| legionella pneumophila secretes an endoglucanase that belongs to the family-5 of glycosyl hydrolases and is dependent upon type ii secretion. | examination of cell-free culture supernatants revealed that legionella pneumophila strains secrete an endoglucanase activity. legionella pneumophila lspf mutants were deficient for this activity, indicating that the endoglucanase is secreted by the bacterium's type ii protein secretion (t2s) system. inactivation of cela, encoding a member of the family-5 of glycosyl hydrolases, abolished the endoglucanase activity in l. pneumophila culture supernatants. the cloned cela gene conferred activity up ... | 2009 | 19817866 |
| transcriptome profiling defines a novel regulon modulated by the lysr-type transcriptional regulator mext in pseudomonas aeruginosa. | the lysr-family regulator mext modulates the expression of the mexef-oprn efflux system in the human pathogen pseudomonas aeruginosa. recently, we demonstrated that mext regulates certain virulence phenotypes, including the type-three secretion system and early attachment independent of its role in regulating mexef-oprn. in this study, transcriptome profiling was utilized to investigate the global nature of mext regulation in p. aeruginosa pao1 and an isogenic mexef mutant. twelve genes of unkno ... | 2009 | 19846594 |
| pantothenate kinase from the thermoacidophilic archaeon picrophilus torridus. | pantothenate kinase (coaa) catalyzes the first step of the coenzyme a (coa) biosynthetic pathway and controls the intracellular concentrations of coa through feedback inhibition in bacteria. an alternative enzyme found in archaea, pantoate kinase, is missing in the order thermoplasmatales. the pto0232 gene from picrophilus torridus, a thermoacidophilic euryarchaeon, is shown to be a distant homologue of the prokaryotic type i coaa. the cloned gene clearly complements the poor growth of the tempe ... | 2010 | 19854913 |
| pantothenate kinase from the thermoacidophilic archaeon picrophilus torridus. | pantothenate kinase (coaa) catalyzes the first step of the coenzyme a (coa) biosynthetic pathway and controls the intracellular concentrations of coa through feedback inhibition in bacteria. an alternative enzyme found in archaea, pantoate kinase, is missing in the order thermoplasmatales. the pto0232 gene from picrophilus torridus, a thermoacidophilic euryarchaeon, is shown to be a distant homologue of the prokaryotic type i coaa. the cloned gene clearly complements the poor growth of the tempe ... | 2010 | 19854913 |
| enhanced adaptability of sesbania rostrata to pb/zn tailings via stem nodulation. | sesbania rostrata is wellknown for its stem nodulation, but the roles of stem nodulation in root nodulation and adaptation of s. rostrata to pb/zn-enriched tailings environment has been poorly understood. we investigated the effects of inoculating (with stem nodule treatment) and non-inoculating (without stem nodule treatment) azorhizobium caulinodans on the growth, root nodulation, and n fixation of s. rostrata grown on three different types of soil substrata: pb/zn tailings, garden soil amende ... | 2009 | 19862929 |
| tetralin-induced and thnr-regulated aldehyde dehydrogenase and beta-oxidation genes in sphingomonas macrogolitabida strain tfa. | a new cluster of genes has been found downstream of the previously identified thna2 gene. the gene products are similar to nonacylating aldehyde dehydrogenases (thng) and to proteins representing a complete beta-oxidation pathway (thnh to thnp). thng has a nonacylating nad-dependent pimelic semialdehyde dehydrogenase activity that renders pimelic acid a seven-carbon dicarboxylic acid. for further metabolism via beta-oxidation, pimelic acid could be acylated by a constitutive acyl coenzyme a (acy ... | 2010 | 19897762 |
| tetralin-induced and thnr-regulated aldehyde dehydrogenase and beta-oxidation genes in sphingomonas macrogolitabida strain tfa. | a new cluster of genes has been found downstream of the previously identified thna2 gene. the gene products are similar to nonacylating aldehyde dehydrogenases (thng) and to proteins representing a complete beta-oxidation pathway (thnh to thnp). thng has a nonacylating nad-dependent pimelic semialdehyde dehydrogenase activity that renders pimelic acid a seven-carbon dicarboxylic acid. for further metabolism via beta-oxidation, pimelic acid could be acylated by a constitutive acyl coenzyme a (acy ... | 2010 | 19897762 |
| [identification and functional characterization of genes induced by seed exudates in azorhizobium caulinodans ors571]. | to identify genes induced by plant seed exudates in azorhizobium caulinodans ors571. | 2009 | 20030054 |
| the sinorhizobium meliloti rna chaperone hfq mediates symbiosis of s. meliloti and alfalfa. | there exist commonalities between symbiotic sinorhizobium meliloti and pathogenic brucella bacteria in terms of extensive gene synteny and the requirements for intracellular survival in their respective hosts. the rna chaperone hfq is essential for virulence for several bacterial groups, including brucella; however, its role in s. meliloti has not been investigated. our studies of an s. meliloti loss-of-function hfq mutant have revealed that hfq plays a key role in the establishment of the symbi ... | 2010 | 20081033 |
| characterization of the sesbania rostrata phytochelatin synthase gene: alternative splicing and function of four isoforms. | phytochelatins (pcs) play an important role in detoxification of heavy metals in plants. pcs are synthesized from glutathione by phytochelatin synthase (pcs), a dipeptidyltransferase. sesbania rostrata is a tropical legume plant that can tolerate high concentrations of cd and zn. in this study, the s. rostrata pcs gene (srpcs) and cdnas were isolated and characterized. southern blot and sequence analysis revealed that a single copy of the srpcs gene occurs in the s. rostrata genome, and produces ... | 2009 | 20111680 |
| role of the sinorhizobium meliloti global regulator hfq in gene regulation and symbiosis. | the rna-binding protein hfq is a global regulator which controls diverse cellular processes in bacteria. to begin understanding the role of hfq in the sinorhizobium meliloti-medicago truncatula nitrogen-fixing symbiosis, we defined free-living and symbiotic phenotypes of an hfq mutant. over 500 transcripts were differentially accumulated in the hfq mutant of s. meliloti rm1021 when grown in a shaking culture. consistent with transcriptome-wide changes, the hfq mutant displayed dramatic alteratio ... | 2010 | 20192823 |
| the sinorhizobium meliloti rna chaperone hfq influences central carbon metabolism and the symbiotic interaction with alfalfa. | the bacterial hfq protein is able to interact with diverse rna molecules, including regulatory small non-coding rnas (srnas), and thus it is recognized as a global post-transcriptional regulator of gene expression. loss of hfq has an extensive impact in bacterial physiology which in several animal pathogens influences virulence. sinorhizobium meliloti is a model soil bacterium known for its ability to establish a beneficial nitrogen-fixing intracellular symbiosis with alfalfa. despite the predic ... | 2010 | 20205931 |
| phrr-like gene prar of azorhizobium caulinodans ors571 is essential for symbiosis with sesbania rostrata and is involved in expression of reb genes. | this study focuses on the function of the gene prar that encodes a putative transcription factor in azorhizobium caulinodans ors571, a microsymbiont of sesbania rostrata. the prar gene is a homolog of the phrr gene of sinorhizobium medicae wsm419, and the prar and phrr homologs are distributed throughout the class alphaproteobacteria. the growth and nitrogen fixation activity of an a. caulinodans prar deletion mutant in the free-living state were not significantly different from those of the wil ... | 2010 | 20382809 |
| characterization of the nifa-rpon regulon in rhizobium etli in free life and in symbiosis with phaseolus vulgaris. | the nifa-rpon complex is a master regulator of the nitrogen fixation genes in alphaproteobacteria. based on the complete rhizobium etli genome sequence, we constructed an r. etli cfn42 oligonucleotide (70-mer) microarray and utilized this tool, reverse transcription (rt)-pcr analysis (transcriptomics), proteomics, and bioinformatics to decipher the nifa-rpon regulon under microaerobic conditions (free life) and in symbiosis with bean plants. the r. etli nifa-rpon regulon was determined to contai ... | 2010 | 20453139 |
| disruption of the glycine cleavage system enables sinorhizobium fredii usda257 to form nitrogen-fixing nodules on agronomically improved north american soybean cultivars. | the symbiosis between sinorhizobium fredii usda257 and soybean [glycine max (l.) merr.] exhibits a high degree of cultivar specificity. usda257 nodulates primitive soybean cultivars but fails to nodulate agronomically improved cultivars such as mccall. in this study we provide evidence for the involvement of a new genetic locus that controls soybean cultivar specificity. this locus was identified in usda257 by tn5 transposon mutagenesis followed by nodulation screening on mccall soybean. we have ... | 2010 | 20453144 |
| the complete genome sequence of cupriavidus metallidurans strain ch34, a master survivalist in harsh and anthropogenic environments. | many bacteria in the environment have adapted to the presence of toxic heavy metals. over the last 30 years, this heavy metal tolerance was the subject of extensive research. the bacterium cupriavidus metallidurans strain ch34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. this tolerance is mostly achieved by rapid ion efflux but al ... | 2010 | 20463976 |
| {gamma}-glutamylmethylamide is an essential intermediate in the metabolism of methylamine by methylocella silvestris. | methylocella silvestris bl2, a facultative methane utilizer, can grow on monomethylamine (mma) as a sole carbon and nitrogen source. no activity of mma dehydrogenase was detectable. instead, this bacterium utilizes a methylated amino acid pathway (gamma-glutamylmethylamide [gma] and n-methylglutamate [nmg]) for mma metabolism. the activities of the two key enzymes in this pathway, gma synthetase and nmg dehydrogenase, were found when the bacterium was grown on mma. gma was detected by high-perfo ... | 2010 | 20472738 |
| crystal structures of the apo and atp bound mycobacterium tuberculosis nitrogen regulatory pii protein. | pii constitutes a family of signal transduction proteins that act as nitrogen sensors in microorganisms and plants. mycobacterium tuberculosis (mtb) has a single homologue of pii whose precise role has as yet not been explored. we have solved the crystal structures of the mtb pii protein in its apo and atp bound forms to 1.4 and 2.4 a resolutions, respectively. the protein forms a trimeric assembly in the crystal lattice and folds similarly to the other pii family proteins. the mtb pii:atp binar ... | 2010 | 20521335 |
| bathy phytochromes in rhizobial soil bacteria. | phytochromes are biliprotein photoreceptors that are found in plants, bacteria, and fungi. prototypical phytochromes have a pr ground state that absorbs in the red spectral range and is converted by light into the pfr form, which absorbs longer-wavelength, far-red light. recently, some bacterial phytochromes have been described that undergo dark conversion of pr to pfr and thus have a pfr ground state. we show here that such so-called bathy phytochromes are widely distributed among bacteria that ... | 2010 | 20675484 |
| symbiotic legume nodules employ both rhizobial exo- and endo-hydrogenases to recycle hydrogen produced by nitrogen fixation. | in symbiotic legume nodules, endosymbiotic rhizobia (bacteroids) fix atmospheric n(2), an atp-dependent catalytic process yielding stoichiometric ammonium and hydrogen gas (h(2)). while in most legume nodules this h(2) is quantitatively evolved, which loss drains metabolic energy, certain bacteroid strains employ uptake hydrogenase activity and thus evolve little or no h(2). rather, endogenous h(2) is efficiently respired at the expense of o(2), driving oxidative phosphorylation, recouping atp u ... | 2010 | 20838423 |
| complete genome and comparative analysis of the chemolithoautotrophic bacterium oligotropha carboxidovorans om5. | oligotropha carboxidovorans om5 t. (dsm 1227, atcc 49405) is a chemolithoautotrophic bacterium capable of utilizing co (carbon monoxide) and fixing co2 (carbon dioxide). we previously published the draft genome of this organism and recently submitted the complete genome sequence to genbank. | 2010 | 20863402 |
| from alpaca to zebrafish: hammerhead ribozymes wherever you look. | the hammerhead ribozyme was originally discovered in subviral plant pathogens and was subsequently also found in a few other genomic locations. using a secondary structure-based descriptor, we have searched publicly accessible sequence databases for new examples of type iii hammerhead ribozymes. the more than 60,000 entries fulfilling the descriptor were filtered with respect to folding and stability parameters that were experimentally validated. this resulted in a set of 284 unique motifs, of w ... | 2010 | 21081661 |
| methylthioadenosine/s-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism. | the importance of methylthioadenosine/s-adenosylhomocysteine (mta/sah) nucleosidase in bacteria has started to be appreciated only in the past decade. a comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through s-adenosylmethionine (sam)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (ai-2). sam is also essential for synthesis of ... | 2010 | 21166890 |
| methylthioadenosine/s-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism. | the importance of methylthioadenosine/s-adenosylhomocysteine (mta/sah) nucleosidase in bacteria has started to be appreciated only in the past decade. a comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through s-adenosylmethionine (sam)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (ai-2). sam is also essential for synthesis of ... | 2010 | 21166890 |
| naringenin regulates expression of genes involved in cell wall synthesis in herbaspirillum seropedicae. | five thousand mutants of herbaspirillum seropedicae smr1 carrying random insertions of transposon ptnmod-ogmkmlacz were screened for differential expression of lacz in the presence of naringenin. among the 16 mutants whose expression was regulated by naringenin were genes predicted to be involved in the synthesis of exopolysaccharides, lipopolysaccharides, and auxin. these loci are probably involved in establishing interactions with host plants. | 2011 | 21257805 |
| bosr (bb0647) controls the rpon-rpos regulatory pathway and virulence expression in borrelia burgdorferi by a novel dna-binding mechanism. | in borrelia burgdorferi (bb), the lyme disease spirochete, the alternative s factor s54 (rpon) directly activates transcription of another alternative s factor, s(s) (rpos) which, in turn, controls the expression of virulence-associated membrane lipoproteins. as is customary in s54-dependent gene control, a putative ntrc-like enhancer-binding protein, rrp2, is required to activate the rpon-rpos pathway. however, recently it was found that rpos transcription in bb also requires another regulator, ... | 2011 | 21347346 |
| alanine zipper-like coiled-coil domains are necessary for homotypic dimerization of plant gaga-factors in the nucleus and nucleolus. | gaga-motif binding proteins control transcriptional activation or repression of homeotic genes. interestingly, there are no sequence similarities between animal and plant proteins. plant bbr/bpc-proteins can be classified into two distinct groups: previous studies have elaborated on group i members only and so little is known about group ii proteins. here, we focused on the initial characterization of atbpc6, a group ii protein from arabidopsis thaliana. comparison of orthologous bbr/bpc sequenc ... | 2011 | 21347358 |
| the maturation factors hoxr and hoxt contribute to oxygen tolerance of membrane-bound [nife] hydrogenase in ralstonia eutropha h16. | the membrane-bound [nife] hydrogenase (mbh) of ralstonia eutropha h16 undergoes a complex maturation process comprising cofactor assembly and incorporation, subunit oligomerization, and finally twin-arginine-dependent membrane translocation. due to its outstanding o(2) and co tolerance, the mbh is of biotechnological interest and serves as a molecular model for a robust hydrogen catalyst. adaptation of the enzyme to oxygen exposure has to take into account not only the catalytic reaction but als ... | 2011 | 21441514 |
| azorhirobial chromosome partition gene (para) is involved in the onset of bacteroid differentiation in sesbania rostrata stem-nodule development. | a para gene in-frame deletion mutant of azorhizobium caulinodans ors571 (ors571-δpara) was constructed to evaluate the roles of the chromosome partitioning gene on various bacterial traits and on the development of stem-positioned nodules. the δpara mutant showed a pleiomorphic cell shape phenotype, and was polyploidy with differences in nucleoid sizes due to dramatic defects in chromosome partitioning. upon inoculating the δpara mutant onto the stem of sesbania rostrata, three types of immature ... | 2011 | 21571889 |
| identification of hammerhead ribozymes in all domains of life reveals novel structural variations. | hammerhead ribozymes are small self-cleaving rnas that promote strand scission by internal phosphoester transfer. comparative sequence analysis was used to identify numerous additional representatives of this ribozyme class than were previously known, including the first representatives in fungi and archaea. moreover, we have uncovered the first natural examples of "type ii" hammerheads, and our findings reveal that this permuted form occurs in bacteria as frequently as type i and iii architectu ... | 2011 | 21573207 |
| variations in outer-membrane characteristics of two stem-nodulating bacteria of sesbania rostrata and its role in tolerance towards diverse stress. | outer-membrane characteristics may determine the survivability of rhizobia under diverse abiotic and biotic stresses. therefore, the role of lipopolysaccharides (lps) and membrane proteins of two stem-nodulating bacteria of sesbania rostrata (azorhizobium caulinodans ors571 and rhizobium sp. we7) in determining tolerance towards abiotic and biotic stresses (hydrophobics and phages) was investigated. outer-membrane characteristics (lps and membrane-protein profiles) of ors571, we7 and thirteen st ... | 2011 | 21573832 |
| tonb-dependent receptors in nitrogen-fixing nodulating bacteria. | tonb-dependent receptors (tbdrs) allow gram-negative bacteria to uptake scarce resources from competitive environments with very high affinity. early reports on tbdrs focused on the uptake of siderophore-iron complexes but recent studies have showed that the spectrum of ligands includes sugars, vitamins, heme, and other non-ferrous cations. to investigate the possible roles of tbdrs in nitrogen-fixing, nodulating bacteria, a bioinformatics approach was adopted to identify their presence in the g ... | 2010 | 21576856 |
| patchwork assembly of nag-like nitroarene dioxygenase genes and 3-chlorocatechol degradation cluster for the pathway evolution of 2-chloronitrobenzene catabolism in pseudomonas stutzeri zwlr2-1. | pseudomonas stutzeri zwlr2-1 utilizes 2-chloronitrobenzene (2cnb) as a sole source of carbon, nitrogen and energy. to identify genes involved in this pathway, a 16.2-kb dna fragment containing putative 2-chloronitrobenzene dioxygenase genes was cloned and sequenced. of the products from the 19 open reading frames that resulted from this fragment, cnbac and cnbad exhibited striking identities to the respective α- and β- subunits of the nag-like ring-hydroxylating dioxygenases involved in the meta ... | 2011 | 21602392 |
| a novel sensor kinase is required for bordetella bronchiseptica to colonize the lower respiratory tract. | bacterial virulence is influenced by the activity of two-component regulator systems (tcs), which consist of membrane-bound sensor kinases that allow bacteria to sense the external environment, and cytoplasmic, dna-binding response regulator proteins that control appropriate gene expression. respiratory pathogens of the bordetella genus require the well-studied tcs bvgas to control the expression of many genes required for colonization of the mammalian respiratory tract. here we describe the ide ... | 2011 | 21606184 |
| characterization of cyclic ╬▓-glucans of bradyrhizobium by maldi-tof mass spectrometry. | periplasmic, cyclic ╬▓-glucans isolated from bradyrhizobium elkanii, bradyrhizobium liaoningense, and bradyrhizobium yuanmingense strains have been investigated by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tof ms), 1d and 2d nuclear magnetic resonance (nmr), as well as standard chemical methods. these compounds are built of 10-13 d-glucose residues. the main fractions contain molecules assembled of 12 hexose units (m(w)=1945.363da). glucose mono ... | 2011 | 21665197 |
| genomic insights into the versatility of the plant growth-promoting bacterium azospirillum amazonense. | abstract: | 2011 | 21838888 |
| pseudomonas aeruginosa d-arabinofuranose biosynthetic pathway and its role in type iv pilus assembly. | pseudomonas aeruginosa strains pa7 and pa5196 glycosylate their type iva pilins with +¦1,5-linked d-arabinofuranose (d-araf), a rare sugar configuration identical to that found in cell wall polymers of the corynebacterineae. despite this chemical identity, the pathway for biosynthesis of +¦1,5-d-araf in gram-negative bacteria is unknown. bioinformatics analyses pointed to a cluster of seven p. aeruginosa genes, including homologues of the mycobacterium tuberculosis genes rv3806c, rv3790, and rv3 ... | 2011 | 21676874 |
| Biochemical and Mutational Studies of the Bacillus cereus CECT 5050T Formamidase Support the Existence of a C-E-E-K Tetrad in Several Members of the Nitrilase Superfamily. | Formamidases (EC 3.5.1.49) are poorly characterized proteins. In spite of this scarce knowledge, ammonia has been described as playing a central role in the pathogenesis of human pathogens such as Helicobacter pylori, for which formamidase has been shown to participate in the nitrogen metabolic pathway. Sequence analysis has revealed that at least two different groups of formamidases are classified as EC 3.5.1.49: on the one hand, the derivatives of the FmdA-AmdA superfamily, which are the best ... | 2011 | 21705545 |
| Identification of a novel gene for biosynthesis of a bacteroid-specific electron carrier menaquinone. | Ubiquinone (UQ) has been considered as an electron mediator in electron transfer that generates ATP in Rhizobium under both free-living and symbiosis conditions. When mutated, the dmtH gene has a symbiotic phenotype of forming ineffective nodules on Astragalus sinicus. The gene was isolated from a Mesorhizobium huakuii 7653R transposon-inserted mutant library. The DNA sequence and conserved protein domain analyses revealed that dmtH encodes demethylmenaquinone (DMK) methyltransferase, which cata ... | 2011 | 22194970 |
| the rhizome of reclinomonas americana, homo sapiens, pediculus humanus and saccharomyces cerevisiae mitochondria. | mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. in this study, we investigated the phenomenon of chimerism in mitochondria to shed light on the origin of these organelles by determining which species played a role in their formation. we used the mitochondria of four distinct organisms, reclinomonas americana, homo sapiens, saccharomyces cerevisiae and multichromosome pediculus humanus, and attempte ... | 2011 | 22014084 |
| Environmental signals and regulatory pathways that influence exopolysaccharide production in rhizobia. | Rhizobia are Gram-negative bacteria that can exist either as free-living bacteria or as nitrogen-fixing symbionts inside root nodules of leguminous plants. The composition of the rhizobial outer surface, containing a variety of polysaccharides, plays a significant role in the adaptation of these bacteria in both habitats. Among rhizobial polymers, exopolysaccharide (EPS) is indispensable for the invasion of a great majority of host plants which form indeterminate-type nodules. Various functions ... | 2011 | 22174640 |
| a photolyase-like protein from agrobacterium tumefaciens with an iron-sulfur cluster. | photolyases and cryptochromes are evolutionarily related flavoproteins with distinct functions. while photolyases can repair uv-induced dna lesions in a light-dependent manner, cryptochromes regulate growth, development and the circadian clock in plants and animals. here we report about two photolyase-related proteins, named phra and phrb, found in the phytopathogen agrobacterium tumefaciens. phra belongs to the class iii cyclobutane pyrimidine dimer (cpd) photolyases, the sister class of plant ... | 2011 | 22066008 |
| new beta rhizobial strains able to efficiently nodulate parapiptadenia rigida (benth.) brenan. | among the leguminous trees natives to uruguay parapiptadenia rigida (angico), a mimosoideae legume, is one of the most promising species for agroforestry. like many other legumes, it is able to establish symbiotic associations with rhizobia and belongs to the group known as "nitrogen fixing trees", which are major components of agroforestry systems. information about rhizobial symbionts for this genus is scarce, and thus the aim of this work was to identify and characterize rhizobia associated w ... | 2012 | 22226956 |
| complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha proteobacterium starkeya novella type strain (atcc 8093(t)). | starkeya novella (starkey 1934) kelly et al. 2000 is a member of the family xanthobacteraceae in the order 'rhizobiales', which is thus far poorly characterized at the genome level. cultures from this species are most interesting due to their facultatively chemolithoautotrophic lifestyle, which allows them to both consume carbon dioxide and to produce it. this feature makes s. novella an interesting model organism for studying the genomic basis of regulatory networks required for the switch betw ... | 2012 | 23450099 |
| genomic basis of broad host range and environmental adaptability of rhizobium tropici ciat 899 and rhizobium sp. prf 81 which are used in inoculants for common bean (phaseolus vulgaris l.). | rhizobium tropici ciat 899 and rhizobium sp. prf 81 are α-proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. these strains are broadly used in commercial inoculants for application to common bean (phaseolus vulgaris) in south america and africa. both strains display intrinsic resistance to several abiotic stressful conditions such as low soil ph and high temperatures, which are common in tropical environments, and to several antimicrobials, including pesticides ... | 2012 | 23270491 |
| 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 |
| genome signature difference between deinococcus radiodurans and thermus thermophilus. | the extremely radioresistant bacteria of the genus deinococcus and the extremely thermophilic bacteria of the genus thermus belong to a common taxonomic group. considering the distinct living environments of deinococcus and thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor. their guanine-cytosine (gc) contents are similar; however, we hypothesized that their genomic signatures would be different. our findings indicate ... | 2012 | 22500246 |
| the novel regulatory ncrna, nfis, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifk mrna in pseudomonas stutzeri a1501. | unlike most pseudomonas, the root-associated bacterium pseudomonas stutzeri a1501 fixes nitrogen after the horizontal acquisition of a nitrogen-fixing (nif) island. a genome-wide search for small noncoding rnas (ncrnas) in p. stutzeri a1501 identified the novel p. stutzeri-specific ncrna nfis in the core genome, whose synthesis was significantly induced under nitrogen fixation or sorbitol stress conditions. the expression of nfis was rna chaperone hfq-dependent and activated by the sigma factor ... | 2016 | 27407147 |
| a persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. | acute exacerbations of chronic obstructive pulmonary disease (copd) are a major source of morbidity and contribute significantly to healthcare costs. although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in copd airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. the aim of this study was to comprehensively profile airway bacterial com ... | 2010 | 20141328 |
| azoarcus sp. cib, an anaerobic biodegrader of aromatic compounds shows an endophytic lifestyle. | endophytic bacteria that have plant growth promoting traits are of great interest in green biotechnology. the previous thought that the azoarcus genus comprises bacteria that fit into one of two major eco-physiological groups, either free-living anaerobic biodegraders of aromatic compounds or obligate endophytes unable to degrade aromatics under anaerobic conditions, is revisited here. | 2014 | 25340341 |
| anaerobic catabolism of aromatic compounds: a genetic and genomic view. | aromatic compounds belong to one of the most widely distributed classes of organic compounds in nature, and a significant number of xenobiotics belong to this family of compounds. since many habitats containing large amounts of aromatic compounds are often anoxic, the anaerobic catabolism of aromatic compounds by microorganisms becomes crucial in biogeochemical cycles and in the sustainable development of the biosphere. the mineralization of aromatic compounds by facultative or obligate anaerobi ... | 2009 | 19258534 |
| phylogenetic co-occurrence of exor, exos, and chvi, components of the rsi bacterial invasion switch, suggests a key adaptive mechanism regulating the transition between free-living and host-invading phases in rhizobiales. | both bacterial symbionts and pathogens rely on their host-sensing mechanisms to activate the biosynthetic pathways necessary for their invasion into host cells. the gram-negative bacterium sinorhizobium meliloti relies on its rsi (exor-exos-chvi) invasion switch to turn on the production of succinoglycan, an exopolysaccharide required for its host invasion. recent whole-genome sequencing efforts have uncovered putative components of rsi-like invasion switches in many other symbiotic and pathogen ... | 2015 | 26309130 |
| anthropogenic impact on diazotrophic diversity in the mangrove rhizosphere revealed by nifh pyrosequencing. | diazotrophs in the mangrove rhizosphere play a major role in providing new nitrogen to the mangrove ecosystem and their composition and activity are strongly influenced by anthropogenic activity and ecological conditions. in this study, the diversity of the diazotroph communities in the rhizosphere sediment of five tropical mangrove sites with different levels of pollution along the north and south coastline of singapore were studied by pyrosequencing of the nifh gene. bioinformatics analysis re ... | 2015 | 26539189 |
| genomes of the symbiotic nitrogen-fixing bacteria of legumes. | | 2007 | 17556525 |
| respiratory membrane endo-hydrogenase activity in the microaerophile azorhizobium caulinodans is bidirectional. | the microaerophilic bacterium azorhizobium caulinodans, when fixing n(2) both in pure cultures held at 20 µm dissolved o(2) tension and as endosymbiont of sesbania rostrata legume nodules, employs a novel, respiratory-membrane endo-hydrogenase to oxidize and recycle endogenous h(2) produced by soluble mo-dinitrogenase activity at the expense of o(2). | 2012 | 22662125 |
| the sinorhizobium meliloti ntrx gene is involved in succinoglycan production, motility, and symbiotic nodulation on alfalfa. | rhizobia establish a symbiotic relationship with their host legumes to induce the formation of nitrogen-fixing nodules. this process is regulated by many rhizobium regulators, including some two-component regulatory systems (tcss). ntry/ntrx, a tcs that was first identified in azorhizobium caulinodans, is required for free-living nitrogen metabolism and symbiotic nodulation on sesbania rostrata. however, its functions in a typical rhizobium such as sinorhizobium meliloti remain unclear. here we ... | 2013 | 24038694 |
| characterization of an ntrx mutant of neisseria gonorrhoeae reveals a response regulator that controls expression of respiratory enzymes in oxidase-positive proteobacteria. | ntryx is a sensor-histidine kinase/response regulator two-component system that has had limited characterization in a small number of alphaproteobacteria. phylogenetic analysis of the response regulator ntrx showed that this two-component system is extensively distributed across the bacterial domain, and it is present in a variety of betaproteobacteria, including the human pathogen neisseria gonorrhoeae. microarray analysis revealed that the expression of several components of the respiratory ch ... | 2013 | 23564168 |
| a genomic survey of reb homologs suggests widespread occurrence of r-bodies in proteobacteria. | bacteria and eukaryotes are involved in many types of interaction in nature, with important ecological consequences. however, the diversity, occurrence, and mechanisms of these interactions often are not fully known. the obligate bacterial endosymbionts of paramecium provide their hosts with the ability to kill sensitive paramecium strains through the production of r-bodies, highly insoluble coiled protein ribbons. r-bodies have been observed in a number of free-living bacteria, where their func ... | 2013 | 23450193 |
| ehrlichia chaffeensis proliferation begins with ntry/ntrx and puta/glna upregulation and ctra degradation induced by proline and glutamine uptake. | how the obligatory intracellular bacterium ehrlichia chaffeensis begins to replicate upon entry into human monocytes is poorly understood. here, we examined the potential role of amino acids in initiating intracellular replication. puta converts proline to glutamate, and glna converts glutamate to glutamine. e. chaffeensis puta and glna complemented escherichia coli puta and glna mutants. methionine sulfoximine, a glutamine synthetase inhibitor, inhibited e. chaffeensis glna activity and e. chaf ... | 2014 | 25425236 |
| the emergence of 2-oxoglutarate as a master regulator metabolite. | the metabolite 2-oxoglutarate (also known as α-ketoglutarate, 2-ketoglutaric acid, or oxoglutaric acid) lies at the intersection between the carbon and nitrogen metabolic pathways. this compound is a key intermediate of one of the most fundamental biochemical pathways in carbon metabolism, the tricarboxylic acid (tca) cycle. in addition, 2-oxoglutarate also acts as the major carbon skeleton for nitrogen-assimilatory reactions. experimental data support the conclusion that intracellular levels of ... | 2015 | 26424716 |
| genome wide transcriptional profiling of herbaspirillum seropedicae smr1 grown in the presence of naringenin. | herbaspirillum seropedicae is a diazotrophic bacterium which associates endophytically with economically important gramineae. flavonoids such as naringenin have been shown to have an effect on the interaction between h. seropedicae and its host plants. we used a high-throughput sequencing based method (rna-seq) to access the influence of naringenin on the whole transcriptome profile of h. seropedicae. three hundred and four genes were downregulated and seventy seven were upregulated by naringeni ... | 2015 | 26052319 |
| interaction between nitrogen and phosphate stress responses in sinorhizobium meliloti. | bacteria have developed various stress response pathways to improve their assimilation and allocation of limited nutrients, such as nitrogen and phosphate. while both the nitrogen stress response (nsr) and phosphate stress response (psr) have been studied individually, there are few experiments reported that characterize effects of multiple stresses on one or more pathways in sinorhizobium meliloti, a facultatively symbiotic, nitrogen-fixing bacteria. the pii proteins, glnb and glnk, regulate th ... | 2016 | 27965651 |
| a developmental and molecular view of formation of auxin-induced nodule-like structures in land plants. | several studies have shown that plant hormones play important roles during legume-rhizobia symbiosis. for instance, auxins induce the formation of nodule-like structures (nlss) on legume roots in the absence of rhizobia. furthermore, these nls can be colonized by nitrogen-fixing bacteria, which favor nitrogen fixation compared to regular roots and subsequently increase plant yield. interestingly, auxin also induces similar nls in cereal roots. while several genetic studies have identified plant ... | 2016 | 27891144 |
| a chemotaxis receptor modulates nodulation during the azorhizobium caulinodans-sesbania rostrata symbiosis. | azorhizobium caulinodans ors571 is a free-living nitrogen-fixing bacterium which can induce nitrogen-fixing nodules both on the root and the stem of its legume host sesbania rostrata this bacterium, which is an obligate aerobe that moves by means of a polar flagellum, possesses a single chemotaxis signal transduction pathway. the objective of this work was to examine the role that chemotaxis and aerotaxis play in the lifestyle of the bacterium in free-living and symbiotic conditions. in bacteria ... | 2016 | 26994081 |
| occurrence of an unusual hopanoid-containing lipid a among lipopolysaccharides from bradyrhizobium species. | the chemical structures of the unusual hopanoid-containing lipid a samples of the lipopolysaccharides (lps) from three strains of bradyrhizobium (slow-growing rhizobia) have been established. they differed considerably from other gram-negative bacteria in regards to the backbone structure, the number of ester-linked long chain hydroxylated fatty acids, as well as the presence of a tertiary residue that consisted of at least one molecule of carboxyl-bacteriohopanediol or its 2-methyl derivative. ... | 2014 | 25371196 |
| comparison of bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometer to bd phoenix automated microbiology system for identification of gram-negative bacilli. | we compared the bd phoenix automated microbiology system to the bruker biotyper (version 2.0) matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry (ms) system for identification of gram-negative bacilli, using biochemical testing and/or genetic sequencing to resolve discordant results. the bd phoenix correctly identified 363 (83%) and 330 (75%) isolates to the genus and species level, respectively. the bruker biotyper correctly identified 408 (93%) and 360 (82 ... | 2011 | 21209160 |
| bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control. | under a shortage of oxygen, bacterial growth can be faced mainly by two atp-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. this bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells ... | 2012 | 22098259 |
| bacterial rubisco is required for efficient bradyrhizobium/aeschynomene symbiosis. | rhizobia and legume plants establish symbiotic associations resulting in the formation of organs specialized in nitrogen fixation. in such organs, termed nodules, bacteria differentiate into bacteroids which convert atmospheric nitrogen and supply the plant with organic nitrogen. as a counterpart, bacteroids receive carbon substrates from the plant. this rather simple model of metabolite exchange underlies symbiosis but does not describe the complexity of bacteroids' central metabolism. a previo ... | 2011 | 21750740 |
| ethanolamine utilization in vibrio alginolyticus. | ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. previous studies have revealed the presence of eutbc genes encoding ethanolamine-ammonia lyase, a key enzyme that breaks ethanolamine into acetaldehyde and ammonia, in about 100 bacterial genomes including members of gamma-proteobacteria. however, ethanolamine utilization has not been reported for any member of the vibrio genus. our comparati ... | 2012 | 23234435 |
| natural products genomics. | | 2008 | 21261848 |
| an evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. | to test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. among the arch ... | 2012 | 22355196 |
| new-old hemoglobin-like proteins of symbiotic dinoflagellates. | symbiotic dinoflagellates are unicellular photosynthetic algae that live in mutualistic symbioses with many marine organisms. within the transcriptome of coral endosymbionts symbiodinium sp. (type c3), we discovered the sequences of two novel and highly polymorphic hemoglobin-like genes and proposed their 3d protein structures. at the protein level, four isoforms shared between 87 and 97% sequence identity for hb-1 and 78-99% for hb-2, whereas between hb-1 and hb-2 proteins, only 15-21% sequence ... | 2013 | 23610627 |
| multiple in vivo roles for the -12-region elements of sigma 54 promoters. | alignment of sigma 54-dependent promoters indicates conservation of two sequence elements. six nucleotides in the downstream -12 element were mutated individually to each nonconsensus nucleotide. mrna levels were measured in vivo for each promoter under strongly activating conditions. the results showed that the consensus sequence was not the strongest promoter. instead, the -12 consensus element consists of two subregions that behave differently when mutated. single changes in the upstream ttt ... | 1998 | 9791111 |
| ethylene-mediated phenotypic plasticity in root nodule development on sesbania rostrata. | leguminous plants in symbiosis with rhizobia form either indeterminate nodules with a persistent meristem or determinate nodules with a transient meristematic region. sesbania rostrata was thought to possess determinate stem and root nodules. however, the nature of nodule development is hybrid, and the early stages resemble those of indeterminate nodules. here we show that, depending on the environmental conditions, mature root nodules can be of the indeterminate type. in situ hybridizations wit ... | 1998 | 9770553 |
| analysis of stable low-molecular-weight rna profiles of members of the family rhizobiaceae. | staircase electrophoresis in polyacrylamide gels was used to analyze the stable low-molecular-weight (lmw) rna profiles of 24 type strains belonging to the family rhizobiaceae. this new electrophoretic technique results in good separation of the molecules forming the lmw rna profiles. differences in the number and distribution of the rna bands in these profiles allowed us to identify differences among the 24 strains assayed. species assignments based on lmw rnas proved to be consistent with the ... | 1998 | 9575134 |
| evidence that the plant host synthesizes the heme moiety of leghemoglobin in root nodules | although it is well established that the plant host encodes and synthesizes the apoprotein for leghemoglobin in root nodules, the source of the heme moiety has been uncertain. we recently found that the transcript for coproporphyrinogen iii oxidase, one of the later enzymes of heme synthesis, is highly elevated in soybean (glycine max l.) nodules compared with roots. in this study we measured enzyme activity and carried out western-blot analysis and in situ hybridization of mrna to investigate t ... | 1998 | 9536042 |
| regulation of sigma 54-dependent transcription by core promoter sequences: role of -12 region nucleotides. | the tetranucleotide core recognition sequence (ttgc) of the sigma 54 promoter -12 recognition element was altered by random substitution. the resulting promoter mutants were characterized in vivo and in vitro. deregulated promoters were identified, implying that this core element can mediate the response to enhancer-binding proteins. these promoters had in common a substitution at position -12 (consensus c), indicating its importance for keeping basal transcription in check. in another screen, n ... | 1999 | 10601214 |
| the mechanism of synthesis of a mixed-linkage (1-->3), (1-->4)beta-d-glucan in maize. evidence for multiple sites of glucosyl transfer in the synthase complex | we examined the mechanism of synthesis in vitro of (1-->3), (1-->4)beta-d-glucan (beta-glucan), a growth-specific cell wall polysaccharide found in grasses and cereals. beta-glucan is composed primarily of cellotriosyl and cellotetraosyl units linked by single (1-->3)beta-linkages. the ratio of cellotriosyl and cellotetraosyl units in the native polymer is strictly controlled at between 2 and 3 in all grasses, whereas the ratios of these units in beta-glucan formed in vitro vary from 1.5 with 5 ... | 1999 | 10444094 |
| reactive oxygen species and ethylene play a positive role in lateral root base nodulation of a semiaquatic legume. | lateral root base nodulation on the tropical, semiaquatic legume sesbania rostrata results from two coordinated, nod factor-dependent processes: formation of intercellular infection pockets and induction of cell division. infection pocket formation is associated with cell death and production of hydrogen peroxide. pharmacological experiments showed that ethylene and reactive oxygen species mediate nod factor responses and are required for nodule initiation, whereby induction of division and infe ... | 2003 | 12975522 |
| srsymrk, a plant receptor essential for symbiosome formation. | the symbiosis between legumes and rhizobia is essential for the nitrogen input into the life cycle on our planet. new root organs, the nodules, are established, which house n2-fixing bacteria internalized into the host cell cytoplasm as horizontally acquired organelles, the symbiosomes. the interaction is initiated by bacterial invasion via epidermal root hair curling and cell division in the cortex, both triggered by bacterial nodulation factors. of the several genes involved in nodule initiati ... | 2005 | 16006516 |
| patterns of expansion and expression divergence in the plant polygalacturonase gene family. | polygalacturonases (pgs) belong to a large gene family in plants and are believed to be responsible for various cell separation processes. pg activities have been shown to be associated with a wide range of plant developmental programs such as seed germination, organ abscission, pod and anther dehiscence, pollen grain maturation, fruit softening and decay, xylem cell formation, and pollen tube growth, thus illustrating divergent roles for members of this gene family. a close look at phylogenetic ... | 2006 | 17010199 |
| phylogenetic analysis indicates evolutionary diversity and environmental segregation of marine podovirus dna polymerase gene sequences. | the distribution of viral genotypes in the ocean and their evolutionary relatedness remain poorly constrained. this paper presents data on the genetic diversity and evolutionary relationships of 1.2-kb dna polymerase (pol) gene fragments from podoviruses. a newly designed set of pcr primers was used to amplify dna directly from coastal sediment and water samples collected from inlets adjacent to the strait of georgia, british columbia, canada, and from the northeastern gulf of mexico. restrictio ... | 2009 | 19363063 |
| structure-function relationship of the chloroplastic glutaredoxin s12 with an atypical wcsys active site. | glutaredoxins (grxs) are efficient catalysts for the reduction of mixed disulfides in glutathionylated proteins, using glutathione or thioredoxin reductases for their regeneration. using gfp fusion, we have shown that poplar grxs12, which possesses a monothiol (28)wcsys(32) active site, is localized in chloroplasts. in the presence of reduced glutathione, the recombinant protein is able to reduce in vitro substrates, such as hydroxyethyldisulfide and dehydroascorbate, and to regenerate the gluta ... | 2009 | 19158074 |
| ubiquitous presence of the hammerhead ribozyme motif along the tree of life. | examples of small self-cleaving rnas embedded in noncoding regions already have been found to be involved in the control of gene expression, although their origin remains uncertain. in this work, we show the widespread occurrence of the hammerhead ribozyme (hhr) motif among genomes from the bacteria, chromalveolata, plantae, and metazoa kingdoms. intergenic hhrs were detected in three different bacterial genomes, whereas metagenomic data from galapagos islands showed the occurrence of similar ri ... | 2010 | 20705646 |
| characterization of indigenous rhizobia from caatinga. | the aim of this study was to characterize rhizobial isolates from cratylia mollis mart. ex benth, calliandra depauperata benth. and mimosa tenuiflora (willd.) poir. by means of rhizobial colonies morphology and restriction analysis of the 16s ribosomal gene (16s rdna-ardra). nodules were collected in the field and from plants cultivated in a greenhouse experiment using caatinga soil samples. sixty seven isolates were described by morphological analysis. forty seven representative isolates were u ... | 2010 | 24031482 |
| genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order rhizobiales. | species belonging to the rhizobiales are intriguing and extensively researched for including both bacteria with the ability to fix nitrogen when in symbiosis with leguminous plants and pathogenic bacteria to animals and plants. similarities between the strategies adopted by pathogenic and symbiotic rhizobiales have been described, as well as high variability related to events of horizontal gene transfer. although it is well known that chromosomal rearrangements, mutations and horizontal gene tra ... | 2010 | 20144182 |
| complete genome sequence of the soybean symbiont bradyrhizobium japonicum strain usda6t. | the complete nucleotide sequence of the genome of the soybean symbiont bradyrhizobium japonicum strain usda6t was determined. the genome of usda6t is a single circular chromosome of 9,207,384 bp. the genome size is similar to that of the genome of another soybean symbiont, b. japonicum usda110 (9,105,828 bp). comparison of the whole-genome sequences of usda6t and usda110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. a significantly high l ... | 2011 | 24710291 |
| sequence variability of rhizobiales orthologs and relationship with physico-chemical characteristics of proteins. | chromosomal orthologs can reveal the shared ancestral gene set and their evolutionary trends. additionally, physico-chemical properties of encoded proteins could provide information about functional adaptation and ecological niche requirements. | 2011 | 21970442 |
| cloning of a novel 6-chloronicotinic acid chlorohydrolase from the newly isolated 6-chloronicotinic acid mineralizing bradyrhizobiaceae strain sg-6c. | a 6-chloronicotinic acid mineralizing bacterium was isolated from enrichment cultures originating from imidacloprid-contaminated soil samples. this bradyrhizobiaceae, designated strain sg-6c, hydrolytically dechlorinated 6-chloronicotinic acid to 6-hydroxynicotinic acid, which was then further metabolised via the nicotinic acid pathway. this metabolic pathway was confirmed by growth and resting cell assays using hplc and lc-ms studies. a candidate for the gene encoding the initial dechlorination ... | 2012 | 23226482 |
| isolation of fucosyltransferase-producing bacteria from marine environments. | fucose-containing oligosaccharides on the cell surface of some pathogenic bacteria are thought to be important for host-microbe interactions and to play a major role in the pathogenicity of bacterial pathogens. here, we screened marine bacteria for glycosyltransferases using two methods: a one-pot glycosyltransferase assay method and a lectin-staining method. using this approach, we isolated marine bacteria with fucosyltransferase activity. there have been no previous reports of marine bacteria ... | 2012 | 23100020 |
| re-annotation of the cazy genes of trichoderma reesei and transcription in the presence of lignocellulosic substrates. | trichoderma reesei is a soft rot ascomycota fungus utilised for industrial production of secreted enzymes, especially lignocellulose degrading enzymes. about 30 carbohydrate active enzymes (cazymes) of t. reesei have been biochemically characterised. genome sequencing has revealed a large number of novel candidates for cazymes, thus increasing the potential for identification of enzymes with novel activities and properties. plenty of data exists on the carbon source dependent regulation of the c ... | 2012 | 23035824 |
| genetic and symbiotic diversity of nitrogen-fixing bacteria isolated from agricultural soils in the western amazon by using cowpea as the trap plant. | cowpea is a legume of great agronomic importance that establishes symbiotic relationships with nitrogen-fixing bacteria. however, little is known about the genetic and symbiotic diversity of these bacteria in distinct ecosystems. our study evaluated the genetic diversity and symbiotic efficiencies of 119 bacterial strains isolated from agriculture soils in the western amazon using cowpea as a trap plant. these strains were clustered into 11 cultural groups according to growth rate and ph. the 57 ... | 2012 | 22798370 |
| lon protease of azorhizobium caulinodans ors571 is required for suppression of reb gene expression. | bacterial lon proteases play important roles in a variety of biological processes in addition to housekeeping functions. in this study, we focused on the lon protease of azorhizobium caulinodans, which can fix nitrogen both during free-living growth and in stem nodules of the legume sesbania rostrata. the nitrogen fixation activity of an a. caulinodans lon mutant in the free-living state was not significantly different from that of the wild-type strain. however, the stem nodules formed by the lo ... | 2012 | 22752172 |
| defining sequence space and reaction products within the cyanuric acid hydrolase (atzd)/barbiturase protein family. | cyanuric acid hydrolases (atzd) and barbiturases are homologous, found almost exclusively in bacteria, and comprise a rare protein family with no discernible linkage to other protein families or an x-ray structural class. there has been confusion in the literature and in genome projects regarding the reaction products, the assignment of individual sequences as either cyanuric acid hydrolases or barbiturases, and spurious connection of this family to another protein family. the present study has ... | 2012 | 22730121 |
| regen: ancestral genome reconstruction for bacteria. | ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. we present a new computational system called regen for ancestral bacterial genome reconstruction at both the gene and replicon levels. regen reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. along each branch of the phylogenetic tree, regen infers evolutionary events, including gene creation and deletion ... | 2012 | 24704978 |
| proteomic phenotyping of novosphingobium nitrogenifigens reveals a robust capacity for simultaneous nitrogen fixation, polyhydroxyalkanoate production, and resistance to reactive oxygen species. | novosphingobium nitrogenifigens y88(t) (y88) is a free-living, diazotrophic alphaproteobacterium, capable of producing 80% of its biomass as the biopolymer polyhydroxybutyrate (phb). we explored the potential utility of this species as a polyhydroxybutyrate production strain, correlating the effects of glucose, nitrogen availability, dissolved oxygen concentration, and extracellular ph with polyhydroxybutyrate production and changes in the y88 proteomic profile. using two-dimensional differentia ... | 2012 | 22582058 |
| expression of phenazine biosynthetic genes during the arbuscular mycorrhizal symbiosis of glomus intraradices. | to explore the molecular mechanisms that prevail during the establishment of the arbuscular mycorrhiza symbiosis involving the genus glomus, we transcriptionally analysed spores of glomus intraradices be3 during early hyphal growth. among 458 transcripts initially identified as being expressed at presymbiotic stages, 20% of sequences had homology to previously characterized eukaryotic genes, 30% were homologous to fungal coding sequences, and 9% showed homology to previously characterized bacter ... | 2012 | 24031884 |
| comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. | the rhizobium-legume symbiosis has been widely studied as the model of mutualistic evolution and the essential component of sustainable agriculture. extensive genetic and recent genomic studies have led to the hypothesis that many distinct strategies, regardless of rhizobial phylogeny, contributed to the varied rhizobium-legume symbiosis. we sequenced 26 genomes of sinorhizobium and bradyrhizobium nodulating soybean to test this hypothesis. the bradyrhizobium core genome is disproportionally enr ... | 2012 | 22586130 |
| nontarget effects of foliar fungicide application on the rhizosphere: diversity of nifh gene and nodulation in chickpea field. | this study explores nontarget effects of fungicide application on field-grown chickpea. | 2012 | 22335393 |
| the ubiquitous hammerhead ribozyme. | the hammerhead ribozyme is a small catalytic rna motif capable of endonucleolytic (self-) cleavage. it is composed of a catalytic core of conserved nucleotides flanked by three helices, two of which form essential tertiary interactions for fast self-scission under physiological conditions. originally discovered in subviral plant pathogens, its presence in several eukaryotic genomes has been reported since. more recently, this catalytic rna motif has been shown to reside in a large number of geno ... | 2012 | 22454536 |