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structural insights into the subclass b3 metallo-β-lactamase smb-1 and the mode of inhibition by the common metallo-β-lactamase inhibitor mercaptoacetate.a novel subclass b3 metallo-β-lactamase (mbl), smb-1, recently identified from a serratia marcescens clinical isolate, showed a higher hydrolytic activity against a wide range of β-lactams than did the other subclass b3 mbls, i.e., bjp-1 and fez-1, from environmental bacteria. to identify the mechanism underlying the differences in substrate specificity among the subclass b3 mbls, we determined the structure of smb-1, using 1.6-å diffraction data. consequently, we found that smb-1 reserves a spa ...201323070156
biochemical and functional characterization of spda, a 2', 3'cyclic nucleotide phosphodiesterase from sinorhizobium meliloti.3', 5'camp signaling in sinorhizobium meliloti was recently shown to contribute to the autoregulation of legume infection. in planta, three adenylate cyclases cyad1, cyad2 and cyak, synthesizing 3', 5'camp, together with the crp-like transcriptional regulator clr and smc02178, a gene of unknown function, are involved in controlling plant infection.201324279347
the myxococcus xanthus two-component system corsr regulates expression of a gene cluster involved in maintaining copper tolerance during growth and development.myxococcus xanthus is a soil-dwelling member of the δ-proteobacteria that exhibits a complex developmental cycle upon starvation. development comprises aggregation and differentiation into environmentally resistant myxospores in an environment that includes fluctuations in metal ion concentrations. while copper is essential for m. xanthus cells because several housekeeping enzymes use it as a cofactor, high copper concentrations are toxic. these opposing effects force cells to maintain a tight c ...201323874560
lateral transfers of insertion sequences between wolbachia, cardinium and rickettsia bacterial endosymbionts.various bacteria live exclusively within arthropod cells and collectively act as an important driver of arthropod evolutionary ecology. whereas rampant intra-generic dna transfers were recently shown to have a pivotal role in the evolution of the most common of these endosymbionts, wolbachia, the present study show that inter-generic dna transfers also commonly take place, constituting a potent source of rapid genomic change. bioinformatic, molecular and phylogenetic data provide evidence that a ...201323759724
global transcriptional response to heat shock of the legume symbiont mesorhizobium loti maff303099 comprises extensive gene downregulation.rhizobia, the bacterial legume symbionts able to fix atmospheric nitrogen inside root nodules, have to survive in varied environmental conditions. the aim of this study was to analyse the transcriptional response to heat shock of mesorhizobium loti maff303099, a rhizobium with a large multipartite genome of 7.6 mb that nodulates the model legume lotus japonicus. using microarray analysis, extensive transcriptomic changes were detected in response to heat shock: 30% of the protein-coding genes we ...201324277738
global transcriptional response to heat shock of the legume symbiont mesorhizobium loti maff303099 comprises extensive gene downregulation.rhizobia, the bacterial legume symbionts able to fix atmospheric nitrogen inside root nodules, have to survive in varied environmental conditions. the aim of this study was to analyse the transcriptional response to heat shock of mesorhizobium loti maff303099, a rhizobium with a large multipartite genome of 7.6 mb that nodulates the model legume lotus japonicus. using microarray analysis, extensive transcriptomic changes were detected in response to heat shock: 30% of the protein-coding genes we ...201324277738
the tetr family of regulators.the most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a dna-binding domain. among the >20 classes of one-component systems, the tetr family of regulators (tfrs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. however, tfrs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and ma ...201324006471
cytochrome bd-i in escherichia coli is less sensitive than cytochromes bd-ii or bo'' to inhibition by the carbon monoxide-releasing molecule, corm-3: n-acetylcysteine reduces co-rm uptake and inhibition of respiration.co-releasing molecules (co-rms) are potential therapeutic agents, able to deliver co - a critical gasotransmitter - in biological environments. co-rms are also effective antimicrobial agents; although the mechanisms of action are poorly defined, haem-containing terminal oxidases are primary targets. nevertheless, it is clear from several studies that the effects of co-rms on biological systems are frequently not adequately explained by the release of co: co-rms are generally more potent inhibito ...201323624261
iron homeostasis in the rhodobacter genus.metals are utilized for a variety of critical cellular functions and are essential for survival. however cells are faced with the conundrum of needing metals coupled with e fact that some metals, iron in particular are toxic if present in excess. maintaining metal homeostasis is therefore of critical importance to cells. in this review we have systematically analyzed sequenced genomes of three members of the rhodobacter genus, r. capsulatus sb1003, r. sphaeroides 2.4.1 and r. ferroxidans sw2 to ...201324382933
shallow breathing: bacterial life at low o(2).competition for molecular oxygen (o(2)) among respiratory microorganisms is intense because o(2) is a potent electron acceptor. this competition leads to the formation of microoxic environments wherever microorganisms congregate in aquatic, terrestrial and host-associated communities. bacteria can harvest o(2) present at low, even nanomolar, concentrations using high-affinity terminal oxidases. here, we report the results of surveys searching for high-affinity terminal oxidase genes in sequenced ...201323411864
rnd multidrug efflux pumps: what are they good for?multidrug efflux pumps are chromosomally encoded genetic elements capable of mediating resistance to toxic compounds in several life forms. in bacteria, these elements are involved in intrinsic and acquired resistance to antibiotics. unlike other well-known horizontally acquired antibiotic resistance determinants, genes encoding for multidrug efflux pumps belong to the core of bacterial genomes and thus have evolved over millions of years. the selective pressure stemming from the use of antibiot ...201323386844
genomic analysis of melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within bacteriodetes/chlorobi group.melioribacter roseus is a moderately thermophilic facultatively anaerobic organotrophic bacterium representing a novel deep branch within bacteriodetes/chlorobi group. to better understand the metabolic capabilities and possible ecological functions of m. roseus and get insights into the evolutionary history of this bacterial lineage, we sequenced the genome of the type strain p3m-2(t). a total of 2838 open reading frames was predicted from its 3.30 mb genome. the whole proteome analysis support ...201323301019
extraordinary expansion of a sorangium cellulosum genome from an alkaline milieu.complex environmental conditions can significantly affect bacterial genome size by unknown mechanisms. the so0157-2 strain of sorangium cellulosum is an alkaline-adaptive epothilone producer that grows across a wide ph range. here, we show that the genome of this strain is 14,782,125 base pairs, 1.75-megabases larger than the largest bacterial genome from s. cellulosum reported previously. the total 11,599 coding sequences (cdss) include massive duplications and horizontally transferred genes, r ...201323812535
whole-proteome analysis of twelve species of alphaproteobacteria links four pathogens.thousands of whole-genome and whole-proteome sequences have been made available through advances in sequencing technology, and sequences of millions more organisms will become available in the coming years. this wealth of genetic information will provide numerous opportunities to enhance our understanding of these organisms including a greater understanding of relationships among species. researchers have used 16s rrna and other gene sequences to study the evolutionary origins of bacteria, but t ...201325437336
the sinorhizobium fredii hh103 lipopolysaccharide is not only relevant at early soybean nodulation stages but also for symbiosome stability in mature nodules.in this work we have characterised the sinorhizobium fredii hh103 grea lpsb lpscde genetic region and analysed for the first time the symbiotic performance of sinorhizobium fredii lps mutants on soybean. the organization of the s. fredii hh103 grea, lpsb, and lpscde genes was equal to that of sinorhizobium meliloti 1021. s. fredii hh103 grea, lpsb, and lpse mutant derivatives produced altered lps profiles that were characteristic of the gene mutated. in addition, s. fredii hh103 grea mutants sho ...201324098345
phylogenetic analysis of erythritol catabolic loci within the rhizobiales and proteobacteria.the ability to use erythritol as a sole carbon source is not universal among the rhizobiaceae. based on the relatedness to the catabolic genes in brucella it has been suggested that the eryabcd operon may have been horizontally transferred into rhizobium. during work characterizing a locus necessary for the transport and catabolism of erythritol, adonitol and l-arabitol in sinorhizobium meliloti, we became interested in the differences between the erythritol loci of s. meliloti and r. leguminosa ...201323432981
evolutionary diversification and characterization of the eubacterial gene family encoding dxr type ii, an alternative isoprenoid biosynthetic enzyme.isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. in most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (mep) pathway. the production of mep is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (dxr-i) but a few organisms use an alternative dxr-like enzyme (dxr-ii).201324004839
the herbaspirillum seropedicae smr1 fnr orthologs controls the cytochrome composition of the electron transport chain.the transcriptional regulatory protein fnr, acts as an intracellular redox sensor regulating a wide range of genes in response to changes in oxygen levels. genome sequencing of herbaspirillum seropedicae smr1 revealed the presence of three fnr-like genes. in this study we have constructed single, double and triple fnr deletion mutant strains of h. seropedicae. transcriptional profiling in combination with expression data from reporter fusions, together with spectroscopic analysis, demonstrates t ...201323996052
high-resolution transcriptomic analyses of sinorhizobium sp. ngr234 bacteroids in determinate nodules of vigna unguiculata and indeterminate nodules of leucaena leucocephala.the rhizobium-legume symbiosis is a model system for studying mutualistic interactions between bacteria and eukaryotes. sinorhizobium sp. ngr234 is distinguished by its ability to form either indeterminate nodules or determinate nodules with diverse legumes. here, we presented a high-resolution rna-seq transcriptomic analysis of ngr234 bacteroids in indeterminate nodules of leucaena leucocephala and determinate nodules of vigna unguiculata. in contrast to exponentially growing free-living bacter ...201323936444
the sinorhizobium meliloti essential porin ropa1 is a target for numerous bacteriophages.the symbiotic nitrogen-fixing bacterium sinorhizobium meliloti harbors a gene, smc02396, which encodes a predicted outer membrane porin that is conserved in many symbiotic and pathogenic bacteria in the order rhizobiales. here, this gene (renamed ropa1) is shown to be required for infection by two commonly utilized transducing bacteriophages (φm12 and n3). mapping of s. meliloti mutations conferring resistance to φm12, n3, or both phages simultaneously revealed diverse mutations mapping within t ...201323749981
brucella bior regulator defines a complex regulatory mechanism for bacterial biotin metabolism.the enzyme cofactor biotin (vitamin h or b7) is an energetically expensive molecule whose de novo biosynthesis requires 20 atp equivalents. it seems quite likely that diverse mechanisms have evolved to tightly regulate its biosynthesis. unlike the model regulator bira, a bifunctional biotin protein ligase with the capability of repressing the biotin biosynthetic pathway, bior has been recently reported by us as an alternative machinery and a new type of gntr family transcriptional factor that ca ...201323729648
cyanuric acid hydrolase: evolutionary innovation by structural concatenation.the cyanuric acid hydrolase, atzd, is the founding member of a newly identified family of ring-opening amidases. we report the first x-ray structure for this family, which is a novel fold (termed the 'toblerone' fold) that likely evolved via the concatenation of monomers of the trimeric yjgf superfamily and the acquisition of a metal binding site. structures of atzd with bound substrate (cyanuric acid) and inhibitors (phosphate, barbituric acid and melamine), along with mutagenesis studies, allo ...201323651355
serologic prevalence of amoeba-associated microorganisms in intensive care unit pneumonia patients.patients admitted to intensive care units are frequently exposed to pathogenic microorganisms present in their environment. exposure to these microbes may lead to the development of hospital-acquired infections that complicate the illness and may be fatal. amoeba-associated microorganisms (aams) are frequently isolated from hospital water networks and are reported to be associated to cases of community and hospital-acquired pneumonia.201323469263
2-nitrobenzoate 2-nitroreductase (nbaa) switches its substrate specificity from 2-nitrobenzoic acid to 2,4-dinitrobenzoic acid under oxidizing conditions.2-nitrobenzoate 2-nitroreductase (nbaa) of pseudomonas fluorescens strain ku-7 is a unique enzyme, transforming 2-nitrobenzoic acid (2-nba) and 2,4-dinitrobenzoic acid (2,4-dnba) to the 2-hydroxylamine compounds. sequence comparison reveals that nbaa contains a conserved cysteine residue at position 141 and two variable regions at amino acids 65 to 74 and 193 to 216. the truncated mutant δ65-74 exhibited markedly reduced activity toward 2,4-dnba, but its 2-nba reduction activity was unaffected; ...201323123905
genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in methylocystis sp. strain sc2.methylocystis sp. strain sc2 can adapt to a wide range of methane concentrations. this is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. to gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 mb chromosome and two large plasmids.201324130670
[novel nadph-dependent l-aspartate dehydrogenases from the mesophilic nitrogen-fixing bacteria rhodopseudomonas palustris and bradyrhizobium japonicum].the genes encoding putative l-aspartate dehydrogenases (ec 1.4.1.21, adh) from the mesophilic nitrogen-fixing bacteria rhodopseudomonas palustris and bradyrhizobium japonicum were cloned and expressed in escherichia coli. the respective enzymes in the form of hybrid proteins with n-terminal hexahistidine tags were purified to apparent homogeneity. both enzymes catalyzed in vitro the reductive amination of oxaloacetate to l-aspartate by an order faster than the reverse reaction at a respective ph ...201323795474
transcription analyses of gmichg, a gene coding for a β-glucosidase that catalyzes the specific hydrolysis of isoflavone conjugates in glycine max (l.) merr.isoflavone conjugate-hydrolyzing β-glucosidase (gmichg) of soybeans [glycine max (l.) merr.] catalyzes the specific hydrolysis of isoflavone conjugates (β-7-o-(malonyl)glucosides of isoflavones) to produce free isoflavones. in this study, changes in the transcription levels of gmichg in the individual organs of soybean seedlings (cv. enrei) in response to microbial infection and abiotic stresses were analyzed and compared with those of genes coding for 2-hydroxyisoflavanone synthase (gmifs) and ...201323683924
polyphasic evidence supporting the reclassification of bradyrhizobium japonicum group ia strains as bradyrhizobium diazoefficiens sp. nov.bradyrhizobium japonicum was described from soybean root-nodule bacterial isolates. since its description, several studies have revealed heterogeneities among rhizobia assigned to this species. strains assigned to b. japonicum group ia have been isolated in several countries, and many of them are outstanding soybean symbionts used in inoculants worldwide, but they have also been isolated from other legume hosts. here, we summarize published studies that indicate that group ia strains are differe ...201323504968
an overview of the metabolic differences between bradyrhizobium japonicum 110 bacteria and differentiated bacteroids from soybean (glycine max) root nodules: an in vitro 13c- and 31p-nuclear magnetic resonance spectroscopy study.bradyrhizobium japonicum is a symbiotic nitrogen-fixing soil bacteria that induce root nodules formation in legume soybean (glycine max.). using (13)c- and (31)p-nuclear magnetic resonance (nmr) spectroscopy, we have analysed the metabolite profiles of cultivated b. japonicum cells and bacteroids isolated from soybean nodules. our results revealed some quantitative and qualitative differences between the metabolite profiles of bacteroids and their vegetative state. this includes in bacteroids a ...201323480054
ethyl tert-butyl ether (etbe) biodegradation by a syntrophic association of rhodococcus sp. ifp 2042 and bradyrhizobium sp. ifp 2049 isolated from a polluted aquifer.ethyl tert-butyl ether (etbe) enrichment was obtained by adding contaminated groundwater to a mineral medium containing etbe as the sole carbon and energy source. etbe was completely degraded to biomass and co2 with a transient production of tert-butanol (tba) and a final biomass yield of 0.37 ± 0.08 mg biomass (dry weight).mg(-1) etbe. two bacterial strains, ifp 2042 and ifp 2049, were isolated from the enrichment, and their 16s rrna genes (rrs) were similar to rhodococcus sp. (99 % similarity ...201323474617
keeping pase with weft: shweft-pase pulse sequences for 1h nmr spectra of highly paramagnetic molecules.metalloproteins are a category of biomolecules in which the metal site is usually the locus of activity or function. in many cases, the metal ions are paramagnetic or have accessible paramagnetic states, many of which can be studied using nmr spectroscopy. extracting useful information from (1)h nmr spectra of highly paramagnetic proteins can be difficult because the paramagnetism leads to large resonance shifts (~400 ppm), extremely broad lines, extreme baseline nonlinearity, and peak shape dis ...201323401036
bradyrhizobium arachidis sp. nov., isolated from effective nodules of arachis hypogaea grown in china.twenty-three bacterial strains isolated from root nodules of arachis hypogaea and lablab purpureus grown in five provinces of china were classified as a novel group within the genus bradyrhizobium by analyses of pcr-based rflp of the 16s rrna gene and 16s-23s igs. to determine their taxonomic position, four representative strains were further characterized. the comparative sequence analyses of 16s rrna and six housekeeping genes clustered the four strains into a distinctive group closely related ...201323295123
response of soybean to seed inoculation with bradyrhizobium japonicum and with mixed inoculants of b. japonicum and azotobacter chroococcum.effects of pre-sowing soybean seed inoculation with bradyrhizobium japonicum alone or with mixed inoculants containing soybean rhizobia and azotobacter chroococcum were compared. in the pot experiment all the tested strains of soybean rhizobia in pure cultures or in mixtures with a. chroococcum significantly improved nodulation of soybean plants and seed yields of this crop. in micro-plot experiments pre-sowing soybean seeds treatment with the inoculant containing the most effective strain 94p o ...201324730143
a simple and effective strategy for solving the problem of inclusion bodies in recombinant protein technology: his-tag deletions enhance soluble expression.the formation of inclusion bodies (ibs) in recombinant protein biotechnology has become one of the most frequent undesirable occurrences in both research and industrial applications. so far, the pet system is the most powerful system developed for the production of recombinant proteins when escherichia coli is used as the microbial cell factory. also, using fusion tags to facilitate detection and purification of the target protein is a commonly used tactic. however, there is still a large fracti ...201323250226
arsenic effect on the model crop symbiosis bradyrhizobium-soybean.soybean (glycine max) is often being cultivated in soils with moderate to high arsenic (as) concentrations or under irrigation with as contaminated groundwater. the purpose of this study was to determine the effect of as on soybean germination, development and nodulation in soybean-bradyrhizobium japonicum e109 symbiosis, as a first-step approach to evaluate the impact of as on soybean production. semi-hydroponic assays were conducted using soybean seedlings inoculated and non-inoculated with b. ...201323228549
fixk₂, a key regulator in bradyrhizobium japonicum, is a substrate for the protease clpap in vitro.fixk₂ is a crp-like transcription factor that controls the endosymbiotic lifestyle of bradyrhizobium japonicum. the reason for its noticeable protease sensitivity was explored here. the repertoire of clp chaperone-proteases in b. japonicum was examined, and specifically clpap₁ and clpxp₁ were purified and tested. fixk₂ was found to be degraded by clpap₁ but not by clpxp₁. degradation was inhibited by the clps₁ adaptor protein, indicating that fixk₂ is a direct substrate for clpap₁. the last 12 a ...201323187170
swarming motility in bradyrhizobium japonicum.flagellar-driven bacterial motility is an important trait for colonization of natural environments. bradyrhizobium japonicum is a soil species that possesses two different flagellar systems: one subpolar and the other lateral, each with a filament formed by a different set of flagellins. while synthesis of subpolar flagellins is constitutive, translation of lateral flagellins was detected in rhizobia grown with l-arabinose, but not with d-mannitol as sole carbon source, independently of whether ...201323124116
prokaryotic squalene-hopene cyclases can be converted to citronellal cyclases by single amino acid exchange.squalene-hopene cyclases (shcs) are prokaryotic enzymes that catalyse the cyclisation of the linear precursor squalene to pentacyclic hopene. recently, we discovered that a shc cloned from zymomonas mobilis (zmo-1548 gene product) has the unique property to cyclise the monoterpenoid citronellal to isopulegol. in this study, we performed saturation mutagenesis of three amino acids of the catalytic centre of zmo-1548 (f428, f486 and w555), which had been previously identified to interact with enzy ...201322526778
agrobacterium rhizogenes transformed soybean roots differ in their nodulation and nitrogen fixation response to genistein and salt stress.we evaluated response differences of normal and transformed (so-called 'hairy') roots of soybean (glycine max l. (merr.), cv l17) to the nod-factor inducing isoflavone genistein and salinity by quantifying growth, nodulation, nitrogen fixation and biochemical changes. composite soybean plants were generated using agrobacterium rhizogenes-mediated transformation of non-nodulating mutant nod139 (gmnfr5α minus) with complementing a. rhizogenes k599 carrying the wild-type gmnfr5α gene under control ...201323430716
antioxidant defense system responses and role of nitrate reductase in the redox balance maintenance in bradyrhizobium japonicum strains exposed to cadmium.in this work, we evaluated the effects of cadmium (cd) on the antioxidant defense system responses and the role of nitrate reductase (nr) in the redox balance maintenance in bradyrhizobium japonicum strains. for that, b. japonicum usda110 and its nr defective mutant strain (grpa1) were used. results showed that the addition of 10μm cd did not modify the aerobic growth of the wild type strain while the mutant strain was strongly affected. anaerobic growth revealed that only the parental strain wa ...201324034434
inoculation with bradyrhizobium japonicum enhances the organic and fatty acids content of soybean (glycine max (l.) merrill) seeds.soybean (glycine max (l.) merrill) is one of the most important food crops for human and animal consumption, providing oil and protein at relatively low cost. the least expensive source of nitrogen for soybean is the biological fixation of atmospheric nitrogen by the symbiotic association with soil bacteria, belonging mainly to the genus bradyrhizobium. this study was conducted to assess the effect of the inoculation of g. max with bradyrhizobium japonicum on the metabolite profile and antioxida ...201323993531
efficiency of different formulations of bradyrhizobium japonicum and effect of co-inoculation of bacillus subtilis with two different strains of bradyrhizobium japonicum.a key constraint in successfully obtaining an effective inoculant is overcoming difficulties in formulating a viable and user-friendly final product and maintaining the microbial cells in a competent state. co-cultures of rhizobia and pgpr (plant growth promoting rhizobacteria) are a logical next subject for formulation researchers as they can influence the efficacy of rhizobia. a greenhouse experiment was set to assess the formulation effect of one strain i.e. bradyrhizobium japonicum, 532c (gr ...201222806160
thioredoxin-like protein tlpa from bradyrhizobium japonicum is a reductant for the copper metallochaperone scoi.tlpa and scoi of bradyrhizobium japonicum are membrane-anchored thioredoxin-like proteins oriented towards the periplasm. tlpa is a protein-disulfide reductase. scoi is a copper chaperone for cytochrome oxidase biogenesis. tlpa with its negative redox potential (e(o') -256 mv) was shown here to reduce oxidized scoi, for which we determined a less negative e(o') (-160 mv). the fast forward reaction (rate constant 9.4×10(4) m(-1) s(-1)) was typical for physiologically relevant disulfide exchange r ...201223123159
increased hydrogen production in co-culture of chlamydomonas reinhardtii and bradyrhizobium japonicum.co-cultivation of bradyrhizobium japonicum with chlamydomonas reinhardtii strain cc849 or the transgenic strain lba, which was hetero-expressed the gene of the soybean leghemoglobin apoprotein lba in chloroplasts of the strain cc849, in tris-acetate-phosphate (tap) or tap-sulfur free media, improved h(2) yield. h(2) production was 14 times and growth was 26% higher when strain lba and b. japonicum were co-cultured, as compared with cultivation of the algal strain alone under the same conditions. ...201222940317
transient nod factor-dependent gene expression in the nodulation-competent zone of soybean (glycine max [l.] merr.) roots.all lateral organ development in plants, such as nodulation in legumes, requires the temporal and spatial regulation of genes and gene networks. a total mrna profiling approach using rna-seq to target the specific soybean (glycine max) root tissues responding to compatible rhizobia [i.e. the zone of nodulation (zon)] revealed a large number of novel, often transient, mrna changes occurring during the early stages of nodulation. focusing on the zon enabled us to discard the majority of root tissu ...201222863334
soybean seed lectin prevents the accumulation of s-adenosyl methionine synthetase and the s1 30s ribosomal protein in bradyrhizobium japonicum under c and n starvation.soybean lectin (sbl) participates in the recognition between bradyrhizobium japonicum and soybean although its role remains unknown. to search for changes in the proteome in response to sbl, b. japonicum usda 110 was incubated for 12 h in a c- and n-free medium with or without sbl (10 μg ml(-1)), and the soluble protein profiles were compared. two polypeptides, s-adenosyl-methionine synthetase (metk) and the 30s ribosomal protein s1 (rpsa), were found only in the fractions from rhizobia incubate ...201222782468
a comparative proteomics analysis in roots of soybean to compatible symbiotic bacteria under flooding stress.a proteomics approach was used to evaluate the effects of flooding stress on early symbiotic interaction between soybean roots and soil bacteria, bradyrhizobium japonicum. three-day-old soybean was inoculated with b. japonicum followed by flooding. the number of root hairs in seedlings, without or with flooding stress, was increased after 3 days of inoculation. proteins were extracted from roots and separated by two-dimensional polyacrylamide gel electrophoresis. out of 219 protein spots, 14 and ...201222692703
identification of systemic responses in soybean nodulation by xylem sap feeding and complete transcriptome sequencing reveal a novel component of the autoregulation pathway.establishment of the nitrogen-fixing nodulation symbiosis between legumes and rhizobia requires plant-wide reprogramming to allow infection and development of nodules. nodulation is regulated principally via a mechanism called autoregulation of nodulation (aon). aon is dependent on shoot and root factors and is maintained by the nodulation autoregulation receptor kinase (nark) in soybean. we developed a bioassay to detect root-derived signalling molecules in xylem sap of soybean plants which may ...201222624681
production and function of jasmonates in nodulated roots of soybean plants inoculated with bradyrhizobium japonicum.little is known regarding production and function of endogenous jasmonates (jas) in root nodules of soybean plants inoculated with bradyrhizobium japonicum. we investigated (1) production of jasmonic acid (ja) and 12-oxophytodienoic acid (opda) in roots of control and inoculated plants and in isolated nodules; (2) correlations between jas levels, nodule number, and plant growth during the symbiotic process; and (3) effects of exogenous ja and opda on nodule cell number and size. in roots of cont ...201222547296
expression, and molecular and enzymatic characterization of cu-containing nitrite reductase from a marine ammonia-oxidizing gammaproteobacterium, nitrosococcus oceani.ammonia-oxidizing bacteria (aob) remove intracellular nitrite to prevent its toxicity by a nitrifier denitrification pathway involving two denitrifying enzymes, nitrite reductase and nitric oxide reductase. here, a cu-containing nitrite reductase from nitrosococcus oceani strain ns58, a gammaproteobacterial marine aob, was expressed in escherichia coli and purified to homogeneity. sequence homology analysis indicated that the nitrite reductase from n. oceani was phylogenetically closer to its co ...201222641151
hfq influences multiple transport systems and virulence in the plant pathogen agrobacterium tumefaciens.the hfq protein mediates gene regulation by small rnas (srnas) in about 50% of all bacteria. depending on the species, phenotypic defects of an hfq mutant range from mild to severe. here, we document that the purified hfq protein of the plant pathogen and natural genetic engineer agrobacterium tumefaciens binds to the previously described srna abcr1 and its target mrna atu2422, which codes for the substrate binding protein of an abc transporter taking up proline and γ-aminobutyric acid (gaba). s ...201222821981
role of the irr protein in the regulation of iron metabolism in rhodobacter sphaeroides.in rhizobia the irr protein is an important regulator for iron-dependent gene expression. we studied the role of the irr homolog rsp_3179 in the photosynthetic alpha-proteobacterium rhodobacter sphaeroides. while irr had little effect on growth under iron-limiting or non-limiting conditions its deletion resulted in increased resistance to hydrogen peroxide and singlet oxygen. this correlates with an elevated expression of kate for catalase in the irr mutant compared to the wild type under non-st ...201222879920
the bhuq gene encodes a heme oxygenase that contributes to the ability of brucella abortus 2308 to use heme as an iron source and is regulated by irr.the brucella bhuq protein is a homolog of the bradyrhizobium japonicum heme oxygenases hmud and hmuq. to determine if this protein plays a role in the ability of brucella abortus 2308 to use heme as an iron source, an isogenic bhuq mutant was constructed and its phenotype evaluated. although the brucella abortus bhuq mutant dco1 did not exhibit a defect in its capacity to use heme as an iron source or evidence of increased heme toxicity in vitro, this mutant produced increased levels of sideroph ...201222636783
stressed by a lov triangle. 201222447905
a comparative genomics screen identifies a sinorhizobium meliloti 1021 sodm-like gene strongly expressed within host plant nodules.we have used the genomic data in the integrated microbial genomes system of the department of energy's joint genome institute to make predictions about rhizobial open reading frames that play a role in nodulation of host plants. the genomic data was screened by searching for orfs conserved in α-proteobacterial rhizobia, but not conserved in closely-related non-nitrogen-fixing α-proteobacteria.201222587634
structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria.α-proteobacteria uniquely integrate features of two-component signal transduction (tcs) and alternative sigma factor (σ) regulation to control transcription in response to general stress. the core of this regulatory system is the phyr protein, which contains a σ-like (sl) domain and a tcs receiver domain. aspartyl phosphorylation of the phyr receiver in response to stress signals promotes binding of the anti-σ factor, nepr, to phyr-sl. this mechanism, whereby nepr switches binding between its co ...201222550172
manganese is required for oxidative metabolism in unstressed bradyrhizobium japonicum cells.recent studies of mn(2+) transport mutants indicate that manganese is essential for unstressed growth in some bacterial species, but is required primarily for induced stress responses in others. a bradyrhizobium japonicum mutant defective in the high-affinity mn(2+) transporter gene mnth has a severe growth phenotype under manganese limitation, suggesting a requirement for the metal under unstressed growth. here, we found that activities of superoxide dismutase and the glycolytic enzyme pyruvate ...201222463793
absence of membrane phosphatidylcholine does not affect virulence and stress tolerance phenotypes in the opportunistic pathogen pseudomonas aeruginosa.during growth in presence of choline, both laboratory and clinical pseudomonas aeruginosa strains synthesize phosphatidylcholine (pc), and pc makes up ∼4% of the total membrane phospholipid content. in all the strains tested, pc synthesis occurred only when choline is provided exogenously. mutants defective in synthesis of pc were generated in the strain backgrounds pao1 and pa14. minimum inhibitory concentration studies testing sensitivity of pc-deficient strains towards various antibiotics and ...201222363496
fur in magnetospirillum gryphiswaldense influences magnetosomes formation and directly regulates the genes involved in iron and oxygen metabolism.magnetospirillum gryphiswaldense strain msr-1 has the unique capability of taking up large amounts of iron and synthesizing magnetosomes (intracellular magnetic particles composed of fe(3)o(4)). the unusual high iron content of msr-1 makes it a useful model for studying biological mechanisms of iron uptake and homeostasis. the ferric uptake regulator (fur) protein plays a key role in maintaining iron homeostasis in many bacteria. we identified and characterized a fur-homologous gene (mgr_1314) i ...201222238623
investigation of the bacterial communities associated with females of lutzomyia sand fly species from south america.phlebotomine sand flies are vectors of leishmania that are acquired by the female sand fly during blood feeding on an infected mammal. leishmania parasites develop exclusively in the gut lumen during their residence in the insect before transmission to a suitable host during the next blood feed. female phlebotomine sand flies are blood feeding insects but their life style of visiting plants as well as animals, and the propensity for larvae to feed on detritus including animal faeces means that t ...201222880020
crystal structure of the mobile metallo-β-lactamase aim-1 from pseudomonas aeruginosa: insights into antibiotic binding and the role of gln157.metallo-β-lactamase (mbl) genes confer resistance to virtually all β-lactam antibiotics and are rapidly disseminated by mobile genetic elements in gram-negative bacteria. mbls belong to three different subgroups, b1, b2, and b3, with the mobile mbls largely confined to subgroup b1. the b3 mbls are a divergent subgroup of predominantly chromosomally encoded enzymes. aim-1 (adelaide imipenmase 1) from pseudomonas aeruginosa was the first b3 mbl to be identified on a readily mobile genetic element. ...201222664968
carf mediates signaling by singlet oxygen, generated via photoexcited protoporphyrin ix, in myxococcus xanthus light-induced carotenogenesis.blue light triggers carotenogenesis in the nonphototrophic bacterium myxococcus xanthus by inducing inactivation of an anti-σ factor, carr, and the consequent liberation of the cognate extracytoplasmic function (ecf) σ factor, carq. carf, the protein implicated earliest in the response to light, does not resemble any known photoreceptor. it interacts physically with carr and is required for its light-driven inactivation, but the mechanism is unknown. blue-light sensing in m. xanthus has been att ...201222267513
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 ...201223234435
prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. the existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. ...201223185476
working together for the common good: cell-cell communication in bacteria.the 4th asm conference on cell-cell communication in bacteria was held in miami, fl, from 6 to 9 november 2011. this review highlights three key themes that emerged from the many exciting talks and poster presentations in the area of quorum sensing: sociomicrobiology, signal transduction mechanisms, and interspecies communication.201222389476
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 ...201223226482
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 ...201223100020
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 ...201222798370
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 ...201222730121
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 ...201224704978
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 ...201222586130
effect of soybean coumestrol on bradyrhizobium japonicum nodulation ability, biofilm formation, and transcriptional profile.flavonoids, secondary plant metabolites which mainly have a polyphenolic structure, play an important role in plant-microbe communications for nitrogen-fixing symbiosis. among 10 polyphenolic compounds isolated from soybean roots in our previous study, coumestrol showed the highest antioxidant activity. in this study, its effect on the soybean nodulation was tested. the soybean symbiont bradyrhizobium japonicum usda110 pretreated with 20 μm coumestrol enhanced soybean nodulation by increasing th ...201222307307
nad(p)+-malic enzyme mutants of sinorhizobium sp. strain ngr234, but not azorhizobium caulinodans ors571, maintain symbiotic n2 fixation capabilities.c(4)-dicarboxylic acids appear to be metabolized via the tricarboxylic acid (tca) cycle in n(2)-fixing bacteria (bacteroids) within legume nodules. in sinorhizobium meliloti bacteroids from alfalfa, nad(+)-malic enzyme (dme) is required for n(2) fixation, and this activity is thought to be required for the anaplerotic synthesis of pyruvate. in contrast, in the pea symbiont rhizobium leguminosarum, pyruvate synthesis occurs via either dme or a pathway catalyzed by phosphoenolpyruvate carboxykinas ...201222307295
the genetics of symbiotic nitrogen fixation: comparative genomics of 14 rhizobia strains by resolution of protein clusters.the symbiotic relationship between legumes and nitrogen fixing bacteria is critical for agriculture, as it may have profound impacts on lowering costs for farmers, on land sustainability, on soil quality, and on mitigation of greenhouse gas emissions. however, despite the importance of the symbioses to the global nitrogen cycling balance, very few rhizobial genomes have been sequenced so far, although there are some ongoing efforts in sequencing elite strains. in this study, the genomes of fourt ...201224704847
comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia.tropical aquatic species of the legume genus aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (nd) or a nod gene-independent (ni) pathway to enter into symbiosis with legumes. in this study we used a comparative genomics approach on nine aeschynomene symbionts representative of their phylogenetic diversity. we produced draft genomes of bradyrhizobial strains representing differen ...201224704842
comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia.tropical aquatic species of the legume genus aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (nd) or a nod gene-independent (ni) pathway to enter into symbiosis with legumes. in this study we used a comparative genomics approach on nine aeschynomene symbionts representative of their phylogenetic diversity. we produced draft genomes of bradyrhizobial strains representing differen ...201224704842
paralogous outer membrane proteins mediate uptake of different forms of iron and synergistically govern virulence in francisella tularensis tularensis.francisella tularensis subsp. tularensis is a highly infectious bacterium causing acute disease in mammalian hosts. mechanisms for the acquisition of iron within the iron-limiting host environment are likely to be critical for survival of this intracellular pathogen. fsle (ftt0025) and fupa (ftt0918) are paralogous proteins that are predicted to form β-barrels in the outer membrane of virulent strain schu s4 and are unique to francisella species. previous studies have implicated both fupa, initi ...201222661710
the unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink.nitrous oxide (n(2)o) is a major radiative forcing and stratospheric ozone-depleting gas emitted from terrestrial and aquatic ecosystems. it can be transformed to nitrogen gas (n(2)) by bacteria and archaea harboring the n(2)o reductase (n(2)or), which is the only known n(2)o sink in the biosphere. despite its crucial role in mitigating n(2)o emissions, knowledge of the n(2)or in the environment remains limited. here, we report a comprehensive phylogenetic analysis of the nosz gene coding the n( ...201223151640
the unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink.nitrous oxide (n(2)o) is a major radiative forcing and stratospheric ozone-depleting gas emitted from terrestrial and aquatic ecosystems. it can be transformed to nitrogen gas (n(2)) by bacteria and archaea harboring the n(2)o reductase (n(2)or), which is the only known n(2)o sink in the biosphere. despite its crucial role in mitigating n(2)o emissions, knowledge of the n(2)or in the environment remains limited. here, we report a comprehensive phylogenetic analysis of the nosz gene coding the n( ...201223151640
dual role of hupf in the biosynthesis of [nife] hydrogenase in rhizobium leguminosarum.[nife] hydrogenases are enzymes that catalyze the oxidation of hydrogen into protons and electrons, to use h₂ as energy source, or the production of hydrogen through proton reduction, as an escape valve for the excess of reduction equivalents in anaerobic metabolism. biosynthesis of [nife] hydrogenases is a complex process that occurs in the cytoplasm, where a number of auxiliary proteins are required to synthesize and insert the metal cofactors into the enzyme structural units. the endosymbioti ...201223136881
copper starvation-inducible protein for cytochrome oxidase biogenesis in bradyrhizobium japonicum.microarray analysis of bradyrhizobium japonicum grown under copper limitation uncovered five genes named pcuabcde, which are co-transcribed and co-regulated as an operon. the predicted gene products are periplasmic proteins (pcua, pcuc, and pcud), a tonb-dependent outer membrane receptor (pcub), and a cytoplasmic membrane-integral protein (pcue). homologs of pcuc and pcue had been discovered in other bacteria, namely pcu(a)c and ycnj, where they play a role in cytochrome oxidase biogenesis and c ...201223012364
the periplasmic nitrate reductase nap is required for anaerobic growth and involved in redox control of magnetite biomineralization in magnetospirillum gryphiswaldense.the magnetosomes of many magnetotactic bacteria consist of membrane-enveloped magnetite crystals, whose synthesis is favored by a low redox potential. however, the cellular redox processes governing the biomineralization of the mixed-valence iron oxide have remained unknown. here, we show that in the alphaproteobacterium magnetospirillum gryphiswaldense, magnetite biomineralization is linked to dissimilatory nitrate reduction. a complete denitrification pathway, including gene functions for nitr ...201222730130
nitrous oxide production and consumption: regulation of gene expression by gas-sensitive transcription factors.several biochemical mechanisms contribute to the biological generation of nitrous oxide (n(2)o). n(2)o generating enzymes include the respiratory nitric oxide (no) reductase, an enzyme from the flavo-diiron family, and flavohaemoglobin. on the other hand, there is only one enzyme that is known to use n(2)o as a substrate, which is the respiratory n(2)o reductase typically found in bacteria capable of denitrification (the respiratory reduction of nitrate and nitrite to dinitrogen). this article w ...201222451107
mechanistic stoichiometry of proton translocation by cytochrome cbb3.cytochrome cbb(3) belongs to the superfamily of respiratory heme-copper oxidases that couple the reduction of molecular oxygen to proton translocation across the bacterial or mitochondrial membrane. the cbb(3)-type enzymes are found only in bacteria, and are both structurally and functionally the most distant from their mitochondrial counterparts. the mechanistic h(+)/e(-) stoichiometry of proton translocation in these cbb(3)-type cytochrome c oxidases has remained controversial. a stoichiometri ...201222529361
the genome sequence of polymorphum gilvum sl003b-26a1(t) reveals its genetic basis for crude oil degradation and adaptation to the saline soil.polymorphum gilvum sl003b-26a1(t) is the type strain of a novel species in the recently published novel genus polymorphum isolated from saline soil contaminated with crude oil. it is capable of using crude oil as the sole carbon and energy source and can adapt to saline soil at a temperature of 45°c. the polymorphum gilvum genome provides a genetic basis for understanding how the strain could degrade crude oil and adapt to a saline environment. genome analysis revealed the versatility of the str ...201222359583
crystal structures and kinetics of monofunctional proline dehydrogenase provide insight into substrate recognition and conformational changes associated with flavin reduction and product release.proline dehydrogenase (prodh) catalyzes the fad-dependent oxidation of proline to δ(1)-pyrroline-5-carboxylate, which is the first step of proline catabolism. here, we report the structures of proline dehydrogenase from deinococcus radiodurans in the oxidized state complexed with the proline analogue l-tetrahydrofuroic acid and in the reduced state with the proline site vacant. the analogue binds against the si face of the fad isoalloxazine and is protected from bulk solvent by helix α8 and the ...201223151026
molecular characterization of nad+-dependent dna ligase from wolbachia endosymbiont of lymphatic filarial parasite brugia malayi.the lymphatic filarial parasite, brugia malayi contains wolbachia endobacteria that are essential for development, viability and fertility of the parasite. therefore, wolbachial proteins have been currently seen as the potential antifilarial drug targets. nad(+)-dependent dna ligase is characterized as a promising drug target in several organisms due to its crucial, indispensable role in dna replication, recombination and dna repair. we report here the cloning, expression and purification of nad ...201222815933
the scoi homologue senc is a copper binding protein that interacts directly with the cbb₃-type cytochrome oxidase in rhodobacter capsulatus.sco proteins are widespread assembly factors for the cu(a) centre of aa₃-type cytochrome oxidases in eukaryotic and prokaryotic organisms. however, sco homologues are also found in bacteria like rhodobacter capsulatus which lack aa₃-type cytochrome oxidases and instead use a cbb₃-type cytochrome oxidase (cbb₃ cox) without a cu(a) centre as a terminal oxidase. in the current study, we have analyzed the role of sco (senc) during cbb₃ cox assembly in r. capsulatus. in agreement with earlier works, ...201222771512
role of trehalose in salinity and temperature tolerance in the model halophilic bacterium chromohalobacter salexigens.the disaccharide trehalose is considered as a universal stress molecule, protecting cells and biomolecules from injuries imposed by high osmolarity, heat, oxidation, desiccation and freezing. chromohalobacter salexigens is a halophilic and extremely halotolerant γ-proteobacterium of the family halomonadaceae. in this work, we have investigated the role of trehalose as a protectant against salinity, temperature and desiccation in c. salexigens. a mutant deficient in the trehalose-6-phosphate synt ...201222448254
cytosolic ni(ii) sensor in cyanobacterium: nickel detection follows nickel affinity across four families of metal sensors.efflux of surplus ni(ii) across the outer and inner membranes of synechocystis pcc 6803 is mediated by the nrs system under the control of a sensor of periplasmic ni(ii), nrss. here, we show that the product of orf sll0176, which encodes a csor/rcnr-like protein now designated inrs (for internal nickel-responsive sensor), represses nrsd (nrsd is deduced to efflux ni(ii) across the inner membrane) from a cryptic promoter between the final two orfs in the nrs operon. transcripts initiated from the ...201222356910
the roles of rhodobacter sphaeroides copper chaperones pcu(a)c and sco (prrc) in the assembly of the copper centers of the aa(3)-type and the cbb(3)-type cytochrome c oxidases.the α proteobacter rhodobacter sphaeroides accumulates two cytochrome c oxidases (cco) in its cytoplasmic membrane during aerobic growth: a mitochondrial-like aa(3)-type cco containing a di-copper cu(a) center and mono-copper cu(b), plus a cbb(3)-type cco that contains cu(b) but lacks cu(a). three copper chaperones are located in the periplasm of r. sphaeroides, pcu(a)c, prrc (sco) and cox11. cox11 is required to assemble cu(b) of the aa(3)-type but not the cbb(3)-type cco. prrc is homologous to ...201222248670
characterization of the flavonoid-responsive regulator frra and its binding sites.previous microarray analyses revealed that in bradyrhizobium japonicum, about 100 genes are induced by genistein, an isoflavonoid secreted by soybean. this includes the three genes frec, frea, and freb (systematic designations bll4319, bll4320, and bll4321), which are likely to form a genistein-, daidzein-, and coumestrol-inducible operon and to encode a multidrug efflux system. upstream of frecab and in the opposite orientation, frra (systematic designation blr4322), which has similarity to tet ...201222389485
fluorescence-based rapid detection of microbiological contaminants in water samples.microbiological contamination of process waters is a current issue for pharmaceutical industries. traditional methods require several days to obtain results; therefore, rapid microbiological methods are widely requested to shorten time-to-result. milliflex quantum was developed for the rapid detection and enumeration of microorganisms in filterable samples. it combines membrane filtration to universal fluorescent staining of viable microorganisms. this new alternative method was validated using ...201222623887
nitrilases in nitrile biocatalysis: recent progress and forthcoming research.over the past decades, nitrilases have drawn considerable attention because of their application in nitrile degradation as prominent biocatalysts. nitrilases are derived from bacteria, filamentous fungi, yeasts, and plants. in-depth investigations on their natural sources function mechanisms, enzyme structure, screening pathways, and biocatalytic properties have been conducted. moreover, the immobilization, purification, gene cloning and modifications of nitrilase have been dwelt upon. some nitr ...201223106943
discovery of a novel (+)-γ-lactamase from bradyrhizobium japonicum usda 6 by rational genome mining.a novel (+)-γ-lactamase used for the resolution of racemic γ-lactam from bradyrhizobium japonicum usda 6 was found as a result of sequence-structure guided genome mining. it consists of 409 amino acids, only 49% of which are identical to the amino acid sequences of the known (+)-γ-lactamase from sulfolobus solfataricus. this is only the third (+)-γ-lactamase gene to be reported.201222885756
identification of cys94 as the distal ligand to the fe(iii) heme in the transcriptional regulator rcom-2 from burkholderia xenovorans.the co-responsive transcriptional regulator rcom from burkholderia xenovorans (bxrcom) was recently identified as a cys(thiolate)-ligated heme protein that undergoes a redox-mediated ligand switch; however, the cys bound to the fe(iii) heme was not identified. to that end, we generated and purified three cys-to-ser variants of bxrcom-2--c94s, c127s, and c130s--and examined their spectroscopic properties in order to identify the native cys(thiolate) ligand. electronic absorption, resonance raman, ...201222855237
rhizobium promotes non-legumes growth and quality in several production steps: towards a biofertilization of edible raw vegetables healthy for humans.the biofertilization of crops with plant-growth-promoting microorganisms is currently considered as a healthy alternative to chemical fertilization. however, only microorganisms safe for humans can be used as biofertilizers, particularly in vegetables that are raw consumed, in order to avoid sanitary problems derived from the presence of pathogenic bacteria in the final products. in the present work we showed that rhizobium strains colonize the roots of tomato and pepper plants promoting their g ...201222675441
distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone.pyrroloquinoline quinone (pqq) is a small, redox active molecule that serves as a cofactor for several bacterial dehydrogenases, introducing pathways for carbon utilization that confer a growth advantage. early studies had implicated a ribosomally translated peptide as the substrate for pqq production. this study presents a sequence- and structure-based analysis of the components of the pqq operon. we find the necessary components for pqq production are present in 126 prokaryotes, most of which ...201222324760
leveraging proteomics to understand plant-microbe interactions.understanding the interactions of plants with beneficial and pathogenic microbes is a promising avenue to improve crop productivity and agriculture sustainability. proteomic techniques provide a unique angle to describe these intricate interactions and test hypotheses. the various approaches for proteomic analysis generally include protein/peptide separation and identification, but can also provide quantification and the characterization of post-translational modifications. in this review, we di ...201222645586
detection, characterization, and biological effect of quorum-sensing signaling molecules in peanut-nodulating bradyrhizobia.bacteria of the genus bradyrhizobium are able to establish a symbiotic relationship with peanut (arachis hypogaea) root cells and to fix atmospheric nitrogen by converting it to nitrogenous compounds. quorum sensing (qs) is a cell-cell communication mechanism employed by a variety of bacterial species to coordinate behavior at a community level through regulation of gene expression. the qs process depends on bacterial production of various signaling molecules, among which the n-acylhomoserine la ...201222736981
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