Genetic characterization of biohydrogen-producing purple non-sulfur bacteria Rhodobacter johrii MAY2 isolate via whole genome analysis.

Purple non-sulfur bacteria (PNSB) are a diverse group of bacteria studied for various possible applications. They are commonly surveyed in bioenergy research as they produce biohydrogen, a candidate for clean alternative energy. This study aimed to assess the biohydrogen production ability and genetically characterize a high biohydrogen-producing PNSB (MAY2) isolated from Los Baños, Laguna, Philippines via whole genome sequencing (WGS). MAY2, when grown in mixed volatile fatty acids, produced biogas with 38% hydrogen. WGS results revealed that the isolate is positively classified under the genus Rhodobacter johrii. Also, 82 genetic hallmarks for biohydrogen production were found in the isolated genome which are involved in the production of key enzymes and proteins relevant to the photofermentative and hydrogen regulation pathways. Its nitrogenase gene cluster is stringently regulated by two genes, nifA and rofN, whose function and expression are easily affected by several environmental factors.

Anoxygenic phototrophic arsenite oxidation by a Rhodobacter strain.

Microbially mediated arsenic redox transformations are key for arsenic speciation and mobility in rice paddies. Whereas anaerobic anoxygenic photosynthesis coupled to arsenite (As(III)) oxidation has been widely examined in arsenic-replete ecosystems, it remains unknown whether this light-dependent process exists in paddy soils. Here, we isolated a phototrophic purple bacteria, Rhodobacter strain CZR27, from an arsenic-contaminated paddy soil and demonstrated its capacity to oxidize As(III) to arsenate (As(V)) using malate as a carbon source photosynthetically. Genome sequencing revealed an As(III)-oxidizing gene cluster (aioXSRBA) encoding an As(III) oxidase. Functional analyses showed that As(III) oxidation under anoxic phototrophic conditions correlated with transcription of the large subunit of the As(III) oxidase aioA gene. Furthermore, the non-As(III) oxidizer Rhodobacter capsulatus SB1003 heterologously expressing aioBA from strain CZR27 was able to oxidize As(III), indicating that aioBA was responsible for the observed As(III) oxidation in strain CZR27. Our study provides evidence for the presence of anaerobic photosynthesis-coupled As(III) oxidation in paddy soils, highlighting the importance of light-dependent, microbe-mediated arsenic redox changes in paddy arsenic biogeochemistry.

Rhodobacter kunshanensis sp. nov., a Novel Bacterium Isolated from Activated Sludge.

Strain HX-7-19T was isolated from the activated sludge collected from an abandoned herbicide manufacturing plant in Kunshan, China. Cells were Gram-reaction-negative, rod-shaped, and non-motile. The phylogenetic analysis based on 16S rRNA gene indicated that strain HX-7-19T formed a clade with Rhodobacter blasticus CGMCC 1.3365T (96.3% sequence similarity). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain HX-7-19T and R. blasticus CGMCC 1.3365T were 76.2% and 20.3%, respectively. The genomic DNA G + C content of strain HX-7-19T was 65.9%. The major fatty acids (> 10% of the total fatty acids) were C18:1 ω7c and C18:1 ω7c 11-methyl. The major respiratory quinone was quinone Q-10. The major polar lipid profile consists of phosphatidylglycerol (PG), diphosphatidyl-glycerol (DPG), phosphatidylethanolamine (PE), and phosphatidylcholine (PC). Photosynthesis pigments bacteriochlorophyll a and carotenoids were formed and photosynthesis genes pufL and pufM were detected. On the basis of phenotypic and phylogenetic evidences, strain HX-7-19T is considered as a novel species in the genus Rhodobacter, for which the name Rhodobacter kunshanensis sp. nov. is proposed. The type strain is HX-7-19T (= KCTC 72471T = CCTCC AB 2020148T).

Rhodobacter xinxiangensis sp. nov., isolated from pakchoi-cultivated soil contaminated with heavy metal and its potential to reduce Cd and Pb accumulation in pakchoi (Brassica campestris L.).

A Gram-stain-negative, aerobic, and motile strain, TJ48T, was isolated from pakchoi-cultivated soil contaminated with Cd and Pb in Xinxiang (China). Cells of the strain were rod-shaped and colonies on LB agar were faint yellow. Strain TJ48T was positive for catalase and oxidase and the optimal condition for growth was 28 °C, with 1% (w/v) NaCl and at pH 7.0. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain TJ48T was closely related to the genus Rhodobacter and the closest relatives were Rhodobacter ovatus JA234T (97.4%, 16S rRNA gene sequence similarity) and Rhodobacter azotoformans KA25T (96.5%). The DNA G + C content of strain TJ48T was 64.7 mol%. Genome-to-genome distance calculations (GGDC) and ANIb values from genomic comparison between the genomes of strain TJ48T and the related reference species were less than 70% and 95%, respectively. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C17:0. The only isoprenoid quinone detected was Ubiquinone-10 (Q-10). The polar lipid profile contains diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipids, and three unidentified lipids. Strain TJ48T significantly increased the dry weight of roots (26.2-66.3%) and shoots (16.7-37.8%) of pakchoi and reduced the Cd (50.2-60.1%) and Pb (55.6-60.9%) contents in pakchoi shoots and roots. On the basis of the physiological, genotypic and genomic characteristics, the strain TJ48T represent a novel species of the genus Rhodobacter, and the name Rhodobacter xinxiangensis sp. nov. is proposed (type strain TJ48T = CCTCC AB2019120T = KCTC 72510T).

Anoxic growth optimization for metal respiration and photobiological hydrogen production by arsenic-resistant Rhodopseudomonas and Rhodobacter species.

The current research focuses on anaerobic respiration of arsenic and other toxic metals by purple nonsulfur bacteria (PNSB). Among the optimization assays performed were carbon utilization, cross metal resistance, and metal respiration, along with a comparison of each assay in photoheterotrophic and chemoheterotrophic growth. The bacteria were identified by the classification of 16S ribosomal RNA gene sequences. Rhodobacter sp. PI3 proved to be more versatile in carbon source utilization (acetate, lactate, citrate, and oxalate), whereas Rhodopseudomonas palustris PI5 proved to be more versatile in metal resistance (arsenate, arsenite, cobalt, lead, selenium, and nickel). Both the strains were found to be positive for photofermentative hydrogen production along with arsenic respiration. This study reveals that anaerobic conditions are more appropriate for better efficiency of PNSB. Our study demonstrates that R. palustris PI5 and Rhodobacter sp. PI3 can be promising candidates for the biohydrogen production along with metal detoxification using heavy metal-polluted effluents as a substrate.

Rhodobacter thermarum sp. nov., a novel phototrophic bacterium isolated from sediment of a hot spring.

An ovoid to rod-shaped, phototrophic, purple non-sulfur bacterium was isolated from a sediment sample of a hot spring in Tibet, China. Cells of strain YIM 73036T were Gram-stain negative, non-motile and multiplied by binary fission. Strain YIM 73036T grew optimally at pH 7.0-7.5 at 37-45 °C. Growth occurred in 0.5-3.5% (w/v) NaCl. Vitamins were not required for growth. The presence of photosynthesis genes pufL and pufM were shown and photosynthesis pigments were formed. Bacteriochlorophyll α, the bacteriopheophytin and carotenoids were present as photosynthetic pigments. Internal cytoplasmic membranes were of the lamellar type. The organism YIM 73036T was able to grow chemo-organoheterophically, chemo-lithoautotrophically and photo-organoheterotrophically but photo-lithoautotrophic and fermentative growth were not demonstrated. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain YIM 73036T is closely related to Rhodobacter blasticus ATCC 33485T (96.65% sequence similarity) and clustered with species of the genus Rhodobacter of the family Rhodobacteraceae. Whole-genome sequence analyses based on the average nucleotide BLAST identity (ANI < 82%) indicated that this isolate belongs to a novel species. The genomic DNA G+C content of organism YIM 73036T was determined to be 66.0 mol%. Strain YIM 73036T contained Q-10 as the predominant ubiquinone and C18:1ω7c, C18:1ω7c 11-methyl and C18:0 as the major fatty acids. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified phospholipid. Differential phenotypic and chemotaxonomic properties, together with the phylogenetic distinctiveness, demonstrated that strain YIM 73036T is distinguishable from other species of the genus Rhodobacter. On the basis of the data presented, strain YIM 73036T is considered to represent a novel species of the genus Rhodobacter, for which the name Rhodobacter thermarum sp. nov. [type strain YIM 73036T (= KCTC 52712T = CCTCC AB 2016298T)] is proposed.

Rhodobacter alkalitolerans sp. nov., isolated from an alkaline brown pond.

An alkali-tolerant, Gram-stain-negative, motile, rod-to-oval-shaped, yellowish brown-colored, phototrophic bacterium, designated as strain JA916T, was isolated from an alkaline brown pond in Gujarat, India. The DNA G + C content of the strain JA916T was 65.1 mol%. Strain JA916T grew well at pH 10. Respiratory quinone was Q-10 and major fatty acid was C18:1ω7c/C18:1ω6c, with significant quantities of C15:02OH observed. Strain JA916T shared the highest 16S rRNA gene sequence similarity with the type strains of Rhodobacter johrii (98.4%), followed by Rhodobacter megalophilus (98.3%), Rhodobacter sphaeroides (98.3%), Rhodobacter azotoformans (97.9%) and other members of the genus Rhodobacter (< 97%). 16S rRNA gene-based phylogenetic tree shows that strain JA916T formed a distinct sub-clade with Rhodobacter johrii, Rhodobacter megalophilus, Rhodobacter sphaeroides and Rhodobacter azotoformans. Further, rpoB-based phylogenetic analysis showed lower similarity with closely related species (≤ 93.0%) of the genus Rhodobacter, which suggests that JA916T is a novel species of the genus Rhodobacter. DNA-DNA hybridization values between strain JA916T and related type strains were less than 40%. Phenotypic, chemotaxonomical and phylogenetic differences showed that strain JA916T was distinct from other species of the genus Rhodobacter, suggesting strain JA916T represents a new species of the genus for which the name Rhodobacter alkalitolerans sp. nov. is proposed. Type strain is JA916T (= KCTC 15473T = LMG 28749T).

Rhodobacter sp. Rb3, an aerobic anoxygenic phototroph which thrives in the polyextreme ecosystem of the Salar de Huasco, in the Chilean Altiplano.

The Salar de Huasco is an evaporitic basin located in the Chilean Altiplano, which presents extreme environmental conditions for life, i.e. high altitude (3800 m.a.s.l.), negative water balance, a wide salinity range, high daily temperature changes and the occurrence of the highest registered solar radiation on the planet (> 1200 W m-2). This ecosystem is considered as a natural laboratory to understand different adaptations of microorganisms to extreme conditions. Rhodobacter, an anoxygenic aerobic phototrophic bacterial genus, represents one of the most abundant groups reported based on taxonomic diversity surveys in this ecosystem. The bacterial mat isolate Rhodobacter sp. strain Rb3 was used to study adaptation mechanisms to stress-inducing factors potentially explaining its success in a polyextreme ecosystem. We found that the Rhodobacter sp. Rb3 genome was characterized by a high abundance of genes involved in stress tolerance and adaptation strategies, among which DNA repair and oxidative stress were the most conspicuous. Moreover, many other molecular mechanisms associated with oxidative stress, photooxidation and antioxidants; DNA repair and protection; motility, chemotaxis and biofilm synthesis; osmotic stress, metal, metalloid and toxic anions resistance; antimicrobial resistance and multidrug pumps; sporulation; cold shock and heat shock stress; mobile genetic elements and toxin-antitoxin system were detected and identified as potential survival mechanism features in Rhodobacter sp. Rb3. In total, these results reveal a wide set of strategies used by the isolate to adapt and thrive under environmental stress conditions as a model of polyextreme environmental resistome.

Dissection of membrane-binding and -remodeling regions in two classes of bacterial phospholipid N-methyltransferases.

Bacterial phospholipid N-methyltransferases (Pmts) catalyze the formation of phosphatidylcholine (PC) via successive N-methylation of phosphatidylethanolamine (PE). They are classified into Sinorhizobium-type and Rhodobacter-type enzymes. The Sinorhizobium-type PmtA protein from the plant pathogen Agrobacterium tumefaciens is recruited to anionic lipids in the cytoplasmic membrane via two amphipathic helices called αA and αF. Besides its enzymatic activity, PmtA is able to remodel membranes mediated by the αA domain. According to the Heliquest program, αA- and αF-like amphipathic helices are also present in other Sinorhizobium- and Rhodobacter-type Pmt enzymes suggesting a conserved architecture of α-helical membrane-binding regions in these methyltransferases. As representatives of the two Pmt families, we investigated the membrane binding and remodeling capacity of Bradyrhizobium japonicum PmtA (Sinorhizobium-type) and PmtX1 (Rhodobacter-type), which act cooperatively to produce PC in consecutive methylation steps. We found that the αA regions in both enzymes bind anionic lipids similar to αA of A. tumefaciens PmtA. Membrane binding of PmtX1 αA is enhanced by its substrate monomethyl-PE indicating a substrate-controlled membrane association. The αA regions of all investigated enzymes remodel spherical liposomes into tubular filaments suggesting a conserved membrane-remodeling capacity of bacterial Pmts. Based on these results we propose that the molecular details of membrane-binding and remodeling are conserved among bacterial Pmts.

Description of Rhodobacter azollae sp. nov. and Rhodobacter lacus sp. nov.

Three strains (JA826T, JA912T and JA913), which were yellowish brown colour, rod to oval shaped, Gram-stain-negative, motile, phototrophic bacteria with a vesicular architecture of intracytoplasmic membranes, were isolated from different pond samples. The DNA G+C content of the three strains was between 64.6 and 65.5 mol%. The highest 16S rRNA gene sequence similarity of all three strains was with the type strains of the genus Rhodobacter sensu stricto in the family Rhodobacteraceae. Strain JA826T had highest sequence similarity with Rhodobacter maris JA276T (98.5 %), Rhodobacter viridis JA737T (97.5 %) and other members of the genus Rhodobacter (<97 %). Strain JA912T had highest sequence similarity with Rhodobacter viridis JA737T (99.6 %), Rhodobacter sediminis N1T (99.3 %), Rhodobacter capsulatus ATCC 11166T (98.8 %) and less than 97 % similarity with other members of the genus Rhodobacter. The 16S rRNA gene sequence similarity between strains JA826T and JA912T was 96.9 %. DNA-DNA hybridization showed that strains JA826T and JA912T (values among themselves and between the type strains of nearest members <44 %) did not belong to any of the nearest species of the genus Rhodobacter. However, strains JA912T and JA913 were closely related (DNA-DNA hybridization value >90 %). The genomic distinction was also supported by differences in phenotypic and chemotaxonomic characteristics in order to propose strains JA826T (=KCTC 15478T=LMG 28758T) and JA912T (=KCTC 15475T=LMG 28748T) as new species in the genus Rhodobacter sensu stricto with the names Rhodobacter lacus and Rhodobacter azollae, respectively.

Genomic Analysis of the Evolution of Phototrophy among Haloalkaliphilic Rhodobacterales.

A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photoheterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and facultatively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter thiooxidans, and aerobic heterotrophic bacterium Natronohydrobacter thiooxidans. These three haloalcaliphilic species are phylogenetically related and share many common characteristics with the Rhodobacter species, forming together the Rhodobacter-Rhodobaca (RR) group. A comparative genomic analysis showed close homology of photosynthetic proteins and similarity in photosynthesis gene organization among the investigated phototrophic RR species. On the other hand, Rhodobaca barguzinensis and Roseinatronobacter thiooxidans lack an inorganic carbon fixation pathway and outer light-harvesting genes. This documents the reduction of their photosynthetic machinery towards a mostly photoheterotrophic lifestyle. Moreover, both phototrophic species contain 5-aminolevulinate synthase (encoded by the hemA gene) incorporated into their photosynthesis gene clusters, which seems to be a common feature of all aerobic anoxygenic phototrophic Alphaproteobacteria. Interestingly, the chrR-rpoE (sigma24) operon, which is part of singlet oxygen defense in phototrophic species, was found in the heterotrophic strain Natronohydrobacter thiooxidans. This suggests that this organism evolved from a photoheterotrophic ancestor through the loss of its photosynthesis genes. The overall evolution of phototrophy among the haloalkaliphilic members of the RR group is discussed.

Falsirhodobacter sp. alg1 Harbors Single Homologs of Endo and Exo-Type Alginate Lyases Efficient for Alginate Depolymerization.

Alginate-degrading bacteria play an important role in alginate degradation by harboring highly efficient and unique alginolytic genes. Although the general mechanism for alginate degradation by these bacteria is fairly understood, much is still required to fully exploit them. Here, we report the isolation of a novel strain, Falsirhodobacter sp. alg1, the first report for an alginate-degrading bacterium from the family Rhodobacteraceae. Genome sequencing reveals that strain alg1 harbors a primary alginate degradation pathway with only single homologs of an endo- and exo-type alginate lyase, AlyFRA and AlyFRB, which is uncommon among such bacteria. Subsequent functional analysis showed that both enzymes were extremely efficient to depolymerize alginate suggesting evolutionary interests in the acquirement of these enzymes. The exo-type alginate lyase, AlyFRB in particular could depolymerize alginate without producing intermediate products making it a highly efficient enzyme for the production of 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH). Based on our findings, we believe that the discovery of Falsirhodobacter sp. alg1 and its alginolytic genes hints at the potentiality of a more diverse and unique population of alginate-degrading bacteria.

Rhodobacter sediminis sp. nov., isolated from lagoon sediments.

Two Gram-stain-negative, rod-shaped phototrophic bacteria (designated strains N1T and C7) were isolated from lagoon sediments. Both strains were positive for catalase and oxidase activity. Casein, starch, urea and Tween 20 were hydrolysed by both strains while chitin, gelatin and Tween 80 were not. In both strains, C16 : 0, C18 : 0,C16 : 1ω6c/C16 : 1ω7c and C18 : 1ω6c/ C18 : 1ω7c were the predominant fatty acids, with minor amounts of C8 : 0 3-OH, anteiso-C14 : 0, C17 : 0, C14 : 1ω5c, C17 : 1 10-methyl and C18 : 1ω5c. Strains N1T and C7 contained phosphatidylglycerol and phosphatidylethanolamine as major polar lipids with minor amounts of phosphatidylcholine, unidentified lipids and an unidentified phospholipid. The mean genomic DNA G+C content was 70.6±1 mol% and the two strains were closely related (mean DNA-DNA hybridization >90 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. Strain N1T has a 16S rRNA gene sequence similarity of 99.2 % with Rhodobacter capsulatus ATCC 11166T, 99.1 % with Rhodobacter viridis JA737T and <96.6 % with other members of the genus Rhodobacter. Strain N1T and C7 shared 100 % 16S rRNA gene sequence similarity. DNA- DNA hybridization values between strain N1T and the type strains of the nearest species were clearly below the 70 % threshold. On the basis of phenotypic and genotypic data, it is proposed that strain N1T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter sediminis sp. nov. is proposed. The type strain is N1T (=KEMB 563-471T=JCM 31175T), and strain C7 is an additional strain of the species.

Translocator Protein 18 kDa (TSPO): An Old Protein with New Functions?

Translocator protein 18 kDa (TSPO) was previously known as the peripheral benzodiazepine receptor (PBR) in eukaryotes, where it is mainly localized to the mitochondrial outer membrane. Considerable evidence indicates that it plays regulatory roles in steroidogenesis and apoptosis and is involved in various human diseases, such as metastatic cancer, Alzheimer's and Parkinson's disease, inflammation, and anxiety disorders. Ligands of TSPO are widely used as diagnostic tools and treatment options, despite there being no clear understanding of the function of TSPO. An ortholog in the photosynthetic bacterium Rhodobacter was independently discovered as the tryptophan-rich sensory protein (TspO) and found to play a role in the response to changes in oxygen and light conditions that regulate photosynthesis and respiration. As part of this highly conserved protein family found in all three kingdoms, the rat TSPO is able to rescue the knockout phenotype in Rhodobacter, indicating functional as well as structural conservation. Recently, a major breakthrough in the field was achieved: the determination of atomic-resolution structures of TSPO from different species by several independent groups. This now allows us to reexamine the function of TSPO with a molecular perspective. In this review, we focus on recently determined structures of TSPO and their implications for potential functions of this ubiquitous multifaceted protein. We suggest that TSPO is an ancient bacterial receptor/stress sensor that has developed additional interactions, partners, and roles in its mitochondrial outer membrane environment in eukaryotes.

The RegA regulon exhibits variability in response to altered growth conditions and differs markedly between Rhodobacter species.

The RegB/RegA two-component system from Rhodobacter capsulatus regulates global changes in gene expression in response to alterations in oxygen levels. Studies have shown that RegB/RegA controls many energy-generating and energy-utilizing systems such as photosynthesis, nitrogen fixation, carbon fixation, hydrogen utilization, respiration, electron transport and denitrification. In this report, we utilized RNA-seq and ChIP-seq to analyse the breadth of genes indirectly and directly regulated by RegA. A comparison of mRNA transcript levels in wild type cells relative to a RegA deletion strain shows that there are 257 differentially expressed genes under photosynthetic defined minimal growth medium conditions and 591 differentially expressed genes when grown photosynthetically in a complex rich medium. ChIP-seq analysis also identified 61 unique RegA binding sites with a well-conserved recognition sequence, 33 of which exhibit changes in neighbouring gene expression. These transcriptome results define new members of the RegA regulon including genes involved in iron transport and motility. These results also reveal that the set of genes that are regulated by RegA are growth medium specific. Similar analyses under dark aerobic conditions where RegA is thought not to be phosphorylated by RegB reveal 40 genes that are differentially expressed in minimal medium and 20 in rich medium. Finally, a comparison of the R. capsulatus RegA regulon with the orthologous PrrA regulon in Rhodobacter sphaeroides shows that the number of photosystem genes regulated by RegA and PrrA are similar but that the identity of genes regulated by RegA and PrrA beyond those involved in photosynthesis are quite distinct.

Biodegradation of Various Aromatic Compounds by Enriched Bacterial Cultures: Part A-Monocyclic and Polycyclic Aromatic Hydrocarbons.

Present study focused on the screening of bacterial consortium for biodegradation of monocyclic aromatic hydrocarbon (MAH) and polycyclic aromatic hydrocarbons (PAHs). Target compounds in the present study were naphthalene, acenaphthene, phenanthrene (PAHs), and benzene (MAH). Microbial consortia enriched with the above target compounds were used in screening experiments. Naphthalene-enriched consortium was found to be the most efficient consortium, based on its substrate degradation rate and its ability to degrade other aromatic pollutants with significantly high efficiency. Substrate degradation rate with naphthalene-enriched culture followed the order benzene > naphthalene > acenaphthene > phenanthrene. Chryseobacterium and Rhodobacter were discerned as the predominant species in naphthalene-enriched culture. They are closely associated to the type strain Chryseobacterium arthrosphaerae and Rhodobacter maris, respectively. Single substrate biodegradation studies with naphthalene (PAH) and benzene (MAH) were carried out using naphthalene-enriched microbial consortium (NAPH). Phenol and 2-hydroxybenzaldehyde were identified as the predominant intermediates during benzene and naphthalene degradation, respectively. Biodegradation of toluene, ethyl benzene, xylene, phenol, and indole by NAPH was also investigated. Monod inhibition model was able to simulate biodegradation kinetics for benzene, whereas multiple substrate biodegradation model was able to simulate biodegradation kinetics for naphthalene.

Metabolic engineering in chemolithoautotrophic hosts for the production of fuels and chemicals.

The ability of autotrophic organisms to fix CO2 presents an opportunity to utilize this 'greenhouse gas' as an inexpensive substrate for biochemical production. Unlike conventional heterotrophic microorganisms that consume carbohydrates and amino acids, prokaryotic chemolithoautotrophs have evolved the capacity to utilize reduced chemical compounds to fix CO2 and drive metabolic processes. The use of chemolithoautotrophic hosts as production platforms has been renewed by the prospect of metabolically engineered commodity chemicals and fuels. Efforts such as the ARPA-E electrofuels program highlight both the potential and obstacles that chemolithoautotrophic biosynthetic platforms provide. This review surveys the numerous advances that have been made in chemolithoautotrophic metabolic engineering with a focus on hydrogen oxidizing bacteria such as the model chemolithoautotrophic organism (Ralstonia), the purple photosynthetic bacteria (Rhodobacter), and anaerobic acetogens. Two alternative strategies of microbial chassis development are considered: (1) introducing or enhancing autotrophic capabilities (carbon fixation, hydrogen utilization) in model heterotrophic organisms, or (2) improving tools for pathway engineering (transformation methods, promoters, vectors etc.) in native autotrophic organisms. Unique characteristics of autotrophic growth as they relate to bioreactor design and process development are also discussed in the context of challenges and opportunities for genetic manipulation of organisms as production platforms.

New methods for determining proton pumping ability and electron transfer activity of the cytochrome bc1 complex.

It is important to determine the electron transfer activity and proton pumping ability of the cytochrome bc1 complex for better understanding its structure and function. In this study, several methods for determining the electron transfer and proton pumping of the bc1 complex, including the traditional and the new methods, are presented and evaluated. For determining the proton pumping ability of the bc1 complex, the new stopped-flow method has a higher accuracy than the traditional pH meter method, and the new spectrophotometer method is more convenient than the traditional pH meter method. In measuring the electron transfer activity of the bc1 complex, the new stopped-flow method is more accurate and has a higher separating capacity than the traditional spectrophotometer method.

[Characterization of a new strain of a purple nonsulfur bacterium from a thermal spring].

A new budding nonsulfur purple bacterium of the genus Rhodobacter (strain Ku-2) was isolated from a mat of a moderately thermal spring (Baikal rift zone, Buryat Republic, Russia). The bacterium had lamellar photosynthetic membranes, which are typica of only one Rhodobacter species, Rba. blasticus. The cells contined spheroidene carotenoids and bacteriochlorophyll a (Bchl a). In vivo absorption spectrum of the cells had the major maximum at 863 nm and an additional peak at 887 nm, which is characteristic of the pigment-protein complexes of Bchl a-containing membranes. The previously described Rba. blasticus strains did not exhibit a 887-nm maximum. The new isolate was photoheterotrophic, with optimal growth occurring at 35 degrees C, 3 g/L NaCl, and pH 7-8. The DNA G+C content was 64.4 mol %. The similarity between the 16S rRNA gene sequences of strain Ku-2 and the Rba. blasticus type strain was 98.7%. The similarity between the PufM amino acid sequences of strain Ku-2 and the previously studied Rba. blasticus strain was 89.0%. Thus, the bacterial strain Ku-2 belonged to the genus Rhodobacter and was phylogenetically related to Rba. blasticus.

Insilico model for prediction of lateral gene transfer in Rhodopseudomonas paulistris.

Study of evolutionary phenomenon is of great interest to biologists in discovering the secrets of life. The presence of reticulation events due to lateral gene transfer (LGT) among species poses new challenges for such evolutionary studies. In this paper an attempt has been made to develop an insilico model to predict LGT in the Rhodopseudomonas paulistris. Neighbour Joining method is employed to generate phylogenetic tree of 26 sequences of Alphaproteobacteria and one sequence of Cyanobacteria used as an out group. Then Least Squares approach is employed to predict the reticulation branches. Three reticulation branches were detected among these 27 sequences. The lateral gene transfer was predicted between Rhodopseudomonas paulistris 99 D and Rhodobacter sphaeroides, Rhodopseudomonas paulistris HMD 88 and Bradyrhizobium japonicum USDA and Bradyrhizobium japonicum USDA and Rhodobacter blasticus. The results obtained are in agreement with the results obtained by earlier research workers.