Dependence of the Genotypic Characteristics of <Emphasis Type="Italic">Acidithiobacillus ferrooxidans</Emphasis> on the Physical,Chemical, and Electrophysical Properties of Pyrites

This study focused on the effect of physical, chemical, and electrophysical properties of two pyrites, pyrite 1, which had electron-type (n-type) conductivity, and pyrite 2, with hole-type (p-type) conductivity, on the genotypic characteristics of Acidithiobacillus ferrooxidans strains TFV-1 and TFBk, which were isolated from different substrates. After the adaptation of the strains to the pyrites at a pulp density of 1%, pulsed-field electrophoresis revealed changes in the chromosomal DNA of strain TFV-1 adapted to pyrite 1, and strain TFBk adapted to either of the pyrite types. In pyrite-adapted strain TFBk, the plasmid composition was the same as after growth on a medium containing ferrous iron, whereas, in strain TFV-1, changes in plasmid sizes or both in plasmid sizes and plasmid number occurred. After an increase in the density of the pyrite 2 pulp from 1 to 10%, the plasmid number increased from three to four, and, after an increase in the density of the pyrite 1 pulp from 1 to 7%, the plasmid number increased from two to six.     

Dependence of the genotypic characteristics of Acidithiobacillus ferrooxidans on the physical, chemical, and electrophysical properties of pyrites

Comparison of Acidithiobacillus ferrooxidans strains TFV-1 and TFBk with respect to their capacity to oxidize pyrite 1, with hole-type (p-type) conductivity, or pyrite 2, with an electron-type (n-type) conductivity, showed that, at a pulp density of 1%, both before and after its adaptation to the pyrites, strain TFBk, isolated from a substrate with a more complex mineral composition, grew faster and oxidized the pyrites of both conductivity types more efficiently than strain TFV-1, which was isolated from a mineralogically simple ore. At a pulp density of 3-5%, the oxidation of pyrite 1 by strain TFV-1 and both of the pyrites by strain TFBk began only after an artificial increase in Eh to 600 mV. If the pulp density was increased gradually, strain TFBk could oxidize the pyrites at its higher values than strain TFV-1, with the rate of pyrite 2 oxidation being higher than that of pyrite 1. During chemical oxidation of both of the pyrites, an increase was observed in the absolute values of the coefficients of thermoelectromotive force (KTEMF); during bacterial-chemical oxidation, the KTEMF of pyrite 1 changed insignificantly, whereas the KTEMF of pyrite 2 decreased.     

Patterns of growth and oxidation of natural pyrites by the representatives of acidophilic chemolithotrophic microorganisms

The patterns of the growth and oxidation of different types of natural pyrites were studied for the three microbial species adapted to these substrates and belonging to phylogenetically remote groups: gram-negative bacterium Acidithiobacillus ferrooxidans, gram-positive bacterium Sulfobacillus thermotolerans, and the archaeon Ferroplasma acidiphilum. For both A. ferrooxidans strains, TFV-1 and TFBk, pyrite 4 appeared to be the most difficult to oxidize and grow; pyrite 5 was oxidized by both strains at an average rate, and pyrite 3 was the most readily oxidized. On each of the three pyrites, growth and oxidation by TFBk were more active than by TFV-1. The effectiveness of the adaptation of S. thermotolerans Kr1^T was low compared to the A. ferrooxidans strains; however, the adapted strain Kr1^T showed the highest growth rate on pyrite 3 among all the cultures studied. No adaptation of strain Kr1^T to pyrite 5 was observed; the rates of growth and pyrite oxidation in the third transfer were lower than in the first transfer. The strain F. acidiphilum Y^T was not adapted to pyrites 3 and 5; the rates of growth and pyrite oxidation were the same in the first five transfers. The strains of three species of the microorganisms studied, A. ferrooxidans, S. thermotolerans, and F. acidiphilum, grew on pyrite 3 (holetype (p) conductivity) and oxidized it better than pyrite 5 (mixed-type (n-p) conductivity). The most readily oxidized were the pyrites with a density of 5.6–5.7 g/cm³ and high resistance values (ln R = 8.8). The pyrite oxidation rate did not depend on the type of conductivity. Changes in the chromosomal DNA structure were revealed in strain TFBk on adaptation to pyrites 3 and 4 and in the TFV-1 plasmid profile on adaptation to pyrite 3. Correlation between genetic variability and adaptive capabilities was shown for A. ferrooxidans. No changes in the chromosomal DNA structure were found in S. thermotolerans Kr1^T and F. acidiphilum Y^T on adaptation to pyrites 3 and 5. Plasmids were absent in the cells of these cultures.     

Patterns of pyrite oxidation by different microorganisms

The bacterial-chemical oxidation of natural pyrites with different physical, chemical, and electrophysical characteristics by bacteria Acidithiobacillus ferrooxidans, Sulfobacillus thermotolerans, and the archaeon Ferroplasma acidiphilum were studied. The electrophysical characteristics of three natural pyrites differed in the K _thermoEMF value (pyrites 3, 4, hole conduction (p-type conductivity); pyrite 5, mixed type conductivity (n-p)) and in the logarithm of electric resistance. Chemical oxidation of pyrites 3 and 5 resulted in no changes of K _thermoEMF. When pyrite 4 was oxidized chemically, the K _thermoEMF values remained in the same range as in the initial sample, but the ratio of grains with different K _thermoEMF values in the sample was changed: the number of grains with a higher K _thermoEMF value increased. The same changes were also observed in the course of bacterio-chemical oxidation of pyrite 4. Of the three pyrites studied, an increase in the logarithm of resistance was observed only for chemical oxidation of pyrite 4 at 28°C. At higher experimental temperatures, the logarithm of resistance increased accordingly; more active bacterial-chemical oxidation resulted in a more pronounced increase in the logarithm of resistance than chemical oxidation. On bacterial-chemical oxidation of pyrites 3 and 5 by A. ferrooxidans and S. thermotolerans strains, iron was leached more actively than sulfur. Preferred bacterial-chemical oxidation of certain fractions from the pyrite samples was shown, namely of the pyrite 3 fraction with higher K _thermoEMF values by the F. acidiphilum strain and of a fraction from the pyrite 5 sample with medium K _thermoEMF values by the A. ferrooxidans and S. thermotolerans strains. The comparative assessment of bacterial-chemical pyrite oxidation by three types of microorganisms showed the direction of changes in the K _thermoEMF values to be the same in the case of bacteria Acidithiobacillus ferrooxidans and Sulfobacillus thermotolerans and different in the case of the archaeon Ferroplasma acidiphilum.     

Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) hydraulic conductivity links to leaf venation architecture under well-watered condition rather than PEG-induced water deficit

Higher plant hydraulic conductivity (K _plant) is vital for plant growth, especially under PEG-induced water deficit stress (PEG-IWDS). Leaf venation architecture is a key determinant of leaf hydraulic conductivity (K _leaf) and K _leaf is a major component of K _plant across different plant species. However, there is little information about (1) varietal difference in leaf vein development in cereal crops, such as rice plants; (2) the effects of PEG-IWDS on leaf vein development; (3) the coordination between leaf venation architecture and K _plant as well as K _leaf under PEG-IWDS. In the present study, widely cultivated eight rice cultivars were grown hydroponically under well-watered condition (WWC) and PEG-IWDS, simulated by adding 15 % (w/v) PEG6000. Leaf venation architecture, including total longitudinal leaf vein number, leaf vein numbers per unit width (LVNW), vein thickness and leaf mass per area, as well as K _plant and K _leaf were measured to address above-mentioned questions. The results showed that leaf venation architecture exhibited significant varietal differences and PEG-IWDS significantly increased LVNW while decreased vein thickness. PEG-IWDS suppressed both K _plant and K _leaf but the decrease was much higher in K _plant than K _leaf. There was a significant and positive correlation observed between LVNW and K _leaf under both WWC and PEG-IWDS but the correlation between LVNW and K _plant was only significant under WWC. K _leaf was significantly and positively correlated with K _plant under WWC but not under PEG-IWDS. It is concluded that K _leaf is a major determinant for K _plant under WWC but not under PEG-IWDS; therefore, breeding or selecting rice cultivars with high LVNW can improve shoot water supplement under WWC but not under PEG-IWDS condition.     

Construction of flavocytochrome <Emphasis Type="Italic">b</Emphasis><Subscript>2</Subscript>-overproducing strains of the thermotolerant methylotrophic yeast <Emphasis Type="Italic">Hansenula polymorpha</Emphasis> (<Emphasis Type="Italic">Pichia angusta</Emphasis>)

L-Lactate cytochrome c oxidoreductase (flavocytochrome b ₂, FC b ₂) from the thermotolerant methylotrophic yeast Hansenula polymorpha (Pichia angusta) is, unlike the enzyme form baker’s yeast, a thermostable enzyme potentially important for bioanalytical technologies for highly selective assays of L-lactate in biological fluids and foods. This paper describes the construction of flavocytochrome b ₂ producers with over-expression of the H. polymorpha CYB2 gene, encoding FC b ₂. The HpCYB2 gene under the control of the strong H. polymorpha alcohol oxidase promoter in a plasmid for multicopy integration was transformed into the recipient strain H. polymorpha C-105 (grc1 catX), impaired in glucose repression and devoid of catalase activity. A method was developed for preliminary screening of the transformants with increased FC b ₂ activity in permeabilized yeast cells. The optimal cultivation conditions providing for the maximal yield of the target enzyme were found. The constructed strain is a promising FC b ₂ producer characterized by a sixfold increased (to 3 μmol min^?1 mg^?1 protein in cell-free extract) activity of the enzyme.     

Photosynthetic activity and components of the electron transport chain in the aerobic bacteriochlorophyll <Emphasis Type="Italic">a</Emphasis>-containing bacterium <Emphasis Type="Italic">Roseinatronobacter thiooxidans</Emphasis>

Bioenergetics of the aerobic bacteriochlorophyll a-containing (BCl a) bacterium (ABC bacterium) Roseinatronobacter thiooxidans is a combination of photosynthesis, oxygen respiration, and oxidation of sulfur compounds under alkaliphilic conditions. The photosynthetic activity of Rna. thiooxidans cells was established by the photoinhibition of cell respiration and reversible photobleaching discoloration of the BCl a of reaction centers (RC), connected by the chain of electron transfer with cytochrome c ₅₅₁ oxidation. The species under study, like many purple bacteria and some of the known ABC bacteria, possesses a light-harvesting pigment-protein (LHI) complex with the average number of 30 molecules of antenna BCl a per one photosynthetic RC. Under microaerobic growth conditions, the cells contained bc ₁ complex and two terminal oxidases: cbb ₃-cytochrome oxidase and the alternative cytochrome oxidase of the a ₃ type. Besides, Rna. thiooxidans was shown to have several different soluble low- and high-potential cytochromes c, probably associated with the ability of utilizing sulfur compounds as additional electron donors.     

A <Emphasis Type="Italic">bean common mosaic virus</Emphasis> (BCMV)-resistance gene is fine-mapped to the same region as <Emphasis Type="Italic">Rsv1</Emphasis>-<Emphasis Type="Italic">h</Emphasis> in the soybean cultivar Suweon 97

Key message

In the soybean cultivar Suweon 97, BCMV-resistance gene was fine-mapped to a 58.1-kb region co-localizing with the Soybean mosaic virus (SMV)-resistance gene, Rsv1-h raising a possibility that the same gene is utilized against both viral pathogens.

Abstract

Certain soybean cultivars exhibit resistance against soybean mosaic virus (SMV) or bean common mosaic virus (BCMV). Although several SMV-resistance loci have been reported, the understanding of the mechanism underlying BCMV resistance in soybean is limited. Here, by crossing a resistant cultivar Suweon 97 with a susceptible cultivar Williams 82 and inoculating 220 F₂ individuals with a BCMV strain (HZZB011), we observed a 3:1 (resistant/susceptible) segregation ratio, suggesting that Suweon 97 possesses a single dominant resistance gene against BCMV. By performing bulked segregant analysis with 186 polymorphic simple sequence repeat (SSR) markers across the genome, the resistance gene was determined to be linked with marker BARSOYSSR_13_1109. Examining the genotypes of nearby SSR markers on all 220 F₂ individuals then narrowed down the gene between markers BARSOYSSR_13_1109 and BARSOYSSR_13_1122. Furthermore, 14 previously established F_2:3 lines showing crossovers between the two markers were assayed for their phenotypes upon BCMV inoculation. By developing six more SNP (single nucleotide polymorphism) markers, the resistance gene was finally delimited to a 58.1-kb interval flanked by BARSOYSSR_13_1114 and SNP-49. Five genes were annotated in this interval of the Williams 82 genome, including a characteristic coiled-coil nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR, CNL)-type of resistance gene, Glyma13g184800. Coincidentally, the SMV-resistance allele Rsv1-h was previously mapped to almost the same region, thereby suggesting that soybean Suweon 97 likely relies on the same CNL-type R gene to resist both viral pathogens.

     

Antirestriction and antimodification activities of T7 Ocr: Effects of amino acid substitutions in the interface

The T7 antirestriction protein Ocr, encoded by 0.3 (ocr), specifically inhibits ATP-dependent type I restriction-modification systems. T7 0.3 (ocr) was cloned in pUC18. Ocr inhibited both restriction and modification activities of the type I restriction-modification system (EcoKI) in Escherichia coli K12. The Ocr F53D A57E mutant was obtained and proved to inhibit only restriction activity of EcoKI. The 0.3 (ocr) and Photorhabdus luminescens luxCDABE genes were cloned in pZ-series vectors with the P _ltetO-1 promoter, strongly controlled by the TetR repressor. The bioluminescence intensity and luciferase content varied up to 5000-fold in E. coli K12 MG1655Z1 tetR⁺ (pZE21-luxCDABE) cells, depending on the environmental concentration of the inductor anhydrotetracycline. The antirestriction activity of Ocr and Ocr F53D A57E was studied as a function of their concentration in the cell. The dissociation constant K _d, characterizing the binding with EcoKI, differed 1000-fold between Ocr and Ocr F53D A57E (10^?10 M versus 10^?7 M).     

Identification and transcriptional analysis of dehydrin gene family in cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis>)

Dehydrins (DHNs) are a group II late embryogenesis abundant (LEA) proteins that play essential roles in plant growth, development and responses to diverse environmental stimuli. Here, four DHNs in cucumber genome were identified using bioinformatics-based methods according to the highly conserved K-, Y- and S-segments, including 1 Y_nK_n-type, 2 Y_nSK_n-type, and 1 SK_n-type DHNs. All of them are intrinsically disordered proteins (IDPs) and possess a large number of disorder-promoting amino acids. Secondary structure prediction revealed that each of them is composed of high proportion of alpha helix and random coil. Gene structure and phylogenetic analyses with DHNs from cucumber and several other species revealed that some closely related DHN genes had similar gene structures. A number of cis-elements involved in stress responses and phytohormones were found in each CsDHN promoter. The tissue expression profiles suggested that the CsDHN genes have overlapping, but different expression patterns. qRT-PCR results showed that three selected CsDHN genes could respond to heat, cold, osmotic and salt stresses, as well as to signaling molecules such as H₂O₂ and ABA. These results lay a solid foundation for future functional investigation of the cucumber dehydrin gene family in tissue development and stress responses in plants.     

Microbial arsenite oxidation with oxygen,nitrate, or an electrode as the sole electron acceptor

The purpose of this study was to identify bacteria that can perform As(III) oxidation for environmental bioremediation. Two bacterial strains, named JHS3 and JHW3, which can autotrophically oxidize As(III)–As(V) with oxygen as an electron acceptor, were isolated from soil and water samples collected in the vicinity of an arsenic-contaminated site. According to 16S ribosomal RNA sequence analysis, both strains belong to the ?-Proteobacteria class and share 99% sequence identity with previously described strains. JHS3 appears to be a new strain of the Acinetobacter genus, whereas JHW3 is likely to be a novel strain of the Klebsiella genus. Both strains possess the aioA gene encoding an arsenite oxidase and are capable of chemolithoautotrophic growth in the presence of As(III) up to 10 mM as a primary electron donor. Cell growth and As(III) oxidation rate of both strains were significantly enhanced during cultivation under heterotrophic conditions. Under anaerobic conditions, only strain JHW3 oxidized As(III) using nitrate or a solid-state electrode of a bioelectrochemical system as a terminal electron acceptor. Kinetic studies of As(III) oxidation under aerobic condition demonstrated a higher V _max and K _m from strain JHW3 than strain JHS3. This study indicated the potential application of strain JHW3 for remediation of subsurface environments contaminated with arsenic.     

Phosphorus deprivation effects on water relations of <Emphasis Type="Italic">Nicotiana tabacum</Emphasis> plant via reducing plasma membrane permeability

Plants grown in phosphorus-deprived solutions often exhibit disruption of water transport due to reduction in root hydraulic conductivity (Lp_r). To uncover the relationship between root Lp_r and water permeability coefficient (P_f) of plasma membrane and the role of aquaporins, we evaluated P_f of plasma membrane and also PIP-type aquaporin gene expression in tobacco (Nicotiana tabacum L.) plant roots after seven days P-deprivation. The results showed significant reduction in sap flow rate (J_v) and osmotic root hydraulic conductivity (L_pr-o) in P-deprived roots. These effects were reversed 24 h after P-resupplying. Interestingly, the P_f of root protoplasts was 57% lower in P-deprived plants compared with P-sufficient ones. The expression of NtPIP1;1 and NtPIP2;1 aquaporins did not change significantly in P-deprived plants compared with P-sufficient ones, but the copy number of NtAQP1 increased significantly in P-deprived plants. P-deprivation did not change Lpr-o significantly in antisense NtAQP1 plants. Taken together, these findings suggest that P-deprivation may play an important role in modulation of root hydraulic conductivity by affecting P_f in transcellular pathway of water flow across roots and aquaporins. Finally, we concluded that dominant water transport pathway under P-deprivation was transcellular one.     

Cloning and characterization of two distinct water-forming NADH oxidases from <Emphasis Type="Italic">Lactobacillus pentosus</Emphasis> for the regeneration of NAD

Two uncharacterized nicotinamide adenine dinucleotide (NADH) oxidases (named as LpNox1, LpNox2) from Lactobacillus pentosus ATCC 8041 were cloned and overexpressed in Escherichia coli BL21 (DE3). The sequence analysis revealed that the two enzymes are water-forming Noxs with 64 % and 52 % identity to LbNox from Lactobacillus brevis DSM 20054. The optimal pH and temperature of the purified LpNox1 and LpNox2 were 7.0 and 8.0 and 35 and 40 °C, respectively, with K _M of 99.0 μM (LpNox1) and 27.6 μM (LpNox2), and yielding catalytic efficiency k _cat/K _M of 1.0 and 0.2 μM^?1 s^?1, respectively. Heat inactivation studies revealed that the two enzymes are relatively instable. The application of LpNox1 for the regeneration of NAD⁺ was demonstrated by coupling with a glycerol dehydrogenase-catalyzed oxidation of glycerol to 1,3-dihydroxyacetone. The characteristics of the LpNox1 could prove to be of interest in industrial application such as NAD⁺ regeneration in dehydrogenase-catalyzed oxidations.     

Stimulation of dopamine oxidation in liver mitochondria by palmitic acid in the presence of ATP and <Emphasis Type="Italic">tert</Emphasis>-butylhydroperoxide

The effect of palmitic acid on the oxidation of dopamine, i.e., on the monoamine oxidase (MA-oxidase) activity, was investigated on deenergized liver mitochondria, upon energization by ATP and also in the presence of an oxidizing agent tert-butylhydroperoxide (TBH). It was found that palmitic acid reduces the value of the apparent K _m for dopamine without alteration of the apparent V _max. This points to stimulation of the mitochondrial MA-oxidase activity by palmitic acid at low concentrations of dopamine. Stimulatory effect of palmitic acid may be related to the ability of amphiphilic compounds to increase the negative charge density on the outer mitochondrial membrane. This leads to an increase in the local concentration of positively charged ions of dopamine in the layer adjacent to the membrane near the active site of monoamine oxidase. ATP eliminates the ability of palmitic acid to stimulate the MA-oxidase activity of mitochondria. This effect of ATP is not observed in the presence of the F _O F ₁-ATP-synthase inhibitor oligomycin. Apparently, in the case of vector transport of H⁺ from the matrix induced by ATP-hydrolysis, protonation of palmitic acid anions occurs on the outer mitochondrial membrane, followed by the movement of the neutral molecules to the outer and then to the inner monolayer of the inner membrane. It was found that TBH at a concentration of 300 μM has no significant effect on the ATPase activity of mitochondria and in the presence of ATP and palmitic acid reduces the value of the apparent K _m for dopamine without alteration of the apparent V _max. Antioxidant thiourea eliminates this effect of TBH. We propose that the TBH-induced oxidative stress in the case of ATP-energized mitochondria results in the movement of palmitic acid molecules from the inner to the outer membrane. This leads to an increase in the density of negative charges on the surface of this membrane and, therefore, to the stimulation of the dopamine oxidation.     

<Emphasis Type="Italic">Flavobacterium zaozhuangense</Emphasis> sp. nov., a new member of the family <Emphasis Type="Italic">Flavobacteriaceae</Emphasis>, isolated from metolachlor-contaminated soil

Strain ZZ-8^T, a Gram-negative, aerobic, non-spore-forming, non-motile, yellow-pigmented, rod-shaped bacterium, was isolated from metolachlor-contaminated soil in China. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZZ-8^T is a member of the genus Flavobacterium and shows high sequence similarity to Flavobacterium humicola UCM-46^T (97.2%) and Flavobacterium pedocola UCM-R36^T (97.1%), and lower (<?97%) sequence similarity to other known Flavobacterium species. Chemotaxonomic analysis revealed that strain ZZ-8^T possessed MK-6 as the major respiratory quinone; and iso-C_15:0 (28.5%), summed feature 9 (iso-C_17:1 w9c/C_16:0 10-methyl, 22.9%), iso-C_17:0 3-OH (17.0%), iso-C_15:0 3-OH (8.9%), iso-C_15:1 G (8.6%) and summed feature 3 (C_16:1 w7c/C_16:1 w6c, 5.7%) as the predominant fatty acids. The polar lipids of strain ZZ-8^T were determined to be lipids, a glycolipid, aminolipids and phosphatidylethanolamine. Strain ZZ-8^T showed low DNA–DNA relatedness with F. pedocola UCM-R36^T (43.23?±?4.1%) and F. humicola UCM-46^T (29.17?±?3.8%). The DNA G+C content was 43.3 mol%. Based on the phylogenetic and phenotypic characteristics, chemotaxonomic data and DNA–DNA hybridization, strain ZZ-8^T is considered a novel species of the genus Flavobacterium, for which the name Flavobacterium zaozhuangense sp. nov. (type strain ZZ-8^T?=?KCTC 62315 ^T?=?CCTCC AB 2017243^T) is proposed.     

Extracellular targeting of an active endoxylanase by a TolB negative mutant of <Emphasis Type="Italic">Gluconobacter oxydans</Emphasis>

Gluconobacter (G.) oxydans strains have great industrial potential due to their ability to incompletely oxidize a wide range of carbohydrates. But there is one major limitation preventing their full production potential. Hydrolysis of polysaccharides is not possible because extracellular hydrolases are not encoded in the genome of Gluconobacter species. Therefore, as a first step for the generation of exoenzyme producing G. oxydans, a leaky outer membrane mutant was created by deleting the TolB encoding gene gox1687. As a second step the xynA gene encoding an endo-1,4-β-xylanase from Bacillus subtilis was expressed in G. oxydans ΔtolB. More than 70 % of the total XynA activity (0.91 mmol h^?1 l culture^?1) was detected in the culture supernatant of the TolB mutant and only 10 % of endoxylanase activity was observed in the supernatant of G. oxydans xynA. These results showed that a G. oxydans strain with an increased substrate spectrum that is able to use the renewable polysaccharide xylan as a substrate to produce the prebiotic compounds xylobiose and xylooligosaccharides was generated. This is the first report about the combination of the process of incomplete oxidation with the degradation of renewable organic materials from plants for the production of value-added products.     

<Emphasis Type="Italic">Nibribacter flagellatus</Emphasis> sp. nov., isolated from rhizosphere of <Emphasis Type="Italic">Hibiscus syriacus</Emphasis> and emended description of the genus <Emphasis Type="Italic">Nibribacter</Emphasis>

A Gram-stain negative, aerobic, motile by flagella, rod-shaped strain (THG-T16^T) was isolated from rhizosphere of Hibiscus syriacus. Growth occurred at 10–40 °C (optimum 28–30 °C), at pH 6.0–8.0 (optimum 7.0) and at 0–1.0% NaCl (optimum 0%). Based on 16S rRNA gene sequence analysis, the near phylogenetic neighbours of strain THG-T16^T were identified as Nibribacter koreensis KACC 16450^T (98.6%), Rufibacter roseus KCTC 42217^T (94.7%), Rufibacter immobilis CCTCC AB 2013351^T (94.5%) and Rufibacter tibetensis CCTCC AB 208084^T (94.4%). The DNA G+C content of strain THG-T16^T was determined to be 46.7 mol%. DNA–DNA hybridization values between strain THG-T16^T and N. koreensis KACC 16450^T, R. roseus KCTC 42217^T, R. immobilis CCTCC AB 2013351^T, R.tibetensis CCTCC AB 208084^T were 33.5?±?0.5% (31.7?±?0.7% reciprocal analysis), 28.1?±?0.2% (25.2?±?0.2%), 17.1?±?0.9% (10.2?±?0.6%) and 8.1?±?0.3% (5.2?±?0.1%). The polar lipids were identified as phosphatidylethanolamine, two unidentified aminophospholipids, an unidentified aminolipid and three unidentified lipids. The quinone was identified as MK-7 and the polyamine as sym-homospermidine. The major fatty acids were identified as C_16:1 ω5c, C_17:1 ω6c, iso-C_15:0, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and summed feature 4 (iso-C_17:1 I and/or anteiso-C_17:1 B). On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics, and DNA–DNA hybridization data, strain THG-T16^T represents a novel species of the genus Nibribacter, for which the name Nibribacter flagellatus sp. nov. is proposed. The type strain is THG-T16^T(=?KACC 19188^T?=?CCTCC AB 2016246^T).     

Analysis of the expression of the <Emphasis Type="Italic">Rhodobacter sphaeroides lexA</Emphasis> gene

The regulation of the Rhodobacter sphaeroides lexA gene has been analyzed using both gel-mobility experiments and lacZ gene fusions. PCR-mediated mutagenesis demonstrated that the second GAAC motif in the sequence GAACN₇GAACN₇GAAC located upstream of the R. sphaeroides lexA gene is absolutely necessary for its DNA damage-mediated induction. Moreover, mutagenesis of either the first or the third GAAC motif in this sequence reduced, but did not abolish, the inducibility of the R. sphaeroides lexA gene. A R. sphaeroides lexA-defective (Def) mutant has also been constructed by replacing the active lexA gene with an inactivated gene copy constructed in vitro. Crude extracts of the R. sphaeroides lexA(Def) strain are unable to form any protein-DNA complex when added to the wild-type lexA promoter of R. sphaeroides. Likewise, the R. sphaeroides lexA(Def) cells constitutively express the recA and lexA genes. All these data clearly indicate that the lexA gene product is the negative regulator of the R. sphaeroides SOS response. Furthermore, the morphology, growth and viability of R. sphaeroides lexA(Def) cultures do not show any significant change relative to those of the wild-type strain. Hence, R. sphaeroides is so far the only bacterial species whose viability is known not to be affected by the presence of a lexA(Def) mutation.