Penicillin-binding proteins of pathogenic Escherichia coli strains

The penicillin-binding proteins of 11 pathogenic Escherichia coli strains, including enteropathogenic, enterotoxigenic, enteroinvasive, enteroaggregative, and enterohemorrhagic E. coli, were detected in gels following the labeling of isolated cell envelopes with [³H]benzylpenicillin. The electrophoretic profiles, sensitivities to and morphological changes induced by β-lactam antibiotics showed that the penicillin-binding proteins of most pathogenic E. coli possess structural and physiological functions similar to those of E. coli K12.     

Coupling site-directed mutagenesis with high-level expression: large scale production of mutant porins from E. coli

Combination of an origin repair mutagenesis system with a new mutS host strain increased the efficiency of mutagenesis from 46% to 75% mutant clones. Overexpression with the T7 expression system afforded large quantities of proteins from mutant strains. A series of E. coli B^E host strains devoid of major outer membrane proteins was constructed, facilitating the purification of mutant porins to homogeneity. This allowed preparation of 149 porin mutants in E. coli used in detailed explorations of the structure and function of this membrane protein to high resolution.     

Mycobacterium tuberculosis AtsG (Rv0296c), GlmU (Rv1018c) and SahH (Rv3248c) Proteins Function as the Human IL-8-Binding Effectors and Contribute to Pathogen Entry into Human Neutrophils

Mycobacterium tuberculosis is an extremely successful intracellular pathogen that has evolved a broad spectrum of pathogenic mechanisms that enable its manipulation of host defense elements and its survival in the hostile environment inside phagocytes. Cellular influx into the site of mycobacterial entry is mediated by a variety of chemokines, including interleukin-8 (IL-8), and the innate cytokine network is critical for the development of an adaptive immune response and infection control. Using affinity chromatography, liquid chromatography electrospray ionization tandem mass spectrometry and surface plasmon resonance techniques, we identified M. tuberculosis AtsG arylsulphatase, bifunctional glucosamine-1-phosphate acetyltransferase and N-acetylglucosamine-1-phosphate uridyl transferase (GlmU) and S-adenosyl-L-homocysteine hydrolase (SahH) as the pathogen proteins that bind to human IL-8. The interactions of all of the identified proteins (AtsG, GlmU and SahH) with IL-8 were characterized by high binding affinity with K_D values of 6.83x10^-6 M, 5.24x10^-6 M and 7.14x10^-10 M, respectively. Furthermore, the construction of Mtb mutant strains overproducing AtsG, GlmU or SahH allowed determination of the contribution of these proteins to mycobacterial entry into human neutrophils. The significantly increased number of intracellularly located bacilli of the overproducing M. tuberculosis mutant strains compared with those of “wild-type” M. tuberculosis and the binding interaction of AtsG, GlmU and SahH proteins with human IL-8 may indicate that these proteins participate in the modulation of the early events of infection with tubercle bacilli and could affect pathogen attachment to target cells.     

Genetic diversity of Rhodopirellula strains

Rhodopirellula baltica SH1^T is a marine planctomycete with 7,325 genes in its genome. Ten strains of the genus Rhodopirellula were studied in whole genome microarray experiments to assess the extent of their genetic relatedness to R. baltica SH1^T. DNA of strains which were previously affiliated with the species R. baltica (OTU A) hybridized with 3,645–5,728 genes of the type strain on the microarray. Strains SH398 and 6C (OTU B), representing a closely related species with an average nucleotide identity of 88 %, showed less hybridization signals: 1,816 and 3,302 genes gave a hybridization signal, respectively. Comparative genomics of eight permanent draft genomes revealed the presence of over 4,000 proteins common in R. baltica SH1^T and strains of OTU A or B. The genus Rhodopirellula is characterized by large genomes, with over 7,000 genes per genome and a core genome of around 3000 genes. Individual Rhodopirellula strains have a large portion of strain-specific genes.     

The virally encoded killer proteins from Ustilago maydis

Several strains of Ustilago maydis, a causal agent of corn smut disease, exhibit a ‘killer’ phenotype that is due to persistent infection by double-stranded RNA Totiviruses. These viruses produce potent killer proteins that are secreted by the host. This is a rare example of virus/host symbiosis in that these viruses are dependent upon host survival and, to that end, produce antifungal proteins that kill competing, uninfected strains of U. maydis. Two of the best-studied examples of this killer phenomenon are U. maydis strains P4 and P6 that secrete killer proteins KP4 and KP6, respectively. The mature form of KP4 is comprised of 105 residues while KP6 consists of two subunits, a and b chains, 76 and 82 residues in length, respectively. KP6 is not homologous to any known protein, and only recently has KP4 been shown to have possible homologs in pathogenic fungi. While very little is known as to the mode of action of KP6, we have shown that KP4 blocks L-type Ca²⁺ channels in fungi and animal cells in a reversible and cytostatic manner. In contrast, preliminary results suggest that KP6 acts via a completely different mechanism and is a potent cytolytic antifungal protein. When KP4 is expressed in maize, the resulting transgenic lines are nearly immune to U. maydis infection. Therefore, a greater understanding of the modes of action of these potent antifungal proteins could lead to development of broad-spectrum antifungal agents.     

Two-dimensional electrophoresis of membrane proteins factors affecting resolution of rat-liver microsomal proteins

A comparison has been made of published techniques for the resolution of rat liver microsomal proteins by two-dimensional electrophoresis. The method of Kaderbhai and Freedman (Biochim. Biophys. Acta 601 (1980) 21-20) gives good resolution of acidic proteins but excludes hydrophobic integral membrane proteins of pI > 7, including cytochrome P-450 apoproteins. The method of Vlasuk and Walz (Anal. Biochem. 105 (1980) 112–120) gives good resolution of proetins of pI 5–8, including cytochromes P-450, but fails to resolve a major acidic protein of pI < 5. Isoelectric focusing of microsomal proteins is improved by the use of high concentrations of urea and low concentrations of sample proteins. Zwitterionic detergents of the general formula R·N⁺(CH₃)₂·CH₂CH₂CH₂SO₃^? are effective in solubilizing microsomal proteins, either alone or in presence of non-ionic detergent; compounds with a long alkyl chain (C₁₄ or C₁₆) are most effective. Isoelectric focusing of microsomal proteins solubilized by zwitterionic detergents did not give good resolution, probably because of incomplete dissociation and denaturation of the proteins. These detergents could not be used in the presence of high concentrations of urea. Although no single method of two-dimensional electrophoresis gives complete resolution of the whole range of microsomal proteins, conditions can be optimized for specific sets of proteins of interest. The technique can be used to monitor differences in microsomal composition between rat strains, or following induction, and for a variety of other studies.     

The virally encoded killer proteins from Ustilago maydis

Several strains of Ustilago maydis, a causal agent of corn smut disease, exhibit a ‘killer’ phenotype that is due to persistent infection by double-stranded RNA Totiviruses. These viruses produce potent killer proteins that are secreted by the host. This is a rare example of virus/host symbiosis in that these viruses are dependent upon host survival and, to that end, produce antifungal proteins that kill competing, uninfected strains of U. maydis. Two of the best-studied examples of this killer phenomenon are U. maydis strains P4 and P6 that secrete killer proteins KP4 and KP6, respectively. The mature form of KP4 is comprised of 105 residues while KP6 consists of two subunits, a and b chains, 76 and 82 residues in length, respectively. KP6 is not homologous to any known protein, and only recently has KP4 been shown to have possible homologs in pathogenic fungi. While very little is known as to the mode of action of KP6, we have shown that KP4 blocks L-type Ca²⁺ channels in fungi and animal cells in a reversible and cytostatic manner. In contrast, preliminary results suggest that KP6 acts via a completely different mechanism and is a potent cytolytic antifungal protein. When KP4 is expressed in maize, the resulting transgenic lines are nearly immune to U. maydis infection. Therefore, a greater understanding of the modes of action of these potent antifungal proteins could lead to development of broad-spectrum antifungal agents.     

Transcriptional analysis for carbon metabolism and kinetic modeling for heterologous proteins productions by Pichia pastoris in induction process with methanol/sorbitol co-feeding

It is difficult to control concentrations of methanol/dissolved oxygen at high levels simultaneously in heterologous proteins productions by Pichia pastoris during induction phase. Two strains, a methanol utilization slow (Mut^S) type and a plus (Mut⁺) type were used with methanol/sorbitol co-feeding strategy to induce porcine interferon-α and human serum albumin-human granulocyte colony stimulating factor respectively, under the conditions of “methanol sufficient-oxygen limited (MS-OL)” and “methanol limited-oxygen sufficient (ML-OS)”. For the Mut^S/Mut⁺ strains, the target proteins titers under “MS-OL” were 6-fold/19.2% of those under “ML-OS”. The key genes in methanol metabolism of the Mut^S strain were up-regulated under “MS-OL”, but they were not differently expressed in the Mut⁺ strain. Methanol utilization rate (r_MeOH) of the Mut^S strain reduced when decreasing methanol concentration, but r_MeOH of the Mut⁺ strain unchanged unless methanol concentration decreased to a low-limit of 0.6 g/L. Finally, kinetic models were designed to describe the methanol/sorbitol co-feeding process.     

Interactions of Cations with Membrane Fractions of Smooth and Rough Strains of Salmonella typhimurium and Other Gram-Negative Bacteria

Addition of cations (20 to 50 mM for Mg²⁺ or Ca²⁺ or 100 to 500 mM for Na⁺) to N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid buffer during preparation of membranes from smooth and rough strains of Salmonella typhimurium LT2, Salmonella minnesota, and Escherichia coli O8 had two effects on the composition of the membranes isolated. First, in rough strains of chemotypes Ra to Re the “total membranes” (pellets from high-speed centrifugation) were deficient in the proteins of the outer membrane. The missing proteins were found to have been sedimented in a prior low-speed centrifugation in a fraction we call “cation-aggregated membranes.” Since these membranes were enriched for lipopolysaccharide and for outer membrane proteins, deficient in succinic dehydrogenase, and contained primarily the dense peak after sucrose gradient centrifugation, it appears to be relatively pure outer membrane. About 10% of the membrane protein of smooth strains and up to 50% that of rough strains were cation-aggregated membranes, appearing to contain most of the outer membrane of rough strains. Thus, cation aggregation may be a useful means of preparation of outer membrane samples. The second effect was that with cation addition, several high-molecular-weight proteins not seen when membranes were prepared without cation addition were found in the total membranes of both smooth and rough strains after high-speed centrifugation. These proteins were bound by cations to the inner membranes, since they were soluble in Triton X-100 and separated into the less dense peak upon sucrose gradient centrifugation. They originated from the cytoplasm or the periplasm, since they corresponded to soluble proteins found in the supernatant after high-speed centrifugation and were depleted from this supernatant when preparation was done in the presence of cations.     

Repair of O4-Alkylthymine by O6-Alkylguanine-DNA Alkyltransferases

O⁶-Alkylguanine-DNA alkyltransferase (AGT) plays a major role in repair of the cytotoxic and mutagenic lesion O⁶-methylguanine (m⁶G) in DNA. Unlike the Escherichia coli alkyltransferase Ogt that also repairs O⁴-methylthymine (m⁴T) efficiently, the human AGT (hAGT) acts poorly on m⁴T. Here we made several hAGT mutants in which residues near the cysteine acceptor site were replaced by corresponding residues from Ogt to investigate the basis for the inefficiency of hAGT in repair of m⁴T. Construct hAGT-03 (where hAGT sequence -V¹⁴⁹CSSGAVGN¹⁵⁷- was replaced with the corresponding Ogt -I¹⁴³GRNGTMTG¹⁵¹-) exhibited enhanced m⁴T repair activity in vitro compared with hAGT. Three AGT proteins (hAGT, hAGT-03, and Ogt) exhibited similar protection from killing by N-methyl-N′-nitro-N-nitrosoguanidine and caused a reduction in m⁶G-induced G:C to A:T mutations in both nucleotide excision repair (NER)-proficient and -deficient Escherichia coli strains that lack endogenous AGTs. hAGT-03 resembled Ogt in totally reducing the m⁴T-induced T:A to C:G mutations in NER-proficient and -deficient strains. Surprisingly, wild type hAGT expression caused a significant but incomplete decrease in NER-deficient strains but a slight increase in T:A to C:G mutation frequency in NER-proficient strains. The T:A to C:G mutations due to O⁴-alkylthymine formed by ethylating and propylating agents were also efficiently reduced by either hAGT-03 or Ogt, whereas hAGT had little effect irrespective of NER status. These results show that specific alterations in the hAGT active site facilitate efficient recognition and repair of O⁴-alkylthymines and reveal damage-dependent interactions of base and nucleotide excision repair.     

Construction of leaky strains and extracellular production of exogenous proteins in recombinant Escherichia coli

In this study, a strategy of the construction of leaky strains for the extracellular production of target proteins was exploited, in which the genes mrcA, mrcB, pal and lpp (as a control) from Escherichia coli were knocked out by using single- and/or double-gene deletion methods. Then the recombinant strains for the expression of exogenous target proteins including Trx-hPTH (human parathyroid hormone 1–84 coupled with thioredoxin as a fusion partner) and reteplase were reconstructed to test the secretory efficiency of the leaky strains. Finally, the fermentation experiments of the target proteins from these recombinant leaky strains were carried out in basic media (Modified R media) and complex media (Terrific Broth media) in flasks or fermenters. The results demonstrated that the resultant leaky strains were genetically stable and had a similar growth profile in the complex media as compared with the original strain, and the secretory levels of target proteins into Modified R media from the strains with double-gene deletion (up to 88.9%/mrcA lpp-pth) are higher than the excretory levels from the strains with single-gene deletion (up to 71.1%/lpp-pth) and the host E. coli JM109 (DE3) (near zero). The highest level of extracellular production of Trx-hPTH in fermenters is up to 680 mg l⁻¹.     

Establishment of an efficient transformation protocol and its application in marine-derived Bacillus strain

Marine-derived Bacillus strains have been proved to be a very promising source for natural product leads.However,transformation of environmental strains is much more difficult than that of domesticated strains.Here,we report the development of an efficient and robust electroporation-based transformation system for marine-derived Bacillus marinus B-9987,which is a macrolactin antibiotics producer and a very promising biological control agent against fungal plant diseases.The transformation efficiency was greatly enhanced 103-fold by using unmethylated plasmid to bypass modification-restriction barrier,and using glycine betaine to protect cells from electrical damages during electroporation.Addition of HEPES and 2 mmol L?1MgCl2 further improved the efficiency by additional 2-fold,with a maximum value of 7.1×104 cfu/μg pHT3101.To demonstrate the feasibility and efficiency of the protocol,a green fluorescent protein reporter system was constructed;furthermore,phosphopantetheinyl transferase gene sfp,which is essential to the biosynthesis of polyketides and nonribosomal peptides,was overexpressed in B-9987,leading to increased production of macrolactin A by about 1.6-fold.In addition,this protocol is also applicable to marine-derived Bacillus licheniforms EI-34-6,indicating it could be a reference for other undomesticated Bacillus strains.To our knowledge,this is the first report regarding the transformation of marine-derived Bacillus strain.     

Homology of plasmids in strains of unicellular Cyanobacteria.

Six strains of unicellular cyanobacteria were examined for the presence of plasmids. Analysis of lysates of these strains by CsCl-ethidium bromide density centrifugation yielded a major chromosomal DNA band and a minor band containing covalently closed circular plasmid DNA, as shown by electron microscopy and agarose gel electrophoresis. The sizes of the various plasmid species were determined; in each of the Synechococcus strains 6301, 6707, and 6908 two plasmid species were found with molecular weights of 5.3 × 10⁶ and 32.7 × 10⁶. Synechococcus strain 7425 had two plasmids of molecular weight 5.4 × 10⁶ and 24 × 10⁶. Synechococcus strain 6312 and Synechocystis strain 7005 each contained one plasmid species with molecular weight of 15.9 × 10⁶ and 2.0 × 10⁶, respectively. Restriction enzyme analysis revealed identical cleavage patterns for the plasmids of identical molecular weight.     

Variant forms of matrix protein in Escherichia coli B/r bearing N plasmids

Plasmids of the N incompatibility group have been found to decrease or virtually eliminate the synthesis of the 36 500 dalton outer membrane matrix protein of their Escherichia coli B/r hosts (Iyer, R. (1977) Biochim. Biophys. Acta 470, 258–272 and Iyer, R., Darby, V. and Holland, I.B. (1978) FEBS Lett. 85, 127–132) or modify its composition. Although the 34 000 dalton tol G protein is slightly increased in some strains, it is identical in composition to the homologous protein from the plasmidless host. In three of five N⁺ strains, the synthesis of the modified matrix proteins depends on the temperature of cultivation of the strains in which they occur. The alterations to the matrix proteins are non-identical and do not affect the expression of several plasmid-coded functions including those of sensitivity to the N plasmid-specific filamentous bacteriophage IKe (Khatoon, H. and Iyer, R. (1971) Can. J. Microbiol. 17, 669–675), or their interbacterial transfer via conjugation to appropriate recipient strains. Thus, although the significance of the variant matrix proteins in N⁺ strains with respect to plasmid-mediated functions remains unclear, N plasmids nevertheless provide a convenient system which might be used to elucidate the events that precede the insertion of this protein into the outer membrane of E. coli B/r hosts.     

Both the full-length and the N-terminal domain of the meningococcal transferrin-binding protein B discriminate between human iron-loaded and apo-transferrin

We have readdressed the ability of the transferrin-binding protein B (TbpB) from Neisseria meningitidis to discriminate between the iron-loaded and the iron-free human transferrin (hTf) by using the BIAcore technology, a powerful experimental technique for the observation of direct interactions between a receptor and its ligands, without the use of labels. Recombinant full-length TbpB from five N. meningitidis strains were produced and purified from Escherichia coli as fusion proteins. They showed a preference for the binding to iron-loaded hTf. As for the full-length molecule, we have demonstrated that the minimal N-terminal hTf binding domain of meningococcal TbpB from B16B6 and M982 strains was able to discriminate between both hTf forms.     

Characterization of the Lactobacillus casei group based on the profiling of ribosomal proteins coded in S10-spc-alpha operons as observed by MALDI-TOF MS

The taxonomy of the members of the Lactobacillus casei group is complicated because of their phylogenetic similarity and controversial nomenclatural status. In this study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of ribosomal proteins coded in the S10-spc-alpha operon, termed S10-GERMS, was applied in order to classify 33 sample strains belonging to the L. casei group. A total of 14 types of ribosomal protein genes coded in the operon were first sequenced from four type strains of the L. casei group (L. casei JCM 1134^T, L. paracasei subsp. paracasei JCM 8130^T, L. paracasei subsp. tolerans JCM 1171^T, and L. rhamnosus JCM 1136^T) together with L. casei JCM 11302, which is the former type strain of ‘L. zeae’. The theoretical masses of the 14 types of ribosomal proteins used as biomarkers were classified into five types and compiled into a ribosomal protein database. The observed ribosomal proteins of each strain, identified by MALDI-TOF MS, were categorized into types based on their masses, summarized as ribosomal protein profiles, and they were used to construct a phylogenetic tree. The 33 sample strains, together with seven genome-sequenced strains, could be classified into four major clusters, which coincided precisely with the taxa of the (sub)species within the L. casei group. Three “ancient” strains, identified as L. acidophilus and L. casei, were correctly re-identified as L. paracasei subsp. paracasei by S10-GERMS. S10-GERMS would thus appear to be a powerful tool for phylogenetic characterization, with considerable potential for management of culture collections.     

Construction of a Kluyveromyces lactis ku80 − Host Strain for Recombinant Protein Production: Extracellular Secretion of Pectin Lyase and a Streptavidin–Pectin Lyase Chimera

In several organisms used for recombinant protein production, integration of the expression cassette into the genome depends on site-specific recombination. In general, the yeast Kluyveromyces lactis shows low gene-targeting efficiency. In this work, two K. lactis ku80 ^? strains defective in the non-homologous end-joining pathway (NHEJ) were constructed using a split-marker strategy and tested as hosts for heterologous gene expression. The NHEJ pathway mediates random integration of exogenous DNA into the genome, and its function depends on the KU80 gene. KU80-defective mutants were constructed using a split-marker strategy. The vectors pKLAC1/Plg1 and pKLAC1/cStpPlg1 were used to evaluate the recovered mutants as hosts for expression of pectin lyase (PNL) and the fusion protein streptavidin–PNL, respectively. The transformation efficiency of the ku80 ^? mutants was higher than the respective parental strains (HP108 and JA6). In addition, PNL secretion was detected by PNL assay in both of the K. lactis ku80 ^? strains. In HP108ku80^?/cStpPlg1 and JA6ku80^?/Plg1 cultures, the PNL extracellular specific activity was 551.48 (±38.66) and 369.04 (±66.33) U/mg protein. This study shows that disruption of the KU80 gene is an effective strategy to increase the efficiency of homologous recombination with pKLAC1 vectors and the production and secretion of recombinant proteins in K. lactis transformants.     

Oxidative phosphorylation in Escherichia coli K-12: The genetic and biochemical characterisation of a strain carrying a mutation in the uncB gene

1. A mutant strain of Escherichia coli unable to grow with succinate as sole carbon source was isolated. This mutant was found to carry a mutation in a gene (designated uncB) mapping at about minute 73.5 on the E. coli chromosome and close to the uncA gene which is probably the structural gene for (Mg²⁺,Ca²⁺)-stimulated ATPase.2. The uncB401 allele was transduced into two other strains of E. coli and the transductants compared with the parent strains.3. Strains carrying the uncB401 allele have low aerobic growth yields when grown on limiting concentrations of glucose, but unlike mutations in the uncA gene, mutations in the uncB gene do not impair anaerobic growth on a glucose-mineral salts medium.4. Oxidase activities in membranes from the normal strains and strains carrying the uncB401 allele were similar.5. Measurement of P/O ratios indicated that a mutation in the uncB gene causes uncoupling of phosphorylation associated with electron transport with d-lactate as substrate.6. (Mg²⁺,Ca²⁺)-stimulated ATPase activities in the normal strains and in strains carrying the uncB401 allele are similar.7. Estimation of the energy-linked and non-energy-linked transhydrogenase activities in membrane preparations from both the normal and mutant strains indicated that the protein affected by a mutation in the uncB gene is essential for the functioning of the ATP-dependent energy-linked transhydrogenase.8. It is concluded that two proteins, specified by the uncA and uncB genes, are essential for phosphorylation coupled to d-lactate oxidation and also for the energy-linked transhydrogenase activity using ATP as the energy source.     

Protein composition and architecture of the photosynthetic membranes from the cyanobacterium, Anacystis nidulans R2

The protein composition of the photosynthetic membrane from the cyanobacterium, Anacystis nidulans R2, was analyzed by acrylamide gel electrophoresis following solubilization with lithium dodecyl sulfate. Autoradiograms of ³⁵S-labelled membranes revealed over 90 bands by this procedure. The effect of solubilization conditions on protein resolution was analyzed by modifying temperature and sulfhydryl concentrations. Labelling cells with ⁵⁹Fe yielded nine iron-containing bands on these gels. Three of these bands, at 33, 19, and 14 kDa, were also heme proteins as determined by tetramethylbenzidine staining, and represent cytochromes f, b₆ and c-552, respectively. The remaining iron proteins are highly sensitive to solubilization conditions, especially the presence of 2-mercaptoethanol, and we suggest that these bands may be Fe-S proteins. Lactoperoxidase-catalyzed iodination of the membranes indicated that at least 41 proteins have surface-exposed domains. Some of the known proteins with external surfaces include cytochrome c-552 and the chlorophyll-binding proteins of Photosystems I and II. Neither cytochrome f nor b₆ appear to be accessible to external labelling. When this structural information was combined with the isolation of functional submembrane complexes, we constructed a topological model of the membrane. Using this model we have discussed the protein architecture of the cyanobacterial membrane.