| correctly identifying the streptothricin resistance gene cassette. | | 2005 | 16082007 |
| seven lotus japonicus genes required for transcriptional reprogramming of the root during fungal and bacterial symbiosis. | a combined genetic and transcriptome analysis was performed to study the molecular basis of the arbuscular mycorrhiza (am) symbiosis. by testing the am phenotype of nodulation-impaired mutants and complementation analysis, we defined seven lotus japonicus common symbiosis genes (symrk, castor, pollux, sym3, sym6, sym15, and sym24) that are required for both fungal and bacterial entry into root epidermal or cortical cells. to describe the phenotype of these mutants at the molecular level, we scre ... | 2005 | 15980262 |
| microbial k+ channels. | | 2005 | 15897296 |
| peace talks and trade deals. keys to long-term harmony in legume-microbe symbioses. | | 2005 | 15824283 |
| extracellular atp in plants. visualization, localization, and analysis of physiological significance in growth and signaling. | extracellular atp (eatp) in animals is well documented and known to play an important role in cellular signaling (e.g. at the nerve synapse). the existence of eatp has been postulated in plants; however, there is no definitive experimental evidence for its presence or an explanation as to how such a polar molecule could exit the plant cell and what physiological role it may play in plant growth and development. the presence of eatp in plants (medicago truncatula) was detected by constructing a n ... | 2006 | 16963521 |
| biosynthesis of ascorbic acid in legume root nodules. | ascorbic acid (vitamin c) is a major antioxidant and redox buffer, but is also involved in other critical processes of plants. recently, the hypothesis has been proposed that legume nodules are unable to synthesize ascorbate and have to import it from the shoot or root, thus providing a means by which the plant regulates nodule senescence. the last step of ascorbate biosynthesis in plants is catalyzed by l-galactono-1,4-lactone dehydrogenase (galldh). the mrnas encoding galldh and three other en ... | 2006 | 16766673 |
| invited lectures : overviews purinergic signalling: past, present and future. | | 2006 | 18404494 |
| isolation and biochemical characterization of two novel metagenome-derived esterases. | the metagenomes of uncultured microbial communities are rich sources for novel biocatalysts. in this study, esterase esta3 was derived from a drinking water metagenome, and esterase estce1 was derived from a soil metagenome. both esterases are approximately 380 amino acids in size and show similarity to beta-lactamases, indicating that they belong to family viii of the lipases/esterases. esta3 had a temperature optimum at 50 degrees c and a ph optimum at ph 9.0. it was remarkably active and very ... | 2006 | 16672512 |
| tracing nonlegume orthologs of legume genes required for nodulation and arbuscular mycorrhizal symbioses. | most land plants can form a root symbiosis with arbuscular mycorrhizal (am) fungi for assimilation of inorganic phosphate from the soil. in contrast, the nitrogen-fixing root nodule symbiosis is almost completely restricted to the legumes. the finding that the two symbioses share common signaling components in legumes suggests that the evolutionarily younger nitrogen-fixing symbiosis has recruited functions from the more ancient am symbiosis. the recent advances in cloning of the genes required ... | 2006 | 16452143 |
| function, structure, and evolution of the rubisco-like proteins and their rubisco homologs. | about 30 years have now passed since it was discovered that microbes synthesize rubisco molecules that differ from the typical plant paradigm. rubiscos of forms i, ii, and iii catalyze co(2) fixation reactions, albeit for potentially different physiological purposes, while the rubisco-like protein (rlp) (form iv rubisco) has evolved, thus far at least, to catalyze reactions that are important for sulfur metabolism. rubisco is the major global co(2) fixation catalyst, and rlp is a somewhat relate ... | 2007 | 18063718 |
| tilling mutants of lotus japonicus reveal that nitrogen assimilation and fixation can occur in the absence of nodule-enhanced sucrose synthase. | in all plant species studied to date, sucrose synthase occurs as multiple isoforms. the specific functions of the different isoforms are for the most part not clear. six isoforms of sucrose synthase have been identified in the model legume lotus japonicus, the same number as in arabidopsis (arabidopsis thaliana) and rice (oryza sativa). the genes encoding these isoforms are differentially expressed in all plant organs examined, although one, ljsus4, is only expressed in flowers. ljsus1 is the mo ... | 2007 | 17468221 |
| recombinant nucleases cel i from celery and sp i from spinach for mutation detection. | the detection of unknown mutations is important in research and medicine. for this purpose, a mismatch-specific endonuclease cel i from celery has been established as a useful tool in high throughput projects. previously, cel i-like activities were described only in a variety of plants and could not be expressed in an active form in bacteria. | 2007 | 17543120 |
| an unusual intrinsically disordered protein from the model legume lotus japonicus stabilizes proteins in vitro. | intrinsic structural disorder is a prevalent feature of proteins with chaperone activity. using a complementary set of techniques, we have structurally characterized ljidp1 (intrinsically disordered protein 1) from the model legume lotus japonicus, and our results provide the first structural characterization of a member of the lea5 protein family (pf03242). contrary to in silico predictions, we show that ljidp1 is intrinsically disordered and probably exists as an ensemble of conformations with ... | 2008 | 18779323 |
| extent of voltage sensor movement during gating of shaker k+ channels. | voltage-driven activation of kv channels results from conformational changes of four voltage sensor domains (vsds) that surround the k(+) selective pore domain. how the vsd helices rearrange during gating is an area of active research. luminescence resonance energy transfer (lret) is a powerful spectroscopic ruler uniquely suitable for addressing the conformational trajectory of these helices. using a geometric analysis of numerous lret measurements, we were able to estimate lret probe positions ... | 2008 | 18614032 |
| structural and energetic analysis of activation by a cyclic nucleotide binding domain. | mlotik1 is a prokaryotic homolog of cyclic-nucleotide-dependent ion channels that contains an intracellular c-terminal cyclic nucleotide binding (cnb) domain. x-ray structures of the cnb domain have been solved in the absence of ligand and bound to camp. both the full-length channel and cnb domain fragment are easily expressed and purified, making mlotik1 a useful model system for dissecting activation by ligand binding. we have used x-ray crystallography to determine three new mlotik1 cnb domai ... | 2008 | 18619611 |
| structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel. | the six-transmembrane helix (6 tm) tetrameric cation channels form the largest ion channel family, some members of which are voltage-gated and others are not. there are no reported channel structures to match the wealth of functional data on the non-voltage-gated members. we determined the structure of the transmembrane regions of the bacterial cyclic nucleotide-regulated channel mlotik1, a non-voltage-gated 6 tm channel. the structure showed how the s1-s4 domain and its associated linker can se ... | 2008 | 18216238 |
| covariation of branch lengths in phylogenies of functionally related genes. | recent studies have shown evidence for the coevolution of functionally-related genes. this coevolution is a result of constraints to maintain functional relationships between interacting proteins. the studies have focused on the correlation in gene tree branch lengths of proteins that are directly interacting with each other. we here hypothesize that the correlation in branch lengths is not limited only to proteins that directly interact, but also to proteins that operate within the same pathway ... | 2009 | 20041191 |
| evidence for horizontally transferred genes involved in the biosynthesis of vitamin b(1), b(5), and b(7) in heterodera glycines. | heterodera glycines is a nematode that is highly adapted to manipulate and parasitize plant hosts. the molecular players involved in these interactions have only recently begun to be identified. here, the sequencing of the second stage juvenile transcriptome, followed by a bioinformatic screen for novel genes, identified seven new genes involved in biosynthesis and salvage of vitamins b₁, b₅, and b₇. with no confirmed reports in the literature, each of these biosynthesis pathways is believed to ... | 2009 | 22736827 |
| tilling in lotus japonicus identified large allelic series for symbiosis genes and revealed a bias in functionally defective ethyl methanesulfonate alleles toward glycine replacements. | we have established tools for forward and reverse genetic analysis of the legume lotus (lotus japonicus). a structured population of m2 progeny of 4,904 ethyl methanesulfonate-mutagenized m1 embryos is available for single nucleotide polymorphism mutation detection, using a tilling (for targeting induced local lesions in genomes) protocol. scanning subsets of this population, we identified a mutation load of one per 502 kb of amplified fragment. moreover, we observed a 1:10 ratio between homozyg ... | 2009 | 19641028 |
| exploiting structural classifications for function prediction: towards a domain grammar for protein function. | the ability to assign function to proteins has become a major bottleneck for comprehensively understanding cellular mechanisms at the molecular level. here we discuss the extent to which structural domain classifications can help in deciphering the complex relationship between the functions of proteins and their sequences and structures. structural classifications are particularly helpful in understanding the mosaic manner in which new proteins and functions emerge through evolution. this is par ... | 2009 | 19398323 |
| the constancy of gene conservation across divergent bacterial orders. | orthologous genes are frequently presumed to perform similar functions. however, outside of model organisms, this is rarely tested. one means of inferring changes in function is if there are changes in the level of gene conservation and selective constraint. here we compare levels of gene conservation across three bacterial groups to test for changes in gene functionality. | 2009 | 19128452 |
| a suite of lotus japonicus starch mutants reveals both conserved and novel features of starch metabolism. | the metabolism of starch is of central importance for many aspects of plant growth and development. information on leaf starch metabolism other than in arabidopsis (arabidopsis thaliana) is scarce. furthermore, its importance in several agronomically important traits exemplified by legumes remains to be investigated. to address this issue, we have provided detailed information on the genes involved in starch metabolism in lotus japonicus and have characterized a comprehensive collection of forwa ... | 2010 | 20699404 |
| cloning-independent expression and analysis of omega-transaminases by use of a cell-free protein synthesis system. | herewith we report the expression and screening of microbial enzymes without involving cloning procedures. computationally predicted putative omega-transaminase (omega-ta) genes were pcr amplified from the bacterial colonies and expressed in a cell-free protein synthesis system for subsequent analysis of their enzymatic activity and substrate specificity. through the cell-free expression analysis of the putative omega-ta genes, a number of enzyme-substrate pairs were identified in a matter of ho ... | 2010 | 20656866 |
| effect of abscisic acid on symbiotic nitrogen fixation activity in the root nodules of lotus japonicus. | the phytohormone abscisic acid (aba) is known to be a negative regulator of legume root nodule formation. by screening lotus japonicus seedlings for survival on an agar medium containing 70 μm aba, we obtained mutants that not only showed increased root nodule number, but also enhanced nitrogen fixation. the mutant was designated enf1 (enhanced nitrogen fixation 1) and was confirmed to be monogenic and incompletely dominant. in long-term growth experiments with m. loti, although some yield param ... | 2010 | 20118670 |
| analysis of two potential long-distance signaling molecules, ljcle-rs1/2 and jasmonic acid, in a hypernodulating mutant too much love. | legume plants tightly control the number and development of root nodules. this is partly regulated by a long-distance signaling known as auto-regulation of nodulation (aon). aon signaling involves at least two potential long-distance signals: root-derived signal and shoot-derived signal. however, their molecular characteristics and the mode of action remain unclear. in our recent study, we isolated a novel lotus japonicus hypernodulating mutant too much love (tml). based on several grafting expe ... | 2010 | 20061808 |
| glycolysis and the tricarboxylic acid cycle are linked by alanine aminotransferase during hypoxia induced by waterlogging of lotus japonicus. | the role of nitrogen metabolism in the survival of prolonged periods of waterlogging was investigated in highly flood-tolerant, nodulated lotus japonicus plants. alanine production revealed to be a critical hypoxic pathway. alanine is the only amino acid whose biosynthesis is not inhibited by nitrogen deficiency resulting from rna interference silencing of nodular leghemoglobin. the metabolic changes that were induced following waterlogging can be best explained by the activation of alanine meta ... | 2010 | 20089769 |
| tertiary alcohol preferred: hydroxylation of trans-3-methyl-l-proline with proline hydroxylases. | the enzymatic synthesis of tertiary alcohols by the stereospecific oxidation of tertiary alkyl centers is a most-straightforward but challenging approach, since these positions are sterically hindered. in contrast to p450-monooxygenases, there is little known about the potential of non-heme iron(ii) oxygenases to catalyze such reactions. we have studied the hydroxylation of trans-3-methyl-l-proline with the α-ketoglutarate (α-kg) dependent oxygenases, cis-3-proline hydroxylase type ii and cis-4- ... | 2011 | 22238542 |
| gating of the mlotik1 potassium channel involves large rearrangements of the cyclic nucleotide-binding domains. | cyclic nucleotide-regulated ion channels are present in bacteria, plants, vertebrates, and humans. in higher organisms, they are closely involved in signaling networks of vision and olfaction. binding of camp or cgmp favors the activation of these ion channels. despite a wealth of structural and studies, there is a lack of structural data describing the gating process in a full-length cyclic nucleotide-regulated channel. we used high-resolution atomic force microscopy (afm) to directly observe t ... | 2011 | 22135457 |
| characterization of highly efficient heavy-ion mutagenesis in arabidopsis thaliana. | heavy-ion mutagenesis is recognised as a powerful technology to generate new mutants, especially in higher plants. heavy-ion beams show high linear energy transfer (let) and thus more effectively induce dna double-strand breaks than other mutagenic techniques. previously, we determined the most effective heavy-ion let (letmax: 30.0 kev μm(-1)) for arabidopsis mutagenesis by analysing the effect of let on mutation induction. however, the molecular structure of mutated dna induced by heavy ions wi ... | 2011 | 22085561 |
| expression screening of fusion partners from an e. coli genome for soluble expression of recombinant proteins in a cell-free protein synthesis system. | while access to soluble recombinant proteins is essential for a number of proteome studies, preparation of purified functional proteins is often limited by the protein solubility. in this study, potent solubility-enhancing fusion partners were screened from the repertoire of endogenous e. coli proteins. based on the presumed correlation between the intracellular abundance and folding efficiency of proteins, pcr-amplified orfs of a series of highly abundant e. coli proteins were fused with aggreg ... | 2011 | 22073212 |
| the evolution of function in strictosidine synthase-like proteins. | the exponential growth of sequence data provides abundant information for the discovery of new enzyme reactions. correctly annotating the functions of highly diverse proteins can be difficult, however, hindering use of this information. global analysis of large superfamilies of related proteins is a powerful strategy for understanding the evolution of reactions by identifying catalytic commonalities and differences in reaction and substrate specificity, even when only a few members have been bio ... | 2011 | 21948213 |
| bacterial community assembly based on functional genes rather than species. | the principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. we previously analyzed the community membership of bacterial communities associated with the green macroalga ulva australis, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. here we extend the prev ... | 2011 | 21825123 |
| peroxiredoxins and nadph-dependent thioredoxin systems in the model legume lotus japonicus. | peroxiredoxins (prxs), thioredoxins (trxs), and nadph-thioredoxin reductases (ntrs) constitute central elements of the thiol-disulfide redox regulatory network of plant cells. this study provides a comprehensive survey of this network in the model legume lotus japonicus. the aims were to identify and characterize these gene families and to assess whether the ntr-trx systems are operative in nodules. quantitative reverse transcription-polymerase chain reaction and immunological and proteomic appr ... | 2011 | 21562331 |
| evolution of abscisic acid synthesis and signaling mechanisms. | the plant hormone abscisic acid (aba) mediates seed dormancy, controls seedling development and triggers tolerance to abiotic stresses, including drought. core aba signaling components consist of a recently identified group of aba receptor proteins of the pyrabactin resistance (pyr)/regulatory component of aba receptor (rcar) family that act as negative regulators of members of the protein phosphatase 2c (pp2c) family. inhibition of pp2c activity enables activation of snf1-related kinase 2 (snrk ... | 2011 | 21549957 |
| proteinortho: detection of (co-)orthologs in large-scale analysis. | orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. the ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. the rapid pace at which new data become available, furthermore, makes it desirable to compute ... | 2011 | 21526987 |
| interaction of diverse voltage sensor homologs with lipid bilayers revealed by self-assembly simulations. | voltage sensors (vs) domains couple the activation of ion channels/enzymes to changes in membrane voltage. we used molecular dynamics simulations to examine interactions with lipids of several vs homologs. vss in intact channels in the activated state are exposed to phospholipids, leading to a characteristic local distortion of the lipid bilayer which decreases its thickness by ∼10 å. this effect is mediated by a conserved hydrophilic stretch in the s4-s5 segment linking the vs and the pore doma ... | 2011 | 21320431 |
| rhizobial and mycorrhizal symbioses in lotus japonicus require lectin nucleotide phosphohydrolase, which acts upstream of calcium signaling. | nodulation in legumes requires the recognition of rhizobially made nod factors. genetic studies have revealed that the perception of nod factors involves lysm domain receptor-like kinases, while biochemical approaches have identified lectin nucleotide phosphohydrolase (lnp) as a nod factor-binding protein. here, we show that antisense inhibition of lnp blocks nodulation in lotus japonicus. this absence of nodulation was due to a defect in nod factor signaling based on the observations that the e ... | 2012 | 23136382 |
| rhizobial and mycorrhizal symbioses in lotus japonicus require lectin nucleotide phosphohydrolase, which acts upstream of calcium signaling. | nodulation in legumes requires the recognition of rhizobially made nod factors. genetic studies have revealed that the perception of nod factors involves lysm domain receptor-like kinases, while biochemical approaches have identified lectin nucleotide phosphohydrolase (lnp) as a nod factor-binding protein. here, we show that antisense inhibition of lnp blocks nodulation in lotus japonicus. this absence of nodulation was due to a defect in nod factor signaling based on the observations that the e ... | 2012 | 23136382 |
| st proteins, a new family of plant tandem repeat proteins with a duf2775 domain mainly found in fabaceae and asteraceae. | many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: i) repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. ii) repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (iii) longer repeats in the order of 100 amino acids th ... | 2012 | 23134664 |
| rhizobia with 16s rrna and nifh similar to mesorhizobium huakuii but novel reca, glnii, noda and nodc genes are symbionts of new zealand carmichaelinae. | new zealand became geographically isolated about 80 million years ago and this separation gave rise to a unique native flora including four genera of legume, carmichaelia, clianthus and montigena in the carmichaelinae clade, tribe galegeae, and sophora, tribe sophoreae, sub-family papilionoideae. ten bacterial strains isolated from nz carmichaelinae growing in natural ecosystems grouped close to the mesorhizobium huakuii type strain in relation to their 16s rrna and nifh gene sequences. however, ... | 2012 | 23118889 |
| the accessory sec protein asp2 modulates glcnac deposition onto the serine-rich repeat glycoprotein gspb. | the accessory sec system is a specialized transport system that exports serine-rich repeat (srr) glycoproteins of gram-positive bacteria. this system contains two homologues of the general secretory (sec) pathway (seca2 and secy2) and several other essential proteins (asp1 to asp5) that share no homology to proteins of known function. in streptococcus gordonii, asp2 is required for the transport of the srr adhesin gspb, but its role in export is unknown. tertiary structure predictions suggest th ... | 2012 | 22885294 |
| genetic diversity, symbiotic evolution, and proposed infection process of bradyrhizobium strains isolated from root nodules of aeschynomene americana l. in thailand. | the diversity of bacteria nodulating aeschynomene americana l. in thailand was determined from phenotypic characteristics and multilocus sequence analysis of the 16s rrna gene and 3 housekeeping genes (dnak, reca, and glnb). the isolated strains were nonphotosynthetic bacteria and were assigned to the genus bradyrhizobium, in which b. yuanmingense was the dominant species. some of the other species, including b. japonicum, b. liaoningense, and b. canariense, were minor species. these isolated st ... | 2012 | 22752179 |
| allosteric mutants show that prfa activation is dispensable for vacuole escape but required for efficient spread and listeria survival in vivo. | the transcriptional regulator prfa controls key virulence determinants of the facultative intracellular pathogen listeria monocytogenes. prfa-dependent gene expression is strongly induced within host cells. while the basis of this activation is unknown, the structural homology of prfa with the camp receptor protein (crp) and the finding of constitutively activated prfa* mutants suggests it may involve ligand-induced allostery. here, we report the identification of a solvent-accessible cavity wit ... | 2012 | 22646689 |
| plant hormonal regulation of nitrogen-fixing nodule organogenesis. | legumes have evolved symbiotic interactions with rhizobial bacteria to efficiently utilize nitrogen. recent progress in symbiosis has revealed several key components of host plants required for nitrogen-fixing nodule organogenesis, in which complicated metabolic and signaling pathways in the host plant are reprogrammed to generate nodules in the cortex upon perception of the rhizobial nod factor. following the recognition of nod factors, plant hormones are likely to be essential throughout nodul ... | 2012 | 22820920 |
| the plant growth promoting substance, lumichrome, mimics starch, and ethylene-associated symbiotic responses in lotus and tomato roots. | symbiosis involves responses that maintain the plant host and symbiotic partner's genetic program; yet these cues are far from elucidated. here we describe the effects of lumichrome, a flavin identified from rhizobium spp., applied to lotus (lotus japonicus) and tomato (solanum lycopersicum). combined transcriptional and metabolite analyses suggest that both species shared common pathways that were altered in response to this application under replete, sterile conditions. these included genes in ... | 2012 | 22701462 |
| ss-sl2, a novel cell wall protein with pan modules, is essential for sclerotial development and cellular integrity of sclerotinia sclerotiorum. | the sclerotium is an important dormant body for many plant fungal pathogens. here, we reported that a protein, named ss-sl2, is involved in sclerotial development of sclerotinia sclerotiorum. ss-sl2 does not show significant homology with any protein of known function. ss-sl2 contains two putative pan modules which were found in other proteins with diverse adhesion functions. ss-sl2 is a secreted protein, during the initial stage of sclerotial development, copious amounts of ss-sl2 are secreted ... | 2012 | 22558105 |
| towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes. | tyrosine-based site-specific recombinases (tbssrs) are dna breaking-rejoining enzymes. in bacterial genomes, they play a major role in the comings and goings of mobile genetic elements (mges), such as temperate phage genomes, integrated conjugative elements (ices) or integron cassettes. tbssrs are also involved in the segregation of plasmids and chromosomes, the resolution of plasmid dimers and of co-integrates resulting from the replicative transposition of transposons. with the aim of improvin ... | 2012 | 22502997 |
| draft genome sequence of mesorhizobium alhagi ccnwxj12-2t, a novel salt-resistant species isolated from the desert of northwestern china. | mesorhizobium alhagi strain ccnwxj12-2(t) is a novel species of soil-dwelling, nitrogen-fixing bacteria that can form symbiotic root nodules with alhagi sparsifolia. moreover, the strain has high resistance to salt and alkali. here we report the draft genome sequence of mesorhizobium alhagi strain ccnwxj12-2(t). a large number of osmotic regulation-related genes have been identified. | 2012 | 22328758 |
| draft genome sequence of plant growth-promoting rhizobium mesorhizobium amorphae, isolated from zinc-lead mine tailings. | here, we describe the draft genome sequence of mesorhizobium amorphae strain ccnwgs0123, isolated from nodules of robinia pseudoacacia growing on zinc-lead mine tailings. a large number of metal(loid) resistance genes, as well as genes reported to promote plant growth, were identified, presenting a great future potential for aiding phytoremediation in metal(loid)-contaminated soil. | 2012 | 22247533 |
| transaminases for the synthesis of enantiopure beta-amino acids. | optically pure β-amino acids constitute interesting building blocks for peptidomimetics and a great variety of pharmaceutically important compounds. their efficient synthesis still poses a major challenge. transaminases (also known as aminotransferases) possess a great potential for the synthesis of optically pure β-amino acids. these pyridoxal 5'-dependent enzymes catalyze the transfer of an amino group from a donor substrate to an acceptor, thus enabling the synthesis of a wide variety of chir ... | 2012 | 22293122 |
| salicylic acids: local, systemic or inter-systemic regulators? | salicylic acid is well known phytohormone, emerging recently as a new paradigm of an array of manifestations of growth regulators. the area unleashed yet encompassed the applied agriculture sector to find the roles to strengthen the crops against plethora of abiotic and biotic stresses. the skipped part of integrated picture, however, was the evolutionary insight of salicylic acid to either allow or discard the microbial invasion depending upon various internal factors of two interactants under ... | 2012 | 22301975 |
| cris-a novel camp-binding protein controlling spermiogenesis and the development of flagellar bending. | the second messengers camp and cgmp activate their target proteins by binding to a conserved cyclic nucleotide-binding domain (cnbd). here, we identify and characterize an entirely novel cnbd-containing protein called cris (cyclic nucleotide receptor involved in sperm function) that is unrelated to any of the other members of this protein family. cris is exclusively expressed in sperm precursor cells. cris-deficient male mice are either infertile due to a lack of sperm resulting from spermatogen ... | 2013 | 24339785 |
| evolution of tryptophan biosynthetic pathway in microbial genomes: a comparative genetic study. | biosynthetic pathway evolution needs to consider the evolution of a group of genes that code for enzymes catalysing the multiple chemical reaction steps leading to the final end product. tryptophan biosynthetic pathway has five chemical reaction steps that are highly conserved in diverse microbial genomes, though the genes of the pathway enzymes show considerable variations in arrangements, operon structure (gene fusion and splitting) and regulation. we use a combined bioinformatic and statistic ... | 2013 | 24592292 |
| evolution of tryptophan biosynthetic pathway in microbial genomes: a comparative genetic study. | biosynthetic pathway evolution needs to consider the evolution of a group of genes that code for enzymes catalysing the multiple chemical reaction steps leading to the final end product. tryptophan biosynthetic pathway has five chemical reaction steps that are highly conserved in diverse microbial genomes, though the genes of the pathway enzymes show considerable variations in arrangements, operon structure (gene fusion and splitting) and regulation. we use a combined bioinformatic and statistic ... | 2013 | 24592292 |
| characterization of inta, a bidirectional site-specific recombinase required for conjugative transfer of the symbiotic plasmid of rhizobium etli cfn42. | site-specific recombination occurs at short specific sequences, mediated by the cognate recombinases. inta is a recombinase from rhizobium etli cfn42 and belongs to the tyrosine recombinase family. it allows cointegration of plasmid p42a and the symbiotic plasmid via site-specific recombination between attachment regions (atta and attd) located in each replicon. cointegration is needed for conjugative transfer of the symbiotic plasmid. to characterize this system, two plasmids harboring the corr ... | 2013 | 23935046 |
| optimization of dairy sludge for growth of rhizobium cells. | in this study dairy sludge was evaluated as an alternative cultivation medium for rhizobium. growth of bacterial strains at different concentrations of dairy sludge was monitored. maximum growth of all strains was observed at 60% dairy sludge concentration. at 60% optical density (od) values are 0.804 for rhizobium trifolii (mtcc905), 0.825 for rhizobium trifolii (mtcc906), and 0.793 for rhizobium meliloti (mtcc100). growth pattern of strains was observed at 60% dairy sludge along with different ... | 2013 | 24089690 |
| the thuefgkab operon of rhizobia and agrobacterium tumefaciens codes for transport of trehalose, maltitol, and isomers of sucrose and their assimilation through the formation of their 3-keto derivatives. | the thu operon (thuefgkab) in sinorhizobium meliloti codes for transport and utilization functions of the disaccharide trehalose. sequenced genomes of members of the rhizobiaceae reveal that some rhizobia and agrobacterium possess the entire thu operon in similar organizations and that mesorhizobium loti maff303099 lacks the transport (thuefgk) genes. in this study, we show that this operon is dedicated to the transport and assimilation of maltitol and isomers of sucrose (leucrose, palatinose, a ... | 2013 | 23772075 |
| genomic and evolutionary aspects of phytoplasmas. | parasitic bacteria that infect eukaryotes, such as animals and plants, often have reduced genomes, having lost important metabolic genes as a result of their host-dependent life cycles. genomic sequencing of these bacteria has revealed their survival strategies and adaptations to parasitism. phytoplasmas (class mollicutes, genus 'candidatus phytoplasma') are intracellular bacterial pathogens of plants and insects and cause devastating yield losses in diverse low- and high-value crops worldwide. ... | 2013 | 23966988 |
| biotransformation of trichoderma spp. and their tolerance to aromatic amines, a major class of pollutants. | trichoderma spp. are cosmopolitan soil fungi that are highly resistant to many toxic compounds. here, we show that trichoderma virens and t. reesei are tolerant to aromatic amines (aa), a major class of pollutants including the highly toxic pesticide residue 3,4-dichloroaniline (3,4-dca). in a previous study, we provided proof-of-concept remediation experiments in which another soil fungus, podospora anserina, detoxifies 3,4-dca through its arylamine n-acetyltransferase (nat), a xenobiotic-metab ... | 2013 | 23728813 |
| minimal genome encoding proteins with constrained amino acid repertoire. | minimal bacterial gene set comprises the genetic elements needed for survival of engineered bacterium on a rich medium. this set is estimated to include 300-350 protein-coding genes. one way of simplifying an organism with such a minimal genome even further is to constrain the amino acid content of its proteins. in this study, comparative genomics approaches and the results of gene knockout experiments were used to extrapolate the minimal gene set of mollicutes, and bioinformatics combined with ... | 2013 | 23873957 |
| small rna pathways and diversity in model legumes: lessons from genomics. | small non-coding rnas (smrna) participate in the regulation of development, cell differentiation, adaptation to environmental constraints and defense responses in plants. they negatively regulate gene expression by degrading specific mrna targets, repressing their translation or modifying chromatin conformation through homologous interaction with target loci. micrornas (mirna) and short-interfering rnas (sirna) are generated from long double stranded rna (dsrna) that are cleaved into 20-24-nucle ... | 2013 | 23847640 |
| structure and catalytic mechanism of yeast 4-amino-4-deoxychorismate lyase. | saccharomyces cerevisiae abz2 is a pyridoxal 5'-phosphate (plp)-dependent lyase that converts 4-amino-4-deoxychorismate (adc) to para-aminobenzoate and pyruvate. to investigate the catalytic mechanism, we determined the 1.9 å resolution crystal structure of abz2 complexed with plp, representing the first eukaryotic adc lyase structure. unlike escherichia coli adc lyase, whose dimerization is critical to the formation of the active site, the overall structure of abz2 displays as a monomer of two ... | 2013 | 23818518 |
| arylamine n-acetyltransferases: a structural perspective. | arylamine n-acetyltransferase (nat) plays an important role in metabolism and detoxification of many compounds including drugs and environmental carcinogens through chemical modification of the amine group with an acetyl group. recent studies have suggested that nats are also involved in cancer cell growth and inhibition of the enzymes may be a potential target for cancer chemotherapy. three-dimensional (3d) structures are available for nats from both prokaryotes and eukaryotes. these structures ... | 2013 | 23517104 |
| carbohydrate kinase (rhak)-dependent abc transport of rhamnose in rhizobium leguminosarum demonstrates genetic separation of kinase and transport activities. | in rhizobium leguminosarum the abc transporter responsible for rhamnose transport is dependent on rhak, a sugar kinase that is necessary for the catabolism of rhamnose. this has led to a working hypothesis that rhak has two biochemical functions: phosphorylation of its substrate and affecting the activity of the rhamnose abc transporter. to address this hypothesis, a linker-scanning random mutagenesis of rhak was carried out. thirty-nine linker-scanning mutations were generated and mapped. allel ... | 2013 | 23708135 |
| commonalities and differences among symbiosis islands of three mesorhizobium loti strains. | to shed light on the breadth of the host range of mesorhizobium loti strain nzp2037, we determined the sequence of the nzp2037 symbiosis island and compared it with those of strain maff303099 and r7a islands. the determined 533 kb sequence of nzp2037 symbiosis island, on which 504 genes were predicted, implied its integration into a phenylalanine-trna gene and subsequent genome rearrangement. comparative analysis revealed that the core regions of the three symbiosis islands consisted of 165 gene ... | 2013 | 23666538 |
| myo-inositol and d-ribose ligand discrimination in an abc periplasmic binding protein. | the periplasmic binding protein (pbp) ibpa mediates the uptake of myo-inositol by the iatp-iata atp-binding cassette transmembrane transporter. we report a crystal structure of caulobacter crescentus ibpa bound to myo-inositol at 1.45 å resolution. this constitutes the first structure of a pbp bound to inositol. ibpa adopts a type i pbp fold consisting of two α-β lobes that surround a central hinge. a pocket positioned between the lobes contains the myo-inositol ligand, which binds with submicro ... | 2013 | 23504019 |
| genome-wide transcriptional responses of two metal-tolerant symbiotic mesorhizobium isolates to zinc and cadmium exposure. | mesorhizobium metallidurans stm 2683t and mesorhizobium sp. strain stm 4661 were isolated from nodules of the metallicolous legume anthyllis vulneraria from distant mining spoils. they tolerate unusually high zinc and cadmium concentrations as compared to other mesorhizobia. this work aims to study the gene expression profiles associated with zinc or cadmium exposure and to identify genes involved in metal tolerance in these two metallicolous mesorhizobium strains of interest for mine phytostabi ... | 2013 | 23631387 |
| comparative genomic analysis of the genus nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability. | the genus nocardiopsis, a widespread group in phylum actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. to shed light on speciation, gene content evolution, and e ... | 2013 | 23626695 |
| atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands. | membrane proteins are embedded in lipid bilayers and facilitate the communication between the external environment and the interior of the cell. this communication is often mediated by the binding of ligands to the membrane protein. understanding the nature of the interaction between a ligand and a membrane protein is required to both understand the mechanism of action of these proteins and for the development of novel pharmacological drugs. the highly hydrophobic nature of membrane proteins and ... | 2013 | 23603221 |
| atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands. | membrane proteins are embedded in lipid bilayers and facilitate the communication between the external environment and the interior of the cell. this communication is often mediated by the binding of ligands to the membrane protein. understanding the nature of the interaction between a ligand and a membrane protein is required to both understand the mechanism of action of these proteins and for the development of novel pharmacological drugs. the highly hydrophobic nature of membrane proteins and ... | 2013 | 23603221 |
| carotenoid cleavage dioxygenase 7 modulates plant growth, reproduction, senescence, and determinate nodulation in the model legume lotus japonicus. | strigolactones (sls) are newly identified hormones that regulate multiple aspects of plant development, infection by parasitic weeds, and mutualistic symbiosis in the roots. in this study, the role of sls was studied for the first time in the model plant lotus japonicus using transgenic lines silenced for carotenoid cleavage dioxygenase 7 (ljccd7), the orthologue of arabidopsis more axillary growth 3. transgenic ljccd7-silenced plants displayed reduced height due to shorter internodes, and more ... | 2013 | 23567864 |
| mechanistic studies of fosb: a divalent-metal-dependent bacillithiol-s-transferase that mediates fosfomycin resistance in staphylococcus aureus. | fosb is a divalent-metal-dependent thiol-s-transferase implicated in fosfomycin resistance among many pathogenic gram-positive bacteria. in the present paper, we describe detailed kinetic studies of fosb from staphylococcus aureus (safosb) that confirm that bacillithiol (bsh) is its preferred physiological thiol substrate. safosb is the first to be characterized among a new class of enzyme (bacillithiol-s-transferases), which, unlike glutathione transferases, are distributed among many low-g+c g ... | 2013 | 23256780 |
| modularity of plant metabolic gene clusters: a trio of linked genes that are collectively required for acylation of triterpenes in oat. | operon-like gene clusters are an emerging phenomenon in the field of plant natural products. the genes encoding some of the best-characterized plant secondary metabolite biosynthetic pathways are scattered across plant genomes. however, an increasing number of gene clusters encoding the synthesis of diverse natural products have recently been reported in plant genomes. these clusters have arisen through the neo-functionalization and relocation of existing genes within the genome, and not by hori ... | 2013 | 23532069 |
| cessation of photosynthesis in lotus japonicus leaves leads to reprogramming of nodule metabolism. | symbiotic nitrogen fixation (snf) involves global changes in gene expression and metabolite accumulation in both rhizobia and the host plant. in order to study the metabolic changes mediated by leaf-root interaction, photosynthesis was limited in leaves by exposure of plants to darkness, and subsequently gene expression was profiled by real-time reverse transcription-pcr (rt-pcr) and metabolite levels by gas chromatography-mass spectrometry in the nodules of the model legume lotus japonicus. pho ... | 2013 | 23404899 |
| voltage sensor ring in a native structure of a membrane-embedded potassium channel. | voltage-gated ion channels support electrochemical activity in cells and are largely responsible for information flow throughout the nervous systems. the voltage sensor domains in these channels sense changes in transmembrane potential and control ion flux across membranes. the x-ray structures of a few voltage-gated ion channels in detergents have been determined and have revealed clear structural variations among their respective voltage sensor domains. more recent studies demonstrated that li ... | 2013 | 23401554 |
| grafting analysis indicates that malfunction of tricot in the root causes a nodulation-deficient phenotype in lotus japonicus. | leguminous plants develop root nodules in symbiosis with soil rhizobia. nodule formation occurs following rhizobial infection of the host root that induces dedifferentiation of some cortical cells and the initiation of a new developmental program to form nodule primordia. in a recent study, we identified a novel gene, tricot (tco), that acts as a positive regulator of nodulation in lotus japonicus. in addition to its role in nodulation, tco mutant plants display pleiotropic defects including abn ... | 2013 | 23333956 |
| structure and function of a bacterial fasciclin i domain protein elucidates function of related cell adhesion proteins such as tgfbip and periostin. | fasciclin i (fas1) domains have important roles in cell adhesion, which are not understood despite many structural and functional studies. examples of fas1 domain proteins include tgfbip (βig-h3) and periostin, which function in angiogenesis and development of cornea and bone, and are also highly expressed in cancer tissues. here we report the structure of a single-domain bacterial fasciclin i protein, fdp, in the free-living photosynthetic bacterium rhodobacter sphaeroides, and show that it con ... | 2013 | 23772377 |
| kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein. | many receptors and ion channels are activated by ligands. one key question concerns the binding mechanism. does the ligand induce conformational changes in the protein via the induced-fit mechanism? or does the protein preexist as an ensemble of conformers and the ligand selects the most complementary one, via the conformational selection mechanism? here, we study ligand binding of a tetrameric cyclic nucleotide-gated channel from mesorhizobium loti and of its monomeric binding domain (cnbd) usi ... | 2013 | 23332059 |
| how does (e)-2-(acetamidomethylene)succinate bind to its hydrolase? from the binding process to the final result. | the binding of (e)-2-(acetamidomethylene)succinate (e-2ams) to e-2ams hydrolase is crucial for biological function of the enzyme and the last step reaction of vitamin b(6) biological degradation. in the present study, several molecular simulation methods, including molecular docking, conventional molecular dynamics (md), steered md (smd), and free energy calculation methods, were properly integrated to investigate the detailed binding process of e-2ams to its hydrolase and to assign the optimal ... | 2013 | 23308285 |
| global transcriptome analysis of mesorhizobium alhagi ccnwxj12-2 under salt stress. | mesorhizobium alhagi ccnwxj12-2 is a α-proteobacterium which could be able to fix nitrogen in the nodules formed with alhagi sparsifolia in northwest of china. desiccation and high salinity are the two major environmental problems faced by m. alhagi ccnwxj12-2. in order to identify genes involved in salt-stress adaption, a global transcriptional analysis of m. alhagi ccnwxj12-2 growing under salt-free and high salt conditions was carried out. the next generation sequencing technology, rna-seq, w ... | 2014 | 25539655 |
| fundamental shift in vitamin b12 eco-physiology of a model alga demonstrated by experimental evolution. | a widespread and complex distribution of vitamin requirements exists over the entire tree of life, with many species having evolved vitamin dependence, both within and between different lineages. vitamin availability has been proposed to drive selection for vitamin dependence, in a process that links an organism's metabolism to the environment, but this has never been demonstrated directly. moreover, understanding the physiological processes and evolutionary dynamics that influence metabolic dem ... | 2014 | 25526368 |
| fundamental shift in vitamin b12 eco-physiology of a model alga demonstrated by experimental evolution. | a widespread and complex distribution of vitamin requirements exists over the entire tree of life, with many species having evolved vitamin dependence, both within and between different lineages. vitamin availability has been proposed to drive selection for vitamin dependence, in a process that links an organism's metabolism to the environment, but this has never been demonstrated directly. moreover, understanding the physiological processes and evolutionary dynamics that influence metabolic dem ... | 2014 | 25526368 |
| genome sequence of the lotus spp. microsymbiont mesorhizobium loti strain nzp2037. | mesorhizobium loti strain nzp2037 was isolated in 1961 in palmerston north, new zealand from a lotus divaricatus root nodule. compared to most other m. loti strains, it has a broad host range and is one of very few m. loti strains able to form effective nodules on the agriculturally important legume lotus pedunculatus. nzp2037 is an aerobic, gram negative, non-spore-forming rod. this report reveals that the genome of m. loti strain nzp2037 does not harbor any plasmids and contains a single scaff ... | 2014 | 25780500 |
| genome sequence of the lotus spp. microsymbiont mesorhizobium loti strain r7a. | mesorhizobium loti strain r7a was isolated in 1993 in lammermoor, otago, new zealand from a lotus corniculatus root nodule and is a reisolate of the inoculant strain icmp3153 (nzp2238) used at the site. r7a is an aerobic, gram-negative, non-spore-forming rod. the symbiotic genes in the strain are carried on a 502-kb integrative and conjugative element known as the symbiosis island or icemlsym(r7a). m. loti is the microsymbiont of the model legume lotus japonicus and strain r7a has been used exte ... | 2014 | 25780499 |
| genome sequence of the lotus corniculatus microsymbiont mesorhizobium loti strain r88b. | mesorhizobium loti strain r88b was isolated in 1993 in the rocklands range in otago, new zealand from a lotus corniculatus root nodule. r88b is an aerobic, gram-negative, non-spore-forming rod. this report reveals the genome of m. loti strain r88b contains a single scaffold of size 7,195,110 bp which encodes 6,950 protein-coding genes and 66 rna-only encoding genes. this genome does not harbor any plasmids but contains the integrative and conjugative element icemlsym(r7a), also known as the r7a ... | 2014 | 25780496 |
| spontaneous symbiotic reprogramming of plant roots triggered by receptor-like kinases. | symbiosis receptor-like kinase (symrk) is indispensable for the development of phosphate-acquiring arbuscular mycorrhiza (am) as well as nitrogen-fixing root nodule symbiosis, but the mechanisms that discriminate between the two distinct symbiotic developmental fates have been enigmatic. in this study, we show that upon ectopic expression, the receptor-like kinase genes nod factor receptor 1 (nfr1), nfr5, and symrk initiate spontaneous nodule organogenesis and nodulation-related gene expression ... | 2014 | 25422918 |
| accumulation of novel glycolipids and ornithine lipids in mesorhizobium loti under phosphate deprivation. | glycolipids are found mainly in photosynthetic organisms (plants, algae, and cyanobacteria), gram-positive bacteria, and a few other bacterial phyla. they serve as membrane lipids and play a role under phosphate deprivation as surrogates for phospholipids. mesorhizobium loti accumulates different di- and triglycosyl diacylglycerols, synthesized by the processive glycosyltransferase pgt-ml, and two so far unknown glycolipids, which were identified in this study by mass spectrometry (ms) and nucle ... | 2014 | 25404698 |
| accumulation of novel glycolipids and ornithine lipids in mesorhizobium loti under phosphate deprivation. | glycolipids are found mainly in photosynthetic organisms (plants, algae, and cyanobacteria), gram-positive bacteria, and a few other bacterial phyla. they serve as membrane lipids and play a role under phosphate deprivation as surrogates for phospholipids. mesorhizobium loti accumulates different di- and triglycosyl diacylglycerols, synthesized by the processive glycosyltransferase pgt-ml, and two so far unknown glycolipids, which were identified in this study by mass spectrometry (ms) and nucle ... | 2014 | 25404698 |
| islander: a database of precisely mapped genomic islands in trna and tmrna genes. | genomic islands are mobile dnas that are major agents of bacterial and archaeal evolution. integration into prokaryotic chromosomes usually occurs site-specifically at trna or tmrna gene (together, tdna) targets, catalyzed by tyrosine integrases. this splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. we applied this principle to search for islands in genomic dna sequenc ... | 2014 | 25378302 |
| islander: a database of precisely mapped genomic islands in trna and tmrna genes. | genomic islands are mobile dnas that are major agents of bacterial and archaeal evolution. integration into prokaryotic chromosomes usually occurs site-specifically at trna or tmrna gene (together, tdna) targets, catalyzed by tyrosine integrases. this splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. we applied this principle to search for islands in genomic dna sequenc ... | 2014 | 25378302 |
| a nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase. | cog5598 comprises a large number of proteins related to mttb, the trimethylamine:corrinoid methyltransferase. mttb has a genetically encoded pyrrolysine residue proposed essential for catalysis. mttb is the only known trimethylamine methyltransferase, yet the great majority of members of cog5598 lack pyrrolysine, leaving the activity of these proteins an open question. here, we describe the function of one of the nonpyrrolysine members of this large protein family. three nonpyrrolysine mttb homo ... | 2014 | 25313086 |
| divergent nod-containing bradyrhizobium sp. doa9 with a megaplasmid and its host range. | bradyrhizobium sp. doa9, a non-photosynthetic bacterial strain originally isolated from the root nodules of the legume aeschynomene americana, is a divergent nod-containing strain. it exhibits a broad host range, being able to colonize and efficiently nodulate the roots of most plants from the dalbergioid, millettioid, and robinioid tribes (7 species of papilionoideae). in all cases, nodulation was determinate. the morphology and size of doa9 bacteroids isolated from the nodules of various speci ... | 2014 | 25283477 |
| conformational selection in protein binding and function. | protein binding and function often involves conformational changes. advanced nuclear magnetic resonance (nmr) experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may "select" protein conformations for binding (or unbinding). in this review, we argue that this conformational selection requires transition times for ligand binding and unbinding that are small compared to the dwell times of proteins in diff ... | 2014 | 25155241 |
| orthology detection combining clustering and synteny for very large datasets. | the elucidation of orthology relationships is an important step both in gene function prediction as well as towards understanding patterns of sequence evolution. orthology assignments are usually derived directly from sequence similarities for large data because more exact approaches exhibit too high computational costs. here we present poff, an extension for the standalone tool proteinortho, which enhances orthology detection by combining clustering, sequence similarity, and synteny. in the cou ... | 2014 | 25137074 |
| the first complete genome sequence of the class fimbriimonadia in the phylum armatimonadetes. | in this study, we present the complete genome of fimbriimonas ginsengisoli gsoil 348t belonging to the class fimbriimonadia of the phylum armatimonadetes, formerly called as candidate phylum op10. the complete genome contains a single circular chromosome of 5.23 mb including a 45.5 kb prophage. of the 4820 open reading frames (orfs), 3,000 (62.2%) genes could be classified into clusters of orthologous groups (cog) families. with the split of rrna genes, strain gsoil 348t had no typical 16s-23s-5 ... | 2014 | 24967843 |
| genome sequencing of two neorhizobium galegae strains reveals a noet gene responsible for the unusual acetylation of the nodulation factors. | the species neorhizobium galegae comprises two symbiovars that induce nodules on galega plants. strains of both symbiovars, orientalis and officinalis, induce nodules on the same plant species, but fix nitrogen only in their own host species. the mechanism behind this strict host specificity is not yet known. in this study, genome sequences of representatives of the two symbiovars were produced, providing new material for studying properties of n. galegae, with a special interest in genomic diff ... | 2014 | 24948393 |
| structure of d-tagatose 3-epimerase-like protein from methanocaldococcus jannaschii. | the crystal structure of a d-tagatose 3-epimerase-like protein (mj1311p) encoded by a hypothetical open reading frame, mj1311, in the genome of the hyperthermophilic archaeon methanocaldococcus jannaschii was determined at a resolution of 2.64 å. the asymmetric unit contained two homologous subunits, and the dimer was generated by twofold symmetry. the overall fold of the subunit proved to be similar to those of the d-tagatose 3-epimerase from pseudomonas cichorii and the d-psicose 3-epimerases ... | 2014 | 25005083 |
| structural basis for catalysis in a cdp-alcohol phosphotransferase. | the cdp-alcohol phosphotransferase (cdp-ap) family of integral membrane enzymes catalyses the transfer of a substituted phosphate group from a cdp-linked donor to an alcohol acceptor. this is an essential reaction for phospholipid biosynthesis across all kingdoms of life, and it is catalysed solely by cdp-aps. here we report the 2.0 å resolution crystal structure of a representative cdp-ap from archaeoglobus fulgidus. the enzyme (af2299) is a homodimer, with each protomer consisting of six trans ... | 2014 | 24923293 |
| land-use influences the distribution and activity of high affinity co-oxidizing bacteria associated to type i-coxl genotype in soil. | soil carboxydovore bacteria are the biological sink of atmospheric carbon monoxide (co). the initial oxidation of co is catalyzed by a co-dehydrogenase (codh), and the gene coxl encodes the large subunit of the enzyme. only a few carboxydovore isolates were shown to oxidize atmospheric co and little is known about the potential impact of global change on the ecophysiology of this functional group. the main objective of this study was to assess the impact of land-use and soil properties on coxl g ... | 2014 | 24971077 |
| common symbiosis genes cerberus and nsp1 provide additional insight into the establishment of arbuscular mycorrhizal and root nodule symbioses in lotus japonicus. | arbuscular mycorrhizal symbiosis (ams) and root nodule symbiosis (rns) share several common symbiotic components, and many of the common symbiosis mutants block the entry of symbionts into the roots. we recently reported that cerberus (an e3 ubiquitin ligase) and nsp1 (a gras family transcription factor), required for rns, also modulate ams development in lotus japonicus. the novel common symbiosis mutants, cerberus and nsp1, have low colonization of arbuscular mycorrhiza (am) fungi, caused by a ... | 2014 | 24705023 |