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toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress. 200010633087
roles of dna adenine methylation in regulating bacterial gene expression and virulence. 200111705888
type ii secretion and pathogenesis. 200111349009
ecological fitness, genomic islands and bacterial pathogenicity. a darwinian view of the evolution of microbes.the compositions of bacterial genomes can be changed rapidly and dramatically through a variety of processes including horizontal gene transfer. this form of change is key to bacterial evolution, as it leads to 'evolution in quantum leaps'. horizontal gene transfer entails the incorporation of genetic elements transferred from another organism-perhaps in an earlier generation-directly into the genome, where they form 'genomic islands', i.e. blocks of dna with signatures of mobile genetic element ...200111375927
virulence functions of autotransporter proteins. 200111179284
a hitchhiker's guide to cell biology: exploitation of host-cell functions by intracellular pathogens.a report on the 'pathogen-host cell interactions' minisymposium at the 41st annual meeting of the american society for cell biology, washington dc, usa, 8-12 december 2001.200211897021
conjugative plasmid transfer in gram-positive bacteria.conjugative transfer of bacterial plasmids is the most efficient way of horizontal gene spread, and it is therefore considered one of the major reasons for the increase in the number of bacteria exhibiting multiple-antibiotic resistance. thus, conjugation and spread of antibiotic resistance represents a severe problem in antibiotic treatment, especially of immunosuppressed patients and in intensive care units. while conjugation in gram-negative bacteria has been studied in great detail over the ...200312794193
microorganisms and cancer: quest for a therapy. 200312700245
type v protein secretion pathway: the autotransporter story.gram-negative bacteria possess an outer membrane layer which constrains uptake and secretion of solutes and polypeptides. to overcome this barrier, bacteria have developed several systems for protein secretion. the type v secretion pathway encompasses the autotransporter proteins, the two-partner secretion system, and the recently described type vc or at-2 family of proteins. since its discovery in the late 1980s, this family of secreted proteins has expanded continuously, due largely to the adv ...200415590781
global analysis of predicted proteomes: functional adaptation of physical properties.the physical characteristics of proteins are fundamentally important in organismal function. we used the complete predicted proteomes of >100 organisms spanning the three domains of life to investigate the comparative biology and evolution of proteomes. theoretical 2d gels were constructed with axes of protein mass and charge (pi) and converted to density estimates comparable across all types and sizes of proteome. we asked whether we could detect general patterns of proteome conservation and va ...200415150418
the ins and outs of dna transfer in bacteria.transformation and conjugation permit the passage of dna through the bacterial membranes and represent dominant modes for the transfer of genetic information between bacterial cells or between bacterial and eukaryotic cells. as such, they are responsible for the spread of fitness-enhancing traits, including antibiotic resistance. both processes usually involve the recognition of double-stranded dna, followed by the transfer of single strands. elaborate molecular machines are responsible for nego ...200516322448
different catalytic mechanisms in mammalian selenocysteine- and cysteine-containing methionine-r-sulfoxide reductases.selenocysteine (sec) is found in active sites of several oxidoreductases in which this residue is essential for catalytic activity. however, many selenoproteins have fully functional orthologs, wherein cysteine (cys) occupies the position of sec. the reason why some enzymes evolve into selenoproteins if the cys versions may be sufficient is not understood. among three mammalian methionine-r-sulfoxide reductases (msrbs), msrb1 is a sec-containing protein, whereas msrb2 and msrb3 contain cys in th ...200516262444
comparative and evolutionary analysis of the bacterial homologous recombination systems.homologous recombination is a housekeeping process involved in the maintenance of chromosome integrity and generation of genetic variability. although detailed biochemical studies have described the mechanism of action of its components in model organisms, there is no recent extensive assessment of this knowledge, using comparative genomics and taking advantage of available experimental data on recombination. using comparative genomics, we assessed the diversity of recombination processes among ...200516132081
mechanisms of protein export across the bacterial outer membrane. 200515968039
weighted genome trees: refinements and applications.there are many ways to group completed genome sequences in hierarchical patterns (trees) reflecting relationships between their genes. such groupings help us organize biological information and bear crucially on underlying processes of genome and organismal evolution. genome trees make use of all comparable genes but can variously weight the contributions of these genes according to similarity, congruent patterns of similarity, or prevalence among genomes. here we explore such possible weighting ...200515687194
secretion by numbers: protein traffic in prokaryotes.almost all aspects of protein traffic in bacteria were covered at the asm-fems meeting on the topic in iraklio, crete in may 2006. the studies presented ranged from mechanistic analysis of specific events leading proteins to their final destinations to the physiological roles of the targeted proteins. among the highlights from the meeting that are reviewed here are the molecular dynamics of seca protein, membrane protein insertion, type iii secretion needles and chaperones, type iv secretion, th ...200617020575
bacterial response to siderophore and quorum-sensing chemical signals in the seawater microbial community.oceans are iron-deficient and nutrient-poor environments. these conditions impart limitations on our understanding of and our ability to identify microorganisms from the marine environment. however, less of knowledge on the influence of siderophores and n-acyl homoserinelactone as interspecies communication signals on the bacterial diversity of seawater has been understood.200111716787
ability of the microscan rapid gram-negative id type 3 panel to identify nonenteric glucose-fermenting and nonfermenting gram-negative bacilli.the microscan rapid neg id3 panel is designed for the identification of enterobacteriaceae and nonenteric glucose-fermenting and nonfermenting gram-negative bacilli. we evaluated this panel for its ability to identify gram-negative non-enterobacteriaceae bacteria. a total of 134 strains, representing 26 genera and 42 species, were taken from storage at -70(o)c, passaged three times before testing, and inoculated into the panels according to the manufacturer's directions before being inserted int ...200212354875
comparative analysis of superintegrons: engineering extensive genetic diversity in the vibrionaceae.integrons are natural tools for bacterial evolution and innovation. their involvement in the capture and dissemination of antibiotic-resistance genes among gram-negative bacteria is well documented. recently, massive ancestral versions, the superintegrons (sis), were discovered in the genomes of diverse proteobacterial species. si gene cassettes with an identifiable activity encode proteins related to simple adaptive functions, including resistance, virulence, and metabolic activities, and their ...200312618374
bacterial contamination of pediatric whole blood transfusions in a kenyan hospital.hospitalized children in sub-saharan africa frequently receive whole blood transfusions for severe anemia. the risk from bacterial contamination of blood for transfusion in sub-saharan africa is not known. this study assessed the frequency of bacterial contamination of pediatric whole blood transfusions at a referral hospital in kenya.200919682331
mob psychology. 200211807045
prokaryotic development: emerging insights. 200312562781
decoding microbial chatter: cell-cell communication in bacteria. 200516077095
stimulus perception in bacterial signal-transducing histidine kinases.two-component signal-transducing systems are ubiquitously distributed communication interfaces in bacteria. they consist of a histidine kinase that senses a specific environmental stimulus and a cognate response regulator that mediates the cellular response, mostly through differential expression of target genes. histidine kinases are typically transmembrane proteins harboring at least two domains: an input (or sensor) domain and a cytoplasmic transmitter (or kinase) domain. they can be identifi ...200617158704
dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain.recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under lexa regulation in several proteobacteria species. in this work, we have traced down instances of this multiple gene cassette across the bacteria domain. phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, ...200616407325
biofilms 2007: broadened horizons and new emphases. 200717766421
comparative genomic reconstruction of transcriptional regulatory networks in bacteria. 200717636889
cell-cell communication in bacteria: united we stand. 200818456806
bacterial responses to photo-oxidative stress.singlet oxygen is one of several reactive oxygen species that can destroy biomolecules, microorganisms and other cells. traditionally, the response to singlet oxygen has been termed photo-oxidative stress, as light-dependent processes in photosynthetic cells are major biological sources of singlet oxygen. recent work identifying a core set of singlet oxygen stress response genes across various bacterial species highlights the importance of this response for survival by both photosynthetic and no ...200919881522
quorum sensing and social networking in the microbial world.for many years, bacterial cells were considered primarily as selfish individuals, but, in recent years, it has become evident that, far from operating in isolation, they coordinate collective behaviour in response to environmental challenges using sophisticated intercellular communication networks. cell-to-cell communication between bacteria is mediated by small diffusible signal molecules that trigger changes in gene expression in response to fluctuations in population density. this process, ge ...200919674996
optimal tuning of bacterial sensing potential.through production and sensing of small signal molecules, quorum sensing (qs) enables bacteria to detect changes in their density and regulate their functions accordingly. qs systems are tremendously diverse in terms of their specific sensory components, the biochemical and transport properties of signaling molecules, their target functions and the context in which qs-mediated functions are activated. cutting across this diversity, however, the central architecture of qs systems is universal; it ...200919584835
protein secretion systems in bacterial-host associations, and their description in the gene ontology.protein secretion plays a central role in modulating the interactions of bacteria with their environments. this is particularly the case when symbiotic bacteria (whether pathogenic, commensal or mutualistic) are interacting with larger host organisms. in the case of gram-negative bacteria, secretion requires translocation across the outer as well as the inner membrane, and a diversity of molecular machines have been elaborated for this purpose. a number of secreted proteins are destined to enter ...200919278550
biosynthesis and function of polyacetylenes and allied natural products.polyacetylenic natural products are a substantial class of often unstable compounds containing a unique carbon-carbon triple bond functionality, that are intriguing for their wide variety of biochemical and ecological functions, economic potential, and surprising mode of biosynthesis. isotopic tracer experiments between 1960 and 1990 demonstrated that the majority of these compounds are derived from fatty acid and polyketide precursors. during the past decade, research into the metabolism of pol ...200818387369
a subset of the diverse cog0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life.cog0523 proteins are, like the nickel chaperones of the ureg family, part of the g3e family of gtpases linking them to metallocenter biosynthesis. even though the first cog0523-encoding gene, cobw, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family.200919822009
analysis of stable low-molecular-weight rna profiles of members of the family rhizobiaceae.staircase electrophoresis in polyacrylamide gels was used to analyze the stable low-molecular-weight (lmw) rna profiles of 24 type strains belonging to the family rhizobiaceae. this new electrophoretic technique results in good separation of the molecules forming the lmw rna profiles. differences in the number and distribution of the rna bands in these profiles allowed us to identify differences among the 24 strains assayed. species assignments based on lmw rnas proved to be consistent with the ...19989575134
the mechanism of synthesis of a mixed-linkage (1-->3), (1-->4)beta-d-glucan in maize. evidence for multiple sites of glucosyl transfer in the synthase complexwe examined the mechanism of synthesis in vitro of (1-->3), (1-->4)beta-d-glucan (beta-glucan), a growth-specific cell wall polysaccharide found in grasses and cereals. beta-glucan is composed primarily of cellotriosyl and cellotetraosyl units linked by single (1-->3)beta-linkages. the ratio of cellotriosyl and cellotetraosyl units in the native polymer is strictly controlled at between 2 and 3 in all grasses, whereas the ratios of these units in beta-glucan formed in vitro vary from 1.5 with 5 ...199910444094
unusual spectral properties of bacteriophytochrome agp2 result from a deprotonation of the chromophore in the red-absorbing form pr.phytochromes are widely distributed photoreceptors with a bilin chromophore that undergo a typical reversible photoconversion between the two spectrally different forms, pr and pfr. the phytochrome agp2 from agrobacterium tumefaciens belongs to the group of bathy phytochromes that have a pfr ground state as a result of the pr to pfr dark conversion. agp2 has untypical spectral properties in the pr form reminiscent of a deprotonated chromophore as confirmed by resonance raman spectroscopy. uv/vis ...201324036118
brucella bior regulator defines a complex regulatory mechanism for bacterial biotin metabolism.the enzyme cofactor biotin (vitamin h or b7) is an energetically expensive molecule whose de novo biosynthesis requires 20 atp equivalents. it seems quite likely that diverse mechanisms have evolved to tightly regulate its biosynthesis. unlike the model regulator bira, a bifunctional biotin protein ligase with the capability of repressing the biotin biosynthetic pathway, bior has been recently reported by us as an alternative machinery and a new type of gntr family transcriptional factor that ca ...201323729648
riboregulation in plant-associated α-proteobacteria.the symbiotic α-rhizobia sinorhizobium meliloti, bradyrhizobium japonicum, rhizobium etli and the related plant pathogen agrobacterium tumefaciens are important model organisms for studying plant-microbe interactions. these metabolically versatile soil bacteria are characterized by complex lifestyles and large genomes. here we summarize the recent knowledge on their small non-coding rnas (srnas) including conservation, function, and interaction of the srnas with the rna chaperone hfq. in each of ...201425003187
paracoccus denitrificans possesses two bior homologs having a role in regulation of biotin metabolism.recently, we determined that bior, the gntr family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent brucella melitensis and the plant pathogen agrobacterium tumefaciens. however, the scenario is unusual in paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. not only does it encode two bior homologs pden_1431 and pd ...201526037461
the class iii cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways.photolyases are proteins with an fad chromophore that repair uv-induced pyrimidine dimers on the dna in a light-dependent manner. the cyclobutane pyrimidine dimer class iii photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. here we present the crystal structure of a class iii photolyase termed photolyase-related protein a (phra) of agrobacterium tumefaciens at 1.67-å resolution. phra contains 5,10-methenyltetrahydrofolate (m ...201525784552
origin of an alternative genetic code in the extremely small and gc-rich genome of a bacterial symbiont.the genetic code relates nucleotide sequence to amino acid sequence and is shared across all organisms, with the rare exceptions of lineages in which one or a few codons have acquired novel assignments. recoding of uga from stop to tryptophan has evolved independently in certain reduced bacterial genomes, including those of the mycoplasmas and some mitochondria. small genomes typically exhibit low guanine plus cytosine (gc) content, and this bias in base composition has been proposed to drive ug ...200919609354
long chain n-acyl homoserine lactone production by enterobacter sp. isolated from human tongue surfaces.we report the isolation of n-acyl homoserine lactone-producing enterobacter sp. isolate t1-1 from the posterior dorsal surfaces of the tongue of a healthy individual. spent supernatants extract from enterobacter sp. isolate t1-1 activated the biosensor agrobacterium tumefaciens ntl4(pzlr4), suggesting production of long chain ahls by these isolates. high resolution mass spectrometry analysis of these extracts confirmed that enterobacter sp. isolate t1-1 produced a long chain n-acyl homoserine la ...201223202161
applying horizontal gene transfer phenomena to enhance non-viral gene therapy.horizontal gene transfer (hgt) is widespread amongst prokaryotes, but eukaryotes tend to be far less promiscuous with their genetic information. however, several examples of hgt from pathogens into eukaryotic cells have been discovered and mimicked to improve non-viral gene delivery techniques. for example, several viral proteins and dna sequences have been used to significantly increase cytoplasmic and nuclear gene delivery. plant genetic engineering is routinely performed with the pathogenic b ...201323994344
catalytic bioscavengers against toxic esters, an alternative approach for prophylaxis and treatments of poisonings.bioscavengers are biopharmaceuticals that specifically react with toxicants. thus, enzymes reacting with poisonous esters can be used as bioscavengers for neutralization of toxic molecules before they reach physiological targets. parenteral administration of bioscavengers is, therefore, intended for prophylaxis or pre-treatments, emergency and post-exposure treatments of intoxications. these enzymes can also be used for application on skin, mucosa and wounds as active components of topical skin ...200922649587
wind river conference on prokaryotic biology--2002. 200312486034
n6-methyladenine: the other methylated base of dna.contrary to mammalian dna, which is thought to contain only 5-methylcytosine (m5c), bacterial dna contains two additional methylated bases, namely n6-methyladenine (m6a), and n4-methylcytosine (m4c). however, if the main function of m5c and m4c in bacteria is protection against restriction enzymes, the roles of m6a are multiple and include, for example, the regulation of virulence and the control of many bacterial dna functions such as the replication, repair, expression and transposition of dna ...200616479578
"alternative" endocytic mechanisms exploited by pathogens: new avenues for therapeutic delivery?some pathogens utilize unique routes to enter cells that may evade the intracellular barriers encountered by the typical clathrin-mediated endocytic pathway. retrograde transport and caveolar uptake are among the better characterized pathways, as alternatives to clathrin-mediated endocytosis, that are known to facilitate entry of pathogens and potential delivery agents. recent characterization of the trafficking mechanisms of prion proteins and certain bacteria may present new paradigms for stra ...200717707545
factors affecting the concordance between orthologous gene trees and species tree in bacteria.as originally defined, orthologous genes implied a reflection of the history of the species. in recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. these studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual phylogenetic reconstructions. here, using a method that allows the detection and exclusion of false positives during identification of orthologous gene ...200818973688
shedding (blue) light on algal gene expression. 200818172200
deciphering evolutionary mechanisms between mutualistic and pathogenic symbioses.the continuum between mutualistic and pathogenic symbioses has been an underlying theme for understanding the evolution of infection and disease in a number of eukaryotic-microbe associations. the ability to monitor and then predict the spread of infectious diseases may depend upon our knowledge and capabilities of anticipating the behavior of virulent pathogens by studying related, benign symbioses. for instance, the ability of a symbiotic species to infect, colonize, and proliferate efficientl ...200819655044
the photobiology of microbial pathogenesis. 200919956669
lights, rhythms, infection: the role of light and the circadian clock in determining the outcome of plant-pathogen interactions.the importance of light with respect to the outcome of plant-pathogen interactions is becoming increasingly evident: light affects both the host response and the virulence of some pathogens. the response of plants to environmental signals and stresses is modulated by the circadian clock, and it is apparent that this may include immune responses. photo and temporal regulation of immune responses may allow plants to anticipate and react more effectively to particular pathogen infections. these asp ...200919789275
hfq influences multiple transport systems and virulence in the plant pathogen agrobacterium tumefaciens.the hfq protein mediates gene regulation by small rnas (srnas) in about 50% of all bacteria. depending on the species, phenotypic defects of an hfq mutant range from mild to severe. here, we document that the purified hfq protein of the plant pathogen and natural genetic engineer agrobacterium tumefaciens binds to the previously described srna abcr1 and its target mrna atu2422, which codes for the substrate binding protein of an abc transporter taking up proline and γ-aminobutyric acid (gaba). s ...201222821981
acid-induced type vi secretion system is regulated by exor-chvg/chvi signaling cascade in agrobacterium tumefaciens.the type vi secretion system (t6ss) is a widespread, versatile protein secretion system in pathogenic proteobacteria. several t6sss are tightly regulated by various regulatory systems at multiple levels. however, the signals and/or regulatory mechanisms of many t6sss remain unexplored. here, we report on an acid-induced regulatory mechanism activating t6ss in agrobacterium tumefaciens, a plant pathogenic bacterium causing crown gall disease in a wide range of plants. we monitored the secretion o ...201223028331
agrobacteria lacking ornithine lipids induce more rapid tumour formation.ornithine lipids (ols) are phosphorus-free membrane lipids that are widespread among gram-negative bacteria. their basic structure consists of a 3-hydroxy fatty acyl group attached in amide linkage to the α-amino group of ornithine and a second fatty acyl group ester-linked to the 3-hydroxy position of the first fatty acid. it has been shown that ols can be hydroxylated within the amide-linked fatty acyl moiety, the secondary fatty acyl moiety or within the ornithine moiety. these modifications ...201222958119
identification of two small regulatory rnas linked to virulence in brucella abortus 2308.hfq is an rna-binding protein that functions in post-transcriptional gene regulation by mediating interactions between mrnas and small regulatory rnas (srnas). two proteins encoded by bab1_1794 and bab2_0612 are highly over-produced in a brucella abortus hfq mutant compared with the parental strain, and recently, expression of orthologues of these proteins in agrobacterium tumefaciens was shown to be regulated by two srnas, called abcr1 and abcr2. orthologous srnas (likewise designated abcr1 and ...201222690807
polar growth in the alphaproteobacterial order rhizobiales.elongation of many rod-shaped bacteria occurs by peptidoglycan synthesis at discrete foci along the sidewall of the cells. however, within the rhizobiales, there are many budding bacteria, in which new cell growth is constrained to a specific region. the phylogeny of the rhizobiales indicates that this mode of zonal growth may be ancestral. we demonstrate that the rod-shaped bacterium agrobacterium tumefaciens grows unidirectionally from the new pole generated after cell division and has an atyp ...201222307633
independent activity of the homologous small regulatory rnas abcr1 and abcr2 in the legume symbiont sinorhizobium meliloti.the legume symbiont sinorhizobium meliloti expresses a plethora of small noncoding rnas (srnas) whose function is mostly unknown. here, we have functionally characterized two tandemly encoded s. meliloti rm1021 srnas that are similar in sequence and structure. homologous srnas (designated abcr1 and abcr2) have been shown to regulate several abc transporters in the related α-proteobacteria agrobacterium tumefaciens and brucella abortus. in rm1021, abcr1 and abcr2 exhibit divergent unlinked regula ...201323869210
coordination of division and development influences complex multicellular behavior in agrobacterium tumefaciens.the α-proteobacterium agrobacterium tumefaciens has proteins homologous to known regulators that govern cell division and development in caulobacter crescentus, many of which are also conserved among diverse α-proteobacteria. in light of recent work demonstrating similarity between the division cycle of c. crescentus and that of a. tumefaciens, the functional conservation for this presumptive control pathway was examined. in c. crescentus the ctra response regulator serves as the master regulato ...201323437210
profound impact of hfq on nutrient acquisition, metabolism and motility in the plant pathogen agrobacterium tumefaciens.as matchmaker between mrna and srna interactions, the rna chaperone hfq plays a key role in riboregulation of many bacteria. often, the global influence of hfq on the transcriptome is reflected by substantially altered proteomes and pleiotropic phenotypes in hfq mutants. using quantitative proteomics and co-immunoprecipitation combined with rna-sequencing (rip-seq) of hfq-bound rnas, we demonstrate the pervasive role of hfq in nutrient acquisition, metabolism and motility of the plant pathogen a ...201425330313
agrobacterium tumefaciens exor controls acid response genes and impacts exopolysaccharide synthesis, horizontal gene transfer, and virulence gene expression.agrobacterium tumefaciens is a facultative plant pathogen and the causative agent of crown gall disease. the initial stage of infection involves attachment to plant tissues, and subsequently, biofilms may form at these sites. this study focuses on the periplasmic exor regulator, which was identified based on the severe biofilm deficiency of a. tumefaciens exor mutants. genome-wide expression analysis was performed to elucidate the complete exor regulon. overproduction of the exopolysaccharide su ...201424982308
identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems.the cell cycle of caulobacter crescentus is controlled by a complex signalling network that co-ordinates events. genome sequencing has revealed many c. crescentus cell cycle genes are conserved in other alphaproteobacteria, but it is not clear to what extent their function is conserved. as many cell cycle regulatory genes are essential in c. crescentus, the essential genes of two alphaproteobacteria, agrobacterium tumefaciens (rhizobiales) and brevundimonas subvibrioides (caulobacterales), were ...201424975755
peptidoglycan synthesis machinery in agrobacterium tumefaciens during unipolar growth and cell division.the synthesis of peptidoglycan (pg) in bacteria is a crucial process controlling cell shape and vitality. in contrast to bacteria such as escherichia coli that grow by dispersed lateral insertion of pg, little is known of the processes that direct polar pg synthesis in other bacteria such as the rhizobiales. to better understand polar growth in the rhizobiales agrobacterium tumefaciens, we first surveyed its genome to identify homologs of (~70) well-known pg synthesis components. since most of t ...201424865559
two separate modules of the conserved regulatory rna abcr1 address multiple target mrnas in and outside of the translation initiation region.the small rna abcr1 regulates the expression of abc transporters in the plant pathogen agrobacterium tumefaciens, the plant symbiont sinorhizobium meliloti, and the human pathogen brucella abortus. a combination of proteomic and bioinformatic approaches suggested dozens of abcr1 targets in a. tumefaciens. several of these newly discovered targets are involved in the uptake of amino acids, their derivatives, and sugars. among the latter is the periplasmic sugar-binding protein chve, a component o ...201424921646
mechanisms and regulation of surface interactions and biofilm formation in agrobacterium.for many pathogenic bacteria surface attachment is a required first step during host interactions. attachment can proceed to invasion of host tissue or cells or to establishment of a multicellular bacterial community known as a biofilm. the transition from a unicellular, often motile, state to a sessile, multicellular, biofilm-associated state is one of the most important developmental decisions for bacteria. agrobacterium tumefaciens genetically transforms plant cells by transfer and integratio ...201424834068
a signaling pathway involving the diguanylate cyclase celr and the response regulator divk controls cellulose synthesis in agrobacterium tumefaciens.the production of cellulose fibrils is involved in the attachment of agrobacterium tumefaciens to its plant host. consistent with previous studies, we reported recently that a putative diguanylate cyclase, celr, is required for synthesis of this polymer in a. tumefaciens. in this study, the effects of celr and other components of the regulatory pathway of cellulose production were explored. mutational analysis of celr demonstrated that the cyclase requires the catalytic ggeef motif, as well as t ...201424443526
a pterin-dependent signaling pathway regulates a dual-function diguanylate cyclase-phosphodiesterase controlling surface attachment in agrobacterium tumefaciens.the motile-to-sessile transition is an important lifestyle switch in diverse bacteria and is often regulated by the intracellular second messenger cyclic diguanylate monophosphate (c-di-gmp). in general, high c-di-gmp concentrations promote attachment to surfaces, whereas cells with low levels of signal remain motile. in the plant pathogen agrobacterium tumefaciens, c-di-gmp controls attachment and biofilm formation via regulation of a unipolar polysaccharide (upp) adhesin. the levels of c-di-gm ...201526126849
cultivation of denitrifying bacteria: optimization of isolation conditions and diversity study.an evolutionary algorithm was applied to study the complex interactions between medium parameters and their effects on the isolation of denitrifying bacteria, both in number and in diversity. growth media with a ph of 7 and a nitrogen concentration of 3 mm, supplemented with 1 ml of vitamin solution but not with sodium chloride or riboflavin, were the most successful for the isolation of denitrifiers from activated sludge. the use of ethanol or succinate as a carbon source and a molar c/n ratio ...200616597968
in vitro activities of bal9141, a novel broad-spectrum pyrrolidinone cephalosporin, against gram-negative nonfermenters.the activities of bal9141 (formerly ro 63-9141), a novel pyrrolidinone-3-ylidenemethyl cephalosporin, against 244 strains of gram-negative nonfermenters were evaluated. the overall mic at which 50% of isolates are inhibited (mic50) and the overall mic90 were 2 and 64 microg/ml, respectively, which are similar to those of imipenem, lower than those of the other cephalosporins tested, amoxicillin, and the ticarcillin-clavulanic acid combination, and much higher than those of ciprofloxacin. bal9141 ...200211850276
biochemical and susceptibility tests useful for identification of nonfermenting gram-negative rods.six hundred nineteen strains of nonfermenting gram-negative rods were tested for alkaline phosphatase, benzyl-arginine arylamidase, pyrrolidonyl arylamidase, ethylene glycol acidification, and susceptibility to desferrioxamine and colistin. the results were highly discriminant. therefore, the proposed tests may be helpful for the identification of this group of organisms.200211880447
performances of vitek 2 colorimetric cards for identification of gram-positive and gram-negative bacteria.the purpose of this study was to evaluate the new vitek 2 identification cards that use colorimetric reading to identify gram-positive and gram-negative bacteria (gp and gn cards, respectively) in comparison to fluorimetric cards (id-gpc and id-gnb, respectively). a total of 580 clinical isolates and stock collection strains belonging to 116 taxa were included in the study. of the 249 gram-positive strains tested with both the id-gpc and gp cards, 218 (87.5%) and 235 (94.4%) strains were correct ...200516145083
quantitative determination of free-dna uptake in river bacteria at the single-cell level by in situ rolling-circle amplification.detection of plasmid dna uptake in river bacteria at the single-cell level was carried out by rolling-circle amplification (rca). uptake of a plasmid containing the green fluorescent protein gene (gfp) by indigenous bacteria from two rivers in osaka, japan, was monitored for 506 h using this in situ gene amplification technique with optimized cell permeabilization conditions. plasmid uptake determined by in situ rca was compared to direct counts of cells expressing gfp under fluorescence microsc ...200616957252
characterization of two-step deglycosylation via oxidation by glycoside oxidoreductase and defining their subfamily.herein, we report a two-step deglycosylation mediated by the oxidation of glycoside which is different from traditional glycoside hydrolase (gh) mechanism. previously, we reported a novel flavin adenine dinucleotide (fad)-dependent glycoside oxidoreductase (fad-go) having deglycosylation activity. various features of the reaction of fad-go such as including mechanism and catalytic residue and substrate specificity were studied. in addition, classification of novel fad-go subfamily was attempted. ...201526057169
metacyc: a multiorganism database of metabolic pathways and enzymes.metacyc is a database of metabolic pathways and enzymes located at http://metacyc.org/. its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. most of the pathways in metacyc occur in microorganisms and plants, although animal pathways are also represented. metacyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and revie ...200516381923
metacyc: a multiorganism database of metabolic pathways and enzymes.metacyc is a database of metabolic pathways and enzymes located at http://metacyc.org/. its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. most of the pathways in metacyc occur in microorganisms and plants, although animal pathways are also represented. metacyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and revie ...200516381923
novel approaches to bacterial infection therapy by interfering with bacteria-to-bacteria signaling.the growing challenge of antimicrobial resistance and the paucity of novel antibiotics underscore the importance of developing novel therapeutics. bacterial cell-to-cell signaling constitutes a novel drug target. quorum sensing (qs) is a cell-to-cell signaling mechanism that refers to the ability of bacteria to respond to chemical hormone-like molecules called autoinducers. qs is responsible for controlling a plethora of virulence genes in several bacterial pathogens. antagonists to autoinducers ...200717402841
expanding the paradigms of plant pathogen life history and evolution of parasitic fitness beyond agricultural boundaries. 200920041212
recombinase polymerase amplification (rpa) of camv-35s promoter and nos terminator for rapid detection of genetically modified crops.recombinase polymerase amplification (rpa) is a novel isothermal dna amplification and detection technology that enables the amplification of dna within 30 min at a constant temperature of 37-42 °c by simulating in vivo dna recombination. in this study, based on the regulatory sequence of the cauliflower mosaic virus 35s (camv-35s) promoter and the agrobacterium tumefaciens nopaline synthase gene (nos) terminator, which are widely incorporated in genetically modified (gm) crops, we designed two ...201425310647
fha interaction with phosphothreonine of tssl activates type vi secretion in agrobacterium tumefaciens.the type vi secretion system (t6ss) is a widespread protein secretion system found in many gram-negative bacteria. t6sss are highly regulated by various regulatory systems at multiple levels, including post-translational regulation via threonine (thr) phosphorylation. the ser/thr protein kinase ppka is responsible for this thr phosphorylation regulation, and the forkhead-associated (fha) domain-containing fha-family protein is the sole t6ss phosphorylation substrate identified to date. here we d ...201424626341
compost-induced suppression of pythium damping-off is mediated by fatty-acid-metabolizing seed-colonizing microbial communities.leaf composts were studied for their suppressive effects on pythium ultimum sporangium germination, cottonseed colonization, and the severity of pythium damping-off of cotton. a focus of the work was to assess the role of fatty-acid-metabolizing microbial communities in disease suppression. suppressiveness was expressed within the first few hours of seed germination as revealed by reduced p. ultimum sporangium germination, reduced seed colonization, and reduced damping-off in transplant experime ...200312514027
the metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases.metacyc (metacyc.org) is a universal database of metabolic pathways and enzymes from all domains of life. the pathways in metacyc are curated from the primary scientific literature, and are experimentally determined small-molecule metabolic pathways. each reaction in a metacyc pathway is annotated with one or more well-characterized enzymes. because metacyc contains only experimentally elucidated knowledge, it provides a uniquely high-quality resource for metabolic pathways and enzymes. biocyc ( ...200717965431
the metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases.metacyc (metacyc.org) is a universal database of metabolic pathways and enzymes from all domains of life. the pathways in metacyc are curated from the primary scientific literature, and are experimentally determined small-molecule metabolic pathways. each reaction in a metacyc pathway is annotated with one or more well-characterized enzymes. because metacyc contains only experimentally elucidated knowledge, it provides a uniquely high-quality resource for metabolic pathways and enzymes. biocyc ( ...200717965431
metabolic modeling of denitrification in agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway.a metabolic network model for facultative denitrification was developed based on experimental data obtained with agrobacterium tumefaciens. the model includes kinetic regulation at the enzyme level and transcription regulation at the enzyme synthesis level. the objective of this work was to study the key factors regulating the metabolic response of the denitrification pathway to transition from oxic to anoxic respiration and to find parameter values for the biological processes that were modeled ...201223087683
estimating the number of integrations in transformed plants by quantitative real-time pcr.when generating transformed plants, a first step in their characterization is to obtain, for each new line, an estimate of how many copies of the transgene have been integrated in the plant genome because this can deeply influence the level of transgene expression and the ease of stabilizing expression in following generations. this task is normally achieved by southern analysis, a procedure that requires relatively large amounts of plant material and is both costly and labour-intensive. moreove ...200212398792
de-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features.function prediction frequently relies on comparing genes or gene products to search for relevant similarities. because the number of protein structures with unknown function is mushrooming, however, we asked here whether such comparisons could be improved by focusing narrowly on the key functional features of protein structures, as defined by the evolutionary trace (et). therefore a series of algorithms was built to (a) extract local motifs (3d templates) from protein structures based on et rank ...200818461181
metal a and metal b sites of nuclear rna polymerases pol iv and pol v are required for sirna-dependent dna methylation and gene silencing.plants are unique among eukaryotes in having five multi-subunit nuclear rna polymerases: the ubiquitous rna polymerases i, ii and iii plus two plant-specific activities, nuclear rna polymerases iv and v (previously known as polymerases iva and ivb). pol iv and pol v are not required for viability but play non-redundant roles in small interfering rna (sirna)-mediated pathways, including a pathway that silences retrotransposons and endogenous repeats via sirna-directed dna methylation. rna polymer ...200919119310
comparative analysis of eubacterial dna polymerase iii alpha subunits.dna polymerase iii is one of the five eubacterial dna polymerases that is responsible for the replication of dna duplex. among the ten subunits of the dna polymerase iii core enzyme, the alpha subunit catalyzes the reaction for polymerizing both dna strands. in this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. we found that all eubacterial genomes have one or more alpha subu ...200617531796
comparative analysis of eubacterial dna polymerase iii alpha subunits.dna polymerase iii is one of the five eubacterial dna polymerases that is responsible for the replication of dna duplex. among the ten subunits of the dna polymerase iii core enzyme, the alpha subunit catalyzes the reaction for polymerizing both dna strands. in this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. we found that all eubacterial genomes have one or more alpha subu ...200617531796
nuclear photosynthetic gene expression is synergistically modulated by rates of protein synthesis in chloroplasts and mitochondria.arabidopsis thaliana mutants prors1-1 and -2 were identified on the basis of a decrease in effective photosystem ii quantum yield. mutations were localized to the 5'-untranslated region of the nuclear gene prolyl-trna synthetase1 (prors1), which acts in both plastids and mitochondria. in prors1-1 and -2, prors1 expression is reduced, along with protein synthesis in both organelles. prors1 null alleles (prors1-3 and -4) result in embryo sac and embryo development arrest. in mutants with the leaky ...200616517761
genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes.serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. while studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. current analysis is aimed at understanding the distribution and probable b ...200819019219
molecular characterization of organelle-type nudix hydrolases in arabidopsis.nudix (for nucleoside diphosphates linked to some moiety x) hydrolases act to hydrolyze ribonucleoside and deoxyribonucleoside triphosphates, nucleotide sugars, coenzymes, or dinucleoside polyphosphates. arabidopsis (arabidopsis thaliana) contains 27 genes encoding nudix hydrolase homologues (atnudx1 to -27) with a predicted distribution in the cytosol, mitochondria, and chloroplasts. previously, cytosolic nudix hydrolases (atnudx1 to -11 and -25) were characterized. here, we conducted a charact ...200818815383
diversity surveys and evolutionary relationships of aoxb genes in aerobic arsenite-oxidizing bacteria.a new primer set was designed to specifically amplify ca. 1,100 bp of aoxb genes encoding the as(iii) oxidase catalytic subunit from taxonomically diverse aerobic as(iii)-oxidizing bacteria. comparative analysis of aoxb protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. aoxb phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16s rrna phylogeny. alphaproteobacteria-, betaproteo ...200818502920
estimating the fraction of non-coding rnas in mammalian transcriptomes.recent studies of mammalian transcriptomes have identified numerous rna transcripts that do not code for proteins; their identity, however, is largely unknown. here we explore an approach based on sequence randomness patterns to discern different rna classes. the relative z-score we use helps identify the known ncrna class from the genome, intergene and intron classes. this leads us to a fractional ncrna measure of putative ncrna datasets which we model as a mixture of genuine ncrnas and other t ...200819812767
identification and biochemical characterization of molybdenum cofactor-binding proteins from arabidopsis thaliana.the molybdenum cofactor (moco) forms part of the catalytic center in all eukaryotic molybdenum enzymes and is synthesized in a highly conserved pathway. among eukaryotes, very little is known about the processes taking place subsequent to moco biosynthesis, i.e. moco transfer, allocation, and insertion into molybdenum enzymes. in the model plant arabidopsis thaliana, we identified a novel protein family consisting of nine members that after recombinant expression are able to bind moco with k(d) ...200920040598
crystal structure of a prokaryotic (6-4) photolyase with an fe-s cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore.the (6-4) photolyases use blue light to reverse uv-induced (6-4) photoproducts in dna. this (6-4) photorepair was thought to be restricted to eukaryotes. here we report a prokaryotic (6-4) photolyase, phrb from agrobacterium tumefaciens, and propose that (6-4) photolyases are broadly distributed in prokaryotes. the crystal structure of photolyase related protein b (phrb) at 1.45 å resolution suggests a dna binding mode different from that of the eukaryotic counterparts. a his-his-x-x-arg motif i ...201323589886
discovery and validation of novel and distinct rna regulators for ribosomal protein s15 in diverse bacterial phyla.autogenous cis-regulators of ribosomal protein synthesis play a critical role in maintaining the stoichiometry of ribosome components. structured portions within an mrna transcript typically interact with specific ribosomal proteins to prevent expression of the entire operon, thus balancing levels of ribosomal proteins across transcriptional units. three distinct rna structures from different bacterial phyla have demonstrated interactions with s15 to regulate gene expression; however, these rnas ...201425104606
structural characterization of antibiotic self-immunity trna synthetase in plant tumour biocontrol agent.antibiotic-producing microbes evolved self-resistance mechanisms to avoid suicide. the biocontrol agrobacterium radiobacter k84 secretes the trojan horse antibiotic agrocin 84 that is selectively transported into the plant pathogen a. tumefaciens and processed into the toxin tm84. we previously showed that tm84 employs a unique trna-dependent mechanism to inhibit leucyl-trna synthetase (leurs), while the tm84-producer prevents self-poisoning by expressing a resistant leurs agnb2. we now identify ...201627713402
horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in alphaproteobacteria: the repabc operon.the repabc plasmid family, which is extensively present within alphaproteobacteria, and some secondary chromosomes of the rhizobiales have the particular feature that all the elements involved in replication and partitioning reside within one transcriptional unit, the repabc operon. given the functional interactions among the elements of the repabc operon, and the fact that they all reside in the same operon, a common evolutionary history would be expected if the entire operon had been horizonta ...200919919719
characterization of a novel agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of d-galactarolactone to 3-deoxy-2-keto-l-threo-hexarate.microorganisms use different pathways for d-galacturonate catabolism. in the known microbial oxidative pathway, d-galacturonate is oxidized to d-galactarolactone, the lactone hydrolyzed to galactarate, which is further converted to 3-deoxy-2-keto-hexarate and α-ketoglutarate. we have shown recently that agrobacterium tumefaciens strain c58 contains an uronate dehydrogenase (at udh) that oxidizes d-galacturonic acid to d-galactarolactone. here we report identification of a novel enzyme from the s ...201222493433
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