Publications

Substitutions in the BamA ß-Barrel Domain Overcome the Conditional Lethal Phenotype of a {Delta}bamB {Delta}bamE Strain of Escherichia coli.	BamA interacts with the BamBCDE lipoproteins, and together they constitute the essential ß-barrel assembly machine (BAM) of Escherichia coli. The simultaneous absence of BamB and BamE confers a conditional lethal phenotype and a severe ß-barrel outer membrane protein (OMP) biogenesis defect. Without BamB and BamE, wild-type BamA levels are significantly reduced, and the folding of the BamA ß-barrel, as assessed by the heat-modifiability assay, is drastically compromised. Single-amino-acid substi ...	2012	22037403
Biogeography of symbiotic and other endophytic bacteria isolated from medicinal Glycyrrhiza species in China.	A total of 159 endophytic bacteria were isolated from surface-sterilized root nodules of wild perennial Glycyrrhiza legumes growing on 40 sites in central and northwestern China. Amplified fragment length polymorphism (AFLP) genomic fingerprinting and sequencing of partial 16S rRNA genes revealed that the collection mainly consisted of Mesorhizobium, Rhizobium, Sinorhizobium, Agrobacterium and Paenibacillus species. Based on symbiotic properties with the legume hosts Glycyrrhiza uralensis and Gl ...	2011	22066910
protein domain of unknown function 3233 is a translocation domain of autotransporter secretory mechanism in gamma proteobacteria.	vibrio cholerae, the enteropathogenic gram negative bacteria is one of the main causative agents of waterborne diseases like cholera. about 1/3(rd) of the organism's genome is uncharacterised with many protein coding genes lacking structure and functional information. these proteins form significant fraction of the genome and are crucial in understanding the organism's complete functional makeup. in this study we report the general structure and function of a family of hypothetical proteins, dom ...	2011	22073138
contribution of nfp lysm domains to the recognition of nod factors during the medicago truncatula/sinorhizobium meliloti symbiosis.	the root nodule nitrogen fixing symbiosis between legume plants and soil bacteria called rhizobia is of great agronomical and ecological interest since it provides the plant with fixed atmospheric nitrogen. the establishment of this symbiosis is mediated by the recognition by the host plant of lipo-chitooligosaccharides called nod factors (nfs), produced by the rhizobia. this recognition is highly specific, as precise nf structures are required depending on the host plant. here, we study the imp ...	2011	22087221
A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas.	Evolutionary relationships of 120 root-nodulating bacteria isolated from the nodules of Pisum sativum cultivated at 22 different locations of the trans-Himalayan valleys of Lahaul and Spiti in the state of Himachal Pradesh of India were studied using 16S rRNA gene PCR-RFLP, ERIC-PCR, sequencing of 16S rRNA, atpD, recA, nodC and nifH genes, carbon-source utilization pattern (BIOLOG™), and whole-cell fatty acid profiling. The results demonstrated that all isolates belonged to Rhizobium leguminosar ...	2012	22092487
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
bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control.	under a shortage of oxygen, bacterial growth can be faced mainly by two atp-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. this bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells ...	2012	22098259
production of 7-o-methyl aromadendrin, a medicinally valuable flavonoid, in escherichia coli.	7-o-methyl aromadendrin (7-oma) is an aglycone moiety of one of the important flavonoid-glycosides found in several plants such as populus alba and eucalyptus maculata with various medicinal applications. to produce such valuable natural flavonoids in large quantity, e. coli cell factory has been developed to employ various plant biosynthetic pathways. here, we report the generation of 7-oma from its precursor p-coumaric acid in e. coli for the first time. primarily, naringenin (nrn) (flavanone) ...	2011	22101053
mur regulates the gene encoding the manganese transporter mnth in brucella abortus 2308.	mnth is the only high-affinity manganese transporter identified in brucella. a previous study showed that mnth is required for the wild-type virulence of brucella abortus 2308 in mice (anderson es, et al., infect. immun. 77:3466-3474, 2009) and indicated that the mnth gene is regulated in a manganese-responsive manner in this strain by a mur homolog. in the study presented here, the transcriptional start site for mnth in b. abortus 2308 was determined by primer extension analysis. specific inter ...	2011	22101848
Characterization of the galacturonosyl transferase genes rgtA, B, C, D, and E responsible for lipopolysaccharide synthesis in the nitrogen-fixing endosymbiont Rhizobium leguminosarum: Lipopolysaccharide core and lipid A galacturonosyl residues confer membrane stability.	Rhizobium lipopolysaccharide (LPS) contains four terminally linked galacturonic acid (GalA) residues: one attached to the lipid A and three attached to the core oligosaccharide moiety. Attachment of the GalA residues requires the lipid donor dodecaprenyl-phosphate GalA (Dod-P-GalA) which is synthesized by the GalA transferase (GalAT) RgtE reported here. The galacturonosyl transferases (GalATs) RgtA, B, and C utilize Dod-P-GalA to attach GalAs on the LPS core region and RgtD attaches GalA to the ...	2011	22110131
Characterization of the galacturonosyl transferase genes rgtA, B, C, D, and E responsible for lipopolysaccharide synthesis in the nitrogen-fixing endosymbiont Rhizobium leguminosarum: Lipopolysaccharide core and lipid A galacturonosyl residues confer membrane stability.	Rhizobium lipopolysaccharide (LPS) contains four terminally linked galacturonic acid (GalA) residues: one attached to the lipid A and three attached to the core oligosaccharide moiety. Attachment of the GalA residues requires the lipid donor dodecaprenyl-phosphate GalA (Dod-P-GalA) which is synthesized by the GalA transferase (GalAT) RgtE reported here. The galacturonosyl transferases (GalATs) RgtA, B, and C utilize Dod-P-GalA to attach GalAs on the LPS core region and RgtD attaches GalA to the ...	2011	22110131
Comparative genomics of the type VI secretion systems of Pantoea and Erwinia species reveals the presence of putative effector islands that may be translocated by the VgrG and Hcp proteins.	ABSTRACT:	2011	22115407
Mutation of the sensor kinase chvG in Rhizobium leguminosarum negatively impacts cellular metabolism, outer membrane stability, and symbiosis.	Two component signal transduction systems (TCS) are a main strategy used by bacteria to sense and adapt to changes in their environment. In the legume symbiont Rhizobium leguminosarum biovar viciae VF39, mutation of the histidine kinase, chvG, caused a number of pleiotropic phenotypes. ChvG mutants are unable to grow on proline, glutamate, histidine, or arginine as the sole carbon source. The chvG mutant secreted lower amounts of acidic and neutral surface polysaccharides, and accumulated abnorm ...	2011	22155778
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
Genomes and Virulence Factors of Novel Bacterial Pathogens Causing Bleaching Disease in the Marine Red Alga Delisea pulchra.	Nautella sp. R11, a member of the marine Roseobacter clade, causes a bleaching disease in the temperate-marine red macroalga, Delisea pulchra. To begin to elucidate the molecular mechanisms underpinning the ability of Nautella sp. R11 to colonize, invade and induce bleaching of D. pulchra, we sequenced and analyzed its genome. The genome encodes several factors such as adhesion mechanisms, systems for the transport of algal metabolites, enzymes that confer resistance to oxidative stress, cytolys ...	2011	22162749
reproducible hairy root transformation and spot-inoculation methods to study root symbioses of pea.	abstract: pea has lagged behind other model legumes in the molecular study of nodulation and mycorrhizae-formation because of the difficulty to transform its roots and its poor growth on agar plates. here we describe for pea 1) a transformation technique which permits the complementation of two known non-nodulating pea mutants, 2) a rhizobial inoculation method which allows the study of early cellular events giving rise to nodule primordia, and 3) a targeted fungal inoculation method which allow ...	2011	22172023
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
arabitol metabolism of corynebacterium glutamicum and its regulation by atlr.	expression profiling of corynebacterium glutamicum in comparison to a derivative deficient of the transcriptional regulator atlr (previously known as sugr or mtlr) revealed eight genes showing more than fourfold higher mrna levels in the mutant. four of these are located in direct vicinity of the atlr gene, i.e., xylb, rbtt, mtld, and sixa, annotated as encoding xylulokinase, ribitol transporter, mannitol 2-dehydrogenase, and phosphohistidine phosphatase, respectively. transcriptional analysis i ...	2011	22178972
Global Transcriptomic and Proteomic Responses of Dehalococcoides ethenogenes Strain 195 to Fixed Nitrogen Limitation.	Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing D. ethenogenes strain 195 to fixed nitrogen limitation (FNL) as dechlorination activity and cell yield both decrease during FNL. As expected, the nitrogen-fixing (nif) genes were differentially up-regulated in the transcriptome and proteome of stra ...	2011	22179257
mads-box transcription factor mbx2/pvg4 regulates invasive growth and flocculation by inducing gsf2+ expression in fission yeast.	the fission yeast schizosaccharomyces pombe exhibits invasive growth and nonsexual flocculation in response to nitrogen limitation. gsf2, a flocculin of fission yeast, is required for not only nonsexual flocculation but also invasive growth through recognition of galactose residues on cell-surface glycoconjugates. we found that pyruvylation negatively regulates nonsexual flocculation by capping the galactose residues of n-linked galactomannan. we investigated whether pyruvylation also regulates ...	2011	22180499
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
sinorhizobium meliloti chea complexed with ches exhibits enhanced binding to chey1 resulting in accelerated chey1-p dephosphorylation.	retrophosphorylation of the histidine kinase chea in the chemosensory transduction chain is a widespread mechanism for efficient dephosphorylation of the activated response regulator. first discovered in sinorhizobium meliloti, the main response regulator chey2-p shuttles its phosphoryl group back to chea, while a second response regulator, chey1, serves as sink for surplus phosphoryl groups from chea-p. we have identified a new component in this phospho-relay system, a small 97-aa protein, name ...	2011	22194454
Identification of a novel gene for biosynthesis of a bacteroid-specific electron carrier menaquinone.	Ubiquinone (UQ) has been considered as an electron mediator in electron transfer that generates ATP in Rhizobium under both free-living and symbiosis conditions. When mutated, the dmtH gene has a symbiotic phenotype of forming ineffective nodules on Astragalus sinicus. The gene was isolated from a Mesorhizobium huakuii 7653R transposon-inserted mutant library. The DNA sequence and conserved protein domain analyses revealed that dmtH encodes demethylmenaquinone (DMK) methyltransferase, which cata ...	2011	22194970
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
role for rhizobium rhizogenes k84 cell envelope polysaccharides in surface interactions.	rhizobium rhizogenes strain k84 is a commercial biocontrol agent used worldwide to control crown gall disease. the organism binds tightly to polypropylene substrate and efficiently colonizes root surfaces as complex, multilayered biofilms. a genetic screen identified two mutants in which these surface interactions were affected. one of these mutants failed to attach and form biofilms on the abiotic surface; although, interestingly, it exhibited normal biofilm formation on the biological root tip ...	2011	22210213
plasmid localization and organization of melamine degradation genes in rhodococcus sp. strain mel.	rhodococcus sp. strain mel was isolated from soil by enrichment and grew in minimal medium with melamine as the sole n source with a doubling time of 3.5 h. stoichiometry studies showed that all six nitrogen atoms of melamine were assimilated. the genome was sequenced by roche 454 pyrosequencing to 13x coverage and a 22.3 kb dna region was found to contain a homolog to the melamine deaminase gene trza. mutagenesis studies showed that the cyanuric acid hydrolase and biuret hydrolase genes were cl ...	2011	22210223
the gtar protein negatively regulates transcription of the gtari operon and modulates gene transfer agent (rcgta) expression in rhodobacter capsulatus.	the gtai gene of rhodobacter capsulatus encodes an n-acyl-homoserine lactone (acyl-hsl) synthase. immediately 5' of the gtai gene is orf rcc00328 that encodes a potential acyl-hsl receptor protein. a combination of genetic and biochemical approaches showed that rcc00328 (renamed gtar) modulates the production of a genetic exchange element called the gene transfer agent (rcgta), and regulates the transcription of gtai. although gtai mutants exhibited decreased levels of rcgta production, mutagene ...	2012	22211723
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
synthetic biological approaches to natural product biosynthesis.	small molecules produced in nature possess exquisite chemical diversity and continue to be an inspiration for the development of new therapeutic agents. in their host organisms, natural products are assembled and modified using dedicated biosynthetic pathways. by rationally reprogramming and manipulating these pathways, unnatural metabolites containing enhanced structural features that were otherwise inaccessible can be obtained. additionally, new chemical entities can be synthesized by developi ...	2012	22221832
intruders below the radar: molecular pathogenesis of bartonella spp.	summary: bartonella spp. are facultative intracellular pathogens that employ a unique stealth infection strategy comprising immune evasion and modulation, intimate interaction with nucleated cells, and intraerythrocytic persistence. infections with bartonella are ubiquitous among mammals, and many species can infect humans either as their natural host or incidentally as zoonotic pathogens. upon inoculation into a naive host, the bartonellae first colonize a primary niche that is widely accepted ...	2012	22232371
fur in magnetospirillum gryphiswaldense influences magnetosomes formation and directly regulates the genes involved in iron and oxygen metabolism.	magnetospirillum gryphiswaldense strain msr-1 has the unique capability of taking up large amounts of iron and synthesizing magnetosomes (intracellular magnetic particles composed of fe(3)o(4)). the unusual high iron content of msr-1 makes it a useful model for studying biological mechanisms of iron uptake and homeostasis. the ferric uptake regulator (fur) protein plays a key role in maintaining iron homeostasis in many bacteria. we identified and characterized a fur-homologous gene (mgr_1314) i ...	2012	22238623
bacterial iron-sulfur regulatory proteins as biological sensor-switches.	in recent years, bacterial iron-sulfur cluster proteins that function as regulators of gene transcription have emerged as a major new group. in all cases, the cluster acts as a sensor of the environment and enables the organism to adapt to the prevailing conditions. this can range from mounting a response to oxidative or nitrosative stress to switching between anaerobic and aerobic respiratory pathways. the sensitivity of these ancient cofactors to small molecule reactive oxygen and nitrogen spe ...	2012	22239203
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
mercury-resistant rhizobial bacteria isolated from nodules of leguminous plants growing in high hg-contaminated soils.	a survey of symbiotic bacteria from legumes grown in high mercury-contaminated soils (almadén, spain) was performed to produce a collection of rhizobia which could be well adapted to the environmental conditions of this region and be used for restoration practices. nineteen hg-tolerant rhizobia were isolated from nodules of 11 legume species (of the genera medicago, trifolium, vicia, lupinus, phaseolus, and retama) and characterized. based on their growth on hg-supplemented media, the isolates w ...	2012	22246528
wide variation in antibiotic resistance proteins identified by functional metagenomic screening of a soil dna library.	most genes for antibiotic resistance present in soil microbes remain unexplored because most environmental microbes cannot be cultured. only recently has the identification of these genes become feasible through the use of culture-independent methods. we screened a soil metagenomic dna library in an escherichia coli host for genes that can confer resistance to kanamycin, gentamicin, rifampin, trimethoprim, chloramphenicol, or tetracycline. the screen revealed 41 genes that encode novel protein v ...	2012	22247132
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
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
nad(p)+-malic enzyme mutants of sinorhizobium sp. strain ngr234, but not azorhizobium caulinodans ors571, maintain symbiotic n2 fixation capabilities.	c(4)-dicarboxylic acids appear to be metabolized via the tricarboxylic acid (tca) cycle in n(2)-fixing bacteria (bacteroids) within legume nodules. in sinorhizobium meliloti bacteroids from alfalfa, nad(+)-malic enzyme (dme) is required for n(2) fixation, and this activity is thought to be required for the anaplerotic synthesis of pyruvate. in contrast, in the pea symbiont rhizobium leguminosarum, pyruvate synthesis occurs via either dme or a pathway catalyzed by phosphoenolpyruvate carboxykinas ...	2012	22307295
identification and characterization of γ-aminobutyric acid uptake system gabpcg (ncgl0464) in corynebacterium glutamicum.	corynebacterium glutamicum is widely used for industrial production of various amino acids and vitamins, and there is growing interest in engineering this bacterium for more commercial bioproducts such as γ-aminobutyric acid (gaba). in this study, a c. glutamicum gaba-specific transporter (gabp(cg)) encoded by ncgl0464 was identified and characterized. gabp(cg) plays a major role in gaba uptake and is essential to c. glutamicum growing on gaba. gaba uptake by gabp(cg) was weakly competed by l-as ...	2012	22307305
[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
in silico insights into the symbiotic nitrogen fixation in sinorhizobium meliloti via metabolic reconstruction.	sinorhizobium meliloti is a soil bacterium, known for its capability to establish symbiotic nitrogen fixation (snf) with leguminous plants such as alfalfa. s. meliloti 1021 is the most extensively studied strain to understand the mechanism of snf and further to study the legume-microbe interaction. in order to provide insight into the metabolic characteristics underlying the snf mechanism of s. meliloti 1021, there is an increasing demand to reconstruct a metabolic network for the stage of snf i ...	2012	22319621
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
nontarget effects of foliar fungicide application on the rhizosphere: diversity of nifh gene and nodulation in chickpea field.	this study explores nontarget effects of fungicide application on field-grown chickpea.	2012	22335393
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
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
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
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
contribution of a genomic accessory region encoding a putative cellobiose phosphotransferase system to virulence of streptococcus pneumoniae.	streptococcus pneumoniae (the pneumococcus) is a formidable human pathogen, responsible for massive global morbidity and mortality. the ability to utilize carbohydrates in a variety of host niches appears to be integral to pneumococcal pathogenesis. in this study we investigated a genomic island, which includes a rok family protein, a putative cellobiose phosphotransferase system (pts) and a putative sulfatase. this accessory region is widespread in the pneumococcus in strains of various serotyp ...	2012	22363821
neisseria conserved protein dmp19 is a dna mimic protein that prevents dna binding to a hypothetical nitrogen-response transcription factor.	dna mimic proteins occupy the dna binding sites of dna-binding proteins, and prevent these sites from being accessed by dna. we show here that the neisseria conserved hypothetical protein dmp19 acts as a dna mimic. the crystal structure of dmp19 shows a dsdna-like negative charge distribution on the surface, suggesting that this protein should be added to the short list of known dna mimic proteins. the crystal structure of another related protein, nhtf (neisseria hypothetical transcription facto ...	2012	22373915
characterization of the flavonoid-responsive regulator frra and its binding sites.	previous microarray analyses revealed that in bradyrhizobium japonicum, about 100 genes are induced by genistein, an isoflavonoid secreted by soybean. this includes the three genes frec, frea, and freb (systematic designations bll4319, bll4320, and bll4321), which are likely to form a genistein-, daidzein-, and coumestrol-inducible operon and to encode a multidrug efflux system. upstream of frecab and in the opposite orientation, frra (systematic designation blr4322), which has similarity to tet ...	2012	22389485
icmf family protein tssm exhibits atpase activity and energizes type vi secretion.	the type vi secretion system (t6ss) with diversified functions is widely distributed in pathogenic proteobacteria. the icmf (intracellular multiplication protein f) family protein tssm is a conserved t6ss inner membrane protein. despite the conservation of its walker a nucleotide-binding motif, the ntpase activity of tssm and its role in t6ss remain obscure. in this study, we characterized tssm in the plant pathogen agrobacterium tumefaciens and provided the first biochemical evidence for tssm e ...	2012	22393043
the lovk-lovr two-component system is a regulator of the general stress pathway in caulobacter crescentus.	a conserved set of regulators control the general stress response in caulobacter crescentus, including σ(t), its anti-σ factor nepr, the anti-anti-σ factor phyr, and the transmembrane sensor kinase phyk. we report that the soluble histidine kinase lovk and the single-domain response regulator lovr also function within the c. crescentus general stress pathway. our genetic data support a model in which lovk-lovr functions upstream of σ(t) by controlling the phosphorylation state and thus anti-anti ...	2012	22408156
metagenomic analysis of streptomyces lividans reveals host-dependent functional expression.	most functional metagenomic studies have been limited by the poor expression of many genes derived from metagenomic dna in escherichia coli, which has been the predominant surrogate host to date. to expand the range of expressed genes, we developed tools for construction and functional screening of metagenomic libraries in streptomyces lividans. we expanded on previously published protocols by constructing a system that enables retrieval and characterization of the metagenomic dna from biologica ...	2012	22427497
thiol synthetases of legumes: immunogold localization and differential gene regulation by phytohormones.	in plants and other organisms, glutathione (gsh) biosynthesis is catalysed sequentially by γ-glutamylcysteine synthetase (γecs) and glutathione synthetase (gshs). in legumes, homoglutathione (hgsh) can replace gsh and is synthesized by γecs and a specific homoglutathione synthetase (hgshs). the subcellular localization of the enzymes was examined by electron microscopy in several legumes and gene expression was analysed in lotus japonicus plants treated for 1-48 h with 50 μm of hormones. immunog ...	2012	22442424
interrogation of global active site occupancy of a fungal iterative polyketide synthase reveals strategies for maintaining biosynthetic fidelity.	nonreducing iterative polyketide synthases (nr-pkss) are responsible for assembling the core of fungal aromatic natural products with diverse biological properties. despite recent advances in the field, many mechanistic details of polyketide assembly by these megasynthases remain unknown. to expand our understanding of substrate loading, polyketide elongation, cyclization, and product release, active site occupancy and product output were explored by fourier transform mass spectrometry using the ...	2012	22452347
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
a positive correlation between bacterial autoaggregation and biofilm formation in native sinorhizobium meliloti isolates from argentina.	sinorhizobium meliloti is a symbiotic nitrogen-fixing bacterium that elicits nodule formation on roots of alfalfa plants. s. meliloti produces two exopolysaccharides (epss), termed eps i and eps ii, that are both able to promote symbiosis. eps i and eps ii are secreted in two major fractions that reflect differing degrees of subunit polymerization, designated high- and low-molecular-weight fractions. we reported previously that epss are crucial for autoaggregation and biofilm formation in s. mel ...	2012	22492433
simple absolute quantification method correcting for quantitative pcr efficiency variations for microbial community samples.	real-time quantitative pcr (qpcr) is a widely used technique in microbial community analysis, allowing the quantification of the number of target genes in a community sample. currently, the standard-curve (sc) method of absolute quantification is widely employed for these kinds of analysis. however, the sc method assumes that the amplification efficiency (e) is the same for both the standard and the sample target template. we analyzed 19 bacterial strains and nine environmental samples in qpcr a ...	2012	22492459
regulation and evolution of malonate and propionate catabolism in proteobacteria.	bacteria catabolize malonate via two pathways, encoded by the mdc and mat genes. in various bacteria, transcription of these genes is controlled by the gntr family transcription factors (tfs) matr/mdcy and/or the lysr family transcription factor mdcr. propionate is metabolized via the methylcitrate pathway, comprising enzymes encoded by the prp and acn genes. prpr, the fis family sigma 54-dependent transcription factor, is known to be a transcriptional activator of the prp genes. here, we report ...	2012	22505679
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
the languages spoken in the water body (or the biological role of cyanobacterial toxins).	although intensification of toxic cyanobacterial blooms over the last decade is a matter of growing concern due to bloom impact on water quality, the biological role of most of the toxins produced is not known. in this critical review we focus primarily on the biological role of two toxins, microcystins and cylindrospermopsin, in inter- and intra-species communication and in nutrient acquisition. we examine the experimental evidence supporting some of the dogmas in the field and raise several op ...	2012	22529842
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
signature tagged mutagenesis in the functional genetic analysis of gastrointestinal pathogens.	signature tagged mutagenesis is a genetic approach that was developed to identify novel bacterial virulence factors. it is a negative selection method in which unique identification tags allow analysis of pools of mutants in mixed populations. the approach is particularly well suited to functional genetic analysis of the gastrointestinal phase of infection in foodborne pathogens and has the capacity to guide the development of novel vaccines and therapeutics. in this review we outline the techni ...	2012	22555467
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
[influence of environmental factors on the generation of nitric oxide in the roots of etiolated pea seedlings].	the article studies the nitric oxide (no) levels in the roots of etiolated seedlings of garden peas (pisum sativum l.) using the daf-2da fluorescent probe and fluorescent microscopy. cross sections of roots of 100-150 microm (the site of a root which is 10-15 mm from the apex) are analyzed. it is shown that the level of no in the roots after 24 h increased by more than a factor of 2 in the versions with nano2 and sodium nitroprusside. at feeding the seedlings with kno3, a peak in the accumulatio ...	2015	22567891
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
comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations.	the rhizobium-legume symbiosis has been widely studied as the model of mutualistic evolution and the essential component of sustainable agriculture. extensive genetic and recent genomic studies have led to the hypothesis that many distinct strategies, regardless of rhizobial phylogeny, contributed to the varied rhizobium-legume symbiosis. we sequenced 26 genomes of sinorhizobium and bradyrhizobium nodulating soybean to test this hypothesis. the bradyrhizobium core genome is disproportionally enr ...	2012	22586130
keys to eukaryality: planctomycetes and ancestral evolution of cellular complexity.	planctomycetes are known to display compartmentalization via internal membranes, thus resembling eukaryotes. significantly, the planctomycete gemmata obscuriglobus has not only a nuclear region surrounded by a double-membrane, but is also capable of protein uptake via endocytosis. in order to clearly analyze implications for homology of their characters with eukaryotes, a correct understanding of planctomycete structure is an essential starting point. here we outline the major features of such s ...	2012	22586422
a comparative genomics screen identifies a sinorhizobium meliloti 1021 sodm-like gene strongly expressed within host plant nodules.	we have used the genomic data in the integrated microbial genomes system of the department of energy's joint genome institute to make predictions about rhizobial open reading frames that play a role in nodulation of host plants. the genomic data was screened by searching for orfs conserved in α-proteobacterial rhizobia, but not conserved in closely-related non-nitrogen-fixing α-proteobacteria.	2012	22587634
the lipopolysaccharide core of brucella abortus acts as a shield against innate immunity recognition.	innate immunity recognizes bacterial molecules bearing pathogen-associated molecular patterns to launch inflammatory responses leading to the activation of adaptive immunity. however, the lipopolysaccharide (lps) of the gram-negative bacterium brucella lacks a marked pathogen-associated molecular pattern, and it has been postulated that this delays the development of immunity, creating a gap that is critical for the bacterium to reach the intracellular replicative niche. we found that a b. abort ...	2012	22589715
delineation of the caffeine c-8 oxidation pathway in pseudomonas sp. strain cbb1 via characterization of a new trimethyluric acid monooxygenase and genes involved in trimethyluric acid metabolism.	the molecular basis of the ability of bacteria to live on caffeine via the c-8 oxidation pathway is unknown. the first step of this pathway, caffeine to trimethyluric acid (tmu), has been attributed to poorly characterized caffeine oxidases and a novel quinone-dependent caffeine dehydrogenase. here, we report the detailed characterization of the second enzyme, a novel nadh-dependent trimethyluric acid monooxygenase (tmum), a flavoprotein that catalyzes the conversion of tmu to 1,3,7-trimethyl-5- ...	2012	22609920
evolution of burkholderia pseudomallei in recurrent melioidosis.	burkholderia pseudomallei, the etiologic agent of human melioidosis, is capable of causing severe acute infection with overwhelming septicemia leading to death. a high rate of recurrent disease occurs in adult patients, most often due to recrudescence of the initial infecting strain. pathogen persistence and evolution during such relapsing infections are not well understood. bacterial cells present in the primary inoculum and in late infections may differ greatly, as has been observed in chronic ...	2012	22615773
phylogenomics of prokaryotic ribosomal proteins.	archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. we developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 arch ...	2012	22615861
stereochemical insignificance discovered in acinetobacter baumannii quorum sensing.	stereochemistry is a key aspect of molecular recognition for biological systems. as such, receptors and enzymes are often highly stereospecific, only recognizing one stereoisomer of a ligand. recently, the quorum sensing signaling molecules used by the nosocomial opportunistic pathogen, acinetobacter baumannii, were identified, and the primary signaling molecule isolated from this species was n-(3-hydroxydodecanoyl)-l-homoserine lactone. a plethora of bacterial species have been demonstrated to ...	2012	22629354
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
sinorhizobium meliloti exor is the target of periplasmic proteolysis.	sinorhizobium meliloti exor regulates the production of succinoglycan and flagella through the exos/chvi two-component regulatory system. exor has been proposed to inhibit the exos sensor through direct interaction in the periplasm. to understand how exor suppression of exos is relieved, which is required for the expression of exos/chvi-regulated symbiosis genes, we characterized wild-type exor and exor95 mutant proteins. in addition to the previously identified precursor and mature forms of exo ...	2012	22636773
sequence, structure and functional diversity of pd-(d/e)xk phosphodiesterase superfamily.	proteins belonging to pd-(d/e)xk phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, dna repair and trna-intron splicing. their malfunction in humans triggers severe diseases, such as fanconi anemia and xeroderma pigmentosum. to date there have been several attempts to identify and classify new pd-(d/e)kk phosphodiesterases using remote homology detection methods. such efforts are complicated, because the superfamily exhibit ...	2012	22638584
effect of arabinogalactan proteins from the root caps of pea and brassica napus on aphanomyces euteiches zoospore chemotaxis and germination.	root tips of many plant species release a number of border, or border-like, cells that are thought to play a major role in the protection of root meristem. however, little is currently known on the structure and function of the cell wall components of such root cells. here, we investigate the sugar composition of the cell wall of the root cap in two species: pea (pisum sativum), which makes border cells, and brassica napus, which makes border-like cells. we find that the cell walls are highly en ...	2012	22645070
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
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
respiratory membrane endo-hydrogenase activity in the microaerophile azorhizobium caulinodans is bidirectional.	the microaerophilic bacterium azorhizobium caulinodans, when fixing n(2) both in pure cultures held at 20 µm dissolved o(2) tension and as endosymbiont of sesbania rostrata legume nodules, employs a novel, respiratory-membrane endo-hydrogenase to oxidize and recycle endogenous h(2) produced by soluble mo-dinitrogenase activity at the expense of o(2).	2012	22662125
rhizobium promotes non-legumes growth and quality in several production steps: towards a biofertilization of edible raw vegetables healthy for humans.	the biofertilization of crops with plant-growth-promoting microorganisms is currently considered as a healthy alternative to chemical fertilization. however, only microorganisms safe for humans can be used as biofertilizers, particularly in vegetables that are raw consumed, in order to avoid sanitary problems derived from the presence of pathogenic bacteria in the final products. in the present work we showed that rhizobium strains colonize the roots of tomato and pepper plants promoting their g ...	2012	22675441
[genetic structure of introduced and natural populations of rhizobium leguminosarum in systems "plant-soil"].		2012	22693834
genome, integration, and transduction of a novel temperate phage of helicobacter pylori.	helicobacter pylori is a common human pathogen that has been identified to be carcinogenic. this study isolated the temperate bacteriophage 1961p from the lysate of a clinical strain of h. pylori isolated in taiwan. the bacteriophage has an icosahedral head and a short tail, typical of the podoviridae family. its double-stranded dna genome is 26,836 bp long and has 33 open reading frames. only 9 of the predicted proteins have homologs of known functions, while the remaining 24 are only similar t ...	2012	22696647
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
transcriptomic profiling of bacillus amyloliquefaciens fzb42 in response to maize root exudates.	plant root exudates have been shown to play an important role in mediating interactions between plant growth-promoting rhizobacteria (pgpr) and their host plants. most investigations were performed on gram-negative rhizobacteria, while much less is known about gram-positive rhizobacteria. to elucidate early responses of pgpr to root exudates, we investigated changes in the transcriptome of a gram-positive pgpr to plant root exudates.	2012	22720735
defining sequence space and reaction products within the cyanuric acid hydrolase (atzd)/barbiturase protein family.	cyanuric acid hydrolases (atzd) and barbiturases are homologous, found almost exclusively in bacteria, and comprise a rare protein family with no discernible linkage to other protein families or an x-ray structural class. there has been confusion in the literature and in genome projects regarding the reaction products, the assignment of individual sequences as either cyanuric acid hydrolases or barbiturases, and spurious connection of this family to another protein family. the present study has ...	2012	22730121
detection, characterization, and biological effect of quorum-sensing signaling molecules in peanut-nodulating bradyrhizobia.	bacteria of the genus bradyrhizobium are able to establish a symbiotic relationship with peanut (arachis hypogaea) root cells and to fix atmospheric nitrogen by converting it to nitrogenous compounds. quorum sensing (qs) is a cell-cell communication mechanism employed by a variety of bacterial species to coordinate behavior at a community level through regulation of gene expression. the qs process depends on bacterial production of various signaling molecules, among which the n-acylhomoserine la ...	2012	22736981
lon protease of azorhizobium caulinodans ors571 is required for suppression of reb gene expression.	bacterial lon proteases play important roles in a variety of biological processes in addition to housekeeping functions. in this study, we focused on the lon protease of azorhizobium caulinodans, which can fix nitrogen both during free-living growth and in stem nodules of the legume sesbania rostrata. the nitrogen fixation activity of an a. caulinodans lon mutant in the free-living state was not significantly different from that of the wild-type strain. however, the stem nodules formed by the lo ...	2012	22752172
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
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
light regulates attachment, exopolysaccharide production, and nodulation in rhizobium leguminosarum through a lov-histidine kinase photoreceptor.	rhizobium leguminosarum is a soil bacterium that infects root hairs and induces the formation of nitrogen-fixing nodules on leguminous plants. light, oxygen, and voltage (lov)-domain proteins are blue-light receptors found in higher plants and many algae, fungi, and bacteria. the genome of r. leguminosarum bv. viciae 3841, a pea-nodulating endosymbiont, encodes a sensor histidine kinase containing a lov domain at the n-terminal end (r-lov-hk). r-lov-hk has a typical lov domain absorption spectru ...	2012	22773814
arabinogalactan proteins in root and pollen-tube cells: distribution and functional aspects.	arabinogalactan proteins (agps) are complex proteoglycans of the cell wall found in the entire plant kingdom and in almost all plant organs. agps encompass a large group of heavily glycosylated cell-wall proteins which share common features, including the presence of glycan chains especially enriched in arabinose and galactose and a protein backbone particularly rich in hydroxyproline residues. however, agps also exhibit strong heterogeneities among their members in various plant species. agp ub ...	2012	22786747
modifications of xanthomonas axonopodis pv. citri lipopolysaccharide affect the basal response and the virulence process during citrus canker.	xanthomonas axonopodis pv. citri (xac) is the phytopathogen responsible for citrus canker, one of the most devastating citrus diseases in the world. a broad range of pathogens is recognized by plants through so-called pathogen-associated molecular patterns (pamps), which are highly conserved fragments of pathogenic molecules. in plant pathogenic bacteria, lipopolisaccharyde (lps) is considered a virulence factor and it is being recognized as a pamp. the study of the participation of xac lps in c ...	2012	22792211
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
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
identification of olivetolic acid cyclase from cannabis sativa reveals a unique catalytic route to plant polyketides.	δ(9)-tetrahydrocannabinol (thc) and other cannabinoids are responsible for the psychoactive and medicinal properties of cannabis sativa l. (marijuana). the first intermediate in the cannabinoid biosynthetic pathway is proposed to be olivetolic acid (oa), an alkylresorcinolic acid that forms the polyketide nucleus of the cannabinoids. oa has been postulated to be synthesized by a type iii polyketide synthase (pks) enzyme, but so far type iii pkss from cannabis have been shown to produce catalytic ...	2012	22802619