| analysis of hydroxycinnamic acid degradation in agrobacterium fabrum reveals a coenzyme a-dependent, beta-oxidative deacetylation pathway. | the soil- and rhizosphere-inhabiting bacterium agrobacterium fabrum (genomospecies g8 of the agrobacterium tumefaciens species complex) is known to have species-specific genes involved in ferulic acid degradation. here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme a (feruloyl-coa), 4-hydroxy-3-methoxyphenyl-β-hydroxypropionyl-coa, 4-hydroxy-3-methoxyphenyl-β-ketopropionyl-coa, vanillic acid, and protocatechuic acid. the genes atu1416, atu14 ... | 2014 | 24657856 |
| comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. | a comprehensive investigation of ribosomal genes in complete genomes from 66 different species allows us to address the distribution of r-proteins between and within the three primary domains. thirty-four r-protein families are represented in all domains but 33 families are specific to archaea and eucarya, providing evidence for specialisation at an early stage of evolution between the bacterial lineage and the lineage leading to archaea and eukaryotes. with only one specific r-protein, the arch ... | 2002 | 12490706 |
| the phage n4 virion rna polymerase catalytic domain is related to single-subunit rna polymerases. | in vitro, bacteriophage n4 virion rna polymerase (vrnap) recognizes in vivo sites of transcription initiation on single-stranded templates. n4 vrnap promoters are comprised of a hairpin structure and conserved sequences. here, we show that vrnap consists of a single 3500 amino acid polypeptide, and we define and characterize a transcriptionally active 1106 amino acid domain (mini-vrnap). biochemical and genetic characterization of this domain indicates that, despite its peculiar promoter specifi ... | 2002 | 12411499 |
| congruent evolution of different classes of non-coding dna in prokaryotic genomes. | prokaryotic genomes are considered to be 'wall-to-wall' genomes, which consist largely of genes for proteins and structural rnas, with only a small fraction of the genomic dna allotted to intergenic regions, which are thought to typically contain regulatory signals. the majority of bacterial and archaeal genomes contain 6-14% non-coding dna. significant positive correlations were detected between the fraction of non-coding dna and inter- and intra-operonic distances, suggesting that different cl ... | 2002 | 12364605 |
| molecular basis of bacterial outer membrane permeability revisited. | gram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. this review summarizes the development in the field since ... | 2003 | 14665678 |
| ccpa-dependent carbon catabolite repression in bacteria. | carbon catabolite repression (ccr) by transcriptional regulators follows different mechanisms in gram-positive and gram-negative bacteria. in gram-positive bacteria, ccpa-dependent ccr is mediated by phosphorylation of the phosphoenolpyruvate:sugar phosphotransferase system intermediate hpr at a serine residue at the expense of atp. the reaction is catalyzed by hpr kinase, which is activated by glycolytic intermediates. in this review, the distribution of ccpa-dependent ccr among bacteria is inv ... | 2003 | 14665673 |
| bidirectional replication from an internal ori site of the linear n15 plasmid prophage. | the prophage of coliphage n15 is not integrated into the chromosome but exists as a linear plasmid molecule with covalently closed hairpin ends (telomeres). upon infection the injected phage dna circularizes via its cohesive ends. then, a phage-encoded enzyme, protelomerase, cuts the circle and forms the hairpin telomeres. n15 protelomerase acts as a telomere-resolving enzyme during prophage dna replication. we characterized the n15 replicon and found that replication of circular n15 miniplasmid ... | 2003 | 14602914 |
| pharmacological inhibition of quorum sensing for the treatment of chronic bacterial infections. | traditional treatment of infectious diseases is based on compounds that aim to kill or inhibit bacterial growth. a major concern with this approach is the frequently observed development of resistance to antimicrobial compounds. the discovery of bacterial-communication systems (quorum-sensing systems), which orchestrate important temporal events during the infection process, has afforded a novel opportunity to ameliorate bacterial infection by means other than growth inhibition. compounds able t ... | 2003 | 14597754 |
| ancient origin of the tryptophan operon and the dynamics of evolutionary change. | the seven conserved enzymatic domains required for tryptophan (trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. a comparative bioinformatics evaluation of the conservation and organization of the genes of trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and oper ... | 2003 | 12966138 |
| evolutionary connection between the catalytic subunits of dna-dependent rna polymerases and eukaryotic rna-dependent rna polymerases and the origin of rna polymerases. | the eukaryotic rna-dependent rna polymerase (rdrp) is involved in the amplification of regulatory micrornas during post-transcriptional gene silencing. this enzyme is highly conserved in most eukaryotes but is missing in archaea and bacteria. no evolutionary relationship between rdrp and other polymerases has been reported so far, hence the origin of this eukaryote-specific polymerase remains a mystery. | 2003 | 12553882 |
| hgt-db: a database of putative horizontally transferred genes in prokaryotic complete genomes. | the horizontal gene transfer database (hgt-db) is a genomic database that includes statistical parameters such as g+c content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer. the current version of the database contains 88 bacterial and arch ... | 2003 | 12519978 |
| common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. | transmembrane receptors in microorganisms, such as sensory histidine kinases and methyl-accepting chemotaxis proteins, are molecular devices for monitoring environmental changes. we report here that sensory domain sharing is widespread among different classes of transmembrane receptors. we have identified two novel conserved extracellular sensory domains, named chase2 and chase3, that are found in at least four classes of transmembrane receptors: histidine kinases, adenylate cyclases, predicted ... | 2003 | 12486065 |
| inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy. | the growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. we have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underp ... | 2004 | 15214963 |
| sigi: score-based identification of genomic islands. | genomic islands can be observed in many microbial genomes. these stretches of dna have a conspicuous composition with regard to sequence or encoded functions. genomic islands are assumed to be frequently acquired via horizontal gene transfer. for the analysis of genome structure and the study of horizontal gene transfer, it is necessary to reliably identify and characterize these islands. | 2004 | 15113412 |
| comparative genomic analyses of the bacterial phosphotransferase system. | we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ... | 2005 | 16339738 |
| assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria. | identification of a bacterial protein's subcellular localization (scl) is important for genome annotation, function prediction and drug or vaccine target identification. subcellular fractionation techniques combined with recent proteomics technology permits the identification of large numbers of proteins from distinct bacterial compartments. however, the fractionation of a complex structure like the cell into several subcellular compartments is not a trivial task. contamination from other compar ... | 2005 | 16288665 |
| differentiation of regions with atypical oligonucleotide composition in bacterial genomes. | complete sequencing of bacterial genomes has become a common technique of present day microbiology. thereafter, data mining in the complete sequence is an essential step. new in silico methods are needed that rapidly identify the major features of genome organization and facilitate the prediction of the functional class of orfs. we tested the usefulness of local oligonucleotide usage (ou) patterns to recognize and differentiate types of atypical oligonucleotide composition in dna sequences of ba ... | 2005 | 16225667 |
| phylogenetic detection of conserved gene clusters in microbial genomes. | microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. however, the conservation can be a result of many factors such as vertical inheritance, or functional selection. thus, identification of conserved gene clusters that are under functional selection provides an effective channel for gene annotation, microarray screening, and pathway reconstruction. the problem of devising a robust method to identify these conserved gene clusters and to eval ... | 2005 | 16202130 |
| comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. | whole-genome transporter analyses have been conducted on 141 organisms whose complete genome sequences are available. for each organism, the complete set of membrane transport systems was identified with predicted functions, and classified into protein families based on the transporter classification system. organisms with larger genome sizes generally possessed a relatively greater number of transport systems. in prokaryotes and unicellular eukaryotes, the significant factor in the increase in ... | 2005 | 16118665 |
| genome-wide selection of unique and valid oligonucleotides. | functional genomics methods are used to investigate the huge amount of information contained in genomes. numerous experimental methods rely on the use of oligo- or polynucleotides. nucleotide strand hybridization forms the underlying principle for these methods. for all these techniques, the probes should be unique for analyzed genes. in addition to being unique for the studied genes, the probes should fulfill a large number of criteria to be usable and valid. the criteria include for example, a ... | 2005 | 16049019 |
| protein length in eukaryotic and prokaryotic proteomes. | we analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. comparing eukaryotes and prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the vast majority of protein families. the magnitude of these differences suggests that the evolution of eukaryotic proteins was influenced by processes of fusion of single-function proteins into extended m ... | 2005 | 15951512 |
| systematic association of genes to phenotypes by genome and literature mining. | one of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. so far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. here, we use an unsupervised, systematic approach for associating genes and phenotypic characteristics that combines literature mining with comparative genome analysis. we first mine the medline literature database for terms that reflect phenotypic simil ... | 2005 | 15799710 |
| clustering the annotation space of proteins. | current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas. | 2005 | 15703069 |
| coverage of whole proteome by structural genomics observed through protein homology modeling database. | we have been developing famsbase, a protein homology-modeling database of whole orfs predicted from genome sequences. the latest update of famsbase ( http://daisy.nagahama-i-bio.ac.jp/famsbase/ ), which is based on the protein three-dimensional (3d) structures released by november 2003, contains modeled 3d structures for 368,724 open reading frames (orfs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. those 276 genomes are pr ... | 2006 | 17146617 |
| the glycolytic pathway of trimastix pyriformis is an evolutionary mosaic. | glycolysis and subsequent fermentation is the main energy source for many anaerobic organisms. the glycolytic pathway consists of ten enzymatic steps which appear to be universal amongst eukaryotes. however, it has been shown that the origins of these enzymes in specific eukaryote lineages can differ, and sometimes involve lateral gene transfer events. we have conducted an expressed sequence tag (est) survey of the anaerobic flagellate trimastix pyriformis to investigate the nature of the evolut ... | 2006 | 17123440 |
| the selective value of bacterial shape. | why do bacteria have shape? is morphology valuable or just a trivial secondary characteristic? why should bacteria have one shape instead of another? three broad considerations suggest that bacterial shapes are not accidental but are biologically important: cells adopt uniform morphologies from among a wide variety of possibilities, some cells modify their shape as conditions demand, and morphology can be tracked through evolutionary lineages. all of these imply that shape is a selectable featur ... | 2006 | 16959965 |
| a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins. | lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ... | 2006 | 16585737 |
| paths of lateral gene transfer of lysyl-aminoacyl-trna synthetases with a unique evolutionary transition stage of prokaryotes coding for class i and ii varieties by the same organisms. | while the premise that lateral gene transfer (lgt) is a dominant evolutionary force is still in considerable dispute, the case for widespread lgt in the family of aminoacyl-trna synthetases (aars) is no longer contentious. aarss are ancient enzymes, guarding the fidelity of the genetic code. they are clustered in two structurally unrelated classes. only lysine aminoacyl-trna synthetase (lysrs) is found both as a class 1 and a class 2 enzyme (lysrs1-2). remarkably, in several extant prokaryotes b ... | 2006 | 16529662 |
| assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. | comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. this is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. | 2007 | 18047665 |
| separating the effects of mutation and selection in producing dna skew in bacterial chromosomes. | many bacterial chromosomes display nucleotide asymmetry, or skew, between the leading and lagging strands of replication. mutational differences between these strands result in an overall pattern of skew that is centered about the origin of replication. such a pattern could also arise from selection coupled with a bias for genes coded on the leading strand. the relative contributions of selection and mutation in producing compositional skew are largely unknown. | 2007 | 17935620 |
| selection against spurious promoter motifs correlates with translational efficiency across bacteria. | because binding of rnap to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of dna motifs capable of rnap-binding across the genome. here we analyze the distribution of the -10 promoter motifs that bind the sigma(70) subunit of rnap in 42 bacterial genomes. we show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequ ... | 2007 | 17710145 |
| linear chromosomes in bacteria: no straight edge advantage? | | 2007 | 17504473 |
| transcriptional regulatory network discovery via multiple method integration: application to e. coli k12. | transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ... | 2007 | 17397539 |
| phylogenetic distribution of translational gtpases in bacteria. | translational gtpases are a family of proteins in which gtpase activity is stimulated by the large ribosomal subunit. conserved sequence features allow members of this family to be identified. | 2007 | 17214893 |
| minimum contradiction matrices in whole genome phylogenies. | minimum contradiction matrices are a useful complement to distance-based phylogenies. a minimum contradiction matrix represents phylogenetic information under the form of an ordered distance matrix y(i) (,) (j) (n). a matrix element corresponds to the distance from a reference vertex n to the path (i, j). for an x-tree or a split network, the minimum contradiction matrix is a robinson matrix. it therefore fulfills all the inequalities defining perfect order: y(i) (,) (j) (n) >or= y(i) (,) (k) (n ... | 2008 | 19204821 |
| inter-kingdom signalling: communication between bacteria and their hosts. | microorganisms and their hosts communicate with each other through an array of hormonal signals. this cross-kingdom cell-to-cell signalling involves small molecules, such as hormones that are produced by eukaryotes and hormone-like chemicals that are produced by bacteria. cell-to-cell signalling between bacteria, usually referred to as quorum sensing, was initially described as a means by which bacteria achieve signalling in microbial communities to coordinate gene expression within a population ... | 2008 | 18197168 |
| sculpting the bacterial cell. | prokaryotes come in a wide variety of shapes, determined largely by natural selection, physical constraints, and patterns of cell growth and division. because of their relative simplicity, bacterial cells are excellent models for how genes and proteins can directly determine morphology. recent advances in cytological methods for bacteria have shown that distinct cytoskeletal filaments composed of actin and tubulin homologs are important for guiding growth patterns of the cell wall in bacteria, a ... | 2009 | 19906583 |
| genomic basis for natural product biosynthetic diversity in the actinomycetes. | | 2009 | 19844637 |
| linear chromosome-generating system of agrobacterium tumefaciens c58: protelomerase generates and protects hairpin ends. | agrobacterium tumefaciens c58, the pathogenic bacteria that causes crown gall disease in plants, harbors one circular and one linear chromosome and two circular plasmids. the telomeres of its unusual linear chromosome are covalently closed hairpins. the circular and linear chromosomes co-segregate and are stably maintained in the organism. we have determined the sequence of the two ends of the linear chromosome thus completing the previously published genome sequence of a. tumefaciens c58. we fo ... | 2012 | 22582388 |
| membrane lipids in agrobacterium tumefaciens: biosynthetic pathways and importance for pathogenesis. | many cellular processes critically depend on the membrane composition. in this review, we focus on the biosynthesis and physiological roles of membrane lipids in the plant pathogen agrobacterium tumefaciens. the major components of a. tumefaciens membranes are the phospholipids (pls), phosphatidylethanolamine (pe), phosphatidylglycerol, phosphatidylcholine (pc) and cardiolipin, and ornithine lipids (ols). under phosphate-limited conditions, the membrane composition shifts to phosphate-free lipid ... | 2014 | 24723930 |
| a bifunctional glycosyltransferase from agrobacterium tumefaciens synthesizes monoglucosyl and glucuronosyl diacylglycerol under phosphate deprivation. | glycolipids are mainly found in phototrophic organisms (like plants and cyanobacteria), in gram-positive bacteria, and a few other bacterial phyla. besides the function as bulk membrane lipids, they often play a role under phosphate deprivation as surrogates for phospholipids. the gram-negative agrobacterium tumefaciens accumulates four different glycolipids under phosphate deficiency, including digalactosyl diacylglycerol and glucosylgalactosyl diacylglycerol synthesized by a processive glycosy ... | 2014 | 24558041 |
| cyclic di-gmp regulates multiple cellular functions in the symbiotic alphaproteobacterium sinorhizobium meliloti. | sinorhizobium meliloti undergoes major lifestyle changes between planktonic states, biofilm formation, and symbiosis with leguminous plant hosts. in many bacteria, the second messenger 3',5'-cyclic di-gmp (c-di-gmp, or cdg) promotes a sessile lifestyle by regulating a plethora of processes involved in biofilm formation, including motility and biosynthesis of exopolysaccharides (eps). here, we systematically investigated the role of cdg in s. meliloti rm2011 encoding 22 proteins putatively associ ... | 2016 | 26574513 |
| tmrdb (tmrna database). | maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the bioinformatics research center, aarhus, denmark (http://www.bioinf.au.dk/tmrdb/). the tmrdb collects and distributes information relevant to the study of tmrna. in trans-translation, this molecule combines propert ... | 2003 | 12520048 |
| biofilms 2003: emerging themes and challenges in studies of surface-associated microbial life. | | 2004 | 15231774 |
| how phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. | the phosphoenolpyruvate(pep):carbohydrate phosphotransferase system (pts) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. to carry out its catalytic function in sugar transport and phosphorylation, the pts uses pep as an energy source and phosphoryl donor. the phosphoryl group of pep is usually transferred via four distinct proteins (domains) to the transported sugar bo ... | 2006 | 17158705 |
| agrobacterium tumefaciens zur regulates the high-affinity zinc uptake system trocba and the putative metal chaperone ycic, along with zint and znuabc, for survival under zinc-limiting conditions. | agrobacterium tumefaciens has a cluster of genes (atu3178, atu3179, and atu3180) encoding an abc-type transporter, here named troa, trob, and troc, respectively, which is shown here to be a zinc-specific uptake system. reverse transcription (rt)-pcr analysis confirmed that troa, trob, and troc are cotranscribed, with troc as the first gene of the operon. the ycic (atu3181) gene is transcribed in the opposite orientation to that of the trocba operon and belongs to a metal-binding gtpase family. e ... | 2016 | 27060116 |
| the accelerating convergence of genomics and microbiology. | | 2001 | 11305936 |
| atp-binding cassette transporters are targets for the development of antibacterial vaccines and therapies. | | 2004 | 15557595 |
| construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks. | to infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. in contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional r ... | 2006 | 16753070 |
| an enhancer mutant of arabidopsis salt overly sensitive 3 mediates both ion homeostasis and the oxidative stress response. | the myristoylated calcium sensor sos3 and its interacting protein kinase, sos2, play critical regulatory roles in salt tolerance. mutations in either of these proteins render arabidopsis thaliana plants hypersensitive to salt stress. we report here the isolation and characterization of a mutant called enh1-1 that enhances the salt sensitivity of sos3-1 and also causes increased salt sensitivity by itself. enh1 encodes a chloroplast-localized protein with a pdz domain at the n-terminal region and ... | 2007 | 17485445 |
| nicotine dehydrogenase complexed with 6-hydroxypseudooxynicotine oxidase involved in the hybrid nicotine-degrading pathway in agrobacterium tumefaciens s33. | nicotine, a major toxic alkaloid in tobacco wastes, is degraded by bacteria, mainly via pyridine and pyrrolidine pathways. previously, we discovered a new hybrid of the pyridine and pyrrolidine pathways in agrobacterium tumefaciens s33 and characterized its key enzyme 6-hydroxy-3-succinoylpyridine (hsp) hydroxylase. here, we purified the nicotine dehydrogenase initializing the nicotine degradation from the strain and found that it forms a complex with a novel 6-hydroxypseudooxynicotine oxidase. ... | 2016 | 26729714 |
| amidoligases with atp-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. | recent studies have shown that the ubiquitin system had its origins in ancient cofactor/amino acid biosynthesis pathways. preliminary studies also indicated that conjugation systems for other peptide tags on proteins, such as pupylation, have evolutionary links to cofactor/amino acid biosynthesis pathways. following up on these observations, we systematically investigated the non-ribosomal amidoligases of the atp-grasp, glutamine synthetase-like and acetyltransferase folds by classifying the kno ... | 2009 | 20023723 |
| comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. | the prokaryotic toxin-antitoxin systems (tas, also referred to as ta loci) are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addictive for replicons and cells in which they reside, but also possess "normal" cellular functions in various forms of stress response and management of prokaryotic population. several distinct tas of type 1, where the toxin is a protein and the antitoxin is an antisense rna, and numerous, unr ... | 2009 | 19493340 |
| insertion sequences. | insertion sequences (iss) constitute an important component of most bacterial genomes. over 500 individual iss have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. the last 10 years have also seen some striking advances in our understanding of the transposition process itself. not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic e ... | 1998 | 9729608 |
| sporangium-specific gene expression in the oomycete phytopathogen phytophthora infestans. | the oomycete genus phytophthora includes many of the world's most destructive plant pathogens, which are generally disseminated by asexual sporangia. to identify factors relevant to the biology of these propagules, genes induced in sporangia of the potato late blight pathogen phytophthora infestans were isolated using cdna macroarrays. of approximately 1,900 genes known to be expressed in sporangia, 61 were up-regulated >5-fold in sporangia versus hyphae based on the arrays, including 17 that we ... | 2003 | 14665470 |
| identification and characterization of phytoplasmal genes, employing a novel method of isolating phytoplasmal genomic dna. | phytoplasmas are unculturable, insect-transmissible plant pathogens belonging to the class mollicutes. to be transmitted, the phytoplasmas replicate in the insect body and are delivered to the insect's salivary glands, from where they are injected into the recipient plant. because phytoplasmas cannot be cultured, any attempt to recover phytoplasmal dna from infected plants or insects has resulted in preparations with a large background of host dna. thus, studies of the phytoplasmal genome have b ... | 2003 | 14594823 |
| computing prokaryotic gene ubiquity: rescuing the core from extinction. | the genomic core concept has found several uses in comparative and evolutionary genomics. defined as the set of all genes common to (ubiquitous among) all genomes in a phylogenetically coherent group, core size decreases as the number and phylogenetic diversity of the relevant group increases. here, we focus on methods for defining the size and composition of the core of all genes shared by sequenced genomes of prokaryotes (bacteria and archaea). there are few (almost certainly less than 50) gen ... | 2004 | 15574825 |
| genomes are covered with ubiquitous 11 bp periodic patterns, the "class a flexible patterns". | the genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. this bias is present throughout a given genome, both in coding and non-coding sequences. until now this bias remained of unknown origin. | 2005 | 16120222 |
| the tyra family of aromatic-pathway dehydrogenases in phylogenetic context. | the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size. | 2005 | 15888209 |
| the signaling helix: a common functional theme in diverse signaling proteins. | the mechanism by which the signals are transmitted between receptor and effector domains in multi-domain signaling proteins is poorly understood. | 2006 | 16953892 |
| rna secondary structure prediction by centroids in a boltzmann weighted ensemble. | prediction of rna secondary structure by free energy minimization has been the standard for over two decades. here we describe a novel method that forsakes this paradigm for predictions based on boltzmann-weighted structure ensemble. we introduce the notion of a centroid structure as a representative for a set of structures and describe a procedure for its identification. in comparison with the minimum free energy (mfe) structure using diverse types of structural rnas, the centroid of the ensemb ... | 2005 | 16043502 |
| differences in lexa regulon structure among proteobacteria through in vivo assisted comparative genomics. | the lexa regulon encompasses an ensemble of genes involved in preserving cell viability under massive dna damage and is present in most bacterial phyla. up to date, however, the scope of this network had only been assessed in the gamma proteobacteria. here, we report the structure of the lexa regulon in the alpha proteobacteria, using a combined approach that makes use of in vitro and in vivo techniques to assist and validate the comparative genomics in silico methodology. this leads to the firs ... | 2004 | 15604457 |
| the origin of mitochondria in light of a fluid prokaryotic chromosome model. | biologists agree that the ancestor of mitochondria was an alpha-proteobacterium. but there is no consensus as to what constitutes an alpha-proteobacterial gene. is it a gene found in all or several alpha-proteobacteria, or in only one? here, we examine the proportion of alpha-proteobacterial genes in alpha-proteobacterial genomes by means of sequence comparisons. we find that each alpha-proteobacterium harbours a particular collection of genes and that, depending upon the lineage examined, betwe ... | 2007 | 17251118 |
| the origin of mitochondria in light of a fluid prokaryotic chromosome model. | biologists agree that the ancestor of mitochondria was an alpha-proteobacterium. but there is no consensus as to what constitutes an alpha-proteobacterial gene. is it a gene found in all or several alpha-proteobacteria, or in only one? here, we examine the proportion of alpha-proteobacterial genes in alpha-proteobacterial genomes by means of sequence comparisons. we find that each alpha-proteobacterium harbours a particular collection of genes and that, depending upon the lineage examined, betwe ... | 2007 | 17251118 |
| molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. | bacterial community structure and diversity in rhizospheres in two types of grassland, distinguished by both plant species and fertilization regimen, were assessed by performing a 16s ribosomal dna (rdna) sequence analysis of dnas extracted from triplicate soil plots. pcr products were cloned, and 45 to 48 clones from each of the six libraries were partially sequenced. phylogenetic analysis of the resultant 275 clone sequences indicated that there was considerable variation in abundance in repli ... | 1999 | 10103273 |
| evolution of the chaperone/usher assembly pathway: fimbrial classification goes greek. | many proteobacteria use the chaperone/usher pathway to assemble proteinaceous filaments on the bacterial surface. these filaments can curl into fimbrial or nonfimbrial surface structures (e.g., a capsule or spore coat). this article reviews the phylogeny of operons belonging to the chaperone/usher assembly class to explore the utility of establishing a scheme for subdividing them into clades of phylogenetically related gene clusters. based on usher amino acid sequence comparisons, our analysis s ... | 2007 | 18063717 |
| enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse european sediments. | anaerobic, nitrate-dependent microbial oxidation of ferrous iron was recently recognized as a new type of metabolism. in order to study the occurrence of three novel groups of ferrous iron-oxidizing, nitrate-reducing bacteria (represented by strains brg1, brg2, and brg3), 16s rrna-targeted oligonucleotide probes were developed. in pure-culture experiments, these probes were shown to be suitable for fluorescent in situ hybridization, as well as for hybridization analysis of denaturing gradient ge ... | 1998 | 9835573 |
| improved assessment of denitrifying, n2-fixing, and total-community bacteria by terminal restriction fragment length polymorphism analysis using multiple restriction enzymes. | a database of terminal restriction fragments (trfs) of the 16s rrna gene was set up utilizing 13 restriction enzymes and 17,327 genbank sequences. a computer program, termed trefid, was developed to allow identification of any of these 17,327 sequences by means of polygons generated from the specific trfs of each bacterium. the trefid program complements and exceeds in its data content the web-based phylogenetic assignment tool recently described by a. d. kent, d. j. smith, b. j. benson, and e. ... | 2005 | 15812035 |
| computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria. | we used comparative genomics to investigate the distribution of conserved dna-binding motifs in the regulatory regions of genes involved in iron and manganese homeostasis in alpha-proteobacteria. combined with other computational approaches, this allowed us to reconstruct the metal regulatory network in more than three dozen species with available genome sequences. we identified several classes of cis-acting regulatory dna motifs (irr-boxes or ices, rira-boxes, iron-rhodo-boxes, fur-alpha-boxes, ... | 2006 | 17173478 |
| genomes of the symbiotic nitrogen-fixing bacteria of legumes. | | 2007 | 17556525 |
| bacteriophytochrome controls carotenoid-independent response to photodynamic stress in a non-photosynthetic rhizobacterium, azospirillum brasilense sp7. | ever since the discovery of the role of bacteriophytochrome (bphp) in inducing carotenoid synthesis in deinococcus radiodurans in response to light the role of bphps in other non-photosynthetic bacteria is not clear yet. azospirillum brasilense, a non-photosynthetic rhizobacterium, harbours a pair of bphps out of which abbphp1 is a homolog of atbphp1 of agrobacterium tumefaciens. by overexpression, purification, biochemical and spectral characterization we have shown that abbphp1 is a photochrom ... | 2012 | 23173079 |
| novel bacterium isolated from a lung transplant patient with cystic fibrosis. | the major clinical problem for patients with cystic fibrosis (cf) is progressive loss of pulmonary function, usually due to chronic bacterial infections. a patient with cf and a lung transplant was severely infected with a previously unidentified gram-negative bacterium. we isolated this organism (strain ds15158) from the patient and characterized it by phylogenetic analysis of the small-subunit rrna and biochemically by the biolog gn microplate assay, fatty acid analysis, and various standard l ... | 1999 | 10565895 |
| amplified-fragment length polymorphism analysis: the state of an art. | | 1999 | 10488158 |
| nomenclature for new tetracycline resistance determinants. | letters of the english alphabet have heretofore been used to name tetracycline resistance determinants. since all 26 letters have now been used, a nomenclature employing numerals is recommended for future determinants, and one laboratory has offered to coordinate the assignment of numerals. | 1999 | 10348788 |
| the arabidopsis huellenlos gene, which is essential for normal ovule development, encodes a mitochondrial ribosomal protein. | the huellenlos (hll) gene participates in patterning and growth of the arabidopsis ovule. we have isolated the hll gene and shown that it encodes a protein homologous to the l14 proteins of eubacterial ribosomes. the arabidopsis genome also includes a highly similar gene, huellenlos paralog (hlp), and genes for both cytosolic (l23) and chloroplast ribosome l14 proteins. phylogenetic analysis shows that hll and hlp differ significantly from these other two classes of such proteins. hll and hlp fu ... | 2001 | 11752383 |
| bacterial autoinduction: looking outside the cell for new metabolic engineering targets. | recent evidence has demonstrated that cell-to-cell signaling is a fundamental activity carried out by numerous microorganisms. a number of specialized processes are reported to be regulated by density-dependent signaling molecules including antibiotic production, bioluminescence, biofilm formation, genetic competence, sporulation, swarming motility and virulence. however, a more centralized role for quorum sensing is emerging where quorum signaling pathways overlap with stress and starvation cir ... | 2002 | 12537600 |
| chemical communication among bacteria. | cell-cell communication in bacteria is accomplished through the exchange of chemical signal molecules called autoinducers. this process, called quorum sensing, allows bacteria to monitor their environment for the presence of other bacteria and to respond to fluctuations in the number and/or species present by altering particular behaviors. most quorum-sensing systems are species- or group-specific, which presumably prevents confusion in mixed-species environments. however, some quorum-sensing ci ... | 2003 | 12949263 |
| the versatile bacterial type iv secretion systems. | bacteria use type iv secretion systems for two fundamental objectives related to pathogenesis--genetic exchange and the delivery of effector molecules to eukaryotic target cells. whereas gene acquisition is an important adaptive mechanism that enables pathogens to cope with a changing environment during invasion of the host, interactions between effector and host molecules can suppress defence mechanisms, facilitate intracellular growth and even induce the synthesis of nutrients that are benefic ... | 2003 | 15035043 |
| microbial genome jambalaya. | | 2003 | 12702204 |
| evolutionary history, structural features and biochemical diversity of the nlpc/p60 superfamily of enzymes. | peptidoglycan is hydrolyzed by a diverse set of enzymes during bacterial growth, development and cell division. the n1pc/p60 proteins define a family of cell-wall peptidases that are widely represented in various bacterial lineages. currently characterized members are known to hydrolyze d-gamma-glutamyl-meso-diaminopimelate or n-acetylmuramate-l-alanine linkages. | 2003 | 12620121 |
| computational inference of scenarios for alpha-proteobacterial genome evolution. | the alpha-proteobacteria, from which mitochondria are thought to have originated, display a 10-fold genome size variation and provide an excellent model system for studies of genome size evolution in bacteria. here, we use computational approaches to infer ancestral gene sets and to quantify the flux of genes along the branches of the alpha-proteobacterial species tree. our study reveals massive gene expansions at branches diversifying plant-associated bacteria and extreme losses at branches sep ... | 2004 | 15210995 |
| unraveling the secret lives of bacteria: use of in vivo expression technology and differential fluorescence induction promoter traps as tools for exploring niche-specific gene expression. | a major challenge for microbiologists is to elucidate the strategies deployed by microorganisms to adapt to and thrive in highly complex and dynamic environments. in vitro studies, including those monitoring genomewide changes, have proven their value, but they can, at best, mimic only a subset of the ensemble of abiotic and biotic stimuli that microorganisms experience in their natural habitats. the widely used gene-to-phenotype approach involves the identification of altered niche-related phen ... | 2005 | 15944455 |
| prokaryotic phylogenies inferred from protein structural domains. | the determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. in this work, we explore a new source of phylogenetic information, the distribution of protein structural domains within fully sequenced prokaryotic genomes. the evolution of the structura ... | 2005 | 15741510 |
| relative predicted protein levels of functionally associated proteins are conserved across organisms. | we show that the predicted protein levels of functionally related proteins change in a coordinated fashion over many unicellular organisms. for each protein, we created a profile containing a protein abundance measure in each of a set of organisms. we show that for functionally related proteins these profiles tend to be correlated. using the codon adaptation index as a predictor of protein abundance in 48 unicellular organisms, we demonstrated this phenomenon for two types of functional relation ... | 2005 | 15718304 |
| divergent evolution of a structural proteome: phenomenological models. | we develop models of the divergent evolution of genomes; the elementary object of sequence dynamics is the protein structural domain. to identify patterns of organization that reflect mechanisms of evolution, we consider the individual genomes of many procaryote species, studying the arrangement of protein structural domains in the space of all polypeptide structures. we view the network of structural similarities as a graph, called the organismal protein domain universe graph (opdug); vertices ... | 2006 | 17071665 |
| divergent evolution of a structural proteome: phenomenological models. | we develop models of the divergent evolution of genomes; the elementary object of sequence dynamics is the protein structural domain. to identify patterns of organization that reflect mechanisms of evolution, we consider the individual genomes of many procaryote species, studying the arrangement of protein structural domains in the space of all polypeptide structures. we view the network of structural similarities as a graph, called the organismal protein domain universe graph (opdug); vertices ... | 2006 | 17071665 |
| the [fefe] hydrogenase of nyctotherus ovalis has a chimeric origin. | the hydrogenosomes of the anaerobic ciliate nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. the hydrogenase permits direct reoxidation of nadh because it consists of a [fefe] hydrogenase module that is fused to two modules, which are homologous to the 24 kda and the 51 kda subunits of a mitochondrial complex i. | 2007 | 18021395 |
| bacterial heme-transport proteins and their heme-coordination modes. | efficient iron acquisition is critical for an invading microbe's survival and virulence. most of the iron in mammals is incorporated into heme, which can be plundered by certain bacterial pathogens as a nutritional iron source. utilization of exogenous heme by bacteria involves the binding of heme or hemoproteins to the cell surface receptors, followed by the transport of heme into cells. once taken into the cytosol, heme is presented to heme oxygenases where the tetrapyrrole ring is cleaved in ... | 2008 | 18977196 |
| bacterial heme-transport proteins and their heme-coordination modes. | efficient iron acquisition is critical for an invading microbe's survival and virulence. most of the iron in mammals is incorporated into heme, which can be plundered by certain bacterial pathogens as a nutritional iron source. utilization of exogenous heme by bacteria involves the binding of heme or hemoproteins to the cell surface receptors, followed by the transport of heme into cells. once taken into the cytosol, heme is presented to heme oxygenases where the tetrapyrrole ring is cleaved in ... | 2008 | 18977196 |
| metasim: a sequencing simulator for genomics and metagenomics. | the new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. next-generation sequencing technologies are producing a rapid increase of environmental data in public databases. there is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets. | 2008 | 18841204 |
| application of tilling and ecotilling as reverse genetic approaches to elucidate the function of genes in plants and animals. | with the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequencing efficiency and accuracy, many species of animals, plants, and microbes have annotated genomic information publicly available. the focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. reverse genetic approaches have been used for many years to advance from sequence data to the resulting phenotype in an effort to ded ... | 2008 | 19452039 |
| on the evolution and expression of chlamydomonas reinhardtii nucleus-encoded transfer rna genes. | in chlamydomonas reinhardtii, 259 trna genes were identified and classified into 49 trna isoaccepting families. by constructing phylogenetic trees, we determined the evolutionary history for each trna gene family. the majority of the trna sequences are more closely related to their plant counterparts than to animals ones. northern experiments also permitted us to show that at least one member of each trna isoacceptor family is transcribed and correctly processed in vivo. a short stretch of t res ... | 2008 | 18493044 |
| the structural biology of type iv secretion systems. | type iv secretion systems (t4sss) are versatile secretion systems that are found in both gram-negative and gram-positive bacteria and secrete a wide range of substrates, from single proteins to protein-protein and protein-dna complexes. they usually consist of 12 components that are organized into atp-powered, double-membrane-spanning complexes. the structures of single soluble components or domains have been solved, but an understanding of how these structures come together has only recently be ... | 2009 | 19756009 |
| gram-negative bacterial sensors for eukaryotic signal molecules. | ample evidence exists showing that eukaryotic signal molecules synthesized and released by the host can activate the virulence of opportunistic pathogens. the sensitivity of prokaryotes to host signal molecules requires the presence of bacterial sensors. these prokaryotic sensors, or receptors, have a double function: stereospecific recognition in a complex environment and transduction of the message in order to initiate bacterial physiological modifications. as messengers are generally unable t ... | 2009 | 22399982 |
| atlast4ss: a curated database for type iv secretion systems. | the type iv secretion system (t4ss) can be classified as a large family of macromolecule transporter systems, divided into three recognized sub-families, according to the well-known functions. the major sub-family is the conjugation system, which allows transfer of genetic material, such as a nucleoprotein, via cell contact among bacteria. also, the conjugation system can transfer genetic material from bacteria to eukaryotic cells; such is the case with the t-dna transfer of agrobacterium tumefa ... | 2012 | 22876890 |
| crystal structure of the hiv neutralizing antibody 2g12 in complex with a bacterial oligosaccharide analog of mammalian oligomannose. | human immunodeficiency virus-1 (hiv-1) is a major public health threat that continues to infect millions of people worldwide each year. a prophylactic vaccine remains the most cost-effective way of globally reducing and eliminating the spread of the virus. the hiv envelope spike, which is the target of many vaccine design efforts, is densely mantled with carbohydrate and several potent broadly neutralizing antibodies to hiv-1 recognize carbohydrate on the envelope spike as a major part of their ... | 2014 | 25380763 |
| counterselectable markers: untapped tools for bacterial genetics and pathogenesis. | | 1998 | 9712740 |
| chloroplast-targeted erd1 protein declines but its mrna increases during senescence in arabidopsis. | arabidopsis erd1 is a clpc-like protein that sequence analysis suggests may interact with the chloroplast-localized clpp protease to facilitate proteolysis. the mrna encoded by the erd1 gene has previously been shown to accumulate in response to senescence and to a variety of stresses and hormones. here we show that the erd1 protein, in contrast to the erd1 mrna, strongly declines in abundance with age, becoming undetectable in fully expanded leaves. sequence analysis also suggests that erd1 is ... | 1999 | 10198079 |
| mutation frequencies and antibiotic resistance. | | 2000 | 10858329 |
| a functional-phylogenetic classification system for transmembrane solute transporters. | a comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the international union of biochemistry and molecular biology. this system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. almost all of the more than 250 identified families of transporters in ... | 2000 | 10839820 |