| haemophilus parainfluenzae expresses diverse lipopolysaccharide o-antigens using abc transporter and wzy polymerase-dependent mechanisms. | lipopolysaccharide o-antigens are the basis of serotyping schemes for gram negative bacteria and help to determine the nature of host-bacterial interactions. haemophilus parainfluenzae is a normal commensal of humans but is also an occasional pathogen. the prevalence, diversity and biosynthesis of o-antigens were investigated in this species for the first time. 18/18 commensal h. parainfluenzae isolates contain a o-antigen biosynthesis gene cluster flanked by glna and pepb, the same position as ... | 2013 | 24035104 |
| 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 ... | 2013 | 24277738 |
| 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 ... | 2013 | 24277738 |
| corbi: a new r package for biological network alignment and querying. | in the last decade, plenty of biological networks are built from the large scale experimental data produced by the rapidly developing high-throughput techniques as well as literature and other sources. but the huge amount of network data have not been fully utilized due to the limited biological network analysis tools. as a basic and essential bioinformatics method, biological network alignment and querying have been applied in many fields such as predicting new protein-protein interactions (ppi ... | 2013 | 24565104 |
| 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 ... | 2013 | 24382933 |
| reconstruction of phyletic trees by global alignment of multiple metabolic networks. | in the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. in contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information. | 2013 | 23368411 |
| perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline. | plants are continuously monitoring the presence of microorganisms to establish an adapted response. plants commonly use pattern recognition receptors (prrs) to perceive microbe- or pathogen-associated molecular patterns (mamps/pamps) which are microorganism molecular signatures. located at the plant plasma membrane, the prrs are generally receptor-like kinases (rlks) or receptor-like proteins (rlps). mamp detection will lead to the establishment of a plant defense program called mamp-triggered i ... | 2015 | 25904927 |
| contributions of sinorhizobium meliloti transcriptional regulator dksa to bacterial growth and efficient symbiosis with medicago sativa. | the stringent response, mediated by the (p)ppgpp synthetase rela and the rna polymerase-binding protein dksa, is triggered by limiting nutrient conditions. for some bacteria, it is involved in regulation of virulence. we investigated the role of two dksa-like proteins from the gram-negative nitrogen-fixing symbiont sinorhizobium meliloti in free-living culture and in interaction with its host plant medicago sativa the two paralogs, encoded by the genes smc00469 and smc00049, differ in the consti ... | 2016 | 26883825 |
| subglacial lake vostok (antarctica) accretion ice contains a diverse set of sequences from aquatic, marine and sediment-inhabiting bacteria and eukarya. | lake vostok, the 7(th) largest (by volume) and 4(th) deepest lake on earth, is covered by more than 3,700 m of ice, making it the largest subglacial lake known. the combination of cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier), limited nutrients and complete darkness presents extreme challenges to life. here, we report metagenomic/metatranscriptomic sequence analyses from four accretion ice sections from the vostok 5g ice core. two sections accreted in t ... | 2013 | 23843994 |
| ecological fitness, genomic islands and bacterial pathogenicity. a darwinian view of the evolution of microbes. | the compositions of bacterial genomes can be changed rapidly and dramatically through a variety of processes including horizontal gene transfer. this form of change is key to bacterial evolution, as it leads to 'evolution in quantum leaps'. horizontal gene transfer entails the incorporation of genetic elements transferred from another organism-perhaps in an earlier generation-directly into the genome, where they form 'genomic islands', i.e. blocks of dna with signatures of mobile genetic element ... | 2001 | 11375927 |
| type v protein secretion pathway: the autotransporter story. | gram-negative bacteria possess an outer membrane layer which constrains uptake and secretion of solutes and polypeptides. to overcome this barrier, bacteria have developed several systems for protein secretion. the type v secretion pathway encompasses the autotransporter proteins, the two-partner secretion system, and the recently described type vc or at-2 family of proteins. since its discovery in the late 1980s, this family of secreted proteins has expanded continuously, due largely to the adv ... | 2004 | 15590781 |
| different catalytic mechanisms in mammalian selenocysteine- and cysteine-containing methionine-r-sulfoxide reductases. | selenocysteine (sec) is found in active sites of several oxidoreductases in which this residue is essential for catalytic activity. however, many selenoproteins have fully functional orthologs, wherein cysteine (cys) occupies the position of sec. the reason why some enzymes evolve into selenoproteins if the cys versions may be sufficient is not understood. among three mammalian methionine-r-sulfoxide reductases (msrbs), msrb1 is a sec-containing protein, whereas msrb2 and msrb3 contain cys in th ... | 2005 | 16262444 |
| new findings on evolution of metal homeostasis genes: evidence from comparative genome analysis of bacteria and archaea. | in order to examine the natural history of metal homeostasis genes in prokaryotes, open reading frames with homology to characterized p(ib)-type atpases from the genomes of 188 bacteria and 22 archaea were investigated. major findings were as follows. first, a high diversity in n-terminal metal binding motifs was observed. these motifs were distributed throughout bacterial and archaeal lineages, suggesting multiple loss and acquisition events. second, the copa locus separated into two distinct p ... | 2005 | 16269744 |
| phenotypic heterogeneity, a phenomenon that may explain why quorum sensing does not always result in truly homogenous cell behavior. | phenotypic heterogeneity describes the occurrence of "nonconformist" cells within an isogenic population. the nonconformists show an expression profile partially different from that of the remainder of the population. phenotypic heterogeneity affects many aspects of the different bacterial lifestyles, and it is assumed that it increases bacterial fitness and the chances for survival of the whole population or smaller subpopulations in unfavorable environments. well-known examples for phenotypic ... | 2015 | 26025903 |
| swimming performance of bradyrhizobium diazoefficiens is an emergent property of its two flagellar systems. | many bacterial species use flagella for self-propulsion in aqueous media. in the soil, which is a complex and structured environment, water is found in microscopic channels where viscosity and water potential depend on the composition of the soil solution and the degree of soil water saturation. therefore, the motility of soil bacteria might have special requirements. an important soil bacterial genus is bradyrhizobium, with species that possess one flagellar system and others with two different ... | 2016 | 27053439 |
| metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in shanghai, china. | activated sludge of wastewater treatment plants carries a diverse microflora. however, up to 80-90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. in this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in shanghai, china, by a culture-independent metagenomic approach. three sets of consensus degenerate hybrid oligonucleotide primers (codehops) target ... | 2013 | 24860282 |
| metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in shanghai, china. | activated sludge of wastewater treatment plants carries a diverse microflora. however, up to 80-90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. in this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in shanghai, china, by a culture-independent metagenomic approach. three sets of consensus degenerate hybrid oligonucleotide primers (codehops) target ... | 2013 | 24860282 |
| possibility of bacterial recruitment of plant genes associated with the biosynthesis of secondary metabolites. | | 2003 | 12857798 |
| molecular details of camp generation in mammalian cells: a tale of two systems. | the second messenger camp has been extensively studied for half a century, but the plethora of regulatory mechanisms controlling camp synthesis in mammalian cells is just beginning to be revealed. in mammalian cells, camp is produced by two evolutionary related families of adenylyl cyclases, soluble adenylyl cyclases (sac) and transmembrane adenylyl cyclases (tmac). these two enzyme families serve distinct physiological functions. they share a conserved overall architecture in their catalytic do ... | 2006 | 16934836 |
| dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain. | recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under lexa regulation in several proteobacteria species. in this work, we have traced down instances of this multiple gene cassette across the bacteria domain. phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, ... | 2006 | 16407325 |
| comparative genomic reconstruction of transcriptional regulatory networks in bacteria. | | 2007 | 17636889 |
| cell-cell communication in bacteria: united we stand. | | 2008 | 18456806 |
| protein secretion systems in bacterial-host associations, and their description in the gene ontology. | protein secretion plays a central role in modulating the interactions of bacteria with their environments. this is particularly the case when symbiotic bacteria (whether pathogenic, commensal or mutualistic) are interacting with larger host organisms. in the case of gram-negative bacteria, secretion requires translocation across the outer as well as the inner membrane, and a diversity of molecular machines have been elaborated for this purpose. a number of secreted proteins are destined to enter ... | 2009 | 19278550 |
| networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. | lateral gene transfer (lgt) is an important mechanism of natural variation among prokaryotes. over the full course of evolution, most or all of the genes resident in a given prokaryotic genome have been affected by lgt, yet the frequency of lgt can vary greatly across genes and across prokaryotic groups. the proteobacteria are among the most diverse of prokaryotic taxa. the prevalence of lgt in their genome evolution calls for the application of network-based methods instead of tree-based method ... | 2010 | 21059789 |
| networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. | lateral gene transfer (lgt) is an important mechanism of natural variation among prokaryotes. over the full course of evolution, most or all of the genes resident in a given prokaryotic genome have been affected by lgt, yet the frequency of lgt can vary greatly across genes and across prokaryotic groups. the proteobacteria are among the most diverse of prokaryotic taxa. the prevalence of lgt in their genome evolution calls for the application of network-based methods instead of tree-based method ... | 2010 | 21059789 |
| evolution and diversity of the ras superfamily of small gtpases in prokaryotes. | the ras superfamily of small gtpases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain gtpases also control complex functions such as cell polarity, motility, predation, development and antibiot ... | 2014 | 25480683 |
| evolution and diversity of the ras superfamily of small gtpases in prokaryotes. | the ras superfamily of small gtpases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain gtpases also control complex functions such as cell polarity, motility, predation, development and antibiot ... | 2014 | 25480683 |
| molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen ix. | tetrapyrroles such as heme and chlorophyll are essential for biological processes, including oxygenation, respiration, and photosynthesis. in the tetrapyrrole biosynthesis pathway, protoporphyrinogen ix oxidase (protox) catalyzes the formation of protoporphyrin ix, the last common intermediate for the biosynthesis of heme and chlorophyll. three nonhomologous isofunctional enzymes, hemg, hemj, and hemy, for protox have been identified. to reveal the distribution and evolution of the three protox ... | 2014 | 25108393 |
| type iii secretion systems: the bacterial flagellum and the injectisome. | the flagellum and the injectisome are two of the most complex and fascinating bacterial nanomachines. at their core, they share a type iii secretion system (t3ss), a transmembrane export complex that forms the extracellular appendages, the flagellar filament and the injectisome needle. recent advances, combining structural biology, cryo-electron tomography, molecular genetics, in vivo imaging, bioinformatics and biophysics, have greatly increased our understanding of the t3ss, especially the str ... | 2015 | 26370933 |
| genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. | two component systems (tcs) are signalling complexes manifested by a histidine kinase (receptor) and a response regulator (effector). they are the most abundant signalling pathways in prokaryotes and control a wide range of biological processes. the pairing of these two components is highly specific, often requiring costly and time-consuming experimental characterisation. therefore, there is considerable interest in developing accurate prediction tools to lessen the burden of experimental work a ... | 2015 | 26384938 |
| evolutionary insights about bacterial glxrs from whole genome analyses: is glurs2 a chimera? | evolutionary histories of glutamyl-trna synthetase (glurs) and glutaminyl-trna synthetase (glnrs) in bacteria are convoluted. after the divergence of eubacteria and eukarya, bacterial glurs glutamylated both trnagln and trnaglu until glnrs appeared by horizontal gene transfer (hgt) from eukaryotes or a duplicate copy of glurs (glurs2) that only glutamylates trnagln appeared. the current understanding is based on limited sequence data and not always compatible with available experimental results. ... | 2014 | 24521160 |
| 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 |
| 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 |
| 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 |
| 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 ... | 2012 | 22307295 |
| thiol synthetases of legumes: immunogold localization and differential gene regulation by phytohormones. | in plants and other organisms, glutathione (gsh) biosynthesis is catalysed sequentially by γ-glutamylcysteine synthetase (γecs) and glutathione synthetase (gshs). in legumes, homoglutathione (hgsh) can replace gsh and is synthesized by γecs and a specific homoglutathione synthetase (hgshs). the subcellular localization of the enzymes was examined by electron microscopy in several legumes and gene expression was analysed in lotus japonicus plants treated for 1-48 h with 50 μm of hormones. immunog ... | 2012 | 22442424 |
| 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 ... | 2012 | 24704847 |
| a survey of srna families in α-proteobacteria. | we have performed a computational comparative analysis of six small non-coding rna (srna) families in α-proteobacteria. members of these families were first identified in the intergenic regions of the nitrogen-fixing endosymbiont s. meliloti by a combined bioinformatics screen followed by experimental verification. consensus secondary structures inferred from covariance models for each srna family evidenced in some cases conserved motifs putatively relevant to the function of trans-encoded base- ... | 2012 | 22418845 |
| 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). | 2013 | 24004839 |
| 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 ... | 2013 | 23749981 |
| 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 ... | 2013 | 23729648 |
| interaction of medicago truncatula lysin motif receptor-like kinases, nfp and lyk3, produced in nicotiana benthamiana induces defence-like responses. | receptor(-like) kinases with lysin motif (lysm) domains in their extracellular region play crucial roles during plant interactions with microorganisms; e.g. arabidopsis thaliana cerk1 activates innate immunity upon perception of fungal chitin/chitooligosaccharides, whereas medicago truncatula nfp and lyk3 mediate signalling upon perception of bacterial lipo-chitooligosaccharides, termed nod factors, during the establishment of mutualism with nitrogen-fixing rhizobia. however, little is still kno ... | 2013 | 23750228 |
| riboregulation in plant-associated α-proteobacteria. | the symbiotic α-rhizobia sinorhizobium meliloti, bradyrhizobium japonicum, rhizobium etli and the related plant pathogen agrobacterium tumefaciens are important model organisms for studying plant-microbe interactions. these metabolically versatile soil bacteria are characterized by complex lifestyles and large genomes. here we summarize the recent knowledge on their small non-coding rnas (srnas) including conservation, function, and interaction of the srnas with the rna chaperone hfq. in each of ... | 2014 | 25003187 |
| the complete genome of burkholderia phenoliruptrix strain br3459a, a symbiont of mimosa flocculosa: highlighting the coexistence of symbiotic and pathogenic genes. | burkholderia species play an important ecological role related to xenobiosis, the promotion of plant growth, the biocontrol of agricultural diseases, and symbiotic and non-symbiotic biological nitrogen fixation. here, we highlight our study as providing the first complete genome of a symbiotic strain of b. phenoliruptrix, br3459a (=cla1), which was originally isolated in brazil from nodules of mimosa flocculosa and is effective in fixing nitrogen in association with this leguminous species. | 2014 | 24972629 |
| phenotypic characterization of astragalus glycyphyllos symbionts and their phylogeny based on the 16s rdna sequences and rflp of 16s rrna gene. | in this study, the nitrogen fixing astragalus glycyphyllos symbionts were characterized by phenotypic properties, restriction fragment length polymorphism (rflp), and sequences of 16s rdna. the generation time of a. glycyphyllos rhizobia in yeast extract mannitol medium was in the range 4-6 h. the studied isolates exhibited a low resistance to antibiotics, a moderate tolerance to nacl, assimilated di- and trisaccharides, and produced acid in medium containing mannitol as a sole carbon source. in ... | 2014 | 24710996 |
| the growth of steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to rhizobiales. | an agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. the growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order rhizobiales. phylogenetic analysis based on 16s rrna gene sequences indicated the novel bacterium, strain ka5-b(t), belonged to the genus steroidobacter in gammaproteobacteria, but differed from its closest relative, steroidobacter denitrificans fs(t), at the species level with 96.5% similarity. st ... | 2014 | 24621511 |
| a proteomic approach of bradyrhizobium/aeschynomene root and stem symbioses reveals the importance of the fixa locus for symbiosis. | rhizobia are soil bacteria that are able to form symbiosis with plant hosts of the legume family. these associations result in the formation of organs, called nodules in which bacteria fix atmospheric nitrogen to the benefit of the plant. most of our knowledge on the metabolism and the physiology of the bacteria during symbiosis derives from studying roots nodules of terrestrial plants. here we used a proteomics approach to investigate the bacterial physiology of photosynthetic bradyrhizobium sp ... | 2014 | 24590127 |
| a legume genetic framework controls infection of nodules by symbiotic and endophytic bacteria. | legumes have an intrinsic capacity to accommodate both symbiotic and endophytic bacteria within root nodules. for the symbionts, a complex genetic mechanism that allows mutual recognition and plant infection has emerged from genetic studies under axenic conditions. in contrast, little is known about the mechanisms controlling the endophytic infection. here we investigate the contribution of both the host and the symbiotic microbe to endophyte infection and development of mixed colonised nodules ... | 2015 | 26042417 |
| genome analysis of a novel bradyrhizobium sp. doa9 carrying a symbiotic plasmid. | bradyrhizobium sp. doa9 isolated from the legume aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the bradyrhizobiaceae. genome analysis of doa9 revealed that its genome comprised a single chromosome of 7.1 mbp and a plasmid of 0.7 mbp. the chromosome showed highest similarity with that of the nod gene-harboring soybean symbiont b. japonicum usda110, whereas the plasmid showed highest similarity with pbbta01 of the nod gene-l ... | 2015 | 25710540 |
| nitrogen fixation and molecular oxygen: comparative genomic reconstruction of transcription regulation in alphaproteobacteria. | biological nitrogen fixation plays a crucial role in the nitrogen cycle. an ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of bacteria and archaea. the transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class alphaproteobacteria. this regulatory network includes the activator of nitrogen fixation nifa, working in tandem with the alternative sigma-factor rpon as well as oxygen-respons ... | 2016 | 27617010 |
| bacterial molecular signals in the sinorhizobium fredii-soybean symbiosis. | sinorhizobium (ensifer) fredii (s. fredii) is a rhizobial species exhibiting a remarkably broad nodulation host-range. thus, s. fredii is able to effectively nodulate dozens of different legumes, including plants forming determinate nodules, such as the important crops soybean and cowpea, and plants forming indeterminate nodules, such as glycyrrhiza uralensis and pigeon-pea. this capacity of adaptation to different symbioses makes the study of the molecular signals produced by s. fredii strains ... | 2016 | 27213334 |
| genetic analysis reveals the essential role of nitrogen phosphotransferase system components in sinorhizobium fredii ccbau 45436 symbioses with soybean and pigeonpea plants. | the nitrogen phosphotransferase system (pts(ntr)) consists of ei(ntr), npr, and eiia(ntr). the active phosphate moiety derived from phosphoenolpyruvate is transferred through ei(ntr) and npr to eiia(ntr). sinorhizobium fredii can establish a nitrogen-fixing symbiosis with the legume crops soybean (as determinate nodules) and pigeonpea (as indeterminate nodules). in this study, s. fredii strains with mutations in ptsp and ptso (encoding ei(ntr) and npr, respectively) formed ineffective nodules on ... | 2016 | 26682851 |
| predicting transmembrane beta-barrels in proteomes. | very few methods address the problem of predicting beta-barrel membrane proteins directly from sequence. one reason is that only very few high-resolution structures for transmembrane beta-barrel (tmb) proteins have been determined thus far. here we introduced the design, statistics and results of a novel profile-based hidden markov model for the prediction and discrimination of tmbs. the method carefully attempts to avoid over-fitting the sparse experimental data. while our model training and sc ... | 2004 | 15141026 |
| origin of an alternative genetic code in the extremely small and gc-rich genome of a bacterial symbiont. | the genetic code relates nucleotide sequence to amino acid sequence and is shared across all organisms, with the rare exceptions of lineages in which one or a few codons have acquired novel assignments. recoding of uga from stop to tryptophan has evolved independently in certain reduced bacterial genomes, including those of the mycoplasmas and some mitochondria. small genomes typically exhibit low guanine plus cytosine (gc) content, and this bias in base composition has been proposed to drive ug ... | 2009 | 19609354 |
| genome analysis and characterisation of the exopolysaccharide produced by bifidobacterium longum subsp. longum 35624™. | the bifibobacterium longum subsp. longum 35624™ strain (formerly named bifidobacterium longum subsp. infantis) is a well described probiotic with clinical efficacy in irritable bowel syndrome clinical trials and induces immunoregulatory effects in mice and in humans. this paper presents (a) the genome sequence of the organism allowing the assignment to its correct subspeciation longum; (b) a comparative genome assessment with other b. longum strains and (c) the molecular structure of the 35624 e ... | 2016 | 27656878 |
| the lysr-type transcription factor hbrl is a global regulator of iron homeostasis and porphyrin synthesis in rhodobacter capsulatus. | the purple bacterium rhodobacter capsulatus is unique among rhodobacteriacae as it contains a putative iron response regulator (irr) but does not possess a copy of the ferric uptake regulator (fur). interestingly, an in-frame deletion mutant of irr shows no major role in iron homeostasis. instead, we showed that the previously identified activator of haem gene expression hbrl is a crucial regulator of iron homeostasis. we demonstrated that an hbrl deletion strain is unable to grow in iron-limite ... | 2013 | 24134691 |
| deciphering evolutionary mechanisms between mutualistic and pathogenic symbioses. | the continuum between mutualistic and pathogenic symbioses has been an underlying theme for understanding the evolution of infection and disease in a number of eukaryotic-microbe associations. the ability to monitor and then predict the spread of infectious diseases may depend upon our knowledge and capabilities of anticipating the behavior of virulent pathogens by studying related, benign symbioses. for instance, the ability of a symbiotic species to infect, colonize, and proliferate efficientl ... | 2008 | 19655044 |
| the histidine kinase pdhs controls cell cycle progression of the pathogenic alphaproteobacterium brucella abortus. | bacterial differentiation is often associated with the asymmetric localization of regulatory proteins, such as histidine kinases. pdhs is an essential and polarly localized histidine kinase in the pathogenic alphaproteobacterium brucella abortus. after cell division, pdhs is asymmetrically segregated between the two sibling cells, highlighting a differentiation event. however, the function(s) of pdhs in the b. abortus cell cycle remains unknown. we used an original approach, the pentapeptide sca ... | 2012 | 22843843 |
| agrobacteria lacking ornithine lipids induce more rapid tumour formation. | ornithine lipids (ols) are phosphorus-free membrane lipids that are widespread among gram-negative bacteria. their basic structure consists of a 3-hydroxy fatty acyl group attached in amide linkage to the α-amino group of ornithine and a second fatty acyl group ester-linked to the 3-hydroxy position of the first fatty acid. it has been shown that ols can be hydroxylated within the amide-linked fatty acyl moiety, the secondary fatty acyl moiety or within the ornithine moiety. these modifications ... | 2012 | 22958119 |
| agrobacteria lacking ornithine lipids induce more rapid tumour formation. | ornithine lipids (ols) are phosphorus-free membrane lipids that are widespread among gram-negative bacteria. their basic structure consists of a 3-hydroxy fatty acyl group attached in amide linkage to the α-amino group of ornithine and a second fatty acyl group ester-linked to the 3-hydroxy position of the first fatty acid. it has been shown that ols can be hydroxylated within the amide-linked fatty acyl moiety, the secondary fatty acyl moiety or within the ornithine moiety. these modifications ... | 2012 | 22958119 |
| comparative genomics of early-diverging brucella strains reveals a novel lipopolysaccharide biosynthesis pathway. | brucella species are gram-negative bacteria that infect mammals. recently, two unusual strains (brucella inopinata bo1(t) and b. inopinata-like bo2) have been isolated from human patients, and their similarity to some atypical brucellae isolated from australian native rodent species was noted. here we present a phylogenomic analysis of the draft genome sequences of bo1(t) and bo2 and of the australian rodent strains 83-13 and nf2653 that shows that they form two groups well separated from the ot ... | 2012 | 22930339 |
| 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. | 2012 | 22587634 |
| 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 ... | 2012 | 22550172 |
| 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 ... | 2013 | 25437336 |
| mechanistic aspects of carotenoid biosynthesis. | | 2013 | 24175570 |
| mechanistic aspects of carotenoid biosynthesis. | | 2013 | 24175570 |
| identification and characterization of ribn, a novel family of riboflavin transporters from rhizobium leguminosarum and other proteobacteria. | rhizobia are symbiotic bacteria able to invade and colonize the roots of legume plants, inducing the formation of nodules, where bacteria reduce atmospheric nitrogen (n2) to ammonia (nh3). riboflavin availability influences the capacity of rhizobia to survive in the rhizosphere and to colonize roots. in this study, we identified the rl1692 gene of rhizobium leguminosarum downstream of a flavin mononucleotide (fmn) riboswitch. rl1692 encodes a putative transmembrane permease with two eama domains ... | 2013 | 23935051 |
| independent activity of the homologous small regulatory rnas abcr1 and abcr2 in the legume symbiont sinorhizobium meliloti. | the legume symbiont sinorhizobium meliloti expresses a plethora of small noncoding rnas (srnas) whose function is mostly unknown. here, we have functionally characterized two tandemly encoded s. meliloti rm1021 srnas that are similar in sequence and structure. homologous srnas (designated abcr1 and abcr2) have been shown to regulate several abc transporters in the related α-proteobacteria agrobacterium tumefaciens and brucella abortus. in rm1021, abcr1 and abcr2 exhibit divergent unlinked regula ... | 2013 | 23869210 |
| 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 ... | 2013 | 23432981 |
| molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. | the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ... | 2014 | 25492513 |
| molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. | the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ... | 2014 | 25492513 |
| molecular characterization of a novel temperate sinorhizobium bacteriophage, фlm21, encoding dna methyltransferase with ccrm-like specificity. | φlm21 is a temperate phage isolated from sinorhizobium sp. strain lm21 (alphaproteobacteria). genomic analysis and electron microscopy suggested that φlm21 is a member of the family siphoviridae. the phage has an isometric head and a long noncontractile tail. the genome of φlm21 has 50,827 bp of linear double-stranded dna encoding 72 putative proteins, including proteins responsible for the assembly of the phage particles, dna packaging, transcription, replication, and lysis. virion proteins wer ... | 2014 | 25187538 |
| a putative bifunctional histidine kinase/phosphatase of the hwe family exerts positive and negative control on the sinorhizobium meliloti general stress response. | the ecfg-type sigma factor rpoe2 is the regulator of the general stress response in sinorhizobium meliloti. rpoe2 activity is negatively regulated by two nepr-type anti-sigma factors (rsia1/a2), themselves under the control of two anti-anti-sigma factors (rsib1/b2) belonging to the phyr family of response regulators. the current model of rpoe2 activation suggests that in response to stress, rsib1/b2 are activated by phosphorylation of an aspartate residue in their receiver domain. once activated ... | 2014 | 24794560 |
| rna-seq and microarrays analyses reveal global differential transcriptomes of mesorhizobium huakuii 7653r between bacteroids and free-living cells. | mesorhizobium huakuii 7653r occurs either in nitrogen-fixing symbiosis with its host plant, astragalus sinicus, or free-living in the soil. the m. huakuii 7653r genome has recently been sequenced. to better understand the complex biochemical and developmental changes that occur in 7653r during bacteroid development, rna-seq and microarrays were used to investigate the differential transcriptomes of 7653r bacteroids and free-living cells. the two approaches identified several thousand differentia ... | 2014 | 24695521 |
| comparative phylogenomics and evolution of the brucellae reveal a path to virulence. | brucella species include important zoonotic pathogens that have a substantial impact on both agriculture and human health throughout the world. brucellae are thought of as "stealth pathogens" that escape recognition by the host innate immune response, modulate the acquired immune response, and evade intracellular destruction. we analyzed the genome sequences of members of the family brucellaceae to assess its evolutionary history from likely free-living soil-based progenitors into highly success ... | 2014 | 24336939 |
| structured and dynamic disordered domains regulate the activity of a multifunctional anti-σ factor. | the anti-σ factor nepr plays a central role in regulation of the general stress response (gsr) in alphaproteobacteria. this small protein has two known interaction partners: its cognate extracytoplasmic function (ecf) σ factor and the anti-anti-σ factor, phyr. stress-dependent phosphorylation of phyr initiates a protein partner switch that promotes phospho-phyr binding to nepr, which frees ecf σ to activate transcription of genes required for cell survival under adverse or fluctuating conditions ... | 2015 | 26220965 |
| thermodynamic matchers for the construction of the cuckoo rna family. | rna family models describe classes of functionally related, non-coding rnas based on sequence and structure conservation. the most important method for modeling rna families is the use of covariance models, which are stochastic models that serve in the discovery of yet unknown, homologous rnas. however, the performance of covariance models in finding remote homologs is poor for rna families with high sequence conservation, while for families with high structure but low sequence conservation, the ... | 2015 | 25779873 |
| genetic analysis of signal integration by the sinorhizobium meliloti sensor kinase feuq. | two-component signalling systems allow bacteria to recognize and respond to diverse environmental stimuli. auxiliary proteins can provide an additional layer of control to these systems. the sinorhizobium meliloti feupq two-component system is required for symbiotic development and is negatively regulated by the auxiliary small periplasmic protein feun. this study explores the mechanistic basis of this regulation. we provide evidence that feun directly interacts with the sensor kinase feuq. isol ... | 2015 | 25479839 |
| discovery and structural characterisation of new fold type iv-transaminases exemplify the diversity of this enzyme fold. | transaminases are useful biocatalysts for the production of amino acids and chiral amines as intermediates for a broad range of drugs and fine chemicals. here, we describe the discovery and characterisation of new transaminases from microorganisms which were enriched in selective media containing (r)-amines as sole nitrogen source. while most of the candidate proteins were clearly assigned to known subgroups of the fold iv family of plp-dependent enzymes by sequence analysis and characterisation ... | 2016 | 27905516 |
| genome of rhizobium leucaenae strains cfn 299(t) and cpao 29.8: searching for genes related to a successful symbiotic performance under stressful conditions. | common bean (phaseolus vulgaris l.) is the most important legume cropped worldwide for food production and its agronomic performance can be greatly improved if the benefits from symbiotic nitrogen fixation are maximized. the legume is known for its high promiscuity in nodulating with several rhizobium species, but those belonging to the rhizobium tropici "group" are the most successful and efficient in fixing nitrogen in tropical acid soils. rhizobium leucaenae belongs to this group, which is ab ... | 2016 | 27485828 |
| biochemistry and genetics of acc deaminase: a weapon to "stress ethylene" produced in plants. | 1-aminocyclopropane-1-carboxylate deaminase (accd), a pyridoxal phosphate-dependent enzyme, is widespread in diverse bacterial and fungal species. owing to accd activity, certain plant associated bacteria help plant to grow under biotic and abiotic stresses by decreasing the level of "stress ethylene" which is inhibitory to plant growth. accd breaks down acc, an immediate precursor of ethylene, to ammonia and α-ketobutyrate, which can be further metabolized by bacteria for their growth. acc deam ... | 2015 | 26441873 |
| molecular characterization of a novel n-acetyltransferase from chryseobacterium sp. | n-acetyltransferase from chryseobacterium sp. strain 5-3b is an acetyl coenzyme a (acetyl-coa)-dependent enzyme that catalyzes the enantioselective transfer of an acetyl group from acetyl-coa to the amino group of l-2-phenylglycine to produce (2s)-2-acetylamino-2-phenylacetic acid. we purified the enzyme from strain 5-3b and deduced the n-terminal amino acid sequence. the gene, designated nata, was cloned with two other hypothetical protein genes; the three genes probably form a 2.5-kb operon. t ... | 2014 | 24375143 |
| plant growth promotion potential is equally represented in diverse grapevine root-associated bacterial communities from different biopedoclimatic environments. | plant-associated bacteria provide important services to host plants. environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. however, whether these environmental factors may influence the plant growth promoting (pgp) potential of the root-associated bacteria is not widely understood. to address this issue, the diversity and pgp potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three medit ... | 2013 | 23878810 |
| a positive correlation between bacterial autoaggregation and biofilm formation in native sinorhizobium meliloti isolates from argentina. | sinorhizobium meliloti is a symbiotic nitrogen-fixing bacterium that elicits nodule formation on roots of alfalfa plants. s. meliloti produces two exopolysaccharides (epss), termed eps i and eps ii, that are both able to promote symbiosis. eps i and eps ii are secreted in two major fractions that reflect differing degrees of subunit polymerization, designated high- and low-molecular-weight fractions. we reported previously that epss are crucial for autoaggregation and biofilm formation in s. mel ... | 2012 | 22492433 |
| growth and survival of mesorhizobium loti inside acanthamoeba enhanced its ability to develop more nodules on lotus corniculatus. | the importance of protozoa as environmental reservoirs of pathogens is well recognized, while their impact on survival and symbiotic properties of rhizobia has not been explored. the possible survival of free-living rhizobia inside amoebae could influence bacterial abundance in the rhizosphere of legume plants and the nodulation competitiveness of microsymbionts. two well-characterized strains of mesorhizobium: mesorhizobium loti nzp2213 and mesorhizobium huakuii symbiovar loti maff303099 were a ... | 2015 | 25779926 |
| 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 ... | 2012 | 22359583 |
| comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. | metal sulfide mineral dissolution during bioleaching and acid mine drainage (amd) formation creates an environment that is inhospitable to most life. despite dominance by a small number of bacteria, amd microbial biofilm communities contain a notable variety of coexisting and closely related euryarchaea, most of which have defied cultivation efforts. for this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring amd arch ... | 2013 | 23865623 |
| crystal structure of an (r)-selective ω-transaminase from aspergillus terreus. | chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5'-phosphate (plp) as cofactor. in nature, (s)-selective amine transaminases are more abundant than the (r)-selective enzymes, and therefore more information concerning their structures is av ... | 2014 | 24498081 |
| active-site engineering of ω-transaminase for production of unnatural amino acids carrying a side chain bulkier than an ethyl substituent. | ω-transaminase (ω-ta) is a promising enzyme for use in the production of unnatural amino acids from keto acids using cheap amino donors such as isopropylamine. the small substrate-binding pocket of most ω-tas permits entry of substituents no larger than an ethyl group, which presents a significant challenge to the preparation of structurally diverse unnatural amino acids. here we report on the engineering of an (s)-selective ω-ta from ochrobactrum anthropi (oata) to reduce the steric constraint ... | 2015 | 26231640 |
| bruce: a program for the detection of transfer-messenger rna genes in nucleotide sequences. | a computer program, bruce, was developed for the identification of transfer-messenger rna (tmrna) genes. the program employs heuristic algorithms to search for a trna(ala)-like secondary structure surrounding a short sequence encoding the tag peptide. in the 57 completely sequenced bacterial genomes where tmrna genes have been reported previously, bruce identified all with no false positives. in addition, bruce found 99 of the 100 tmrnas identified previously in other bacteria, red chloroplasts ... | 2002 | 12140330 |
| shear rate moderates community diversity in freshwater biofilms. | the development of freshwater multispecies biofilms at solid-liquid interfaces occurs both in quiescent waters and under conditions of high shear rates. however, the influence of hydrodynamic shear rates on bacterial biofilm diversity is poorly understood. we hypothesized that different shear rates would significantly influence biofilm diversity and alter the relative proportions of coaggregating and autoaggregating community isolates. in order to study this hypothesis, freshwater biofilms were ... | 2004 | 15574945 |
| genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes. | serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. while studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. current analysis is aimed at understanding the distribution and probable b ... | 2008 | 19019219 |
| argonaute protein as a linker to command center of physiological processes. | micrornas (mirnas) post-transcriptionally regulate gene expression by binding to target mrnas with perfect or imperfect complementarity, recruiting an argonaute (ago) protein complex that usually results in degradation or translational repression of the target mrna. ago proteins function as the slicer enzyme in mirna and small interfering rna (sirna) pathways involved in human physiological and pathophysiological processes, such as antiviral responses and disease formation. although the past dec ... | 2013 | 23997530 |
| application of representational difference analysis to identify genomic differences between bradyrhizobium elkanii and b. japonicum species. | bradyrhizobium elkanii is successfully used in the formulation of commercial inoculants and, together with b. japonicum, it fully supplies the plant nitrogen demands. despite the similarity between b. japonicum and b. elkanii species, several works demonstrated genetic and physiological differences between them. in this work representational difference analysis (rda) was used for genomic comparison between b. elkanii semia 587, a crop inoculant strain, and b. japonicum usda 110, a reference stra ... | 2010 | 24031597 |
| discovery of novel haloalkane dehalogenase inhibitors. | haloalkane dehalogenases (hlds) have recently been discovered in a number of bacteria, including symbionts and pathogens of both plants and humans. however, the biological roles of hlds in these organisms are unclear. the development of efficient hld inhibitors serving as molecular probes to explore their function would represent an important step toward a better understanding of these interesting enzymes. here we report the identification of inhibitors for this enzyme family using two different ... | 2016 | 26773086 |
| use of cdna microarrays to monitor transcriptional responses of the chestnut blight fungus cryphonectria parasitica to infection by virulence-attenuating hypoviruses. | hypoviruses are a family of cytoplasmically replicating rna viruses of the chestnut blight fungus cryphonectria parasitica. members of this mycovirus family persistently alter virulence (hypovirulence) and related fungal developmental processes, including asexual and sexual sporulation. in order to gain a better understanding of the molecular basis for these changes, we have developed a c. parasitica cdna microarray to monitor global transcriptional responses to hypovirus infection. in this repo ... | 2003 | 14665460 |