| purification and characterization of acetoin:2,6-dichlorophenolindophenol oxidoreductase, dihydrolipoamide dehydrogenase, and dihydrolipoamide acetyltransferase of the pelobacter carbinolicus acetoin dehydrogenase enzyme system. | dihydrolipoamide dehydrogenase (dhldh), dihydrolipoamide acetyltransferase (dhlta), and acetoin: 2,6-dichlorophenolindophenol oxidoreductase (ao:dcpip or) were purified from acetoin-grown cells of pelobacter carbinolicus. dhldh had a native mr of 110,000, consisted of two identical subunits of mr 54,000, and reacted only with nad(h) as a coenzyme. the n-terminal amino acid sequence included the flavin adenine dinucleotide-binding site and exhibited a high degree of homology to other dhldhs. dhlt ... | 1991 | 1898934 |
| fe(iii) and s0 reduction by pelobacter carbinolicus. | there is a close phylogenetic relationship between pelobacter species and members of the genera desulfuromonas and geobacter, and yet there has been a perplexing lack of physiological similarities. pelobacter species have been considered to have a fermentative metabolism. in contrast, desulfuromonas and geobacter species have a respiratory metabolism with fe(iii) serving as the common terminal electron acceptor in all species. however, the ability of pelobacter species to reduce fe(iii) had not ... | 1995 | 7793935 |
| identification and molecular characterization of the aco genes encoding the pelobacter carbinolicus acetoin dehydrogenase enzyme system. | use of oligonucleotide probes, which were deduced from the n-terminal sequences of the purified enzyme components, identified the structural genes for the alpha and beta subunits of e1 (acetoin:2,6-dichlorophenolindophenol oxidoreductase), e2 (dihydrolipoamide acetyltransferase), and e3 (dihydrolipoamide dehydrogenase) of the pelobacter carbinolicus acetoin dehydrogenase enzyme system, which were designated acoa, acob, acoc, and acol, respectively. the nucleotide sequences of acoa (979 bp), acob ... | 1994 | 8110297 |
| biochemical and molecular characterization of the clostridium magnum acetoin dehydrogenase enzyme system. | e2 (dihydrolipoamide acetyltransferase) and e3 (dihydrolipoamide dehydrogenase) of the clostridium magnum acetoin dehydrogenase enzyme system were copurified in a three-step procedure from acetoin-grown cells. the denatured e2-e3 preparation comprised two polypeptides with m(r)s of 49,000 and 67,000, respectively. microsequencing of both proteins revealed identical amino acid sequences. by use of oligonucleotide probes based on the n-terminal sequences of the alpha and beta subunits of e1 (aceto ... | 1994 | 8206840 |
| evidence of two oxidative reaction steps initiating anaerobic degradation of resorcinol (1,3-dihydroxybenzene) by the denitrifying bacterium azoarcus anaerobius. | the denitrifying bacterium azoarcus anaerobius lufres1 grows anaerobically with resorcinol (1,3-dihydroxybenzene) as the sole source of carbon and energy. the anaerobic degradation of this compound was investigated in cell extracts. resorcinol reductase, the key enzyme for resorcinol catabolism in fermenting bacteria, was not present in this organism. instead, resorcinol was hydroxylated to hydroxyhydroquinone (hhq; 1,2,4-trihydroxybenzene) with nitrate or k3fe(cn)6 as the electron acceptor. hhq ... | 1998 | 9658009 |
| dissimilatory reduction of fe(iii) and other electron acceptors by a thermus isolate. | a thermophilic bacterium that can use o2, no3-, fe(iii), and s0 as terminal electron acceptors for growth was isolated from groundwater sampled at a 3.2-km depth in a south african gold mine. this organism, designated sa-01, clustered most closely with members of the genus thermus, as determined by 16s rrna gene (rdna) sequence analysis. the 16s rdna sequence of sa-01 was >98% similar to that of thermus strain nmx2 a.1, which was previously isolated by other investigators from a thermal spring i ... | 1999 | 10049886 |
| rhodococcus erythropolis dcl14 contains a novel degradation pathway for limonene. | strain dcl14, which is able to grow on limonene as a sole source of carbon and energy, was isolated from a freshwater sediment sample. this organism was identified as a strain of rhodococcus erythropolis by chemotaxonomic and genetic studies. r. erythropolis dcl14 also assimilated the terpenes limonene-1,2-epoxide, limonene-1,2-diol, carveol, carvone, and (-)-menthol, while perillyl alcohol was not utilized as a carbon and energy source. induction tests with cells grown on limonene revealed that ... | 1999 | 10224006 |
| biochemical and molecular characterization of the bacillus subtilis acetoin catabolic pathway. | a recent study indicated that bacillus subtilis catabolizes acetoin by enzymes encoded by the acu gene cluster (f. j. grundy, d. a. waters, t. y. takova, and t. m. henkin, mol. microbiol. 10:259-271, 1993) that are completely different from those in the multicomponent acetoin dehydrogenase enzyme system (aodh es) encoded by aco gene clusters found before in all other bacteria capable of utilizing acetoin as the sole carbon source for growth. by hybridization with a dna probe covering acoa and ac ... | 1999 | 10368162 |
| isolation and characterization of a sulfate-reducing bacterium that anaerobically degrades alkanes. | an alkane-degrading, sulfate-reducing bacterial strain, ak-01, was isolated from an estuarine sediment with a history of chronic petroleum contamination. the bacterium is a short, nonmotile, non-spore-forming, gram-negative rod. it is mesophilic and grows optimally at ph 6.9 to 7.0 and at an nacl concentration of 1%. formate, fatty acids (c4 to c16) and hydrogen were readily utilized as electron donors. sulfate, sulfite, and thiosulfate were used as electron acceptors, but sulfur, nitrite, and n ... | 1999 | 10388691 |
| ferric iron reduction by bacteria associated with the roots of freshwater and marine macrophytes. | in vitro assays of washed, excised roots revealed maximum potential ferric iron reduction rates of >100 micromol g (dry weight)(-1) day(-1) for three freshwater macrophytes and rates between 15 and 83 micromol (dry weight)(-1) day(-1) for two marine species. the rates varied with root morphology but not consistently (fine root activity exceeded smooth root activity in some but not all cases). sodium molybdate added at final concentrations of 0.2 to 20 mm did not inhibit iron reduction by roots o ... | 1999 | 10508065 |
| the legionella pneumophila iraab locus is required for iron assimilation, intracellular infection, and virulence. | legionella pneumophila, a facultative intracellular parasite of human alveolar macrophages and protozoa, causes legionnaires' disease. using mini-tn10 mutagenesis, we previously isolated a l. pneumophila mutant that was hypersensitive to iron chelators. this mutant, nu216, and its allelic equivalent, nu216r, were also defective for intracellular infection, particularly in iron-deficient host cells. to determine whether nu216r was attenuated for virulence, we assessed its ability to cause disease ... | 2000 | 10678909 |
| regulation of the acetoin catabolic pathway is controlled by sigma l in bacillus subtilis. | bacillus subtilis grown in media containing amino acids or glucose secretes acetate, pyruvate, and large quantities of acetoin into the growth medium. acetoin can be reused by the bacteria during stationary phase when other carbon sources have been depleted. the acoabcl operon encodes the e1alpha, e1beta, e2, and e3 subunits of the acetoin dehydrogenase complex in b. subtilis. expression of this operon is induced by acetoin and repressed by glucose in the growth medium. the acor gene is located ... | 2001 | 11274109 |
| purification of synechocystis sp. strain pcc6308 cyanophycin synthetase and its characterization with respect to substrate and primer specificity. | synechocystis sp. strain pcc6308 cyanophycin synthetase was purified 72-fold in three steps by anion exchange chromatography on q sepharose, affinity chromatography on the triazine dye matrix procion blue he-rd sepharose, and gel filtration on superdex 200 hr from recombinant cells of escherichia coli. the native enzyme, which catalyzed the incorporation of arginine and aspartic acid into cyanophycin, has an apparent molecular mass of 240 +/- 30 kda and consists of identical subunits of 85 +/- 5 ... | 2001 | 11319097 |
| photosynthetic and phylogenetic primers for detection of anoxygenic phototrophs in natural environments. | primer sets were designed to target specific 16s ribosomal dna (rdna) sequences of photosynthetic bacteria, including the green sulfur bacteria, the green nonsulfur bacteria, and the members of the heliobacteriaceae (a gram-positive phylum). due to the phylogenetic diversity of purple sulfur and purple nonsulfur phototrophs, the 16s rdna gene was not an appropriate target for phylogenetic rdna primers. thus, a primer set was designed that targets the pufm gene, encoding the m subunit of the phot ... | 2001 | 11425703 |
| enrichment of members of the family geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments. | stimulating microbial reduction of soluble u(vi) to insoluble u(iv) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments. in order to learn more about which microorganisms might be involved in u(vi) reduction in situ, the changes in the microbial community when u(vi) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the san juan river in shiprock, n ... | 2002 | 11976101 |
| sequence versus structure for the direct detection of 16s rrna on planar oligonucleotide microarrays. | a two-probe proximal chaperone detection system consisting of a species-specific capture probe for the microarray and a labeled, proximal chaperone probe for detection was recently described for direct detection of intact rrnas from environmental samples on oligonucleotide arrays. in this study, we investigated the physical spacing and nucleotide mismatch tolerance between capture and proximal chaperone detector probes that are required to achieve species-specific 16s rrna detection for the diss ... | 2003 | 12732571 |
| characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as desulfuromonas michiganensis sp. nov. | two tetrachlorethene (pce)-dechlorinating populations, designated strains bb1 and brs1, were isolated from pristine river sediment and chloroethene-contaminated aquifer material, respectively. pce-to-cis-1,2-dichloroethene-dechlorinating activity could be transferred in defined basal salts medium with acetate as the electron donor and pce as the electron acceptor. taxonomic analysis based on 16s rrna gene sequencing placed both isolates within the desulfuromonas cluster in the delta subdivision ... | 2003 | 12732573 |
| differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient. | the hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. the microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. using a suite of methods (denaturing gradient gel electrophoresis, 16s rrna phylogeny, phospholipid fatty a ... | 2003 | 12957946 |
| in situ expression of nifd in geobacteraceae in subsurface sediments. | in order to determine whether the metabolic state of geobacteraceae involved in bioremediation of subsurface sediments might be inferred from levels of mrna for key genes, in situ expression of nifd, a highly conserved gene involved in nitrogen fixation, was investigated. when geobacter sulfurreducens was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and fe(iii) as the electron acceptor, levels of nifd transcripts were 4 to 5 orders o ... | 2004 | 15574924 |
| a novel geobacteraceae-specific outer membrane protein j (ompj) is essential for electron transport to fe(iii) and mn(iv) oxides in geobacter sulfurreducens. | metal reduction is thought to take place at or near the bacterial outer membrane and, thus, outer membrane proteins in the model dissimilatory metal-reducing organism geobacter sulfurreducens are of interest to understand the mechanisms of fe(iii) reduction in the geobacter species that are the predominant fe(iii) reducers in many environments. previous studies have implicated periplasmic and outer membrane cytochromes in electron transfer to metals. here we show that the most abundant outer mem ... | 2005 | 16000176 |
| characterization of citrate synthase from geobacter sulfurreducens and evidence for a family of citrate synthases similar to those of eukaryotes throughout the geobacteraceae. | members of the family geobacteraceae are commonly the predominant fe(iii)-reducing microorganisms in sedimentary environments, as well as on the surface of energy-harvesting electrodes, and are able to effectively couple the oxidation of acetate to the reduction of external electron acceptors. citrate synthase activity of these organisms is of interest due to its key role in acetate metabolism. prior sequencing of the genome of geobacter sulfurreducens revealed a putative citrate synthase sequen ... | 2005 | 16000798 |
| potential for quantifying expression of the geobacteraceae citrate synthase gene to assess the activity of geobacteraceae in the subsurface and on current-harvesting electrodes. | the geobacteraceae citrate synthase is phylogenetically distinct from those of other prokaryotes and is a key enzyme in the central metabolism of geobacteraceae. therefore, the potential for using levels of citrate synthase mrna to estimate rates of geobacter metabolism was evaluated in pure culture studies and in four different geobacteraceae-dominated environments. quantitative reverse transcription-pcr studies with mrna extracted from cultures of geobacter sulfurreducens grown in chemostats w ... | 2005 | 16269721 |
| characterization of dissimilatory fe(iii) versus no3- reduction in the hyperthermophilic archaeon pyrobaculum aerophilum. | the hyperthermophilic archaeon pyrobaculum aerophilum used 20 mm fe(iii) citrate, 100 mm poorly crystalline fe(iii) oxide, and 10 mm kno3 as terminal electron acceptors. the two forms of iron were reduced at different rates but with equal growth yields. the insoluble iron was reduced when segregated spatially by dialysis tubing, indicating that direct contact with the iron was not necessary for growth. when partitioned, there was no detectable fe(iii) or fe(ii) outside of the tubing after growth ... | 2006 | 16385043 |
| suspension array analysis of 16s rrna from fe- and so(4)2- reducing bacteria in uranium-contaminated sediments undergoing bioremediation. | a 16s rrna-targeted tunable bead array was developed and used in a retrospective analysis of metal- and sulfate-reducing bacteria in contaminated subsurface sediments undergoing in situ u(vi) bioremediation. total rna was extracted from subsurface sediments and interrogated directly, without a pcr step. bead array validation studies with total rna derived from 24 isolates indicated that the behavior and response of the 16s rrna-targeted oligonucleotide probes could not be predicted based on the ... | 2006 | 16820459 |
| c-type cytochromes in pelobacter carbinolicus. | previous studies failed to detect c-type cytochromes in pelobacter species despite the fact that other close relatives in the geobacteraceae, such as geobacter and desulfuromonas species, have abundant c-type cytochromes. analysis of the recently completed genome sequence of pelobacter carbinolicus revealed 14 open reading frames that could encode c-type cytochromes. transcripts for all but one of these open reading frames were detected in acetoin-fermenting and/or fe(iii)-reducing cells. three ... | 2006 | 16936056 |
| tungsten transport protein a (wtpa) in pyrococcus furiosus: the first member of a new class of tungstate and molybdate transporters. | a novel tungstate and molybdate binding protein has been discovered from the hyperthermophilic archaeon pyrococcus furiosus. this tungstate transport protein a (wtpa) is part of a new abc transporter system selective for tungstate and molybdate. wtpa has very low sequence similarity with the earlier-characterized transport proteins moda for molybdate and tupa for tungstate. its structural gene is present in the genome of numerous archaea and some bacteria. the identification of this new tungstat ... | 2006 | 16952940 |
| evolution of sensory complexity recorded in a myxobacterial genome. | myxobacteria are single-celled, but social, eubacterial predators. upon starvation they build multicellular fruiting bodies using a developmental program that progressively changes the pattern of cell movement and the repertoire of genes expressed. development terminates with spore differentiation and is coordinated by both diffusible and cell-bound signals. the growth and development of myxococcus xanthus is regulated by the integration of multiple signals from outside the cells with physiologi ... | 2006 | 17015832 |
| role of relgsu in stress response and fe(iii) reduction in geobacter sulfurreducens. | geobacter species are key members of the microbial community in many subsurface environments in which dissimilatory metal reduction is an important process. the genome of geobacter sulfurreducens contains a gene designated rel(gsu), which encodes a rela homolog predicted to catalyze both the synthesis and the degradation of guanosine 3',5'-bispyrophosphate (ppgpp), a regulatory molecule that signals slow growth in response to nutrient limitation in bacteria. to evaluate the physiological role of ... | 2006 | 17041036 |
| helicobacter pylori flhb function: the flhb c-terminal homologue hp1575 acts as a "spare part" to permit flagellar export when the hp0770 flhbcc domain is deleted. | in helicobacter pylori 26695, a gene annotated hp1575 encodes a putative protein of unknown function which shows significant similarity to part of the c-terminal domain of the flagellar export protein flhb. in salmonella enterica, this part (flhb(cc)) is proteolytically cleaved from the full-length flhb, a processing event that is required for flagellar protein export and, thus, motility. the role of flhb (hp0770) and its c-terminal homologue hp1575 was studied in h. pylori using a range of nonp ... | 2006 | 17050924 |
| transposon tn7 is widespread in diverse bacteria and forms genomic islands. | we find that relatives of the bacterial transposon tn7 are widespread in disparate environments and phylogenetically diverse species. these elements form functionally diverse genomic islands at the specific site of tn7 insertion adjacent to glms. this work presents the first example of genomic island formation by a dde type transposon. | 2007 | 17194796 |
| transposon tn7 is widespread in diverse bacteria and forms genomic islands. | we find that relatives of the bacterial transposon tn7 are widespread in disparate environments and phylogenetically diverse species. these elements form functionally diverse genomic islands at the specific site of tn7 insertion adjacent to glms. this work presents the first example of genomic island formation by a dde type transposon. | 2007 | 17194796 |
| structure of the type iii pantothenate kinase from bacillus anthracis at 2.0 a resolution: implications for coenzyme a-dependent redox biology. | coenzyme a (coash) is the major low-molecular weight thiol in staphylococcus aureus and a number of other bacteria; the crystal structure of the s. aureus coenzyme a-disulfide reductase (coadr), which maintains the reduced intracellular state of coash, has recently been reported [mallett, t.c., wallen, j.r., karplus, p.a., sakai, h., tsukihara, t., and claiborne, a. (2006) biochemistry 45, 11278-89]. in this report we demonstrate that coash is the major thiol in bacillus anthracis; a bioinformat ... | 2007 | 17323930 |
| a novel giardia lamblia nitroreductase, glnr1, interacts with nitazoxanide and other thiazolides. | the nitrothiazole analogue nitazoxanide [ntz; 2-acetolyloxy-n-(5-nitro-2-thiazolyl)benzamide] represents the parent compound of a class of drugs referred to as thiazolides and exhibits a broad spectrum of activities against a wide variety of helminths, protozoa, and enteric bacteria infecting animals and humans. ntz and other thiazolides are active against a wide range of other intracellular and extracellular protozoan parasites in vitro and in vivo, but their mode of action and respective subce ... | 2007 | 17438059 |
| co-existence of physiologically similar sulfate-reducing bacteria in a full-scale sulfidogenic bioreactor fed with a single organic electron donor. | a combination of culture-dependent and independent methods was used to study the co-existence of different sulfate-reducing bacteria (srb) in an upflow anaerobic sludge bed reactor treating sulfate-rich wastewater. the wastewater was fed with ethanol as an external electron donor. twenty six strains of srb were randomly picked and isolated from the highest serial dilution that showed growth (i.e. 10(8)). repetitive enterobacterial palindromic polymerase chain reaction and whole cell protein prof ... | 2007 | 17440719 |
| the genome of syntrophus aciditrophicus: life at the thermodynamic limit of microbial growth. | biochemically, the syntrophic bacteria constitute the missing link in our understanding of anaerobic flow of carbon in the biosphere. the completed genome sequence of syntrophus aciditrophicus sb, a model fatty acid- and aromatic acid-degrading syntrophic bacterium, provides a glimpse of the composition and architecture of the electron transfer and energy-transducing systems needed to exist on marginal energy economies of a syntrophic lifestyle. the genome contains 3,179,300 base pairs and 3,169 ... | 2007 | 17442750 |
| lack of electricity production by pelobacter carbinolicus indicates that the capacity for fe(iii) oxide reduction does not necessarily confer electron transfer ability to fuel cell anodes. | the ability of pelobacter carbinolicus to oxidize electron donors with electron transfer to the anodes of microbial fuel cells was evaluated because microorganisms closely related to pelobacter species are generally abundant on the anodes of microbial fuel cells harvesting electricity from aquatic sediments. p. carbinolicus could not produce current in a microbial fuel cell with electron donors which support fe(iii) oxide reduction by this organism. current was produced using a coculture of p. c ... | 2007 | 17574993 |
| evolution and functional characterization of the rh50 gene from the ammonia-oxidizing bacterium nitrosomonas europaea. | the family of ammonia and ammonium channel proteins comprises the amt proteins, which are present in all three domains of life with the notable exception of vertebrates, and the homologous rh proteins (rh50 and rh30) that have been described thus far only in eukaryotes. the existence of an rh50 gene in bacteria was first revealed by the genome sequencing of the ammonia-oxidizing bacterium nitrosomonas europaea. here we have used a phylogenetic approach to study the evolution of the n. europaea r ... | 2007 | 17921289 |
| a high-affinity molybdate transporter in eukaryotes. | molybdenum is an essential element for almost all living beings, which, in the form of a molybdopterin-cofactor, participates in the active site of enzymes involved in key reactions of carbon, nitrogen, and sulfur metabolism. this metal is taken up by cells in form of the oxyanion molybdate. bacteria acquire molybdate by an atp-binding-cassette (abc) transport system in a widely studied process, but how eukaryotic cells take up molybdenum is unknown because molybdate transporters have not been i ... | 2007 | 18077439 |
| genome evolution and the emergence of fruiting body development in myxococcus xanthus. | lateral gene transfer (lgt) is thought to promote speciation in bacteria, though well-defined examples have not been put forward. | 2007 | 18159227 |
| "candidatus cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division. | many microorganisms live in anaerobic environments. most of these microorganisms have not yet been cultivated. here, we present, from a metagenomic analysis of an anaerobic digester of a municipal wastewater treatment plant, a reconstruction of the complete genome of a bacterium belonging to the wwe1 candidate division. in silico proteome analysis indicated that this bacterium might derive most of its carbon and energy from the fermentation of amino acids, and hence, it was provisionally classif ... | 2008 | 18245282 |
| a complete collection of single-gene deletion mutants of acinetobacter baylyi adp1. | we have constructed a collection of single-gene deletion mutants for all dispensable genes of the soil bacterium acinetobacter baylyi adp1. a total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium. this essentiality data set is 88% consistent with the escherichia coli data set inferred from the keio mutant collection profiled for growth on minimal medium, while 80% of the orthologous genes described as esse ... | 2008 | 18319726 |
| rcom: a new single-component transcriptional regulator of co metabolism in bacteria. | genomic analysis suggested the existence of a co-sensing bacterial transcriptional regulator that couples an n-terminal pas fold domain to a c-terminal dna-binding lyttr domain. uv/visible-light spectral analyses of heterologously expressed, purified full-length proteins indicated that they contained a hexacoordinated b-type heme moiety that avidly binds co and no. studies of protein variants strongly suggested that the pas domain residues his74 and met104 serve as the heme fe(ii) axial ligands, ... | 2008 | 18326575 |
| isolation of the exoelectrogenic bacterium ochrobactrum anthropi yz-1 by using a u-tube microbial fuel cell. | exoelectrogenic bacteria have potential for many different biotechnology applications due to their ability to transfer electrons outside the cell to insoluble electron acceptors, such as metal oxides or the anodes of microbial fuel cells (mfcs). very few exoelectrogens have been directly isolated from mfcs, and all of these organisms have been obtained by techniques that potentially restrict the diversity of exoelectrogenic bacteria. a special u-tube-shaped mfc was therefore developed to enrich ... | 2008 | 18359834 |
| a widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. | we have identified a highly conserved rna motif located upstream of genes encoding molybdate transporters, molybdenum cofactor (moco) biosynthesis enzymes, and proteins that utilize moco as a coenzyme. bioinformatics searches have identified 176 representatives in gamma-proteobacteria, delta-proteobacteria, clostridia, actinobacteria, deinococcus-thermus species and dnas from environmental samples. using genetic assays, we demonstrate that a moco rna in escherichia coli associated with the moco ... | 2008 | 18363797 |
| the mosaic genome of anaeromyxobacter dehalogenans strain 2cp-c suggests an aerobic common ancestor to the delta-proteobacteria. | anaeromyxobacter dehalogenans strain 2cp-c is a versaphilic delta-proteobacterium distributed throughout many diverse soil and sediment environments. 16s rrna gene phylogenetic analysis groups a. dehalogenans together with the myxobacteria, which have distinguishing characteristics including strictly aerobic metabolism, sporulation, fruiting body formation, and surface motility. analysis of the 5.01 mb strain 2cp-c genome substantiated that this organism is a myxobacterium but shares genotypic t ... | 2008 | 18461135 |
| genome-wide gene expression patterns and growth requirements suggest that pelobacter carbinolicus reduces fe(iii) indirectly via sulfide production. | although pelobacter species are closely related to geobacter species, recent studies suggested that pelobacter carbinolicus may reduce fe(iii) via a different mechanism because it lacks the outer-surface c-type cytochromes that are required for fe(iii) reduction by geobacter sulfurreducens. investigation into the mechanisms for fe(iii) reduction demonstrated that p. carbinolicus had growth yields on both soluble and insoluble fe(iii) consistent with those of other fe(iii)-reducing bacteria. comp ... | 2008 | 18515480 |
| metagenomic analysis of lysogeny in tampa bay: implications for prophage gene expression. | phage integrase genes often play a role in the establishment of lysogeny in temperate phage by catalyzing the integration of the phage into one of the host's replicons. to investigate temperate phage gene expression, an induced viral metagenome from tampa bay was sequenced by 454/pyrosequencing. the sequencing yielded 294,068 reads with 6.6% identifiable. one hundred-three sequences had significant similarity to integrases by blastx analysis (e < or =0.001). four sequences with strongest amino-a ... | 2008 | 18810270 |
| geobacter sulfurreducens contains separate c- and a-adding trna nucleotidyltransferases and a poly(a) polymerase. | the genome of geobacter sulfurreducens contains three genes whose sequences are quite similar to sequences encoding known members of an rna nucleotidyltransferase superfamily that includes trna nucleotidyltransferases and poly(a) polymerases. reverse transcription-pcr using g. sulfurreducens total rna demonstrated that the genes encoding these three proteins are transcribed. these genes, encoding proteins designated ntsfi, ntsfii, and ntsfiii, were cloned and overexpressed in escherichia coli. t ... | 2009 | 18952795 |
| geobacter sulfurreducens contains separate c- and a-adding trna nucleotidyltransferases and a poly(a) polymerase. | the genome of geobacter sulfurreducens contains three genes whose sequences are quite similar to sequences encoding known members of an rna nucleotidyltransferase superfamily that includes trna nucleotidyltransferases and poly(a) polymerases. reverse transcription-pcr using g. sulfurreducens total rna demonstrated that the genes encoding these three proteins are transcribed. these genes, encoding proteins designated ntsfi, ntsfii, and ntsfiii, were cloned and overexpressed in escherichia coli. t ... | 2009 | 18952795 |
| structure-function analysis of 2-keto-3-deoxy-d-glycero-d-galactonononate-9-phosphate phosphatase defines specificity elements in type c0 haloalkanoate dehalogenase family members. | the phosphotransferases of the haloalkanoate dehalogenase superfamily (hadsf) act upon a wide range of metabolites in all eukaryotes and prokaryotes and thus constitute a significant force in cell function. the challenge posed for biochemical function assignment of hadsf members is the identification of the structural determinants that target a specific metabolite. the "8kdop" subfamily of the hadsf is defined by the known structure and catalytic activity of 2-keto-3-deoxy-8-phospho-d-manno-octu ... | 2009 | 18986982 |
| genome sequence of desulfobacterium autotrophicum hrm2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. | sulfate-reducing bacteria (srb) belonging to the metabolically versatile desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. desulfobacterium autotrophicum hrm2 is the first member of this ecophysiologically important group with a now available genome sequence. with 5.6 megabasepairs (mbp) the genome of db. autotrophicum hrm2 is about 2 mbp larger than the sequenced genomes of other sulfate reducers (srb). a h ... | 2009 | 19187283 |
| a comparative genomics study of genetic products potentially encoding ladderane lipid biosynthesis. | the fatty acids of anaerobic ammonium oxidizing (anammox) bacteria contain linearly concatenated cyclobutane moieties, so far unique to biology. these moieties are under high ring strain and are synthesised by a presently unknown biosynthetic pathway. | 2009 | 19220888 |
| evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six geobacteraceae species. | the anaerobic degradation of organic matter in natural environments, and the biotechnical use of anaerobes in energy production and remediation of subsurface environments, both require the cooperative activity of a diversity of microorganisms in different metabolic niches. the geobacteraceae family contains members with three important anaerobic metabolisms: fermentation, syntrophic degradation of fermentation intermediates, and anaerobic respiration. | 2009 | 19284579 |
| acetoin catabolism and acetylbutanediol formation by bacillus pumilus in a chemically defined medium. | most low molecular diols are highly water-soluble, hygroscopic, and reactive with many organic compounds. in the past decades, microbial research to produce diols, e.g. 1,3-propanediol and 2,3-butanediol, were considerably expanded due to their versatile usages especially in polymer synthesis and as possible alternatives to fossil based feedstocks from the bioconversion of renewable natural resources. this study aimed to provide a new way for bacterial production of an acetylated diol, i.e. acet ... | 2009 | 19461961 |
| anode biofilm transcriptomics reveals outer surface components essential for high density current production in geobacter sulfurreducens fuel cells. | the mechanisms by which geobacter sulfurreducens transfers electrons through relatively thick (>50 microm) biofilms to electrodes acting as a sole electron acceptor were investigated. biofilms of geobacter sulfurreducens were grown either in flow-through systems with graphite anodes as the electron acceptor or on the same graphite surface, but with fumarate as the sole electron acceptor. fumarate-grown biofilms were not immediately capable of significant current production, suggesting substantia ... | 2009 | 19461962 |
| anaerobic respiration of elemental sulfur and thiosulfate by shewanella oneidensis mr-1 requires psra, a homolog of the phsa gene of salmonella enterica serovar typhimurium lt2. | shewanella oneidensis mr-1, a facultatively anaerobic gammaproteobacterium, respires a variety of anaerobic terminal electron acceptors, including the inorganic sulfur compounds sulfite (so3(2-)), thiosulfate (s2o3(2-)), tetrathionate (s4o6(2-)), and elemental sulfur (s(0)). the molecular mechanism of anaerobic respiration of inorganic sulfur compounds by s. oneidensis, however, is poorly understood. in the present study, we identified a three-gene cluster in the s. oneidensis genome whose trans ... | 2009 | 19542325 |
| connecting quorum sensing, c-di-gmp, pel polysaccharide, and biofilm formation in pseudomonas aeruginosa through tyrosine phosphatase tpba (pa3885). | with the opportunistic pathogen pseudomonas aeruginosa, quorum sensing based on homoserine lactones was found to influence biofilm formation. here we discern a mechanism by which quorum sensing controls biofilm formation by screening 5850 transposon mutants of p. aeruginosa pa14 for altered biofilm formation. this screen identified the pa3885 mutant, which had 147-fold more biofilm than the wild-type strain. loss of pa3885 decreased swimming, abolished swarming, and increased attachment, althoug ... | 2009 | 19543378 |
| novel genetic environment of the carbapenem-hydrolyzing beta-lactamase kpc-2 among enterobacteriaceae in china. | thirty-nine bla(kpc)-producing isolates of the family enterobacteriaceae with carbapenem resistance or reduced carbapenem susceptibility were obtained from inpatients from eight hospitals in six cities of three provinces in eastern china. the pulsed-field gel electrophoresis analysis of all 36 klebsiella pneumoniae isolates revealed six major patterns. the resistant plasmids of most isolates were successfully transferred by conjugation and evaluated experimentally to be 40 to 180 kb in size. a 2 ... | 2009 | 19620332 |
| crystal structure and catalytic properties of bacillus anthracis coadr-rhd: implications for flavin-linked sulfur trafficking. | rhodanese homology domains (rhds) play important roles in sulfur trafficking mechanisms essential to the biosynthesis of sulfur-containing cofactors and nucleosides. we have now determined the crystal structure at 2.10 a resolution for the bacillus anthracis coenzyme a-disulfide reductase isoform (bacoadr-rhd) containing a c-terminal rhd domain; this is the first structural representative of the multidomain proteins class of the rhodanese superfamily. the catalytic cys44 of the coadr module is s ... | 2009 | 19725515 |
| cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. | aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ... | 2009 | 19946135 |
| characterization of camh from methanosarcina thermophila, founding member of a subclass of the {gamma} class of carbonic anhydrases. | the homotrimeric enzyme mt-cam from methanosarcina thermophila is the archetype of the gamma class of carbonic anhydrases. a search of databases queried with mt-cam revealed that a majority of the homologs comprise a putative subclass (camh) in which there is major conservation of all of the residues essential for the archetype mt-cam except glu62 and an acidic loop containing the essential proton shuttle residue glu84. the camh homolog from m. thermophila (mt-camh) was overproduced in escherich ... | 2010 | 20023030 |
| characterization of camh from methanosarcina thermophila, founding member of a subclass of the {gamma} class of carbonic anhydrases. | the homotrimeric enzyme mt-cam from methanosarcina thermophila is the archetype of the gamma class of carbonic anhydrases. a search of databases queried with mt-cam revealed that a majority of the homologs comprise a putative subclass (camh) in which there is major conservation of all of the residues essential for the archetype mt-cam except glu62 and an acidic loop containing the essential proton shuttle residue glu84. the camh homolog from m. thermophila (mt-camh) was overproduced in escherich ... | 2010 | 20023030 |
| predicting the pathway involved in post-translational modification of elongation factor p in a subset of bacterial species. | background: the bacterial elongation factor p (ef-p) is strictly conserved in bacteria and essential for protein synthesis. it is homologous to the eukaryotic translation initiation factor 5a (eif5a). a highly conserved eif5a lysine is modified into an unusual amino acid derived from spermidine, hypusine. hypusine is absolutely required for eif5a's role in translation in saccharomyces cerevisiae. the homologous lysine of ef-p is also modified to a spermidine derivative in escherichia coli. howev ... | 2010 | 20070887 |
| carbon-dependent control of electron transfer and central carbon pathway genes for methane biosynthesis in the archaean, methanosarcina acetivorans strain c2a. | the archaeon, methanosarcina acetivorans strain c2a forms methane, a potent greenhouse gas, from a variety of one-carbon substrates and acetate. whereas the biochemical pathways leading to methane formation are well understood, little is known about the expression of the many of the genes that encode proteins needed for carbon flow, electron transfer and/or energy conservation. quantitative transcript analysis was performed on twenty gene clusters encompassing over one hundred genes in m. acetiv ... | 2010 | 20178638 |
| bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium deferribacter desulfuricans ssm1. | the complete genome sequence of the thermophilic sulphur-reducing bacterium, deferribacter desulfuricans smm1, isolated from a hydrothermal vent chimney has been determined. the genome comprises a single circular chromosome of 2,234,389 bp and a megaplasmid of 308,544 bp. many genes encoded in the genome are most similar to the genes of sulphur- or sulphate-reducing bacterial species within deltaproteobacteria. the reconstructed central metabolisms showed a heterotrophic lifestyle primarily driv ... | 2010 | 20189949 |
| bacterial genes in the aphid genome: absence of functional gene transfer from buchnera to its host. | genome reduction is typical of obligate symbionts. in cellular organelles, this reduction partly reflects transfer of ancestral bacterial genes to the host genome, but little is known about gene transfer in other obligate symbioses. aphids harbor anciently acquired obligate mutualists, buchnera aphidicola (gammaproteobacteria), which have highly reduced genomes (420-650 kb), raising the possibility of gene transfer from ancestral buchnera to the aphid genome. in addition, aphids often harbor oth ... | 2010 | 20195500 |
| twisting of the dna-binding surface by a beta-strand-bearing proline modulates dna gyrase activity. | dna gyrase is the only topoisomerase capable of introducing (-) supercoils into relaxed dna. the c-terminal domain of the gyrase a subunit (gyra-ctd) and the presence of a gyrase-specific 'gyra-box' motif within this domain are essential for this unique (-) supercoiling activity by allowing gyrase to wrap dna around itself. here we report the crystal structure of xanthomonas campestris gyra-ctd and provide the first view of a canonical gyra-box motif. this structure resembles the gyra-box-disord ... | 2010 | 20215433 |
| the hp0256 gene product is involved in motility and cell envelope architecture of helicobacter pylori. | helicobacter pylori is the causative agent for gastritis, and peptic and duodenal ulcers. the bacterium displays 5-6 polar sheathed flagella that are essential for colonisation and persistence in the gastric mucosa. the biochemistry and genetics of flagellar biogenesis in h. pylori has not been fully elucidated. bioinformatics analysis suggested that the gene hp0256, annotated as hypothetical, was a flij homologue. in salmonella, flij is a chaperone escort protein for flgn and flit, two proteins ... | 2010 | 20377912 |
| the dissemination of c10 cysteine protease genes in bacteroides fragilis by mobile genetic elements. | the c10 family of cysteine proteases includes enzymes that contribute to the virulence of bacterial pathogens, such as speb in streptococcus pyogenes. the presence of homologues of cysteine protease genes in human commensal organisms has not been examined. bacteroides fragilis is a member of the dominant bacteroidetes phylum of the human intestinal microbiota, and is a significant opportunistic pathogen. | 2010 | 20416045 |
| interference with histidyl-trna synthetase by a crispr spacer sequence as a factor in the evolution of pelobacter carbinolicus. | pelobacter carbinolicus, a bacterium of the family geobacteraceae, cannot reduce fe(iii) directly or produce electricity like its relatives. how p. carbinolicus evolved is an intriguing problem. the genome of p. carbinolicus contains clustered regularly interspaced short palindromic repeats (crispr) separated by unique spacer sequences, which recent studies have shown to produce rna molecules that interfere with genes containing identical sequences. | 2010 | 20667132 |
| comparative metagenomics of bathypelagic plankton and bottom sediment from the sea of marmara. | to extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the sea of marmara, the gateway between the eastern mediterranean and the black seas. data from small subunit ribosomal rna (ssu rrna) gene libraries and direct pyrosequencing of the same samples indicated that gamma- and alpha-proteobacteria, followed by bacteroidetes, dominated the bacterial fraction in marmara d ... | 2011 | 20668488 |
| comparative metagenomics of bathypelagic plankton and bottom sediment from the sea of marmara. | to extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the sea of marmara, the gateway between the eastern mediterranean and the black seas. data from small subunit ribosomal rna (ssu rrna) gene libraries and direct pyrosequencing of the same samples indicated that gamma- and alpha-proteobacteria, followed by bacteroidetes, dominated the bacterial fraction in marmara d ... | 2011 | 20668488 |
| the escherichia coli crispr system protects from λ lysogenization, lysogens, and prophage induction. | we show that phage lysogenization, lysogens, and prophage induction are all targeted by crispr. the results demonstrate that genomic dna is not immune to the crispr system, that the crispr system does not require noncytoplasmic elements, and that the system protects from phages entering and exiting the lysogenic cycle. | 2010 | 20889749 |
| constraint-based modeling analysis of the metabolism of two pelobacter species. | pelobacter species are commonly found in a number of subsurface environments, and are unique members of the geobacteraceae family. they are phylogenetically intertwined with both geobacter and desulfuromonas species. pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells. | 2010 | 21182788 |
| a dual function of the crispr-cas system in bacterial antivirus immunity and dna repair. | clustered regularly interspaced short palindromic repeats (crisprs) and the associated proteins (cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes. cas1 is a crispr-associated protein that is common to all crispr-containing prokaryotes but its function remains obscure. here we show that the purified cas1 protein of escherichia coli (ygbt) exhibits nuclease activity against single-stranded and branched dnas including holliday junctions, replication forks and ... | 2010 | 21219465 |
| a dual function of the crispr-cas system in bacterial antivirus immunity and dna repair. | clustered regularly interspaced short palindromic repeats (crisprs) and the associated proteins (cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes. cas1 is a crispr-associated protein that is common to all crispr-containing prokaryotes but its function remains obscure. here we show that the purified cas1 protein of escherichia coli (ygbt) exhibits nuclease activity against single-stranded and branched dnas including holliday junctions, replication forks and ... | 2010 | 21219465 |
| parallel evolution and horizontal gene transfer of the pst operon in firmicutes from oligotrophic environments. | the high affinity phosphate transport system (pst) is crucial for phosphate uptake in oligotrophic environments. cuatro cienegas basin (ccb) has extremely low p levels and its endemic bacillus are closely related to oligotrophic marine firmicutes. thus, we expected the pst operon of ccb to share the same evolutionary history and protein similarity to marine firmicutes. orthologs of the pst operon were searched in 55 genomes of firmicutes and 13 outgroups. phylogenetic reconstructions were perfor ... | 2011 | 21461370 |
| bioinformatic characterization of the trimeric intracellular cation-specific channel protein family. | trimeric intracellular cation-specific (tric) channels are integral to muscle excitation-contraction coupling. tric channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. until recently, knowledge of the presence of these proteins was limited to animals. we analyzed the tric family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. prokaryotic memb ... | 2011 | 21519847 |
| crispr inhibition of prophage acquisition in streptococcus pyogenes. | streptococcus pyogenes, one of the major human pathogens, is a unique species since it has acquired diverse strain-specific virulence properties mainly through the acquisition of streptococcal prophages. in addition, s. pyogenes possesses clustered regularly interspaced short palindromic repeats (crispr)/cas systems that can restrict horizontal gene transfer (hgt) including phage insertion. therefore, it was of interest to examine the relationship between crispr and acquisition of prophages in s ... | 2011 | 21573110 |
| widespread occurrence of secondary lipid biosynthesis potential in microbial lineages. | bacterial production of long-chain omega-3 polyunsaturated fatty acids (pufas), such as eicosapentaenoic acid (epa, 20:5n-3) and docosahexaenoic acid (dha, 22:6n-3), is constrained to a narrow subset of marine γ-proteobacteria. the genes responsible for de novo bacterial pufa biosynthesis, designated pfaeabcd, encode large, multi-domain protein complexes akin to type i iterative fatty acid and polyketide synthases, herein referred to as "pfa synthases". in addition to the archetypal pfa synthase ... | 2011 | 21629834 |
| the atypical two-component sensor kinase lpl0330 from legionella pneumophila controls the bifunctional diguanylate cyclase-phosphodiesterase lpl0329 to modulate c-di-gmp synthesis. | a significant part of bacterial two-component system response regulators contain effector domains predicted to be involved in metabolism of c-di-gmp, a second messenger which plays a key role in many physiological processes. intracellular level of c-di-gmp is controlled by diguanylate cyclases (dgcs) and phosphodiesterases (pdes) activities associated with ggdef and eal domains, respectively. the legionella pneumophila lens genome displays 22 ggdef/eal domain-encoding genes. one of them, lpl0329 ... | 2011 | 21757706 |
| identification and characterization of rhodopseudomonas palustris tie-1 hopanoid biosynthesis mutants. | hopanes preserved in both modern and ancient sediments are recognized as the molecular fossils of bacteriohopanepolyols, pentacyclic hopanoid lipids. based on the phylogenetic distribution of hopanoid production by extant bacteria, hopanes have been used as indicators of specific bacterial groups and/or their metabolisms. however, our ability to interpret them ultimately depends on understanding the physiological roles of hopanoids in modern bacteria. toward this end, we set out to identify gene ... | 2012 | 22221333 |
| complete genome sequence of syntrophobacter fumaroxidans strain (mpob(t)). | syntrophobacter fumaroxidans strain mpob(t) is the best-studied species of the genus syntrophobacter. the species is of interest because of its anaerobic syntrophic lifestyle, its involvement in the conversion of propionate to acetate, h2 and co2 during the overall degradation of organic matter, and its release of products that serve as substrates for other microorganisms. the strain is able to ferment fumarate in pure culture to co2 and succinate, and is also able to grow as a sulfate reducer w ... | 2012 | 23450070 |
| crispr regulation of intraspecies diversification by limiting is transposition and intercellular recombination. | mobile genetic elements (mges) and genetic rearrangement are considered as major driving forces of bacterial diversification. previous comparative genome analysis of porphyromonas gingivalis, a pathogen related to periodontitis, implied such an important relationship. as a counterpart system to mges, clustered regularly interspaced short palindromic repeats (crisprs) in bacteria may be useful for genetic typing. we found that crispr typing could be a reasonable alternative to conventional method ... | 2013 | 23661565 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| noncellulosomal cohesin- and dockerin-like modules in the three domains of life. | the high-affinity cohesin-dockerin interaction was originally discovered as modular components, which mediate the assembly of the various subunits of the multienzyme cellulosome complex that characterizes some cellulolytic bacteria. until recently, the presence of cohesins and dockerins within a bacterial proteome was considered a definitive signature of a cellulosome-producing bacterium. widespread genome sequencing has since revealed a wealth of putative cohesin- and dockerin-containing protei ... | 2009 | 19025568 |
| noncellulosomal cohesin- and dockerin-like modules in the three domains of life. | the high-affinity cohesin-dockerin interaction was originally discovered as modular components, which mediate the assembly of the various subunits of the multienzyme cellulosome complex that characterizes some cellulolytic bacteria. until recently, the presence of cohesins and dockerins within a bacterial proteome was considered a definitive signature of a cellulosome-producing bacterium. widespread genome sequencing has since revealed a wealth of putative cohesin- and dockerin-containing protei ... | 2009 | 19025568 |
| in silico characterization of pectate lyase protein sequences from different source organisms. | a total of 121 protein sequences of pectate lyases were subjected to homology search, multiple sequence alignment, phylogenetic tree construction, and motif analysis. the phylogenetic tree constructed revealed different clusters based on different source organisms representing bacterial, fungal, plant, and nematode pectate lyases. the multiple accessions of bacterial, fungal, nematode, and plant pectate lyase protein sequences were placed closely revealing a sequence level similarity. the multip ... | 2010 | 21048874 |
| novel metagenome-derived, cold-adapted alkaline phospholipase with superior lipase activity as an intermediate between phospholipase and lipase. | a novel lipolytic enzyme was isolated from a metagenomic library obtained from tidal flat sediments on the korean west coast. its putative functional domain, designated mplag, showed the highest similarity to phospholipase a from grimontia hollisae cip 101886, though it was screened from an emulsified tricaprylin plate. phylogenetic analysis showed that mplag is far from family i.6 lipases, including staphylococcus hyicus lipase, a unique lipase which can hydrolyze phospholipids, and is more evo ... | 2012 | 22544255 |
| dissemination of 6s rna among bacteria. | 6s rna is a highly abundant small non-coding rna widely spread among diverse bacterial groups. by competing with dna promoters for binding to rna polymerase (rnap), the rna regulates transcription on a global scale. rnap produces small product rnas derived from 6s rna as template, which rearranges the 6s rna structure leading to dissociation of 6s rna:rnap complexes. although 6s rna has been experimentally analysed in detail for some species, such as escherichia coli and bacillus subtilis, and w ... | 2014 | 25483037 |
| impact of small repeat sequences on bacterial genome evolution. | intergenic regions of prokaryotic genomes carry multiple copies of terminal inverted repeat (tir) sequences, the nonautonomous miniature inverted-repeat transposable element (mite). in addition, there are the repetitive extragenic palindromic (rep) sequences that fold into a small stem loop rich in g-c bonding. and the clustered regularly interspaced short palindromic repeats (crisprs) display similar small stem loops but are an integral part of a complex genetic element. other classes of repeat ... | 2011 | 21803768 |
| turnover-dependent covalent inactivation of staphylococcus aureus coenzyme a-disulfide reductase by coenzyme a-mimetics: mechanistic and structural insights. | disruption of the unusual thiol-based redox homeostasis mechanisms in staphylococcus aureus represents a unique opportunity to identify new metabolic processes and new targets for intervention. targeting uncommon aspects of coash biosynthetic and redox functions in s. aureus, the antibiotic cj-15,801 has recently been demonstrated to be an antimetabolite of the coash biosynthetic pathway in this organism; coas-mimetics containing α,β-unsaturated sulfone and carboxyl moieties have also been explo ... | 2012 | 22954034 |
| evolution of the f0f1 atp synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes. | bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation and reduction, sulfate reduction, and methanogenesis. most bioenergetic pathways have a similar general ... | 2014 | 25188293 |
| self-targeting by crispr: gene regulation or autoimmunity? | the recently discovered prokaryotic immune system known as crispr (clustered regularly interspaced short palindromic repeats) is based on small rnas ('spacers') that restrict phage and plasmid infection. it has been hypothesized that crisprs can also regulate self gene expression by utilizing spacers that target self genes. by analyzing crisprs from 330 organisms we found that one in every 250 spacers is self-targeting, and that such self-targeting occurs in 18% of all crispr-bearing organisms. ... | 2010 | 20598393 |
| molecular evolution of the oxygen-binding hemerythrin domain. | the evolution of oxygenic photosynthesis during precambrian times entailed the diversification of strategies minimizing reactive oxygen species-associated damage. four families of oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of arthropodan and molluscan hemocyanins) are known to have evolved independently the capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolutionary pressure of oxygen accumulation. oxygen-binding hem ... | 2016 | 27336621 |
| reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes. | the increasing number of sequenced prokaryotic genomes contains a wealth of genomic data that needs to be effectively analysed. a set of statistical tools exists for such analysis, but their strengths and weaknesses have not been fully explored. the statistical methods we are concerned with here are mainly used to examine similarities between archaeal and bacterial dna from different genomes. these methods compare observed genomic frequencies of fixed-sized oligonucleotides with expected values, ... | 2008 | 18307761 |
| intergenic transposable elements are not randomly distributed in bacteria. | insertion sequences (iss) are mobile genetic elements in bacterial genomes. in general, intergenic is elements are probably less deleterious for their hosts than intragenic iss, simply because they have a lower likelihood of disrupting native genes. however, since promoters, shine-dalgarno sequences, and transcription factor binding sites are intergenic and upstream of genes, i hypothesized that not all neighboring gene orientations (ngos) are selectively equivalent for is insertion. to test thi ... | 2010 | 20697140 |
| recovery of humic-reducing bacteria from a diversity of environments. | to evaluate which microorganisms might be responsible for microbial reduction of humic substances in sedimentary environments, humic-reducing bacteria were isolated from a variety of sediment types. these included lake sediments, pristine and contaminated wetland sediments, and marine sediments. in each of the sediment types, all of the humic reducers recovered with acetate as the electron donor and the humic substance analog, 2,6-anthraquinone disulfonate (aqds), as the electron acceptor were m ... | 1998 | 9546186 |
| the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. | ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ... | 2006 | 16859499 |
| molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. | bacterial community structure and diversity in rhizospheres in two types of grassland, distinguished by both plant species and fertilization regimen, were assessed by performing a 16s ribosomal dna (rdna) sequence analysis of dnas extracted from triplicate soil plots. pcr products were cloned, and 45 to 48 clones from each of the six libraries were partially sequenced. phylogenetic analysis of the resultant 275 clone sequences indicated that there was considerable variation in abundance in repli ... | 1999 | 10103273 |