| a ubiquitin ligase of symbiosis receptor kinase involved in nodule organogenesis. | the symbiosis receptor kinase (symrk) is required for morphological changes of legume root hairs triggered by rhizobial infection. how protein turnover of symrk is regulated and how the nodulation factor signals are transduced downstream of symrk are not known. in this report, a symrk-interacting e3 ubiquitin ligase (sie3) was shown to bind and ubiquitinate symrk. the sie3-symrk interaction and the ubiquitination of symrk were shown to occur in vitro and in planta. sie3 represents a new class of ... | 2012 | 22822209 |
| genetic diversity of rhizobia isolates from amazon soils using cowpea (vigna unguiculata) as trap plant. | the aim of this work was to characterize rhizobia isolated from the root nodules of cowpea (vigna unguiculata) plants cultivated in amazon soils samples by means of ardra (amplified rdna restriction analysis) and sequencing analysis, to know their phylogenetic relationships. the 16s rrna gene of rhizobia was amplified by pcr (polymerase chain reaction) using universal primers y1 and y3. the amplification products were analyzed by the restriction enzymes hinfi, mspi and ddei and also sequenced wi ... | 2012 | 24031880 |
| multilocus sequence analysis (mlsa) of bradyrhizobium strains: revealing high diversity of tropical diazotrophic symbiotic bacteria. | symbiotic association of several genera of bacteria collectively called as rhizobia and plants belonging to the family leguminosae (=fabaceae) results in the process of biological nitrogen fixation, playing a key role in global n cycling, and also bringing relevant contributions to the agriculture. bradyrhizobium is considered as the ancestral of all nitrogen-fixing rhizobial species, probably originated in the tropics. the genus encompasses a variety of diverse bacteria, but the diversity captu ... | 2012 | 24031882 |
| lotus japonicus e3 ligase seven in absentia4 destabilizes the symbiosis receptor-like kinase symrk and negatively regulates rhizobial infection. | the lotus japonicus symbiosis receptor-like kinase (symrk) is required for symbiotic signal transduction upon stimulation of root cells by microbial signaling molecules. here, we identified members of the seven in absentia (sina) e3 ubiquitin-ligase family as symrk interactors and confirmed their predicted ubiquitin-ligase activity. in nicotiana benthamiana leaves, symrk-yellow fluorescent protein was localized at the plasma membrane, and interaction with sinas, as determined by bimolecular fluo ... | 2012 | 22534128 |
| the small gtpase rop6 interacts with nfr5 and is involved in nodule formation in lotus japonicus. | nod factor receptor5 (nfr5) is an atypical receptor-like kinase, having no activation loop in the protein kinase domain. it forms a heterodimer with nfr1 and is required for the early plant responses to rhizobium infection. a rho-like small gtpase from lotus japonicus was identified as an nfr5-interacting protein. the amino acid sequence of this rho-like gtpase is closest to the arabidopsis (arabidopsis thaliana) rop6 and medicago truncatula rop6 and was designated as ljrop6. the interaction bet ... | 2012 | 22434040 |
| a map kinase kinase interacts with symrk and regulates nodule organogenesis in lotus japonicus. | the symbiosis receptor kinase, symrk, is required for root nodule development. a symrk-interacting protein (sip2) was found to form protein complex with symrk in vitro and in planta. the interaction between symrk and sip2 is conserved in legumes. the sip2 gene was expressed in all lotus japonicus tissues examined. sip2 represents a typical plant mitogen-activated protein kinase kinase (mapkk) and exhibited autophosphorylation and transphosphorylation activities. recombinant sip2 protein could ph ... | 2012 | 22353370 |
| nuclear-localized and deregulated calcium- and calmodulin-dependent protein kinase activates rhizobial and mycorrhizal responses in lotus japonicus. | the common symbiosis pathway is at the core of symbiosis signaling between plants and soil microbes. in this pathway, calcium- and calmodulin-dependent protein kinase (ccamk) plays a crucial role in integrating the signals both in arbuscular mycorrhizal symbiosis (ams) and in root nodule symbiosis (rns). however, the molecular mechanism by which ccamk coordinates ams and rns is largely unknown. here, we report that the gain-of-function (gof) variants of ccamk without the regulatory domains activ ... | 2012 | 22337918 |
| the national bioresource project (nbrp) lotus and glycine in japan. | the objective of the national bioresource project (nbrp) in japan is to collect, conserve and distribute biological materials for life sciences research. the project consists of twenty-eight bioresources, including animal, plant, microorganism and dna resources. nbrp lotus and glycine aims to support the development of legume research through the collection, conservation, and distribution of these bioresources. lotus japonicus is a perennial legume that grows naturally throughout japan and is wi ... | 2012 | 23136485 |
| functional domain analysis of the remorin protein ljsymrem1 in lotus japonicus. | in legumes rhizobial infection during root nodule symbiosis (rns) is controlled by a conserved set of receptor proteins and downstream components. mtsymrem1, a protein of the remorin family in medicago truncatula, was shown to interact with at least three receptor-like kinases (rlks) that are essential for rns. remorins are comprised of a conserved c-terminal domain and a variable n-terminal region that defines the six different remorin groups. while both n- and c-terminal regions of remorins be ... | 2012 | 22292047 |
| rhizobial and fungal symbioses show different requirements for calmodulin binding to calcium calmodulin-dependent protein kinase in lotus japonicus. | ca(2+)/calmodulin (cam)-dependent protein kinase (ccamk) is a key regulator of root nodule and arbuscular mycorrhizal symbioses and is believed to be a decoder for ca(2+) signals induced by microbial symbionts. however, it is unclear how ccamk is activated by these microbes. here, we investigated in vivo activation of ccamk in symbiotic signaling, focusing mainly on the significance of and epistatic relationships among functional domains of ccamk. loss-of-function mutations in ef-hand motifs rev ... | 2012 | 22253228 |
| rhizobial infection does not require cortical expression of upstream common symbiosis genes responsible for the induction of ca(2+) spiking. | for the establishment of an effective root nodule symbiosis, a coordinated regulation of the infection processes between the epidermis and cortex is required. however, it remains unclear whether the symbiotic genes identified so far are involved in epidermal and/or cortical infection, e.g. epidermal and cortical infection thread formation or cortical cell division. to analyze the symbiotic gene requirements of the infection process, we have developed an epidermis-specific expression system (pepi ... | 2013 | 24329948 |
| rhizobial infection does not require cortical expression of upstream common symbiosis genes responsible for the induction of ca(2+) spiking. | for the establishment of an effective root nodule symbiosis, a coordinated regulation of the infection processes between the epidermis and cortex is required. however, it remains unclear whether the symbiotic genes identified so far are involved in epidermal and/or cortical infection, e.g. epidermal and cortical infection thread formation or cortical cell division. to analyze the symbiotic gene requirements of the infection process, we have developed an epidermis-specific expression system (pepi ... | 2013 | 24329948 |
| nodule inception directly targets nf-y subunit genes to regulate essential processes of root nodule development in lotus japonicus. | the interactions of legumes with symbiotic nitrogen-fixing bacteria cause the formation of specialized lateral root organs called root nodules. it has been postulated that this root nodule symbiosis system has recruited factors that act in early signaling pathways (common sym genes) partly from the ancestral mycorrhizal symbiosis. however, the origins of factors needed for root nodule organogenesis are largely unknown. nodule inception (nin) is a nodulation-specific gene that encodes a putative ... | 2013 | 23555278 |
| metabolic and functional diversity of saponins, biosynthetic intermediates and semi-synthetic derivatives. | saponins are widely distributed plant natural products with vast structural and functional diversity. they are typically composed of a hydrophobic aglycone, which is extensively decorated with functional groups prior to the addition of hydrophilic sugar moieties, to result in surface-active amphipathic compounds. the saponins are broadly classified as triterpenoids, steroids or steroidal glycoalkaloids, based on the aglycone structure from which they are derived. the saponins and their biosynthe ... | 2014 | 25286183 |
| nodule inception creates a long-distance negative feedback loop involved in homeostatic regulation of nodule organ production. | autoregulatory negative-feedback loops play important roles in fine-balancing tissue and organ development. such loops are composed of short-range intercellular signaling pathways via cell-cell communications. on the other hand, leguminous plants use a long-distance negative-feedback system involving root-shoot communication to control the number of root nodules, root lateral organs that harbor symbiotic nitrogen-fixing bacteria known as rhizobia. this feedback system, known as autoregulation of ... | 2014 | 25246578 |
| mir171h restricts root symbioses and shows like its target nsp2 a complex transcriptional regulation in medicago truncatula. | legumes have the unique capability to undergo root nodule and arbuscular mycorrhizal symbiosis. both types of root endosymbiosis are regulated by nsp2, which is a target of microrna171h (mir171h). although, recent data implies that mir171h specifically restricts arbuscular mycorrhizal symbiosis in the root elongation zone of medicago truncatula roots, there is limited knowledge available about the spatio-temporal regulation of mir171h expression at different physiological and symbiotic condition ... | 2014 | 25928247 |
| lotus japonicus sunergos1 encodes a predicted subunit a of a dna topoisomerase vi that is required for nodule differentiation and accommodation of rhizobial infection. | a symbiotic mutant of lotus japonicus, called sunergos1-1 (suner1-1), originated from a har1-1 suppressor screen. suner1-1 supports epidermal infection by mesorhizobium loti and initiates cell divisions for organogenesis of nodule primordia. however, these processes appear to be temporarily stalled early during symbiotic interaction, leading to a low nodule number phenotype. this defect is ephemeral and near wild-type nodule numbers are reached by suner1-1 at a later point after infection. using ... | 2014 | 24661810 |
| a positive regulator of nodule organogenesis, nodule inception, acts as a negative regulator of rhizobial infection in lotus japonicus. | legume-rhizobium symbiosis occurs in specialized root organs called nodules. to establish the symbiosis, two major genetically controlled events, rhizobial infection and organogenesis, must occur. for a successful symbiosis, it is essential that the two phenomena proceed simultaneously in different root tissues. although several symbiotic genes have been identified during genetic screenings of nonsymbiotic mutants, most of the mutants harbor defects in both infection and organogenesis pathways, ... | 2014 | 24722550 |
| genome sequence of ensifer adhaerens ov14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes. | recently it has been shown that ensifer adhaerens can be used as a plant transformation technology, transferring genes into several plant genomes when equipped with a ti plasmid. for this study, we have sequenced the genome of ensifer adhaerens ov14 (ov14) and compared it with those of agrobacterium tumefaciens c58 (c58) and sinorhizobium meliloti 1021 (1021); the latter of which has also demonstrated a capacity to genetically transform crop genomes, albeit at significantly reduced frequencies. | 2014 | 24708309 |
| lotus japonicus cytokinin receptors work partially redundantly to mediate nodule formation. | previous analysis of the lotus histidine kinase1 (lhk1) cytokinin receptor gene has shown that it is required and also sufficient for nodule formation in lotus japonicus. the l. japonicus mutant carrying the loss-of-function lhk1-1 allele is hyperinfected by its symbiotic partner, mesorhizobium loti, in the initial absence of nodule organogenesis. at a later time point following bacterial infection, lhk1-1 develops a limited number of nodules, suggesting the presence of an lhk1-independent mecha ... | 2014 | 24585837 |
| scarn a novel class of scar protein that is required for root-hair infection during legume nodulation. | rhizobial infection of legume root hairs requires a rearrangement of the actin cytoskeleton to enable the establishment of plant-made infection structures called infection threads. in the scar/wave (suppressor of camp receptor defect/wasp family verpolin homologous protein) actin regulatory complex, the conserved n-terminal domains of scar proteins interact with other components of the scar/wave complex. the conserved c-terminal domains of scar proteins bind to and activate the actin-related pro ... | 2015 | 26517270 |
| ethylene resistance in flowering ornamental plants - improvements and future perspectives. | various strategies of plant breeding have been attempted in order to improve the ethylene resistance of flowering ornamental plants. these approaches span from conventional techniques such as simple cross-pollination to new breeding techniques which modify the plants genetically such as precise genome-editing. the main strategies target the ethylene pathway directly; others focus on changing the ethylene pathway indirectly via pathways that are known to be antagonistic to the ethylene pathway, e ... | 2015 | 26504580 |
| proteomic analysis of the soybean symbiosome identifies new symbiotic proteins. | legumes form a symbiosis with rhizobia in which the plant provides an energy source to the rhizobia bacteria that it uses to fix atmospheric nitrogen. this nitrogen is provided to the legume plant, allowing it to grow without the addition of nitrogen fertilizer. as part of the symbiosis, the bacteria in the infected cells of a new root organ, the nodule, are surrounded by a plant-derived membrane, the symbiosome membrane, which becomes the interface between the symbionts. fractions containing th ... | 2015 | 25724908 |
| lotus japonicus clathrin heavy chain1 is associated with rho-like gtpase rop6 and involved in nodule formation. | mechanisms underlying nodulation factor signaling downstream of the nodulation factor receptors (nfrs) have not been fully characterized. in this study, clathrin heavy chain1 (chc1) was shown to interact with the rho-like gtpase rop6, an interaction partner of nfr5 in lotus japonicus. the chc1 gene was found to be expressed constitutively in all plant tissues and induced in mesorhizobium loti-infected root hairs and nodule primordia. when expressed in leaves of nicotiana benthamiana, chc1 and ro ... | 2015 | 25717037 |
| network of gras transcription factors involved in the control of arbuscule development in lotus japonicus. | arbuscular mycorrhizal (am) fungi, in symbiosis with plants, facilitate acquisition of nutrients from the soil to their host. after penetration, intracellular hyphae form fine-branched structures in cortical cells termed arbuscules, representing the major site where bidirectional nutrient exchange takes place between the host plant and fungus. transcriptional mechanisms underlying this cellular reprogramming are still poorly understood. gras proteins are an important family of transcriptional re ... | 2015 | 25560877 |
| intraradical colonization by arbuscular mycorrhizal fungi triggers induction of a lipochitooligosaccharide receptor. | functional divergence of paralogs following gene duplication is one of the mechanisms leading to evolution of novel pathways and traits. here we show that divergence of lys11 and nfr5 lysm receptor kinase paralogs of lotus japonicus has affected their specificity for lipochitooligosaccharides (lcos) decorations, while the innate capacity to recognize and induce a downstream signalling after perception of rhizobial lcos (nod factors) was maintained. regardless of this conserved ability, lys11 was ... | 2016 | 27435342 |
| transfer of dna from bacteria to eukaryotes. | historically, the members of the agrobacterium genus have been considered the only bacterial species naturally able to transfer and integrate dna into the genomes of their eukaryotic hosts. yet, increasing evidence suggests that this ability to genetically transform eukaryotic host cells might be more widespread in the bacterial world. indeed, analyses of accumulating genomic data reveal cases of horizontal gene transfer from bacteria to eukaryotes and suggest that it represents a significant fo ... | 2016 | 27406565 |
| medicago truncatula gaertn. as a model for understanding the mechanism of growth promotion by bacteria from rhizosphere and nodules of alfalfa. | the present study showed all the 16 strains isolated and identified from the alfalfa rhizosphere and nodules, and registered in genbank, to be good candidates for targeted use in studies addressing the rather weak known mechanism of plant growth promotion, including that of medicago truncatula, a molecular crop model. based on physiological, biochemical and molecular analysis, the 16 isolates obtained were ascribed to the following five families: bacillaceae, rhizobiaceae, xantomonadaceae, enter ... | 2016 | 26861677 |
| inoculation insensitive promoters for cell type enriched gene expression in legume roots and nodules. | establishment and maintenance of mutualistic plant-microbial interactions in the rhizosphere and within plant roots involve several root cell types. the processes of host-microbe recognition and infection require complex signal exchange and activation of downstream responses. these molecular events coordinate host responses across root cell layers during microbe invasion, ultimately triggering changes of root cell fates. the progression of legume root interactions with rhizobial bacteria has bee ... | 2016 | 26807140 |
| the repertoire of ice in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. | horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. conjugation allows the broadest range and the highest gene transfer input per transfer event. while conjugative plasmids have been studied for decades, the number and diversity of integrative conjugative elements (ice) in prokaryotes remained unknown. we defined a large set of protein profiles of the conjugation machinery to scan over 1,000 genomes of prokaryotes. we found 682 pu ... | 2011 | 21876676 |
| 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 |
| genetic characterization of a novel rhizobial plasmid conjugation system in rhizobium leguminosarum bv. viciae strain vf39sm. | rhizobium leguminosarum strain vf39sm contains two plasmids that have previously been shown to be self-transmissible by conjugation. one of these plasmids, prlevf39b, is shown in this study to carry a set of plasmid transfer genes that differs significantly from conjugation systems previously studied in the rhizobia but is similar to an uncharacterized set of genes found in r. leguminosarum bv. trifolii strain wsm2304. the entire sequence of the transfer region on prlevf39b was determined as par ... | 2013 | 23144250 |
| the use of fosmid metagenomic libraries in preliminary screening for various biological activities. | it is generally believed that there are many natural sources of as yet unknown bioactive compounds with a high biotechnological potential. however, the common method based on the use of cell extracts in the preliminary screening for particular molecules or activities is problematic as amounts of obtained compounds may be low, and such experiments are hardly reproducible. therefore, the aim of this work was to test whether a novel strategy to search for previously unknown biological activities ca ... | 2014 | 25048369 |
| a mrna-based thermosensor controls expression of rhizobial heat shock genes. | expression of several heat shock operons, mainly coding for small heat shock proteins, is under the control of rose (repression of heat shock gene expression) in various rhizobial species. this negatively cis-acting element confers temperature control by preventing expression at physiological temperatures. we provide evidence that rose-mediated regulation occurs at the post-transcriptional level. a detailed mutational analysis of rose(1)-hspa translationally fused to lacz revealed that its highl ... | 2001 | 11726689 |
| codon usage bias from trna's point of view: redundancy, specialization, and efficient decoding for translation optimization. | the selection-mutation-drift theory of codon usage plays a major role in the theory of molecular evolution by explaining the co-evolution of codon usage bias and trna content in the framework of translation optimization. because most studies have focused only on codon usage, we analyzed the trna gene pool of 102 bacterial species. we show that as minimal generation times get shorter, the genomes contain more trna genes, but fewer anticodon species. surprisingly, despite the wide g+c variation of ... | 2004 | 15479947 |
| cpndb: a chaperonin sequence database. | type i chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. sequences of cpn60 genes, encoding 60-kda chaperonin protein subunits (cpn60, also known as groel or hsp60), are useful for phylogenetic studies and as targets for detection and identification of organisms. conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal pcr primers. here, we introduce cpndb, a curated collectio ... | 2004 | 15289485 |
| trends between gene content and genome size in prokaryotic species with larger genomes. | although the evolution process and ecological benefits of symbiotic species with small genomes are well understood, these issues remain poorly elucidated for free-living species with large genomes. we have compared 115 completed prokaryotic genomes by using the clusters of orthologous groups database to determine whether there are changes with genome size in the proportion of the genome attributable to particular cellular processes, because this may reflect both cellular and ecological strategie ... | 2004 | 14973198 |
| nutrient sharing between symbionts. | | 2007 | 17556524 |
| responses of the model legume medicago truncatula to the rhizobial exopolysaccharide succinoglycan. | many species of rhizobial bacteria can invade their plant hosts and induce development of symbiotic nitrogen-fixing nodules only if they are able to produce an acidic exopolysaccharide (eps) with certain structural and molecular weight characteristics.1-3sinorhizobium meliloti that produces the functional form of the exopolysaccharide succinoglycan induces formation of invasion structures called infection threads in the root hair cells of its plant hosts alfalfa and medicago truncatula. however, ... | 2008 | 19704531 |
| trifle, a program for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets. | we describe trifle, a freely accessible computer program that generates theoretical terminal restriction fragments (t-rfs) from any user-supplied sequence set tailored to a particular group of organisms, sequences from clone libraries, or sequences from specific genes. the program allows a rapid identification of the most polymorphic enzymes, creates a collection of t-rfs for the data set, and can potentially identify specific t-rfs in t-rf length polymorphism (t-rflp) patterns by comparing theo ... | 2008 | 18757578 |
| genetic diversity of indigenous common bean (phaseolus vulgaris l.) rhizobia from the state of minas gerais, brazil. | we characterized indigenous common bean rhizobia from five districts of the state of minas gerais, brazil. the isolates were trapped by two common bean varieties, the mineiro precoce (andean origin) and ouro negro (mesoamerican origin). analysis by box-pcr of selected isolates detected a high level of genetic diversity. | 2009 | 24031433 |
| a fosmid cloning strategy for detecting the widest possible spectrum of microbes from the international space station drinking water system. | in this study, fosmid cloning strategies were used to assess the microbial populations in water from the international space station (iss) drinking water system (henceforth referred to as prebiocide and tank a water samples). the goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16s rrna-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. initially, ... | 2012 | 23346038 |
| 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 |
| conservation of gene order and content in the circular chromosomes of 'candidatus liberibacter asiaticus' and other rhizobiales. | 'ca. liberibacter asiaticus,' an insect-vectored, obligate intracellular bacterium associated with citrus-greening disease, also called "hlb," is a member of the rhizobiales along with nitrogen-fixing microsymbionts sinorhizobium meliloti and bradyrhizobium japonicum, plant pathogen agrobacterium tumefaciens and facultative intracellular mammalian pathogen bartonella henselae. comparative analyses of their circular chromosomes identified 514 orthologous genes shared among all five species. share ... | 2012 | 22496839 |
| metabolomics of forage plants: a review. | forage plant breeding is under increasing pressure to deliver new cultivars with improved yield, quality and persistence to the pastoral industry. new innovations in dna sequencing technologies mean that quantitative trait loci analysis and marker-assisted selection approaches are becoming faster and cheaper, and are increasingly used in the breeding process with the aim to speed it up and improve its precision. high-throughput phenotyping is currently a major bottle neck and emerging technologi ... | 2012 | 22351485 |
| isolation and characterization of two novel bacteria afipia cberi and mesorhizobium hominis from blood of a patient afflicted with fatal pulmonary illness. | we recently isolated and discovered new bradyrhizobiaceae microbes from the cryopreserved culture broth of blood samples from 3 patients with poorly defined illnesses using modified sp4 media and culture conditions coupled with genomic sequencing. using a similar protocol, we studied a previously cryopreserved culture broth of blood sample from a patient who had succumbed to an acute onset of fulminant pulmonary illness. we report that two phases of microbial growth were observed in the re-initi ... | 2013 | 24367538 |
| cyanobase and rhizobase: databases of manually curated annotations for cyanobacterial and rhizobial genomes. | to understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. we have extended cyanobase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed rhizobase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. both databases focus on the representation and reusability of reference genome a ... | 2013 | 24275496 |
| cyanobase and rhizobase: databases of manually curated annotations for cyanobacterial and rhizobial genomes. | to understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. we have extended cyanobase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed rhizobase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. both databases focus on the representation and reusability of reference genome a ... | 2013 | 24275496 |
| hijacking of leguminous nodulation signaling by the rhizobial type iii secretion system. | root-nodule symbiosis between leguminous plants and nitrogen-fixing bacteria (rhizobia) involves molecular communication between the two partners. key components for the establishment of symbiosis are rhizobium-derived lipochitooligosaccharides (nod factors; nfs) and their leguminous receptors (nfrs) that initiate nodule development and bacterial entry. here we demonstrate that the soybean microsymbiont bradyrhizobium elkanii uses the type iii secretion system (t3ss), which is known for its deli ... | 2013 | 24082124 |
| disclosure of the differences of mesorhizobium loti under the free-living and symbiotic conditions by comparative proteome analysis without bacteroid isolation. | rhizobia are symbiotic nitrogen-fixing soil bacteria that show a symbiotic relationship with their host legume. rhizobia have 2 different physiological conditions: a free-living condition in soil, and a symbiotic nitrogen-fixing condition in the nodule. the lifestyle of rhizobia remains largely unknown, although genome and transcriptome analyses have been carried out. to clarify the lifestyle of bacteria, proteome analysis is necessary because the protein profile directly reflects in vivo reacti ... | 2013 | 23898917 |
| proteogenomic analysis of bradyrhizobium japonicum usda110 using genosuite, an automated multi-algorithmic pipeline. | we present genosuite, an integrated proteogenomic pipeline to validate, refine and discover protein coding genes using high-throughput mass spectrometry (ms) data from prokaryotes. to demonstrate the effectiveness of genosuite, we analyzed proteomics data of bradyrhizobium japonicum (usda110), a model organism to study agriculturally important rhizobium-legume symbiosis. our analysis confirmed 31% of known genes, refined 49 gene models for their translation initiation site (tis) and discovered 5 ... | 2013 | 23882027 |
| genome analysis suggests that the soil oligotrophic bacterium agromonas oligotrophica (bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of aeschynomene indica. | agromonas oligotrophica (bradyrhizobium oligotrophicum) s58(t) is a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. here, the complete genome sequence of s58 was determined. the s58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average gc content of 65.1% lacking nodabc genes and the typical symbiosis island. the genome showed a high level of similarity to the genomes of bradyrhizobium sp. ... | 2013 | 23396330 |
| comparative genomics of the core and accessory genomes of 48 sinorhizobium strains comprising five genospecies. | the sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. while the alfalfa symbiont sinorhizobium meliloti rm 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group. | 2013 | 23425606 |
| the nifa-rpon regulon of mesorhizobium loti strain r7a and its symbiotic activation by a novel laci/galr-family regulator. | mesorhizobium loti is the microsymbiont of lotus species, including the model legume l. japonicus. m. loti differs from other rhizobia in that it contains two copies of the key nitrogen fixation regulatory gene nifa, nifa1 and nifa2, both of which are located on the symbiosis island icemlsym(r7a). m. loti r7a also contains two rpon genes, rpon1 located on the chromosome outside of icemlsym(r7a) and rpon2 that is located on icemlsym(r7a). the aims of the current work were to establish how nifa ex ... | 2013 | 23308282 |
| relationship between soil type and n₂o reductase genotype (nosz) of indigenous soybean bradyrhizobia: nosz-minus populations are dominant in andosols. | bradyrhizobium japonicum strains that have the nosz gene, which encodes n2o reductase, are able to mitigate n2o emissions from soils (15). to examine the distribution of nosz genotypes among japanese indigenous soybean bradyrhizobia, we isolated bradyrhizobia from the root nodules of soybean plants inoculated with 32 different soils and analyzed their nosz and nodc genotypes. the 1556 resultant isolates were classified into the nosz+/nodc+ genotype (855 isolates) and nosz-/nodc+ genotype (701 is ... | 2014 | 25476067 |
| ectopic expression of mir156 represses nodulation and causes morphological and developmental changes in lotus japonicus. | the effects of microrna156 overexpression on general plant architecture, branching, flowering time and nodulation were investigated in the model legume, lotus japonicus. we cloned an mir156 homolog, ljmir156a, from l. japonicus, and investigated its squamosa promoter binding protein like (spl) genes and its biological function at enhancing vegetative biomass yield, extending flowering time, and its impact on nodulation. thirteen potential targets for ljmir156 were identified in vitro and their e ... | 2014 | 25293935 |
| ectopic expression of mir156 represses nodulation and causes morphological and developmental changes in lotus japonicus. | the effects of microrna156 overexpression on general plant architecture, branching, flowering time and nodulation were investigated in the model legume, lotus japonicus. we cloned an mir156 homolog, ljmir156a, from l. japonicus, and investigated its squamosa promoter binding protein like (spl) genes and its biological function at enhancing vegetative biomass yield, extending flowering time, and its impact on nodulation. thirteen potential targets for ljmir156 were identified in vitro and their e ... | 2014 | 25293935 |
| rna-seq analysis of the multipartite genome of rhizobium etli ce3 shows different replicon contributions under heat and saline shock. | regulation of transcription is essential for any organism and rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. this bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (phaseolus vulgaris) in a symbiotic relationship. abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of r. etli and therefore its symbiotic interaction with p. vulgaris. however, it is still unc ... | 2014 | 25201548 |
| differing courses of genetic evolution of bradyrhizobium inoculants as revealed by long-term molecular tracing in acacia mangium plantations. | introducing nitrogen-fixing bacteria as an inoculum in association with legume crops is a common practice in agriculture. however, the question of the evolution of these introduced microorganisms remains crucial, both in terms of microbial ecology and agronomy. we explored this question by analyzing the genetic and symbiotic evolution of two bradyrhizobium strains inoculated on acacia mangium in malaysia and senegal 15 and 5 years, respectively, after their introduction. based on typing of sever ... | 2014 | 25002434 |
| proteomic analysis of free-living bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis. | strain cpac 7 (=semia 5080) was recently reclassified into the new species bradyrhizobium diazoefficiens; due to its outstanding efficiency in fixing nitrogen, it has been used in commercial inoculants for application to crops of soybean [glycine max (l.) merr.] in brazil and other south american countries. although the efficiency of b. diazoefficiens inoculant strains is well recognized, few data on their protein expression are available. | 2014 | 25086822 |
| identification of a dominant gene in medicago truncatula that restricts nodulation by sinorhizobium meliloti strain rm41. | leguminous plants are able to form a root nodule symbiosis with nitrogen-fixing soil bacteria called rhizobia. this symbiotic association shows a high level of specificity. beyond the specificity for the legume family, individual legume species/genotypes can only interact with certain restricted group of bacterial species or strains. specificity in this system is regulated by complex signal exchange between the two symbiotic partners and thus multiple genetic mechanisms could be involved in the ... | 2014 | 24934080 |
| comparative genomics of bradyrhizobium japonicum cpac 15 and bradyrhizobium diazoefficiens cpac 7: elite model strains for understanding symbiotic performance with soybean. | the soybean-bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. b. japonicum cpac 15 (=semia 5079) is outstanding in its saprophytic capacity and competitiveness, whereas b. diazoefficiens cpac 7 (=semia 5080) is known for its high efficiency in fixing nitrogen. both are well ada ... | 2014 | 24888481 |
| the role of symbiotic nitrogen fixation in sustainable production of biofuels. | with the ever-increasing population of the world (expected to reach 9.6 billion by 2050), and altered life style, comes an increased demand for food, fuel and fiber. however, scarcity of land, water and energy accompanied by climate change means that to produce enough to meet the demands is getting increasingly challenging. today we must use every avenue from science and technology available to address these challenges. the natural process of symbiotic nitrogen fixation, whereby plants such as l ... | 2014 | 24786096 |
| mixed group of rhizobiales microbes in lung and blood of a patient with fatal pulmonary illness. | we examined the microbial composition in the diseased lung and early-phase microbial cultures from the blood of a patient with a rapidly progressing fatal pulmonary illness. although no microbes could be isolated from such cultures during the initial study, the hts-microbiome study revealed the presence of a unique mixture of alphaproteobacteria, composed mainly of different families of rhizobiales microbes. microbial 16s rdna sequences matching closely to afipia cberi were identified mainly in ... | 2015 | 26823697 |
| legume-rhizobia signal exchange: promiscuity and environmental effects. | although signal exchange between legumes and their rhizobia is among the best-known examples of this biological process, most of the more characterized data comes from just a few legume species and environmental stresses. although a relative wealth of information is available for some model legumes and some of the major pulses such as soybean, little is known about tropical legumes. this relative disparity in current knowledge is also apparent in the research on the effects of environmental stre ... | 2015 | 26441880 |
| the control of auxin transport in parasitic and symbiotic root-microbe interactions. | most field-grown plants are surrounded by microbes, especially from the soil. some of these, including bacteria, fungi and nematodes, specifically manipulate the growth and development of their plant hosts, primarily for the formation of structures housing the microbes in roots. these developmental processes require the correct localization of the phytohormone auxin, which is involved in the control of cell division, cell enlargement, organ development and defense, and is thus a likely target fo ... | 2015 | 27135343 |
| symbiosis island shuffling with abundant insertion sequences in the genomes of extra-slow-growing strains of soybean bradyrhizobia. | extra-slow-growing bradyrhizobia from root nodules of field-grown soybeans harbor abundant insertion sequences (iss) and are termed highly reiterated sequence-possessing (hrs) strains. we analyzed the genome organization of hrs strains with the focus on is distribution and symbiosis island structure. using pulsed-field gel electrophoresis, we consistently detected several plasmids (0.07 to 0.4 mb) in the hrs strains (nk5, nk6, usda135, 2281, usda123, and t2), whereas no plasmids were detected in ... | 2015 | 25862225 |
| preferential association of endophytic bradyrhizobia with different rice cultivars and its implications for rice endophyte evolution. | plant colonization by bradyrhizobia is found not only in leguminous plants but also in nonleguminous species such as rice. to understand the evolution of the endophytic symbiosis of bradyrhizobia, the effect of the ecosystems of rice plantations on their associations was investigated. samples were collected from various rice (oryza sativa) tissues and crop rotational systems. the rice endophytic bradyrhizobia were isolated on the basis of oligotrophic properties, selective medium, and nodulation ... | 2015 | 25710371 |
| a genomic encyclopedia of the root nodule bacteria: assessing genetic diversity through a systematic biogeographic survey. | root nodule bacteria are free-living soil bacteria, belonging to diverse genera within the alphaproteobacteria and betaproteobacteria, that have the capacity to form nitrogen-fixing symbioses with legumes. the symbiosis is specific and is governed by signaling molecules produced from both host and bacteria. sequencing of several model rnb genomes has provided valuable insights into the genetic basis of symbiosis. however, the small number of sequenced rnb genomes available does not currently ref ... | 2015 | 25685260 |
| identification of ferredoxin ii as a major calcium binding protein in the nitrogen-fixing symbiotic bacterium mesorhizobium loti. | legumes establish with rhizobial bacteria a nitrogen-fixing symbiosis which is of the utmost importance for both plant nutrition and a sustainable agriculture. calcium is known to act as a key intracellular messenger in the perception of symbiotic signals by both the host plant and the microbial partner. regulation of intracellular free ca(2+) concentration, which is a fundamental prerequisite for any ca(2+)-based signalling system, is accomplished by complex mechanisms including ca(2+) binding ... | 2015 | 25648224 |
| search for nodulation and nodule development-related cystatin genes in the genome of soybean (glycine max). | nodulation, nodule development and senescence directly affects nitrogen fixation efficiency, and previous studies have shown that inhibition of some cysteine proteases delay nodule senescence, so their nature inhibitors, cystatin genes, are very important in nodulation, nodule development, and senescence. although several cystatins are actively transcribed in soybean nodules, their exact roles and functional diversities in legume have not been well explored in genome-wide survey studies. in this ... | 2016 | 27826313 |
| exopolysaccharide production by sinorhizobium fredii hh103 is repressed by genistein in a nodd1-dependent manner. | in the rhizobia-legume symbiotic interaction, bacterial surface polysaccharides, such as exopolysaccharide (eps), lipopolysaccharide (lps), k-antigen polysaccharide (kps) or cyclic glucans (cg), appear to play crucial roles either acting as signals required for the progression of the interaction and/or preventing host defence mechanisms. the symbiotic significance of each of these polysaccharides varies depending on the specific rhizobia-legume couple. in this work we show that the production of ... | 2016 | 27486751 |
| region 4 of rhizobium etli primary sigma factor (siga) confers transcriptional laxity in escherichia coli. | sigma factors are rna polymerase subunits engaged in promoter recognition and dna strand separation during transcription initiation in bacteria. primary sigma factors are responsible for the expression of housekeeping genes and are essential for survival. rpod, the primary sigma factor of escherichia coli, a γ-proteobacteria, recognizes consensus promoter sequences highly similar to those of some α-proteobacteria species. despite this resemblance, rpod is unable to sustain transcription from mos ... | 2016 | 27468278 |
| origin and evolution of nitrogen fixation genes on symbiosis islands and plasmid in bradyrhizobium. | the nitrogen fixation (nif) genes of nodule-forming bradyrhizobium strains are generally located on symbiosis islands or symbiosis plasmids, suggesting that these genes have been transferred laterally. the nif genes of rhizobial and non-rhizobial bradyrhizobium strains were compared in order to infer the evolutionary histories of nif genes. based on all codon positions, the phylogenetic tree of concatenated nifd and nifk sequences showed that nifdk on symbiosis islands formed a different clade f ... | 2016 | 27431195 |
| rhizobial gibberellin negatively regulates host nodule number. | in legume-rhizobia symbiosis, the nodule number is controlled to ensure optimal growth of the host. in lotus japonicus, the nodule number has been considered to be tightly regulated by host-derived phytohormones and glycopeptides. however, we have discovered a symbiont-derived phytohormonal regulation of nodule number in mesorhizobium loti. in this study, we found that m. loti synthesized gibberellic acid (ga) under symbiosis. hosts inoculated with a ga-synthesis-deficient m. loti mutant formed ... | 2016 | 27307029 |
| metabolomic profiling of bradyrhizobium diazoefficiens-induced root nodules reveals both host plant-specific and developmental signatures. | bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. our previous studies described b. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. in order to further characterize nodule metabolism, we here determine by flow injection-time-of-flight mass spectrometry analysis the metabolome of (i) nodules and roots fr ... | 2016 | 27240350 |
| draft genome sequence of mesorhizobium sp. ufla 01-765, a multitolerant, efficient symbiont and plant growth-promoting strain isolated from zn-mining soil using leucaena leucocephala as a trap plant. | we report the 7.4-mb draft genome sequence of mesorhizobium sp. strain ufla 01-765, a gram-negative bacterium of the phyllobacteriaceae isolated from zn-mining soil in minas gerais, brazil. this strain promotes plant growth, efficiently fixes n2 in symbiosis with leucaena leucocephala on multicontaminated soil, and has potential for application in bioremediation of marginal lands. | 2016 | 26966214 |
| discrete responses to limitation for iron and manganese in agrobacterium tumefaciens: influence on attachment and biofilm formation. | transition metals such as iron and manganese are crucial trace nutrients for the growth of most bacteria, functioning as catalytic cofactors for many essential enzymes. dedicated uptake and regulatory systems have evolved to ensure their acquisition for growth, while preventing toxicity. transcriptomic analysis of the iron- and manganese-responsive regulons of agrobacterium tumefaciens revealed that there are discrete regulatory networks that respond to changes in iron and manganese levels. comp ... | 2016 | 26712936 |
| conservation and occurrence of trans-encoded srnas in the rhizobiales. | post-transcriptional regulation by trans-encoded srnas, for example via base-pairing with target mrnas, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. several studies based on computational and rna-seq approaches identified approximately 180 trans-encoded srnas in sinorhizobium meliloti. the initial point of this report is a set of 52 trans-encoded srnas derived from the former studies. sequence homology combined with structural conservat ... | 2011 | 24710299 |
| prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment. | the commercial availability of next generation sequencing (ngs) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with ngs technologies. studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which m ... | 2013 | 24046766 |
| genes encoding conserved hypothetical proteins localized in the conjugative transfer region of plasmid pret42a from rhizobium etli cfn42 participate in modulating transfer and affect conjugation from different donors. | among sequenced genomes, it is common to find a high proportion of genes encoding proteins that cannot be assigned a known function. in bacterial genomes, genes related to a similar function are often located in contiguous regions. the presence of genes encoding conserved hypothetical proteins (chp) in such a region may suggest that they are related to that particular function. plasmid pret42a from rhizobium etli cfn42 is a conjugative plasmid containing a segment of approximately 30 kb encoding ... | 2014 | 25642223 |
| genes encoding conserved hypothetical proteins localized in the conjugative transfer region of plasmid pret42a from rhizobium etli cfn42 participate in modulating transfer and affect conjugation from different donors. | among sequenced genomes, it is common to find a high proportion of genes encoding proteins that cannot be assigned a known function. in bacterial genomes, genes related to a similar function are often located in contiguous regions. the presence of genes encoding conserved hypothetical proteins (chp) in such a region may suggest that they are related to that particular function. plasmid pret42a from rhizobium etli cfn42 is a conjugative plasmid containing a segment of approximately 30 kb encoding ... | 2014 | 25642223 |
| characterization of rhizobium grahamii extrachromosomal replicons and their transfer among rhizobia. | rhizobium grahamii belongs to a new phylogenetic group of rhizobia together with rhizobium mesoamericanum and other species. r. grahamii has a broad-host-range that includes leucaena leucocephala and phaseolus vulgaris, although it is a poor competitor for p. vulgaris nodulation in the presence of rhizobium etli or rhizobium phaseoli strains. this work analyzed the genome sequence and transfer properties of r. grahamii plasmids. | 2014 | 24397311 |
| phylogeny of symbiotic genes and the symbiotic properties of rhizobia specific to astragalus glycyphyllos l. | the phylogeny of symbiotic genes of astragalus glycyphyllos l. (liquorice milkvetch) nodule isolates was studied by comparative sequence analysis of noda, nodc, nodh and nifh loci. in all these genes phylograms, liquorice milkvetch rhizobia (closely related to bacteria of three species, i.e. mesorhizobium amorphae, mesorhizobium septentrionale and mesorhizobium ciceri) formed one clearly separate cluster suggesting the horizontal transfer of symbiotic genes from a single ancestor to the bacteria ... | 2015 | 26496493 |
| evolution of intra-specific regulatory networks in a multipartite bacterial genome. | reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. the evolution of such networks within and outside the species boundary is however still obscure. sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a signifi ... | 2015 | 26340565 |
| high-quality draft genome sequence of rhizobium mesoamericanum strain stm6155, a mimosa pudica microsymbiont from new caledonia. | rhizobium mesoamericanum stm6155 (inscd = atyy01000000) is an aerobic, motile, gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume mimosa pudica l.. stm6155 was isolated in 2009 from a nodule of the trap host m. pudica grown in nickel-rich soil collected near mont dore, new caledonia. r. mesoamericanum stm6155 was selected as part of the doe joint genome institute 2010 genomic encyclopedia for bacteria and archae ... | 2017 | 28116041 |
| use of subtractive hybridization to design habitat-based oligonucleotide probes for investigation of natural bacterial communities. | we describe a rapid oligonucleotide probe design strategy based on subtractive hybridization which yields probes for 16s rrna or rrna genes of individual members of microbial communities that are specific within the context of those communities. this strategy circumvents the need to sequence many similar or identical clones of dominant members of a community. radioactively labeled subfragments of a cloned 16s rrna gene sequence for which a probe is required (target) were hybridized with biotinyl ... | 1998 | 9435075 |
| oxygen regulation of a nodule-located carbonic anhydrase in alfalfa. | control of the permeability to oxygen is critical for the function of symbiotic nitrogen fixation in legume nodules. the inner cortex (ic) seems to be a primary site for this regulation. in alfalfa (medicago sativa) nodules, expression of the msca1 gene encoding a carbonic anhydrase (ca) was previously found to be restricted to the ic. we have now raised antibodies against recombinant msca1 protein and used them, together with antibodies raised against potato leaf ca, to demonstrate the presence ... | 2000 | 11080283 |
| voltage-dependent cation channels permeable to nh(+)(4), k(+), and ca(2+) in the symbiosome membrane of the model legume lotus japonicus. | the symbiosome of nitrogen fixing root nodules mediates metabolite exchange between endosymbiotic rhizobia bacteria and the legume host. in the present study, the ion currents of the symbiosome membrane of the model legume lotus japonicus were analyzed by patch-clamp recording. both excised and symbiosome-attached patches exhibited a large inward (toward the cytosolic side of the membrane) current that is activated in a time-dependent manner by negative (on the cytosolic side) potentials. based ... | 2002 | 11842141 |
| biochemistry and molecular biology of antioxidants in the rhizobia-legume symbiosis. | | 2003 | 14555779 |
| comparative genomics of physcomitrella patens gametophytic transcriptome and arabidopsis thaliana: implication for land plant evolution. | the mosses and flowering plants diverged >400 million years ago. the mosses have haploid-dominant life cycles, whereas the flowering plants are diploid-dominant. the common ancestors of land plants have been inferred to be haploid-dominant, suggesting that genes used in the diploid body of flowering plants were recruited from the genes used in the haploid body of the ancestors during the evolution of land plants. to assess this evolutionary hypothesis, we constructed an est library of the moss p ... | 2003 | 12808149 |
| analysis and functional classification of transcripts from the nematode meloidogyne incognita. | plant parasitic nematodes are major pathogens of most crops. molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches. as an entrée to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ests) from second-stage larvae (l2) of the root-knot nematode meloidogyne incognita. | 2003 | 12702207 |
| evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences. | we have determined the complete mitochondrial dna (mtdna) sequences of three chytridiomycete fungi, monoblepharella15, harpochytrium94 and harpochytrium105. our phylogenetic analysis based on concatenated mitochondrial protein sequences confirms the placement of mono blepharella15 together with harpochytrium spp. and hyaloraphidium curvatum within the taxonomic order monoblepharidales, with overwhelming support. these four mtdna sequences encode the standard fungal mitochondrial gene complement ... | 2003 | 12626702 |
| proteome analysis. novel proteins identified at the peribacteroid membrane from lotus japonicus root nodules. | the peribacteroid membrane (pbm) forms the structural and functional interface between the legume plant and the rhizobia. the model legume lotus japonicus was chosen to study the proteins present at the pbm by proteome analysis. pbm was purified from root nodules by an aqueous polymer two-phase system. extracted proteins were subjected to a global trypsin digest. the peptides were separated by nanoscale liquid chromatography and analyzed by tandem mass spectrometry. searching the nonredundant pr ... | 2003 | 12644660 |
| the sym35 gene required for root nodule development in pea is an ortholog of nin from lotus japonicus. | comparative phenotypic analysis of pea (pisum sativum) sym35 mutants and lotus japonicus nin mutants suggested a similar function for the pssym35 and ljnin genes in early stages of root nodule formation. both the pea and l. japonicus mutants are non-nodulating but normal in their arbuscular mycorrhizal association. both are characterized by excessive root hair curling in response to the bacterial microsymbiont, lack of infection thread initiation, and absence of cortical cell divisions. to inves ... | 2003 | 12644653 |
| exploring symbiotic nitrogen fixation and assimilation in pea root nodules by in vivo 15n nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry. | nitrogen (n) fixation and assimilation in pea (pisum sativum) root nodules were studied by in vivo (15)n nuclear magnetic resonance (nmr) by exposing detached nodules to (15)n(2) via a perfusion medium, while recording a time course of spectra. in vivo (31)p nmr spectroscopy was used to monitor the physiological state of the metabolically active nodules. the nodules were extracted after the nmr studies and analyzed for total soluble amino acid pools and (15)n labeling of individual amino acids b ... | 2003 | 12529544 |
| evolutionarily conserved regions and hydrophobic contacts at the superfamily level: the case of the fold-type i, pyridoxal-5'-phosphate-dependent enzymes. | the wealth of biological information provided by structural and genomic projects opens new prospects of understanding life and evolution at the molecular level. in this work, it is shown how computational approaches can be exploited to pinpoint protein structural features that remain invariant upon long evolutionary periods in the fold-type i, plp-dependent enzymes. a nonredundant set of 23 superposed crystallographic structures belonging to this superfamily was built. members of this family typ ... | 2004 | 15498941 |
| islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their dna site specificities. | prokaryotic chromosomes often contain islands, such as temperate phages or pathogenicity islands, delivered by site-specific integrases. integration usually occurs within a trna or tmrna gene, splitting the gene, yet sequences within the island restore the disrupted gene. the regenerated rna gene and the displaced fragment of that gene thus mark the endpoints of the island. we applied this principle to search for islands in genomic dna sequences. our algorithm generates a list of trna and tmrna ... | 2004 | 14681358 |
| the two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure. | the origin of the nuclear compartment has been extensively debated, leading to several alternative views on the evolution of the eukaryotic nucleus. until recently, too little phylogenetic information was available to address this issue by using multiple characters for many lineages. | 2005 | 16207356 |
| activation of olfactory-type cyclic nucleotide-gated channels is highly cooperative. | cyclic nucleotide-gated (cng) ion channels play a key role in the sensory transduction of vision and olfaction. the channels are opened by the binding of cyclic nucleotides. native olfactory cng channels are heterotetramers of cnga2, cnga4, and cngb1b subunits. upon heterologous expression, only cnga2 subunits can form functional homotetrameric channels. it is presently not known how the binding of the ligands to the four subunits is translated to channel opening. we studied activation of olfact ... | 2005 | 16081488 |