| conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families. | the heme-copper oxidase (hco) superfamily includes hcos in aerobic respiratory chains and nitric oxide reductases (nors) in the denitrification pathway. the hco/nor catalytic subunit has a core structure consisting of 12 transmembrane helices (tmhs) arranged in three-fold rotational pseudosymmetry, with six conserved histidines for heme and metal binding. using sensitive sequence similarity searches, we detected a number of novel hco/nor homologs and named them hco homology (hcoh) proteins. seve ... | 2014 | 24931479 |
| comparative genomic and phylogenetic analyses of gammaproteobacterial glg genes traced the origin of the escherichia coli glycogen glgbxcap operon to the last common ancestor of the sister orders enterobacteriales and pasteurellales. | production of branched α-glucan, glycogen-like polymers is widely spread in the bacteria domain. the glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species escherichia coli (order enterobacteriales, class gammaproteobacteria), in which the cognate genes (branching enzyme glgb, debranching enzyme glgx, adp-glucose pyrophosphorylase glgc, glycogen synthase glga, and glycogen phosphorylase glgp) are clustered in a glgbxcap operon arrang ... | 2015 | 25607991 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics. | the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ... | 2014 | 24688489 |
| biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics. | the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ... | 2014 | 24688489 |
| olsg (sinac_1600) is an ornithine lipid n-methyltransferase from the planctomycete singulisphaera acidiphila. | ornithine lipids (ols) are phosphorus-free membrane lipids widespread in bacteria but absent from archaea and eukaryotes. in addition to the unmodified ols, a variety of ol derivatives hydroxylated in different structural positions has been reported. recently, methylated derivatives of ols were described in several planctomycetes isolated from a peat bog in northern russia, although the gene/enzyme responsible for the n-methylation of ol remained obscure. here we identify and characterize the ol ... | 2015 | 25925947 |
| the aspergillus fumigatus dihydroxyacid dehydratase ilv3a/ilvc is required for full virulence. | dihydroxyacid dehydratase (dhad) is a key enzyme in the branched-chain amino acid biosynthetic pathway that exists in a variety of organisms, including fungi, plants and bacteria, but not humans. in this study we identified four putative dhad genes from the filamentous fungus aspergillus fumigatus by homology to saccharomyces cerevisiae ilv3. two of these genes, afua_2g14210 and afua_1g03550, initially designated afilv3a and afilv3b for this study, clustered in the same group as s. cerevisiae il ... | 2012 | 23028460 |
| two c or not two c: recurrent disruption of zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. | ribosomal proteins are encoded in all genomes of cellular life forms and are, generally, well conserved during evolution. in prokaryotes, the genes for most ribosomal proteins are clustered in several highly conserved operons, which ensures efficient co-regulation of their expression. duplications of ribosomal-protein genes are infrequent, and given their coordinated expression and functioning, it is generally assumed that ribosomal-protein genes are unlikely to undergo horizontal transfer. howe ... | 2001 | 11574053 |
| 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 |
| 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 |
| classification and evolutionary history of the single-strand annealing proteins, rect, redbeta, erf and rad52. | the dna single-strand annealing proteins (ssaps), such as rect, redbeta, erf and rad52, function in reca-dependent and reca-independent dna recombination pathways. recently, they have been shown to form similar helical quaternary superstructures. however, despite the functional similarities between these diverse ssaps, their actual evolutionary affinities are poorly understood. | 2002 | 11914131 |
| alpha-crystallin-type heat shock proteins: socializing minichaperones in the context of a multichaperone network. | alpha-crystallins were originally recognized as proteins contributing to the transparency of the mammalian eye lens. subsequently, they have been found in many, but not all, members of the archaea, bacteria, and eucarya. most members of the diverse alpha-crystallin family have four common structural and functional features: (i) a small monomeric molecular mass between 12 and 43 kda; (ii) the formation of large oligomeric complexes; (iii) the presence of a moderately conserved central region, the ... | 2002 | 11875128 |
| superfamily: hmms representing all proteins of known structure. scop sequence searches, alignments and genome assignments. | the superfamily database contains a library of hidden markov models representing all proteins of known structure. the database is based on the scop 'superfamily' level of protein domain classification which groups together the most distantly related proteins which have a common evolutionary ancestor. there is a public server at http://supfam.org which provides three services: sequence searching, multiple alignments to sequences of known structure, and structural assignments to all complete genom ... | 2002 | 11752312 |
| 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 |
| 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 |
| genomic and proteomic adaptations to growth at high temperature. | most positively selected mutations cause changes in metabolism, resulting in a better-adapted phenotype. but as well as acting on the information content of genes, natural selection may also act directly on nucleic acid and protein molecules. we review the evidence for direct temperature-dependent natural selection acting on genomes, transcriptomes and proteomes. | 2004 | 15461805 |
| 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 |
| sequence motifs that distinguish atp(ctp):trna nucleotidyl transferases from eubacterial poly(a) polymerases. | atp(ctp):trna nucleotidyl transferases, trna maturing enzymes found in all organisms, and eubacterial poly(a) polymerases, enzymes involved in mrna degradation, are so similar that until now their biochemical functions could not be distinguished by their amino acid sequence. blast searches and analysis with the program "sequence space" for the prediction of functional residues revealed sequence motifs which define these two protein families. one of the poly(a) polymerase defining motifs specifie ... | 2004 | 15146073 |
| 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 |
| automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. | the increasing volume of genomic data opens new possibilities for analysis of protein function. we introduce a method for automated selection of residues that determine the functional specificity of proteins with a common general function (the specificity-determining positions [sdp] prediction method). such residues are assumed to be conserved within groups of orthologs (that may be assumed to have the same specificity) and to vary between paralogs. thus, considering a multiple sequence alignmen ... | 2004 | 14739328 |
| 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 |
| 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 |
| 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 |
| protein subunit interfaces: heterodimers versus homodimers. | protein dimers are either homodimers (complexation of identical monomers) or heterodimers (complexation of non-identical monomers). these dimers are common in catalysis and regulation. however, the molecular principles of protein dimer interactions are difficult to understand mainly due to the geometrical and chemical characteristics of proteins. nonetheless, the principles of protein dimer interactions are often studied using a dataset of 3d structural complexes determined by x-ray crystallogra ... | 2005 | 17597849 |
| 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 |
| identification of genomic features using microsyntenies of domains: domain teams. | the detection, across several genomes, of local conservation of gene content and proximity considerably helps the prediction of features of interest, such as gene fusions or physical and functional interactions. here, we want to process realistic models of chromosomes, in which genes (or genomic segments of several genes) can be duplicated within a chromosome, or be absent from some other chromosome(s). our approach adopts the technique of temporarily forgetting genes and working directly with p ... | 2005 | 15899966 |
| 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 |
| transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in is element gene expression. | transcription slippage occurs on certain patterns of repeat mononucleotides, resulting in synthesis of a heterogeneous population of mrnas. individual mrna molecules within this population differ in the number of nucleotides they contain that are not specified by the template. when transcriptional slippage occurs in a coding sequence, translation of the resulting mrnas yields more than one protein product. except where the products of the resulting mrnas have distinct functions, transcription sl ... | 2005 | 15774026 |
| 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 |
| comparative genomics and evolution of the hsp90 family of genes across all kingdoms of organisms. | hsp90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. hsp90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. in this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in genbank, and address the diversity, evolution, gene structure, conservation and nomenclature ... | 2006 | 16780600 |
| 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 |
| 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 |
| 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 |
| 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 |
| target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. | to study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common tim barrel fold and catalyze a wide range of chemical reactions. here, we describe a collaboration between the enzyme specificity consortium (enspec) and the new york sgx research center for structural genomics (nysgxrc) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. using sequence- and s ... | 2009 | 19219566 |
| cubic time algorithms of amalgamating gene trees and building evolutionary scenarios. | a long recognized problem is the inference of the supertree s that amalgamates a given set {g(j)} of trees g(j), with leaves in each g(j) being assigned homologous elements. we ground on an approach to find the tree s by minimizing the total cost of mappings α(j) of individual gene trees g(j) into s. traditionally, this cost is defined basically as a sum of duplications and gaps in each α(j). the classical problem is to minimize the total cost, where s runs over the set of all trees that contain ... | 2012 | 23259766 |
| meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling. | in the last two decades, a large number of whole-genome phylogenies have been inferred to reconstruct the tree of life (tol). underlying data models range from gene or functionality content in species to phylogenetic gene family trees and multiple sequence alignments of concatenated protein sequences. diversity in data models together with the use of different tree reconstruction techniques, disruptive biological effects and the steadily increasing number of genomes have led to a huge diversity ... | 2012 | 22915837 |
| molecular mechanisms and clinical impact of acquired and intrinsic fosfomycin resistance. | bacterial infections caused by antibiotic-resistant isolates have become a major health problem in recent years, since they are very difficult to treat, leading to an increase in morbidity and mortality. fosfomycin is a broad-spectrum bactericidal antibiotic that inhibits cell wall biosynthesis in both gram-negative and gram-positive bacteria. this antibiotic has a unique mechanism of action and inhibits the initial step in peptidoglycan biosynthesis by blocking the enzyme, mura. fosfomycin has ... | 2013 | 27029300 |
| the shoct domain: a widespread domain under-represented in model organisms. | we have identified a new protein domain, which we have named the shoct domain (short c-terminal domain). this domain is widespread in bacteria with over a thousand examples. but we found it is missing from the most commonly studied model organisms, despite being present in closely related species. it's predominantly c-terminal location, co-occurrence with numerous other domains and short size is reminiscent of the gram-positive anchor motif, however it is present in a much wider range of species ... | 2013 | 23451277 |
| 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 |
| distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives. | it is well known that patterns of nucleotide composition vary within and among genomes, although the reasons why these variations exist are not completely understood. between-genome compositional variation has been exploited to assign environmental shotgun sequences to their most likely originating genomes, whereas within-genome variation has been used to identify recently acquired genetic material such as pathogenicity islands. recent sequence assignment techniques have achieved high levels of ... | 2010 | 20333228 |
| 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 |
| structural classification of bacterial response regulators: diversity of output domains and domain combinations. | chey-like phosphoacceptor (or receiver [rec]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. in this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. transcriptional regulators of the ompr, narl, and ntrc families w ... | 2006 | 16740923 |
| the influence of smoking on the peri-implant microbiome. | smokers are at high risk for 2 bacterially driven oral diseases: peri-implant mucositis and peri-implantitis. therefore, the purpose of this investigation was to use a deep-sequencing approach to identify the effect of smoking on the peri-implant microbiome in states of health and disease. peri-implant biofilm samples were collected from 80 partially edentulous subjects with peri-implant health, peri-implant mucositis, and peri-implantitis. bacterial dna was isolated and 16s ribsomal rna gene li ... | 2015 | 26124222 |
| a golden age for microbial genomics. | | 2003 | 14611656 |
| protein-translocating trimeric autotransporters of gram-negative bacteria. | | 2006 | 16885434 |
| 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 |
| mining high-throughput experimental data to link gene and function. | nearly 2200 genomes that encode around 6 million proteins have now been sequenced. around 40% of these proteins are of unknown function, even when function is loosely and minimally defined as 'belonging to a superfamily'. in addition to in silico methods, the swelling stream of high-throughput experimental data can give valuable clues for linking these unknowns with precise biological roles. the goal is to develop integrative data-mining platforms that allow the scientific community at large to ... | 2011 | 21310501 |
| a second-generation protein-protein interaction network of helicobacter pylori. | helicobacter pylori infections cause gastric ulcers and play a major role in the development of gastric cancer. in 2001, the first protein interactome was published for this species, revealing over 1500 binary protein interactions resulting from 261 yeast two-hybrid screens. here we roughly double the number of previously published interactions using an orfeome-based, proteome-wide yeast two-hybrid screening strategy. we identified a total of 1515 protein-protein interactions, of which 1461 are ... | 2014 | 24627523 |
| carnitine in bacterial physiology and metabolism. | carnitine is a quaternary amine compound found at high concentration in animal tissues, particularly muscle, and is most well studied for its contribution to fatty acid transport into mitochondria. in bacteria, carnitine is an important osmoprotectant, and can also enhance thermotolerance, cryotolerance and barotolerance. carnitine can be transported into the cell or acquired from metabolic precursors, where it can serve directly as a compatible solute for stress protection or be metabolized thr ... | 2015 | 25787873 |
| extensive identification of bacterial riboflavin transporters and their distribution across bacterial species. | riboflavin, the precursor for the cofactors flavin mononucleotide (fmn) and flavin adenine dinucleotide, is an essential metabolite in all organisms. while the functions for de novo riboflavin biosynthesis and riboflavin import may coexist in bacteria, the extent of this co-occurrence is undetermined. the ribm, ribn, rfuabcd and the energy-coupling factor-ribu bacterial riboflavin transporters have been experimentally characterized. in addition, impx, rfnt and ribxy are proposed as riboflavin tr ... | 2015 | 25938806 |
| the tryptophan pathway genes of the sargasso sea metagenome: new operon structures and the prevalence of non-operon organization. | the enormous database of microbial dna generated from the sargasso sea metagenome provides a unique opportunity to locate genes participating in different biosynthetic pathways and to attempt to understand the relationship and evolution of those genes. in this article, an analysis of the sargasso sea metagenome is made with respect to the seven genes of the tryptophan pathway. | 2008 | 18221558 |
| 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 |
| a gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen bartonella. | gene transfer agents (gtas) randomly transfer short fragments of a bacterial genome. a novel putative gta was recently discovered in the mouse-infecting bacterium bartonella grahamii. although gtas are widespread in phylogenetically diverse bacteria, their role in evolution is largely unknown. here, we present a comparative analysis of 16 bartonella genomes ranging from 1.4 to 2.6 mb in size, including six novel genomes from bartonella isolated from a cow, two moose, two dogs, and a kangaroo. a ... | 2013 | 23555299 |
| expansion of the biocyc collection of pathway/genome databases to 160 genomes. | the biocyc database collection is a set of 160 pathway/genome databases (pgdbs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. each pgdb in the biocyc collection describes the genome and predicted metabolic network of a single organism, inferred from the metacyc database, which is a reference source on metabolic pathways from multiple organisms. in addition, each bacterial pgdb includes predicted operons for the corresponding species. the biocyc ... | 2005 | 16246909 |
| a computational approach for identifying pathogenicity islands in prokaryotic genomes. | pathogenicity islands (pais), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (gis) that have been acquired by horizontal gene transfer event. up to now, computational approaches for identifying pais have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. these approaches often lead to the identification of genomic islands, rather than pais. | 2005 | 16033657 |
| 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 |
| intergenic transposable elements are not randomly distributed in bacteria. | insertion sequences (iss) are mobile genetic elements in bacterial genomes. in general, intergenic is elements are probably less deleterious for their hosts than intragenic iss, simply because they have a lower likelihood of disrupting native genes. however, since promoters, shine-dalgarno sequences, and transcription factor binding sites are intergenic and upstream of genes, i hypothesized that not all neighboring gene orientations (ngos) are selectively equivalent for is insertion. to test thi ... | 2010 | 20697140 |
| characterization of nitric oxide-inducing lipid a derived from mesorhizobium loti lipopolysaccharide. | mesorhizobium loti is a member of the rhizobia and forms nitrogen-fixing symbioses with several lotus species. recently, it was reported that m. loti bacterial cells and their lipopolysaccharide (lps) preparations transiently induced nitric oxide (no) production in the roots of l. japonicus. we subsequently found that polysaccharides and the lipid a moiety were responsible for this no induction. in this study, we elucidated the chemical structure of m. loti lipid a and characterized its no-induc ... | 2012 | 23059724 |
| whole genome sequencing revealed host adaptation-focused genomic plasticity of pathogenic leptospira. | leptospirosis, caused by pathogenic leptospira spp., has recently been recognized as an emerging infectious disease worldwide. despite its severity and global importance, knowledge about the molecular pathogenesis and virulence evolution of leptospira spp. remains limited. here we sequenced and analyzed 102 isolates representing global sources. a high genomic variability were observed among different leptospira species, which was attributed to massive gene gain and loss events allowing for adapt ... | 2016 | 26833181 |
| conserved amino acid sequence features in the alpha subunits of mofe, vfe, and fefe nitrogenases. | this study examines the structural features and phylogeny of the alpha subunits of 69 full-length nifd (mofe subunit), vnfd (vfe subunit), and anfd (fefe subunit) sequences. | 2009 | 19578539 |
| distribution of genes encoding nucleoid-associated protein homologs in plasmids. | bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ... | 2011 | 21350637 |
| the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. | ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ... | 2006 | 16859499 |
| structure of potassium channels. | potassium channels ubiquitously exist in nearly all kingdoms of life and perform diverse but important functions. since the first atomic structure of a prokaryotic potassium channel (kcsa, a channel from streptomyces lividans) was determined, tremendous progress has been made in understanding the mechanism of potassium channels and channels conducting other ions. in this review, we discuss the structure of various kinds of potassium channels, including the potassium channel with the pore-forming ... | 2015 | 26070303 |
| 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 |
| coevolution of the atpase clpv, the sheath proteins tssb and tssc, and the accessory protein tagj/hsie1 distinguishes type vi secretion classes. | the type vi secretion system (t6ss) is a bacterial nanomachine for the transport of effector molecules into prokaryotic and eukaryotic cells. it involves the assembly of a tubular structure composed of tssb and tssc that is similar to the tail sheath of bacteriophages. the sheath contracts to provide the energy needed for effector delivery. the aaa(+) atpase clpv disassembles the contracted sheath, which resets the systems for reassembly of an extended sheath that is ready to fire again. this me ... | 2014 | 25305017 |
| diversity of nitrogen-fixing bacteria associated with switchgrass in the native tallgrass prairie of northern oklahoma. | switchgrass (panicum virgatum l.) is a perennial c4 grass native to north america that is being developed as a feedstock for cellulosic ethanol production. industrial nitrogen fertilizers enhance switchgrass biomass production but add to production and environmental costs. a potential sustainable alternative source of nitrogen is biological nitrogen fixation. as a step in this direction, we studied the diversity of nitrogen-fixing bacteria (nfb) associated with native switchgrass plants from the ... | 2014 | 25002418 |
| bacterial genome instability. | bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile dna elements. this implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. in this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. we ... | 2014 | 24600039 |
| evolutionary and functional relationships of the dha regulon by genomic context analysis. | 3-hydroxypropionaldehyde (3-hpa) and 1,3-propanediol (1,3-pd) are subproducts of glycerol degradation and of economical interest as they are used for polymers synthesis, such as polyesters and polyurethanes. some few characterized bacterial species (mostly from firmicutes and gamma-proteobacteria groups) are able to catabolize these monomers from glycerol using the gene products from the dha regulon. to expand our knowledge and direct further experimental studies on the regulon and related genes ... | 2016 | 26938861 |
| molecular analysis of microbial community structures in pristine and contaminated aquifers: field and laboratory microcosm experiments. | this study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (fc) or aerobic and noncontaminated (nc) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). the latter objective was addressed by using the nc and fc aquifer materials for anaerobic microcosm studie ... | 1999 | 10224013 |
| 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 |
| reactive oxygen species-inducible ecf σ factors of bradyrhizobium japonicum. | extracytoplasmic function (ecf) σ factors control the transcription of genes involved in different cellular functions, such as stress responses, metal homeostasis, virulence-related traits, and cell envelope structure. the genome of bradyrhizobium japonicum, the nitrogen-fixing soybean endosymbiont, encodes 17 putative ecf σ factors belonging to nine different ecf σ factor families. the genes for two of them, ecfq (bll1028) and ecff (blr3038), are highly induced in response to the reactive oxyge ... | 2012 | 22916258 |
| an underground tale: contribution of microbial activity to plant iron acquisition via ecological processes. | iron (fe) deficiency in crops is a worldwide agricultural problem. plants have evolved several strategies to enhance fe acquisition, but increasing evidence has shown that the intrinsic plant-based strategies alone are insufficient to avoid fe deficiency in fe-limited soils. soil micro-organisms also play a critical role in plant fe acquisition; however, the mechanisms behind their promotion of fe acquisition remain largely unknown. | 2013 | 24265348 |
| an underground tale: contribution of microbial activity to plant iron acquisition via ecological processes. | iron (fe) deficiency in crops is a worldwide agricultural problem. plants have evolved several strategies to enhance fe acquisition, but increasing evidence has shown that the intrinsic plant-based strategies alone are insufficient to avoid fe deficiency in fe-limited soils. soil micro-organisms also play a critical role in plant fe acquisition; however, the mechanisms behind their promotion of fe acquisition remain largely unknown. | 2013 | 24265348 |
| aliphatic, cyclic, and aromatic organic acids, vitamins, and carbohydrates in soil: a review. | organic acids, vitamins, and carbohydrates represent important organic compounds in soil. aliphatic, cyclic, and aromatic organic acids play important roles in rhizosphere ecology, pedogenesis, food-web interactions, and decontamination of sites polluted by heavy metals and organic pollutants. carbohydrates in soils can be used to estimate changes of soil organic matter due to management practices, whereas vitamins may play an important role in soil biological and biochemical processes. the aim ... | 2013 | 24319374 |
| discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria. | root nodule bacteria (rnb) or "rhizobia" are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. in this study, we sequenced the genomes of 110 rnb from diverse hosts and biogeographical regions, and undertook a global exploration of all available rnb genera with the aim of identifying novel genetic determinants of symbio ... | 2015 | 26584898 |
| impact of microalgae-bacteria interactions on the production of algal biomass and associated compounds. | a greater insight on the control of the interactions between microalgae and other microorganisms, particularly bacteria, should be useful for enhancing the efficiency of microalgal biomass production and associated valuable compounds. little attention has been paid to the controlled utilization of microalgae-bacteria consortia. however, the studies of microalgal-bacterial interactions have revealed a significant impact of the mutualistic or parasitic relationships on algal growth. the algal grow ... | 2016 | 27213407 |
| elucidation of a novel lipid a α-(1,1)-gala transferase gene (rgtf) from mesorhizobium loti: heterologous expression of rgtf causes rhizobium etli to synthesize lipid a with α-(1,1)-gala. | an unusual α-(1,1)-galacturonic acid (gala) lipid a modification has been reported in the lipopolysaccharide of a number of interesting gram-negative bacteria, including the nitrogen-fixing bacteria azospirillum lipoferum, mesorhizobium huakuii and m. loti, the stalk-forming bacterium caulobacter crescentus and the hyperthermophilic bacterium aquifex aeolicus. however, the α-(1,1)-gala transferase (galat) gene, which we have named rgtf, was not identified. species of the rhizobium genera produce ... | 2013 | 23283001 |
| occurrence of an unusual hopanoid-containing lipid a among lipopolysaccharides from bradyrhizobium species. | the chemical structures of the unusual hopanoid-containing lipid a samples of the lipopolysaccharides (lps) from three strains of bradyrhizobium (slow-growing rhizobia) have been established. they differed considerably from other gram-negative bacteria in regards to the backbone structure, the number of ester-linked long chain hydroxylated fatty acids, as well as the presence of a tertiary residue that consisted of at least one molecule of carboxyl-bacteriohopanediol or its 2-methyl derivative. ... | 2014 | 25371196 |
| new insights into 1-aminocyclopropane-1-carboxylate (acc) deaminase phylogeny, evolution and ecological significance. | the main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (acc) deaminase, the activity of which represents one of the most important and studied mechanisms used by plant growth-promoting microorganisms. the acc deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis w ... | 2014 | 24905353 |
| genome-wide discovery of putative srnas in paracoccus denitrificans expressed under nitrous oxide emitting conditions. | nitrous oxide (n2o) is a stable, ozone depleting greenhouse gas. emissions of n2o into the atmosphere continue to rise, primarily due to the use of nitrogen-containing fertilizers by soil denitrifying microbes. it is clear more effective mitigation strategies are required to reduce emissions. one way to help develop future mitigation strategies is to address the currently poor understanding of transcriptional regulation of the enzymes used to produce and consume n2o. with this ultimate aim in mi ... | 2016 | 27895629 |
| 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 |
| 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 |
| 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 |
| global network alignment using multiscale spectral signatures. | protein interaction networks provide an important system-level view of biological processes. one of the fundamental problems in biological network analysis is the global alignment of a pair of networks, which puts the proteins of one network into correspondence with the proteins of another network in a manner that conserves their interactions while respecting other evidence of their homology. by providing a mapping between the networks of different species, alignments can be used to inform hypot ... | 2012 | 23047556 |
| 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 |