| efficient recombinant expression and secretion of a thermostable gh26 mannan endo-1,4-beta-mannosidase from bacillus licheniformis in escherichia coli. | mannans are one of the key polymers in hemicellulose, a major component of lignocellulose. the mannan endo-1,4-beta-mannosidase or 1,4-beta-d-mannanase (ec 3.2.1.78), commonly named beta-mannanase, is an enzyme that can catalyze random hydrolysis of beta-1,4-mannosidic linkages in the main chain of mannans, glucomannans and galactomannans. the enzyme has found a number of applications in different industries, including food, feed, pharmaceutical, pulp/paper industries, as well as gas well stimul ... | 2010 | 20380743 |
| monomethylamine as a nitrogen source for a nonmethylotrophic bacterium, agrobacterium tumefaciens. | monomethylamine can be used by nonmethylotrophs as a sole nitrogen source but not as a carbon source; however, little is known about the genes and enzymes involved. the gamma-glutamylmethylamide/n-methylglutamate pathway for monomethylamine utilization by methylotrophs has recently been resolved. we have identified genes encoding key enzymes of this pathway in nonmethylotrophs (e.g., agrobacterium tumefaciens) and demonstrated that this pathway is also involved in the utilization of monomethylam ... | 2010 | 20400554 |
| expression and function of four carbonic anhydrase homologs in the deep-sea chemolithoautotroph thiomicrospira crunogena. | the hydrothermal vent chemolithoautotroph thiomicrospira crunogena grows rapidly in the presence of low concentrations of dissolved inorganic carbon (dic) (= co(2) + hco(3)(-) + co(3)(-2)). its genome encodes alpha-carbonic anhydrase (alpha-ca), beta-ca, carboxysomal beta-like ca (csosca), and a protein distantly related to gamma-ca. the purposes of this work were to characterize the gene products, determine whether they were differentially expressed, and identify those that are necessary for di ... | 2010 | 20400567 |
| regulation of glycogen metabolism in yeast and bacteria. | microorganisms have the capacity to utilize a variety of nutrients and adapt to continuously changing environmental conditions. many microorganisms, including yeast and bacteria, accumulate carbon and energy reserves to cope with the starvation conditions temporarily present in the environment. glycogen biosynthesis is a main strategy for such metabolic storage, and a variety of sensing and signaling mechanisms have evolved in evolutionarily distant species to ensure the production of this homop ... | 2010 | 20412306 |
| characterization of strains unlike mesorhizobium loti that nodulate lotus spp. in saline soils of granada, spain. | lotus species are forage legumes with potential as pastures in low-fertility and environmentally constrained soils, owing to their high persistence and yield under those conditions. the aim of this work was the characterization of phenetic and genetic diversity of salt-tolerant bacteria able to establish efficient symbiosis with lotus spp. a total of 180 isolates able to nodulate lotus corniculatus and lotus tenuis from two locations in granada, spain, were characterized. molecular identificatio ... | 2010 | 20435777 |
| resonance assignments of the nucleotide-free wildtype mlok1 cyclic nucleotide-binding domain. | cyclic nucleotide-sensitive ion channels, known as hcn and cng channels play crucial roles in neuronal excitability and signal transduction of sensory cells. these channels are activated by binding of cyclic nucleotides to their intracellular cyclic nucleotide-binding domain (cnbd). a comparison of the structures of wildtype ligand-free and ligand-bound cnbd is essential to elucidate the mechanism underlying nucleotide-dependent activation of cnbds. we recently reported the solution structure of ... | 2010 | 20449776 |
| characterization of the nifa-rpon regulon in rhizobium etli in free life and in symbiosis with phaseolus vulgaris. | the nifa-rpon complex is a master regulator of the nitrogen fixation genes in alphaproteobacteria. based on the complete rhizobium etli genome sequence, we constructed an r. etli cfn42 oligonucleotide (70-mer) microarray and utilized this tool, reverse transcription (rt)-pcr analysis (transcriptomics), proteomics, and bioinformatics to decipher the nifa-rpon regulon under microaerobic conditions (free life) and in symbiosis with bean plants. the r. etli nifa-rpon regulon was determined to contai ... | 2010 | 20453139 |
| disruption of the glycine cleavage system enables sinorhizobium fredii usda257 to form nitrogen-fixing nodules on agronomically improved north american soybean cultivars. | the symbiosis between sinorhizobium fredii usda257 and soybean [glycine max (l.) merr.] exhibits a high degree of cultivar specificity. usda257 nodulates primitive soybean cultivars but fails to nodulate agronomically improved cultivars such as mccall. in this study we provide evidence for the involvement of a new genetic locus that controls soybean cultivar specificity. this locus was identified in usda257 by tn5 transposon mutagenesis followed by nodulation screening on mccall soybean. we have ... | 2010 | 20453144 |
| the complete genome sequence of cupriavidus metallidurans strain ch34, a master survivalist in harsh and anthropogenic environments. | many bacteria in the environment have adapted to the presence of toxic heavy metals. over the last 30 years, this heavy metal tolerance was the subject of extensive research. the bacterium cupriavidus metallidurans strain ch34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. this tolerance is mostly achieved by rapid ion efflux but al ... | 2010 | 20463976 |
| evolutionary ancestry and novel functions of the mammalian glucose transporter (glut) family. | in general, sugar porters function by proton-coupled symport or facilitative transport modes. symporters, coupled to electrochemical energy, transport nutrients against a substrate gradient. facilitative carriers transport sugars along a concentration gradient, thus transport is dependent upon extracellular nutrient levels. across bacteria, fungi, unicellular non-vertebrates and plants, proton-coupled hexose symport is a crucial process supplying energy under conditions of nutrient flux. in mamm ... | 2010 | 20487568 |
| transcriptome analysis of the mobile genome iceclc in pseudomonas knackmussii b13. | integrative and conjugative elements (ice) form a diverse group of dna elements that are integrated in the chromosome of the bacterial host, but can occasionally excise and horizontally transfer to a new host cell. ice come in different families, typically with a conserved core for functions controlling the element's behavior and a variable region providing auxiliary functions to the host. the iceclc element of pseudomonas knackmussii strain b13 is representative for a large family of chromosoma ... | 2010 | 20504315 |
| crystallization and preliminary x-ray analysis of sdr-type pyridoxal dehydrogenase from mesorhizobium loti. | pyridoxal 4-dehydrogenase from mesorhizobium loti maff303099 was overexpressed in escherichia coli. the recombinant selenomethionine-substituted enzyme was purified and crystallized by the sitting-drop vapour-diffusion method using peg 4000 as precipitant. crystals grew in the presence of 0.45 mm nad(+). the crystals diffracted to 2.9 a resolution and belonged to the monoclinic space group p2(1), with unit-cell parameters a = 86.20, b = 51.11, c = 91.73 a, beta = 89.36 degrees. the calculated v( ... | 2010 | 20516609 |
| the phosphatomes of the multicellular myxobacteria myxococcus xanthus and sorangium cellulosum in comparison with other prokaryotic genomes. | analysis of the complete genomes from the multicellular myxobacteria myxococcus xanthus and sorangium cellulosum identified the highest number of eukaryotic-like protein kinases (elks) compared to all other genomes analyzed. high numbers of protein phosphatases (pps) could therefore be anticipated, as reversible protein phosphorylation is a major regulation mechanism of fundamental biological processes. | 2010 | 20567509 |
| agrobacterium tumefaciens exor represses succinoglycan biosynthesis and is required for biofilm formation and motility. | the ubiquitous plant pathogen agrobacterium tumefaciens attaches efficiently to plant tissues and abiotic surfaces and can form complex biofilms. a genetic screen for mutants unable to form biofilms on pvc identified disruptions in a homologue of the exor gene. exor is a predicted periplasmic protein, originally identified in sinorhizobium meliloti, but widely conserved among alphaproteobacteria. disruptions in the a. tumefaciens exor gene result in severely compromised attachment to abiotic sur ... | 2010 | 20576688 |
| the bridge-region of the ku superfamily is an atypical zinc ribbon domain. | members of the ku superfamily are dna-end-binding proteins involved in non-homologous end-joining (nhej) dna repair. the published crystal structure of human ku-dna complex reveals a heterodimer that forms a ring around dsdna by means of the ku core modules. these modules contain a highly conserved seven-stranded β-barrel, which in turn contains an insertion, termed the bridge-region, between its second and third β-strands. the bridge-region adopts an unusual β-strand-rich structure critical for ... | 2010 | 20580930 |
| gene transfer into solanum tuberosum via rhizobium spp. | agrobacterium tumefaciens-mediated transformation (atmt) is the preferred technique for gene transfer into crops. a major disadvantage of the technology remains the complexity of the patent landscape that surrounds atmt which restricts its use for commercial applications. an alternative system has been described (broothaerts et al. in nature 433:629-633, 2005) detailing the propensity of three rhizobia to transform the model crop arabidopsis thaliana, the non-food crop nicotiana tabacum and, at ... | 2011 | 20582626 |
| identification of two flavin monooxygenases from an effluent treatment plant sludge metagenomic library. | oxygenases are useful for the production of many industrially important molecules. screening of an effluent treatment plant (etp) sludge metagenomic library identified two clones encoding proteins, b1 and b2, with similarity to putative flavin monooxygenases from mesorhizobium loti and sphingomonas wittichi, respectively. the deduced amino acid sequences show only 20% identity, but both have a paired rossman fold and a flavin monooxygenase (fmo) motif. b1 and b2 appear to be members of the flavi ... | 2010 | 20591656 |
| a cell-type-specific protein-protein interaction modulates transcriptional activity of a master regulator in caulobacter crescentus. | progression through the caulobacter cell cycle is driven by the master regulator ctra, an essential two-component signaling protein that regulates the expression of nearly 100 genes. ctra is abundant throughout the cell cycle except immediately prior to dna replication. however, the expression of ctra-activated genes is generally restricted to s phase. we identify the conserved protein scip (small ctra inhibitory protein) and show that it accumulates during g1, where it inhibits ctra from activa ... | 2010 | 20598601 |
| an alternative route for udp-diacylglucosamine hydrolysis in bacterial lipid a biosynthesis. | the outer leaflet of the outer membranes of gram-negative bacteria is composed primarily of lipid a, the hydrophobic anchor of lipopolysaccharide. like escherichia coli, most gram-negative bacteria encode one copy of each of the nine genes required for lipid a biosynthesis. an important exception exists in the case of the fourth enzyme, lpxh, a peripheral membrane protein that hydrolyzes udp-2,3-diacylglucosamine to form 2,3-diacylglucosamine 1-phosphate and ump by catalyzing the attack of water ... | 2010 | 20608695 |
| inhibitory effect on the tobacco mosaic virus infection by a plant ring finger protein. | in the yeast two-hybrid screening of plant factors interacting with tobacco mosaic virus (tmv) rna-dependent rna polymerase (rdrp), we found a protein containing a ring finger motif in tobacco (nicotiana tabacum) and designated it as tarf (tmv-associated ring finger protein). tarf is a homologue of a lotus japonicus ring finger protein (ljnsring) involved in the symbiotic interaction between l. japonicus and mesorhizobium loti. when tarf was silenced by virus-induced gene silencing (vigs) method ... | 2010 | 20621138 |
| biosynthesis of compatible solutes in rhizobial strains isolated from phaseolus vulgaris nodules in tunisian fields. | associated with appropriate crop and soil management, inoculation of legumes with microbial biofertilizers can improve food legume yield and soil fertility and reduce pollution by inorganic fertilizers. rhizospheric bacteria are subjected to osmotic stress imposed by drought and/or nacl, two abiotic constraints frequently found in semi-arid lands. osmostress response in bacteria involves the accumulation of small organic compounds called compatible solutes. whereas most studies on rhizobial osmo ... | 2010 | 20633304 |
| the omptins of yersinia pestis and salmonella enterica cleave the reactive center loop of plasminogen activator inhibitor 1. | plasminogen activator inhibitor 1 (pai-1) is a serine protease inhibitor (serpin) and a key molecule that regulates fibrinolysis by inactivating human plasminogen activators. here we show that two important human pathogens, the plague bacterium yersinia pestis and the enteropathogen salmonella enterica serovar typhimurium, inactivate pai-1 by cleaving the r346-m347 bait peptide bond in the reactive center loop. no cleavage of pai-1 was detected with yersinia pseudotuberculosis, an oral/fecal pat ... | 2010 | 20639337 |
| how many peas in a pod? legume genes responsible for mutualistic symbioses underground. | the nitrogen-fixing symbiosis between legume plants and rhizobium bacteria is the most prominent plant-microbe endosymbiotic system and, together with mycorrhizal fungi, has critical importance in agriculture. the introduction of two model legume species, lotus japonicus and medicago truncatula, has enabled us to identify a number of host legume genes required for symbiosis. a total of 26 genes have so far been cloned from various symbiotic mutants of these model legumes, which are involved in r ... | 2010 | 20660226 |
| a new family of enzymes catalyzing the first committed step of the methylerythritol 4-phosphate (mep) pathway for isoprenoid biosynthesis in bacteria. | isoprenoids are a large family of compounds with essential functions in all domains of life. most eubacteria synthesize their isoprenoids using the methylerythritol 4-phosphate (mep) pathway, whereas a minority uses the unrelated mevalonate pathway and only a few have both. interestingly, brucella abortus and some other bacteria that only use the mep pathway lack deoxyxylulose 5-phosphate (dxp) reductoisomerase (dxr), the enzyme catalyzing the nadph-dependent production of mep from dxp in the fi ... | 2010 | 20660776 |
| the baca gene homolog, mlr7400, in mesorhizobium loti maff303099 is dispensable for symbiosis with lotus japonicus but partially capable of supporting the symbiotic function of baca in sinorhizobium meliloti. | establishment of rhizobium-legume symbiosis requires a series of mutual authentication, which might involve bacterial evasion of host defense. one such evasion-related genes is sinorhizobium meliloti baca that is essential for bacteroid formation. baca is a transmembrane protein highly similar to escherichia coli sbma, a predicted transporter, and has homologs even in animal pathogens, such as brucella abortus in which the homolog contributes to effective survival in host macrophages. despite su ... | 2010 | 20668224 |
| evolutionary dynamics of insertion sequences in relation to the evolutionary histories of the chromosome and symbiotic plasmid genes of rhizobium etli populations. | insertion sequences (is) are mobile genetic elements that are distributed in many prokaryotes. in particular, in the genomes of the symbiotic nitrogen-fixing bacteria collectively known as rhizobia, is are fairly abundant in plasmids or chromosomal islands that carry the genes needed for symbiosis. here, we report an analysis of the distribution and genetic conservation of the is found in the genome of rhizobium etli cfn42 in a collection of 87 rhizobium strains belonging to populations with dif ... | 2010 | 20675442 |
| nena, a lotus japonicus homolog of sec13, is required for rhizodermal infection by arbuscular mycorrhiza fungi and rhizobia but dispensable for cortical endosymbiotic development. | legumes form symbioses with arbuscular mycorrhiza (am) fungi and nitrogen fixing root nodule bacteria. intracellular root infection by either endosymbiont is controlled by the activation of the calcium and calmodulin-dependent kinase (ccamk), a central regulatory component of the plant's common symbiosis signaling network. we performed a microscopy screen for lotus japonicus mutants defective in am development and isolated a mutant, nena, that aborted fungal infection in the rhizodermis. nena en ... | 2010 | 20675572 |
| structure and functional analysis of lptc, a conserved membrane protein involved in the lipopolysaccharide export pathway in escherichia coli. | lptc is a conserved bitopic inner membrane protein from escherichia coli involved in the export of lipopolysaccharide from its site of synthesis in the cytoplasmic membrane to the outer membrane. lptc forms a complex with the atp-binding cassette transporter, lptbfg, which is thought to facilitate the extraction of lipopolysaccharide from the inner membrane and release it into a translocation pathway that includes the putative periplasmic chaperone lpta. cysteine modification experiments establi ... | 2010 | 20720015 |
| a structural model of anti-anti-σ inhibition by a two-component receiver domain: the phyr stress response regulator. | phyr is a hybrid stress regulator conserved in α-proteobacteria that contains an n-terminal σ-like (sl) domain and a c-terminal receiver domain. phosphorylation of the receiver domain is known to promote binding of the sl domain to an anti-σ factor. phyr thus functions as an anti-anti-σ factor in its phosphorylated state. we present genetic evidence that caulobacter crescentus phyr is a phosphorylation-dependent stress regulator that functions in the same pathway as σ(t) and its anti-σ factor, n ... | 2010 | 20735776 |
| protein networks reveal detection bias and species consistency when analysed by information-theoretic methods. | we apply our recently developed information-theoretic measures for the characterisation and comparison of protein-protein interaction networks. these measures are used to quantify topological network features via macroscopic statistical properties. network differences are assessed based on these macroscopic properties as opposed to microscopic overlap, homology information or motif occurrences. we present the results of a large-scale analysis of protein-protein interaction networks. precise null ... | 2010 | 20805870 |
| characterization of a two-component regulatory system that regulates succinate-mediated catabolite repression in sinorhizobium meliloti. | when they are available, sinorhizobium meliloti utilizes c(4)-dicarboxylic acids as preferred carbon sources for growth while suppressing the utilization of some secondary carbon sources such as α- and β-galactosides. the phenomenon of using succinate as the sole carbon source in the presence of secondary carbon sources is termed succinate-mediated catabolite repression (smcr). genetic screening identified the gene sma0113 as needed for strong smcr when s. meliloti was grown in succinate plus la ... | 2010 | 20817764 |
| symbiotic legume nodules employ both rhizobial exo- and endo-hydrogenases to recycle hydrogen produced by nitrogen fixation. | in symbiotic legume nodules, endosymbiotic rhizobia (bacteroids) fix atmospheric n(2), an atp-dependent catalytic process yielding stoichiometric ammonium and hydrogen gas (h(2)). while in most legume nodules this h(2) is quantitatively evolved, which loss drains metabolic energy, certain bacteroid strains employ uptake hydrogenase activity and thus evolve little or no h(2). rather, endogenous h(2) is efficiently respired at the expense of o(2), driving oxidative phosphorylation, recouping atp u ... | 2010 | 20838423 |
| structure and mechanism of orf36, an amino sugar oxidizing enzyme in everninomicin biosynthesis . | everninomicin is a highly modified octasaccharide that belongs to the orthosomycin family of antibiotics and possesses potent gram-positive antibiotic activity, including broad-spectrum efficacy against multidrug resistant enterococci and staphylococcus aureus. among its distinctive structural features is a nitro sugar, l-evernitrose, analogues of which decorate a variety of natural products. recently, we identified a nitrososynthase enzyme encoded by orf36 from micromonospora carbonacea var. af ... | 2010 | 20866105 |
| role of lupeol synthase in lotus japonicus nodule formation. | • triterpenes are plant secondary metabolites, derived from the cyclization of 2,3-oxidosqualene by oxidosqualene cyclases (oscs). here, we investigated the role of lupeol synthase, encoded by osc3, and its product, lupeol, in developing roots and nodules of the model legume lotus japonicus. • the expression patterns of osc3 in different developmental stages of uninfected roots and in roots infected with mesorhizobium loti were determined. the tissue specificity of osc3 expression was analysed b ... | 2010 | 20868395 |
| r gene-controlled host specificity in the legume-rhizobia symbiosis. | leguminous plants can enter into root nodule symbioses with nitrogen-fixing soil bacteria known as rhizobia. an intriguing but still poorly understood property of the symbiosis is its host specificity, which is controlled at multiple levels involving both rhizobial and host genes. it is widely believed that the host specificity is determined by specific recognition of bacterially derived nod factors by the cognate host receptor(s). here we describe the positional cloning of two soybean genes rj2 ... | 2010 | 20937853 |
| engineered acc deaminase-expressing free-living cells of mesorhizobium loti show increased nodulation efficiency and competitiveness on lotus spp. | ethylene inhibits the establishment of symbiosis between rhizobia and legumes. several rhizobia species express the enzyme acc deaminase, which degrades the ethylene precursor 1-cyclopropane-1-carboxilate (acc), leading to reductions in the amount of ethylene evolved by the plant. m. loti has a gene encoding acc deaminase, but this gene is under the activity of the nifa-rpon-dependent promoter; thus, it is only expressed inside the nodule. the m. loti structural gene acc deaminase (acds) was int ... | 2010 | 20953097 |
| the role of sigma factor rpoh1 in the ph stress response of sinorhizobium meliloti. | environmental ph stress constitutes a limiting factor for s. meliloti survival and development. the response to acidic ph stress in s. meliloti is versatile and characterized by the differential expression of genes associated with various cellular functions. the purpose of this study was to gain detailed insight into the participation of sigma factors in the complex stress response system of s. meliloti 1021 using ph stress as an effector. | 2010 | 20955556 |
| argc orthologs from rhizobiales show diverse profiles of transcriptional efficiency and functionality in sinorhizobium meliloti. | several factors can influence ortholog replacement between closely related species. we evaluated the transcriptional expression and metabolic performance of ortholog substitution complementing a sinorhizobium meliloti argc mutant with argc from rhizobiales (agrobacterium tumefaciens, rhizobium etli, and mesorhizobium loti). the argc gene is necessary for the synthesis of arginine, an amino acid that is central to protein and cellular metabolism. strains were obtained carrying plasmids with argc ... | 2010 | 21075924 |
| argc orthologs from rhizobiales show diverse profiles of transcriptional efficiency and functionality in sinorhizobium meliloti. | several factors can influence ortholog replacement between closely related species. we evaluated the transcriptional expression and metabolic performance of ortholog substitution complementing a sinorhizobium meliloti argc mutant with argc from rhizobiales (agrobacterium tumefaciens, rhizobium etli, and mesorhizobium loti). the argc gene is necessary for the synthesis of arginine, an amino acid that is central to protein and cellular metabolism. strains were obtained carrying plasmids with argc ... | 2010 | 21075924 |
| annotation and structural analysis of sialylated human milk oligosaccharides. | sialylated human milk oligosaccharides (shmos) are important components of human milk oligosaccharides. sialic acids are typically found on the nonreducing end and are known binding sites for pathogens and aid in neonates' brain development. due to their negative charge and hydrophilic nature, they also help modulate cell-cell interactions. it has also been shown that sialic acids are involved in regulating the immune response and aid in brain development. in this study, the enriched shmos from ... | 2011 | 21133381 |
| a c subunit of the plant nuclear factor nf-y required for rhizobial infection and nodule development affects partner selection in the common bean-rhizobium etli symbiosis. | legume plants are able to interact symbiotically with soil bacteria to form nitrogen-fixing root nodules. although specific recognition between rhizobia and legume species has been extensively characterized, plant molecular determinants that govern the preferential colonization by different strains within a single rhizobium species have received little attention. we found that the c subunit of the heterotrimeric nuclear factor nf-y from common bean (phaseolus vulgaris) nf-yc1 plays a key role in ... | 2010 | 21139064 |
| both plant and bacterial nitrate reductases contribute to nitric oxide production in medicago truncatula nitrogen-fixing nodules. | nitric oxide (no) is a signaling and defense molecule of major importance in living organisms. in the model legume medicago truncatula, no production has been detected in the nitrogen fixation zone of the nodule, but the systems responsible for its synthesis are yet unknown and its role in symbiosis is far from being elucidated. in this work, using pharmacological and genetic approaches, we explored the enzymatic source of no production in m. truncatula-sinorhizobium meliloti nodules under normo ... | 2010 | 21139086 |
| both plant and bacterial nitrate reductases contribute to nitric oxide production in medicago truncatula nitrogen-fixing nodules. | nitric oxide (no) is a signaling and defense molecule of major importance in living organisms. in the model legume medicago truncatula, no production has been detected in the nitrogen fixation zone of the nodule, but the systems responsible for its synthesis are yet unknown and its role in symbiosis is far from being elucidated. in this work, using pharmacological and genetic approaches, we explored the enzymatic source of no production in m. truncatula-sinorhizobium meliloti nodules under normo ... | 2010 | 21139086 |
| a novel interaction between ccamk and a protein containing the scythe_n ubiquitin-like domain in lotus japonicus. | in the rhizobium-legume symbiosis, calcium/calmodulin-dependent protein kinase (ccamk) is a key regulator for both rhizobial infection and nodule organogenesis. deregulation of ccamk by either a point mutation in the autophosphorylation site or the deletion of the carboxyl-terminal regulatory domain results in spontaneous nodule formation without rhizobia. however, the underlying biochemical mechanisms are poorly understood. here, using the kinase domain of ccamk as a bait in yeast two-hybrid sc ... | 2011 | 21209278 |
| 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 |
| from defense to symbiosis: limited alterations in the kinase domain of lysm receptor-like kinases are crucial for evolution of legume-rhizobium symbiosis. | nitrogen-fixing symbiosis between legumes and rhizobia is initiated by the recognition of rhizobial nod factors (nfs) by host plants. nfs are diversely modified derivatives of chitin oligosaccharide, a fungal elicitor that induces defense responses in plants. recent evidence has shown that both nfs and chitin elicitors are recognized by structurally related lysm receptor kinases. transcriptome analyses of lotus japonicus roots indicated that nfs not only activate symbiosis genes but also transie ... | 2010 | 21223383 |
| 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 |
| characterization of two novel nodule-enhanced α-type carbonic anhydrases from lotus japonicus. | two cdna clones coding for α-type carbonic anhydrases (ca; ec 4.2.1.1) in the nitrogen-fixing nodules of the model legume lotus japonicus were identified. functionality of the full-length proteins was confirmed by heterologous expression in escherichia coli and purification of the encoded polypeptides. the developmental expression pattern of ljcaa1 and ljcaa2 revealed that both genes code for nodule enhanced carbonic anhydrase isoforms, which are induced early during nodule development. the gene ... | 2011 | 21256984 |
| two novel classes of enzymes are required for the biosynthesis of aurofusarin in fusarium graminearum. | previous studies have reported the functional characterization of 9 out of 11 genes found in the gene cluster responsible for biosynthesis of the polyketide pigment aurofusarin in fusarium graminearum. here we reanalyze the function of a putative aurofusarin pump (aurt) and the two remaining orphan genes, aurz and aurs. targeted gene replacement of aurz resulted in the discovery that the compound ywa1, rather than nor-rubrofusarin, is the primary product of f. graminearum polyketide synthase 12 ... | 2011 | 21296881 |
| nodulation enhances dark co2 fixation and recycling in the model legume lotus japonicus. | during symbiotic nitrogen fixation (snf), the nodule becomes a strong sink for photosynthetic carbon. here, it was studied whether nodule dark co(2) fixation could participate in a mechanism for co(2) recycling through c(4)-type photosynthesis. differences in the natural d(13)c abundance between lotus japonicus inoculated or not with the n-fixing mesorhizobium loti were assessed. (13)c labelling and gene expression of key enzymes of co(2) metabolism were applied in plants inoculated with wild-ty ... | 2011 | 21307384 |
| the crystal structure of sdr-type pyridoxal 4-dehydrogenase of mesorhizobium loti. | pyridoxal 4-dehydrogenase catalyzes the irreversible oxidation of pyridoxal to 4-pyridoxolactone and is involved in degradation pathway i of pyridoxine, a vitamin b(6) compound. its crystal structure was elucidated for the first time. molecular replacement with (s)-1-phenylthanol dehydrogenase (pdb code 2ew8) was adopted to determine the tertiary structure of the nad(+)-bound enzyme. | 2011 | 21307574 |
| nitric oxide production induced in roots of lotus japonicus by lipopolysaccharide from mesorhizobium loti. | lipopolysaccharide (lps) is a bacterial molecule that induces nitric oxide (no) production and triggers defense systems in plant-pathogen interactions. no production is induced in the roots of lotus japonicus after inoculation of the roots with its microsymbiont mesorhizobium loti. however, the rhizobial molecule that induces no production has not yet been identified. we investigated no production in the roots of l. japonicus by treatment with lps of m. loti. lps was prepared by phenol-hot water ... | 2011 | 21330297 |
| 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 |
| structural insights into conformational changes of a cyclic nucleotide-binding domain in solution from mesorhizobium loti k1 channel. | cyclic nucleotide-sensitive ion channels, known as hcn and cng channels, are activated by binding of ligands to a domain (cnbd) located on the cytoplasmic side of the channel. the underlying mechanisms are not well understood. to elucidate the gating mechanism, structures of both the ligand-free and -bound cnbd are required. several crystal structures of the cnbd from hcn2 and a bacterial cng channel (mlok1) have been solved. however, for hcn2, the camp-free and -bound state did not reveal subst ... | 2011 | 21430265 |
| nitric oxide is required for an optimal establishment of the medicago truncatula-sinorhizobium meliloti symbiosis. | nitric oxide (no) is a gaseous molecule that participates in numerous plant signalling pathways. it is involved in plant responses to pathogens and development processes such as seed germination, flowering and stomatal closure. using a permeable no-specific fluorescent probe and a bacterial reporter strain expressing the lacz gene under the control of a no-responsive promoter, we detected no production in the first steps, during infection threads growth, of the medicago truncatula-sinorhizobium ... | 2011 | 21457261 |
| 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 |
| competing formate- and carbon dioxide-utilizing prokaryotes in an anoxic methane-emitting fen soil. | methanogenesis in wetlands is dependent on intermediary substrates derived from the degradation of biopolymers. formate is one such substrate and is stimulatory to methanogenesis and acetogenesis in anoxic microcosms of soil from the fen schlöppnerbrunnen. formate dissimilation also yields co(2) as a potential secondary substrate. the objective of this study was to resolve potential differences between anaerobic formate- and co(2)-utilizing prokaryotes of this fen by stable isotope probing. anox ... | 2011 | 21478308 |
| genetic diversity of root nodule bacteria nodulating lotus corniculatus and anthyllis vulneraria in sweden. | very little is known about the genetic diversity and phylogeny of rhizobia nodulating lotus species in northern temperate regions. we have therefore studied the genetic diversity among a total of 61 root nodule bacteria isolated from lotus corniculatus and anthyllis vulneraria from different geographic sites and habitats in sweden by restriction fragment length polymorphism (rflp) of the internal transcribed spacer between their 16s rrna and 23s rrna (igs) region. a high diversity consisting of ... | 2011 | 21497473 |
| identification of mesorhizobium loti genes relevant to symbiosis by using signature-tagged mutants. | signature-tagged mutagenesis was applied to mesorhizobium loti, a nitrogen-fixing root-nodule symbiont of the leguminous plant lotus japonicus. we arranged 1,887 non-redundant mutant strains of m. loti into 75 sets, each consisting of 24 to 26 strains with a different tag in each strain. these sets were each inoculated en masse onto l. japonicus plants. comparative analysis of total dna extracted from inoculants and resulting nodules based on quantitative pcr led to the selection of 69 strains a ... | 2011 | 21502733 |
| plant growth-promoting fungus, trichoderma koningi suppresses isoflavonoid phytoalexin vestitol production for colonization on/in the roots of lotus japonicus. | the relationship between the colonization of lotus japonicus by plant growth-promoting fungi (pgpf) and biosynthesis of the isoflavonoid phytoalexin vestitol, a major defensive response of leguminous plants, was analyzed. when pgpf including trichoderma koningi, fusarium equiseti, and penicillium simplicissimum were inoculated onto l. japonicus roots, only t. koningi colonized the roots long-term and increased plant dry weight (126%). microscopic observations of transverse sections of roots colo ... | 2011 | 21502738 |
| 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 |
| isolation of xylose isomerases by sequence- and function-based screening from a soil metagenome library. | abstract: background: xylose isomerase (xi) catalyses the isomerization of xylose to xylulose in bacteria and some fungi. currently, only a limited number of xi genes have been functionally expressed in saccharomyces cerevisiae, the microorganism of choice for lignocellulosic ethanol production. the objective of the present study was to search for novel xi genes in the vastly diverse microbial habitat present in soil. as the exploitation of microbial diversity is impaired by the ability to culti ... | 2011 | 21545702 |
| root hair deformation of symbiosis-deficient mutants of lotus japonicus by application of nod factor from mesorhizobium loti. | in the model leguminous plant lotus japonicus, the reception of a symbiotic signal called nod factor (nf), which is secreted by the symbiont bacterium mesorhizobium loti, induces wavy shaped root hairs. this is called root hair deformation. to dissect the root hair deformation process, we studied symbiosis- deficient mutants of l. japonicus, castor, nup85, ccamk and nsp2. the castor, nup85, and ccamk genes are also required for mycorrhizal infection and thus called common symbiotic genes. on the ... | 2009 | 21566365 |
| azorhirobial chromosome partition gene (para) is involved in the onset of bacteroid differentiation in sesbania rostrata stem-nodule development. | a para gene in-frame deletion mutant of azorhizobium caulinodans ors571 (ors571-δpara) was constructed to evaluate the roles of the chromosome partitioning gene on various bacterial traits and on the development of stem-positioned nodules. the δpara mutant showed a pleiomorphic cell shape phenotype, and was polyploidy with differences in nucleoid sizes due to dramatic defects in chromosome partitioning. upon inoculating the δpara mutant onto the stem of sesbania rostrata, three types of immature ... | 2011 | 21571889 |
| tonb-dependent receptors in nitrogen-fixing nodulating bacteria. | tonb-dependent receptors (tbdrs) allow gram-negative bacteria to uptake scarce resources from competitive environments with very high affinity. early reports on tbdrs focused on the uptake of siderophore-iron complexes but recent studies have showed that the spectrum of ligands includes sugars, vitamins, heme, and other non-ferrous cations. to investigate the possible roles of tbdrs in nitrogen-fixing, nodulating bacteria, a bioinformatics approach was adopted to identify their presence in the g ... | 2010 | 21576856 |
| characterization of mesorhizobium loti l-rhamnose isomerase and its application to l-talose production. | the l-rhamnose isomerase gene (rhi) of mesorhizobium loti was cloned and expressed in escherichia coli, and then characterized. the enzyme exhibited activity with respect to various aldoses, including d-allose and l-talose. application of it in l-talose production from galactitol was achieved by a two-step reaction, indicating that it can be utilized in the large-scale production of l-talose. | 2011 | 21597169 |
| s-adenosylmethionine-binding properties of a bacterial phospholipid n-methyltransferase. | the presence of the membrane lipid phosphatidylcholine (pc) in the bacterial membrane is critically important for many host-microbe interactions. the phospholipid n-methyltransferase pmta from the plant pathogen agrobacterium tumefaciens catalyzes the formation of pc by a three-step methylation of phosphatidylethanolamine via monomethyl-phosphatidylethanolamine and dimethylphosphatidylethanolamine. the methyl group is provided by s-adenosylmethionine (sam), which is converted to s-adenosylhomocy ... | 2011 | 21602340 |
| crystal structure of a novel esterase rv0045c from mycobacterium tuberculosis. | there are at least 250 enzymes in mycobacterium tuberculosis (m. tuberculosis) involved in lipid metabolism. some of the enzymes are required for bacterial survival and full virulence. the esterase rv0045c shares little amino acid sequence similarity with other members of the esterase/lipase family. here, we report the 3d structure of rv0045c. our studies demonstrated that rv0045c is a novel member of α/β hydrolase fold family. the structure of esterase rv0045c contains two distinct domains: the ... | 2011 | 21637775 |
| multiple loci are involved in quorum quenching of autoinducer i molecules in the nitrogen-fixing symbiont (sino-) rhizobium sp. ngr234. | rhizobium sp. ngr234 is a unique α-proteobacterium (order - rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other micro-symbiont. since we have previously described the complete genome sequence of ngr234, we now report on a genome wide functional analysis of the genes and enzymes involved in autoinducer i hydrolysis in this microbe. altogether we identified five cosmid clones that repeatedly gave a positive result in our function-based approach for the detection of aut ... | 2011 | 21642401 |
| systems biology of bacterial nitrogen fixation: high-throughput technology and its integrative description with constraint-based modeling. | abstract: background: bacterial nitrogen fixation is the biological process by which atmospheric nitrogen is uptaken by bacteroids located in plant root nodules and converted into ammonium through the enzymatic activity of nitrogenase. in practice, this biological process serves as a natural form of fertilization and its optimization has significant implications in sustainable agricultural programs. currently, the advent of high-throughput technology supplies with valuable data that contribute t ... | 2011 | 21801415 |
| a monogalactosyldiacylglycerol synthase found in the green sulfur bacterium chlorobaculum tepidum reveals important roles for galactolipids in photosynthesis. | monogalactosyldiacylglycerol (mgdg), which is conserved in almost all photosynthetic organisms, is the most abundant natural polar lipid on earth. in plants, mgdg is highly accumulated in the chloroplast membranes and is an important bulk constituent of thylakoid membranes. however, precise functions of mgdg in photosynthesis have not been well understood. here, we report a novel mgdg synthase from the green sulfur bacterium chlorobaculum tepidum. this enzyme, mgda, catalyzes mgdg synthesis usin ... | 2011 | 21764989 |
| identification of xanthomonas fragariae, xanthomonas axonopodis pv. phaseoli, and xanthomonas fuscans subsp. fuscans with novel markers and using a dot blot platform coupled with automatic data analysis. | phytosanitary regulations and the provision of plant health certificates still rely mainly on long and laborious culture-based methods of diagnosis, which are frequently inconclusive. dna-based methods of detection can circumvent many of the limitations of currently used screening methods, allowing a fast and accurate monitoring of samples. the genus xanthomonas includes 13 phytopathogenic quarantine organisms for which improved methods of diagnosis are needed. in this work, we propose 21 new xa ... | 2011 | 21705524 |
| expression and characterization of a mycoplasma genitalium glycosyltransferase in membrane glycolipid biosynthesis. potential target against mycoplasma infections. | mycoplasmas contain glycoglycerolipids in their plasma membrane as key structural components involved in bilayer properties and stability. a membrane-associated glycosyltransferase, gt mg517, has been identified in mycoplasma genitalium, which sequentially produces monoglycosyl- and diglycosyldiacylglycerols (mgdag and dgdag). when recombinantly expressed in e. coli, the enzyme was functional in vivo and yielded membrane glycolipids from which glc+¦1,6glc+¦dag was identified as the main product. ... | 2011 | 21835921 |
| horizontal gene exchange in environmental microbiota. | horizontal gene transfer (hgt) plays an important role in the evolution of life on the earth. this view is supported by numerous occasions of hgt that are recorded in the genomes of all three domains of living organisms. hgt-mediated rapid evolution is especially noticeable among the bacteria, which demonstrate formidable adaptability in the face of recent environmental changes imposed by human activities, such as the use of antibiotics, industrial contamination, and intensive agriculture. at th ... | 2011 | 21845185 |
| phylogenetic analysis reveals gene conversions in multigene families of rhizobia. | gene families are an important and intrinsic trait of rhizobial species. these gene copies can participate in non-reciprocal recombination events, also called gene conversions. gene conversion has diverse roles, but it is usually implicated in the evolution of multigene families. here, we searched for gene conversions in multigene families of six representative rhizobial genomes. we identified 11 gene families with different numbers of copies, genome location and function in cfn42 and ciat652 st ... | 2011 | 21823087 |
| photorespiratory metabolism and nodule function: behavior of lotus japonicus mutants deficient in plastid glutamine synthetase. | two photorespiratory mutants of lotus japonicus deficient in plastid glutamine synthetase (gs(2)) were examined for their capacity to establish symbiotic association with mesorhizobium loti bacteria. biosynthetic glutamine synthetase (gs) activity was reduced by around 40% in crude nodule extracts from mutant plants as compared with the wild type (wt). western blot analysis further confirmed the lack of gs(2) polypeptide in mutant nodules. the decrease in gs activity affected the nodular carbon ... | 2011 | 22007601 |
| Recent Progress in Development of Tnt1 Functional Genomics Platform for Medicago truncatula and Lotus japonicus in Bulgaria. | Legumes, as protein-rich crops, are widely used for human food, animal feed and vegetable oil production. Over the past decade, two legume species, Medicago truncatula and Lotus japonicus, have been adopted as model legumes for genomics and physiological studies. The tobacco transposable element, Tnt1, is a powerful tool for insertional mutagenesis and gene inactivation in plants. A large collection of Tnt1-tagged lines of M. truncatula cv. Jemalong was generated during the course of the project ... | 2011 | 21966253 |
| excision of an unstable pathogenicity island in salmonella enterica serovar enteritidis is induced during infection of phagocytic cells. | the availability of the complete genome sequence of several salmonella enterica serovars has revealed the presence of unstable genetic elements in these bacteria, such as pathogenicity islands and prophages. this is the case of salmonella enterica serovar enteritidis (s. enteritidis), a bacterium that causes gastroenteritis in humans and systemic infection in mice. the whole genome sequence analysis for s. enteritidis unveiled the presence of several genetic regions that are absent in other salm ... | 2011 | 22039432 |
| sequence and role in virulence of the three plasmid complement of the model tumor-inducing bacterium pseudomonas savastanoi pv. savastanoi ncppb 3335. | pseudomonas savastanoi pv. savastanoi ncppb 3335 is a model for the study of the molecular basis of disease production and tumor formation in woody hosts, and its draft genome sequence has been recently obtained. here we closed the sequence of the plasmid complement of this strain, composed of three circular molecules of 78,357 nt (ppsv48a), 45,220 nt (ppsv48b), and 42,103 nt (ppsv48c), all belonging to the ppt23a-like family of plasmids widely distributed in the p. syringae complex. a total of ... | 2011 | 22022435 |
| identification of a eukaryotic reductive dechlorinase and characterization of its mechanism of action on its natural substrate. | chlorinated compounds are important environmental pollutants whose biodegradation may be limited by inefficient dechlorinating enzymes. dictyostelium amoebae produce a chlorinated alkyl phenone called dif which induces stalk cell differentiation during their multicellular development. here we describe the identification of dif dechlorinase. dif dechlorinase is active when expressed in bacteria, and activity is lost from dictyostelium cells when its gene, drca, is knocked out. it has a k(m) for d ... | 2011 | 22035794 |
| Interplay of flg22-induced defence responses and nodulation in Lotus japonicus. | In this study the interplay between the symbiotic and defence signalling pathways in Lotus japonicus was investigated by comparing the responses to Mesorhizobium loti, the symbiotic partner of L. japonicus, and the elicitor flg22, a conserved peptide motif present in flagellar protein of a wide range of bacteria. It was found that defence and symbiotic pathways overlap in the interaction between L. japonicus and M. loti since similar responses were induced by the mutualistic bacteria and flg22. ... | 2012 | 21934117 |
| Interplay of flg22-induced defence responses and nodulation in Lotus japonicus. | In this study the interplay between the symbiotic and defence signalling pathways in Lotus japonicus was investigated by comparing the responses to Mesorhizobium loti, the symbiotic partner of L. japonicus, and the elicitor flg22, a conserved peptide motif present in flagellar protein of a wide range of bacteria. It was found that defence and symbiotic pathways overlap in the interaction between L. japonicus and M. loti since similar responses were induced by the mutualistic bacteria and flg22. ... | 2012 | 21934117 |
| 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 simple method to evaluate the number of bradyrhizobia on soybean seeds and its implication on inoculant quality control. | abstract: soybean seeds are non-sterile and their bacterial population interferes with the enumeration of beneficial bacteria, making it difficult to assess survival under different conditions. within this context, the principal aims of this work were: (1) to improve a selective media for the enumeration of b. japonicum recovered from inoculated soybean seeds; (2) to establish the most representative mathematical function for b. japonicum mortality on soybean seeds after inoculation; (3) to eval ... | 2011 | 21906377 |
| a novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by variovorax sp. strain srs16. | the soil bacterial isolate variovorax sp. strain srs16 mineralizes the phenylurea herbicide linuron. the proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (dca) and n,o-dimethylhydroxylamine, followed by conversion of dca to krebs cycle intermediates. differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (liba), a multicomponent chloroaniline dioxygenase, and enzymes associated with a ... | 2011 | 22003008 |
| 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 |
| nodulin 41, a novel late nodulin of common bean with peptidase activity. | the legume-rhizobium symbiosis requires the formation of root nodules, specialized organs where the nitrogen fixation process takes place. nodule development is accompanied by the induction of specific plant genes, referred to as nodulin genes. important roles in processes such as morphogenesis and metabolism have been assigned to nodulins during the legume-rhizobium symbiosis. | 2011 | 21985276 |
| Lotus japonicus nodulation is photomorphogenetically controlled by sensing the red/far red (R/FR) ratio through jasmonic acid (JA) signaling. | Light is critical for supplying carbon to the energetically expensive, nitrogen-fixing symbiosis between legumes and rhizobia. Here, we show that phytochrome B (phyB) is part of the monitoring system to detect suboptimal light conditions, which normally suppress Lotus japonicus nodule development after Mesorhizobium loti inoculation. We found that the number of nodules produced by L. japonicus phyB mutants is significantly reduced compared with the number produced of WT Miyakojima MG20. To explo ... | 2011 | 21930895 |
| biological consequences of ancient gene acquisition and duplication in the large genome of candidatus solibacter usitatus ellin6076. | members of the bacterial phylum acidobacteria are widespread in soils and sediments worldwide, and are abundant in many soils. acidobacteria are challenging to culture in vitro, and many basic features of their biology and functional roles in the soil have not been determined. candidatus solibacter usitatus strain ellin6076 has a 9.9 mb genome that is approximately 2-5 times as large as the other sequenced acidobacteria genomes. bacterial genome sizes typically range from 0.5 to 10 mb and are in ... | 2011 | 21949776 |
| 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 |
| quantitative trait locus analysis of symbiotic nitrogen fixation activity in the model legume lotus japonicus. | many legumes form nitrogen-fixing root nodules. an elevation of nitrogen fixation in such legumes would have significant implications for plant growth and biomass production in agriculture. to identify the genetic basis for the regulation of nitrogen fixation, quantitative trait locus (qtl) analysis was conducted with recombinant inbred lines derived from the cross miyakojima mg-20 × gifu b-129 in the model legume lotus japonicus. this population was inoculated with mesorhizobium loti maff303099 ... | 2011 | 22009016 |
| Is the sequence-specific binding of aminoacyl-tRNAs by EF-Tu universal among bacteria? | Three base pairs in the T-stem are primarily responsible for the sequence-specific interaction of tRNA with Escherichia coli and Thermus thermophilus EF-Tu. While the amino acids on the surface of EF-Tu that contact aminoacyl-tRNA (aa-tRNA) are highly conserved among bacteria, the T-stem sequences of individual tRNA are variable, making it unclear whether or not this protein-nucleic acid interaction is also sequence specific in other bacteria. We propose and validate a thermodynamic model that p ... | 2011 | 21893586 |
| crystallization and preliminary x-ray analysis of pyridoxine 4-oxidase, the first enzyme in pyridoxine degradation pathway i. | vitamin b(6)-degradation pathway i has recently been identified in mesorhizobium loti maff303099. pyridoxine 4-oxidase, an fad-dependent enzyme, is the first enzyme in this pathway and catalyzes the irreversible oxidation of pyridoxine to pyridoxal. the enzyme was overexpressed in escherichia coli with a his(6) tag and purified. the recombinant enzyme was crystallized at 277 k by the sitting-drop vapour-diffusion method using peg 4000 as the precipitant. the crystal, which belonged to space grou ... | 2012 | 22232175 |
| crystallization and preliminary x-ray analysis of pyridoxine 4-oxidase, the first enzyme in pyridoxine degradation pathway i. | vitamin b(6)-degradation pathway i has recently been identified in mesorhizobium loti maff303099. pyridoxine 4-oxidase, an fad-dependent enzyme, is the first enzyme in this pathway and catalyzes the irreversible oxidation of pyridoxine to pyridoxal. the enzyme was overexpressed in escherichia coli with a his(6) tag and purified. the recombinant enzyme was crystallized at 277 k by the sitting-drop vapour-diffusion method using peg 4000 as the precipitant. the crystal, which belonged to space grou ... | 2012 | 22232175 |
| structure of the pilus assembly protein tadz from eubacterium rectale: implications for polar localization. | the tad (tight adherence) locus encodes a protein translocation system that produces a novel variant of type iv pili. the pilus assembly protein tadz (called cpae in caulobacter crescentus) is ubiquitous in tad loci, but is absent in other type iv pilus biogenesis systems. the crystal structure of tadz from eubacterium rectale (ertadz), in complex with atp and mg(2+) , was determined to 2.1 å resolution. ertadz contains an atypical atpase domain with a variant of a deviant walker-a motif that re ... | 2011 | 22211578 |
| 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 |
| structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site. | l-rhamnose isomerase (l-rhi) catalyzes the reversible isomerization of l-rhamnose to l-rhamnulose. previously determined x-ray structures of l-rhi showed a hydride-shift mechanism for the isomerization of substrates in a linear form, but the mechanism for opening of the sugar-ring is still unclear. to elucidate this mechanism, we determined x-ray structures of a mutant l-rhi in complex with l-rhamnopyranose and d-allopyranose. results suggest that a catalytic water molecule, which acts as an aci ... | 2012 | 23772372 |
| structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site. | l-rhamnose isomerase (l-rhi) catalyzes the reversible isomerization of l-rhamnose to l-rhamnulose. previously determined x-ray structures of l-rhi showed a hydride-shift mechanism for the isomerization of substrates in a linear form, but the mechanism for opening of the sugar-ring is still unclear. to elucidate this mechanism, we determined x-ray structures of a mutant l-rhi in complex with l-rhamnopyranose and d-allopyranose. results suggest that a catalytic water molecule, which acts as an aci ... | 2012 | 23772372 |
| 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 |