Publications

the rhizome of reclinomonas americana, homo sapiens, pediculus humanus and saccharomyces cerevisiae mitochondria.	mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. in this study, we investigated the phenomenon of chimerism in mitochondria to shed light on the origin of these organelles by determining which species played a role in their formation. we used the mitochondria of four distinct organisms, reclinomonas americana, homo sapiens, saccharomyces cerevisiae and multichromosome pediculus humanus, and attempte ...	2011	22014084
modulation of metabolism and switching to biofilm prevail over exopolysaccharide production in the response of rhizobium alamii to cadmium.	heavy metals such as cadmium (cd(2+)) affect microbial metabolic processes. consequently, bacteria adapt by adjusting their cellular machinery. we have investigated the dose-dependent growth effects of cd(2+) on rhizobium alamii, an exopolysaccharide (eps)-producing bacterium that forms a biofilm on plant roots. adsorption isotherms show that the eps of r. alamii binds cadmium in competition with calcium. a metabonomics approach based on ion cyclotron resonance fourier transform mass spectrometr ...	2011	22096497
mutation of a broadly conserved operon (rl3499-rl3502) from rhizobium leguminosarum biovar viciae causes defects in cell morphology and envelope integrity.	the bacterial cell envelope is of critical importance to the function and survival of the cell; it acts as a barrier against harmful toxins while allowing the flow of nutrients into the cell. it also serves as a point of physical contact between a bacterial cell and its host. hence, the cell envelope of rhizobium leguminosarum is critical to cell survival under both free-living and symbiotic conditions. transposon mutagenesis of r. leguminosarum strain 3841 followed by a screen to isolate mutant ...	2011	21357485
role of baca in lipopolysaccharide synthesis, peptide transport, and nodulation by rhizobium sp. strain ngr234.	baca of sinorhizobium meliloti plays an essential role in the establishment of nitrogen-fixing symbioses with medicago plants, where it is involved in peptide import and in the addition of very-long-chain fatty acids (vlcfa) to lipid a of lipopolysaccharide (lps). we investigated the role of baca in rhizobium species strain ngr234 by mutating the baca gene. in the ngr234 baca mutant, peptide import was impaired, but no effect on vlcfa addition was observed. more importantly, the symbiotic abilit ...	2011	21357487
regulation of type vi secretion gene clusters by sigma54 and cognate enhancer binding proteins.	type vi secretion systems (t6ss) are bacteriophage-derived macromolecular machines responsible for the release of at least two proteins in the milieu, which are thought to form an extracellular appendage. although several t6ss have been shown to be involved in the virulence of animal and plant pathogens, clusters encoding these machines are found in the genomes of most species of gram-negative bacteria, including soil, marine, and environmental isolates. t6ss have been associated with several ph ...	2011	21378190
characterization of n-acylhomoserine lactone-degrading bacteria associated with the zingiber officinale (ginger) rhizosphere: co-existence of quorum quenching and quorum sensing in acinetobacter and burkholderia.	cell-to-cell communication (quorum sensing (qs)) co-ordinates bacterial behaviour at a population level. consequently the behaviour of a natural multi-species community is likely to depend at least in part on co-existing qs and quorum quenching (qq) activities. here we sought to discover novel n-acylhomoserine lactone (ahl)-dependent qs and qq strains by investigating a bacterial community associated with the rhizosphere of ginger (zingiber officinale) growing in the malaysian rainforest.	2011	21385437
determination of the electrokinetic potential of rhizobium leguminosarum bv trifolii rt24.2 using laser doppler velocimetry--a methodological study.	electrokinetic potential (+â, zeta potential) is one of the parameters which characterize the physicochemical properties of the bacterial cell envelope. the term is often used in the context of adhesiveness of bacteria and biofilm formation. this work presents the methodological aspects of zeta potential determination in strain rt24.2 of rhizobium leguminosarum using laser doppler velocimetry combined with phase analysis light scattering and changed electric field techniques. the influence of me ...	2011	21397639
multilocus sequence-based analysis delineates a clonal population of agrobacterium (rhizobium) radiobacter (agrobacterium tumefaciens) of human origin.	the genus agrobacterium includes plant-associated bacteria and opportunistic human pathogens. taxonomy and nomenclature within the genus remain controversial. in particular, isolates of human origin were all affiliated with the species agrobacterium (rhizobium) radiobacter, while phytopathogenic strains were designated under the synonym denomination agrobacterium tumefaciens. in order to study the relative distribution of agrobacterium strains according to their origins, we performed a multilocu ...	2011	21398532
development of functional symbiotic white clover root hairs and nodules requires tightly regulated production of rhizobial cellulase celc2.	the establishment of rhizobia as nitrogen-fixing endosymbionts within legume root nodules requires the disruption of the plant cell wall to breach the host barrier at strategic infection sites in the root hair tip and at points of bacterial release from infection threads (it) within the root cortex. we previously found that rhizobium leguminosarum bv. trifolii uses its chromosomally encoded celc2 cellulase to erode the noncrystalline wall at the apex of root hairs, thereby creating the primary p ...	2011	21405987
the maturation factors hoxr and hoxt contribute to oxygen tolerance of membrane-bound [nife] hydrogenase in ralstonia eutropha h16.	the membrane-bound [nife] hydrogenase (mbh) of ralstonia eutropha h16 undergoes a complex maturation process comprising cofactor assembly and incorporation, subunit oligomerization, and finally twin-arginine-dependent membrane translocation. due to its outstanding o(2) and co tolerance, the mbh is of biotechnological interest and serves as a molecular model for a robust hydrogen catalyst. adaptation of the enzyme to oxygen exposure has to take into account not only the catalytic reaction but als ...	2011	21441514
biochemical characterization of sinorhizobium meliloti mutants reveals gene products involved in the biosynthesis of the unusual lipid a very long-chain fatty acid.	sinorhizobium meliloti forms a symbiosis with the legume alfalfa, whereby it differentiates into a nitrogen-fixing bacteroid. the lipid a species of s. meliloti are modified with very long-chain fatty acids (vlcfas), which play a central role in bacteroid development. a six-gene cluster was hypothesized to be essential for the biosynthesis of vlcfa-modified lipid a. previously, two cluster gene products, acpxl and lpxxl, were found to be essential for s. meliloti lipid a vlcfa biosynthesis. in t ...	2011	21454518
housekeeping genes essential for pantothenate biosynthesis are plasmid-encoded in rhizobium etli and rhizobium leguminosarum.	a traditional concept in bacterial genetics states that housekeeping genes, those involved in basic metabolic functions needed for maintenance of the cell, are encoded in the chromosome, whereas genes required for dealing with challenging environmental conditions are located in plasmids. exceptions to this rule have emerged from genomic sequence data of bacteria with multipartite genomes. the genome sequence of r. etli cfn42 predicts the presence of panc and panb genes clustered together on the ...	2011	21463532
heme binding to the second, lower-affinity site of the global iron regulator irr from rhizobium leguminosarum promotes oligomerization.	the iron responsive regulator irr is found in a wide range of α-proteobacteria, where it regulates many genes in response to the essential but toxic metal iron. unlike fur, the transcriptional regulator that is used for iron homeostasis by almost all other bacterial lineages, irr does not sense fe(2+) directly, but, rather, interacts with a physiologically important form of iron, namely heme. recent studies of irr from the n(2) -fixing symbiont rhizobium leguminosarum (irr(rl) ) showed that it b ...	2011	21481185
xerr, a negative regulator of xccr in xanthomonas campestris pv. campestris, relieves its repressor function in planta.	we previously reported that xccr, a luxr-type regulator of xanthomonas campestris pv. campestris (xcc), activates the downstream proline iminopeptidase virulence gene (pip) in response to certain host plant factor(s). in this report, we further show that the expression of the xccr gene was repressed in the culture medium by an ntrc-type response regulator, which we named xerr (xccr expression-related, repressor), and that this repression was relieved when the bacteria were grown in planta. such ...	2011	21483448
a chaperonin subunit with unique structures is essential for folding of a specific substrate.	type i chaperonins are large, double-ring complexes present in bacteria (groel), mitochondria (hsp60), and chloroplasts (cpn60), which are involved in mediating the folding of newly synthesized, translocated, or stress-denatured proteins. in escherichia coli, groel comprises 14 identical subunits and has been exquisitely optimized to fold its broad range of substrates. however, multiple cpn60 subunits with different expression profiles have evolved in chloroplasts. here, we show that, in arabido ...	2011	21483722
molecular diversity and phylogeny of rhizobia associated with lablab purpureus (linn.) grown in southern china.	as an introduced plant, lablab purpureus serves as a vegetable, herbal medicine, forage and green manure in china. in order to investigate the diversity of rhizobia associated with this plant, a total of 49 rhizobial strains isolated from ten provinces of southern china were analyzed in the present study with restriction fragment length polymorphism and/or sequence analyses of housekeeping genes (16s rrna, igs, atpd, glnii and reca) and symbiotic genes (nifh and nodc). the results defined the l. ...	2011	21498018
bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.	trimeric intracellular cation-specific (tric) channels are integral to muscle excitation-contraction coupling. tric channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. until recently, knowledge of the presence of these proteins was limited to animals. we analyzed the tric family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. prokaryotic memb ...	2011	21519847
a bacterial sub-family of luxr regulators that respond to plant compounds.	pseudomonas fluorescens are rhizobacteria known for their biocontrol properties; several antimicrobial functions are crucial for this process; experiments here investigate the modulation of their expression during the plant-bacterial interaction. the role of a luxr family regulator in interkingdom signalling has been investigated using genome-scale transcriptome analysis, gene promoter studies in vivo and in vitro, biocontrol assays and response to plant compounds. psor, a luxr solo or orphan re ...	2011	21531826
hydroxylated ornithine lipids increase stress tolerance in rhizobium tropici ciat899.	ornithine lipids (ols) are widespread among gram-negative bacteria. their basic structure consists of a 3-hydroxy fatty acyl group attached in amide linkage to the α-amino group of ornithine and a second fatty acyl group ester-linked to the 3-hydroxy position of the first fatty acid. ols can be hydroxylated within the secondary fatty acyl moiety and this modification has been related to increased stress tolerance. rhizobium tropici, a nodule-forming α-proteobacterium known for its stress toleran ...	2011	21205018
the transport mechanism of bacterial cu+-atpases: distinct efflux rates adapted to different function.	cu(+)-atpases play a key role in bacterial cu(+) homeostasis by participating in cu(+) detoxification and cuproprotein assembly. characterization of archaeoglobus fulgidus copa, a model protein within the subfamily of p(1b-1) type atpases, has provided structural and mechanistic details on this group of transporters. atomic resolution structures of cytoplasmic regulatory metal binding domains (mbds) and catalytic actuator, phosphorylation, and nucleotide binding domains are available. these, in ...	2011	21210186
cyclic gmp controls rhodospirillum centenum cyst development.	adenylyl cyclases are widely distributed across all kingdoms whereas guanylyl cyclases are generally thought to be restricted to eukaryotes. here we report that the α-proteobacterium rhodospirillum centenum secretes cgmp when developing cysts and that a guanylyl cyclase deletion strain fails to synthesize cgmp and is defective in cyst formation. the r. centenum cyclase was purified and shown to effectively synthesize cgmp from gtp in vitro, demonstrating that it is a functional guanylyl cyclase. ...	2011	21214648
solution structure of 4'-phosphopantetheine - gmacp3 from geobacter metallireducens: a specialized acyl carrier protein with atypical structural features and a putative role in lipopolysaccharide biosynthesis.	gmacp3 from geobacter metallireducens is a specialized acyl carrier protein (acp) whose gene, gmet_2339, is located near genes encoding many proteins involved in lipopolysaccharide (lps) biosynthesis, indicating a likely function for gmacp3 in lps production. by overexpression in escherichia coli, about 50% holo-gmacp3 and 50% apo-gmacp3 were obtained. apo-gmacp3 exhibited slow precipitation and non-monomeric behavior by (15)n nmr relaxation measurements. addition of 4'-phosphopantetheine (4'-pp ...	2011	21235239
a processive glycosyltransferase involved in glycolipid synthesis during phosphate deprivation in mesorhizobium loti.	natural habitats are often characterized by a low availability of phosphate. in plants and many bacteria, phosphate deficiency causes different physiological responses, including the replacement of phosphoglycerolipids in the membranes with nonphosphorous lipids. we describe here a processive glycosyltransferase (pgt) in mesorhizobium loti (rhizobiales) involved in the synthesis of di- and triglycosyldiacylglycerols (dglycd and tglycd) during phosphate deprivation. cells of the corresponding δpg ...	2011	21239587
failure to fix nitrogen by non-reproductive symbiotic rhizobia triggers host sanctions that reduce fitness of their reproductive clonemates.	the legume-rhizobia symbiosis is a classical mutualism where fixed carbon and nitrogen are exchanged between the species. nonetheless, the plant carbon that fuels nitrogen (n(2)) fixation could be diverted to rhizobial reproduction by 'cheaters'--rhizobial strains that fix less n(2) but potentially gain the benefit of fixation by other rhizobia. host sanctions can decrease the relative fitness of less-beneficial reproductive bacteroids and prevent cheaters from breaking down the mutualism. howev ...	2011	21270038
genome sequence analyses of pseudomonas savastanoi pv. glycinea and subtractive hybridization-based comparative genomics with nine pseudomonads.	bacterial blight, caused by pseudomonas savastanoi pv. glycinea (psg), is a common disease of soybean. in an effort to compare a current field isolate with one isolated in the early 1960s, the genomes of two psg strains, race 4 and b076, were sequenced using 454 pyrosequencing. the genomes of both psg strains share more than 4,900 highly conserved genes, indicating very low genetic diversity between psg genomes. though conserved, genome rearrangements and recombination events occur commonly with ...	2011	21304594
biosynthesis of udp-xylose and udp-arabinose in sinorhizobium meliloti 1021: first characterization of a bacterial udp-xylose synthase, and udp-xylose 4-epimerase.	sinorhizobium meliloti is a soil bacterium that fixes nitrogen after being established inside nodules that can form on the roots of several legumes, including medicago truncatula. a mutation in an s. meliloti gene (lpsb) required for lipopolysaccharide synthesis has been reported to result in defective nodulation and an increase in the synthesis of a xylose-containing glycan. glycans containing xylose as well as arabinose are also formed by other rhizobial species, but little is known about thei ...	2011	20847005
solving the problem: genome annotation standards before the data deluge.	the promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. researchers recognize that there is a need for high quality data. however, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. ncbi in collaboratio ...	2011	22180819
discovering the unknown: improving detection of novel species and genera from short reads.	high-throughput sequencing technologies enable metagenome profiling, simultaneous sequencing of multiple microbial species present within an environmental sample. since metagenomic data includes sequence fragments ("reads") from organisms that are absent from any database, new algorithms must be developed for the identification and annotation of novel sequence fragments. homology-based techniques have been modified to detect novel species and genera, but, composition-based methods, have not been ...	2011	21541181
recent advances in bacterial heme protein biochemistry.	recent progress in genetics, fed by the burst in genome sequence data, has led to the identification of a host of novel bacterial heme proteins that are now being characterized in structural and mechanistic terms. the following short review highlights very recent work with bacterial heme proteins involved in the uptake, biosynthesis, degradation, and use of heme in respiration and sensing.	2011	21339081
auxin and plant-microbe interactions.	microbial synthesis of the phytohormone auxin has been known for a long time. this property is best documented for bacteria that interact with plants because bacterial auxin can cause interference with the many plant developmental processes regulated by auxin. auxin biosynthesis in bacteria can occur via multiple pathways as has been observed in plants. there is also increasing evidence that indole-3-acetic acid (iaa), the major naturally occurring auxin, is a signaling molecule in microorganism ...	2011	21084388
plant-bacteria association and symbiosis: are there common genomic traits in alphaproteobacteria?	alphaproteobacteria show a great versatility in adapting to a broad range of environments and lifestyles, with the association between bacteria and plants as one of the most intriguing, spanning from relatively unspecific nonsymbiotic association (as rhizospheric or endophytic strains) to the highly species-specific interaction of rhizobia. to shed some light on possible common genetic features in such a heterogeneous set of plant associations, the genomes of 92 alphaproteobacteria strains were ...	2011	24710303
poles apart: prokaryotic polar organelles and their spatial regulation.	while polar organelles hold the key to understanding the fundamentals of cell polarity and cell biological principles in general, they have served in the past merely for taxonomical purposes. here, we highlight recent efforts in unraveling the molecular basis of polar organelle positioning in bacterial cells. specifically, we detail the role of members of the ras-like gtpase superfamily and coiled-coil-rich scaffolding proteins in modulating bacterial cell polarity and in recruiting effector pro ...	2011	21084387
lipooligosaccharide is required for the generation of infectious elementary bodies in chlamydia trachomatis.	lipopolysaccharides (lps) and lipooligosaccharides (los) are the main lipid components of bacterial outer membranes and are essential for cell viability in most gram-negative bacteria. here we show that small molecule inhibitors of lpxc [udp-3-o-(r-3-hydroxymyristoyl)-glcnac deacetylase], the enzyme that catalyzes the first committed step in the biosynthesis of lipid a, block the synthesis of los in the obligate intracellular bacterial pathogen chlamydia trachomatis. in the absence of los, chlam ...	2011	21628561
competitiveness of rhizobium leguminosarum bv. trifolii strains in mixed inoculation of clover (trifolium pratense).	rhizobium leguminosarum by. trifolii (rlt) establishes beneficial root nodule symbiosis with clover. twenty rlt strains differentially marked with antibiotic-resistance markers were investigated in terms of their competitiveness and plant growth promotion in mixed inoculation of clover in laboratory experiments. the results showed that the studied strains essentially differed in competition ability. these differences seem not to be dependent on bacterial multiplication in the vicinity of roots, ...	2011	21630573
Field monitoring of plant-growth-promoting rhizobacteria by colony immunoblotting.	Inoculant plant-growth-promoting bacteria are emerging as an important component of sustainable agriculture. There is a need to develop inexpensive methods for enumerating these organisms after their application in the field, to better understand their survival and impacts on yields. Immunoblotting is one potential method to measure viable cells, but the high cost of the conventionally used nylon membranes makes this method prohibitive. In this study, less expensive alternative materials such as ...	2011	22017658
contribution of the lipopolysaccharide to resistance of shigella flexneri 2a to extreme acidity.	shigella flexneri is endemic in most underdeveloped countries, causing diarrheal disease and dysentery among young children. in order to reach its target site, the colon, shigella must overcome the acid environment of the stomach. shigella is able to persist in this stressful environment and, because of this ability it can initiate infection following the ingestion of very small inocula. thus, acid resistance is considered an important virulence trait of this bacterium. it has been reported that ...	2011	21984920
comparative characterization of fungal anthracenone and naphthacenedione biosynthetic pathways reveals an α-hydroxylation-dependent claisen-like cyclization catalyzed by a dimanganese thioesterase.	the linear tetracyclic tan-1612 (1) and bms-192548 (2) were isolated from different filamentous fungal strains and have been examined as potential neuropeptide y and neurokinin-1 receptor antagonists, respectively. although the biosynthesis of fungal aromatic polyketides has attracted much interest in recent years, the biosynthetic mechanism for such naphthacenedione-containing products has not been established. using a targeted genome mining approach, we first located the ada gene cluster respo ...	2011	21866960
adaptation of rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics.	abstract: background: the rhizosphere is the microbe-rich zone around plant roots and is a key determinant of the biosphere's productivity. comparative transcriptomics was used to investigate general and plant-specific adaptations during rhizosphere colonization. rhizobium leguminosarum biovar viciae was grown in the rhizospheres of pea (its legume nodulation host), alfalfa (a non-host legume) and sugar beet (non-legume). gene expression data were compared to metabolic and transportome maps to ...	2011	22018401
Environmental signals and regulatory pathways that influence exopolysaccharide production in rhizobia.	Rhizobia are Gram-negative bacteria that can exist either as free-living bacteria or as nitrogen-fixing symbionts inside root nodules of leguminous plants. The composition of the rhizobial outer surface, containing a variety of polysaccharides, plays a significant role in the adaptation of these bacteria in both habitats. Among rhizobial polymers, exopolysaccharide (EPS) is indispensable for the invasion of a great majority of host plants which form indeterminate-type nodules. Various functions ...	2011	22174640
transformation of pwwo in rhizobium leguminosarum dpt to engineer toluene degrading ability for rhizoremediation.	rhizoremediation of organic xenobiotics is based on interactions between plants and their associated micro-organisms. the present work was designed to engineer a bacterial system having toluene degradation ability along with plant growth promoting characteristics for effective rhizoremediation. pwwo harboring the genes responsible for toluene breakdown was isolated from pseudomonas putida mtcc 979 and successfully transformed in rhizobium dpt. this resulted in a bacterial strain (dpt(t)) which h ...	2011	23729882
transformation of pwwo in rhizobium leguminosarum dpt to engineer toluene degrading ability for rhizoremediation.	rhizoremediation of organic xenobiotics is based on interactions between plants and their associated micro-organisms. the present work was designed to engineer a bacterial system having toluene degradation ability along with plant growth promoting characteristics for effective rhizoremediation. pwwo harboring the genes responsible for toluene breakdown was isolated from pseudomonas putida mtcc 979 and successfully transformed in rhizobium dpt. this resulted in a bacterial strain (dpt(t)) which h ...	2011	23729882
characterization of outer membrane vesicles from brucella melitensis and protection induced in mice.	the outer membrane vesicles (omvs) from smooth b. melitensis 16 m and a derived rough mutant, vtrm1 strain, were purified and characterized with respect to protein content and induction of immune responses in mice. proteomic analysis showed 29 proteins present in omvs from b. melitensis 16 m; some of them are well-known brucella immunogens such as sod, groes, omp31, omp25, omp19, bp26, and omp16. omvs from a rough vtrm1 induced significantly higher expression of il-12, tnfα, and ifnγ genes in bo ...	2011	22242036
characterization of outer membrane vesicles from brucella melitensis and protection induced in mice.	the outer membrane vesicles (omvs) from smooth b. melitensis 16 m and a derived rough mutant, vtrm1 strain, were purified and characterized with respect to protein content and induction of immune responses in mice. proteomic analysis showed 29 proteins present in omvs from b. melitensis 16 m; some of them are well-known brucella immunogens such as sod, groes, omp31, omp25, omp19, bp26, and omp16. omvs from a rough vtrm1 induced significantly higher expression of il-12, tnfα, and ifnγ genes in bo ...	2011	22242036
azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.	fossil records indicate that life appeared in marine environments ∼3.5 billion years ago (gyr) and transitioned to terrestrial ecosystems nearly 2.5 gyr. sequence analysis suggests that "hydrobacteria" and "terrabacteria" might have diverged as early as 3 gyr. bacteria of the genus azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. we obtained genome sequences of two azospirillum species and analyzed their gene origins. while m ...	2011	22216014
rhizobia species: a boon for "plant genetic engineering".	since past three decades new discoveries in plant genetic engineering have shown remarkable potentials for crop improvement. agrobacterium ti plasmid based dna transfer is no longer the only efficient way of introducing agronomically important genes into plants. recent studies have explored a novel plant genetic engineering tool, rhizobia sp., as an alternative to agrobacterium, thereby expanding the choice of bacterial species in agricultural plant biotechnology. rhizobia sp. serve as an open l ...	2011	23024417
annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms.	the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ...	2011	24710297
ros-mediated signalling in bacteria: zinc-containing cys-x-x-cys redox centres and iron-based oxidative stress.	bacteria are permanently in contact with reactive oxygen species (ros), both over the course of their life cycle as well that present in their environment. these species cause damage to proteins, lipids, and nucleotides, negatively impacting the organism. to detect these ros molecules and to stimulate the expression of proteins involved in antioxidative stress response, bacteria use a number of different protein-based regulatory and sensory systems. ros-based stress detection mechanisms induce p ...	2011	21977318
ros-mediated signalling in bacteria: zinc-containing cys-x-x-cys redox centres and iron-based oxidative stress.	bacteria are permanently in contact with reactive oxygen species (ros), both over the course of their life cycle as well that present in their environment. these species cause damage to proteins, lipids, and nucleotides, negatively impacting the organism. to detect these ros molecules and to stimulate the expression of proteins involved in antioxidative stress response, bacteria use a number of different protein-based regulatory and sensory systems. ros-based stress detection mechanisms induce p ...	2011	21977318
distribution of genes encoding nucleoid-associated protein homologs in plasmids.	bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ...	2011	21350637
exploring the genetic diversity of ethiopian grass pea (lathyrus sativus l.) using est-ssr markers.	expressed sequence tags (ests) in public databases and cross-species transferable markers are considered to be a cost-effective means for developing sequence-based markers for less-studied species. in this study, est-simple sequence repeat (ssr) markers developed from lathyrus sativus l. est sequences and cross-transferable est-ssrs derived from medicago truncatula l. were utilized to investigate the genetic diversity among grass pea populations from ethiopia. a total of 45 alleles were detected ...	2011	22924019
exploring the genetic diversity of ethiopian grass pea (lathyrus sativus l.) using est-ssr markers.	expressed sequence tags (ests) in public databases and cross-species transferable markers are considered to be a cost-effective means for developing sequence-based markers for less-studied species. in this study, est-simple sequence repeat (ssr) markers developed from lathyrus sativus l. est sequences and cross-transferable est-ssrs derived from medicago truncatula l. were utilized to investigate the genetic diversity among grass pea populations from ethiopia. a total of 45 alleles were detected ...	2011	22924019
bacterial catabolism of dimethylsulfoniopropionate (dmsp).	dimethylsulfoniopropionate (dmsp) is a metabolite produced primarily by marine phytoplankton and is the main precursor to the climatically important gas dimethylsulfide (dms). dms is released upon bacterial catabolism of dmsp, but it is not the only possible fate of dmsp sulfur. an alternative demethylation/demethiolation pathway results in the eventual release of methanethiol, a highly reactive volatile sulfur compound that contributes little to the atmospheric sulfur flux. the activity of thes ...	2011	21886640
vacuolar organization in the nodule parenchyma is important for the functioning of pea root nodules.	different models have been proposed to explain the operation of oxygen diffusion barrier in root nodules of leguminous plants. this barrier participates in protection of oxygen-sensitive nitrogenase, the key enzyme in nitrogen fixation, from inactivation. details concerning structural and biochemical properties of the barrier are still lacking. here, the properties of pea root nodule cortical cells were examined under normal conditions and after shoot removal. microscopic observations, including ...	2011	21957326
determination of symbiotic nodule occupancy in the model vicia tetrasperma using a fluorescence scanner.	fluorescent tagging of nodule bacteria forming symbioses with legume host plants represents a tool for vital tracking of bacteria inside the symbiotic root nodules and monitoring changes in gene activity. the constitutive expression of heterologous fluorescent proteins, such as green fluorescent protein (gfp), also allows screening for nodule occupancy by a particular strain. imaging of the fluorescence signal on a macro-scale is associated with technical problems due to the robustness of nodule ...	2011	21262794
malonyl-coa synthetase, encoded by acyl activating enzyme13, is essential for growth and development of arabidopsis.	malonyl-coa is the precursor for fatty acid synthesis and elongation. it is also one of the building blocks for the biosynthesis of some phytoalexins, flavonoids, and many malonylated compounds. in plants as well as in animals, malonyl-coa is almost exclusively derived from acetyl-coa by acetyl-coa carboxylase (ec 6.4.1.2). however, previous studies have suggested that malonyl-coa may also be made directly from malonic acid by malonyl-coa synthetase (ec 6.2.1.14). here, we report the cloning of ...	2011	21642549
in vitro sensitivity of rhizobium and phosphate solubilising bacteria to herbicides.	nitrogen fixing bacteria, rhizobia and phosphate solubilizing bacteria (psb) are the commonly applied microbial inoculants in grain legumes (pulses). it is important to apply herbicides to control weeds in order to augment yield of the crop. the herbicides may however, be incompatible with the microbial inoculants. this study compared the effect of the recommended pre-plant incorporated herbicide, fluchloralin (20.25 × 10(4) ppm) and pre-emergence herbicide, pendimethalin in two doses (9 × 10(4) ...	2011	22654170
legume pectate lyase required for root infection by rhizobia.	to allow rhizobial infection of legume roots, plant cell walls must be locally degraded for plant-made infection threads (its) to be formed. here we identify a lotus japonicus nodulation pectate lyase gene (ljnpl), which is induced in roots and root hairs by rhizobial nodulation (nod) factors via activation of the nodulation signaling pathway and the nin transcription factor. two ljnpl mutants produced uninfected nodules and most infections arrested as infection foci in root hairs or roots. the ...	2011	22203959
legume pectate lyase required for root infection by rhizobia.	to allow rhizobial infection of legume roots, plant cell walls must be locally degraded for plant-made infection threads (its) to be formed. here we identify a lotus japonicus nodulation pectate lyase gene (ljnpl), which is induced in roots and root hairs by rhizobial nodulation (nod) factors via activation of the nodulation signaling pathway and the nin transcription factor. two ljnpl mutants produced uninfected nodules and most infections arrested as infection foci in root hairs or roots. the ...	2011	22203959
structural interaction between gfp-labeled diazotrophic endophytic bacterium herbaspirillum seropedicae ram10 and pineapple plantlets 'vitória'.	the events involved in the structural interaction between the diazotrophic endophytic bacterium herbaspirillum seropedicae, strain ram10, labeled with green fluorescent protein, and pineapple plantlets 'vitória' were evaluated by means of bright-field and fluorescence microscopy, combined with scanning electron microscopy for 28 days after inoculation. after 6 hours of inoculation, h. seropedicae was already adhered to the roots, colonizing mainly root hair surface and bases, followed by epiderm ...	2011	24031612
micrornas as master regulators of the plant nb-lrr defense gene family via the production of phased, trans-acting sirnas.	legumes and many nonleguminous plants enter symbiotic interactions with microbes, and it is poorly understood how host plants respond to promote beneficial, symbiotic microbial interactions while suppressing those that are deleterious or pathogenic. trans-acting sirnas (tasirnas) negatively regulate target transcripts and are characterized by sirnas spaced in 21-nucleotide (nt) "phased" intervals, a pattern formed by dicer-like 4 (dcl4) processing. a search for phased sirnas (phasirnas) found at ...	2011	22156213
identification and characterization of the endophytic plant growth prompter bacillus cereus strain mq23 isolated from sophora alopecuroides root nodules.	endophytes mq23 and mq23r isolated from sophora alopecuroides root nodules were characterized by observing their ability to promote plant growth and employing molecular analysis techniques. results showed that mq23 and mq23r are potential n2-fixing endophytes and belong to the same species as bacillus cereus. mq23 was shown to be able to produce siderophores, iaa, and demonstrate certain antifungal activity to plant pathogenic fungi. co-inoculation with mq23+mq23ii showed a more significant effe ...	2011	24031669
iron-containing transcription factors and their roles as sensors.	iron-binding transcription factors are widespread throughout the bacterial world and to date are known to bind several types of cofactors, such as fe2+, heme, or iron-sulfur clusters. the known chemistry of these cofactors is exploited by transcription factors, including fur, fnr, and nsrr, to sense molecules such as fe2+, gases (e.g. oxygen and nitric oxide), or reactive oxygen species. new structural data and information generated by genome-wide analysis studies have provided additional detail ...	2011	21292540
does gaba increase the efficiency of symbiotic n2 fixation in legumes?	the ability to regulate the rates of metabolic processes in response to changes in the internal and/or external environment is a fundamental feature which is inherent in all organisms. this adaptability is necessary for conserving the stability of the intercellular environment (homeostasis) which is essential for maintaining an efficient functional state in the organism. symbiotic nitrogen fixation in legumes is an important process which establishes from the complex interaction between the host ...	2011	21307661
characterization of free nitrogen fixing bacteria of the genus azotobacter in organic vegetable-grown colombian soils.	with the purpose of isolating and characterizing free nitrogen fixing bacteria (fnfb) of the genus azotobacter, soil samples were collected randomly from different vegetable organic cultures with neutral ph in different zones of boyacá-colombia. isolations were done in selective free nitrogen ashby-sucrose agar obtaining a recovery of 40%. twenty four isolates were evaluated for colony and cellular morphology, pigment production and metabolic activities. molecular characterization was carried ou ...	2011	24031700
[phylogenetic analysis of symbiotic genes of nodule bacteria in the plants of the genus lathyrus (l.) (fabaceae)].	the comparative analysis of the symbiotic genes nifd, nifh, noda of wild-growing lathyrus l. species (fabaceae) connected by genes sequences of 16s arna to rhizobium leguminosarum bv. viceae, rhizobium tropici, agrobacterium sp., and phyllobacterium sp. was carried out. it was demonstrated that all tested genes of strains taken for analysis had high degree of homology with analogous genes of rhizobium leguminosarum bv. viceae. it was suggested that symbiotic genes were introduced into rhizobium ...	2011	22312895
identification of a nodd repressible gene adjacent to nodm in rhizobium leguminosarum biovar viciae.	the nodfel and nodmnt operons in rhizobium leguminosarum biovar viciae are transcribed in the same orientation and induced by nodd in response to flavonoids secreted by legumes. in the narrow intergenic region between nodfel and nodmnt, we identified a small gene divergently transcribed from nodm to the 3' end of nodl. unlike the promoters upstream of nodf and nodm, the promoter of this gene is constitutively expressed. it appeared that its promoter might partially overlap with that of nodm and ...	2012	22337919
polymorphic infection and organogenesis patterns induced by a rhizobium leguminosarum isolate from lotus root nodules are determined by the host genotype.	to sample the natural variation in genes controlling compatibility in the legume-rhizobium symbiosis, we isolated rhizobia from nodules of endemic lotus species from 21 sites across europe. the majority of isolates were identified as mesorhizobium- or bradyrhizobium-related and formed nitrogen-fixing root nodules on lotus corniculatus and l. pendunculatus, respectively, thus confirming previously defined cross-inoculation groups. rhizobium leguminosarum (rl) strain norway, isolated from l. corni ...	2012	22950721
genetic analysis reveals links between lipid a structure and expression of the outer membrane protein gene, ropb, in rhizobium leguminosarum.	the fabxl genes encode enzymes that synthesize the very-long-chain fatty acid - a unique acyl modification located at the 2' position of the lipid a of gram-negative bacteria in the order rhizobiales. mutation of the fabxl genes causes sensitivity to outer membrane stressors and other envelope-related stresses; however, the underlying mechanisms for increased sensitivity are poorly understood. we found that expression of the outer membrane protein gene ropb is down-regulated in an acpxl mutant. ...	2012	22845832
oligogalacturonides: novel signaling molecules in rhizobium-legume communications.	oligogalacturonides are pectic fragments of the plant cell wall, whose signaling role has been described thus far during plant development and plant-pathogen interactions. in the present work, we evaluated the potential involvement of oligogalacturonides in the molecular communications between legumes and rhizobia during the establishment of nitrogen-fixing symbiosis. oligogalacturonides with a degree of polymerization of 10 to 15 were found to trigger a rapid intracellular production of reactiv ...	2012	22835276
removal of chromium using rhizobium leguminosarum.	the chromium (cr(iii) and cr(vi)) removal capability of rhizobium leguminosarum was checked by estimating the amount of chromium in the medium before and after inoculation. to determine the efficiency of r. leguminosarum in removal of chromium, the influence of physical and chemical parameters such as temperature, ph and different concentrations (0.1-1.0 mm) of trivalent (cr(iii)) and hexavalent (cr(vi)) chromium were studied. the chromium removal in aqueous solution by different size of active ...	2012	22806858
[genetic structure of introduced and natural populations of rhizobium leguminosarum in systems "plant-soil"].		2012	22693834
novel structural and functional insights into the moxr family of aaa+ atpases.	the moxr family of aaa+ atpases is widespread among bacteria and archaea, although their cellular functions are not well characterized. based on recent studies, moxr atpases are proposed to have chaperone-like function for the maturation of specific protein complexes or for the insertion of cofactors into proteins. moxr proteins have been found to be important modulators of multiple stress response pathways in different organisms. for example, the respective moxr proteins have been found to play ...	2012	22491058
application of targeted metagenomics to explore abundance and diversity of co₂-fixing bacterial community using cbbl gene from the rhizosphere of arachis hypogaea.	sequestration of co(2) by autotrophic bacteria is a key process of biogeochemical carbon cycling in soil ecosystem. rhizosphere is a rich niche of microbial activity and diversity, influenced by change in atmospheric co(2). structural changes in rhizosphere composition influence microbial communities and the nutrient cycling. in the present study, the bacterial diversity and population dynamics were established using cbbl and 16s rrna gene targeted metagenomics approach from the rhizosphere of a ...	2012	22766402
glycerol utilization by rhizobium leguminosarum requires an abc transporter and affects competition for nodulation.	plasmid curing has shown that the ability to use glycerol as a carbon source is plasmid-encoded in rhizobium leguminosarum. we isolated the locus responsible for glycerol utilization from plasmid prlevf39c in r. leguminosarum bv. viciae vf39. this region was analyzed by dna sequencing and mutagenesis. the locus encompasses a gene encoding glpr (a deor regulator), genes encoding an abc transporter, and genes glpk and glpd, encoding a kinase and dehydrogenase, respectively. all the genes except th ...	2012	22343359
the pts(ntr) system globally regulates atp-dependent transporters in rhizobium leguminosarum.	mutation of ptsp encoding ei(ntr) of the pts(ntr) system in rhizobium leguminosarum strain rlv3841 caused a pleiotropic phenotype as observed with many bacteria. the mutant formed dry colonies and grew poorly on organic nitrogen or dicarboxylates. most strikingly the ptsp mutant had low activity of a broad range of atp-dependent abc transporters. this lack of activation, which occurred post-translationally, may explain many of the pleiotropic effects. in contrast proton-coupled transport systems ...	2012	22340847
integrated management of foot rot of lentil using biocontrol agents under field condition.	the efficacy of cowdung, bangladesh institute of nuclear agriculture (bina)-biofertilizer, and bangladesh agricultural university (bau)-biofungicide, alone or in combination, was evaluated for controlling foot rot disease of lentil. the results exhibited that bina-biofertilizer and baubiofungicide (peat soil-based rhizobium leguminosarum and black gram bran-based trichoderma harzianum) are compatible and have combined effects in controlling the pathogenic fungi fusarium oxysporum and sclerotium ...	2012	22580305
genetic diversity of rhizobia nodulating lentil (lens culinaris) in bangladesh.	in order to determine the bacterial diversity and the identity of rhizobia nodulating lentil in bangladesh, we performed a phylogenetic analysis of housekeeping genes (16s rrna, reca, atpd and glnii) and nodulation genes (nodc, nodd and noda) of 36 bacterial isolates from 25 localities across the country. maximum likelihood (ml) and bayesian analyses based on 16s rrna sequences showed that most of the isolates (30 out of 36) were related to rhizobium etli and rhizobium leguminosarum. only these ...	2012	22280898
manganese uptake in marine bacteria; the novel mntx transporter is widespread in roseobacters, vibrios, alteromonadales and the sar11 and sar116 clades.	we showed that two very different manganese transporters occur in various important genera of marine bacteria. the abc transporter encoded by sitabcd of the model roseobacter-clade bacterium ruegeria pomeroyi dss-3 is required for mn(2+) import and was repressed by the mur (manganese uptake regulator) transcriptional regulator in mn-replete media. most genome-sequenced roseobacter strains contain sitabcd, which are in at least two sub-groups, judged by their amino-acid sequences. however, a few ...	2012	23190726
manganese uptake in marine bacteria; the novel mntx transporter is widespread in roseobacters, vibrios, alteromonadales and the sar11 and sar116 clades.	we showed that two very different manganese transporters occur in various important genera of marine bacteria. the abc transporter encoded by sitabcd of the model roseobacter-clade bacterium ruegeria pomeroyi dss-3 is required for mn(2+) import and was repressed by the mur (manganese uptake regulator) transcriptional regulator in mn-replete media. most genome-sequenced roseobacter strains contain sitabcd, which are in at least two sub-groups, judged by their amino-acid sequences. however, a few ...	2012	23190726
construction of a new gfp vector and its use for fusaruim oxysporum transformation.	in this study, the gfp fragment as a reporter gene had integrated into the form plasmid vector pbc-hygro which contains an expressive promoter of the fungus to facilitate the transformation of fusarium oxysporum. the resultant plasmid pbc-hygro-gfp was identified by digestion with enzymes. binary plasmids pbc-hygro-gfp were transformed into f. oxysporum by using the peg-cacl2 mediated transformation technique. results show that the recombinant plasmid pbc-hygro-gfp was constructed correctly. the ...	2012	23961215
construction of a new gfp vector and its use for fusaruim oxysporum transformation.	in this study, the gfp fragment as a reporter gene had integrated into the form plasmid vector pbc-hygro which contains an expressive promoter of the fungus to facilitate the transformation of fusarium oxysporum. the resultant plasmid pbc-hygro-gfp was identified by digestion with enzymes. binary plasmids pbc-hygro-gfp were transformed into f. oxysporum by using the peg-cacl2 mediated transformation technique. results show that the recombinant plasmid pbc-hygro-gfp was constructed correctly. the ...	2012	23961215
phosphorus limitation increases attachment in agrobacterium tumefaciens and reveals a conditional functional redundancy in adhesin biosynthesis.	bacterial responses to phosphorus limitation, commonly inorganic phosphate (p(i)), are important survival mechanisms in a variety of environments. the two-component sensor kinase phor and its cognate response regulator phob are central to the p(i) limitation response of many bacteria and control the large pho regulon. limitation for p(i) significantly increased attachment and biofilm formation by the plant pathogen agrobacterium tumefaciens, and this was driven by phob. surprisingly, it was also ...	2012	23103488
characterization of the twin-arginine transport secretome in sinorhizobium meliloti and evidence for host-dependent phenotypes.	the twin-arginine transport (tat) system is essential for cell viability in sinorhizobium meliloti and may play a role during the development of root nodules. utilizing an in vivo recombination strategy, we have constructed 28 strains that contain deletions in predicted tat substrates. testing of these mutations for symbiotic proficiency on the plant hosts alfalfa and sweet clover shows that some of these mutations affect associations with these hosts differentially.	2012	22843517
identifying abnormalities in symbiotic development between trifolium spp. and rhizobium leguminosarum bv. trifolii leading to sub-optimal and ineffective nodule phenotypes.	legumes overcome nitrogen limitations by entering into a mutualistic symbiosis with n(2)-fixing bacteria (rhizobia). fully compatible associations (effective) between trifolium spp. and rhizobium leguminosarum bv. trifolii result from successful recognition of symbiotic partners in the rhizosphere, root hair infection and the formation of nodules where n(2)-fixing bacteroids reside. poorly compatible associations can result in root nodule formation with minimal (sub-optimal) or no (ineffective) ...	2012	22989463
structure of a specialized acyl carrier protein essential for lipid a biosynthesis with very long-chain fatty acids in open and closed conformations.	the solution nuclear magnetic resonance (nmr) structures and backbone (15)n dynamics of the specialized acyl carrier protein (acp), rpacpxl, from rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4'-phosphopantetheine at s37, are virtually identical, monomeric, and correspond to the closed conformation. the structures have an extra α-helix compared to the archetypical acp from escherichia coli, which has four helices, resulting in a larger opening ...	2012	22876860
inability to catabolize galactose leads to increased ability to compete for nodule occupancy in sinorhizobium meliloti.	a mutant unable to utilize galactose was isolated in sinorhizobium meliloti strain rm1021. the mutation was found to be in a gene annotated dgok1, a putative 2-keto-3-deoxygalactonokinase. the genetic region was isolated on a complementing cosmid and subsequently characterized. based on genetic and bioinformatic evidence, the locus encodes all five enzymes (gald, dgok, dgoa, smc00883, and ilvd1) involved in the de ley-doudoroff pathway for galactose catabolism. although all five genes are presen ...	2012	22797764
genome sequence and mutational analysis of plant-growth-promoting bacterium agrobacterium tumefaciens ccnwgs0286 isolated from a zinc-lead mine tailing.	the plant-growth-promoting bacterium agrobacterium tumefaciens ccnwgs0286, isolated from the nodules of robinia pseudoacacia growing in zinc-lead mine tailings, both displayed high metal resistance and enhanced the growth of robinia plants in a metal-contaminated environment. our goal was to determine whether bacterial metal resistance or the capacity to produce phytohormones had a larger impact on the growth of host plants under zinc stress. eight zinc-sensitive mutants and one zinc-sensitive m ...	2012	22636006
"ménage à trois": the presence/absence of thyme shapes the mutualistic interaction between the host plant medicago truncatula (fabaceae) and its symbiotic bacterium sinorhizobium meliloti.	the long-term maintenance of specialized mutualisms remains an evolutionary puzzle. recent focus has been on factors governing the stability of these mutualisms, including sanctions by the host, partner choice, and coevolutionary constraint, that is, the genetic correlation (r(g)) between fitness of both partners. so far these studies have been typically carried out in a single environment. here, we ask if the genetic correlation between fitness of the host plant medicago truncatula (fabaceae) a ...	2012	22957171
technologies for beneficial microorganisms inocula used as biofertilizers.	the increasing need for environmentaly friendly agricultural practices is driving the use of fertilizers based on beneficial microorganisms. the latter belong to a wide array of genera, classes, and phyla, ranging from bacteria to yeasts and fungi, which can support plant nutrition with different mechanisms. moreover, studies on the interactions between plant, soil, and the different microorganisms are shedding light on their interrelationships thus providing new possible ways to exploit them fo ...	2012	22547984
expr is not required for swarming but promotes sliding in sinorhizobium meliloti.	swarming is a mode of translocation dependent on flagellar activity that allows bacteria to move rapidly across surfaces. in several bacteria, swarming is a phenotype regulated by quorum sensing. it has been reported that the swarming ability of the soil bacterium sinorhizobium meliloti rm2011 requires a functional expr/sin quorum-sensing system. however, our previous published results demonstrate that strains rm1021 and rm2011, both known to have a disrupted copy of expr, are able to swarm on s ...	2012	22328673
delivery of iron-sulfur clusters to the hydrogen-oxidizing [nife]-hydrogenases in escherichia coli requires the a-type carrier proteins erpa and isca.	during anaerobic growth escherichia coli synthesizes two membrane-associated hydrogen-oxidizing [nife]-hydrogenases, termed hydrogenase 1 and hydrogenase 2. each enzyme comprises a catalytic subunit containing the [nife] cofactor, an electron-transferring small subunit with a particular complement of [fe-s] (iron-sulfur) clusters and a membrane-anchor subunit. how the [fe-s] clusters are delivered to the small subunit of these enzymes is unclear. a-type carrier (atc) proteins of the isc (iron-su ...	2012	22363723
proteomic profiling of rhizobium tropici prf 81: identification of conserved and specific responses to heat stress.	rhizobium tropici strain prf 81 (= semia 4080) has been used in commercial inoculants for application to common-bean crops in brazil since 1998, due to its high efficiency in fixing nitrogen, competitiveness against indigenous rhizobial populations and capacity to adapt to stressful tropical conditions, representing a key alternative to application of n-fertilizers. the objective of our study was to obtain an overview of adaptive responses to heat stress of strain prf 81, by analyzing differenti ...	2012	22647150
the ruegeria pomeroyi acui gene has a role in dmsp catabolism and resembles yhdh of e. coli and other bacteria in conferring resistance to acrylate.	the escherichia coli yhdh polypeptide is in the mdr012 sub-group of medium chain reductase/dehydrogenases, but its biological function was unknown and no phenotypes of yhdh(-) mutants had been described. we found that an e. coli strain with an insertional mutation in yhdh was hyper-sensitive to inhibitory effects of acrylate, and, to a lesser extent, to those of 3-hydroxypropionate. close homologues of yhdh occur in many bacterial taxa and at least two animals. the acrylate sensitivity of yhdh(- ...	2012	22563425
the plant growth promoting substance, lumichrome, mimics starch, and ethylene-associated symbiotic responses in lotus and tomato roots.	symbiosis involves responses that maintain the plant host and symbiotic partner's genetic program; yet these cues are far from elucidated. here we describe the effects of lumichrome, a flavin identified from rhizobium spp., applied to lotus (lotus japonicus) and tomato (solanum lycopersicum). combined transcriptional and metabolite analyses suggest that both species shared common pathways that were altered in response to this application under replete, sterile conditions. these included genes in ...	2012	22701462
draft genome sequence of plant growth-promoting rhizobium mesorhizobium amorphae, isolated from zinc-lead mine tailings.	here, we describe the draft genome sequence of mesorhizobium amorphae strain ccnwgs0123, isolated from nodules of robinia pseudoacacia growing on zinc-lead mine tailings. a large number of metal(loid) resistance genes, as well as genes reported to promote plant growth, were identified, presenting a great future potential for aiding phytoremediation in metal(loid)-contaminated soil.	2012	22247533
ader, a pucr-type transcription factor, activates expression of l-alanine dehydrogenase and is required for sporulation of bacillus subtilis.	the bacillus subtilis ald gene encodes l-alanine dehydrogenase, which catalyzes the nad(+)-dependent deamination of l-alanine to pyruvate for the generation of energy and is required for normal sporulation. the transcription of ald is induced by alanine, but the mechanism underlying alanine induction remains unknown. here we report that a gene (formerly yukf and now designated ader) located upstream of ald is essential for the basal and alanine-inducible expression of ald. the disruption of the ...	2012	22797752
structure-guided expansion of the substrate range of methylmalonyl coenzyme a synthetase (matb) of rhodopseudomonas palustris.	malonyl coenzyme a (malonyl-coa) and methylmalonyl-coa are two of the most commonly used extender units for polyketide biosynthesis and are utilized to synthesize a vast array of pharmaceutically relevant products with antibacterial, antiparasitic, anticholesterol, anticancer, antifungal, and immunosuppressive properties. heterologous hosts used for polyketide production such as escherichia coli often do not produce significant amounts of methylmalonyl-coa, however, requiring the introduction of ...	2012	22773649
quorum sensing: how bacteria can coordinate activity and synchronize their response to external signals?	quorum sensing is used by a large variety of bacteria to regulate gene expression in a cell-density-dependent manner. bacteria can synchronize population behavior using small molecules called autoinducers that are produced by cognate synthases and recognized by specific receptors. quorum sensing plays critical roles in regulating diverse cellular functions in bacteria, including bioluminescence, virulence gene expression, biofilm formation, and antibiotic resistance. the best-studied autoinducer ...	2012	22825856
analyses of the large subunit histidine-rich motif expose an alternative proton transfer pathway in [nife] hydrogenases.	a highly conserved histidine-rich region with unknown function was recognized in the large subunit of [nife] hydrogenases. the hxhxxhxxhxh sequence occurs in most membrane-bound hydrogenases, but only two of these histidines are present in the cytoplasmic ones. site-directed mutagenesis of the his-rich region of the t. roseopersicina membrane-attached hyn hydrogenase disclosed that the enzyme activity was significantly affected only by the replacement of the his104 residue. computational analysi ...	2012	22511957
isolation and characterization of nodule-associated exiguobacterium sp. from the root nodules of fenugreek (trigonella foenum-graecum) and their possible role in plant growth promotion.	one of the ways to increase the competitive survivability of rhizobial biofertilizers and thus achieve better plant growth under such conditions is by modifying the rhizospheric environment or community by addition of nonrhizobial nodule-associated bacteria (nab) that cause better nodulation and plant growth when coinoculated with rhizobia. a study was performed to investigate the most commonly associated nodule-associated bacteria and the rhizospheric microorganisms associated with the fenugree ...	2012	22518149