| 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 |
| correlations between shine-dalgarno sequences and gene features such as predicted expression levels and operon structures. | this work assesses relationships for 30 complete prokaryotic genomes between the presence of the shine-dalgarno (sd) sequence and other gene features, including expression levels, type of start codon, and distance between successive genes. a significant positive correlation of the presence of an sd sequence and the predicted expression level of a gene based on codon usage biases was ascertained, such that predicted highly expressed genes are more likely to possess a strong sd sequence than avera ... | 2002 | 12270832 |
| evidence for strong selective constraint acting on the nucleotide composition of 16s ribosomal rna genes. | previous studies have shown that the guanine plus cytosine (g+c) content of ribosomal rnas (rrnas) is highly correlated with bacterial growth temperatures. this correlation is strongest in the double-stranded stem regions of the rrna, a fact that can be explained by selection for increased structural stability at high growth temperatures. in this study, we examined the single-stranded regions of 16s rrnas. we reasoned that, since these regions of the molecule are subject to less structural const ... | 2002 | 12034839 |
| on the evolution of structure in aminoacyl-trna synthetases. | the aminoacyl-trna synthetases are one of the major protein components in the translation machinery. these essential proteins are found in all forms of life and are responsible for charging their cognate trnas with the correct amino acid. the evolution of the trna synthetases is of fundamental importance with respect to the nature of the biological cell and the transition from an rna world to the modern world dominated by protein-enzymes. we present a structure-based phylogeny of the aminoacyl-t ... | 2003 | 14665676 |
| 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 |
| 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 |
| 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 |
| 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 |
| prediction of rna-binding proteins from primary sequence by a support vector machine approach. | elucidation of the interaction of proteins with different molecules is of significance in the understanding of cellular processes. computational methods have been developed for the prediction of protein-protein interactions. but insufficient attention has been paid to the prediction of protein-rna interactions, which play central roles in regulating gene expression and certain rna-mediated enzymatic processes. this work explored the use of a machine learning method, support vector machines (svm) ... | 2004 | 14970381 |
| 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 |
| 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 |
| predicted highly expressed genes in archaeal genomes. | based primarily on 16s rrna sequence comparisons, life has been broadly divided into the three domains of bacteria, archaea, and eukarya. archaea is further classified into crenarchaea and euryarchaea. archaea generally thrive in extreme environments as assessed by temperature, ph, and salinity. for many prokaryotic organisms, ribosomal proteins (rp), transcription/translation factors, and chaperone genes tend to be highly expressed. a gene is predicted highly expressed (phx) if its codon usage ... | 2005 | 15883368 |
| 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 |
| p-value based visualization of codon usage data. | two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. both problems can be addressed by multivariate analysis of codon usage data. in particular dimensionality reduction methods for visualization of multivariate data have shown to be effective tools for codon usage analysis. we here propose a multidimensional scaling approach using a novel similarity measure for codon usage tab ... | 2006 | 16808834 |
| phylogenomic analysis of the giy-yig nuclease superfamily. | the giy-yig domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-ltr retrotransposons) and in enzymes involved in dna repair and recombination. however, to date no systematic search for novel members of the giy-yig superfamily or comparative analysis of these enzymes has been reported. | 2006 | 16646971 |
| 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 |
| 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 |
| 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 |
| large deviations for random trees and the branching of rna secondary structures. | we give a large deviation principle (ldp) with explicit rate function for the distribution of vertex degrees in plane trees, a combinatorial model of rna secondary structures. we calculate the typical degree distributions based on nearest neighbor free energies, and compare our results with the branching configurations found in two sets of large rna secondary structures. we find substantial agreement overall, with some interesting deviations which merit further study. | 2008 | 19083065 |
| large deviations for random trees and the branching of rna secondary structures. | we give a large deviation principle (ldp) with explicit rate function for the distribution of vertex degrees in plane trees, a combinatorial model of rna secondary structures. we calculate the typical degree distributions based on nearest neighbor free energies, and compare our results with the branching configurations found in two sets of large rna secondary structures. we find substantial agreement overall, with some interesting deviations which merit further study. | 2008 | 19083065 |
| genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. | the first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. a crucial finding that enables function ... | 2008 | 18948295 |
| 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 |
| evolutionary primacy of sodium bioenergetics. | the f- and v-type atpases are rotary molecular machines that couple translocation of protons or sodium ions across the membrane to the synthesis or hydrolysis of atp. both the f-type (found in most bacteria and eukaryotic mitochondria and chloroplasts) and v-type (found in archaea, some bacteria, and eukaryotic vacuoles) atpases can translocate either protons or sodium ions. the prevalent proton-dependent atpases are generally viewed as the primary form of the enzyme whereas the sodium-transloca ... | 2008 | 18380897 |
| 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 |
| card: a new rna polymerase modulator in mycobacteria. | mycobacteria card is an essential rnap binding protein that regulates many transcripts including rrna. this article will review our present state of knowledge regarding card and compare the known functions of card with other rnap binding proteins in e. coli, emphasizing how this information can guide future investigations. | 2010 | 21326904 |
| card: a new rna polymerase modulator in mycobacteria. | mycobacteria card is an essential rnap binding protein that regulates many transcripts including rrna. this article will review our present state of knowledge regarding card and compare the known functions of card with other rnap binding proteins in e. coli, emphasizing how this information can guide future investigations. | 2010 | 21326904 |
| novel base triples in rna structures revealed by graph theoretical searching methods. | highly hydrogen bonded base interactions play a major part in stabilizing the tertiary structures of complex rna molecules, such as transfer-rnas, ribozymes and ribosomal rnas. | 2011 | 22373013 |
| a computational study of elongation factor g (efg) duplicated genes: diverged nature underlying the innovation on the same structural template. | elongation factor g (efg) is a core translational protein that catalyzes the elongation and recycling phases of translation. a more complex picture of efg's evolution and function than previously accepted is emerging from analyzes of heterogeneous efg family members. whereas the gene duplication is postulated to be a prominent factor creating functional novelty, the striking divergence between efg paralogs can be interpreted in terms of innovation in gene function. | 2011 | 21829651 |
| molecular evolution of urea amidolyase and urea carboxylase in fungi. | urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. urea amidolyase has been found only in some fungal species among eukaryotes. it contains two major domains: the amidase and urea carboxylase domains. a shorter form of urea amidolyase is known as urea carboxylase and has no amidase domain. eukaryotic urea carboxylase has been found only in several fungal species and green algae. in order to elucid ... | 2011 | 21447149 |
| the aeropath project targeting pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery. | bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. a major concern is gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. in an effort to accelerate early steps in drug discovery, the eu-funded aeropath project aims to identify novel targets in the opportunistic pathogen pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization ... | 2012 | 23295481 |
| the aeropath project targeting pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery. | bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. a major concern is gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. in an effort to accelerate early steps in drug discovery, the eu-funded aeropath project aims to identify novel targets in the opportunistic pathogen pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization ... | 2012 | 23295481 |
| a multicenter blinded analysis indicates no association between chronic fatigue syndrome/myalgic encephalomyelitis and either xenotropic murine leukemia virus-related virus or polytropic murine leukemia virus. | the disabling disorder known as chronic fatigue syndrome or myalgic encephalomyelitis (cfs/me) has been linked in two independent studies to infection with xenotropic murine leukemia virus-related virus (xmrv) and polytropic murine leukemia virus (pmlv). although the associations were not confirmed in subsequent studies by other investigators, patients continue to question the consensus of the scientific community in rejecting the validity of the association. here we report blinded analysis of p ... | 2012 | 22991430 |
| comparing the similarity of different groups of bacteria to the human proteome. | numerous aspects of the relationship between bacteria and human have been investigated. one aspect that has recently received attention is sequence overlap at the proteomic level. however, there has not yet been a study that comprehensively characterizes the level of sequence overlap between bacteria and human, especially as it relates to bacterial characteristics like pathogenicity, g-c content, and proteome size. in this study, we began by performing a general characterization of the range of ... | 2012 | 22558081 |
| bactquant: an enhanced broad-coverage bacterial quantitative real-time pcr assay. | bacterial load quantification is a critical component of bacterial community analysis, but a culture-independent method capable of detecting and quantifying diverse bacteria is needed. based on our analysis of a diverse collection of 16 s rrna gene sequences, we designed a broad-coverage quantitative real-time pcr (qpcr) assay--bactquant--for quantifying 16 s rrna gene copy number and estimating bacterial load. we further utilized in silico evaluation to complement laboratory-based qpcr characte ... | 2012 | 22510143 |
| a blueprint for a mutationist theory of replicative strand asymmetries formation. | in the present review, we summarized current knowledge on replicative strand asymmetries in prokaryotic genomes. a cornerstone for the creation of a theory of their formation has been overviewed. according to our recent works, the probability of nonsense mutation caused by replication-associated mutational pressure is higher for genes from lagging strands than for genes from leading strands of both bacterial and archaeal genomes. lower density of open reading frames in lagging strands can be exp ... | 2012 | 22942675 |
| acyl carrier protein structural classification and normal mode analysis. | all acyl carrier protein primary and tertiary structures were gathered into the thyme database. they are classified into 16 families by amino acid sequence similarity, with members of the different families having sequences with statistically highly significant differences. these classifications are supported by tertiary structure superposition analysis. tertiary structures from a number of families are very similar, suggesting that these families may come from a single distant ancestor. normal ... | 2012 | 22374859 |
| biological diversity in the patent system. | biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. to address this problem we text mined 11 million patent documents for 6 million latin species names from the global names index (gni) established by the global biodiversity information facility (gbif) and encyclopedia of life (eol). we identified 76,274 full latin species names from 23,882 genera in 767,955 patent documents. 2 ... | 2013 | 24265714 |
| two homologous ef-g proteins from pseudomonas aeruginosa exhibit distinct functions. | genes encoding two proteins corresponding to elongation factor g (ef-g) were cloned from pseudomonas aeruginosa. the proteins encoded by these genes are both members of the efg i subfamily. the gene encoding one of the forms of ef-g is located in the str operon and the resulting protein is referred to as ef-g1a while the gene encoding the other form of ef-g is located in another part of the genome and the resulting protein is referred to as ef-g1b. these proteins were expressed and purified to 9 ... | 2013 | 24260360 |
| aggregate-reactivation activity of the molecular chaperone clpb from ehrlichia chaffeensis. | rickettsiale diseases, including human monocytic ehrlichiosis caused by ehrlichia chaffeensis, are the second leading cause of the tick-borne infections in the usa and a growing health concern. little is known about how e. chaffeensis survives the host-induced stress in vertebrate and tick hosts. a molecular chaperone clpb from several microorganisms has been reported to reactivate aggregated proteins in cooperation with the co-chaperones dnak/dnaj/grpe (kje). in this study, we performed the fir ... | 2013 | 23667479 |
| insight into centromere-binding properties of parb proteins: a secondary binding motif is essential for bacterial genome maintenance. | parb proteins are one of the three essential components of partition systems that actively segregate bacterial chromosomes and plasmids. in binding to centromere sequences, parb assembles as nucleoprotein structures called partition complexes. these assemblies are the substrates for the partitioning process that ensures dna molecules are segregated to both sides of the cell. we recently identified the sopc centromere nucleotides required for binding to the parb homologue of plasmid f, sopb. this ... | 2013 | 23345617 |
| evolution of the f0f1 atp synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes. | bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation and reduction, sulfate reduction, and methanogenesis. most bioenergetic pathways have a similar general ... | 2014 | 25188293 |
| card integrates three functional modules to promote efficient transcription, antibiotic tolerance, and pathogenesis in mycobacteria. | although the basic mechanisms of prokaryotic transcription are conserved, it has become evident that some bacteria require additional factors to allow for efficient gene transcription. card is an rna polymerase (rnap)-binding protein conserved in numerous bacterial species and essential in mycobacteria. despite the importance of card, its function at transcription complexes remains unclear. we have generated a panel of mutations that individually target three independent functional modules of ca ... | 2014 | 24962732 |
| preliminary x-ray crystallographic analysis of an engineered glutamyl-trna synthetase from escherichia coli. | the nature of interaction between glutamyl-trna synthetase (glurs) and its trna substrate is unique in bacteria in that many bacterial glurs are capable of recognizing two trna substrates: trnaglu and trnagln. to properly understand this distinctive glurs-trna interaction it is important to pursue detailed structure-function studies; however, because of the fact that trna-glurs interaction in bacteria is also associated with phylum-specific idiosyncrasies, the structure-function correlation stud ... | 2014 | 25005090 |
| ge23077 binds to the rna polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides. | using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic ge23077 (ge) binds directly to the bacterial rna polymerase (rnap) active-center 'i' and 'i+1' nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. the target-based resistance spectrum for ge is unusually small, reflecting the fact that the ge binding site on rnap includes residues of the rnap active center that ... | 2014 | 24755292 |
| superoxide dismutases and superoxide reductases. | | 2014 | 24684599 |
| long-term survival of borrelia burgdorferi lacking the hibernation promotion factor homolog in the unfed tick vector. | borrelia burgdorferi, a causative agent of lyme borreliosis, is a zoonotic pathogen that survives in nutrient-limited environments within a tick, prior to transmission to its mammalian host. survival under these prolonged nutrient-limited conditions is thought to be similar to survival during stationary phase, which is characterized by growth cessation and decreased protein production. multiple ribosome-associated proteins are implicated in stationary-phase survival of escherichia coli. these pr ... | 2015 | 26438790 |
| the borrelia afzelii outer membrane protein bapko_0422 binds human factor-h and is predicted to form a membrane-spanning β-barrel. | the deep evolutionary history of the spirochetes places their branch point early in the evolution of the diderms, before the divergence of the present day proteobacteria. as a spirochete, the morphology of the borrelia cell envelope shares characteristics of both gram-positive and gram-negative bacteria. a thin layer of peptidoglycan, tightly associated with the cytoplasmic membrane, is surrounded by a more labile outer membrane (om). this om is rich in lipoproteins but with few known integral m ... | 2015 | 26181365 |
| acylation of biomolecules in prokaryotes: a widespread strategy for the control of biological function and metabolic stress. | acylation of biomolecules (e.g., proteins and small molecules) is a process that occurs in cells of all domains of life and has emerged as a critical mechanism for the control of many aspects of cellular physiology, including chromatin maintenance, transcriptional regulation, primary metabolism, cell structure, and likely other cellular processes. although this review focuses on the use of acetyl moieties to modify a protein or small molecule, it is clear that cells can use many weak organic aci ... | 2015 | 26179745 |
| structure-function dissection of myxococcus xanthus card n-terminal domain, a defining member of the card_cdnl_trcf family of rna polymerase interacting proteins. | two prototypes of the large card_cdnl_trcf family of bacterial rna polymerase (rnap)-binding proteins, myxococcus xanthus card and cdnl, have distinct functions whose molecular basis remain elusive. card, a global regulator linked to the action of several extracytoplasmic function (ecf) σ-factors, binds to the rnap β subunit (rnap-β) and to protein carg via an n-terminal domain, cardnt, and to dna via an intrinsically unfolded c-terminal domain resembling eukaryotic high-mobility-group a (hmga) ... | 2015 | 25811865 |
| complete genome sequence and description of salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat. | during a study of the anaerobic microbial community of a lithifying hypersaline microbial mat of lake 21 on the kiritimati atoll (kiribati republic, central pacific) strain l21-rpul-d2(t) was isolated. the closest phylogenetic neighbor was spirochaeta africana z-7692(t) that shared a 16s rrna gene sequence identity value of 90% with the novel strain and thus was only distantly related. a comprehensive polyphasic study including determination of the complete genome sequence was initiated to chara ... | 2015 | 26203324 |
| the nucleotide excision repair pathway protects borrelia burgdorferi from nitrosative stress in ixodes scapularis ticks. | the lyme disease spirochete borrelia burgdorferi encounters a wide range of environmental conditions as it cycles between ticks of the genus ixodes and its various mammalian hosts. reactive oxygen species (ros) and reactive nitrogen species (rns) are potent antimicrobial molecules generated during the innate immune response to infection, however, it is unclear whether ros and rns pose a significant challenge to b. burgdorferi in vivo. in this study, we screened a library of b. burgdorferi strain ... | 2016 | 27656169 |
| challenges with using names to link digital biodiversity information. | | 2016 | 27346955 |
| independent evolution of six families of halogenating enzymes. | halogenated natural products are widespread in the environment, and the halogen atoms are typically vital to their bioactivities. thus far, six families of halogenating enzymes have been identified: cofactor-free haloperoxidases (hpo), vanadium-dependent haloperoxidases (v-hpo), heme iron-dependent haloperoxidases (hi-hpo), non-heme iron-dependent halogenases (ni-hg), flavin-dependent halogenases (f-hg), and s-adenosyl-l-methionine (sam)-dependent halogenases (s-hg). however, these halogenating ... | 2016 | 27153321 |
| bacterial gcn5-related n-acetyltransferases: from resistance to regulation. | the gcn5-related n-acetyltransferases family (gnat) is an important family of proteins that includes more than 100000 members among eukaryotes and prokaryotes. acetylation appears as a major regulatory post-translational modification and is as widespread as phosphorylation. n-acetyltransferases transfer an acetyl group from acetyl-coa to a large array of substrates, from small molecules such as aminoglycoside antibiotics to macromolecules. acetylation of proteins can occur at two different posit ... | 2016 | 26818562 |
| neisseria meningitidis translation elongation factor p and its active-site arginine residue are essential for cell viability. | translation elongation factor p (ef-p), a ubiquitous protein over the entire range of bacterial species, rescues ribosomal stalling at consecutive prolines in proteins. in escherichia coli and salmonella enterica, the post-translational β-lysyl modification of lys34 of ef-p is important for the ef-p activity. the β-lysyl ef-p modification pathway is conserved among only 26-28% of bacteria. recently, it was found that the shewanella oneidensis and pseudomonas aeruginosa ef-p proteins, containing ... | 2016 | 26840407 |
| hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. | enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of > 80 degrees c), also called hyperthermophilic enzymes, are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures. these enzymes share the same catalytic mechanisms with their mesophilic counterparts. when cloned and expressed in mesophilic hosts, hyperthermophilic enzymes usually retain their thermal properties, ind ... | 2001 | 11238984 |
| the tmrdb and srpdb resources. | 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 royal veterinary and agricultural university, denmark (http://tmrdb.kvl.dk/). the signal recognition particle database (srpdb) at http://psyche.uthct.edu/dbs/srpdb/srpdb.html is mirrored at http://srpdb.kvl.dk/ an ... | 2006 | 16381838 |
| the tmrdb and srpdb resources. | 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 royal veterinary and agricultural university, denmark (http://tmrdb.kvl.dk/). the signal recognition particle database (srpdb) at http://psyche.uthct.edu/dbs/srpdb/srpdb.html is mirrored at http://srpdb.kvl.dk/ an ... | 2006 | 16381838 |
| potential and utilization of thermophiles and thermostable enzymes in biorefining. | in today's world, there is an increasing trend towards the use of renewable, cheap and readily available biomass in the production of a wide variety of fine and bulk chemicals in different biorefineries. biorefineries utilize the activities of microbial cells and their enzymes to convert biomass into target products. many of these processes require enzymes which are operationally stable at high temperature thus allowing e.g. easy mixing, better substrate solubility, high mass transfer rate, and ... | 2007 | 17359551 |
| 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 |
| a predictive model of intein insertion site for use in the engineering of molecular switches. | inteins are intervening protein domains with self-splicing ability that can be used as molecular switches to control activity of their host protein. successfully engineering an intein into a host protein requires identifying an insertion site that permits intein insertion and splicing while allowing for proper folding of the mature protein post-splicing. by analyzing sequence and structure based properties of native intein insertion sites we have identified four features that showed significant ... | 2012 | 22649521 |
| carbohydrate metabolism in archaea: current insights into unusual enzymes and pathways and their regulation. | the metabolism of archaea, the third domain of life, resembles in its complexity those of bacteria and lower eukarya. however, this metabolic complexity in archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. instead, archaea are characterized by the presence of unique, modified variants of classical pathways such as the embden-meyerhof-parnas (emp) pathway and the entner-doudoroff (ed) pathway. the pentose phosphate pathway is only ... | 2014 | 24600042 |
| recent advances in in vivo applications of intein-mediated protein splicing. | intein-mediated protein splicing has become an essential tool in modern biotechnology. fundamental progress in the structure and catalytic strategies of cis- and trans-splicing inteins has led to the development of modified inteins that promote efficient protein purification, ligation, modification and cyclization. recent work has extended these in vitro applications to the cell or to whole organisms. we review recent advances in intein-mediated protein expression and modification, post-translat ... | 2014 | 24490831 |
| global association between thermophilicity and vancomycin susceptibility in bacteria. | exploration of the aquatic microbiota of several circum-neutral (6.0-8.5 ph) mid-temperature (55-85°c) springs revealed rich diversities of phylogenetic relatives of mesophilic bacteria, which surpassed the diversity of the truly-thermophilic taxa. to gain insight into the potentially-thermophilic adaptations of the phylogenetic relatives of gram-negative mesophilic bacteria detected in culture-independent investigations we attempted pure-culture isolation by supplementing the enrichment media w ... | 2016 | 27065976 |
| comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms. | understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. while multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. in this work we compare equivalent clusters of spatially neighboring residues between paired thermophili ... | 2016 | 26741367 |
| flagellin glycosylation in paenibacillus alvei ccm 2051t. | flagellin glycosylation impacts, in several documented cases, the functionality of bacterial flagella. the basis of flagellin glycosylation has been studied for various gram-negative bacteria, but less is known about flagellin glycans of gram-positive bacteria including paenibacillus alvei, a secondary invader of honeybee colonies diseased with european foulbrood. paenibacillus alvei ccm 2051(t) swarms vigorously on solidified culture medium, with swarming relying on functional flagella as evide ... | 2016 | 26405108 |
| flagellin glycosylation in paenibacillus alvei ccm 2051t. | flagellin glycosylation impacts, in several documented cases, the functionality of bacterial flagella. the basis of flagellin glycosylation has been studied for various gram-negative bacteria, but less is known about flagellin glycans of gram-positive bacteria including paenibacillus alvei, a secondary invader of honeybee colonies diseased with european foulbrood. paenibacillus alvei ccm 2051(t) swarms vigorously on solidified culture medium, with swarming relying on functional flagella as evide ... | 2016 | 26405108 |
| structural, bioinformatic, and in vivo analyses of two treponema pallidum lipoproteins reveal a unique trap transporter. | treponema pallidum, the bacterial agent of syphilis, is predicted to encode one tripartite atp-independent periplasmic transporter (trap-t). trap-ts typically employ a periplasmic substrate-binding protein (sbp) to deliver the cognate ligand to the transmembrane symporter. herein, we demonstrate that the genes encoding the putative trap-t components from t. pallidum, tp0957 (the sbp), and tp0958 (the symporter), are in an operon with an uncharacterized third gene, tp0956. we determined the cryst ... | 2012 | 22306465 |
| 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 |
| small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold. | the beta-grasp fold (beta-gf), prototyped by ubiquitin (ub), has been recruited for a strikingly diverse range of biochemical functions. these functions include providing a scaffold for different enzymatic active sites (e.g. nudix phosphohydrolases) and iron-sulfur clusters, rna-soluble-ligand and co-factor-binding, sulfur transfer, adaptor functions in signaling, assembly of macromolecular complexes and post-translational protein modification. to understand the basis for the functional versatil ... | 2007 | 17605815 |
| a homolog of glyceraldehyde-3-phosphate dehydrogenase from riemerella anatipestifer is an extracellular protein and exhibits biological activity. | riemerella anatipestifer is the causative agent of septicemia anserum exsudativa in ducks. its pathogenesis and virulence factors are still unclear. the glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase (gapdh), an anchorless and multifunctional protein on the surface of several pathogenic microorganisms, is involved in virulence and adhesion. whether homologs of gapdh exist, and display similar characteristics in r. anatipestifer (ragapdh) has not been determined. in our research, the ... | 2014 | 25183032 |
| gbtools: interactive visualization of metagenome bins in r. | improvements in dna sequencing technology have increased the amount and quality of sequences that can be obtained from metagenomic samples, making it practical to extract individual microbial genomes from metagenomic assemblies ("binning"). however, while many tools and methods exist for unsupervised binning with various statistical algorithms, there are few options for visualizing the results, even though visualization is vital to exploratory data analysis. we have developed gbtools, a software ... | 2015 | 26732662 |
| crispr-mediated epigenome editing. | mounting evidence has called into question our understanding of the role that the central dogma of molecular biology plays in human pathology. the conventional view that elucidating the mechanisms for translating genes into proteins can account for a panoply of diseases has proven incomplete. landmark studies point to epigenetics as a missing piece of the puzzle. however, technological limitations have hindered the study of specific roles for histone post-translational modifications, dna modific ... | 2016 | 28018139 |
| a comprehensive benchmarking study of protocols and sequencing platforms for 16s rrna community profiling. | in the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. the most common phylogenetic marker for microbial community diversity studies is the 16s ribosomal rna gene and in the last 10 years the field h ... | 2016 | 26763898 |
| capreomycin susceptibility is increased by tlya-directed 2'-o-methylation on both ribosomal subunits. | the binding site of the cyclic peptide antibiotics capreomycin and viomycin is located on the ribosomal subunit interface close to nucleotides c1409 in 16s rrna and c1920 in 23s rrna. in mycobacterium tuberculosis, the 2'-hydroxyls of both nucleotides are methylated by the enzyme tlya. loss of these methylations through inactivation of tlya confers resistance to capreomycin and viomycin. we report here that tlya orthologues occur in diverse bacteria and fall into two distinct groups. one group, ... | 2012 | 22779429 |
| crystallographic characterization of the ribosomal binding site and molecular mechanism of action of hygromycin a. | hygromycin a (hyga) binds to the large ribosomal subunit and inhibits its peptidyl transferase (pt) activity. the presented structural and biochemical data indicate that hyga does not interfere with the initial binding of aminoacyl-trna to the a site, but prevents its subsequent adjustment such that it fails to act as a substrate in the pt reaction. structurally we demonstrate that hyga binds within the peptidyl transferase center (ptc) and induces a unique conformation. specifically in its ribo ... | 2015 | 26464437 |
| distinct trna accommodation intermediates observed on the ribosome with the antibiotics hygromycin a and a201a. | the increase in multi-drug-resistant bacteria is limiting the effectiveness of currently approved antibiotics, leading to a renewed interest in antibiotics with distinct chemical scaffolds. we have solved the structures of the thermus thermophilus 70s ribosome with a-, p-, and e-site trnas bound and in complex with either the aminocyclitol-containing antibiotic hygromycin a (hyga) or the nucleoside antibiotic a201a. both antibiotics bind at the peptidyl transferase center and sterically occlude ... | 2015 | 26028538 |
| 16s rrna gene mutations associated with decreased susceptibility to tetracycline in mycoplasma bovis. | mycoplasma bovis isolates with decreased susceptibilities to tetracyclines are increasingly reported worldwide. the acquired molecular mechanisms associated with this phenomenon were investigated in 70 clinical isolates of m. bovis. sequence analysis of the two 16s rrna-encoding genes (rrs3 and rrs4 alleles) containing the primary binding pocket for tetracycline (tet-1 site) was performed on isolates with tetracycline hydrochloride mics of 0.125 to 16 μg/ml. mutations at positions a965t, a967t/c ... | 2015 | 25403668 |
| the novel aminomethylcycline omadacycline has high specificity for the primary tetracycline-binding site on the bacterial ribosome. | omadacycline is an aminomethylcycline antibiotic with potent activity against many gram-positive and gram-negative pathogens, including strains carrying the major efflux and ribosome protection resistance determinants. this makes it a promising candidate for therapy of severe infectious diseases. omadacycline inhibits bacterial protein biosynthesis and competes with tetracycline for binding to the ribosome. its interactions with the 70s ribosome were, therefore, analyzed in great detail and comp ... | 2016 | 27669321 |
| comparative analysis of the regulation of expression and structures of two evolutionarily divergent genes for delta1-pyrroline-5-carboxylate synthetase from tomato. | we isolated two tomato (lycopersicon esculentum) cdna clones, tompro1 and tompro2, specifying delta1-pyrroline-5-carboxylate synthetase (p5cs), the first enzyme of proline (pro) biosynthesis. tompro1 is unusual because it resembles prokaryotic polycistronic operons (m.g. garcía-ríos, t. fujita, p.c. larosa, r.d. locy, j.m. clithero, r.a. bressan, l.n. csonka [1997] proc natl acad sci usa 94: 8249-8254), whereas tompro2 encodes a full-length p5cs. we analyzed the accumulation of pro and the tompr ... | 1998 | 9765552 |
| search and discovery strategies for biotechnology: the paradigm shift. | profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. the advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. in this ... | 2000 | 10974127 |
| the archaeal origins of the eukaryotic translational system. | among the 78 eukaryotic ribosomal proteins, eleven are specific to eukarya, 33 are common only to archaea and eukarya and 34 are homologous (at least in part) to those of both bacteria and archaea. several other translational proteins are common only to eukarya and archaea (e.g., if2a, srp19, etc.), whereas others are shared by the three phyla (e.g., eftu/ef1a and srp54). although this and other analyses strongly support an archaeal origin for a substantial fraction of the eukaryotic translation ... | 2005 | 16877317 |
| the archaeal origins of the eukaryotic translational system. | among the 78 eukaryotic ribosomal proteins, eleven are specific to eukarya, 33 are common only to archaea and eukarya and 34 are homologous (at least in part) to those of both bacteria and archaea. several other translational proteins are common only to eukarya and archaea (e.g., if2a, srp19, etc.), whereas others are shared by the three phyla (e.g., eftu/ef1a and srp54). although this and other analyses strongly support an archaeal origin for a substantial fraction of the eukaryotic translation ... | 2005 | 16877317 |
| inhibition of bacterial rna polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. | we define the target, mechanism, and structural basis of inhibition of bacterial rna polymerase (rnap) by the tetramic acid antibiotic streptolydigin (stl). stl binds to a site adjacent to but not overlapping the rnap active center and stabilizes an rnap-active-center conformational state with a straight-bridge helix. the results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix rnap-active-center conformations exist and that cycling between st ... | 2005 | 16122422 |
| the application of fast-nmr for the identification of novel drug discovery targets. | the continued success of genome sequencing projects has resulted in a wealth of information, but 40-50% of identified genes correspond to hypothetical proteins or proteins of unknown function. the functional annotation screening technology by nmr (fast-nmr) screen was developed to assign a biological function for these unannotated proteins with a structure solved by the protein structure initiative. fast-nmr is based on the premise that a biological function can be described by a similarity in b ... | 2008 | 18275915 |
| comphy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets. | with the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. we developed a new tool comphy, 'composite distance phylogeny', based on a composite distance matrix calculated from the comparison of complete gene sets between genome pairs to produce a prokaryotic phylogeny. | 2009 | 19208152 |
| diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. | the yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. sensitivity and selectivity have improved because of various technical tricks and experimental designs. here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment comp ... | 2012 | 22688816 |
| cellular function and molecular structure of ecto-nucleotidases. | ecto-nucleotidases play a pivotal role in purinergic signal transmission. they hydrolyze extracellular nucleotides and thus can control their availability at purinergic p2 receptors. they generate extracellular nucleosides for cellular reuptake and salvage via nucleoside transporters of the plasma membrane. the extracellular adenosine formed acts as an agonist of purinergic p1 receptors. they also can produce and hydrolyze extracellular inorganic pyrophosphate that is of major relevance in the c ... | 2012 | 22555564 |
| on the molecular mechanism of gc content variation among eubacterial genomes. | as a key parameter of genome sequence variation, the gc content of bacterial genomes has been investigated for over half a century, and many hypotheses have been put forward to explain this gc content variation and its relationship to other fundamental processes. previously, we classified eubacteria into dnae-based groups (the dimeric combination of dna polymerase iii alpha subunits), according to a hypothesis where gc content variation is essentially governed by genome replication and dna repai ... | 2012 | 22230424 |
| accommodation of profound sequence differences at the interfaces of eubacterial rna polymerase multi-protein assembly. | evolutionarily divergent proteins have been shown to change their interacting partners. rna polymerase assembly is one of the rare cases which retain its component proteins in the course of evolution. this ubiquitous molecular assembly, involved in transcription, consists of four core subunits (alpha, beta, betaprime, and omega), which assemble to form the core enzyme. remarkably, the orientation of the four subunits in the complex is conserved from prokaryotes to eukaryotes although their seque ... | 2012 | 22359428 |
| card uses a minor groove wedge mechanism to stabilize the rna polymerase open promoter complex. | a key point to regulate gene expression is at transcription initiation, and activators play a major role. card, an essential activator in mycobacterium tuberculosis, is found in many bacteria, including thermus species, but absent in escherichia coli. to delineate the molecular mechanism of card, we determined crystal structures of thermus transcription initiation complexes containing card. the structures show card interacts with the unique dna topology presented by the upstream double-stranded/ ... | 2015 | 26349034 |
| structural basis for methyl-donor-dependent and sequence-specific binding to trna substrates by knotted methyltransferase trmd. | the deep trefoil knot architecture is unique to the spou and trna methyltransferase d (trmd) (spout) family of methyltransferases (mtases) in all three domains of life. in bacteria, trmd catalyzes the n(1)-methylguanosine (m(1)g) modification at position 37 in transfer rnas (trnas) with the (36)gg(37) sequence, using s-adenosyl-l-methionine (adomet) as the methyl donor. the m(1)g37-modified trna functions properly to prevent +1 frameshift errors on the ribosome. here we report the crystal struct ... | 2015 | 26183229 |
| recent functional insights into the role of (p)ppgpp in bacterial physiology. | the alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppgpp) are involved in regulating growth and several different stress responses in bacteria. in recent years, substantial progress has been made in our understanding of the molecular mechanisms of (p)ppgpp metabolism and (p)ppgpp-mediated regulation. in this review, we summarize these recent insights, with a focus on the molecular mechanisms governing the activity of the rela/spot homologue (rsh) ... | 2015 | 25853779 |
| superpose3d: a local structural comparison program that allows for user-defined structure representations. | local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. the outcome of such analyses is critically dependent on the representation used to describe the structure. indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. we have therefore developed superpose3d, a novel structural comparison softw ... | 2010 | 20700534 |
| 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 |
| characterization of the genome, proteome, and structure of yersiniophage ϕr1-37. | the bacteriophage vb_yecm-ϕr1-37 (ϕr1-37) is a lytic yersiniophage that can propagate naturally in different yersinia species carrying the correct lipopolysaccharide receptor. this large-tailed phage has deoxyuridine (du) instead of thymidine in its dna. in this study, we determined the genomic sequence of phage ϕr1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. t ... | 2012 | 22973030 |
| mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes. | the sizes of proteins are relevant to their biochemical structure and for their biological function. the statistical distribution of protein lengths across a diverse set of taxa can provide hints about the evolution of proteomes. | 2012 | 22296664 |