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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 ...201324860282
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 ...201324860282
absence of ancient dna in sub-fossil insect inclusions preserved in 'anthropocene' colombian copal.insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. the objective of the work reported in this paper was therefore to determine if ancient dna is present in insects preserved in copal. we prepared dna libraries from two stingless bees (apidae: meliponini: trigonisca ameliae) preserved in 'anthropocene' colombian copal, dat ...201324039876
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 ...201323997530
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 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
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 ...201323750228
elucidation of a novel lipid a α-(1,1)-gala transferase gene (rgtf) from mesorhizobium loti: heterologous expression of rgtf causes rhizobium etli to synthesize lipid a with α-(1,1)-gala.an unusual α-(1,1)-galacturonic acid (gala) lipid a modification has been reported in the lipopolysaccharide of a number of interesting gram-negative bacteria, including the nitrogen-fixing bacteria azospirillum lipoferum, mesorhizobium huakuii and m. loti, the stalk-forming bacterium caulobacter crescentus and the hyperthermophilic bacterium aquifex aeolicus. however, the α-(1,1)-gala transferase (galat) gene, which we have named rgtf, was not identified. species of the rhizobium genera produce ...201323283001
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 ...201324035104
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
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 ...201324565104
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
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.201323368411
an underground tale: contribution of microbial activity to plant iron acquisition via ecological processes.iron (fe) deficiency in crops is a worldwide agricultural problem. plants have evolved several strategies to enhance fe acquisition, but increasing evidence has shown that the intrinsic plant-based strategies alone are insufficient to avoid fe deficiency in fe-limited soils. soil micro-organisms also play a critical role in plant fe acquisition; however, the mechanisms behind their promotion of fe acquisition remain largely unknown.201324265348
an underground tale: contribution of microbial activity to plant iron acquisition via ecological processes.iron (fe) deficiency in crops is a worldwide agricultural problem. plants have evolved several strategies to enhance fe acquisition, but increasing evidence has shown that the intrinsic plant-based strategies alone are insufficient to avoid fe deficiency in fe-limited soils. soil micro-organisms also play a critical role in plant fe acquisition; however, the mechanisms behind their promotion of fe acquisition remain largely unknown.201324265348
aliphatic, cyclic, and aromatic organic acids, vitamins, and carbohydrates in soil: a review.organic acids, vitamins, and carbohydrates represent important organic compounds in soil. aliphatic, cyclic, and aromatic organic acids play important roles in rhizosphere ecology, pedogenesis, food-web interactions, and decontamination of sites polluted by heavy metals and organic pollutants. carbohydrates in soils can be used to estimate changes of soil organic matter due to management practices, whereas vitamins may play an important role in soil biological and biochemical processes. the aim ...201324319374
molecular mechanisms and clinical impact of acquired and intrinsic fosfomycin resistance.bacterial infections caused by antibiotic-resistant isolates have become a major health problem in recent years, since they are very difficult to treat, leading to an increase in morbidity and mortality. fosfomycin is a broad-spectrum bactericidal antibiotic that inhibits cell wall biosynthesis in both gram-negative and gram-positive bacteria. this antibiotic has a unique mechanism of action and inhibits the initial step in peptidoglycan biosynthesis by blocking the enzyme, mura. fosfomycin has ...201327029300
the shoct domain: a widespread domain under-represented in model organisms.we have identified a new protein domain, which we have named the shoct domain (short c-terminal domain). this domain is widespread in bacteria with over a thousand examples. but we found it is missing from the most commonly studied model organisms, despite being present in closely related species. it's predominantly c-terminal location, co-occurrence with numerous other domains and short size is reminiscent of the gram-positive anchor motif, however it is present in a much wider range of species ...201323451277
a gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen bartonella.gene transfer agents (gtas) randomly transfer short fragments of a bacterial genome. a novel putative gta was recently discovered in the mouse-infecting bacterium bartonella grahamii. although gtas are widespread in phylogenetically diverse bacteria, their role in evolution is largely unknown. here, we present a comparative analysis of 16 bartonella genomes ranging from 1.4 to 2.6 mb in size, including six novel genomes from bartonella isolated from a cow, two moose, two dogs, and a kangaroo. a ...201323555299
two lotus japonicus symbiosis mutants impaired at distinct steps of arbuscule development.arbuscular mycorrhiza (am) fungi form nutrient-acquiring symbioses with the majority of higher plants. nutrient exchange occurs via arbuscules, highly branched hyphal structures that are formed within root cortical cells. with a view to identifying host genes involved in am development, we isolated lotus japonicus am-defective mutants via a microscopic screen of an ethyl methanesulfonate-mutagenized population. a standardized mapping procedure was developed that facilitated positioning of the de ...201323627596
crystal structure of pyridoxine 4-oxidase from mesorhizobium loti.pyridoxine 4-oxidase (pnox) from mesorhizobium loti is a monomeric glucose-methanol-choline (gmc) oxidoreductase family enzyme, catalyzes fad-dependent oxidation of pyridoxine (pn) into pyridoxal, and is the first enzyme in pathway i for the degradation of pn. the tertiary structures of pnox with a c-terminal his6-tag and pnox-pyridoxamine (pm) complex were determined at 2.2å and at 2.1å resolutions, respectively. the overall structure consisted of fad-binding and substrate-binding domains. in t ...201323501672
gene cloning and characterization of l-ribulose 3-epimerase from mesorhizobium loti and its application to rare sugar production.a gene encoding l-ribulose 3-epimerase (l-re) from mesorhizobium loti, an important enzyme for rare sugar production by the izumoring strategy, was cloned and overexpressed. the enzyme showed highest activity toward l-ribulose (230 u/mg) among keto-pentoses and keto-hexoses. this is the first report on a ketose 3-epimerase showing highest activity toward keto-pentose. the optimum enzyme reaction conditions for l-re were determined to be sodium phosphate buffer (ph 8.0) at 60 °c. the enzyme showe ...201323470755
down-regulation of nsp2 expression in developmentally young regions of lotus japonicus roots in response to rhizobial inoculation.during the early 1980s, bauer and associates reported that nodulation potential in primary roots of soybean seedlings following inoculation with rhizobia was significantly reduced in developmentally younger regions. they suggested that this phenomenon might be due to a fast-acting regulatory mechanism in the host that prevented excessive nodulation. however, the molecular mechanism of this fast-acting regulatory response remains uncertain. here, we sought to elucidate components of this regulato ...201323335614
conditional requirement for exopolysaccharide in the mesorhizobium-lotus symbiosis.rhizobial surface polysaccharides are required for nodule formation on the roots of at least some legumes but the mechanisms by which they act are yet to be determined. as a first step to investigate the function of exopolysaccharide (eps) in the formation of determinate nodules, we isolated mesorhizobium loti mutants affected in various steps of eps biosynthesis and characterized their symbiotic phenotypes on two lotus spp. the wild-type m. loti r7a produced both high molecular weight eps and l ...201323134480
a widely conserved molecular switch controls quorum sensing and symbiosis island transfer in mesorhizobium loti through expression of a novel antiactivator.icemlsym(r7a) of mesorhizobium loti is an integrative and conjugative element (ice) that confers the ability to form a nitrogen-fixing symbiosis with lotus species. horizontal transfer is activated by trar and n-acyl-homoserine lactone (ahl), which can stimulate ice excision in 100% of cells. however, in wild-type cultures, the ice is excised at low frequency. here we show that qsem, a widely conserved ice-encoded protein, is an antiactivator of trar. mutation of qsem resulted in trar-dependent ...201323106190
mesorhizobium sangaii sp. nov., isolated from the root nodules of astragalus luteolus and astragalus ernestii.our previous published data indicated that the two rhizobial strains scau7(t) and scau27, which were isolated from the root nodules of astragalus luteolus and astragalus ernestii respectively, in sichuan province, china, might be novel species of the genus mesorhizobium. their exact taxonomic position was determined in the present study by using polyphasic approaches. comparative analysis of nearly full-length 16s rrna gene sequences showed that these strains belonged to the genus mesorhizobium, ...201323315406
mesorhizobium qingshengii sp. nov., isolated from effective nodules of astragalus sinicus.in a study on the diversity of rhizobia isolated from root nodules of astragalus sinicus, five strains showed identical 16s rrna gene sequences. they were related most closely to the type strains of mesorhizobium loti, mesorhizobium shangrilense, mesorhizobium ciceri and mesorhizobium australicum, with sequence similarities of 99.6-99.8%. a polyphasic approach, including 16s-23s intergenic spacer (igs) rflp, comparative sequence analysis of 16s rrna, atpd, glnii and reca genes, dna-dna hybridiza ...201323041644
quorum sensing and self-quorum quenching in the intracellular pathogen brucellamelitensis.brucella quorum sensing has been described as an important regulatory system controlling crucial virulence determinants such as the virb type iv secretion system and the flagellar genes. however, the basis of quorum sensing, namely the production of autoinducers in brucella has been questioned. here, we report data obtained from the use of a genetic tool allowing the in situ detection of long-chain n-acyl-homoserine lactones (ahl) activity at single bacterium level in brucella melitensis. these ...201324349302
catalytic mechanism of short ethoxy chain nonylphenol dehydrogenase belonging to a polyethylene glycol dehydrogenase group in the gmc oxidoreductase family.ethoxy (eo) chain nonylphenol dehydrogenase (npeo-dh) from ensifer sp. as08 and eo chain octylphenol dehydrogenase from pseudomonas putida share common molecular characteristics with polyethylene glycol (peg) dehydrogenases (peg-dh) and comprise a peg-dh subgroup in the family of glucose-methanol-choline (gmc) oxidoreductases that includes glucose/alcohol oxidase and glucose/choline dehydrogenase. three-dimensional (3d) molecular modeling suggested that differences in the size, secondary structu ...201323306149
spatio-temporal expression patterns of arabidopsis thaliana and medicago truncatula defensin-like genes.plant genomes contain several hundred defensin-like (defl) genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. little is known about the expression patterns or functions of many defls because most were discovered recently and hence are not well represented on standard microarrays. we designed a custom affymetrix chip consisting of probe sets for 317 and 684 defls from arabidopsis thaliana and medicago truncatula, respectively for ...201323527067
profligate biotin synthesis in α-proteobacteria - a developing or degenerating regulatory system?biotin (vitamin h) is a key enzyme cofactor required in all three domains of life. although this cofactor was discovered over 70 years ago and has long been recognized as an essential nutrient for animals, our knowledge of the strategies bacteria use to sense biotin demand is very limited. the paradigm mechanism is that of escherichia coli in which bira protein, the prototypical bi-functional biotin protein ligase, both covalently attaches biotin to the acceptor proteins of central metabolism an ...201323387333
mutualistic co-evolution of type iii effector genes in sinorhizobium fredii and bradyrhizobium japonicum.two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. in one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. in the opposing model, conflicts between mutualist and host are largely resolved and the interaction is characterized by evolutionary stasis. we tested these opposing frameworks in two line ...201323468637
rhizobial infection does not require cortical expression of upstream common symbiosis genes responsible for the induction of ca(2+) spiking.for the establishment of an effective root nodule symbiosis, a coordinated regulation of the infection processes between the epidermis and cortex is required. however, it remains unclear whether the symbiotic genes identified so far are involved in epidermal and/or cortical infection, e.g. epidermal and cortical infection thread formation or cortical cell division. to analyze the symbiotic gene requirements of the infection process, we have developed an epidermis-specific expression system (pepi ...201324329948
rhizobial infection does not require cortical expression of upstream common symbiosis genes responsible for the induction of ca(2+) spiking.for the establishment of an effective root nodule symbiosis, a coordinated regulation of the infection processes between the epidermis and cortex is required. however, it remains unclear whether the symbiotic genes identified so far are involved in epidermal and/or cortical infection, e.g. epidermal and cortical infection thread formation or cortical cell division. to analyze the symbiotic gene requirements of the infection process, we have developed an epidermis-specific expression system (pepi ...201324329948
nodule inception directly targets nf-y subunit genes to regulate essential processes of root nodule development in lotus japonicus.the interactions of legumes with symbiotic nitrogen-fixing bacteria cause the formation of specialized lateral root organs called root nodules. it has been postulated that this root nodule symbiosis system has recruited factors that act in early signaling pathways (common sym genes) partly from the ancestral mycorrhizal symbiosis. however, the origins of factors needed for root nodule organogenesis are largely unknown. nodule inception (nin) is a nodulation-specific gene that encodes a putative ...201323555278
isolation and characterization of two novel bacteria afipia cberi and mesorhizobium hominis from blood of a patient afflicted with fatal pulmonary illness.we recently isolated and discovered new bradyrhizobiaceae microbes from the cryopreserved culture broth of blood samples from 3 patients with poorly defined illnesses using modified sp4 media and culture conditions coupled with genomic sequencing. using a similar protocol, we studied a previously cryopreserved culture broth of blood sample from a patient who had succumbed to an acute onset of fulminant pulmonary illness. we report that two phases of microbial growth were observed in the re-initi ...201324367538
cyanobase and rhizobase: databases of manually curated annotations for cyanobacterial and rhizobial genomes.to understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. we have extended cyanobase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed rhizobase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. both databases focus on the representation and reusability of reference genome a ...201324275496
cyanobase and rhizobase: databases of manually curated annotations for cyanobacterial and rhizobial genomes.to understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. we have extended cyanobase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed rhizobase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. both databases focus on the representation and reusability of reference genome a ...201324275496
hijacking of leguminous nodulation signaling by the rhizobial type iii secretion system.root-nodule symbiosis between leguminous plants and nitrogen-fixing bacteria (rhizobia) involves molecular communication between the two partners. key components for the establishment of symbiosis are rhizobium-derived lipochitooligosaccharides (nod factors; nfs) and their leguminous receptors (nfrs) that initiate nodule development and bacterial entry. here we demonstrate that the soybean microsymbiont bradyrhizobium elkanii uses the type iii secretion system (t3ss), which is known for its deli ...201324082124
disclosure of the differences of mesorhizobium loti under the free-living and symbiotic conditions by comparative proteome analysis without bacteroid isolation.rhizobia are symbiotic nitrogen-fixing soil bacteria that show a symbiotic relationship with their host legume. rhizobia have 2 different physiological conditions: a free-living condition in soil, and a symbiotic nitrogen-fixing condition in the nodule. the lifestyle of rhizobia remains largely unknown, although genome and transcriptome analyses have been carried out. to clarify the lifestyle of bacteria, proteome analysis is necessary because the protein profile directly reflects in vivo reacti ...201323898917
proteogenomic analysis of bradyrhizobium japonicum usda110 using genosuite, an automated multi-algorithmic pipeline.we present genosuite, an integrated proteogenomic pipeline to validate, refine and discover protein coding genes using high-throughput mass spectrometry (ms) data from prokaryotes. to demonstrate the effectiveness of genosuite, we analyzed proteomics data of bradyrhizobium japonicum (usda110), a model organism to study agriculturally important rhizobium-legume symbiosis. our analysis confirmed 31% of known genes, refined 49 gene models for their translation initiation site (tis) and discovered 5 ...201323882027
genome analysis suggests that the soil oligotrophic bacterium agromonas oligotrophica (bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of aeschynomene indica.agromonas oligotrophica (bradyrhizobium oligotrophicum) s58(t) is a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. here, the complete genome sequence of s58 was determined. the s58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average gc content of 65.1% lacking nodabc genes and the typical symbiosis island. the genome showed a high level of similarity to the genomes of bradyrhizobium sp. ...201323396330
comparative genomics of the core and accessory genomes of 48 sinorhizobium strains comprising five genospecies.the sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. while the alfalfa symbiont sinorhizobium meliloti rm 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group.201323425606
the nifa-rpon regulon of mesorhizobium loti strain r7a and its symbiotic activation by a novel laci/galr-family regulator.mesorhizobium loti is the microsymbiont of lotus species, including the model legume l. japonicus. m. loti differs from other rhizobia in that it contains two copies of the key nitrogen fixation regulatory gene nifa, nifa1 and nifa2, both of which are located on the symbiosis island icemlsym(r7a). m. loti r7a also contains two rpon genes, rpon1 located on the chromosome outside of icemlsym(r7a) and rpon2 that is located on icemlsym(r7a). the aims of the current work were to establish how nifa ex ...201323308282
genetic characterization of a novel rhizobial plasmid conjugation system in rhizobium leguminosarum bv. viciae strain vf39sm.rhizobium leguminosarum strain vf39sm contains two plasmids that have previously been shown to be self-transmissible by conjugation. one of these plasmids, prlevf39b, is shown in this study to carry a set of plasmid transfer genes that differs significantly from conjugation systems previously studied in the rhizobia but is similar to an uncharacterized set of genes found in r. leguminosarum bv. trifolii strain wsm2304. the entire sequence of the transfer region on prlevf39b was determined as par ...201323144250
structural insight into l-ribulose 3-epimerase from mesorhizobium loti.l-ribulose 3-epimerase (l-re) from mesorhizobium loti has been identified as the first ketose 3-epimerase that shows the highest observed activity towards ketopentoses. in the present study, the crystal structure of the enzyme was determined to 2.7 å resolution. the asymmetric unit contained two homotetramers with the monomer folded into an (α/β)8-barrel carrying four additional short α-helices. the overall structure of m. loti l-re showed significant similarity to the structures of ketose 3-epi ...201324311575
prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment.the commercial availability of next generation sequencing (ngs) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with ngs technologies. studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which m ...201324046766
engineering rhizobial bioinoculants: a strategy to improve iron nutrition.under field conditions, inoculated rhizobial strains are at a survival disadvantage as compared to indigenous strains. in order to out-compete native rhizobia it is not only important to develop strong nodulation efficiency but also increase their competence in the soil and rhizosphere. competitive survival of the inoculated strain may be improved by employing strain selection and by genetic engineering of superior nitrogen fixing strains. iron sufficiency is an important factor determining the ...201324319357
an engineered community approach for industrial cultivation of microalgae.although no species lives in isolation in nature, efforts to grow organisms for use in biotechnology have generally focused on a single-species approach, particularly where a product is required at high purity. in such scenarios, preventing the establishment of contaminants requires considerable effort that is economically justified. however, for some applications in biotechnology where the focus is on lower-margin biofuel production, axenic culture is not necessary, provided yields of the desir ...201425729339
functional conservation of the capacity for ent-kaurene biosynthesis and an associated operon in certain rhizobia.bacterial interactions with plants are accompanied by complex signal exchange processes. previously, the nitrogen-fixing symbiotic (rhizo)bacterium bradyrhizobium japonicum was found to carry adjacent genes encoding two sequentially acting diterpene cyclases that together transform geranylgeranyl diphosphate to ent-kaurene, the olefin precursor to the gibberellin plant hormones. species from the three other major genera of rhizobia were found to have homologous terpene synthase genes. cloning an ...201424142247
genes encoding conserved hypothetical proteins localized in the conjugative transfer region of plasmid pret42a from rhizobium etli cfn42 participate in modulating transfer and affect conjugation from different donors.among sequenced genomes, it is common to find a high proportion of genes encoding proteins that cannot be assigned a known function. in bacterial genomes, genes related to a similar function are often located in contiguous regions. the presence of genes encoding conserved hypothetical proteins (chp) in such a region may suggest that they are related to that particular function. plasmid pret42a from rhizobium etli cfn42 is a conjugative plasmid containing a segment of approximately 30 kb encoding ...201425642223
genes encoding conserved hypothetical proteins localized in the conjugative transfer region of plasmid pret42a from rhizobium etli cfn42 participate in modulating transfer and affect conjugation from different donors.among sequenced genomes, it is common to find a high proportion of genes encoding proteins that cannot be assigned a known function. in bacterial genomes, genes related to a similar function are often located in contiguous regions. the presence of genes encoding conserved hypothetical proteins (chp) in such a region may suggest that they are related to that particular function. plasmid pret42a from rhizobium etli cfn42 is a conjugative plasmid containing a segment of approximately 30 kb encoding ...201425642223
characterization of rhizobium grahamii extrachromosomal replicons and their transfer among rhizobia.rhizobium grahamii belongs to a new phylogenetic group of rhizobia together with rhizobium mesoamericanum and other species. r. grahamii has a broad-host-range that includes leucaena leucocephala and phaseolus vulgaris, although it is a poor competitor for p. vulgaris nodulation in the presence of rhizobium etli or rhizobium phaseoli strains. this work analyzed the genome sequence and transfer properties of r. grahamii plasmids.201424397311
the use of fosmid metagenomic libraries in preliminary screening for various biological activities.it is generally believed that there are many natural sources of as yet unknown bioactive compounds with a high biotechnological potential. however, the common method based on the use of cell extracts in the preliminary screening for particular molecules or activities is problematic as amounts of obtained compounds may be low, and such experiments are hardly reproducible. therefore, the aim of this work was to test whether a novel strategy to search for previously unknown biological activities ca ...201425048369
relationship between soil type and n₂o reductase genotype (nosz) of indigenous soybean bradyrhizobia: nosz-minus populations are dominant in andosols.bradyrhizobium japonicum strains that have the nosz gene, which encodes n2o reductase, are able to mitigate n2o emissions from soils (15). to examine the distribution of nosz genotypes among japanese indigenous soybean bradyrhizobia, we isolated bradyrhizobia from the root nodules of soybean plants inoculated with 32 different soils and analyzed their nosz and nodc genotypes. the 1556 resultant isolates were classified into the nosz+/nodc+ genotype (855 isolates) and nosz-/nodc+ genotype (701 is ...201425476067
ectopic expression of mir156 represses nodulation and causes morphological and developmental changes in lotus japonicus.the effects of microrna156 overexpression on general plant architecture, branching, flowering time and nodulation were investigated in the model legume, lotus japonicus. we cloned an mir156 homolog, ljmir156a, from l. japonicus, and investigated its squamosa promoter binding protein like (spl) genes and its biological function at enhancing vegetative biomass yield, extending flowering time, and its impact on nodulation. thirteen potential targets for ljmir156 were identified in vitro and their e ...201425293935
ectopic expression of mir156 represses nodulation and causes morphological and developmental changes in lotus japonicus.the effects of microrna156 overexpression on general plant architecture, branching, flowering time and nodulation were investigated in the model legume, lotus japonicus. we cloned an mir156 homolog, ljmir156a, from l. japonicus, and investigated its squamosa promoter binding protein like (spl) genes and its biological function at enhancing vegetative biomass yield, extending flowering time, and its impact on nodulation. thirteen potential targets for ljmir156 were identified in vitro and their e ...201425293935
rna-seq analysis of the multipartite genome of rhizobium etli ce3 shows different replicon contributions under heat and saline shock.regulation of transcription is essential for any organism and rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. this bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (phaseolus vulgaris) in a symbiotic relationship. abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of r. etli and therefore its symbiotic interaction with p. vulgaris. however, it is still unc ...201425201548
differing courses of genetic evolution of bradyrhizobium inoculants as revealed by long-term molecular tracing in acacia mangium plantations.introducing nitrogen-fixing bacteria as an inoculum in association with legume crops is a common practice in agriculture. however, the question of the evolution of these introduced microorganisms remains crucial, both in terms of microbial ecology and agronomy. we explored this question by analyzing the genetic and symbiotic evolution of two bradyrhizobium strains inoculated on acacia mangium in malaysia and senegal 15 and 5 years, respectively, after their introduction. based on typing of sever ...201425002434
proteomic analysis of free-living bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis.strain cpac 7 (=semia 5080) was recently reclassified into the new species bradyrhizobium diazoefficiens; due to its outstanding efficiency in fixing nitrogen, it has been used in commercial inoculants for application to crops of soybean [glycine max (l.) merr.] in brazil and other south american countries. although the efficiency of b. diazoefficiens inoculant strains is well recognized, few data on their protein expression are available.201425086822
identification of a dominant gene in medicago truncatula that restricts nodulation by sinorhizobium meliloti strain rm41.leguminous plants are able to form a root nodule symbiosis with nitrogen-fixing soil bacteria called rhizobia. this symbiotic association shows a high level of specificity. beyond the specificity for the legume family, individual legume species/genotypes can only interact with certain restricted group of bacterial species or strains. specificity in this system is regulated by complex signal exchange between the two symbiotic partners and thus multiple genetic mechanisms could be involved in the ...201424934080
comparative genomics of bradyrhizobium japonicum cpac 15 and bradyrhizobium diazoefficiens cpac 7: elite model strains for understanding symbiotic performance with soybean.the soybean-bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. b. japonicum cpac 15 (=semia 5079) is outstanding in its saprophytic capacity and competitiveness, whereas b. diazoefficiens cpac 7 (=semia 5080) is known for its high efficiency in fixing nitrogen. both are well ada ...201424888481
the role of symbiotic nitrogen fixation in sustainable production of biofuels.with the ever-increasing population of the world (expected to reach 9.6 billion by 2050), and altered life style, comes an increased demand for food, fuel and fiber. however, scarcity of land, water and energy accompanied by climate change means that to produce enough to meet the demands is getting increasingly challenging. today we must use every avenue from science and technology available to address these challenges. the natural process of symbiotic nitrogen fixation, whereby plants such as l ...201424786096
metabolic and functional diversity of saponins, biosynthetic intermediates and semi-synthetic derivatives.saponins are widely distributed plant natural products with vast structural and functional diversity. they are typically composed of a hydrophobic aglycone, which is extensively decorated with functional groups prior to the addition of hydrophilic sugar moieties, to result in surface-active amphipathic compounds. the saponins are broadly classified as triterpenoids, steroids or steroidal glycoalkaloids, based on the aglycone structure from which they are derived. the saponins and their biosynthe ...201425286183
nodule inception creates a long-distance negative feedback loop involved in homeostatic regulation of nodule organ production.autoregulatory negative-feedback loops play important roles in fine-balancing tissue and organ development. such loops are composed of short-range intercellular signaling pathways via cell-cell communications. on the other hand, leguminous plants use a long-distance negative-feedback system involving root-shoot communication to control the number of root nodules, root lateral organs that harbor symbiotic nitrogen-fixing bacteria known as rhizobia. this feedback system, known as autoregulation of ...201425246578
mir171h restricts root symbioses and shows like its target nsp2 a complex transcriptional regulation in medicago truncatula.legumes have the unique capability to undergo root nodule and arbuscular mycorrhizal symbiosis. both types of root endosymbiosis are regulated by nsp2, which is a target of microrna171h (mir171h). although, recent data implies that mir171h specifically restricts arbuscular mycorrhizal symbiosis in the root elongation zone of medicago truncatula roots, there is limited knowledge available about the spatio-temporal regulation of mir171h expression at different physiological and symbiotic condition ...201425928247
lotus japonicus sunergos1 encodes a predicted subunit a of a dna topoisomerase vi that is required for nodule differentiation and accommodation of rhizobial infection.a symbiotic mutant of lotus japonicus, called sunergos1-1 (suner1-1), originated from a har1-1 suppressor screen. suner1-1 supports epidermal infection by mesorhizobium loti and initiates cell divisions for organogenesis of nodule primordia. however, these processes appear to be temporarily stalled early during symbiotic interaction, leading to a low nodule number phenotype. this defect is ephemeral and near wild-type nodule numbers are reached by suner1-1 at a later point after infection. using ...201424661810
a positive regulator of nodule organogenesis, nodule inception, acts as a negative regulator of rhizobial infection in lotus japonicus.legume-rhizobium symbiosis occurs in specialized root organs called nodules. to establish the symbiosis, two major genetically controlled events, rhizobial infection and organogenesis, must occur. for a successful symbiosis, it is essential that the two phenomena proceed simultaneously in different root tissues. although several symbiotic genes have been identified during genetic screenings of nonsymbiotic mutants, most of the mutants harbor defects in both infection and organogenesis pathways, ...201424722550
genome sequence of ensifer adhaerens ov14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes.recently it has been shown that ensifer adhaerens can be used as a plant transformation technology, transferring genes into several plant genomes when equipped with a ti plasmid. for this study, we have sequenced the genome of ensifer adhaerens ov14 (ov14) and compared it with those of agrobacterium tumefaciens c58 (c58) and sinorhizobium meliloti 1021 (1021); the latter of which has also demonstrated a capacity to genetically transform crop genomes, albeit at significantly reduced frequencies.201424708309
lotus japonicus cytokinin receptors work partially redundantly to mediate nodule formation.previous analysis of the lotus histidine kinase1 (lhk1) cytokinin receptor gene has shown that it is required and also sufficient for nodule formation in lotus japonicus. the l. japonicus mutant carrying the loss-of-function lhk1-1 allele is hyperinfected by its symbiotic partner, mesorhizobium loti, in the initial absence of nodule organogenesis. at a later time point following bacterial infection, lhk1-1 develops a limited number of nodules, suggesting the presence of an lhk1-independent mecha ...201424585837
genome features of the endophytic actinobacterium micromonospora lupini strain lupac 08: on the process of adaptation to an endophytic life style?endophytic microorganisms live inside plants for at least part of their life cycle. according to their life strategies, bacterial endophytes can be classified as "obligate" or "facultative". reports that members of the genus micromonospora, gram-positive actinobacteria, are normal occupants of nitrogen-fixing nodules has opened up a question as to what is the ecological role of these bacteria in interactions with nitrogen-fixing plants and whether it is in a process of adaptation from a terrestr ...201425268993
characterisation of salrab a salicylic acid inducible positively regulated efflux system of rhizobium leguminosarum bv viciae 3841.salicylic acid is an important signalling molecule in plant-microbe defence and symbiosis. we analysed the transcriptional responses of the nitrogen fixing plant symbiont, rhizobium leguminosarum bv viciae 3841 to salicylic acid. two mfs-type multicomponent efflux systems were induced in response to salicylic acid, rmrab and the hitherto undescribed system salrab. based on sequence similarity sala and salb encode a membrane fusion and inner membrane protein respectively. salab are positively reg ...201425133394
soil-borne microbial functional structure across different land uses.land use change alters the structure and composition of microbial communities. however, the links between environmental factors and microbial functions are not well understood. here we interrogated the functional structure of soil microbial communities across different land uses. in a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was c :  ...201425177716
structural characterization and function determination of a nonspecific carboxylate esterase from the amidohydrolase superfamily with a promiscuous ability to hydrolyze methylphosphonate esters.the uncharacterized protein rsp3690 from rhodobacter sphaeroides is a member of the amidohydrolase superfamily of enzymes. in this investigation the gene for rsp3690 was expressed in escherichia coli and purified to homogeneity, and the three-dimensional structure was determined to a resolution of 1.8 å. the protein folds as a distorted (β/α)8-barrel, and the subunits associate as a homotetramer. the active site is localized to the c-terminal end of the β-barrel and is highlighted by the formati ...201424832101
comparative genomic analysis of n2-fixing and non-n2-fixing paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes.we provide here a comparative genome analysis of 31 strains within the genus paenibacillus including 11 new genomic sequences of n2-fixing strains. the heterogeneity of the 31 genomes (15 n2-fixing and 16 non-n2-fixing paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. large numbers of transposable elements might be related to the heterogeneity. we discovered that a minimal and compact nif cluster comprising ...201424651173
utilization of glyphosate as phosphate source: biochemistry and genetics of bacterial carbon-phosphorus lyase.after several decades of use of glyphosate, the active ingredient in weed killers such as roundup, in fields, forests, and gardens, the biochemical pathway of transformation of glyphosate phosphorus to a useful phosphorus source for microorganisms has been disclosed. glyphosate is a member of a large group of chemicals, phosphonic acids or phosphonates, which are characterized by a carbon-phosphorus bond. this is in contrast to the general phosphorus compounds utilized and metabolized by microor ...201424600043
genomic analysis of cyclic-di-gmp-related genes in rhizobial type strains and functional analysis in rhizobium etli.rhizobia are soil bacteria that can fix nitrogen in symbiosis with leguminous plants or exist free living in the rhizosphere. crucial to their complex lifestyle is the ability to sense and respond to diverse environmental stimuli, requiring elaborate signaling pathways. in the majority of bacteria, the nucleotide-based second messenger cyclic diguanosine monophosphate (c-di-gmp) is involved in signal transduction. surprisingly, little is known about the importance of c-di-gmp signaling in rhizob ...201424728599
chemically synthesized 58-mer lysm domain binds lipochitin oligosaccharide.recognition of carbohydrates by proteins is a ubiquitous biochemical process. in legume-rhizobium symbiosis, lipochitin oligosaccharides, also referred to as nodulation (nod) factors, function as primary rhizobial signal molecules to trigger root nodule development. perception of these signal molecules is receptor mediated, and nod factor receptor 5 (nfr5) from the model legume lotus japonicus is predicted to contain three lysm domain binding sites. here we studied the interactions between nod f ...201425154732
genes commonly involved in acid tolerance are not overexpressed in the plant microsymbiont mesorhizobium loti maff303099 upon acidic shock.rhizobia are legume bacterial symbionts that fix nitrogen in the root nodules of plants. the aim of the present study was to investigate the global transcriptional response of rhizobia upon an acidic shock. changes in the transcriptome of cells of mesorhizobium loti strain maff303099 upon an acidic shock at ph 3 for 30 min were analysed. from a total of 7,231 protein-coding genes, 433 were found to be differentially expressed upon acidic shock, of which 322 were overexpressed. although most of t ...201424931309
functional surface engineering by nucleotide-modulated potassium channel insertion into polymer membranes attached to solid supports.planar solid-supported membranes based on amphiphilic block copolymers represent promising systems for the artificial creation of structural surfaces. here we introduce a method for engineering functional planar solid-supported membranes through insertion of active biomolecules. we show that membranes based on poly(dimethylsiloxane)-block-poly(2-methyl-2-oxazoline) (pdms-b-pmoxa) amphiphilic diblock copolymers, which mimic natural membranes, are suitable for hosting biomolecules. our strategy al ...201424912817
knockdown of ljald1, agd2-like defense response protein 1, influences plant growth and nodulation in lotus japonicus.the discovery of the enzyme l,l-diaminopimelate aminotransferase (ll-dap-at, ec 2.6.1.83) uncovered a unique step in the l-lysine biosynthesis pathway in plants. in arabidopsis thaliana, ll-dap-at has been shown to play a key role in plant-pathogen interactions by regulation of the salicylic acid (sa) signaling pathway. here, a full-length cdna of ll-dap-at named as ljald1 from lotus japonicus (regel) larsen was isolated. the deduced amino acid sequence shares 67% identity with the arabidopsis a ...201424797909
microtubule array formation during root hair infection thread initiation and elongation in the mesorhizobium-lotus symbiosis.nuclear migration during infection thread (it) development in root hairs is essential for legume-rhizobium symbiosis. however, little is known about the relationships between it formation, nuclear migration, and microtubule dynamics. to this aim, we used transgenic lotus japonicus expressing a fusion of the green fluorescent protein and tubulin-α6 from arabidopsis thaliana to visualize in vivo dynamics of cortical microtubules (cmt) and endoplasmic microtubules (emts) in root hairs in the presen ...201424488109
glutamine synthetase i-deficiency in mesorhizobium loti differentially affects nodule development and activity in lotus japonicus.in this study, we focused on the effect of glutamine synthetase (gsi) activity in mesorhizobium loti on the symbiosis between the host plant, lotus japonicus, and the bacteroids. we used a signature-tagged mutant of m. loti (stm30) with a transposon inserted into the gsi (mll0343) gene. the l. japonicus plants inoculated with stm30 had significantly more nodules, and the occurrence of senesced nodules was much higher than in plants inoculated with the wild-type. the acetylene reduction activity ...201424484964
endoplasmic reticulum-targeted gfp reveals er remodeling in mesorhizobium-treated lotus japonicus root hairs during root hair curling and infection thread formation.the endoplasmic reticulum (er) of the model legume lotus japonicus was visualized using green fluorescent protein (gfp) fused with the kdel sequence to investigate the changes in the root hair cortical er in the presence or absence of mesorhizobium loti using live fluorescence imaging. uninoculated root hairs displayed dynamic forms of er, ranging from a highly condensed form to an open reticulum. in the presence of m. loti, a highly dynamic condensed form of the er linked with the nucleus was f ...201424337802
knockdown of ljipt3 influences nodule development in lotus japonicus.cytokinins play important roles in legume-rhizobia symbiosis. here we report isolation of six genes encoding isopentenyl transferase (ipt) from lotus japonicus, which catalyze the rate-limiting step of cytokinin biosynthesis. the ljipt3 gene was found to be up-regulated in infected roots and mature nodules. histochemical analysis demonstrated expression of pro(ljipt3):gus (β-glucuronidase) in vegetative and reproductive organs, and was especially high in the vascular bundles of roots. when inocu ...201424285753
the trehalose utilization gene thua ortholog in mesorhizobium loti does not influence competitiveness for nodulation on lotus spp.competitiveness for nodulation is a desirable trait in rhizobia strains used as inoculant. in sinorhizobium meliloti 1021 mutation in either of the trehalose utilization genes thua or thub influences its competitiveness for root colonization and nodule occupancy depending on the interacting host. we have therefore investigated whether mutation in the thua ortholog in mesorhizobium loti maff303099 also leads to a similar competitive phenotype on its hosts. the results show that m. loti thua mutan ...201424142427
biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics.the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ...201424688489
biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics.the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ...201424688489
a second-generation protein-protein interaction network of helicobacter pylori.helicobacter pylori infections cause gastric ulcers and play a major role in the development of gastric cancer. in 2001, the first protein interactome was published for this species, revealing over 1500 binary protein interactions resulting from 261 yeast two-hybrid screens. here we roughly double the number of previously published interactions using an orfeome-based, proteome-wide yeast two-hybrid screening strategy. we identified a total of 1515 protein-protein interactions, of which 1461 are ...201424627523
conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families.the heme-copper oxidase (hco) superfamily includes hcos in aerobic respiratory chains and nitric oxide reductases (nors) in the denitrification pathway. the hco/nor catalytic subunit has a core structure consisting of 12 transmembrane helices (tmhs) arranged in three-fold rotational pseudosymmetry, with six conserved histidines for heme and metal binding. using sensitive sequence similarity searches, we detected a number of novel hco/nor homologs and named them hco homology (hcoh) proteins. seve ...201424931479
membrane lipids in agrobacterium tumefaciens: biosynthetic pathways and importance for pathogenesis.many cellular processes critically depend on the membrane composition. in this review, we focus on the biosynthesis and physiological roles of membrane lipids in the plant pathogen agrobacterium tumefaciens. the major components of a. tumefaciens membranes are the phospholipids (pls), phosphatidylethanolamine (pe), phosphatidylglycerol, phosphatidylcholine (pc) and cardiolipin, and ornithine lipids (ols). under phosphate-limited conditions, the membrane composition shifts to phosphate-free lipid ...201424723930
a bifunctional glycosyltransferase from agrobacterium tumefaciens synthesizes monoglucosyl and glucuronosyl diacylglycerol under phosphate deprivation.glycolipids are mainly found in phototrophic organisms (like plants and cyanobacteria), in gram-positive bacteria, and a few other bacterial phyla. besides the function as bulk membrane lipids, they often play a role under phosphate deprivation as surrogates for phospholipids. the gram-negative agrobacterium tumefaciens accumulates four different glycolipids under phosphate deficiency, including digalactosyl diacylglycerol and glucosylgalactosyl diacylglycerol synthesized by a processive glycosy ...201424558041
coevolution of the atpase clpv, the sheath proteins tssb and tssc, and the accessory protein tagj/hsie1 distinguishes type vi secretion classes.the type vi secretion system (t6ss) is a bacterial nanomachine for the transport of effector molecules into prokaryotic and eukaryotic cells. it involves the assembly of a tubular structure composed of tssb and tssc that is similar to the tail sheath of bacteriophages. the sheath contracts to provide the energy needed for effector delivery. the aaa(+) atpase clpv disassembles the contracted sheath, which resets the systems for reassembly of an extended sheath that is ready to fire again. this me ...201425305017
diversity of nitrogen-fixing bacteria associated with switchgrass in the native tallgrass prairie of northern oklahoma.switchgrass (panicum virgatum l.) is a perennial c4 grass native to north america that is being developed as a feedstock for cellulosic ethanol production. industrial nitrogen fertilizers enhance switchgrass biomass production but add to production and environmental costs. a potential sustainable alternative source of nitrogen is biological nitrogen fixation. as a step in this direction, we studied the diversity of nitrogen-fixing bacteria (nfb) associated with native switchgrass plants from the ...201425002418
bacterial genome instability.bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile dna elements. this implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. in this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. we ...201424600039
occurrence of an unusual hopanoid-containing lipid a among lipopolysaccharides from bradyrhizobium species.the chemical structures of the unusual hopanoid-containing lipid a samples of the lipopolysaccharides (lps) from three strains of bradyrhizobium (slow-growing rhizobia) have been established. they differed considerably from other gram-negative bacteria in regards to the backbone structure, the number of ester-linked long chain hydroxylated fatty acids, as well as the presence of a tertiary residue that consisted of at least one molecule of carboxyl-bacteriohopanediol or its 2-methyl derivative. ...201425371196
new insights into 1-aminocyclopropane-1-carboxylate (acc) deaminase phylogeny, evolution and ecological significance.the main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (acc) deaminase, the activity of which represents one of the most important and studied mechanisms used by plant growth-promoting microorganisms. the acc deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis w ...201424905353
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 ...201425480683
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