| effect of soybean coumestrol on bradyrhizobium japonicum nodulation ability, biofilm formation, and transcriptional profile. | flavonoids, secondary plant metabolites which mainly have a polyphenolic structure, play an important role in plant-microbe communications for nitrogen-fixing symbiosis. among 10 polyphenolic compounds isolated from soybean roots in our previous study, coumestrol showed the highest antioxidant activity. in this study, its effect on the soybean nodulation was tested. the soybean symbiont bradyrhizobium japonicum usda110 pretreated with 20 μm coumestrol enhanced soybean nodulation by increasing th ... | 2012 | 22307307 |
| 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 |
| structures of nodz α1,6-fucosyltransferase in complex with gdp and gdp-fucose. | rhizobial nodz α1,6-fucosyltransferase (α1,6-fuct) catalyzes the transfer of the fucose (fuc) moiety from guanosine 5'-diphosphate-β-l-fucose to the reducing end of the chitin oligosaccharide core during nod-factor (nf) biosynthesis. nf is a key signalling molecule required for successful symbiosis with a legume host for atmospheric nitrogen fixation. to date, only two α1,6-fuct structures have been determined, both without any donor or acceptor molecule that could highlight the structural backg ... | 2012 | 22281745 |
| comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia. | tropical aquatic species of the legume genus aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (nd) or a nod gene-independent (ni) pathway to enter into symbiosis with legumes. in this study we used a comparative genomics approach on nine aeschynomene symbionts representative of their phylogenetic diversity. we produced draft genomes of bradyrhizobial strains representing differen ... | 2012 | 24704842 |
| comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia. | tropical aquatic species of the legume genus aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (nd) or a nod gene-independent (ni) pathway to enter into symbiosis with legumes. in this study we used a comparative genomics approach on nine aeschynomene symbionts representative of their phylogenetic diversity. we produced draft genomes of bradyrhizobial strains representing differen ... | 2012 | 24704842 |
| molecular cloning and characterization of a newly isolated pyrethroid-degrading esterase gene from a genomic library of ochrobactrum anthropi yz-1. | a novel pyrethroid-degrading esterase gene pyty was isolated from the genomic library of ochrobactrum anthropi yz-1. it possesses an open reading frame (orf) of 897 bp. blast search showed that its deduced amino acid sequence shares moderate identities (30% to 46%) with most homologous esterases. phylogenetic analysis revealed that pyty is a member of the esterase vi family. pyty showed very low sequence similarity compared with reported pyrethroid-degrading genes. pyty was expressed, purified, ... | 2013 | 24155944 |
| microbial contents of vacuum cleaner bag dust and emitted bioaerosols and their implications for human exposure indoors. | vacuum cleaners can release large concentrations of particles, both in their exhaust air and from resuspension of settled dust. however, the size, variability, and microbial diversity of these emissions are unknown, despite evidence to suggest they may contribute to allergic responses and infection transmission indoors. this study aimed to evaluate bioaerosol emission from various vacuum cleaners. we sampled the air in an experimental flow tunnel where vacuum cleaners were run, and their airborn ... | 2013 | 23934489 |
| the nodulation factor hydrolase of medicago truncatula: characterization of an enzyme specifically cleaving rhizobial nodulation signals. | nodule formation induced by nitrogen-fixing rhizobia depends on bacterial nodulation factors (nfs), modified chitin oligosaccharides with a fatty acid moiety. certain nfs can be cleaved and inactivated by plant chitinases. however, the most abundant nf of sinorhizobium meliloti, an o-acetylated and sulfated tetramer, is resistant to hydrolysis by all plant chitinases tested so far. nevertheless, this nf is rapidly degraded in the host rhizosphere. here, we identify and characterize mtnfh1 (for m ... | 2013 | 24082029 |
| unusual spectral properties of bacteriophytochrome agp2 result from a deprotonation of the chromophore in the red-absorbing form pr. | phytochromes are widely distributed photoreceptors with a bilin chromophore that undergo a typical reversible photoconversion between the two spectrally different forms, pr and pfr. the phytochrome agp2 from agrobacterium tumefaciens belongs to the group of bathy phytochromes that have a pfr ground state as a result of the pr to pfr dark conversion. agp2 has untypical spectral properties in the pr form reminiscent of a deprotonated chromophore as confirmed by resonance raman spectroscopy. uv/vis ... | 2013 | 24036118 |
| 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 herbaspirillum seropedicae smr1 fnr orthologs controls the cytochrome composition of the electron transport chain. | the transcriptional regulatory protein fnr, acts as an intracellular redox sensor regulating a wide range of genes in response to changes in oxygen levels. genome sequencing of herbaspirillum seropedicae smr1 revealed the presence of three fnr-like genes. in this study we have constructed single, double and triple fnr deletion mutant strains of h. seropedicae. transcriptional profiling in combination with expression data from reporter fusions, together with spectroscopic analysis, demonstrates t ... | 2013 | 23996052 |
| high-resolution transcriptomic analyses of sinorhizobium sp. ngr234 bacteroids in determinate nodules of vigna unguiculata and indeterminate nodules of leucaena leucocephala. | the rhizobium-legume symbiosis is a model system for studying mutualistic interactions between bacteria and eukaryotes. sinorhizobium sp. ngr234 is distinguished by its ability to form either indeterminate nodules or determinate nodules with diverse legumes. here, we presented a high-resolution rna-seq transcriptomic analysis of ngr234 bacteroids in indeterminate nodules of leucaena leucocephala and determinate nodules of vigna unguiculata. in contrast to exponentially growing free-living bacter ... | 2013 | 23936444 |
| 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 |
| crystallization and preliminary x-ray diffraction studies of cyanuric acid hydrolase from azorhizobium caulinodans. | cyanuric acid is synthesized industrially and forms during the microbial metabolism of s-triazine herbicides. cyanuric acid is metabolized by some microorganisms via cyanuric acid hydrolase (cah), which opens the s-triazine ring as a prelude to further metabolism. cah is a member of the rare cyanuric acid hydrolase/barbiturase family. here, the crystallization and preliminary x-ray diffraction analysis of cah from azorhizobium caulinodans are reported. cah was cocrystallized with barbituric acid ... | 2013 | 23908033 |
| 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 |
| cyanuric acid hydrolase: evolutionary innovation by structural concatenation. | the cyanuric acid hydrolase, atzd, is the founding member of a newly identified family of ring-opening amidases. we report the first x-ray structure for this family, which is a novel fold (termed the 'toblerone' fold) that likely evolved via the concatenation of monomers of the trimeric yjgf superfamily and the acquisition of a metal binding site. structures of atzd with bound substrate (cyanuric acid) and inhibitors (phosphate, barbituric acid and melamine), along with mutagenesis studies, allo ... | 2013 | 23651355 |
| serologic prevalence of amoeba-associated microorganisms in intensive care unit pneumonia patients. | patients admitted to intensive care units are frequently exposed to pathogenic microorganisms present in their environment. exposure to these microbes may lead to the development of hospital-acquired infections that complicate the illness and may be fatal. amoeba-associated microorganisms (aams) are frequently isolated from hospital water networks and are reported to be associated to cases of community and hospital-acquired pneumonia. | 2013 | 23469263 |
| queuosine biosynthesis is required for sinorhizobium meliloti-induced cytoskeletal modifications on hela cells and symbiosis with medicago truncatula. | rhizobia are symbiotic soil bacteria able to intracellularly colonize legume nodule cells and form nitrogen-fixing symbiosomes therein. how the plant cell cytoskeleton reorganizes in response to rhizobium colonization has remained poorly understood especially because of the lack of an in vitro infection assay. here, we report on the use of the heterologous hela cell model to experimentally tackle this question. we observed that the model rhizobium sinorhizobium meliloti, and other rhizobia as we ... | 2013 | 23409119 |
| 2-nitrobenzoate 2-nitroreductase (nbaa) switches its substrate specificity from 2-nitrobenzoic acid to 2,4-dinitrobenzoic acid under oxidizing conditions. | 2-nitrobenzoate 2-nitroreductase (nbaa) of pseudomonas fluorescens strain ku-7 is a unique enzyme, transforming 2-nitrobenzoic acid (2-nba) and 2,4-dinitrobenzoic acid (2,4-dnba) to the 2-hydroxylamine compounds. sequence comparison reveals that nbaa contains a conserved cysteine residue at position 141 and two variable regions at amino acids 65 to 74 and 193 to 216. the truncated mutant δ65-74 exhibited markedly reduced activity toward 2,4-dnba, but its 2-nba reduction activity was unaffected; ... | 2013 | 23123905 |
| nitrogen-fixing rhizobial strains isolated from common bean seeds: phylogeny, physiology, and genome analysis. | rhizobial bacteria are commonly found in soil but also establish symbiotic relationships with legumes, inhabiting the root nodules, where they fix nitrogen. endophytic rhizobia have also been reported in the roots and stems of legumes and other plants. we isolated several rhizobial strains from the nodules of noninoculated bean plants and looked for their provenance in the interiors of the seeds. nine isolates were obtained, covering most known bean symbiont species, which belong to the rhizobiu ... | 2014 | 25002426 |
| homogalacturonan-modifying enzymes: structure, expression, and roles in plants. | understanding the changes affecting the plant cell wall is a key element in addressing its functional role in plant growth and in the response to stress. pectins, which are the main constituents of the primary cell wall in dicot species, play a central role in the control of cellular adhesion and thereby of the rheological properties of the wall. this is likely to be a major determinant of plant growth. how the discrete changes in pectin structure are mediated is thus a key issue in our understa ... | 2014 | 25056773 |
| 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 |
| genomic basis of symbiovar mimosae in rhizobium etli. | symbiosis genes (nod and nif) involved in nodulation and nitrogen fixation in legumes are plasmid-borne in rhizobium. rhizobial symbiotic variants (symbiovars) with distinct host specificity would depend on the type of symbiosis plasmid. in rhizobium etli or in rhizobium phaseoli, symbiovar phaseoli strains have the capacity to form nodules in phaseolus vulgaris while symbiovar mimosae confers a broad host range including different mimosa trees. | 2014 | 25005495 |
| mutation of prar in rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins. | in rhizobium leguminosarum bv. viciae, quorum-sensing is regulated by cinr, which induces the cinis operon. cini synthesizes an ahl, whereas cins inactivates prar, a repressor. mutation of prar enhanced biofilms in vitro. we developed a light (lux)-dependent assay of rhizobial attachment to roots and demonstrated that mutation of prar increased biofilms on pea roots. the prar mutant out-competed wild-type for infection of pea nodules in mixed inoculations. analysis of gene expression by microarr ... | 2014 | 24942546 |
| 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 |
| genome sequencing and annotation of afipia septicemium strain ohsu_ii. | we report the 5.1 mb noncontiguous draft genome of afipia septicemium strain ohsu_ii, isolated from blood of a female patient. the genome consists of 5,087,893 bp circular chromosome with no identifiable autonomous plasmid with a g + c content of 61.09% and contains 4898 protein-coding genes and 49 rna genes including 3 rrna genes and 46 trna genes. | 2014 | 25396117 |
| cyanuric acid hydrolase from azorhizobium caulinodans ors 571: crystal structure and insights into a new class of ser-lys dyad proteins. | cyanuric acid hydrolase (cah) catalyzes the hydrolytic ring-opening of cyanuric acid (2,4,6-trihydroxy-1,3,5-triazine), an intermediate in s-triazine bacterial degradation and a by-product from disinfection with trichloroisocyanuric acid. in the present study, an x-ray crystal structure of the cah-barbituric acid inhibitor complex from azorhizobium caulinodans ors 571 has been determined at 2.7 å resolution. the cah protein fold consists of three structurally homologous domains forming a β-barre ... | 2014 | 24915109 |
| the crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein cae31940 from proteobacterium bordetella bronchiseptica rb50, and evolutionary insight into the nmt1/thi5 family. | we report a 2.0 å structure of the cae31940 protein, a proteobacterial nmt1/thi5-like domain-containing protein. we also discuss the primary and tertiary structure similarity with its homologs. the highly conserved fggxmp motif was identified in cae31940, which corresponds to the gcccx motif located in the vicinity of the active center characteristic for thi5-like proteins found in yeast. this suggests that the fggxmp motif may be a unique hallmark of proteobacterial nmt1/thi5-like proteins. | 2014 | 24908050 |
| 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 |
| accumulation of n-acetylglucosamine oligomers in the plant cell wall affects plant architecture in a dose-dependent and conditional manner. | to study the effect of short n-acetylglucosamine (glcnac) oligosaccharides on the physiology of plants, n-acetylglucosaminyltransferase (nodc) of azorhizobium caulinodans was expressed in arabidopsis (arabidopsis thaliana). the corresponding enzyme catalyzes the polymerization of glcnac and, accordingly, β-1,4-glcnac oligomers accumulated in the plant. a phenotype characterized by difficulties in developing an inflorescence stem was visible when plants were grown for several weeks under short-da ... | 2014 | 24664205 |
| 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 |
| trna signatures reveal a polyphyletic origin of sar11 strains among alphaproteobacteria. | molecular phylogenetics and phylogenomics are subject to noise from horizontal gene transfer (hgt) and bias from convergence in macromolecular compositions. extensive variation in size, structure and base composition of alphaproteobacterial genomes has complicated their phylogenomics, sparking controversy over the origins and closest relatives of the sar11 strains. sar11 are highly abundant, cosmopolitan aquatic alphaproteobacteria with streamlined, a+t-biased genomes. a dominant view holds that ... | 2014 | 24586126 |
| genome-wide profiling of hfq-binding rnas uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in sinorhizobium meliloti. | the rna chaperone hfq is a global post-transcriptional regulator in bacteria. here, we used rnaseq to analyze rna populations from the legume symbiont sinorhizobium meliloti that were co-immunoprecipitated (coip-rna) with a flag-tagged hfq in five growth/stress conditions. hfq-bound transcripts (1315) were largely identified in stressed bacteria and derived from small rnas (srnas), both trans-encoded (6.4%) and antisense (asrnas; 6.3%), and mrnas (86%). pull-down with hfq recovered a small propo ... | 2014 | 24786641 |
| structural basis of thermal stability of the tungsten cofactor synthesis protein moab from pyrococcus furiosus. | molybdenum and tungsten cofactors share a similar pterin-based scaffold, which hosts an ene-dithiolate function being essential for the coordination of either molybdenum or tungsten. the biosynthesis of both cofactors involves a multistep pathway, which ends with the activation of the metal binding pterin (mpt) by adenylylation before the respective metal is incorporated. in the hyperthermophilic organism pyrococcus furiosus, the hexameric protein moab (pfumoab) has been shown to catalyse mpt-ad ... | 2014 | 24465852 |
| high-quality permanent draft genome sequence of ensifer medicae strain wsm244, a microsymbiont isolated from medicago polymorpha growing in alkaline soil. | ensifer medicae wsm244 is an aerobic, motile, gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of medicago species. wsm244 was isolated in 1979 from a nodule recovered from the roots of the annual medicago polymorpha l. growing in alkaline soil (ph 8.0) in tel afer, iraq. wsm244 is the only acid-sensitive e. medicae strain that has been sequenced to date. it is effective at fixing nitrogen with m. polymorpha l., as well as with more alkaline-a ... | 2015 | 26664655 |
| high-quality permanent draft genome sequence of bradyrhizobium sp. strain wsm1743 - an effective microsymbiont of an indigofera sp. growing in australia. | bradyrhizobium sp. strain wsm1743 is an aerobic, motile, gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of an indigofera sp. wsm1743 was isolated from a nodule recovered from the roots of an indigofera sp. growing 20 km north of carnarvon in australia. it is slow growing, tolerates up to 1 % nacl and is capable of growth at 37 °c. here we describe the features of bradyrhizobium sp. strain wsm1743, together with genome sequence information an ... | 2015 | 26512312 |
| high-quality permanent draft genome sequence of ensifer meliloti strain 4h41, an effective salt- and drought-tolerant microsymbiont of phaseolus vulgaris. | ensifer meliloti 4h41 is an aerobic, motile, gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of common bean (phaseolus vulgaris). strain 4h41 was isolated in 2002 from root nodules of p. vulgaris grown in south tunisia from the oasis of rjim-maatoug. strain 4h41 is salt- and drought-tolerant and highly effective at fixing nitrogen with p. vulgaris. here we describe the features of e. meliloti 4h41, together with genome sequence information an ... | 2015 | 26380038 |
| genomic characterization of sinorhizobium meliloti ak21, a wild isolate from the aral sea region. | the symbiotic, nitrogen-fixing bacterium sinorhizobium meliloti has been widely studied due to its ability to improve crop yields through direct interactions with leguminous plants. s. meliloti ak21 is a wild type strain that forms nodules on medicago plants in saline and drought conditions in the aral sea region. the aim of this work was to establish the genetic similarities and differences between s. meliloti ak21 and the reference strain s. meliloti 1021. comparative genome hybridization with ... | 2015 | 26090306 |
| high-quality permanent draft genome sequence of bradyrhizobium sp. ai1a-2; a microsymbiont of andira inermis discovered in costa rica. | bradyrhizobium sp. ai1a-2 is is an aerobic, motile, gram-negative, non-spore-forming rod that was isolated from an effective nitrogen fixing root nodule of andira inermis collected from tres piedras in costa rica. in this report we describe, for the first time, the genome sequence information and annotation of this legume microsymbiont. the 9,029,266 bp genome has a gc content of 62.56% with 247 contigs arranged into 246 scaffolds. the assembled genome contains 8,482 protein-coding genes and 102 ... | 2015 | 26380037 |
| 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 |
| paracoccus denitrificans possesses two bior homologs having a role in regulation of biotin metabolism. | recently, we determined that bior, the gntr family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent brucella melitensis and the plant pathogen agrobacterium tumefaciens. however, the scenario is unusual in paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. not only does it encode two bior homologs pden_1431 and pd ... | 2015 | 26037461 |
| candidatus frankia datiscae dg1, the actinobacterial microsymbiont of datisca glomerata, expresses the canonical nod genes nodabc in symbiosis with its host plant. | frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. phylogenetically, symbiotic frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. the strains of cluster ii which form symbioses with actinorhizal rosales and cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. the genome of the first representative of this cluster ... | 2015 | 26020781 |
| bacterial-induced calcium oscillations are common to nitrogen-fixing associations of nodulating legumes and nonlegumes. | plants that form root-nodule symbioses are within a monophyletic 'nitrogen-fixing' clade and associated signalling processes are shared with the arbuscular mycorrhizal symbiosis. central to symbiotic signalling are nuclear-associated oscillations in calcium ions (ca(2+) ), occurring in the root hairs of several legume species in response to the rhizobial nod factor signal. in this study we expanded the species analysed for activation of ca(2+) oscillations, including nonleguminous species within ... | 2015 | 26010117 |
| high-quality permanent draft genome sequence of bradyrhizobium sp. tv2a.2, a microsymbiont of tachigali versicolor discovered in barro colorado island of panama. | bradyrhizobiumsp. tv2a.2 is an aerobic, motile, gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of tachigali versicolor collected in barro colorado island of panama. here we describe the features of bradyrhizobiumsp. tv2a.2, together with high-quality permanent draft genome sequence information and annotation. the 8,496,279 bp high-quality draft genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding genes and 72 rna-on ... | 2015 | 26203338 |
| high-quality permanent draft genome sequence of bradyrhizobium sp. th.b2, a microsymbiont of amphicarpaea bracteata collected in johnson city, new york. | bradyrhizobium sp. th.b2 is an aerobic, motile, gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of amphicarpaea bracteata collected in johnson city, new york. here we describe the features of bradyrhizobium sp. th.b2, together with high-quality permanent draft genome sequence information and annotation. the 10,118,060 high-quality draft genome is arranged in 266 scaffolds of 274 contigs, contains 9,809 protein-coding genes and 108 rna-only enc ... | 2015 | 26203336 |
| role of root microbiota in plant productivity. | the growing human population requires increasing amounts of food, but modern agriculture has limited possibilities for increasing yields. new crop varieties may be bred to have increased yields and be more resistant to environmental stress and pests. however, they still require fertilization to supplement essential nutrients that are normally limited in the soil. soil microorganisms present an opportunity to reduce the requirement for inorganic fertilization in agriculture. microorganisms, due t ... | 2015 | 25908654 |
| the class iii cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways. | photolyases are proteins with an fad chromophore that repair uv-induced pyrimidine dimers on the dna in a light-dependent manner. the cyclobutane pyrimidine dimer class iii photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. here we present the crystal structure of a class iii photolyase termed photolyase-related protein a (phra) of agrobacterium tumefaciens at 1.67-å resolution. phra contains 5,10-methenyltetrahydrofolate (m ... | 2015 | 25784552 |
| an integrated approach to reconstructing genome-scale transcriptional regulatory networks. | transcriptional regulatory networks (trns) program cells to dynamically alter their gene expression in response to changing internal or environmental conditions. in this study, we develop a novel workflow for generating large-scale trn models that integrates comparative genomics data, global gene expression analyses, and intrinsic properties of transcription factors (tfs). an assessment of this workflow using benchmark datasets for the well-studied γ-proteobacterium escherichia coli showed that ... | 2015 | 25723545 |
| 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 |
| ccer and akgr regulate central carbon and energy metabolism in alphaproteobacteria. | many pathways of carbon and energy metabolism are conserved across the phylogeny, but the networks that regulate their expression or activity often vary considerably among organisms. in this work, we show that two previously uncharacterized transcription factors (tfs) are direct regulators of genes encoding enzymes of central carbon and energy metabolism in the alphaproteobacterium rhodobacter sphaeroides. the laci family member ccer (rsp_1663) directly represses genes encoding enzymes in the en ... | 2015 | 25650399 |
| molecular and physiological evidence of genetic assimilation to high co2 in the marine nitrogen fixer trichodesmium. | most investigations of biogeochemically important microbes have focused on plastic (short-term) phenotypic responses in the absence of genetic change, whereas few have investigated adaptive (long-term) responses. however, no studies to date have investigated the molecular progression underlying the transition from plasticity to adaptation under elevated co2 for a marine nitrogen-fixer. to address this gap, we cultured the globally important cyanobacterium trichodesmium at both low and high co2 f ... | 2016 | 27830646 |
| new insights into nod factor biosynthesis: analyses of chitooligomers and lipo-chitooligomers of rhizobium sp. irbg74 mutants. | soil-dwelling, nitrogen-fixing rhizobia signal their presence to legume hosts by secreting lipo-chitooligomers (lcos) that are decorated with a variety of chemical substituents. it has long been assumed, but never empirically shown, that the lco backbone is synthesized first by nodc, nodb, and noda, followed by addition of one or more substituents by other nod proteins. by analyzing a collection of in-frame deletion mutants of key nod genes in the bacterium rhizobium sp. irbg74 by mass spectrome ... | 2016 | 27623438 |
| transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat. | soil microorganisms are key determinants of soil fertility and plant health. soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. microbial biocontrol agents have been extensively studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between them have mainly been characterised in dual cultures, without taking into account the soil microbial community. we used an rna sequencing approach to elucidate the molecul ... | 2016 | 27784266 |
| proteomic studies on the effects of lipo-chitooligosaccharide and thuricin 17 under unstressed and salt stressed conditions in arabidopsis thaliana. | plants, being sessile organisms, are exposed to widely varying environmental conditions throughout their life cycle. compatible plant-microbe interactions favor plant growth and development, and help plants deal with these environmental challenges. microorganisms produce a diverse range of elicitor molecules to establish symbiotic relationships with the plants they associate with, in a given ecological niche. lipo-chitooligosaccharide (lco) and thuricin 17 (th17) are two such compounds shown to ... | 2016 | 27625672 |
| 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 |
| regulation of polyhydroxybutyrate synthesis in the soil bacterium bradyrhizobium diazoefficiens. | polyhydroxybutyrate (phb) is a carbon and energy reserve polymer in various prokaryotic species. we determined that, when grown with mannitol as the sole carbon source, bradyrhizobium diazoefficiens produces a homopolymer composed only of 3-hydroxybutyrate units (phb). conditions of oxygen limitation (such as microoxia, oxic stationary phase, and bacteroids inside legume nodules) were permissive for the synthesis of phb, which was observed as cytoplasmic granules. to study the regulation of phb ... | 2016 | 27208130 |
| high-quality permanent draft genome sequence of ensifer sp. pc2, isolated from a nitrogen-fixing root nodule of the legume tree (khejri) native to the thar desert of india. | ensifer sp. pc2 is an aerobic, motile, gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume p. cineraria (l.) druce (khejri), which is a keystone species that grows in arid and semi-arid regions of the indian thar desert. strain pc2 exists as a dominant saprophyte in alkaline soils of western rajasthan. it is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as speci ... | 2016 | 27340511 |
| 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 |
| articles of significant interest selected from this issue by the editors. | | 2016 | 27207695 |
| review: diversity of microorganisms in global fermented foods and beverages. | culturalable and non-culturable microorganisms naturally ferment majority of global fermented foods and beverages. traditional food fermentation represents an extremely valuable cultural heritage in most regions, and harbors a huge genetic potential of valuable but hitherto undiscovered strains. holistic approaches for identification and complete profiling of both culturalable and non-culturable microorganisms in global fermented foods are of interest to food microbiologists. the application of ... | 2016 | 27047484 |
| gene expression profiling gut microbiota in different races of humans. | the gut microbiome is shaped and modified by the polymorphisms of microorganisms in the intestinal tract. its composition shows strong individual specificity and may play a crucial role in the human digestive system and metabolism. several factors can affect the composition of the gut microbiome, such as eating habits, living environment, and antibiotic usage. thus, various races are characterized by different gut microbiome characteristics. in this present study, we studied the gut microbiomes ... | 2016 | 26975620 |
| ancient evolution and recent evolution converge for the biodegradation of cyanuric acid and related triazines. | cyanuric acid was likely present on prebiotic earth, may have been a component of early genetic materials, and is synthesized industrially today on a scale of more than one hundred million pounds per year in the united states. in light of this, it is not surprising that some bacteria and fungi have a metabolic pathway that sequentially hydrolyzes cyanuric acid and its metabolites to release the nitrogen atoms as ammonia to support growth. the initial reaction that opens the s-triazine ring is ca ... | 2016 | 26729715 |
| using synthetic biology to increase nitrogenase activity. | nitrogen fixation has been established in protokaryotic model escherichia coli by transferring a minimal nif gene cluster composed of 9 genes (nifb, nifh, nifd, nifk, nife, nifn, nifx, hesa and nifv) from paenibacillus sp. wly78. however, the nitrogenase activity in the recombinant e. coli 78-7 is only 10 % of that observed in wild-type paenibacillus. thus, it is necessary to increase nitrogenase activity through synthetic biology. | 2016 | 26897628 |
| 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 |
| the lps o-antigen in photosynthetic bradyrhizobium strains is dispensable for the establishment of a successful symbiosis with aeschynomene legumes. | the photosynthetic bradyrhizobia are able to use a nod-factor independent process to induce nitrogen-fixing nodules on some semi-aquatic aeschynomene species. these bacteria display a unique lps o-antigen composed of a new sugar, the bradyrhizose that is regarded as a key symbiotic factor due to its non-immunogenic character. in this study, to check this hypothesis, we isolated mutants affected in the o-antigen synthesis by screening a transposon mutant library of the ors285 strain for clones al ... | 2016 | 26849805 |
| structure and biological roles of sinorhizobium fredii hh103 exopolysaccharide. | here we report that the structure of the sinorhizobium fredii hh103 exopolysaccharide (eps) is composed of glucose, galactose, glucuronic acid, pyruvic acid, in the ratios 5∶2∶2∶1 and is partially acetylated. a s. fredii hh103 exoa mutant (svq530), unable to produce eps, not only forms nitrogen fixing nodules with soybean but also shows increased competitive capacity for nodule occupancy. mutant svq530 is, however, less competitive to nodulate vigna unguiculata. biofilm formation was reduced in ... | 2014 | 25521500 |
| genetic diversity of indigenous common bean (phaseolus vulgaris l.) rhizobia from the state of minas gerais, brazil. | we characterized indigenous common bean rhizobia from five districts of the state of minas gerais, brazil. the isolates were trapped by two common bean varieties, the mineiro precoce (andean origin) and ouro negro (mesoamerican origin). analysis by box-pcr of selected isolates detected a high level of genetic diversity. | 2009 | 24031433 |
| expanding the cyanuric acid hydrolase protein family to the fungal kingdom. | the known enzymes that open the s-triazine ring, the cyanuric acid hydrolases, have been confined almost exclusively to the kingdom bacteria and are all homologous members of the rare cyanuric acid hydrolase/barbiturase protein family. in the present study, a filamentous fungus, sarocladium sp. strain ca, was isolated from soil by enrichment culturing using cyanuric acid as the sole source of nitrogen. a reverse-genetic approach identified a fungal cyanuric acid hydrolase gene composed of two ex ... | 2013 | 24039269 |
| ethylene, a hormone at the center-stage of nodulation. | nodulation is the result of a beneficial interaction between legumes and rhizobia. it is a sophisticated process leading to nutrient exchange between the two types of symbionts. in this association, within a nodule, the rhizobia, using energy provided as photosynthates, fix atmospheric nitrogen and convert it to ammonium which is available to the plant. nodulation is recognized as an essential process in nitrogen cycling and legume crops are known to enrich agricultural soils in nitrogenous comp ... | 2015 | 26834752 |
| blue light does not inhibit nodulation in sesbania rostrata. | earlier, we reported that root nodulation was inhibited by blue light irradiation of lotus japonicus. because some legumes do not establish nodules exclusively on underground roots, we investigated whether nodule formation in sesbania rostrata, which forms both root and "stem" nodules following inoculation with azorhizobium caulinodans, is inhibited by blue light as are l. japonicus nodules. we found that neither s. rostrata nodulation nor nitrogen fixation was inhibited by blue light exposure. ... | 2017 | 27935414 |
| migration of endophytic diazotroph azorhizobium caulinodans ors571 inside wheat (triticum aestivum l) and its effect on micrornas. | azorhizobium caulinodans ors571, a novel rhizobium, forms endosymbionts with its nature host sesbania rostrata, a semi-aquatic leguminous tree. recent studies showed that a. caulinodans ors571, as endophytic rhizobium, disseminated and colonized inside of cereal plants. however, how this rhizobium infects monocot plants and the regulatory mechanism remains unknown. micrornas (mirnas) are small, endogenous rnas that regulate gene expression at the post-transcriptional levels. in this study, we em ... | 2016 | 27858182 |
| plant nodulation inducers enhance horizontal gene transfer of azorhizobium caulinodans symbiosis island. | horizontal gene transfer (hgt) of genomic islands is a driving force of bacterial evolution. many pathogens and symbionts use this mechanism to spread mobile genetic elements that carry genes important for interaction with their eukaryotic hosts. however, the role of the host in this process remains unclear. here, we show that plant compounds inducing the nodulation process in the rhizobium-legume mutualistic symbiosis also enhance the transfer of symbiosis islands. we demonstrate that the symbi ... | 2016 | 27849579 |
| oxyr-regulated catalase activity is critical for oxidative stress resistance, nodulation and nitrogen fixation in azorhizobium caulinodans. | the legume-rhizobial interaction results in the formation of symbiotic nodules in which rhizobia fix nitrogen. during the process of symbiosis, reactive oxygen species (ros) are generated. thus, the response of rhizobia to ros is important for successful nodulation and nitrogen fixation. in this study, we investigated how azorhizobium caulinodans, a rhizobium that forms both root and stem nodules on its host plant, regulates ros resistance. we found that in-frame deletions of a gene encoding the ... | 2016 | 27190162 |
| removal of methyl acrylate by ceramic-packed biotrickling filter and their response to bacterial community. | methyl acrylate is a widely used raw chemical materials and it is toxic in humans. in order to treat the methyl acrylate waste gas, a 3-layer btf packed with ceramic particles and immobilized with activated sludge was set up. the btf exhibited excellent removal efficiency that no methyl acrylate could be detected when ebrt was larger than 266s and inlet concentration was lower than 0.19g/m(3). the 1st layer performed the best at fixed inlet concentration of 0.42g/m(3). pcr combined with dgge was ... | 2016 | 26970927 |
| effects of alteration in lps structure in azorhizobium caulinodans on nodule development. | the lipopolysaccharide (lps) of azorhizobium caulinodans ors571, which forms n2-fixing nodules on the stems and roots of sesbania rostrata, is known to be a positive signal required for the progression of nodule formation. in this study, four a. caulinodans mutants producing a variety of defective lpss were compared. the lpss of the mutants having tn5 insertion in the rfaf, rfad, and rfae genes were more truncated than the modified lpss of the oac2 mutants. however, the nodule formation by the r ... | 2015 | 26782655 |
| bacterial dynamics during yearlong spontaneous fermentation for production of ngari, a dry fermented fish product of northeast india. | ngari is the most popular traditionally processed non-salted fish product, prepared from sun-dried small cyprinid fish puntius sophore (ham.) in manipur state of northeast india. the microbial involvement in ngari production remained uncertain due to its low moisture content and yearlong incubation in anaerobically sealed earthen pots without any significant change in total microbial count. the culture-independent pcr-dgge analysis used during this study confirmed a drastic bacterial community s ... | 2015 | 25637876 |
| azorhizobium oxalatiphilum sp. nov., and emended description of the genus azorhizobium. | a gram-negative, motile, non-spore-forming rod, designated ns12(t), was isolated from macerated petioles of rumex sp. after enrichment with oxalate. on the basis of 16s rrna gene sequence similarity, strain ns12(t) was phylogenetically related to the genera azorhizobium and xanthobacter in the class alphaproteobacteria. strain ns12(t) was most closely related to azorhizobium doebereinerae br 5401(t) and azorhizobium caulinodans ors 571(t) (98.3 and 97.3 % 16s rrna gene sequence similarity, respe ... | 2013 | 22888185 |
| structure of the o-polysaccharide of azorhizobium caulinodans hambi 216; identification of 3-c-methyl-d-rhamnose as a component of bacterial polysaccharides. | the o-polysaccharide was obtained from the lipopolysaccharide of the stem-nodulating nitrogen-fixing bacterium azorhizobium caulinodans hambi 216 and studied by sugar and methylation analyses along with (1)h and (13)c nmr spectroscopy. the polysaccharide was found to have a linear pentasaccharide repeating unit containing d-rhamnose and its rarely occurring 2-o-methyl (rha2ome) and 3-c-methyl (rha3cme) derivatives and having the following structure: →3)-α-d-rhap2ome-(1→2)-β-d-rhap3cme-(1→3)-α-d- ... | 2012 | 22819626 |
| structure of lipid a from a stem-nodulating bacterium azorhizobium caulinodans. | the structure of the lipid a of the lipopolysaccharide (lps) from azorhizobium caulinodans, a symbiont of the tropical legume sesbania rostrata, was investigated by chemical compositional analyses, mass spectrometry, as well as 1d and 2d nmr spectroscopy techniques. the lipid a backbone was composed of a β-(1→6)-linked 2,3-diamino-2,3-dideoxy-d-glucopyranose (glcpn3n) disaccharide and α-d-glucuronic acid (glcpa). nuclear magnetic resonance spectroscopy revealed that the glcpa was connected to th ... | 2012 | 22456102 |
| plant gene expression during effective and ineffective nodule development of the tropical stem-nodulated legume sesbania rostrata. | the expression of plant genes during symbiosis of sesbania rostrata with rhizobium sp. and azorhizobium caulinodans was studied by comparing two-dimensional page patterns of in vitro translation products of poly(a)(+) rna from uninfected roots and stems with that of root and stem nodules. both types of nodules are essentially similar, particularly when stem nodules are formed in the dark. we detected the specific expression of at least 16 genes in stem and root nodules and observed the stimulate ... | 1988 | 24277625 |