| physiological control and regulation of the rhodobacter capsulatus cbb operons. | the genes encoding enzymes of the calvin-benson-bassham (cbb) reductive pentose phosphate pathway in rhodobacter capsulatus are organized in at least two operons, each preceded by a separate cbbr gene, encoding potential lysr-type transcriptional activators. as a prelude to studies of cbb gene regulation in r. capsulatus, the nucleotide sequence of a 4,537-bp region, which included cbbrii, was determined. this region contained the following open reading frames: a partial pgm gene (encoding phosp ... | 1998 | 9696777 |
| molecular characterization of epiphytic bacterial communities on charophycean green algae | epiphytic bacterial communities within the sheath material of three filamentous green algae, desmidium grevillii, hyalotheca dissiliens, and spondylosium pulchrum (class charophyceae, order zygnematales), collected from a sphagnum bog were characterized by pcr amplification, cloning, and sequencing of 16s ribosomal dna. a total of 20 partial sequences and nine different sequence types were obtained, and one sequence type was recovered from the bacterial communities on all three algae. by phyloge ... | 1998 | 9797295 |
| the "green" form i ribulose 1,5-bisphosphate carboxylase/oxygenase from the nonsulfur purple bacterium rhodobacter capsulatus. | form i ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) of the calvin-benson-bassham cycle may be divided into two broad phylogenetic groups, referred to as red-like and green-like, based on deduced large subunit amino acid sequences. unlike the form i enzyme from the closely related organism rhodobacter sphaeroides, the form i rubisco from r. capsulatus is a member of the green-like group and closely resembles the enzyme from certain chemoautotrophic proteobacteria and cyanobacteria. a ... | 1999 | 10383960 |
| phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms. | the phylogenetic diversity of the ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco, e.c. 4.1.1.39) large-subunit genes of deep-sea microorganisms was analyzed. bulk genomic dna was isolated from seven samples, including samples from the mid-atlantic ridge and various deep-sea habitats around japan. the kinds of samples were hydrothermal vent water and chimney fragment; reducing sediments from a bathyal seep, a hadal seep, and a presumed seep; and symbiont-bearing tissues of the vent muss ... | 2001 | 11282630 |
| partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces. | distinct partitioning has been observed in the composition and diversity of bacterial communities inhabiting the surface and overlying seawater of three coral species infected with black band disease (bbd) on the southern caribbean island of curaçao, netherlands antilles. pcr amplification and sequencing of bacterial 16s rrna genes (rdna) with universally conserved primers have identified over 524 unique bacterial sequences affiliated with 12 bacterial divisions. the molecular sequences exhibite ... | 2002 | 11976091 |
| analysis of dna binding and transcriptional activation by the lysr-type transcriptional regulator cbbr of xanthobacter flavus. | the lysr-type transcriptional regulator cbbr controls the expression of the cbb and gap-pgk operons in xanthobacter flavus, which encode the majority of the enzymes of the calvin cycle required for autotrophic co2 fixation. the cbb operon promoter of this chemoautotrophic bacterium contains three potential cbbr binding sites, two of which partially overlap. site-directed mutagenesis and subsequent analysis of dna binding by cbbr and cbb promoter activity were used to show that the potential cbbr ... | 2003 | 12562794 |
| co2-responsive expression and gene organization of three ribulose-1,5-bisphosphate carboxylase/oxygenase enzymes and carboxysomes in hydrogenovibrio marinus strain mh-110. | hydrogenovibrio marinus strain mh-110, an obligately lithoautotrophic hydrogen-oxidizing bacterium, fixes co2 by the calvin-benson-bassham cycle. strain mh-110 possesses three different sets of genes for ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco): cbbls-1 and cbbls-2, which belong to form i (l8s8), and cbbm, which belongs to form ii (lx). in this paper, we report that the genes for cbbls-1 (cbbls-1) and cbbm (cbbm) are both followed by the cbbqo genes and preceded by the cbbr gene ... | 2004 | 15317772 |
| effector-mediated interaction of cbbri and cbbrii regulators with target sequences in rhodobacter capsulatus. | in rhodobacter capsulatus, genes encoding enzymes of the calvin-benson-bassham reductive pentose phosphate pathway are located in the cbb(i) and cbb(ii) operons. each operon contains a divergently transcribed lysr-type transcriptional activator (cbbr(i) and cbbr(ii)) that regulates the expression of its cognate cbb promoter in response to an as yet unidentified effector molecule(s). both cbbr(i) and cbbr(ii) were purified, and the ability of a variety of potential effector molecules to induce ch ... | 2004 | 15547275 |
| cloning, expression, crystallization and preliminary x-ray characterization of cytochrome c552 from a moderate thermophilic bacterium, hydrogenophilus thermoluteolus. | the amino-acid sequence of cytochrome c552 (ph c552) from a moderately thermophilic bacterium, hydrogenophilus thermoluteolus, was more than 50% identical to that of cytochrome c from an extreme thermophile, hydrogenobacter thermophilus (ht c552), and from a mesophile, pseudomonas aeruginosa (pa c551). the ph c552 gene was overexpressed as a correctly processed holoprotein in the escherichia coli periplasm. the overexpressed ph c552 has been crystallized by vapour diffusion from polyethylene gly ... | 2005 | 16511051 |
| activity of rhodobacter sphaeroides rpohii, a second member of the heat shock sigma factor family. | we have identified a second rpoh homolog, rpoh(ii), in the alpha-proteobacterium rhodobacter sphaeroides. primary amino acid sequence comparisons demonstrate that r. sphaeroides rpoh(ii) belongs to a phylogenetically distinct group with rpoh orthologs from alpha-proteobacteria that contain two rpoh genes. like its previously identified paralog, rpoh(i), rpoh(ii) is able to complement the temperature-sensitive phenotype of an escherichia coli sigma(32) (rpoh) mutant. in addition, we show that rec ... | 2006 | 16885439 |
| the genome of deep-sea vent chemolithoautotroph thiomicrospira crunogena xcl-2. | presented here is the complete genome sequence of thiomicrospira crunogena xcl-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. this gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. it has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. a ... | 2006 | 17105352 |
| the ancestor of the paulinella chromatophore obtained a carboxysomal operon by horizontal gene transfer from a nitrococcus-like gamma-proteobacterium. | paulinella chromatophora is a freshwater filose amoeba with photosynthetic endosymbionts (chromatophores) of cyanobacterial origin that are closely related to free-living prochlorococcus and synechococcus species (ps-clade). members of the ps-clade of cyanobacteria contain a proteobacterial form 1a rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) that was acquired by horizontal gene transfer (hgt) of a carboxysomal operon. in rdna-phylogenies, the paulinella chromatophore diverged basal ... | 2007 | 17550603 |
| the biodiversity and ecology of antarctic lakes: models for evolution. | antarctic lakes are characterised by simplified, truncated food webs. the lakes range from freshwater to hypersaline with a continuum of physical and chemical conditions that offer a natural laboratory in which to study evolution. molecular studies on antarctic lake communities are still in their infancy, but there is clear evidence from some taxonomic groups, for example the cyanobacteria, that there is endemicity. moreover, many of the bacteria have considerable potential as sources of novel b ... | 2007 | 17553775 |
| genes and pathways for co2 fixation in the obligate, chemolithoautotrophic acidophile, acidithiobacillus ferrooxidans, carbon fixation in a. ferrooxidans. | acidithiobacillus ferrooxidans is chemolithoautotrophic γ-proteobacterium that thrives at extremely low ph (ph 1-2). although a substantial amount of information is available regarding co2 uptake and fixation in a variety of facultative autotrophs, less is known about the processes in obligate autotrophs, especially those living in extremely acidic conditions, prompting the present study. | 2010 | 20799944 |
| L-Tryptophan Production by Auxotrophic and Analogue Resistant Mutants of Aureobacterium flavescens. | A number of tyrosine plus phenylalanine double auxotrophic mutants were isolated by N-methyl-N-nitro-N-nitrosoguanidine (MNNG) treatment of a locally isolated strain of Aureobacterium flavescens of which 11A(39) and 11A(17) were selected on the basis of their tryptophan production in a mineral salt medium over other isolated mutant strains. The mutational block in the aromatic amino acid biosynthetic pathway of the selected double auxotrophs were determined. By controlling pH of the production m ... | 2011 | 22084602 |
| further unravelling the regulatory twist - metabolic coinducer-mediated cbbr-cbbi promoter interactions in rhodopseudomonas palustris cga010. | the cbb(i) region of rhodopseudomonas palustris contains the cbbls genes encoding form i ribulose -1, 5 -bisphosphate (rubp) carboxylase oxygenase (rubisco) along with a divergently transcribed regulator gene, cbbr. juxtaposed between cbbr and cbbls are the cbbrrs genes encoding an unusual three protein two-component (cbbrrs) system that modulates the ability of cbbr to influence cbbls expression. the nature of the metabolic signals that rps. palustris cbbr perceives to regulate cbbls transcript ... | 2012 | 22247506 |
| temperature-dependent variations in sulfate-reducing communities associated with a terrestrial hydrocarbon seep. | terrestrial hydrocarbon seeps are an important source of naturally emitted methane over geological time. the exact community compositions responsible for carbon cycling beneath these surface features remain obscure. as sulfate reduction represents an essential process for anoxic organic mineralization, this study collected muddy fluids from a high-temperature hydrocarbon seep in taiwan and analyzed community structures of sulfate-supplemented sediment slurries incubated anoxically at elevated te ... | 2014 | 25273230 |
| isolation and metabolic characteristics of previously uncultured members of the order aquificales in a subsurface gold mine. | culture-dependent and -independent techniques were combined to characterize the physiological properties and the ecological impacts of culture-resistant phylotypes of thermophiles within the order aquificales from a subsurface hot aquifer of a japanese gold mine. thermophilic bacteria phylogenetically associated with previously uncultured phylotypes of aquificales were successfully isolated. 16s ribosomal dna clone analysis of the entire microbial dna assemblage and fluorescence in situ whole-ce ... | 2002 | 12039766 |
| abundance of reverse tricarboxylic acid cycle genes in free-living microorganisms at deep-sea hydrothermal vents. | since the discovery of hydrothermal vents more than 25 years ago, the calvin-bassham-benson (calvin) cycle has been considered the principal carbon fixation pathway in this microbe-based ecosystem. however, on the basis of recent molecular data of cultured free-living and noncultured episymbiotic members of the epsilon subdivision of proteobacteria and earlier carbon isotope data of primary consumers, an alternative autotrophic pathway may predominate. here, genetic and culture-based approaches ... | 2004 | 15466576 |
| ecology of subglacial lake vostok (antarctica), based on metagenomic/metatranscriptomic analyses of accretion ice. | lake vostok is the largest of the nearly 400 subglacial antarctic lakes and has been continuously buried by glacial ice for 15 million years. extreme cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier) and dissolved oxygen (delivered by melting meteoric ice), in addition to limited nutrients and complete darkness, combine to produce one of the most extreme environments on earth. metagenomic/metatranscriptomic analyses of ice that accreted over a shallow embay ... | 2013 | 24832801 |
| average oxidation state of carbon in proteins. | the formal oxidation state of carbon atoms in organic molecules depends on the covalent structure. in proteins, the average oxidation state of carbon (z(c)) can be calculated as an elemental ratio from the chemical formula. to investigate oxidation-reduction (redox) patterns, groups of proteins from different subcellular locations and phylogenetic groups were selected for comparison. extracellular proteins of yeast have a relatively high oxidation state of carbon, corresponding with oxidizing co ... | 2014 | 25165594 |
| plant growth promotion potential is equally represented in diverse grapevine root-associated bacterial communities from different biopedoclimatic environments. | plant-associated bacteria provide important services to host plants. environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. however, whether these environmental factors may influence the plant growth promoting (pgp) potential of the root-associated bacteria is not widely understood. to address this issue, the diversity and pgp potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three medit ... | 2013 | 23878810 |
| during cytochrome c maturation ccmi chaperones the class i apocytochromes until the formation of their b-type cytochrome intermediates. | the c-type cytochromes are electron transfer proteins involved in energy transduction. they have heme-binding (cxxch) sites that covalently ligate heme b via thioether bonds and are classified into different classes based on their protein folds and the locations and properties of their cofactors. rhodobacter capsulatus produces various c-type cytochromes using the cytochrome c maturation (ccm) system i, formed from the ccmabcdefghi proteins. ccmi, a component of the heme ligation complex ccmfhi, ... | 2015 | 25979338 |
| a deeply branching thermophilic bacterium with an ancient acetyl-coa pathway dominates a subsurface ecosystem. | a nearly complete genome sequence of candidatus 'acetothermum autotrophicum', a presently uncultivated bacterium in candidate division op1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. phylogenetic analysis based on the concatenated sequences of proteins common among 367 prokaryotes suggests that ca. 'a. autotrophicum' is one of the earliest diverging bacterial lineages. it possesses a folate-dependent wood-ljungdahl (acetyl-coa) pathway of co(2) fix ... | 2012 | 22303444 |
| function and evolution of the sox multienzyme complex in the marine gammaproteobacterium congregibacter litoralis. | core sets of sox genes were detected in several genome sequenced members of the environmental important om60/nor5 clade of marine gammaproteobacteria. however, emendation of media with thiosulfate did not result in stimulation of growth in two of these strains and cultures of congregibacter litoralis dsm 17192(t) did not oxidize thiosulfate to sulfate in concentrations of one mmol l(-1) or above. on the other hand, a significant production of sulfate was detected upon growth with the organic sul ... | 2014 | 25006520 |
| crystallization and preliminary x-ray analysis of the nad+-reducing [nife] hydrogenase from hydrogenophilus thermoluteolus th-1. | nad+-reducing [nife] hydrogenases catalyze the oxidoreduction of dihydrogen concomitant with the interconversion of nad+ and nadh. here, the isolation, purification and crystallization of the nad+-reducing [nife] hydrogenase from hydrogenophilus thermoluteolus th-1 are reported. crystals of the nad+-reducing [nife] hydrogenase were obtained within one week from a solution containing polyethylene glycol using the sitting-drop vapour-diffusion method and micro-seeding. the crystal diffracted to 2. ... | 2015 | 25615977 |
| cbbr, the master regulator for microbial carbon dioxide fixation. | biological carbon dioxide fixation is an essential and crucial process catalyzed by both prokaryotic and eukaryotic organisms to allow ubiquitous atmospheric co2 to be reduced to usable forms of organic carbon. this process, especially the calvin-bassham-benson (cbb) pathway of co2 fixation, provides the bulk of organic carbon found on earth. the enzyme ribulose 1,5-bisphosphate (rubp) carboxylase/oxygenase (rubisco) performs the key and rate-limiting step whereby co2 is reduced and incorporated ... | 2015 | 26324454 |
| modern subsurface bacteria in pristine 2.7 ga-old fossil stromatolite drillcore samples from the fortescue group, western australia. | several abiotic processes leading to the formation of life-like signatures or later contamination with actual biogenic traces can blur the interpretation of the earliest fossil record. in recent years, a large body of evidence showing the occurrence of diverse and active microbial communities in the terrestrial subsurface has accumulated. considering the time elapsed since archaean sedimentation, the contribution of subsurface microbial communities postdating the rock formation to the fossil bio ... | 2009 | 19396360 |
| microbial communities associated with wet flue gas desulfurization systems. | flue gas desulfurization (fgd) systems are employed to remove so(x) gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. wet fgds represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (tds) of fluids in the interior of the fgd units. despite the potential importance of microbial activities in the performance and operation of fgd systems, th ... | 2012 | 23226147 |
| structural characterization of a newly identified component of α-carboxysomes: the aaa+ domain protein csocbbq. | carboxysomes are bacterial microcompartments that enhance carbon fixation by concentrating ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) and its substrate co2 within a proteinaceous shell. they are found in all cyanobacteria, some purple photoautotrophs and many chemoautotrophic bacteria. carboxysomes consist of a protein shell that encapsulates several hundred molecules of rubisco, and contain carbonic anhydrase and other accessory proteins. genes coding for carboxysome shell compon ... | 2015 | 26538283 |
| functional classification of uncultured "candidatus caldiarchaeum subterraneum" using the maple system. | in this study, the metabolic and physiological potential evaluator system based on kyoto encyclopedia of genes and genomes (kegg) functional modules was employed to establish a functional classification of archaeal species and to determine the comprehensive functions (functionome) of the previously uncultivated thermophile "candidatus caldiarchaeum subterraneum" (ca. c. subterraneum). a phylogenetic analysis based on the concatenated sequences of proteins common among 142 archaea and 2 bacteria, ... | 2015 | 26196861 |
| stable and variable parts of microbial community in siberian deep subsurface thermal aquifer system revealed in a long-term monitoring study. | the goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. a microbial community of a deep subsurface thermal aquifer in the tomsk region, western siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3p, drilled down to a palaeozoic basement. the borehole water discharges with a temperature o ... | 2016 | 28082967 |