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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 ...201425003187
structure of d-tagatose 3-epimerase-like protein from methanocaldococcus jannaschii.the crystal structure of a d-tagatose 3-epimerase-like protein (mj1311p) encoded by a hypothetical open reading frame, mj1311, in the genome of the hyperthermophilic archaeon methanocaldococcus jannaschii was determined at a resolution of 2.64 å. the asymmetric unit contained two homologous subunits, and the dimer was generated by twofold symmetry. the overall fold of the subunit proved to be similar to those of the d-tagatose 3-epimerase from pseudomonas cichorii and the d-psicose 3-epimerases ...201425005083
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
bacterial metabolism of methylated amines and identification of novel methylotrophs in movile cave.movile cave, romania, is an unusual underground ecosystem that has been sealed off from the outside world for several million years and is sustained by non-phototrophic carbon fixation. methane and sulfur-oxidising bacteria are the main primary producers, supporting a complex food web that includes bacteria, fungi and cave-adapted invertebrates. a range of methylotrophic bacteria in movile cave grow on one-carbon compounds including methylated amines, which are produced via decomposition of orga ...201425050523
bacterial metabolism of methylated amines and identification of novel methylotrophs in movile cave.movile cave, romania, is an unusual underground ecosystem that has been sealed off from the outside world for several million years and is sustained by non-phototrophic carbon fixation. methane and sulfur-oxidising bacteria are the main primary producers, supporting a complex food web that includes bacteria, fungi and cave-adapted invertebrates. a range of methylotrophic bacteria in movile cave grow on one-carbon compounds including methylated amines, which are produced via decomposition of orga ...201425050523
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
molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen ix.tetrapyrroles such as heme and chlorophyll are essential for biological processes, including oxygenation, respiration, and photosynthesis. in the tetrapyrrole biosynthesis pathway, protoporphyrinogen ix oxidase (protox) catalyzes the formation of protoporphyrin ix, the last common intermediate for the biosynthesis of heme and chlorophyll. three nonhomologous isofunctional enzymes, hemg, hemj, and hemy, for protox have been identified. to reveal the distribution and evolution of the three protox ...201425108393
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
orthology detection combining clustering and synteny for very large datasets.the elucidation of orthology relationships is an important step both in gene function prediction as well as towards understanding patterns of sequence evolution. orthology assignments are usually derived directly from sequence similarities for large data because more exact approaches exhibit too high computational costs. here we present poff, an extension for the standalone tool proteinortho, which enhances orthology detection by combining clustering, sequence similarity, and synteny. in the cou ...201425137074
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
conformational selection in protein binding and function.protein binding and function often involves conformational changes. advanced nuclear magnetic resonance (nmr) experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may "select" protein conformations for binding (or unbinding). in this review, we argue that this conformational selection requires transition times for ligand binding and unbinding that are small compared to the dwell times of proteins in diff ...201425155241
refined regio- and stereoselective hydroxylation of l-pipecolic acid by protein engineering of l-proline cis-4-hydroxylase based on the x-ray crystal structure.enzymatic regio- and stereoselective hydroxylation are valuable for the production of hydroxylated chiral ingredients. proline hydroxylases are representative members of the nonheme fe(2+)/α-ketoglutarate-dependent dioxygenase family. these enzymes catalyze the conversion of l-proline into hydroxy-l-prolines (hyps). l-proline cis-4-hydroxylases (cis-p4hs) from sinorhizobium meliloti and mesorhizobium loti catalyze the hydroxylation of l-proline, generating cis-4-hydroxy-l-proline, as well as the ...201525171735
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
molecular characterization of a novel temperate sinorhizobium bacteriophage, фlm21, encoding dna methyltransferase with ccrm-like specificity.φlm21 is a temperate phage isolated from sinorhizobium sp. strain lm21 (alphaproteobacteria). genomic analysis and electron microscopy suggested that φlm21 is a member of the family siphoviridae. the phage has an isometric head and a long noncontractile tail. the genome of φlm21 has 50,827 bp of linear double-stranded dna encoding 72 putative proteins, including proteins responsible for the assembly of the phage particles, dna packaging, transcription, replication, and lysis. virion proteins wer ...201425187538
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
alfalfa snakin-1 prevents fungal colonization and probably coevolved with rhizobia.the production of antimicrobial peptides is a common defense strategy of living cells against a wide range of pathogens. plant snakin peptides inhibit bacterial and fungal growth at extremely low concentrations. however, little is known of their molecular and ecological characteristics, including origin, evolutionary equivalence, specific functions and activity against beneficial microbes. the aim of this study was to identify and characterize snakin-1 from alfalfa (mssn1).201425227589
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
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
divergent nod-containing bradyrhizobium sp. doa9 with a megaplasmid and its host range.bradyrhizobium sp. doa9, a non-photosynthetic bacterial strain originally isolated from the root nodules of the legume aeschynomene americana, is a divergent nod-containing strain. it exhibits a broad host range, being able to colonize and efficiently nodulate the roots of most plants from the dalbergioid, millettioid, and robinioid tribes (7 species of papilionoideae). in all cases, nodulation was determinate. the morphology and size of doa9 bacteroids isolated from the nodules of various speci ...201425283477
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
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
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
a nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase.cog5598 comprises a large number of proteins related to mttb, the trimethylamine:corrinoid methyltransferase. mttb has a genetically encoded pyrrolysine residue proposed essential for catalysis. mttb is the only known trimethylamine methyltransferase, yet the great majority of members of cog5598 lack pyrrolysine, leaving the activity of these proteins an open question. here, we describe the function of one of the nonpyrrolysine members of this large protein family. three nonpyrrolysine mttb homo ...201425313086
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
islander: a database of precisely mapped genomic islands in trna and tmrna genes.genomic islands are mobile dnas that are major agents of bacterial and archaeal evolution. integration into prokaryotic chromosomes usually occurs site-specifically at trna or tmrna gene (together, tdna) targets, catalyzed by tyrosine integrases. this splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. we applied this principle to search for islands in genomic dna sequenc ...201425378302
islander: a database of precisely mapped genomic islands in trna and tmrna genes.genomic islands are mobile dnas that are major agents of bacterial and archaeal evolution. integration into prokaryotic chromosomes usually occurs site-specifically at trna or tmrna gene (together, tdna) targets, catalyzed by tyrosine integrases. this splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. we applied this principle to search for islands in genomic dna sequenc ...201425378302
accumulation of novel glycolipids and ornithine lipids in mesorhizobium loti under phosphate deprivation.glycolipids are found mainly in photosynthetic organisms (plants, algae, and cyanobacteria), gram-positive bacteria, and a few other bacterial phyla. they serve as membrane lipids and play a role under phosphate deprivation as surrogates for phospholipids. mesorhizobium loti accumulates different di- and triglycosyl diacylglycerols, synthesized by the processive glycosyltransferase pgt-ml, and two so far unknown glycolipids, which were identified in this study by mass spectrometry (ms) and nucle ...201425404698
accumulation of novel glycolipids and ornithine lipids in mesorhizobium loti under phosphate deprivation.glycolipids are found mainly in photosynthetic organisms (plants, algae, and cyanobacteria), gram-positive bacteria, and a few other bacterial phyla. they serve as membrane lipids and play a role under phosphate deprivation as surrogates for phospholipids. mesorhizobium loti accumulates different di- and triglycosyl diacylglycerols, synthesized by the processive glycosyltransferase pgt-ml, and two so far unknown glycolipids, which were identified in this study by mass spectrometry (ms) and nucle ...201425404698
spontaneous symbiotic reprogramming of plant roots triggered by receptor-like kinases.symbiosis receptor-like kinase (symrk) is indispensable for the development of phosphate-acquiring arbuscular mycorrhiza (am) as well as nitrogen-fixing root nodule symbiosis, but the mechanisms that discriminate between the two distinct symbiotic developmental fates have been enigmatic. in this study, we show that upon ectopic expression, the receptor-like kinase genes nod factor receptor 1 (nfr1), nfr5, and symrk initiate spontaneous nodule organogenesis and nodulation-related gene expression ...201425422918
whole-proteome analysis of twelve species of alphaproteobacteria links four pathogens.thousands of whole-genome and whole-proteome sequences have been made available through advances in sequencing technology, and sequences of millions more organisms will become available in the coming years. this wealth of genetic information will provide numerous opportunities to enhance our understanding of these organisms including a greater understanding of relationships among species. researchers have used 16s rrna and other gene sequences to study the evolutionary origins of bacteria, but t ...201325437336
crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an nad⁺-dependent dismutase from mesorhizobium loti.5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase (fhmpcdh) from mesorhizobium loti is the fifth enzyme in degradation pathway i for pyridoxine. the enzyme catalyzes a dismutation reaction: the oxidation of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid (fhmpc) to 3-hydroxy-2-methylpyridine 4,5-dicarboxylic acid with nad(+) and reduction of fhmpc to 4-pyridoxic acid with nadh. fhmpcdh belongs to the l-3-hydroxyacyl-coa dehydrogenase (had) family. the crystal structure ...201525446130
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
genetic analysis of signal integration by the sinorhizobium meliloti sensor kinase feuq.two-component signalling systems allow bacteria to recognize and respond to diverse environmental stimuli. auxiliary proteins can provide an additional layer of control to these systems. the sinorhizobium meliloti feupq two-component system is required for symbiotic development and is negatively regulated by the auxiliary small periplasmic protein feun. this study explores the mechanistic basis of this regulation. we provide evidence that feun directly interacts with the sensor kinase feuq. isol ...201525479839
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
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
molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis.the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ...201425492513
molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis.the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ...201425492513
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 ...201425521500
fundamental shift in vitamin b12 eco-physiology of a model alga demonstrated by experimental evolution.a widespread and complex distribution of vitamin requirements exists over the entire tree of life, with many species having evolved vitamin dependence, both within and between different lineages. vitamin availability has been proposed to drive selection for vitamin dependence, in a process that links an organism's metabolism to the environment, but this has never been demonstrated directly. moreover, understanding the physiological processes and evolutionary dynamics that influence metabolic dem ...201425526368
fundamental shift in vitamin b12 eco-physiology of a model alga demonstrated by experimental evolution.a widespread and complex distribution of vitamin requirements exists over the entire tree of life, with many species having evolved vitamin dependence, both within and between different lineages. vitamin availability has been proposed to drive selection for vitamin dependence, in a process that links an organism's metabolism to the environment, but this has never been demonstrated directly. moreover, understanding the physiological processes and evolutionary dynamics that influence metabolic dem ...201425526368
global transcriptome analysis of mesorhizobium alhagi ccnwxj12-2 under salt stress.mesorhizobium alhagi ccnwxj12-2 is a α-proteobacterium which could be able to fix nitrogen in the nodules formed with alhagi sparsifolia in northwest of china. desiccation and high salinity are the two major environmental problems faced by m. alhagi ccnwxj12-2. in order to identify genes involved in salt-stress adaption, a global transcriptional analysis of m. alhagi ccnwxj12-2 growing under salt-free and high salt conditions was carried out. the next generation sequencing technology, rna-seq, w ...201425539655
network of gras transcription factors involved in the control of arbuscule development in lotus japonicus.arbuscular mycorrhizal (am) fungi, in symbiosis with plants, facilitate acquisition of nutrients from the soil to their host. after penetration, intracellular hyphae form fine-branched structures in cortical cells termed arbuscules, representing the major site where bidirectional nutrient exchange takes place between the host plant and fungus. transcriptional mechanisms underlying this cellular reprogramming are still poorly understood. gras proteins are an important family of transcriptional re ...201525560877
oricola cellulosilytica gen. nov., sp. nov., a cellulose-degrading bacterium of the family phyllobacteriaceae isolated from surface seashore water, and emended descriptions of mesorhizobium loti and phyllobacterium myrsinacearum.a gram-stain negative, strictly aerobic, rod-shaped, non-spore-forming, motile cellulolytic bacterium, designated strain cc-amh-0(t), was isolated from surface seashore water of hualien, taiwan and subjected to polyphasic taxonomy. strain cc-amh-0(t) exhibited enzymatic saccharification of cellulose and active growth particularly during log-phase under nutrient-limited conditions, whereas enhanced saccharification was found in the declining growth phase under copiotrophic conditions. the novel s ...201525566955
bacterial genospecies that are not ecologically coherent: population genomics of rhizobium leguminosarum.biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. to establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium rhizobium leguminosarum by genomic sequencing of 72 isolates. although all strains have 16s rrna typical of r. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ani). many ...201525589577
comparative genomic and phylogenetic analyses of gammaproteobacterial glg genes traced the origin of the escherichia coli glycogen glgbxcap operon to the last common ancestor of the sister orders enterobacteriales and pasteurellales.production of branched α-glucan, glycogen-like polymers is widely spread in the bacteria domain. the glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species escherichia coli (order enterobacteriales, class gammaproteobacteria), in which the cognate genes (branching enzyme glgb, debranching enzyme glgx, adp-glucose pyrophosphorylase glgc, glycogen synthase glga, and glycogen phosphorylase glgp) are clustered in a glgbxcap operon arrang ...201525607991
the microbiome of the upper airways: focus on chronic rhinosinusitis.upper airway diseases including allergic rhinitis, chronic rhinosinusitis with or without polyps, and cystic fibrosis are characterized by substantially different inflammatory profiles. traditionally, studies on the association of specific bacterial patterns with inflammatory profiles of diseases had been dependent on bacterial culturing. in the past 30 years, molecular biology methods have allowed bacterial culture free studies of microbial communities, revealing microbiota much more diverse th ...201525624972
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
identification of ferredoxin ii as a major calcium binding protein in the nitrogen-fixing symbiotic bacterium mesorhizobium loti.legumes establish with rhizobial bacteria a nitrogen-fixing symbiosis which is of the utmost importance for both plant nutrition and a sustainable agriculture. calcium is known to act as a key intracellular messenger in the perception of symbiotic signals by both the host plant and the microbial partner. regulation of intracellular free ca(2+) concentration, which is a fundamental prerequisite for any ca(2+)-based signalling system, is accomplished by complex mechanisms including ca(2+) binding ...201525648224
genome-wide gene order distances support clustering the gram-positive bacteria.initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...201525653643
genome-wide gene order distances support clustering the gram-positive bacteria.initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...201525653643
insight into cofactor recognition in arylamine n-acetyltransferase enzymes: structure of mesorhizobium loti arylamine n-acetyltransferase in complex with coenzyme a.arylamine n-acetyltransferases (nats) are xenobiotic metabolizing enzymes that catalyze the acetyl-coa-dependent acetylation of arylamines. to better understand the mode of binding of the cofactor by this family of enzymes, the structure of mesorhizobium loti nat1 [(rhilo)nat1] was determined in complex with coa. the f42w mutant of (rhilo)nat1 was used as it is well expressed in escherichia coli and displays enzymatic properties similar to those of the wild type. the apo and holo structures of ( ...201525664736
a genomic encyclopedia of the root nodule bacteria: assessing genetic diversity through a systematic biogeographic survey.root nodule bacteria are free-living soil bacteria, belonging to diverse genera within the alphaproteobacteria and betaproteobacteria, that have the capacity to form nitrogen-fixing symbioses with legumes. the symbiosis is specific and is governed by signaling molecules produced from both host and bacteria. sequencing of several model rnb genomes has provided valuable insights into the genetic basis of symbiosis. however, the small number of sequenced rnb genomes available does not currently ref ...201525685260
the absence of protein y4ys affects negatively the abundance of t3ss mesorhizobium loti secretin, rhcc2, in bacterial membranes.mesorhizobium loti maff303099 has a functional type iii secretion system (t3ss) that is involved in the determination of nodulation competitiveness on lotus. the m. loti t3ss cluster contains gene y4ys (mlr8765) that codes for a protein of unknown function (y4ys). a mutation in the y4ys gene favors the m. loti symbiotic competitive ability on lotus tenuis cv. esmeralda and affects negatively the secretion of proteins through t3ss. here we localize y4ys in the bacterial membrane using a translati ...201525688250
preferential association of endophytic bradyrhizobia with different rice cultivars and its implications for rice endophyte evolution.plant colonization by bradyrhizobia is found not only in leguminous plants but also in nonleguminous species such as rice. to understand the evolution of the endophytic symbiosis of bradyrhizobia, the effect of the ecosystems of rice plantations on their associations was investigated. samples were collected from various rice (oryza sativa) tissues and crop rotational systems. the rice endophytic bradyrhizobia were isolated on the basis of oligotrophic properties, selective medium, and nodulation ...201525710371
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 ...201525710540
lotus japonicus clathrin heavy chain1 is associated with rho-like gtpase rop6 and involved in nodule formation.mechanisms underlying nodulation factor signaling downstream of the nodulation factor receptors (nfrs) have not been fully characterized. in this study, clathrin heavy chain1 (chc1) was shown to interact with the rho-like gtpase rop6, an interaction partner of nfr5 in lotus japonicus. the chc1 gene was found to be expressed constitutively in all plant tissues and induced in mesorhizobium loti-infected root hairs and nodule primordia. when expressed in leaves of nicotiana benthamiana, chc1 and ro ...201525717037
proteomic analysis of the soybean symbiosome identifies new symbiotic proteins.legumes form a symbiosis with rhizobia in which the plant provides an energy source to the rhizobia bacteria that it uses to fix atmospheric nitrogen. this nitrogen is provided to the legume plant, allowing it to grow without the addition of nitrogen fertilizer. as part of the symbiosis, the bacteria in the infected cells of a new root organ, the nodule, are surrounded by a plant-derived membrane, the symbiosome membrane, which becomes the interface between the symbionts. fractions containing th ...201525724908
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
revision of the taxonomic status of type strains of mesorhizobium loti and reclassification of strain usda 3471t as the type strain of mesorhizobiumerdmanii sp. nov. and atcc 33669t as the type strain of mesorhizobiumjarvisii sp. nov.the species mesorhizobim loti was isolated from nodules of lotus corniculatus and its type strain deposited in several collections. some of these type strains, such as those deposited in the usda and atcc collections before 1990, are not coincident with the original strain, nzp 2213t, deposited in the nzp culture collection. the analysis of the 16s rrna gene showed that strains usda 3471t and atcc 33669t formed independent branches from that occupied by mesorhizobium loti nzp 2213t and related t ...201525736411
function of glutathione peroxidases in legume root nodules.glutathione peroxidases (gpxs) are antioxidant enzymes not studied so far in legume nodules, despite the fact that reactive oxygen species are produced at different steps of the symbiosis. the function of two gpxs that are highly expressed in nodules of the model legume lotus japonicus was examined. gene expression analysis, enzymatic and nitrosylation assays, yeast cell complementation, in situ mrna hybridization, immunoelectron microscopy, and ljgpx-green fluorescent protein (gfp) fusions were ...201525740929
thermodynamic matchers for the construction of the cuckoo rna family.rna family models describe classes of functionally related, non-coding rnas based on sequence and structure conservation. the most important method for modeling rna families is the use of covariance models, which are stochastic models that serve in the discovery of yet unknown, homologous rnas. however, the performance of covariance models in finding remote homologs is poor for rna families with high sequence conservation, while for families with high structure but low sequence conservation, the ...201525779873
growth and survival of mesorhizobium loti inside acanthamoeba enhanced its ability to develop more nodules on lotus corniculatus.the importance of protozoa as environmental reservoirs of pathogens is well recognized, while their impact on survival and symbiotic properties of rhizobia has not been explored. the possible survival of free-living rhizobia inside amoebae could influence bacterial abundance in the rhizosphere of legume plants and the nodulation competitiveness of microsymbionts. two well-characterized strains of mesorhizobium: mesorhizobium loti nzp2213 and mesorhizobium huakuii symbiovar loti maff303099 were a ...201525779926
genome sequence of the lotus corniculatus microsymbiont mesorhizobium loti strain r88b.mesorhizobium loti strain r88b was isolated in 1993 in the rocklands range in otago, new zealand from a lotus corniculatus root nodule. r88b is an aerobic, gram-negative, non-spore-forming rod. this report reveals the genome of m. loti strain r88b contains a single scaffold of size 7,195,110 bp which encodes 6,950 protein-coding genes and 66 rna-only encoding genes. this genome does not harbor any plasmids but contains the integrative and conjugative element icemlsym(r7a), also known as the r7a ...201425780496
genome sequence of the lotus spp. microsymbiont mesorhizobium loti strain r7a.mesorhizobium loti strain r7a was isolated in 1993 in lammermoor, otago, new zealand from a lotus corniculatus root nodule and is a reisolate of the inoculant strain icmp3153 (nzp2238) used at the site. r7a is an aerobic, gram-negative, non-spore-forming rod. the symbiotic genes in the strain are carried on a 502-kb integrative and conjugative element known as the symbiosis island or icemlsym(r7a). m. loti is the microsymbiont of the model legume lotus japonicus and strain r7a has been used exte ...201425780499
genome sequence of the lotus spp. microsymbiont mesorhizobium loti strain nzp2037.mesorhizobium loti strain nzp2037 was isolated in 1961 in palmerston north, new zealand from a lotus divaricatus root nodule. compared to most other m. loti strains, it has a broad host range and is one of very few m. loti strains able to form effective nodules on the agriculturally important legume lotus pedunculatus. nzp2037 is an aerobic, gram negative, non-spore-forming rod. this report reveals that the genome of m. loti strain nzp2037 does not harbor any plasmids and contains a single scaff ...201425780500
structural and enzymatic characterization of the choline kinase lica from streptococcus pneumoniae.lica plays a key role in the cell-wall phosphorylcholine biosynthesis of streptococcus pneumonia. here we determined the crystal structures of apo-form lica at 1.94 å and two complex forms lica-choline and lica-amp-mes, at 2.01 and 1.45 å resolution, respectively. the overall structure adopts a canonical protein kinase-like fold, with the active site located in the crevice of the n- and c-terminal domains. the three structures present distinct poses of the active site, which undergoes an open-cl ...201525781969
ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing-activated transfer of a mobile genetic element.symbiosis islands are integrative and conjugative mobile genetic elements that convert nonsymbiotic rhizobia into nitrogen-fixing symbionts of leguminous plants. excision of the mesorhizobium loti symbiosis island icemlsym(r7a) is indirectly activated by quorum sensing through trar-dependent activation of the excisionase gene rdfs. here we show that a +1 programmed ribosomal frameshift (prf) fuses the coding sequences of two trar-activated genes, msi172 and msi171, producing an activator of rdfs ...201525787256
carnitine in bacterial physiology and metabolism.carnitine is a quaternary amine compound found at high concentration in animal tissues, particularly muscle, and is most well studied for its contribution to fatty acid transport into mitochondria. in bacteria, carnitine is an important osmoprotectant, and can also enhance thermotolerance, cryotolerance and barotolerance. carnitine can be transported into the cell or acquired from metabolic precursors, where it can serve directly as a compatible solute for stress protection or be metabolized thr ...201525787873
a census of nuclear cyanobacterial recruits in the plant kingdom.the plastids and mitochondria of the eukaryotic cell are of endosymbiotic origin. these events occurred ~2 billion years ago and produced significant changes in the genomes of the host and the endosymbiont. previous studies demonstrated that the invasion of land affected plastids and mitochondria differently and that the paths of mitochondrial integration differed between animals and plants. other studies examined the reasons why a set of proteins remained encoded in the organelles and were not ...201525794152
the interaction of arabidopsis with piriformospora indica shifts from initial transient stress induced by fungus-released chemical mediators to a mutualistic interaction after physical contact of the two symbionts.piriformospora indica, an endophytic fungus of sebacinales, colonizes the roots of many plant species including arabidopsis thaliana. the symbiotic interaction promotes plant performance, growth and resistance/tolerance against abiotic and biotic stress.201525849363
symbiosis island shuffling with abundant insertion sequences in the genomes of extra-slow-growing strains of soybean bradyrhizobia.extra-slow-growing bradyrhizobia from root nodules of field-grown soybeans harbor abundant insertion sequences (iss) and are termed highly reiterated sequence-possessing (hrs) strains. we analyzed the genome organization of hrs strains with the focus on is distribution and symbiosis island structure. using pulsed-field gel electrophoresis, we consistently detected several plasmids (0.07 to 0.4 mb) in the hrs strains (nk5, nk6, usda135, 2281, usda123, and t2), whereas no plasmids were detected in ...201525862225
perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline.plants are continuously monitoring the presence of microorganisms to establish an adapted response. plants commonly use pattern recognition receptors (prrs) to perceive microbe- or pathogen-associated molecular patterns (mamps/pamps) which are microorganism molecular signatures. located at the plant plasma membrane, the prrs are generally receptor-like kinases (rlks) or receptor-like proteins (rlps). mamp detection will lead to the establishment of a plant defense program called mamp-triggered i ...201525904927
olsg (sinac_1600) is an ornithine lipid n-methyltransferase from the planctomycete singulisphaera acidiphila.ornithine lipids (ols) are phosphorus-free membrane lipids widespread in bacteria but absent from archaea and eukaryotes. in addition to the unmodified ols, a variety of ol derivatives hydroxylated in different structural positions has been reported. recently, methylated derivatives of ols were described in several planctomycetes isolated from a peat bog in northern russia, although the gene/enzyme responsible for the n-methylation of ol remained obscure. here we identify and characterize the ol ...201525925947
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
secondary structural entropy in rna switch (riboswitch) identification.rna regulatory elements play a significant role in gene regulation. riboswitches, a widespread group of regulatory rnas, are vital components of many bacterial genomes. these regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in rna. riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. a typical class of riboswitch has its own unique structural and biological complexity, m ...201525928324
genomic features separating ten strains of neorhizobium galegae with different symbiotic phenotypes.the symbiotic phenotype of neorhizobium galegae, with strains specifically fixing nitrogen with either galega orientalis or g. officinalis, has made it a target in research on determinants of host specificity in nitrogen fixation. the genomic differences between representative strains of the two symbiovars are, however, relatively small. this introduced a need for a dataset representing a larger bacterial population in order to make better conclusions on characteristics typical for a subset of t ...201525933608
extensive identification of bacterial riboflavin transporters and their distribution across bacterial species.riboflavin, the precursor for the cofactors flavin mononucleotide (fmn) and flavin adenine dinucleotide, is an essential metabolite in all organisms. while the functions for de novo riboflavin biosynthesis and riboflavin import may coexist in bacteria, the extent of this co-occurrence is undetermined. the ribm, ribn, rfuabcd and the energy-coupling factor-ribu bacterial riboflavin transporters have been experimentally characterized. in addition, impx, rfnt and ribxy are proposed as riboflavin tr ...201525938806
micro rna 172 (mir172) signals epidermal infection and is expressed in cells primed for bacterial invasion in lotus japonicus roots and nodules.legumes interact with rhizobial bacteria to form nitrogen-fixing root nodules. host signalling following mutual recognition ensures a specific response, but is only partially understood. focusing on the stage of epidermal infection with mesorhizobium loti, we analysed endogenous small rnas (srnas) of the model legume lotus japonicus to investigate their involvement in host response regulation. we used illumina sequencing to annotate the l. japonicus srna-ome and isolate infection-responsive srna ...201525967282
quantitative time-course proteome analysis of mesorhizobium loti during nodule maturation.rhizobia are nitrogen-fixing bacteria that establish a symbiotic relationship with leguminous plants. to understand the mechanism by which rhizobia alter their metabolism to establish successful nitrogen-fixing symbiotic relationship with hosts, lotus japonicus were inoculated with mesorhizobium loti. bacteroids were isolated from nodules harvested at 2weeks (the early stage of nodule development), and at 3 and 4weeks (the intermediate stage of nodule development) post-inoculation. using a quant ...201525982383
phenotypic heterogeneity, a phenomenon that may explain why quorum sensing does not always result in truly homogenous cell behavior.phenotypic heterogeneity describes the occurrence of "nonconformist" cells within an isogenic population. the nonconformists show an expression profile partially different from that of the remainder of the population. phenotypic heterogeneity affects many aspects of the different bacterial lifestyles, and it is assumed that it increases bacterial fitness and the chances for survival of the whole population or smaller subpopulations in unfavorable environments. well-known examples for phenotypic ...201526025903
shoot har1 mediates nitrate inhibition of nodulation in lotus japonicus.nitrate is a major environmental factor in the inhibition of nodulation. in a model legume lotus japonicus, a clv1-like receptor kinase, har1, mediates nitrate inhibition and autoregulation of nodulation. autoregulation of nodulation involves root-to-shoot-to-root long-distance communication, and har1 functions in shoots. however, it remains elusive where har1 functions in the nitrate inhibition of nodulation. we performed grafting experiments with the har1 mutant under various nitrate condition ...201526039467
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 ...201526042417
structure of potassium channels.potassium channels ubiquitously exist in nearly all kingdoms of life and perform diverse but important functions. since the first atomic structure of a prokaryotic potassium channel (kcsa, a channel from streptomyces lividans) was determined, tremendous progress has been made in understanding the mechanism of potassium channels and channels conducting other ions. in this review, we discuss the structure of various kinds of potassium channels, including the potassium channel with the pore-forming ...201526070303
the influence of smoking on the peri-implant microbiome.smokers are at high risk for 2 bacterially driven oral diseases: peri-implant mucositis and peri-implantitis. therefore, the purpose of this investigation was to use a deep-sequencing approach to identify the effect of smoking on the peri-implant microbiome in states of health and disease. peri-implant biofilm samples were collected from 80 partially edentulous subjects with peri-implant health, peri-implant mucositis, and peri-implantitis. bacterial dna was isolated and 16s ribsomal rna gene li ...201526124222
identification of bradyrhizobium elkanii genes involved in incompatibility with soybean plants carrying the rj4 allele.symbioses between leguminous plants and soil bacteria known as rhizobia are of great importance to agricultural production and nitrogen cycling. while these mutualistic symbioses can involve a wide range of rhizobia, some legumes exhibit incompatibility with specific strains, resulting in ineffective nodulation. the formation of nodules in soybean plants (glycine max) is controlled by several host genes, which are referred to as rj genes. the soybean cultivar barc2 carries the rj4 gene, which re ...201526187957
secretion systems and signal exchange between nitrogen-fixing rhizobia and legumes.the formation of symbiotic nitrogen-fixing nodules on the roots and/or stem of leguminous plants involves a complex signal exchange between both partners. since many microorganisms are present in the soil, legumes and rhizobia must recognize and initiate communication with each other to establish symbioses. this results in the formation of nodules. rhizobia within nodules exchange fixed nitrogen for carbon from the legume. symbiotic relationships can become non-beneficial if one partner ceases t ...201526191069
structured and dynamic disordered domains regulate the activity of a multifunctional anti-σ factor.the anti-σ factor nepr plays a central role in regulation of the general stress response (gsr) in alphaproteobacteria. this small protein has two known interaction partners: its cognate extracytoplasmic function (ecf) σ factor and the anti-anti-σ factor, phyr. stress-dependent phosphorylation of phyr initiates a protein partner switch that promotes phospho-phyr binding to nepr, which frees ecf σ to activate transcription of genes required for cell survival under adverse or fluctuating conditions ...201526220965
biochemical and spectroscopic studies of epoxyqueuosine reductase: a novel iron-sulfur cluster- and cobalamin-containing protein involved in the biosynthesis of queuosine.queuosine is a hypermodified nucleoside present in the wobble position of trnas with a 5'-gun-3' sequence in their anticodon (his, asp, asn, and tyr). the 7-deazapurine core of the base is synthesized de novo in prokaryotes from guanosine 5'-triphosphate in a series of eight sequential enzymatic transformations, the final three occurring on trna. epoxyqueuosine reductase (queg) catalyzes the final step in the pathway, which entails the two-electron reduction of epoxyqueuosine to form queuosine. ...201526230193
active-site engineering of ω-transaminase for production of unnatural amino acids carrying a side chain bulkier than an ethyl substituent.ω-transaminase (ω-ta) is a promising enzyme for use in the production of unnatural amino acids from keto acids using cheap amino donors such as isopropylamine. the small substrate-binding pocket of most ω-tas permits entry of substituents no larger than an ethyl group, which presents a significant challenge to the preparation of structurally diverse unnatural amino acids. here we report on the engineering of an (s)-selective ω-ta from ochrobactrum anthropi (oata) to reduce the steric constraint ...201526231640
commentary: the absence of protein y4ys affects negatively the abundance of t3ss mesorhizobium loti secretin, rhcc2, in bacterial membranes. 201526236295
involvement of rop6 and clathrin in nodulation factor signaling.the symbiotic association between the legume lotus japonicus and the nitrogen-fixing bacterium mesorhizobium loti results in the formation of root nodules. this process begins with the recognition of the rhizobial nodulation factor (nf) by the nf receptors (nfr) at the cell surface of the host roots. the downstream signaling cascades after nfr recognition have not been fully characterized. we recently identified a clathrin heavy chain 1 (chc1) from l. japonicus as a potential target of the nf si ...201526251877
phod alkaline phosphatase gene diversity in soil.phosphatase enzymes are responsible for much of the recycling of organic phosphorus in soils. the phod alkaline phosphatase takes part in this process by hydrolyzing a range of organic phosphoesters. we analyzed the taxonomic and environmental distribution of phod genes using whole-genome and metagenome databases. phod alkaline phosphatase was found to be spread across 20 bacterial phyla and was ubiquitous in the environment, with the greatest abundance in soil. to study the great diversity of p ...201526253682
aquaporin-based biomimetic polymeric membranes: approaches and challenges.in recent years, aquaporin biomimetic membranes (abms) for water separation have gained considerable interest. although the first abms are commercially available, there are still many challenges associated with further abm development. here, we discuss the interplay of the main components of abms: aquaporin proteins (aqps), block copolymers for aqp reconstitution, and polymer-based supporting structures. first, we briefly cover challenges and review recent developments in understanding the inter ...201526264033
mesorhizobium waimense sp. nov. isolated from sophora longicarinata root nodules and mesorhizobium cantuariense sp. nov. isolated from sophora microphylla root nodules.in total 14 strains of gram-stain-negative, rod-shaped bacteria were isolated from sophora longicarinata and sophora microphylla root nodules and authenticated as rhizobia on these hosts. based on the 16s rrna gene phylogeny, they were shown to belong to the genus mesorhizobium, and the strains from s. longicarinata were most closely related to mesorhizobium amorphae accc 19665t (99.8–99.9 %), mesorhizobium huakuii iam 14158t (99.8–99.9 %), mesorhizobium loti usda 3471t (99.5–99.9 %) and mesorhi ...201526296780
nitrogen-fixing nodules are an important source of reduced sulfur, which triggers global changes in sulfur metabolism in lotus japonicus.we combined transcriptomic and biochemical approaches to study rhizobial and plant sulfur (s) metabolism in nitrogen (n) fixing nodules (fix(+)) of lotus japonicus, as well as the link of s-metabolism to symbiotic nitrogen fixation and the effect of nodules on whole-plant s-partitioning and metabolism. our data reveal that n-fixing nodules are thiol-rich organs. their high adenosine 5'-phosphosulfate reductase activity and strong (35)s-flux into cysteine and its metabolites, in combination with ...201526296963
comparative genomic analysis of multiple strains of two unusual plant pathogens: pseudomonas corrugata and pseudomonas mediterranea.the non-fluorescent pseudomonads, pseudomonas corrugata (pcor) and p. mediterranea (pmed), are closely related species that cause pith necrosis, a disease of tomato that causes severe crop losses. however, they also show strong antagonistic effects against economically important pathogens, demonstrating their potential for utilization as biological control agents. in addition, their metabolic versatility makes them attractive for the production of commercial biomolecules and bioremediation. an e ...201526300874
evolution of intra-specific regulatory networks in a multipartite bacterial genome.reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. the evolution of such networks within and outside the species boundary is however still obscure. sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a signifi ...201526340565
type iii secretion systems: the bacterial flagellum and the injectisome.the flagellum and the injectisome are two of the most complex and fascinating bacterial nanomachines. at their core, they share a type iii secretion system (t3ss), a transmembrane export complex that forms the extracellular appendages, the flagellar filament and the injectisome needle. recent advances, combining structural biology, cryo-electron tomography, molecular genetics, in vivo imaging, bioinformatics and biophysics, have greatly increased our understanding of the t3ss, especially the str ...201526370933
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