Overexpression of the groESL Operon Enhances the Heat and Salinity Stress Tolerance of the Nitrogen-Fixing Cyanobacterium Anabaena sp. Strain PCC7120

The bicistronic groESL operon, encoding the Hsp60 and Hsp10 chaperonins, was cloned into an integrative expression vector, pFPN, and incorporated at an innocuous site in the Anabaena sp. strain PCC7120 genome. In the recombinant Anabaena strain, the additional groESL operon was expressed from a strong cyanobacterial P_psbA1 promoter without hampering the stress-responsive expression of the native groESL operon. The net expression of the two groESL operons promoted better growth, supported the vital activities of nitrogen fixation and photosynthesis at ambient conditions, and enhanced the tolerance of the recombinant Anabaena strain to heat and salinity stresses.Nitrogen-fixing cyanobacteria, especially strains of Nostoc and Anabaena, are native to tropical agroclimatic conditions, such as those of Indian paddy fields, and contribute to the carbon (C) and nitrogen (N) economy of these soils (22, 30). However, their biofertilizer potential decreases during exposure to high temperature, salinity, and other such stressful environments (1). A common target for these stresses is cellular proteins, which are denatured and inactivated during stress, resulting in metabolic arrest, cessation of growth, and eventually loss of viability. Molecular chaperones play a major role in the conformational homeostasis of cellular proteins (13, 16, 24, 26) by (i) proper folding of nascent polypeptide chains; (ii) facilitating protein translocation and maturation to functional conformation, including multiprotein complex assembly; (iii) refolding of misfolded proteins; (iv) sequestering damaged proteins to aggregates; and (v) solubilizing protein aggregates for refolding or degradation. Present at basal levels under optimum growth conditions in bacteria, the expression of chaperonins is significantly enhanced during heat shock and other stresses (2, 25, 32).The most common and abundant cyanobacterial chaperones are Hsp60 proteins, and nitrogen-fixing cyanobacteria possess two or more copies of the hsp60 or groEL gene (http://genome.kazusa.or.jp/cyanobase). One occurs as a solitary gene, cpn60 (17, 21), while the other is juxtaposed to its cochaperonin encoding genes groES and constitutes a bicistronic operon groESL (7, 19, 31). The two hsp60 genes encode a 59-kDa GroEL and a 61-kDa Cpn60 protein in Anabaena (2, 20). Both the Hsp60 chaperonins are strongly expressed during heat stress, resulting in the superior thermotolerance of Anabaena, compared to the transient expression of the Hsp60 chaperonins in Escherichia coli (20). GroEL and Cpn60 stably associate with thylakoid membranes in Anabaena strain PCC7120 (14) and in Synechocystis sp. strain PCC6803 (15). In Synechocystis sp. strain PCC6803, photosynthetic inhibitors downregulate, while light and redox perturbation induce cpn60 expression (10, 25, 31), and a cpn60 mutant exhibits a light-sensitive phenotype (http://genome.kazusa.or.jp/cyanobase), indicating a possible role for Cpn60 in photosynthesis. GroEL, a lipochaperonin (12, 28), requires a cochaperonin, GroES, for its folding activity and has wider substrate selectivity. In heterotrophic nitrogen-fixing bacteria, such as Klebsiella pneumoniae and Bradyrhizobium japonicum, the GroEL protein has been implicated in nif gene expression and the assembly, stability, and activity of the nitrogenase proteins (8, 9, 11).Earlier work from our laboratory demonstrated that the Hsp60 family chaperonins are commonly induced general-stress proteins in response to heat, salinity, and osmotic stresses in Anabaena strains (2, 4). Our recent work elucidated a major role of the cpn60 gene in the protection from photosynthesis and the nitrate reductase activity of N-supplemented Anabaena cultures (21). In this study, we integrated and constitutively overexpressed an extra copy of the groESL operon in Anabaena to evaluate the importance and contribution of GroEL chaperonin to the physiology of Anabaena during optimal and stressful conditions.Anabaena sp. strain PCC7120 was photoautotrophically grown in combined nitrogen-free (BG11⁻) or 17 mM NaNO₃-supplemented (BG11⁺) BG11 medium (5) at pH 7.2 under continuous illumination (30 μE m⁻² s⁻¹) and aeration (2 liters min⁻¹) at 25°C ± 2°C. Escherichia coli DH5α cultures were grown in Luria-Bertani medium at 37°C at 150 rpm. For E. coli DH5α, kanamycin and carbenicillin were used at final concentrations of 50 μg ml⁻¹ and 100 μg ml⁻¹, respectively. Recombinant Anabaena clones were selected on BG11⁺ agar plates supplemented with 25 μg ml⁻¹ neomycin or in BG11⁻ liquid medium containing 12.5 μg ml⁻¹ neomycin. The growth of cyanobacterial cultures was estimated either by measuring the chlorophyll a content as described previously (18) or the turbidity (optical density at 750 nm). Photosynthesis was measured as light-dependent oxygen evolution at 25 ± 2°C by a Clark electrode (Oxy-lab 2/2; Hansatech Instruments, England) as described previously (21). Nitrogenase activity was estimated by acetylene reduction assays, as described previously (3). Protein denaturation and aggregation were measured in clarified cell extracts containing ∼500 μg cytosolic proteins treated with 100 μM 8-anilino-1-naphthalene sulfonate (ANS). The pellet (protein aggregate) was solubilized in 20 mM Tris-6 M urea-2% sodium dodecyl sulfate (SDS)-40 mM dithiothreitol for 10 min at 50°C. The noncovalently trapped ANS was estimated using a fluorescence spectrometer (model FP-6500; Jasco, Japan) at a λ_excitation of 380 nm and a λ_emission of 485 nm, as described previously (29).The complete bicistronic groESL operon (2.040 kb) (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"FJ608815","term_id":"222354886","term_text":"FJ608815"}}FJ608815) was PCR amplified from PCC7120 genomic DNA using specific primers (Table ​(Table1)1) and the amplicon cloned into the NdeI-BamHI restriction sites of plasmid vector pFPN, which allows integration at a defined innocuous site in the PCC7120 genome and expression from a strong cyanobacterial P_psbA1 promoter (6). The resulting construct, designated pFPNgro (Table ​(Table1),1), was electroporated into PCC7120 using an exponential-decay wave form electroporator (200 J capacitive energy at a full charging voltage of 2 kV; Pune Polytronics, Pune, India), as described previously (6). The electroporation was carried out at 6 kV cm⁻¹ for 5 ms, employing an external autoclavable electrode with a 2-mm gap. The electroporation buffer contained high concentrations of salt (10 mM HEPES, 100 mM LiCl, 50 mM CaCl₂), as have been recommended for plant cells (23) and other cell types (27). The electrotransformants, selected on BG11⁺ agar plates supplemented with 25 μg ml⁻¹ neomycin by repeated subculturing for at least 25 weeks to achieve complete segregation, were designated AnFPNgro.

TABLE 1.

Plasmids, strains, and primers used in this study

Efficient Production of 2-Oxobutyrate from 2-Hydroxybutyrate by Using Whole Cells of Pseudomonas stutzeri Strain SDM

2-Oxobutyrate is an important intermediate in the chemical, drug, and food industries. Whole cells of Pseudomonas stutzeri SDM, containing NAD-independent lactate dehydrogenases, effectively converted 2-hydroxybutyrate into 2-oxobutyrate. Under optimal conditions, the biocatalytic process produced 2-oxobutyrate at a high concentration (44.4 g liter⁻¹) and a high yield (91.5%).2-Oxobutyrate (2-OBA) is used as a raw material in the synthesis of chiral 2-aminobutyric acid, isoleucine, and some kinds of medicines (1, 8). There is no suitable starting material for 2-OBA production by chemical synthesis; therefore, the development of innovative biotechnology-based techniques for 2-OBA production is desirable (12).2-Hydroxybutyrate (2-HBA) is cheaper than 2-OBA and can be substituted for 2-OBA in the production of isoleucine, as reported previously (9, 10). The results of those studies also indicated that it might be possible to produce 2-OBA from 2-HBA by a suitable biocatalytic process. In the presence of NAD, NAD-dependent 2-hydroxybutyrate dehydrogenase can catalyze the oxidation of 2-HBA to 2-OBA (4). However, due to the high cost of pyridine cofactors (11), it is preferable to use a biocatalyst that directly catalyzes the formation of 2-OBA from 2-HBA without any requirement for NAD as a cofactor.In our previous report, we confirmed that NAD-independent lactate dehydrogenases (iLDHs) in the pyruvate-producing strain Pseudomonas stutzeri SDM (China Center for Type Culture Collection no. M206010) could oxidize lactate and 2-HBA (6). Therefore, in addition to pyruvate production from lactate, P. stutzeri SDM might also have a potential application in 2-OBA production.To determine the 2-OBA production capability of P. stutzeri SDM, the strain was first cultured at 30°C in a minimal salt medium (MSM) supplemented with 5.0 g liter⁻¹ dl-lactate as the sole carbon source (5). The whole-cell catalyst was prepared by centrifuging the medium and resuspending the cell pellet, and biotransformation was then carried out under the following conditions using 2-HBA as the substrate and whole cells of P. stutzeri SDM as the biocatalyst: 2-HBA, 10 g liter⁻¹; dry cell concentration, 6 g liter⁻¹; buffer, 100 mM potassium phosphate (pH 7.0); temperature, 30°C; shaking speed, 300 rpm. After 4 h of reaction, the mixture was analyzed by high-performance liquid chromatography (HPLC; Agilent 1100 series; Hewlett-Packard) using a refractive index detector (3). The HPLC system was fitted with a Bio-Rad Aminex HPX-87 H column. The mobile phase consisted of 10 mM H₂SO₄ pumped at 0.4 ml min⁻¹ (55°C). Biotransformation resulted in the production of a compound that had a retention time of 19.57 min, which corresponded to the peak of authentic 2-OBA (see Fig. S1 in the supplemental material).After acidification and vacuum distillation, the new compound was analyzed by negative-ion mass spectroscopy. The molecular ion ([M − H]⁻, m/z 101.1) signal of the compound was consistent with the molecular weight of 2-OBA, i.e., 102.1 (see Fig. S2 in the supplemental material). These results confirmed that 2-HBA was oxidized to 2-OBA by whole cells of P. stutzeri SDM.To investigate whether iLDHs are responsible for 2-OBA production in the above-described biocatalytic process, 2-HBA oxidation activity in P. stutzeri SDM was probed by native polyacrylamide gel electrophoresis. After electrophoresis, the gels were soaked in a substrate solution [50 mM Tris-HCl buffer (pH 8.0) containing 0.1 mM phenazine methosulfate, 0.1 mM 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide, and 1 mM l-lactate, dl-lactate, or dl-2-HBA] and gently shaken. As shown in Fig. ​Fig.1,1, d- and l-iLDH migrated as two bands with distinct mobilities. The activities responsible for d- and l-2-HBA oxidation were located at the same positions as the d- and l-iLDH activities, respectively. No other bands responsible for d- and l-2-HBA oxidation were detected. Moreover, the dialysis of the crude cell extract did not lead to loss of 2-HBA oxidation activity and the addition of 10 mM NAD⁺ could not stimulate the reaction (see Table S1 in the supplemental material). These results implied that in the biocatalytic system, 2-HBA was oxidized to 2-OBA by iLDHs present in P. stutzeri SDM.Open in a separate windowFIG. 1.Activity staining of iLDHs after native polyacrylamide gel electrophoresis with lactate or 2-HBA as the substrate.Although the SDM strain could not use 2-HBA or 2-OBA for growth (see Fig. S3 in the supplemental material), 2-HBA might induce some of the enzymes responsible for 2-OBA production in the biocatalytic process. To exclude this possibility, the SDM strain was cultured in MSM containing dl-lactate or pyruvate as the sole carbon source. As shown in Fig. ​Fig.2,2, the enzyme activities that catalyzed lactate and 2-HBA oxidation were simultaneously present in the cells cultured on lactate and were absent in those cultured on pyruvate. After the lactate or pyruvate was exhausted, 5.05 g liter⁻¹ dl-2-HBA was added to the medium. It was observed that dl-2-HBA was efficiently converted to 2-OBA in the medium containing dl-lactate (Fig. ​(Fig.2a).2a). No 2-OBA production was detected in the medium containing pyruvate. Because 2-HBA addition did not induce the enzymes involved in 2-HBA oxidation (Fig. 2a and b), we concluded that the iLDHs induced by dl-lactate catalyzed 2-HBA oxidation in this biocatalytic process.Open in a separate windowFIG. 2.Time course of P. stutzeri SDM growth on media containing dl-lactate (a) and pyruvate (b). 2-HBA was added to the medium after the exhaustion of lactate or pyruvate. Symbols: ▴, lactate; ▵, pyruvate; •, 2-HBA; ○, 2-OBA; ▪, cell density; ▧, iLDHs activity with dl-lactate as the substrate; ▒, iLDHs activity with dl-2-HBA as the substrate.iLDHs could catalyze the oxidation of the substrate in a flavin-dependent manner and might use membrane quinone as the electron acceptor. Unlike the oxidases, which directly use the oxygen as the electron acceptor, this substrate oxidation mechanism could prevent the formation of H₂O₂ (see Fig. S4 in the supplemental material). The P. stutzeri SDM strain efficiently converted dl-2-HBA to 2-OBA with high yields (4.97 g liter⁻¹ 2-OBA was produced from 5.05 g liter⁻¹ dl-2-HBA); therefore, 2-OBA production by this strain can be a valuable and technically feasible process. To increase the efficiency of P. stutzeri SDM in the biotechnological production of 2-OBA, the conditions for biotransformation using whole cells of P. stutzeri SDM were first optimized. The influence of the reaction pH and 2-HBA concentration on 2-OBA production was determined in 100 mM phosphate buffer containing whole cells harvested from the medium containing dl-lactate as the sole carbon source. The reaction was initiated by adding the whole cells and 2-HBA at 37°C, followed by incubation for 10 min. After stopping the reaction by adding 1 M HCl, the 2-OBA concentration was determined by HPLC.As shown in Fig. ​Fig.3a,3a, ​,2-OBA2-OBA production was highest at pH 7.0. Under acidic or alkaline conditions, the transformation of 2-HBA to 2-OBA decreased. The optimal 2-HBA concentration was found to be 0.4 M, as shown in Fig. ​Fig.3b.3b. 2-OBA production increased as the 2-HBA concentration increased up to about 0.4 M and decreased thereafter. The concentration of the whole-cell catalyst was then optimized using 0.4 M 2-HBA as the substrate at pH 7.0. As shown in Fig. ​Fig.3c,3c, the highest 2-OBA concentration was obtained with 20 g (dry cell weight [DCW]) liter⁻¹ of P. stutzeri SDM. The 2-OBA concentration decreased with any increase beyond this cell concentration.Open in a separate windowFIG. 3.Optimization of the biocatalysis conditions. (a) Effect of pH on 2-OBA production activity. (b) Effect of 2-HBA concentrations on 2-OBA production activity. (c) Effect of the concentration of P. stutzeri SDM on biotransformation. OD, optical density.After optimizing the biocatalytic conditions, we studied the biotechnological production of 2-OBA from 2-HBA by using the whole-cell catalyst P. stutzeri SDM. As shown in Fig. ​Fig.4,4, when 20 g (DCW) liter⁻¹ P. stutzeri SDM was used as the biocatalyst, 48.5 g liter⁻¹ 2-HBA was biotransformed into 44.4 g liter⁻¹ 2-OBA in 24 h.Open in a separate windowFIG. 4.Time course of production of 2-OBA from 2-HBA under the optimum conditions. Symbols: ▪, 2-OBA; •, 2-HBA.Biocatalytic production of 2-OBA was carried out using crotonic acid, propionaldehyde, 1,2-butanediol, or threonine as the substrate (2, 7, 8, 12). Resting cells of the strain Rhodococcus erpi IF0 3730 produced 15.7 g liter⁻¹ 2-OBA from 20 g liter⁻¹ 1,2-butanediol, which is the highest reported yield of 2-OBA to date (8). By using the whole-cell catalyst P. stutzeri SDM, it was possible to produce 2-OBA at a high concentration (44.4 g liter⁻¹) and a high yield (91.5%). Due to the simple composition of the biocatalytic system (see Fig. S5 in the supplemental material), 2-HBA and 2-OBA could be easily separated on a column using a suitable resin. Separation of 2-OBA from the biocatalytic system was relatively inexpensive. The biocatalytic process presented in this report could be a promising alternative for the biotechnological production of 2-OBA.      

Characterization of the Corynebacterium glutamicum ΔpimB′ ΔmgtA Double Deletion Mutant and the Role of Mycobacterium tuberculosis Orthologues Rv2188c and Rv0557 in Glycolipid Biosynthesis

In this study, utilizing a Corynebacterium glutamicum ΔpimB′ ΔmgtA double deletion mutant, we unequivocally assign the in vivo functions of Rv2188c as an Ac₁PIM₁:mannosyltransferase (originally termed PimB′_Mt [Mycobacterium tuberculosis PimB′]) and Rv0557 as a GlcAGroAc₂:mannosyltransferase (originally termed PimB_Mt), which we have reassigned as PimB_Mt and MgtA_Mt, respectively, in Mycobacterium tuberculosis.The current model of mycobacterial phosphatidyl-myo-inositol mannoside (PIM) biosynthesis, supported by biochemical and genetic studies, follows a linear pathway from phosphatidylinositol (PI) → Ac₁PIM₂ → Ac₁PIM₄ → Ac₁PIM₆ (4, 17, 19) as shown in Fig. ​Fig.1.1. In this pathway, mycobacterial PI is glycosylated by an α-mannopyranosyl residue at the 2-OH position of inositol, followed by the acylation and mannosylation at the 6-OH position of PI to form Ac₁PIM₂ (3), which is further mannosylated to form Ac₁PIM₄ and Ac₁PIM₆, extending the 6-OH position of Ac₁PIM₂ (19).Open in a separate windowFIG. 1.Glycolipid biosynthetic pathways in Corynebacterineae. (A) PIM synthesis in M. tuberculosis; (B) PIMs; (C) ManGlcAGroAc₂ synthesis in C. glutamicum.In view of the identification of genes involved in PIM, lipomannan (LM), and lipoarabinomannan (LAM) biosynthesis, Schaeffer et al. (22) proposed Rv0557 as an α-d-mannose-α-(1→6)-phosphatidyl-myo-inositol-mannosyltransferase that transfers mannose from GDP-Man to Ac₁PIM₁ to form Ac₁PIM₂, a precursor of the immunomodulatory lipoglycans LM and LAM (4, 17). The study was based on a cell-free assay using GDP[¹⁴C]Man, Ac₁PIM_1, Mycobacterium smegmatis membranes, and/or partially purified recombinant Rv0557. On the basis of these in vitro studies, Rv0557 was assigned as PimB_Mt (Mycobacterium tuberculosis PimB) in the synthesis of Ac₁PIM₂. However, on the disruption of Rv0557 in Mycobacterium tuberculosis, PIM biosynthesis remains unaffected (G. S. Besra and L. S. Schlesinger, unpublished data), suggesting that either gene duplication or Rv0557 performed another function in M. tuberculosis. Interestingly, in a recent study, Rv0557 was also shown to be involved in the biosynthesis of 1,2-di-O-C₁₆/C_18:1-(α-d-mannopyranosyl)-(1→4)-(α-d-glucopyranosylu- ronic acid)-(1→3)-glycerol (ManGlcAGroAc₂) and an LM-like molecule in Corynebacterium glutamicum and was termed MgtA_Mt (M. tuberculosis MgtA) (25). More recently, Rv2188c was also proposed to be involved in the synthesis of Ac₁PIM₂ as the second α-d-mannose-α-(1→6)-phosphatidyl-myo-inositol-mannosyl transferase (termed PimB′_Mt) (13, 16), which has augmented ongoing confusion in the field. Due to the essentiality of M. tuberculosis PIM biosynthesis (3) in this study, we have generated C. glutamicum ΔpimB′ ΔmgtA, deficient in pimB′_Cg and mgtA_Cg (C. glutamicum pimB′ and mgtA) and subsequently overexpressed Rv2188c and Rv0557 individually to identify their true in vivo and in vitro biochemical activities.     

Streptomyces Development in Colonies and Soils

Streptomyces development was analyzed under conditions resembling those in soil. The mycelial growth rate was much lower than that in standard laboratory cultures, and the life span of the previously named first compartmentalized mycelium was remarkably increased.Streptomycetes are gram-positive, mycelium-forming, soil bacteria that play an important role in mineralization processes in nature and are abundant producers of secondary metabolites. Since the discovery of the ability of these microorganisms to produce clinically useful antibiotics (2, 15), they have received tremendous scientific attention (12). Furthermore, its remarkably complex developmental features make Streptomyces an interesting subject to study. Our research group has extended our knowledge about the developmental cycle of streptomycetes, describing new aspects, such as the existence of young, fully compartmentalized mycelia (5-7). Laboratory culture conditions (dense inocula, rich culture media, and relatively elevated temperatures [28 to 30°C]) result in high growth rates and an orderly-death process affecting these mycelia (first death round), which is observed at early time points (5, 7).In this work, we analyzed Streptomyces development under conditions resembling those found in nature. Single colonies and soil cultures of Streptomyces antibioticus ATCC 11891 and Streptomyces coelicolor M145 were used for this analysis. For single-colony studies, suitable dilutions of spores of these species were prepared before inoculation of plates containing GYM medium (glucose, yeast extract, malt extract) (11) or GAE medium (glucose, asparagine, yeast extract) (10). Approximately 20 colonies per plate were obtained. Soil cultures were grown in petri dishes with autoclaved oak forest soil (11.5 g per plate). Plates were inoculated directly with 5 ml of a spore suspension (1.5 × 10⁷ viable spores ml⁻¹; two independent cultures for each species). Coverslips were inserted into the soil at an angle, and the plates were incubated at 30°C. To maintain a humid environment and facilitate spore germination, the cultures were irrigated with 3 ml of sterile liquid GAE medium each week.The development of S. coelicolor M145 single colonies growing on GYM medium is shown in Fig. ​Fig.1.1. Samples were collected and examined by confocal microscopy after different incubation times, as previously described (5, 6). After spore germination, a viable mycelium develops, forming clumps which progressively extend along the horizontal (Fig. 1a and b) and vertical (Fig. 1c and d) axes of a plate. This mycelium is fully compartmentalized and corresponds to the first compartmentalized hyphae previously described for confluent surface cultures (Fig. 1e, f, and j) (see below) (5); 36 h later, death occurs, affecting the compartmentalized hyphae (Fig. 1e and f) in the center of the colony (Fig. ​(Fig.1g)1g) and in the mycelial layers below the mycelial surface (Fig. 1d and k). This death causes the characteristic appearance of the variegated first mycelium, in which alternating live and dead segments are observed (Fig. 1f and j) (5). The live segments show a decrease in fluorescence, like the decrease in fluorescence that occurs in solid confluent cultures (Fig. ​(Fig.11 h and i) (5, 9). As the cycle proceeds, the intensity of the fluorescence in these segments returns, and the segments begin to enlarge asynchronously to form a new, multinucleated mycelium, consisting of islands or sectors on the colony surfaces (Fig. 1m to o). Finally, death of the deeper layers of the colony (Fig. ​(Fig.1q)1q) and sporulation (Fig. ​(Fig.1r)1r) take place. Interestingly, some of the spores formed germinate (Fig. ​(Fig.1s),1s), giving rise to a new round of mycelial growth, cell death, and sporulation. This process is repeated several times, and typical, morphologically heterogeneous Streptomyces colonies grow (not shown). The same process was observed for S. antibioticus ATCC 11891, with minor differences mainly in the developmental time (not shown).Open in a separate windowFIG. 1.Confocal laser scanning fluorescence microscopy analysis of the development-related cell death of S. coelicolor M145 in surface cultures containing single colonies. Developmental culture times (in hours) are indicated. The images in panels l and n were obtained in differential interference contrast mode and correspond to the same fields as in panels k and m, respectively. The others are culture sections stained with SYTO 9 and propidium iodide. Panels c, d, k, l, p, and q are cross sections; the other images are longitudinal sections (see the methods). Panels h and i are images of the same field taken with different laser intensities, showing low-fluorescence viable hyphae in the center of the colonies that develop into a multinucleated mycelium. The arrows in panels e and s indicate septa (e) and germinated spores (s). See the text for details.Figure ​Figure22 shows the different types of mycelia present in S. coelicolor cultures under the conditions described above, depending on the compartmentalization status. Hyphae were treated with different fluorescent stains (SYTO 9 plus propidium iodide for nucleic acids, CellMask plus FM4-64 for cell membranes, and wheat germ agglutinin [WGA] for cell walls). Samples were processed as previously described (5). The young initial mycelia are fully compartmentalized and have membranous septa (Fig. 2b to c) with little associated cell wall material that is barely visible with WGA (Fig. ​(Fig.2d).2d). In contrast, the second mycelium is a multinucleated structure with fewer membrane-cell wall septa (Fig. 2e to h). At the end of the developmental cycle, multinucleated hyphae begin to undergo the segmentation which precedes the formation of spore chains (Fig. 2i to m). Similar results were obtained for S. antibioticus (not shown), but there were some differences in the numbers of spores formed. Samples of young and late mycelia were freeze-substituted using the methodology described by Porta and Lopez-Iglesias (13) and were examined with a transmission electron microscope (Fig. 2n and o). The septal structure of the first mycelium (Fig. ​(Fig.2n)2n) lacks the complexity of the septal structure in the second mycelium, in which a membrane with a thick cell wall is clearly visible (Fig. ​(Fig.2o).2o). These data coincide with those previously described for solid confluent cultures (4).Open in a separate windowFIG. 2.Analysis of S. coelicolor hyphal compartmentalization with several fluorescent indicators (single colonies). Developmental culture times (in hours) are indicated. (a, e, and i) Mycelium stained with SYTO 9 and propidium iodide (viability). (b, f, and j) Hyphae stained with Cell Mask (a membrane stain). (c, g, and l) Hyphae stained with FM 4-64 (a membrane stain). (d, h, and m) Hyphae stained with WGA (cell wall stain). Septa in all the images in panels a to j, l, and m are indicated by arrows. (k) Image of the same field as panel j obtained in differential interference contrast mode. (n and o) Transmission electron micrographs of S. coelicolor hyphae at different developmental phases. The first-mycelium septa (n) are comprised of two membranes separated by a thin cell wall; in contrast, second-mycelium septa have thick cell walls (o). See the text for details. IP, propidium iodide.The main features of S. coelicolor growing in soils are shown in Fig. ​Fig.3.3. Under these conditions, spore germination is a very slow, nonsynchronous process that commences at about 7 days (Fig. 3c and d) and lasts for at least 21 days (Fig. 3i to l), peaking at around 14 days (Fig. 3e to h). Mycelium does not clump to form dense pellets, as it does in colonies; instead, it remains in the first-compartmentalized-mycelium phase during the time analyzed. Like the membrane septa in single colonies, the membrane septa of the hyphae are stained with FM4-64 (Fig. 3j and k), although only some of them are associated with thick cell walls (WGA staining) (Fig. ​(Fig.3l).3l). Similar results were obtained for S. antibioticus cultures (not shown).Open in a separate windowFIG. 3.Confocal laser scanning fluorescence microscopy analysis of the development-related cell death and hyphal compartmentalization of S. coelicolor M145 growing in soil. Developmental culture times (in days) are indicated. The images in panels b, f, and h were obtained in differential interference contrast mode and correspond to the same fields as the images in panels a, e, and g, respectively. The dark zone in panel h corresponds to a particle of soil containing hyphae. (a, c, d, e, g, i, j, and k) Hyphae stained with SYTO 9, propidium iodide (viability stain), and FM4-64 (membrane stain) simultaneously. (i) SYTO 9 and propidium iodide staining. (j) FM4-64 staining. The image in panel k is an overlay of the images in panels i and j and illustrates that first-mycelium membranous septa are not always apparent when they are stained with nucleic acid stains (SYTO 9 and propidium iodide). (l) Hyphae stained with WGA (cell wall stain), showing the few septa with thick cell walls present in the cells. Septa are indicated by arrows. IP, propidium iodide.In previous work (8), we have shown that the mycelium currently called the substrate mycelium corresponds to the early second multinucleated mycelium, according to our nomenclature, which still lacks the hydrophobic layers characteristic of the aerial mycelium. The aerial mycelium therefore corresponds to the late second mycelium which has acquired hydrophobic covers. This multinucleated mycelium as a whole should be considered the reproductive structure, since it is destined to sporulate (Fig. ​(Fig.4)4) (8). The time course of lysine 6-aminotransferase activity during cephamycin C biosynthesis has been analyzed by other workers using isolated colonies of Streptomyces clavuligerus and confocal microscopy with green fluorescent protein as a reporter (4). A complex medium and a temperature of 29°C were used, conditions which can be considered similar to the conditions used in our work. Interestingly, expression did not occur during the development of the early mycelium and was observed in the mycelium only after 80 h of growth. This suggests that the second mycelium is the antibiotic-producing mycelium, a hypothesis previously confirmed using submerged-growth cultures of S. coelicolor (9).Open in a separate windowFIG. 4.Cell cycle features of Streptomyces growing under natural conditions. Mycelial structures (MI, first mycelium; MII, second mycelium) and cell death are indicated. The postulated vegetative and reproductive phases are also indicated (see text).The significance of the first compartmentalized mycelium has been obscured by its short life span under typical laboratory culture conditions (5, 6, 8). In previous work (3, 7), we postulated that this structure is the vegetative phase of the bacterium, an hypothesis that has been recently corroborated by proteomic analysis (data not shown). Death in confluent cultures begins shortly after germination (4 h) and continues asynchronously for 15 h. The second multinucleated mycelium emerges after this early programmed cell death and is the predominant structure under these conditions. In contrast, as our results here show, the first mycelium lives for a long time in isolated colonies and soil cultures. As suggested in our previous work (5, 6, 8), if we assume that the compartmentalized mycelium is the Streptomyces vegetative growth phase, then this phase is the predominant phase in individual colonies (where it remains for at least 36 h), soils (21 days), and submerged cultures (around 20 h) (9). The differences in the life span of the vegetative phase could be attributable to the extremely high cell densities attained under ordinary laboratory culture conditions, which provoke massive differentiation and sporulation (5-7, 8).But just exactly what are “natural conditions”? Some authors have developed soil cultures of Streptomyces to study survival (16, 17), genetic transfer (14, 17-19), phage-bacterium interactions (3), and antibiotic production (1). Most of these studies were carried out using amended soils (supplemented with chitin and starch), conditions under which growth and sporulation were observed during the first few days (1, 17). These conditions, in fact, might resemble environments that are particularly rich in organic matter where Streptomyces could conceivably develop. However, natural growth conditions imply discontinuous growth and limited colony development (20, 21). To mimic such conditions, we chose relatively poor but more balanced carbon-nitrogen soil cultures (GAE medium-amended soil) and less dense spore inocula, conditions that allow longer mycelium growth times. Other conditions assayed, such as those obtained by irrigating the soil with water alone, did not result in spore germination and mycelial growth (not shown). We were unable to detect death, the second multinucleated mycelium described above, or sporulation, even after 1 month of incubation at 30°C. It is clear that in nature, cell death and sporulation must take place at the end of the long vegetative phase (1, 17) when the imbalance of nutrients results in bacterial differentiation.In summary, the developmental kinetics of Streptomyces under conditions resembling conditions in nature differs substantially from the developmental kinetics observed in ordinary laboratory cultures, a fact that should be born in mind when the significance of development-associated phenomena is analyzed.     

Self-Assembly of the Bacterial Cytoskeleton-Associated RNA Helicase B Protein into Polymeric Filamentous Structures

The Escherichia coli RNA degradosome proteins are organized into a helical cytoskeletal-like structure within the cell. Here we describe the ATP-dependent assembly of the RhlB component of the degradosome into polymeric filamentous structures in vitro, which suggests that extended polymers of RhlB are likely to comprise a basic core element of the degradosome cytoskeletal structures.The RNA degradosome plays an essential role in normal RNA processing and degradation. Within the cell, the degradosome proteins (RNA helicase B [RhlB], RNase E, polynucleotide phosphorylase [PNPase], and enolase) (4, 13, 15, 16) are organized into coiled structures that resemble the pole-to-pole helical structures of the MreB and MinCDE bacterial cytoskeletal systems (4, 12, 13). However, the degradosomal structures are also present in cells that lack the MreB and MinCDE cytoskeletal elements, suggesting that the degradosomal structures may be part of an independent class of prokaryotic cytoskeletal elements (19-21).One of the degradosomal proteins, RhlB, is organized into similar helical cellular structures in cells that lack the other degradosome proteins (Fig. ​(Fig.11 A). In addition, RhlB recruits PNPase to the helical framework in the absence of other degradosome proteins, suggesting that the RhlB structures are core elements of the degradosomal cytoskeletal-like elements of the cell (Fig. ​(Fig.1B)1B) (20). The cellular RhlB structures could be generated in two ways: (i) individual RhlB molecules may bind to an as-yet-undefined underlying track, or (ii) RhlB may polymerize to form the filamentous helical structures independent of any underlying template.Open in a separate windowFIG. 1.The RhlB filamentous cytoskeletal-like structures. (A) Cellular organization of RhlB based on immunofluorescence microscopy using purified anti-RhlB antibody in the absence of RNase E filamentous elements in AT8 cells (rne^1-417), which fail to generate RNase E coiled structures because of the absence of the RNase E cytoskeletal localization domain (20). (B) Proposed model for the cytoskeletal-like organization of the RNA degradosome (modified from reference 20). Arcs depict the RNase E (blue) and RhlB (red) helical strands. It is not known whether the RNase E helical strand is formed by RNase E polymerization or by the association of RNase E with an unknown underlying cytoskeletal structure. Enolase (Eno) and PNPase are shown in gray. Molecular dimensions and stoichiometry of the proteins were arbitrarily chosen to simplify the figure. (C to H) Electron micrographs of uranyl acetate-stained RhlB filaments (C, E, and H) and RhlB sheets (D). Unless otherwise indicated, the sample contained 9 μM RhlB, 2 mM ATP, 5 mM MgCl₂, and 5 mM CaCl₂. (E) Calcium was omitted. (F) ATP was omitted. (G and H) ATP was replaced by ATPγS (G) or AMP-PNP (H). Samples were loaded on glow-discharged 300-mesh carbon-coated copper grids and then stained. Images were taken with a JEOL 100CX transmission electron microscope. Magnification, ×10,000 to 50,000.Here we report that RhlB can self-assemble into extended polymeric structures in vitro in a process that requires ATP binding but not ATP hydrolysis. It is likely that extended RhlB polymers such as those described here are the basic components of the RhlB filamentous helical elements that comprise the core of the degradosomal cytoskeletal structures of the Escherichia coli cell.Evidence that RhlB can self-assemble into filamentous polymeric structures came from electron microscopic studies of purified His-tagged RhlB negatively stained with 2% uranyl acetate. This staining showed large numbers of long uniform filamentous structures when the purified protein was incubated in the presence of ATP and Ca²⁺ (Fig. ​(Fig.1C).1C). The filaments were 25 ± 1.8 nm wide (n = 91; mean ± standard deviation) and were generally more than 10 μm long. Some wider sheets were also observed (Fig. ​(Fig.1D).1D). Optimal assembly of the RhlB filamentous structures required ATP and Ca²⁺, as shown by the observation that only occasional single structures were present when the polymerization reaction was carried out in the absence of Ca²⁺ (Fig. ​(Fig.1E)1E) or ATP (Fig. ​(Fig.1F).1F). The polymeric RhlB-His structures were observed with approximately similar frequencies when ATP was replaced by the nonhydrolyzable ATP analog adenosine 5′-(γ-thiotriphosphate) (ATPγS) or AMP-PNP (Fig. 1G and H).Cellular localization studies showed that the presence of the His tag did not interfere with the ability of RhlB to form the helical cellular structures. Thus, RhlB-His was present in extended helical filamentous structures that were indistinguishable from those formed by untagged RhlB (20, 21). Similarly, the RhlB-His structures recruited PNPase to the helical framework in a manner similar to untagged RhlB (20) (see Fig. S1 in the supplemental material).Immunogold staining showed that the filaments and sheets were decorated with gold particles when stained with mouse anti-His tag antibody and gold-labeled secondary antibody (Fig. ​(Fig.22 A to C), confirming that the structures were composed of RhlB. In contrast, the structures were not decorated with gold particles in the absence of the primary antibody or when mouse anti-His tag antibody was replaced by nonimmune mouse IgG (Fig. ​(Fig.2D2D and E). The polymeric structures were observed with C-terminally His-tagged RhlB, which is functional in terms of helicase activity (8), but not when the tag was present at the amino terminus of the protein, where the His tag may interfere with RhlB self-assembly.Open in a separate windowFIG. 2.Immunogold electron microscopy of RhlB structures. Samples were prepared as describe for Fig. ​Fig.1C,1C, except that the grids were stained with 2% uranyl acetate after exposure to primary and/or secondary antibodies as indicated. (A to C) RhlB structures decorated with 10-nm gold particles in samples stained with mouse anti-His tag monoclonal antibody and gold-labeled secondary antibody. (A) single filaments; (B) clustered filaments; (C) a single RhlB filament and RhlB sheet. Arrows indicate gold particles. (D) The primary mouse anti-His tag antibody was replaced by mouse IgG. (E) The primary antibody was omitted.Changes in light scattering were used to follow the course of polymerization and to compare polymerization conditions in a more quantitative way than is possible by electron microscopy. The initial rate of increase in scattering was used to estimate polymerization rate (see Table S1 in the supplemental material). Significant rates of polymerization were observed in the presence of ATP and Ca²⁺, whereas there was very little increase in light scattering in the absence of nucleotide and/or Ca²⁺ (Fig. ​(Fig.33 A). ADP was less effective than ATP, whereas AMP and cyclic AMP (cAMP) were inactive (Fig. ​(Fig.3B).3B). In the presence of Ca²⁺, the extent and rate of RhlB polymerization varied as a function of ATP concentration (Fig. ​(Fig.3C).3C). Millimolar concentrations of Ca²⁺ were required to produce a measurable rate of polymerization in the light scattering assay (Fig. ​(Fig.3A).3A). It is not known how these relatively high concentrations of Ca²⁺ promote the in vitro polymerization of RhlB and other cytoskeletal proteins, such as MreB and FtsZ (1, 11, 12, 14, 23).Open in a separate windowFIG. 3.RhlB polymerization. (A and B) RhlB polymerization as shown by 90° light scattering is indicated in arbitrary units (a.u.). RhlB polymerization was followed at room temperature in a 1-cm light path quartz cuvette using a Hitachi fluorometer (FL-2500) set to 400 V with excitation and emission wavelengths set at 455 nm and a slit width of 10 nm. The reaction (100 μl volume) was performed in a polymerization buffer (50 mM Tris, 50 mM KCl, 5 mM MgCl₂; pH 8) as indicated. (A) The sample contained 9 μM RhlB-His, 1 mM ATP, and either 10 mM CaCl₂, 7.5 mM CaCl₂, or no CaCl₂ (squares). In the lower three curves the samples lacked ATP or CaCl₂, as indicated. (B) The sample contained 9 μM RhlB-His, 7.5 mM CaCl₂, and 1 mM adenosine nucleotides: ATP, ADP, AMP, cAMP, AMP-PNP, and ATPγS. (C) The sample contained 9 μM RhlB-His, 7.5 mM CaCl₂, and ATP as indicated (1 mM, 0.75 mM, 0.5 mM, 0.25 mM, or 0.1 mM ATP). (D) Effects of Ca²⁺ concentration on RhlB sedimentation in the presence of 2 mM ATP. RhlB in the pellet, expressed as a percentage of total RhlB present in the polymerization reaction mixture, was plotted against calcium concentration. The insert shows an example of a Coomassie blue-stained gel of supernatant (S) and pellet (P) fractions from the sedimentation assay in the presence of ATP and Ca²⁺ (see results for ATP in Table ​Table11).The nonhydrolyzable ATP analogs ATPγS and AMP-PNP were approximately equivalent to ATP in promoting polymerization as monitored by the light scattering assay (Fig. ​(Fig.3B)3B) as well as in the electron microscopic studies. This suggests that nucleotide binding, but not hydrolysis, is required to promote RhlB polymerization. In this regard, RhlB resembles a number of other proteins, including F-actin, MreB, and MinD, where polymerization is induced by nucleotide binding (2, 5, 6, 18, 22). In these systems, subsequent ATP hydrolysis induces depolymerization, providing the basis for the dynamic behavior of the polymers within the cell. RhlB is an RNA-dependent ATPase (7), but it is not yet known whether ATP hydrolysis is associated with depolymerization in the RhlB system.Similar results were obtained when the extent of polymerization was monitored by a sedimentation assay, measuring the proportion of RhlB in the pellet fraction after centrifugation at 278,000 × g for 10 min (Table ​(Table1;1; Fig. ​Fig.3D).3D). Essentially all of the protein was sedimentable at pH 8 in the presence of Ca²⁺ and ATP. RhlB sedimentation returned to background levels when EGTA or EDTA was added to the reaction mixture (Table ​(Table1),1), confirming the Ca²⁺ requirement for RhlB polymerization in the electron microscopic and light scattering analyses. ATPγS was equivalent to ATP in the sedimentation assay, confirming the results described above. The relatively high background of RhlB sedimentation was not affected by prespinning the samples prior to addition of nucleotides and/or Ca²⁺.

TABLE 1.

Sedimentation assay for RhlB polymerization

Evaluation of a Stochastic Inactivation Model for Heat-Activated Spores of Bacillus spp.

Heat activates the dormant spores of certain Bacillus spp., which is reflected in the “activation shoulder” in their survival curves. At the same time, heat also inactivates the already active and just activated spores, as well as those still dormant. A stochastic model based on progressively changing probabilities of activation and inactivation can describe this phenomenon. The model is presented in a fully probabilistic discrete form for individual and small groups of spores and as a semicontinuous deterministic model for large spore populations. The same underlying algorithm applies to both isothermal and dynamic heat treatments. Its construction does not require the assumption of the activation and inactivation kinetics or knowledge of their biophysical and biochemical mechanisms. A simplified version of the semicontinuous model was used to simulate survival curves with the activation shoulder that are reminiscent of experimental curves reported in the literature. The model is not intended to replace current models to predict dynamic inactivation but only to offer a conceptual alternative to their interpretation. Nevertheless, by linking the survival curve''s shape to probabilities of events at the individual spore level, the model explains, and can be used to simulate, the irregular activation and survival patterns of individual and small groups of spores, which might be involved in food poisoning and spoilage.Heat inactivation kinetics of bacterial spores is a well-researched field. Much of the work on its relation to foods has focused on the heat-resistant spores of Clostridia, particularly those of Clostridium botulinum, which to this date serves as the reference organism in sterility calculations of low-acid foods (8, 32). The thermal resistance of Bacilli spores, although also extensively studied, has received less attention in the literature on food preservation. This is primarily because they are unlikely to germinate and produce cells that will survive and divide under the anaerobic conditions in a sterilized food container. Yet the mere possibility of viable Bacillus spores being present in processed foods has become an issue of food safety and a security concern. For this reason, there is a renewed interest in these spores'' heat resistance (2, 3, 6, 7, 16, 30). One of the peculiarities of certain Bacillus spores, like those of Bacillus sporothermodurans or Bacillus stearothermophilus, is that many of them can remain dormant unless activated by heat. The result is a survival curve that exhibits an “activation shoulder,” as shown schematically in Fig. ​Fig.11 and with published data in Fig. ​Fig.2.2. Thus, modeling this survival pattern, where the number of spores initially grows rather than declines, must account for the heat''s dual role of being a lethal agent and activator at the same time.Open in a separate windowFIG. 1.A schematic view of a survival curve having an activation shoulder. S(t) is the ratio between the number N(t) of viable spores at time t and the initial number N₀. Notice the discrepancy between the two ways to estimate the number of dormant spores, represented by the dashed and dotted gray lines.Open in a separate windowFIG. 2.Demonstration of the fit of equation 1 (solid line) and equation 2 (dashed line) to survival curves of B. stearothermophilus spores at two temperatures. Notice the postpeak concavity of the curves. In such cases, the estimated number of dormant spores reached by the tangent method will depend on the experiment duration. The original experimental data are from Sapru et al. (25).Traditionally, the thermal inactivation of both Clostridia and Bacilli spores has been thought to follow first-order kinetics (9, 12, 31), an assumption that has been frequently challenged in recent years (18, 21, 33, 35). The most publicized model of the simultaneous heat activation and inactivation of Bacillus spores in food is that proposed by Sapru et al. (24, 25), which is an improved version of models proposed earlier by Shull et al. (29) and Rodriguez et al. (23). All of these authors and others (1, 17) assumed that the activation of dormant spores follows first-order kinetics and so does their inactivation before and after activation. The temperature dependence of the corresponding exponential rate constants was assumed to follow the Arrhenius equation.Peleg (18, 20) and van Boekel (33, 35) have shown that none of the above assumptions was necessary and that the same survival data on Bacillus stearothermophilus reported by Sapru et al. (25) and other investigators (5) can be described by different kinds of alternative four-parameter empirical models, which have a slightly better fit. This was evident not only visually (Fig. ​(Fig.2)2) but also as judged by statistical criteria (34). Fig. ​Fig.22 shows the fit of the “double Weibullian” model proposed by van Boekel (33). It has the following form: (1) where S(t) = N(t)/N₀ is the survival/activation ratio, N₀ and N(t) are the initial and momentary number of countable spores, respectively, and b₁, b₂, n₁, and n₂ are adjustable temperature-dependent constants. Figure 2 also shows the fit of an ad hoc empirical model, a hybrid between the double Weibullian model and one previously proposed (20) that can be written in the following form: (2) or (3) where a₁, b₁, t_c2, and m₂ are adjustable temperature-dependent parameters. According to this model, a₁ is the asymptote of the first term on the right, b₁ is a time characteristic of the activation, t_c2 is a characteristic time of the inactivation, and m₂ is a parameter that represents the curve''s postpeak concavity. The structure of equation 2 or 3 dictates that the number of dormant spores must be finite and cannot exceed N₀ × 10^a1, if the logarithm is base 10, or N₀ × exp(a₁), if it is base e. (A demonstration that generates realistic-looking activation/inactivation curves using equation 3 as a model is available from Wolfram Research [http://demonstrations.wolfram.com/SurvivalCurvesOfBacilliSporesWithAnActivationShoulder/].)Corradini and Peleg (5) proposed a way to estimate the initial number of dormant spores from survival curves having an activation shoulder using a similar model, which was originally described in Peleg (20). They suggested that the intersection of a tangent to the survival curve drawn at its postpeak region with the time axis (Fig. ​(Fig.1)1) is not a recommended method to estimate the number of dormant spores and that it can render unrealistically high values if used. Also, where there is no evidence that the survival curve in the postpeak region ever becomes a straight line; the same survival curve will yield different estimates of the dormant spores'' initial number depending on the experiment''s duration. Moreover, if in the postpeak region the survival ratio drop rate progressively increases, as it most probably does (Fig. ​(Fig.2)2) (20, 33), then the number of dormant spores estimated by the tangent extrapolation method will grow indefinitely, despite the fact that it must be finite (1). Also, since the exponential inactivation rate can be a function of time as well as of temperature, the applicability of the Arrhenius equation as a secondary model might come into question. The same can also be said about the log-linearity of the D value''s temperature dependence if used instead of the Arrhenius equation.The question that arises in light of all the above is whether one can construct a conceptual population dynamic model of the activation/inactivation of spores without assuming any fixed kinetic order. The biochemical and biophysical mechanisms that govern bacterial spore germination, activation, and inactivation have been thoroughly investigated (11, 13, 14, 15, 22, 26-28). Still, it is not clear how processes within an individual spore can be translated into activation and survival patterns at the population level and how their manifestation can be expressed in a mathematical model. Whenever a system has inherent variability and knowledge of its working is incomplete or merely insufficient to develop a model from basic principles, one can, and sometimes must, resort to a probabilistic modeling approach. The general objective of this work has been to explore the merits and limitations of this option by developing a stochastic model of Bacilli spores'' heat activation and inactivation and examining its properties. The goal has not been to develop a new method to predict the spores'' survival under dynamic conditions—rate versions of the existing empirical models such as equation 1, 2, or 3 seem to be quite suitable for that—but to offer an alternative interpretation of the patterns reported and discussed in the literature.     

F Plasmid TraF and TraH Are Components of an Outer Membrane Complex Involved in Conjugation

F plasmid TraF and TraH are required for F pilus assembly and F plasmid transfer. Using flotation sucrose density gradients, we found that TraF and TraH (as well as TraU and TraW) localized to the outer membrane in the presence of the complete F transfer region, especially TraV, the putative anchor. Mutational analysis of TraH revealed two domains that are important for its function and possible interaction with TrbI, which in turn has a role in stabilizing TraH.The F plasmid (99,159 bp) of Escherichia coli is a model system for the study of the horizontal gene transfer among prokaryotes via conjugation (3, 10, 27). F encodes a 33.3-kb transfer region that is responsible for the formation of mating junctions between donor and recipient cells prior to DNA transfer and establishment in the recipient. The hallmark of F conjugation is the formation of extracellular filaments, F pili, that initiate contact between mating cells and retract, bringing the donor and recipient cells together (5, 19). Synthesis of the F pilus is not well understood, despite the morphological simplicity of this organelle (7, 15, 28). The F transfer region consists of nearly 40 tra genes, with 18 being involved in construction of the transferosome, which is involved in pilus synthesis, mating pair stabilization, and DNA transfer (9). Eight of the encoded Tra proteins (TraA, -B, -C, -E, -G [the N-terminal domain], -K, -L, and -V) correspond to widely conserved members of type IV secretion systems (T4SS), whereas another 9 (TraF, -G [C-terminal domain], -H, -N, -U, and -W and TrbB, -C, and -I) are involved in the F-specific T4SS (4, 18). Two other proteins (TraQ and -X) are specific to the F plasmid itself. The roles of the F-specific proteins that are involved in pilus assembly and DNA transfer are intriguing, since other conjugative T4SS appear to function efficiently without them (18). These tra proteins do not affect F pilin levels, and hence, they have been assigned functions in pilus assembly/retraction and mating pair stabilization, which are characteristics of F-like transfer systems (18). TraF, -H, and -W and TrbC are required for F pilus assembly (9), and mutations in traU reduce the number and the mean length of pili but do not abolish pilus outgrowth (24). TraU is required for DNA transfer and has been tentatively grouped with TraN and -G as proteins involved in mating pair stabilization (18). TrbI is thought to play a role in pilus retraction, since trbI mutants have unusually long pili (21). TrbB contains the thioredoxin-like domain with a C-X-X-C motif and appears to be a periplasmic disulfide bond isomerase (6). Previously, we hypothesized that TrbB and TraF, the latter of which also has the thioredoxin-like domain but lacks the C-X-X-C motif, might have chaperone-like activity. These proteins might help F T4SS proteins such as TraH, -U, and -N, which have 6, 10, and 22 conserved cysteines, respectively, achieve the correct conformation for assembly into the transferosome complex (6). Interestingly, yeast two-hybrid (Y2H) analysis demonstrated that TraF, -H, -U, and -W and TrbB and -I form an interaction group, with TraH directly linked to TraF, TraU, and TrbI (14). TraH is the only one of the three cysteine-rich proteins required for pilus assembly; it is the largest protein (458 amino acids [aa]; 50.2-kDa precursor, processed to 47.8 kDa) in the interaction group and contains a C-terminal coiled-coil domain that can contribute to its oligomerization and interaction with other T4SS proteins (18). Y2H analysis also showed that the C-terminal region of TraH is critical for its interaction with TraF (28 kDa, processed to 25.9 kDa) and TraU (36.8 kDa, processed to 34.3 kDa) and that a deletion within the N-terminal region of TraH enhanced its interaction with TrbI (14.1 kDa) (14).Mutations in traH affect pilus outgrowth but not pilus tip formation at the cell surface, since traH mutants are sensitive to the M13K07 transducing phage, which binds to the pilus tip (1). Membrane fractionation studies of cells containing subclones of the F transfer region originally suggested that TraH fractionates with the inner membrane (IM) (22). TraH contains three N-terminal hydrophobic domains of approximately 20 aa each, which supports this model. In contrast, Ham et al. predicted TraH to be a soluble periplasmic protein (12). Sucrose density gradient sedimentation studies suggested that FLAG-tagged TraH, in the presence of F lac traH80, is in the outer membrane (OM) (23). Since TraH is extracted from membrane preparations with guanidine-HCl or urea but not Triton X-100, Manwaring concluded that TraH is a peripherally associated outer membrane protein (23). By use of subclones of the F transfer region, TraF, -U, -W, and TrbB were localized to the periplasm, whereas TrbI was thought to be an inner membrane protein (21, 24, 29, 30). Using the F plasmid derivative pOX38-Tc (2), which carries the entire F transfer region, we reassessed the localization of TraH as well as TraF, TraU, and TraW (23.6 kDa, processed to 21.7 kDa).E. coli strains were grown at 37°C in Luria-Bertani (LB) broth (1% tryptone [Difco], 0.5% yeast extract [Difco], 1% NaCl [BDH]) with shaking to mid-exponential phase (optical density at 600 nm [OD₆₀₀] of ca. 0.5) with appropriate antibiotics at the following concentrations: 50 μg/ml ampicillin (Ap), 20 μg/ml chloramphenicol (Cm), 25 μg/ml kanamycin (Km), 200 μg/ml streptomycin (Sm), 100 μg/ml spectinomycin (Sp), and 10 μg/ml tetracycline (Tc). Sucrose density flotation studies of cell membrane fractions and immunoblot analysis were performed as previously described (17). Cell pellets corresponding to 0.1 OD₆₀₀ equivalents were used in all immunoblot assays. Samples were boiled in sodium dodecyl sulfate (SDS) sample buffer for 5 min and were analyzed by resolving SDS-15% polyacrylamide gel by using the Bio-Rad Minigel system. The positions of the inner and outer membrane fractions were determined using polyclonal antibodies to the C-terminal region of OmpA, the major outer membrane porin, and CpxA, the inner membrane sensor of the CpxAR two-component system (25). Anti-CpxA, anti-TraE, anti-TraF, anti-TraH, anti-TraU, anti-TraW, and anti-TrbB polyclonal antisera (raised in rabbits) were diluted 1:7,000, 1:5,000, 1:2,000, 1:1,000; 1:500, 1:20,000 and 1:10,000, respectively, in blocking solution and were incubated with the blots at room temperature for 1 h. Anti-OmpA antibodies were used at a 10⁻⁵ dilution in 5% bovine serum albumin (BSA; Roche) to avoid heavy background. Unfortunately, TrbI protein could not be overproduced and specific antibodies could not be raised.Log-phase cultures of E. coli MC4100 (Sm^r) (17) containing pOX38-Tc (2) were separated into periplasmic, cytoplasmic, and membrane fractions according to a previously described method (26). The fractions were tested for the presence of TraH, TraF, TraU, and TraW by SDS-PAGE, followed by immunoblot analysis. All four proteins were found associated with the membrane fraction and not the periplasmic fraction (Fig. ​(Fig.1A).1A). TrbB was found in the periplasmic fraction, in agreement with its proposed role in disulfide bond isomerization (6; data not shown).Open in a separate windowFIG. 1.(A) The F-specific proteins TraH, -F, -U, and -W were detected in the membrane fraction when expressed from MC4100/pOX38-Tc. Proteins were detected by immunoblotting using antisera specific for each protein as described in the text. (B) TraF localization was tested in pOX38-Km and pOX38 ΔtraV::cat. The cells were fractionated into cytoplasmic (C), periplasmic (P), and total membrane (M) fractions, and TraF was detected by immunoblotting with anti-TraF antibodies. TraV was complemented by pRS29 (pRS31 acted as a negative control). The following abbreviations are used: WT, wild type; ΔV, pOX38 ΔtraV::cat; ΔH, pOX38-Tc ΔtraH::cat; and ΔF, pOX38 ΔtraF::kan. The positions of the proteins are indicated by arrows on the right of each panel. The asterisk indicates a band that reacts nonspecifically with anti-F antiserum.Sucrose density flotation gradients of the membrane preparations of MC4100 (Sm^r) cells harboring pOX38-Tc (2), pOX38-Tc ΔtraF::kan (6) and pOX38-Tc ΔtraH::cat were performed to distinguish between OM and IM proteins according to reference 17. pOX38-Tc ΔtraH::cat was constructed according to the method described by Elton et al. (6) by inserting a chloramphenicol acetyltransferase cassette into traH. Gradients were fractionated, and a subset of the fractions (fractions 26 to 54, renamed 1 to 29) that contained the proteins of interest were subjected to SDS-PAGE and immunoblot analyses (Fig. ​(Fig.2).2). OmpA and CpxA were controls for the outer and inner membrane fractions and helped define the subset of fractions examined (Fig. ​(Fig.2,2, panels 1 and 2, respectively). The TraE pilus assembly protein of the F plasmid was used as an IM marker for the F transfer system (Fig. ​(Fig.2,2, panel 9) (9). TraH fractionated as an OM protein in MC4100/pOX38-Tc (Fig. ​(Fig.2,2, panel 3), as did TraF, TraU, and TraW (Fig. ​(Fig.2,2, panels 5, 7, and 8, respectively). TraH did not appear to be required for TraF localization, which was unaffected in a traH mutant (Fig. ​(Fig.2,2, panel 6). In addition, TraF did not appear to be required for TraH localization, although its absence caused a reduction in the levels of TraH (Fig. ​(Fig.2,2, panel 4; see below).Open in a separate windowFIG. 2.The cellular localizations of TraE, TraF, TraH, TraU, and TraW in subcellular fractions of E. coli MC4100/pOX38-Tc and its derivatives. Flotation sucrose density gradients were performed with subsequent immunodetection of tra proteins in a subset of gradient fractions (fractions 26 to 54, renumbered 1 to 29). The positions of the IM and OM fractions are shown above the gels, and the identities of the samples are indicated on the left. The panel numbers are indicated on the right.TraF, -H, -U, and -W appear to be periplasmic proteins that associate with the outer membrane when in the context of the complete transfer apparatus. TrbC, which is fused to TraW in the F-like R27 T4SS, might also be part of this complex (18). Therefore, an as yet unidentified transfer protein should act as an anchor in the outer membrane, directing these proteins to this location. Of the 18 transferosome proteins, only TraV and TraN are known to be located in the OM, with TraV being the only OM protein involved in pilus assembly. Preliminary localization studies using TraF as a test case and a traV insertion mutant, pOX38 ΔtraV::cat (this study, constructed as described above for pOX38-Tc ΔtraH::cat), demonstrated that the levels of TraF decreased dramatically. However, the remaining TraF was found in the periplasm (Fig. ​(Fig.1B).1B). Complementation of the traV mutation with pRS29, but not pRS31 (1), restored TraF localization to the outer membrane. Thus, TraV is probably the anchor protein for both the F-specific transferosome proteins (TraF, -H, -U, and -W) as well as the TraV, -K, and -B complex (13).MC4100 (Sm^r) cells bearing pOX38-Tc (2) or insertion mutant pOX38-Tc ΔtraH::cat, pOX38-Tc ΔtraF::kan (6), pOX38-Tc ΔtrbB::cat (6), pOX38-Tc ΔtraW::cat (this study), pOX38 traU347 (Km^r) (24), or pOX38-trbI472 (Km^r) (21) were used in subsequent experiments. pOX38-Tc ΔtraW::cat was constructed according to the method described by Elton et al. (6) by inserting a chloramphenicol acetyltransferase gene within traW. Mating efficiencies of these mutants were determined according to previously described methods using E. coli ED24 (Sp^r) as the recipient (20). Transconjugants were selected based on double resistance toward chloramphenicol or kanamycin and spectinomycin (Fig. ​(Fig.2).2). Observed mating efficiencies were in agreement with the data obtained previously, as were the results of complementation assays using subclones carrying the appropriate transfer gene (1, 6, 21, 24, 29, 30). These subclones were pK184TraH (Km^r) (this study), pFTraF and pFTrbB (Ap^r) (6), and pKI175 (Ap^r; traWU) (30) (Fig. ​(Fig.2).2). pK184TraH is based on the vector pK184 (Km^r) and contains the traH gene plus its ribosome binding site cloned into the EcoRI and HindIII sites in pK184 (16). Immunoblot analyses revealed that traF, traU, or trbB, but not traW, insertion mutants had slightly reduced levels of TraH in MC4100 cells whereas the trbI insertion mutant had undetectable levels of TraH (Fig. ​(Fig.3).3). Since TraH interacts directly with TrbI, TraF, and TraU in Y2H assays (14), the absence of these proteins would be expected to destabilize TraH. TraH is thought to interact indirectly with TraW via TraU (14); its levels were unaffected in a traW mutant. TraH was destabilized in a dsbA mutant and was undetectable by immunoblotting (data not shown) and decreased slightly in a trbB mutant, suggesting that disulfide bond formation (DsbA) and isomerization (TrbB) are important for TraH.Open in a separate windowFIG. 3.Immunoblot analysis of the levels of TraH in the absence of other members of Y2H interaction group by using pOX38-Tc and its derivatives containing insertion mutations in traH, traF, trbB, traW, traU, or trbI. A loading control is shown in the lower panel, and the mating efficiency (ME) expressed as a percentage of transconjugants relative to donor cells is given below the gels. n.d., not detected; n.a., not applicable. The last line of data are the complementation data (percent complementation mating efficiency [CME]) obtained by use of clones as described in the text. Previously, TraH was found to interact with TraF, TraU, and TrbI, and TraU interacts with TraW (14).The absence of TrbI appeared to have the most profound effect on the level of TraH, although there was only a 20-fold decrease in mating efficiency, suggesting that enough TraH was present to support mating (Fig. ​(Fig.3).3). Complementation assays performed with pOX38-trbI472 and pBAD24TrbI plasmids (this study) restored the levels of TraH, possibly by stabilizing it (Fig. ​(Fig.3).3). pBAD24TrbI is based on the vector pBAD24 (Ap^r) and contains the trbI gene cloned into the EcoRI site in pBAD24 (11). However, complementation with pBAD24TrbI did not restore mating efficiency to wild-type levels, confirming that the insertion mutation within pOX38-trbI472 has a weak polar effect on downstream genes in the tra operon (21). Alternatively, overexpression of TrbI from pBAD24TrbI affected mating efficiency.Y2H analysis revealed two regions within TraH that appeared to be important for TraH-TrbI interactions (14). The deletion of 50 N-terminal amino acids (aa 25 to 75) from the mature TraH gave a 40-fold increase in TraH-TrbI interaction in the Y2H assay (14). This region of TraH also contains the highly conserved residues N31, T44, G60, and R65 (numeration includes the 25-aa signal peptide) (Fig. ​(Fig.4A).4A). Site-directed mutagenesis was performed on plasmid pK184TraH by using the QuikChange kit (Stratagene). The mating abilities of MC4100/pOX38-Tc ΔtraH::cat/pK184TraH and derivatives with amino acid substitutions N31A, T44A, G60A, and R65A were determined according to previously described methods using ED24 (Sp^r) as the recipient (20). Transconjugants were selected based on double resistance toward tetracycline and spectinomycin. TraH levels within the donor cells were monitored by immunoblot analysis. The N31A and T44A substitutions did not affect mating efficiency and did not change the level of TraH within donor cells (Fig. ​(Fig.5).5). The G60A and R65A substitutions decreased mating efficiency to undetectable levels. TraH levels remained unchanged in both mutants (Fig. ​(Fig.5).5). MC4100/pOX38-Tc ΔtraH::cat cells with pK184TraHG60A or pK184TraHR65A were also resistant toward pilus-specific phage f1, suggesting that the pilus was not assembled.Open in a separate windowFIG. 4.Multiple sequence alignment of F-like TraH proteins. (A) Alignment of the N-terminal regions. (B) Alignment of the putative TraH-TrbI interaction region. The leader peptide is cleaved after A24 in F TraH, which is marked by an arrow. The degrees of identity are indicated by black and gray boxes above the sequences, with the tallest black boxes representing conservation over all 7 sequences. Positions with 5 or more different amino acids are marked with the shortest black boxes. The gray boxes in the residue number line indicate gaps in some of the sequences. The putative nucleotide triphosphate (NTP) binding site (aa 193 to 200) and the conserved sequence (aa 220 to 226) are underlined. The regions thought to interact with TrbI are bracketed. Asterisks refer to amino acids selected for mutational analysis. GenBank protein accession numbers for the sequences are as follows: for F, {"type":"entrez-protein","attrs":{"text":"BAA97968","term_id":"8918921","term_text":"BAA97968"}}BAA97968; for SXT, {"type":"entrez-protein","attrs":{"text":"AAL59676","term_id":"21885270","term_text":"AAL59676"}}AAL59676; for R391, {"type":"entrez-protein","attrs":{"text":"AAM08008","term_id":"20095142","term_text":"AAM08008"}}AAM08008; for pNL1, {"type":"entrez-protein","attrs":{"text":"NP_049152","term_id":"10956932","term_text":"NP_049152"}}NP_049152; for RTS1, {"type":"entrez-protein","attrs":{"text":"NP_640201","term_id":"21233903","term_text":"NP_640201"}}NP_640201; for pED208, {"type":"entrez-protein","attrs":{"text":"AAM90722","term_id":"22539465","term_text":"AAM90722"}}AAM90722; and for R27, {"type":"entrez-protein","attrs":{"text":"NP_058340","term_id":"10957316","term_text":"NP_058340"}}NP_058340. Sequence alignment was performed with DNAStar software (LazerGene), using the ClustalW algorithm. Highly conserved amino acids as well as a consensus sequence are given above the residue number line.Open in a separate windowFIG. 5.Immunoblot analysis of intracellular levels of TraH in MC4100/pOX38-Tc ΔtraH::cat complemented with different pK184TraH plasmids. C represents the vector control pK184, WT is the wild-type pK184TraH plasmid, and an asterisk refers to the nonspecific band used as the loading control. Mating efficiency (ME), expressed as a percentage of transconjugants relative to donor cells, is given below the gels. n.d., not detected; MW, molecular mass.Sequence analysis also showed the presence of conserved residues N(L/I/Y)X(W/Y)XX(F/L) (N₂₂₀IMWNAL₂₂₆ in F TraH) within the putative TrbI interaction domain (aa 193 to 226) (Fig. ​(Fig.4B)4B) (14). Substitution of N220 with alanine (N220A) did not change the levels of TraH protein in pOX38-Tc ΔtraH::cat/pK184TraHN220A but decreased the mating ability to undetectable levels. The W223A mutation in TraH decreased the level of TraH within donor cells and reduced the mating efficiency 1,000-fold compared to the wild-type level (Fig. ​(Fig.5).5). The N220A and W223A mutants were resistant to f1 phage and could not assemble functional pili. Thus, mutations in N220 and W223 could affect TraH-TrbI interaction, or they may act independently to block TraH function. If TrbI is in the IM as previously reported (21), then the TrbI:TraH pair could be part of a second envelope-spanning structure analogous to the TraV:TraK:TraB scaffold (8, 13).Primary sequence analysis also revealed the presence of a putative Walker A motif within aa 193 to 226 of TraH (G₁₉₃CTVGGKS₂₀₀) (9). Comparison of seven TraH orthologs revealed that this motif is not conserved among TraH-like sequences (Fig. ​(Fig.4B).4B). To confirm whether this sequence might be important in the F plasmid, a triple mutant (G193A/K199A/S200A) was constructed. It reduced mating efficiency 20-fold but did not change the levels of TraH within donor cells (data not shown). Single substitutions (G193A, K199A, or S200A) did not change the mating efficiency or the level of TraH (data not shown). Thus, TraH, a peripheral OM protein, is probably not an NTPase, nor does it bind nucleotides.Our data also revealed that several conserved amino acid residues are critical for TraH function and structure and that TraH stability is dependent on TrbI as well as DsbA and TrbB, which affect disulfide bond formation and isomerization, respectively. Thus, TrbI, in which mutations have only a minor effect on mating ability, plays a more important role than previously thought (21).     

Structural Study of the Serratia entomophila Antifeeding Prophage: Three-Dimensional Structure of the Helical Sheath

The sheath of the Serratia entomophila antifeeding prophage, which is pathogenic to the New Zealand grass grub Costelytra zealandica, is a 3-fold helix formed by a 4-fold symmetric repeating motif disposed around a helical inner tube. This structure, determined by electron microscopy and image processing, is distinct from that of the other known morphologically similar bacteriophage sheaths.The antifeeding prophage (Afp) of Serratia entomophila and Serratia proteamaculans is a naturally occurring virus tail-like structure which delivers a putative toxin molecule that leads to starvation of the New Zealand grass grub Costelytra zealandica (5). Afp is composed of 18 different gene products (molecular masses of 6.5 to 263 kDa). The first 16 open reading frames have orthologues (Photorhabdus virulence cassettes [PVC]) in the insecticidal bacterium Photorhabdus luminescens TTO1 genome (5). Afp and PVCs morphologically resemble a typical R-type bacteriocin (6, 12, 16) However, Afp is the only known phage tail-like protein complex that is not a bacteriocin-protein complex of considerable medical relevance that targets the same or closely related bacterial strains (1, 3, 8, 12). The major component of Afp is a contractile cylindrical outer sheath encasing an inner tube speculated to house the toxin molecule (6). A dome-shaped “head” defines one extremity of the tube, while the other end is attached to a “bell-shaped” structure with a base morphologically similar to the base plate of the T4 bacteriophage tail (9).Transmission electron micrographs of two-dimensional (2D) projections of negatively stained (Fig. ​(Fig.11 A) or frozen-hydrated and vitrified (Fig. ​(Fig.1B)1B) recombinant Afp particles (see Fig. S1 in the supplemental material) were used for computational image analysis. A globally averaged image of the Afp particle in the major configuration (called E here) (Fig. ​(Fig.1C),1C), generated using negatively stained specimens, clearly distinguished the morphologies of the various constituent structural parts. Thus, the cylindrical sheath appears to be formed by a periodic structure harboring a distinctive, inverted-V-shaped feature. A minor population of Afp particles displays an alternate configuration (called C here) where, concomitant with contraction of the sheath (averaged axial compression of ∼52% [see Table S1 in the supplemental material]), the inner tube, shorn off the bell-shaped structure, is revealed (Fig. ​(Fig.1A)1A) (6). Several other bacteriocins undergo such a high degree of compression, which has been characterized in detail for the tail sheath of bacteriophage T4 (9). We also generated individual global averages for the periodic sheath structure, for the bell-shaped structure, and for the inner tube (Fig. ​(Fig.1C)1C) which provide more accurate dimensions of these different sections (see Table S1 in the supplemental material) than those reported earlier (6).Open in a separate windowFIG. 1.(A) Electron micrograph of a negatively stained preparation of partially purified recombinant Afp particles. The gray, white, and black arrows point to an Afp particle in the extended (E) configuration, to an Afp particle with the sheath contracted, exposing the inner tube in the contracted (C) configuration, and to an inner tube with the bell-shaped structure attached at one end, respectively. (B) Cryoelectron micrograph recorded from a preparation similar to that shown in panel A. (C) Globally averaged images of Afp particles (3,026 images) in the E state and the three distinguishable parts visualized by negative staining. Bars, 200 Å. (D) Averaged power spectrum of the sheath of vitrified Afp particles. The black and white arrows indicate reflections delineating the axial rise (1/78.5 Å) and the helical pitch (1/118 Å), respectively. In panels A and C, lighter regions represent protein and the contrast is reversed in panel B. Global averages were created using classalign2 of the EMAN suite (10) and visualized in bshow (4).For a better insight, we determined the 3D structure of the central periodic section of the Afp particle in the E state. A global power spectrum derived from the cryoimages established the structure to be helical with a clear first meridional reflection at 1/78.5 Å and the first, strongest nonmeridional reflection at 1/118 Å (Fig. ​(Fig.1D).1D). These reflections correspond to the axial rise (Δx) and the pitch of the helix, respectively, and reflect a turn angle (Δψ) of about ±240° (3₂ helix) for the repeating motif. The correct sign, i.e., the hand, of the helix remains to be determined. Computationally excised overlapping segments of this helical section from images of vitrified and negatively stained Afp particles were subjected to 3D reconstruction using the iterative helical real-space reconstruction (IHRSR) algorithm (2) using the determined helical parameters (see Fig. S2 in the supplemental material). After a few iterations, the presence of an in-plane 4-fold symmetry (C4) was apparent in the density map (see Fig. S2 in the supplemental material), which was then imposed in the subsequent reconstruction exercises. However, no stable solution was forthcoming, even after many (e.g., 30) iterative cycles. This is generally indicative of the presence of heterogeneity in the form of variations in helix translation and/or twist angle (15) in the structure. As a first step, we focused our attention on the pitch value, and following classification (see Fig. S3 in the supplemental material), we found that the majority of the image segments correspond to a pitch of 120 Å. These segments were then selected out of the full data set and led to a stable and refined 3D reconstruction. We also obtained very comparable results for the helical section when images of negatively stained Afp sheath sections were used, thus supporting our computational approach (see Fig. S4 in the supplemental material) and general conclusions about the E state described below.Figure ​Figure22 A is an isosurface representation of the density map of the helical Afp sheath in the E state calculated at ∼21.5-Å resolution (see Fig. S5 in the supplemental material). To the best of our knowledge, a 4-fold rotational symmetry has not been seen for any other contractile T4 bacteriophage taillike structure, which points to the unique architecture of the Afp sheath. A power spectrum generated using the 2D projection from the final density map, compared to the experimental global power spectrum (Fig. ​(Fig.2D),2D), showed strong agreement, confirming the fidelity of the computational image analysis. The density map displays protein layers, ∼80 Å thick, that are stacked on each other in a periodic fashion. The uneven outer surface of the sheath is perforated and decorated with ∼35-Å protrusions. When rendered with a raised threshold, a characteristic feature of the map is a contiguous, high-electron-density region having an inverted-Y-shaped structure (Fig. 2C and E; see Fig. S4 in the supplemental material). At the modest ∼21.5-Å resolution, the boundary of the repeating subunit cannot be defined. A 25 ± 3-Å-wide central lumen is seen clearly when viewed along the helix axis (Fig. ​(Fig.2B)2B) and likely represents the pore of the inner tube (see also below). Using scanning transmission electron microscopy (STEM) (see Fig. S6 in the supplemental material), we estimated the averaged molecular mass of the central helical section of an Afp particle to be 9.8 ± 0.4 kDa/Å (Fig. ​(Fig.3)3) (14) and that of only the inner tube to be ∼2.5 kDa/Å, based on a relatively small pool of such images. These values translate to a mass contribution of approximately 145 kDa of the subunit whose periodic arrangement forms the outer component of the sheath (i.e., excluding the inner tube) (see Fig. S6 in the supplemental material). This value is not very different from the cumulative mass of the different proteins, i.e., homologous afp2, afp3, and afp4, thought to be involved in Afp sheath formation (5) (see Fig. S7 in the supplemental material).Open in a separate windowFIG. 2.Orthogonal isosurface rendering, at 1 σ (standard deviation) of the computed ∼21.5-Å density map of the helical sheath of the vitrified Afp particle viewed normal (A) and parallel (B) to the helix. The images were generated using the software package CHIMERA (13). The arrow indicates a surface perforation. (C) The Afp density map rendered at 3.5 σ to highlight the largest contiguous high-electron-density regions; one circumscribed by a black ellipse is computationally extracted and shown in panel E. (D) Comparison of the experimental, averaged power spectrum of the helical sheath of Afp (left) with that computed (right) from the 2D projection of the calculated density map. (F) Global average of the inner tube of the Afp particle and a plot of the surface density variation (scaled from 0 to 1) along the helical (y) axis. The dimension along the tube is plotted on the x axis.Open in a separate windowFIG. 3.(A) Dark-field micrograph of a freeze-dried, unstained preparation of Afp particles used in STEM measurements. An Afp particle in the E state, an Afp inner tube with the attached bell-shaped structure, and a tobacco mosaic virus particle, used as a calibration standard, are marked by the arrowhead and the gray and white arrows, respectively. (B) Histogram plot of the measured distributions of mass per unit length corresponding to the uniform periodic section of the Afp particles overlaid with a fitted Gaussian curve produced by using the ORIGIN6 software package.A paucity of images of the C state (∼5% of the complete data set) precluded a full, refined 3D reconstruction, but based on the available 2,774 overlapping image segments of the isolated inner tube, a global average was calculated. A plot of contrast variation (Fig. ​(Fig.2F)2F) indicates that the surface is characterized by ∼40-Å spaced elevated crests and invaginated grooves, in agreement with the calculated axial rise of ∼39 Å for the subunit (see Fig. S8 in the supplemental material) comprising the tube. Based on these preliminary results, it appears that the helical symmetry of the inner tube is markedly different from that of the sheath.Our observation that the pitch of the helix in the E state can vary by as much as ∼50 Å attests to the flexible nature of the sheath, which is required for compressibility and may be facilitated by the somewhat porous nature of the sheath (Fig. ​(Fig.2).2). Preliminary deductions (data not shown) based on a small pool of images of the C state suggest profound rearrangement of the elements of the sheath. How that translates to extrusion of the toxin remains to be revealed.      

Identification and Characterization of Inorganic Pyrophosphatase and PAP Phosphatase from Thermococcus onnurineus NA1

Two hypothetical genes were functionally verified to be a pyrophosphatase and a PAP phosphatase in Thermococcus onnurineus NA1. This is the first report of the pyrophosphatases and the PAP phosphatases being organized in the gene clusters of the sulfate activation system only in T. onnurineus NA1 and “Pyrococcus abyssi.”Sulfate is assimilated through reduction to sulfite and incorporation into the sulfur metabolites such as cysteine, methionine, or homocysteine (4) and through sulfation of various metabolites by the action of sulfotransferases (13, 15, 22, 27) (Fig. ​(Fig.1).1). The sulfate assimilation pathways require the activation of sulfate, forming adenosine 5′-phosphosulfate (APS) by ATP-sulfurylase (EC 2.7.7.4) and 3′-phosphoadenosine-5′-phosphosulfate (PAPS) by APS kinase (EC 2.7.1.25) (11). Pyrophosphatase (EC 3.6.1.1) favors the former reaction by effectively removing inorganic pyrophosphates (PP_i) to phosphates (6). Soluble pyrophosphatases from a wide variety of sources have been identified and classified to two superfamilies, the inorganic pyrophosphatase superfamily (family I) and the DHH (Asp-His-His) phosphoesterase superfamily (family II) (5, 29, 32). However, a specific enzyme for the reaction has not been pinpointed yet. In the latter reaction, PAPS enters the reductive sulfate assimilation pathway involving PAPS reductase or is utilized as a sulfate donor for sulfotransferase, yielding 3′-phosphoadenosine-5′-phosphate (PAP). The specific PAP phosphatase has been known to remove the 3′-phosphate of PAP to prevent the intracellular trapping of adenine nucleotides and the inhibition of PAPS reductase, sulfotransferase, and oligoribonuclease by the metabolite (19, 28). A 3′(2′),5′-diphosphonucleoside 3′(2′)-phosphohydrolase from Chlorella species and a 2′(3′),5′-bisphosphate nucleotidase from guinea pig liver could dephosphorylate PAP to AMP (17, 26), and the proteins encoded by cysQ, Rv2131c, HAL2, SAL1, and RHL genes from Escherichia coli, Mycobacterium tuberculosis, yeast, and plants, respectively, and murine bisphosphate nucleotidase were also reported to have phosphomonoesterase activity toward PAP (12, 20, 23, 25, 30).Open in a separate windowFIG. 1.Sulfate assimilation pathways. All intermediates are shown in bold, and enzymes are shown alongside the reaction arrows.In the sequenced hyperthermophilic archaeal genome of Thermococcus onnurineus NA1 (16), two genes encoding the ATP sulfurylase (TON_1707) and the APS kinase (TON_1704) could be identified by sequence similarity with their counterparts. Those genes flank two open reading frames, TON_1705 and TON_1706, which are annotated as hypothetical proteins. The Sequence Similarity Database gene cluster search (http://www.genome.jp) of the Kyoto Encyclopedia of Genes and Genomes revealed that clustering of all four genes was maintained in “Pyrococcus abyssi,” while Staphylothermus marinus, Aeropyrum pernix, Ignicoccus hospitalis, and Pyrobaculum islandicum showed clustering of only three genes except the TON_1706 ortholog (Fig. ​(Fig.22).Open in a separate windowFIG. 2.Organization of the gene cluster involved in sulfate activation system. Comparison of T. onnurineus NA1 gene cluster and the corresponding region in other genomes. Open reading frames with sequence similarities are outlined using the same pattern.TON_1705 orthologs are annotated as hypothetical proteins or type I phosphodiesterase/nucleotide pyrophosphatases, which catalyze the cleavage of phosphodiester and phosphosulfate bonds in NAD, deoxynucleotides, and nucleotide sugars. TON_1705 exhibited 36 to 82% similarity in its amino acid sequence to its orthologs and contained residues involved in metal binding or catalysis which are conserved in the members of the alkaline phosphatase superfamily (8-10). A motif search of the protein sequence of TON_1706 using Pfam suggests that it might belong to a DHH phosphoesterase superfamily including functionally related enzymes such as the family II inorganic pyrophosphatases, prune, a cyclic AMPase and RecJ, a single-stranded DNA exonuclease (1). TON_1706 and its ortholog, P. abyssi PAB1596 (a hypothetical protein with 62% identity), bear the characteristic triplet motif, Asp-His-His, that contributes to the active site and also three other motifs conserved in the DHH phosphoesterase superfamily. The phylogenetic tree computed with the multiple sequence alignment produced by T-Coffee revealed that TON_1706 and PAB1596 formed a cluster distinct from all other members of DHH subfamilies 1 and 2 (data not shown).Since TON_1705 and TON_1706 genes are flanked by ATP sulfurylase and APS kinase, we predicted their functionalities by considering which activities the enzymes in the respective superfamily could show in connection with the sulfate assimilation pathway. For TON_1705 belonging to the alkaline phosphatase superfamily, it was predicted to be a phosphatase, a nucleotide pyrophosphatase, or a sulfohydrolase, which is required to modulate the concentrations of various adenylate compounds such as PAPS, APS, AMP, or ADP and pyrophosphate. It has been reported that the sulfohydrolytic activities to degrade PAPS and APS in rat liver and human placenta were due to enzymes having a nucleotide pyrophosphatase nature (7, 31). TON_1706 was predicted to function as a PAP phosphatase by the clue that YtqI from Bacillus subtilis belongs to the DHH phosphoesterase superfamily and has PAP phosphatase activity along with oligoribonuclease activity (7, 18, 31).The TON_1705 and TON_1706 genes were PCR amplified from T. onnurineus NA1 genomic DNA and cloned into the pET-24a(+) vector (Novagen, Madison, WI). Proteins were overexpressed in E. coli Rosetta(DE3)pLysS (Stratagene, La Jolla, CA) in Luria-Bertani medium by induction with 1 mM isopropyl-β-d-thiogalactopyranoside at 37°C. The proteins were purified to homogeneity using Talon metal affinity column chromatography (BD Biosciences Clontech, Palo Alto, CA). The buffer of the proteins was then exchanged with 50 mM Tris-HCl buffer (pH 8.0), which includes 10% glycerol, using Centricon YM-10 (Millipore, Bedford, MA). Each 37-kDa and 56-kDa protein was shown to be the major component of the purified protein samples by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis.The nucleotide pyrophosphatase, the sulfohydrolase, or the phosphatase activity of the TON_1705-encoded protein was examined using adenylate compounds such as ATP, ADP, AMP, 3′-AMP, PAPS, and APS as substrates (2, 3, 11, 24), but little or no phosphohydrolytic or sulfohydrolytic activity was detected for those substrates (Table ​(Table11 and data not shown). However, the protein exhibited very high pyrophosphatase activity, hydrolyzing inorganic pyrophosphate to orthophosphate (Table ​(Table1).1). Thus, this results in expanding the substrate spectrum of the alkaline phosphatase superfamily. The pyrophosphatase activity was pH dependent and evaluated to be maximal in the pH 9.0 to 9.5 range (Fig. ​(Fig.3A).3A). In the absence of metal ions, no activity was detected (data not shown), and the enzyme activity relied on the presence of the Mg²⁺ ion (Fig. ​(Fig.3B).3B). The result confirms the metalloenzymatic nature of the TON_1705-encoded protein, as all the members of the alkaline phosphatase superfamily have strong dependency on divalent cations. Maximal activity of the enzyme was observed with the Mg²⁺ ion at the concentration of 0.2 mM (data not shown). The kinetic parameters of the enzyme, K_m and k_cat, toward pyrophosphate were determined to be 18.8 μM and 2.1 s⁻¹, respectively. The affinity of the enzyme for pyrophosphate was between K_m values of smaller than 10 μM for most family I pyrophosphatases and high K_m values of 90 to 160 μM for family II pyrophosphatases (21). The k_cat/K_m value of 1.1 × 10⁵ M⁻¹ s⁻¹ is 1 or 2 orders of magnitude lower than those of the family I pyrophosphatase from Pyrococcus horikoshii (6.6 × 10⁶) (14) and the family II pyrophosphatase of Bacillus subtilis (2.0 × 10⁷) (21).Open in a separate windowFIG. 3.Effects of pH (A) and divalent metal ions (B) on the pyrophosphatase activity of a TON_1705-encoded protein. (A) pH dependence reactions were run with the following buffers (each at 50 mM) chosen on the basis of pH measured at room temperature: MOPS (4-morpholinepropanesulfonic acid) (triangles) and Tris-HCl (upside-down triangles). (B) Various divalent metal ions were added at a concentration of 1 mM.

TABLE 1.

Substrate specificity of the phosphatase activities of the TON_1705- and TON_1706-encoded proteins

Intestinal Endocellular Symbiotic Bacterium of the Macaque Louse Pedicinus obtusus: Distinct Endosymbiont Origins in Anthropoid Primate Lice and the Old World Monkey Louse

A symbiotic bacterium of the macaque louse, Pedicinus obtusus, was characterized. The symbiont constituted a gammaproteobacterial lineage distinct from the symbionts of anthropoid primate lice, localized in the midgut epithelium and the ovaries and exhibiting AT-biased genes and accelerated molecular evolution. The designation “Candidatus Puchtella pedicinophila” was proposed for it.Sucking lice (Insecta: Phthiraptera: Anoplura), ectoparasitic insects that feed exclusively on the blood of their specific mammalian hosts, are generally associated with endosymbiotic bacteria (2, 13). Recent molecular studies have demonstrated that symbiotic bacteria of sucking lice are of multiple evolutionary origins (1, 8, 10, 16).From primates, three louse genera, Pediculus, Pthirus, and Pedicinus, have been recorded. Three Pediculus and two Pthirus species are known from anthropoid primates, harboring gammaproteobacterial “Candidatus Riesia spp.” in the stomach disc (1, 16). Meanwhile, 14 Pedicinus species, whose symbiotic bacteria have not been characterized, have been recorded from Old World monkeys (3).Samples of Pedicinus obtusus were collected in 2008 at the Jigokudani Monkey Park, Nagano, Japan, where a wild population of the Japanese macaque, Macaca fuscata, is exhibited to the public under careful control. When animals were caught and inspected, samples of P. obtusus were collected from the anesthetized animals under the supervision of a veterinary doctor (permission number 19-26-24, Nagano Prefecture, Japan). Samples of P. obtusus were collected in November 2008 by courtesy of Kiyoyasu Kowaki from a subspecies of the Japanese macaque, M. fuscata yakui, that is endemic in Yakushima Island, Kagoshima, Japan. Each of the insect samples was subjected to DNA extraction, and a 1.5-kb segment of the 16S rRNA gene (5) and a 1.6-kb segment of the groEL gene (7) were amplified by PCR, cloned, and sequenced. Molecular phylogenetic analyses were performed using the programs PAUP 4.0b10 (Sinauer Associates, Sunderland, MA), RAxML version 7.0.0 (17), and MrBayes 3.1.2 (15).The 1,490-bp 16S rRNA gene sequences formed a distinct lineage in the Gammaproteobacteria, exhibiting no phylogenetic affinity to the symbionts of other louse species, including those of human lice and the chimpanzee louse (see Fig. S1 in the supplemental material). The 1,601-bp groEL gene sequences also constituted a gammaproteobacterial lineage, exhibiting no phylogenetic affinity to the symbiont of human lice (Fig. ​(Fig.1)1) These results indicated that the endosymbiotic bacterium of the Old World monkey louse evolved independently of the endosymbiotic bacteria of the anthropoid primate lice. Considering that the date of divergence of Old World monkeys and anthropoid primates has been inferred as 23 to 31 million years ago, the endosymbiotic evolution in the primate lice must have occurred within this time scale (12).Open in a separate windowFIG. 1.groEL gene sequence-based molecular phylogenetic analysis of the symbiont of P. obtusus in the Gammaproteobacteria. A maximum-likelihood tree inferred from 1,040 unambiguously aligned nucleotide sites is shown. Bayesian and neighbor-joining analyses gave essentially the same results (data not shown). Statistical support values higher than 70% are indicated at the nodes in the order of maximum-likelihood/Bayesian/neighbor-joining values. Asterisks indicate statistical support values lower than 70%. Sequence accession numbers are shown in brackets. AT contents of the sequences are also shown. The sequences from the symbionts of human and monkey lice are highlighted in boldface. P-symbiont, primary symbiont; S-symbiont, secondary symbiont.The molecular evolutionary rates of the symbiont gene sequences were analyzed with a relative rate test using the program RRTree (14). The evolutionary rates of the 16S rRNA and groEL gene sequences in the lineage of the P. obtusus symbiont were significantly higher than those in the lineages of related free-living gammaproteobacteria (see Table S1 in the supplemental material).The AT contents of the 16S rRNA and groEL gene sequences of the P. obtusus symbiont were 53.5% and 64.8%, respectively. These values were equivalent to those of obligate endosymbionts of other insects (>50% for the 16S rRNA gene and >60% for the groEL gene) and were remarkably higher than those of allied free-living gammaproteobacteria (∼45% for the 16S rRNA gene and 45 to 50% for the groEL gene) (Fig. ​(Fig.1;1; see Fig. S1 in the supplemental material).Obligate endosymbiotic bacteria that cospeciate with their host insects commonly exhibit peculiar genetic traits, including AT-biased nucleotide composition, an accelerated rate of molecular evolution, and significant genome reduction (18). The AT-biased nucleotide composition and the accelerated evolution observed with the P. obtusus symbiont (Fig. ​(Fig.1;1; see Fig. S1 and Table S1 in the supplemental material) are suggestive of a stable and intimate host-symbiont association over evolutionary time.Fluorescent in situ hybridization targeting 16S rRNA of the symbiont was performed using the Alexa Fluor 555-labeled oligonucleotide probes Al555-ML439 (Al555-5′-ATAATATCTTCTTTCCTACCGA-3′) and Al555-ML1256 (Al555-5′-GCTAATTCTTGCGAATTTGCTT-3′) as described previously (9). In first-, second-, and third-instar nymphs, the symbiont signals were detected in the posterior half of the stomach in the abdomen (Fig. ​(Fig.2A).2A). In the posterior stomach, the signals exhibited a periodical and striated pattern (Fig. ​(Fig.2B).2B). Magnified images located the symbiont signals endocellularly in the intestinal wall tissue (Fig. ​(Fig.2C).2C). In some of the third-instar nymphs, the symbiont signals were found not only in the posterior stomach but also in the ovaries (Fig. ​(Fig.2A).2A). In adult females, the symbiont signals were restricted to the lateral oviducts (Fig. ​(Fig.2A),2A), where many bacteriocytes formed a pair of symbiotic organs called ovarial ampullae (Fig. ​(Fig.2D).2D). The ovarial ampullae were located adjacent to developing oocytes in the ovarioles, where the symbiont was passed to the developing eggs (Fig. ​(Fig.2E2E).Open in a separate windowFIG. 2.Localization of the symbiont in nymphs and adults of P. obtusus. (A) General localization of the symbiont in nymphal and adult insects. The symbiont signals are seen in the posterior stomach (green arrows) and the ovarial ampullae (yellow arrows). (B) An image of the posterior stomach of a second-instar nymph. Periodical and striped regions are densely populated by the symbiont. (C) An image of the posterior stomach of a third-instar nymph. The symbiont signals are restricted to the gut epithelial cells and not detected in the stomach lumen. Bacteriocytes are intercalated with uninfected cells, forming a striated pattern. (D) An enlarged image of the ovarial ampulla, consisting of a number of uninucleated bacteriocytes. (E) An image of the ovary in an adult female, wherein developing oocytes are found in the ovarioles. Ovarial ampullae (yellow arrows) are located at the anterior tip of the lateral oviducts, where symbiont transmission to oocytes occurs (white arrow). Panel A shows epifluorescent images, while panels B to E are confocal optical sectioning images. Red and blue signals reflect the symbiont 16S rRNA and the host nuclear DNA, respectively. Abbreviations: lu, stomach lumen; oc, oocyte.These results suggested that in third-instar female nymphs of P. obtusus, the symbiont localization drastically changes, from the posterior stomach to the ovarial ampullae (Fig. ​(Fig.2A).2A). Presumably, the endocellular symbiont escapes the host cells and somehow moves to the female reproductive organ, establishing a new endocellular association and finding a way to the next host generation. Interestingly, such symbiont migrations from a symbiotic organ to the ovaries in third-instar female nymphs have been reported for the human body louse Pediculus humanus (4, 13) and the slender pigeon louse Columbicola columbae (6, 13). Here it is notable that the symbiotic bacteria of P. obtusus, P. humanus, and C. columbae are phylogenetically not related to each other (see Fig. S1 in the supplemental material). The mechanisms underpinning the symbiont migration are currently unknown. Eberle and McLean (4) suggested by a series of experiments that the ovary of the human body louse might emanate a humoral factor that attracts the symbiotic bacteria to induce the migration. Whether or not this hypothesis is true deserves future experimental studies of these louse species and their symbiotic bacteria.On the basis of these results, we propose the designation “Candidatus Puchtella pedicinophila” for the novel endosymbiont lineage. The generic name honors Otto Puchta, who identified the biological role of the human louse symbiont as the provision of B vitamins (11). The specific name indicates association with a Pedicinus monkey louse. Whether the other monkey lice harbor symbiotic bacteria allied to the symbiont of P. obtusus deserves future studies.     

Simple,Fast, and Sensitive Method for Quantification of Tellurite in Culture Media

A fast, simple, and reliable chemical method for tellurite quantification is described. The procedure is based on the NaBH₄-mediated reduction of TeO₃²⁻ followed by the spectrophotometric determination of elemental tellurium in solution. The method is highly reproducible, is stable at different pH values, and exhibits linearity over a broad range of tellurite concentrations.The tellurium oxyanion tellurite is toxic for most organisms, making important its accurate assessment. Several methods for quantifying tellurite have been described to date. However, most of them are rather complicated and require sophisticated equipment and in some cases the detection is not quite sensitive enough to allow the assessment of TeO₃²⁻ concentrations below 50 μg/ml (200 μM). For example, the analytical determination of tellurium (Te) oxyanions by atomic absorption spectrometry (AAS) is hampered by poor sensitivity. Where flame or electrothermal AAS routinely yields detection limits of less than 10 ppb for iron (16), normal flame AAS tellurium detection limits are 100 to 1,000 times higher and require pretreatment to achieve the +IV oxidation state before analysis (11).On the other hand, hydride generation AAS (HGAAS) is used to achieve ppb-level detection limits for Se and Te as well as arsenic and antimony among others. For Te the volatile hydride gas H₂Te is generated by first converting the metalloid to the +IV oxidation state and then by chemical reduction to the gaseous hydride using—almost universally—sodium borohydride (NaBH₄). In automated HGAAS systems, an inert purge gas sweeps the volatile hydride formed in a glass reaction vessel into a quartz cell heated by the AAS flame where gaseous hydride decomposition and atomization occur. Though tellurite reduction, precipitation, and detection methods have been reported (3, 17), they are temporally relatively unstable and pH dependent.Since tellurium is toxic and environmentally important (7, 8), determining low concentrations in bacterial cultures is very desirable and a simple analysis without pretreatment steps that could quickly establish total metalloid oxyanion content in a liquid sample would be a plus. Here we report a new method for the determination of tellurite in bacterial culture media. This procedure is based on the NaBH₄ reduction of tellurite to the elemental form, which is analyzed spectrophotometrically at 500 nm or 320 nm (see below), by which the light scattered by the particles of elemental metalloid in solution is measured. While the detection limits do not compare to those of HGAAS (14) or capillary electrophoresis (13), they do approach those of old flame AAS but involve a much simpler and quicker procedure requiring only one reagent and a spectrophotometer to determine total content of solutions of +IV oxyanions in solution. Linear calibration range, method development time and probe stability, effect of sample pH, common interferences, and detection limits were investigated.Calibration curves to determine K₂TeO₃ concentrations in routinely used microbiological culture media such as Luria-Bertani (LB) or M9 minimal medium amended with 0.2% glucose (15) were constructed. A set of solutions containing increasing concentrations of K₂TeO₃ (Sigma) were prepared in LB or M9 culture medium, and the tellurium oxyanion was quantitatively reduced using freshly prepared 3.5 mM NaBH₄ (final concentration).The reaction was carried out at 60°C for 10 min (bubbling was overcome by vortexing), and after 5 min at room temperature, the optical density at 500 nm (OD₅₀₀) was determined spectrophotometrically as described previously (4, 5, 9, 12). Blanks contained no borohydride. Figure ​Figure11 shows that in both media good curve linearity was obtained, with r² values of 0.9740 and 0.9963 for LB and M9, respectively. Tellurite concentrations lower than 1 μg/ml or higher than 200 μg/ml were also tested, but OD₅₀₀ values were close to the spectrophotometer error limit at low concentrations or nonlinear above 200 μg/ml (not shown). Thus, the NaBH₄ method allows determination of a wide range of tellurite concentrations in a fast and simple way. Tellurite concentrations lower than 50 μg/ml in both rich and minimal media can be easily determined; the experimental error was about 10%, similar to that reported for the diethyl dithiocarbamate (DDTC) tellurite method (17).Open in a separate windowFIG. 1.Calibration curves to determine K₂TeO₃ concentrations in LB (A) (R² = 0.9963) or M9 minimal (B) (R² = 0.9740) medium. Optical density at 500 nm was determined after reducing the oxyanion with sodium borohydride. Error bars denote 1 standard deviation of three replicates.To analyze the resulting solutions after tellurite reduction by NaBH₄, absorption/scattering spectra were determined. Figure ​Figure22 shows that spectra from LB and those from M9 after tellurite reduction are quite different, which may be a consequence of the different chemical compositions of these culture media. In both cases, absorption spectra showed linearity between optical density at 500 nm and tellurite concentration in the sample. However, high tellurite concentrations (∼100 μg/ml) caused a loss of linearity in LB medium.Open in a separate windowFIG. 2.Absorption spectra after reducing samples of LB (A) or M9 (B) culture medium containing increasing tellurite concentrations with 3.5 mM NaBH₄. Tellurite concentrations used were 20, 40, 60, 80, and 100 (LB) and 2, 4, 6, 8, and 10 (M9) μg/ml. (Inset) Calibration curve in M9 medium using the absorbance maxima at 320 nm.Figure ​Figure2B2B shows that in M9 medium there is a zone around 320 nm exhibiting higher optical density than that at 500 nm, which represents an advantage in the determination of tellurite in chemically defined culture media. This is reflected in a wider range of measurable concentrations at 320 nm (Fig. ​(Fig.2B,2B, inset), as well as in a higher sensitivity of the method as determined by the slope of the calibration curve. The product of tellurite reduction by NaBH₄ showed good stability at both wavelengths in rich and minimal culture media (not shown).Since in M9 medium the method allows the determination of minor tellurite concentrations (1 to 20 μg/ml), it would be of great help in assessing tellurite uptake in tellurite-sensitive microorganisms whose MICs range from 1 to 10 μg/ml. Sulfur-containing salts, commonly present in culture media as sulfites and sulfates, did not interfere with our NaBH₄ method for tellurite assessment at concentrations up to 0.5 M (not shown).As shown in Fig. ​Fig.3,3, tellurite assessment was not affected by the pH of the culture medium. In fact, linearity was observed in a wide pH range with minor slope changes in LB. Similar results were obtained with M9 medium, although tellurite assessment was not possible at pH values higher than 7.0 because of the formation of a precipitate. This may be due to an interaction of the phosphate salts present in the medium and some charged (2⁺) chemical species forming at alkaline pH values, as has been reported earlier (17).Open in a separate windowFIG. 3.Effect of pH in determining tellurite concentrations in LB (A) and M9 minimal (B) media.To date, the most commonly used procedure for determining tellurite in culture media is that involving the spectrophotometric determination (340 nm) of the complex that forms between tellurite and diethyl dithiocarbamate (17). This procedure has been used to assess tellurite uptake by the phototrophic bacterium Rhodobacter capsulatus, which is naturally resistant to K₂TeO₃ (MIC, ∼1.4 mM) (2, 3). However, K₂TeO₃ uptake studies in highly sensitive cells such as Escherichia coli (MIC, ∼4 μM) are difficult to carry out because of the low concentrations of toxicant present in the culture medium, far below the detection limit of the DDTC procedure (17).In this context and for testing the applicability of our method in vivo, we used the tellurite-sensitive bacterium E. coli BW25113 (10) and the tellurite-resistant Aeromonas caviae ST (5, 6). An overnight culture of E. coli BW25113 in M9 minimal medium was diluted 100-fold with fresh M9 supplemented with 0.2% glucose and grown at 37°C with shaking. When the OD₆₀₀ was 0.1, the culture was amended with 20 μg/ml K₂TeO₃ (arrow, Fig. ​Fig.4A).4A). Then aliquots were taken at the indicated times and cells were centrifuged at 8,500 × g for 3 min; supernatants were used to assess extracellular tellurite by our NaBH₄ method. While added tellurite did not affect bacterial growth (Fig. ​(Fig.4A),4A), the remaining tellurite in the supernatant dropped approximately to one-third after 3 h (Fig. ​(Fig.4B).4B). Tellurite determinations were validated using, in parallel, the DDTC method (not shown).Open in a separate windowFIG. 4.Tellurite uptake by Escherichia coli. Time zero in panel B represents the moment of tellurite addition.Regarding the tellurite-resistant bacterium A. caviae ST, a 1:100 dilution of an overnight culture was inoculated into fresh LB medium and the OD₆₀₀ was recorded at the indicated times. When the OD₆₀₀ was ∼0.4, the culture was amended with tellurite (400 μg/ml final concentration) (Fig. ​(Fig.5A,5A, arrow) and the remaining tellurite in the supernatants was assessed as described above. Figure ​Figure5B5B shows that in 4 h ∼27% of the toxic oxyanion was removed from the culture medium.Open in a separate windowFIG. 5.Tellurite uptake by Aeromonas caviae ST. See the text for details.In summary and in comparison to the DDTC procedure, the NaBH₄ method described here allows more sensitive determination of the initial tellurite concentrations as well as the continuous uptake of the toxicant by tellurite-sensitive and tellurite-resistant microorganisms. This method should be of great help in future studies aimed at unveiling the tellurite reductase activity exhibited by some metabolic enzymes such as nitrate reductase (1), catalase (4), and the pyruvate dehydrogenase complex (5, 6). These studies are currently being carried out in our laboratory.     

Structure-Based Rational Design of a Phosphotriesterase

In silico substrate docking of both stereoisomers of the pesticide chlorfenvinphos (CVP) in the phosphotriesterase from Agrobacterium radiobacter identified two residues (F131 and W132) that prevent productive substrate binding and cause stereospecificity. A variant (W131H/F132A) was designed that exhibited ca. 480-fold and 8-fold increases in the rate of Z-CVP and E-CVP hydrolysis, respectively, eliminating stereospecificity.Synthetic organophosphate pesticides (OPs) can cause acute neurotoxicity in insects and humans as a result of their inhibition of acetylcholinesterase at the nerve synapse (15). The >90% identical bacterial phosphotriesterases (PTEs) from Pseudomonas diminuta (oph; PTE_Pd) (5) and Agrobacterium radiobacter (opdA; PTE_Ar) (9) efficiently catalyze the hydrolysis of a broad range of OPs, effectively detoxifying them. This has led to the commercialization of PTE_Ar as a free-enzyme bioremediant (14) and its use in treating OP poisoning in animal studies (1). However, not all OPs are efficiently turned over by the PTEs. For instance, despite having a reasonably reactive leaving group (Fig. ​(Fig.1),1), the turnover of chlorfenvinphos (CVP) by PTE_Ar was not detected in a previous study (9).Open in a separate windowFIG. 1.Structures of the leaving groups of all the substrates discussed in this work. (a) 3,5,6-Trichloro-2-pyridinol for methyl chlorpyrifos oxon; (b) 4-nitrophenol for methyl paraoxon and methyl parathion; (c) 2,2-dichloroethenol for dichlorvos; (d) Z/E-2-chloro-1-(2,4-dichlorophenyl)ethanol for E/Z-CVP; (e) 4-methoxyphenol for EPO.