Microbial & comparative genomics最新文献

{"title":"Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes.","authors":"T Gaasterland,&nbsp;M A Ragan","doi":"10.1089/omi.1.1998.3.199","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.199","url":null,"abstract":"<p><p>We have implemented a statistically based approach to comparative genomics that allows us to define and characterize distributional patterns of conceptually translated open reading frames (ORFs) at different confidence levels based on pairwise FASTA matches. In this report, we apply this methodology to nine microbial genomes, focusing particularly on phyletic and functional patterns of ORF distribution within and between the two prokaryotic domains of life, Bacteria and Archaea. We examine patterns of presence and absence of matches, determine the universal ORF set, analyze features of genome specialization between closely related organisms, and present genomic evidence for the monophyly of Archaea. These analyses illustrate how a quantitative approach to comparative genomics can illuminate questions of fundamental biological significance.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.199","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20901972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Tenth International Genome Sequencing and Analysis Conference, Miami Beach, Florida, September 17-20, 1998.","authors":"D J Doyle","doi":"10.1089/omi.1.1998.3.255","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.255","url":null,"abstract":"","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.255","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20901938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Yeast \"operons\".","authors":"X Zhang,&nbsp;T F Smith","doi":"10.1089/omi.1.1998.3.133","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.133","url":null,"abstract":"<p><p>To achieve coordinate gene regulation, yeast (Saccharomyces cerevisiae) appears to have exploited two distinct multifunction \"operon\" schemas: one, by concatenating originally separate functional domains into single polypeptides, and two, by linking opposite strand genes through common promoter elements. For example, distinct functions found in bacterial operons are often concatenated in yeast. A selective advantage, similar to that for bringing multiple related functions into a single peptide, may also explain the large numbers of yeast opposite-strand, ORF pairs sharing a common regulatory region.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.133","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20613819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping chicken genes using preferential amplification of specific alleles.","authors":"E J Smith,&nbsp;H H Cheng","doi":"10.1089/omi.1.1998.3.13","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.13","url":null,"abstract":"<p><p>To map the chicken genome, an international reference population was developed at our laboratory (East Lansing, MI) using an F2 backcross between inbred jungle fowl (JF) and inbred white leghorns (WL). To augment the number of type I genes on the East Lansing (E) map, segregation of the JF-specific allele was followed using preferential amplification of specific alleles (PASA) in polymerase chain reactions (PCR). Among 15 functional genes that were added to the E map, agrin and mannose-6-phosphate receptor genes were found to occur in conserved syntenic groups. Using this PCR-based approach, six conserved groups spanning more than 243 centimorgans (cM) in the chicken were syntenic with human and mouse.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21847046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Relationship between codon usage and sequence-dependent curvature of genomes.","authors":"R Jáuregui,&nbsp;F O'Reilly,&nbsp;F Bolivar,&nbsp;E Merino","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Static DNA curvature distributions of full-sequenced genomes and large DNA contigs from different organisms were calculated. Very distinctive differences among histogram profiles coming from archaebacteria, eubacteria, and eukaryotes were observed. Eubacterial profiles were, on average, more curved than were archaeal and eukaryotic profiles. A comparative analysis between real and randomized DNA sequences revealed that eubacterial genomes presented, overall, higher curvature values than random sequences. An opposite portrait was exhibited by archaeal and eukaryotic genomes. They displayed a lower frequency of curved regions than their corresponding randomized sequences. The contributions of coding and intergenic regions to the curvature profile were also analyzed. Intergenic regions, on average, were found to be more curved than the overall genomic sequences, especially in prokaryotic organisms. Nevertheless, because of their small size with respect to coding regions, the contribution of intergenic sequences to the overall curvature profile tended to be minor. A clear relationship between codon usage and DNA curvature was demonstrated, and a proposal of the possible coevolution of both systems is discussed. Finally, we present a procedure to quantify the deviation of a curvature profile from randomness through a formal statistical analysis.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20901937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial genescapes: a prokaryotic view of the yeast genome.","authors":"M A Ragan,&nbsp;T Gaasterland","doi":"10.1089/omi.1.1998.3.219","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.219","url":null,"abstract":"<p><p>We examine the translated open reading frames (ORFs) of the yeast Saccharomyces cerevisiae, focusing on those that have FASTA matches in phyletically defined sets of completely sequenced genomes. On this basis, we identify archaeal yeast, bacterial yeast, universal yeast, and yeast ORFs that do not have a match in any of nine prokaryote genomes. Similarly, we examine the yeast mitochondrial genome and the subset of the yeast nuclear ORFs identified as being involved in mitochondrial biogenesis. For the yeast ORFs that match one or more ORFs in these prokaryote genomes, we examine the phyletic and functional distributions of these matches as a function of match strength. These results provide genome level insights into the origin of the eukaryotic cell and the origin of mitochondria. More generally, they exemplify how the growing database of prokaryote genome sequences can help us understand eukaryote genomes.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.219","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20901973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Horizontal transfer of chromosomal DNA between the marine bacterium Vibrio furnissii and Escherichia coli revealed by sequence analysis.","authors":"A Charbit,&nbsp;N Autret","doi":"10.1089/omi.1.1998.3.119","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.119","url":null,"abstract":"<p><p>Previous in silico analysis of the 67.4-76.0 minutes region of the Escherichia coli genome led to the identification of a gene cluster (named aga) comprising five genes encoding homologs of the mannose transporter of E. coli, a member of the sugar-specific phosphoenolypyruvate/sugar phosphotransferase system (PTS). In the present work, we compared the aga gene cluster of E. coli, which has been considered to be involved in N-acetylgalactosamine or N-acetylmannosamine transport and metabolism, to the region comprising the recently identified mannose transporter of the marine bacterium Vibrio furnissii. Our analysis revealed that the proteins encoded by three genes (agaV, agaW, and agaA), located in the proximal portion of the aga gene cluster, shared striking similarities with the proteins encoded by the manX (IIBMan), manY (IICMan), and manD (a putative deacetylase) genes of V. furnissii, respectively (70%-82.3% identity among the three pairs of proteins). Moreover, we found that the two following aga genes (agaS and agaY) were homologous to the sequences flanking the mannose operon of V. furnissii. These observations strongly support the idea of a horizontal transfer of the chromosomally encoded man operon of V. furnissii into the E. coli genome.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.119","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20613818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The CorA magnesium transporter gene family.","authors":"D G Kehres,&nbsp;C H Lawyer,&nbsp;M E Maguire","doi":"10.1089/omi.1.1998.3.151","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.151","url":null,"abstract":"<p><p>The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli. The CorA protein has no homology to any other known family of proteins. It has an unusual membrane topology, with a large, soluble, highly charged periplasmic N-terminal domain with three transmembrane segments in a shorter, hydrophobic C-terminal domain. Previous phenotypic and molecular data had suggested that this transport system was widespread in the Bacteria. In this report we show that CorA is virtually ubiquitous in the Bacteria and Archaea, forming a distinct family of transport proteins. Genomic sequences to date have revealed at least 22 members of the CorA family in the Bacteria and the Archaea, with 6 more distant members in the yeasts. Only three of the smallest bacterial genomes lack a CorA homologue. Strikingly, phylogenetic analysis does not show clustering by related species or even within kingdom. Several species of Bacteria contain two or even three CorA paralogues. Within species, these paralogues are not closely related, however, and we suggest that they might have distinct transport functions. A multiple alignment suggests three extended consensus regions within the N-terminal soluble domain of CorA, which is predicted to be virtually all alpha-helical. A fourth consensus region includes the last 20 residues of the soluble domain and continues through the entire membrane domain. The first half of this last consensus domain may form an amphipathic alpha-helix that extends from the soluble domain into the first transmembrane segment. The degree of charge in the first transmembrane segment is quite variable, and we suggest that this transport family may include members with only two rather than three transmembrane segments. If so, this would place the N-terminal soluble domain on different sides of the membrane in different members of the family. We suggest that the CorA Mg2+ transport system forms the major Mg2+ uptake system in the Bacteria and Archaea but that some family members may have a function other than Mg2+ transport.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.151","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20688591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tenth International Genome Sequencing and Analysis Conference. Miami Beach, Florida, USA. September 17-20, 1998. Proceedings and abstracts.","authors":"","doi":"10.1089/omi.1.1998.3.149","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.149","url":null,"abstract":"","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.149","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20688590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assignment of folds for proteins of unknown function in three microbial genomes.","authors":"I Dubchak,&nbsp;I Muchnik,&nbsp;S H Kim","doi":"10.1089/omi.1.1998.3.171","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.171","url":null,"abstract":"<p><p>Analysis of DNA sequences of several microbial genomes has revealed that a large fraction of predicted coding regions has no known protein function. Information about the three-dimensional folds of these proteins may provide insight into their possible functions. To predict the folds for protein sequences with little or no homology to proteins of known function, we used computational neural networks trained on the database of proteins with known three-dimensional structures. Global descriptions of protein sequences based on physical and structural properties of the constituent amino acids were used as inputs for neural networks. Of the 131, 498, and 868 protein sequences of unknown function from Mycoplasma genitalium, Haemophilus influenzae, and Methanococcus jannaschii (Fleischmann et al. 1995), we have made high-confidence fold assignments for 4, 10, and 19 sequences, respectively.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1998-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1998.3.171","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20688592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}