Microbial & comparative genomics最新文献

{"title":"Mechanisms of spiroplasma genome variation associated with SpV1-like viral DNA inferred from sequence comparisons.","authors":"U Melcher,&nbsp;Y Sha,&nbsp;F Ye,&nbsp;J Fletcher","doi":"10.1089/omi.1.1999.4.29","DOIUrl":"https://doi.org/10.1089/omi.1.1999.4.29","url":null,"abstract":"<p><p>Genomes of Spiroplasma citri strains have rearranged frequently during their evolution, partly due to multiple integrated sequences of spiroplasma viruses. To understand better the role of viral sequences in genome evolution, we examined available nucleotide sequences of viruslike elements in the S. citri chromosome. Comparison of integrated and nonintegrated sequences of spiroplasma virus SpV1-C74 DNA suggested that it is an encapsidated form of the circular transposition intermediate belonging to an insertion sequence (IS3) family member. One SpV1-C74 viral DNA fragment was identified as interrupting the remains of a DNA adenine modification methylase gene. A viral DNA insertion of SpV1-R8A2 B DNA had hallmarks of having suffered an internal deletion by a site-specific recombination system. Homologous recombination likely was responsible for several deletions within viral DNA. A homologous recombination event was inferred between part of a viral DNA insertion and a similar chromosomal sequence. Dispersed sequences from SpV1-like C4 open reading frames (ORFs) were identified as involved in a complex deletion-inversion event. Thus, SpV1-like sequences likely have altered spiroplasma genomes by inserting within active genes, destroying their function, by providing targets for site-specific recombination, by mediating deletions of sequences adjacent to their integration sites, and by providing targets for homologous recombination, leading to inversions.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1999.4.29","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21380071","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":"SST versus EST in gene recognition.","authors":"A A Mironov,&nbsp;P A Pevzner","doi":"10.1089/omi.1.1999.4.167","DOIUrl":"https://doi.org/10.1089/omi.1.1999.4.167","url":null,"abstract":"<p><p>The expressed sequence tag (EST) data provide a powerful tool for identification of transcribed DNA sequences. However, as EST are relatively short, many exons are poorly covered by EST, thus reducing the utility of EST data. Recently, signature sequence tag (SST) fingerprints were proposed as an alternative to EST fingerprints. Given a fingerprint set of probes, SST of a clone is a subset of probes from the fingerprint set that hybridize with the clone. We demonstrate that besides being a powerful technique for screening cDNA libraries, SST technology provides for very accurate gene predictions. Even with a small fingerprint set (600-800 probes), SST-based gene recognition outperforms many conventional and EST-based methods. The increase in the size of the fingerprint set to 1500 probes provides almost perfect gene recognition. Even more importantly, SST-based gene predictions miss very few exons and, therefore, provide an opportunity to bypass the cDNA sequencing step on the way from finished genomic sequence to mutation detection in gene-hunting projects. Because SST data can be obtained in a highly parallel and inexpensive way, SST technology has a potential of complementing EST technology for gene hunting.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1999.4.167","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21446714","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":"Mixed-function supraoperons that exhibit overall conservation, albeit shuffled gene organization, across wide intergenomic distances within eubacteria.","authors":"G Xie,&nbsp;T S Brettin,&nbsp;C A Bonner,&nbsp;R A Jensen","doi":"10.1089/omi.1.1999.4.5","DOIUrl":"https://doi.org/10.1089/omi.1.1999.4.5","url":null,"abstract":"<p><p>Nearly identical mixed-function supraoperons (defined as nested transcriptional units encoding gene products that function in more than one biochemical pathway) have been found recently in Pseudomonas stutzeri and Pseudomonas aeruginosa. The Pseudomonas serC(pdxF)-aroQp.pheA-hisHb-tyrAc-aroF+ ++-cmk-rpsA supraoperon encodes 3-phosphoserine aminotransferase, a bidomain chorismate mutase/prephenate dehydratase, imidazole acetol-phosphate aminotransferase, cyclohexadienyl dehydrogenase, 5-enolpyruvylshikimate 3-phosphate synthase, cytidylate kinase, and 30S ribosomal protein S1. These enzymes participate in the biosynthesis of serine, pyridoxine, histidine, phenylalanine, tyrosine, tryptophan, and aromatic pathway vitamins and cytidylic acid, in addition to the general role of RpsA in the process of protein synthesis. Features that suggest supraoperon-wide translational coupling are the highly compressed intergenic spacing (including overlapping stop and start codons), as well as possible hairpin structures in mRNA, which could sequester many of the ribosome-binding sites. The hisH-tyrA-aroF segment corresponds to the distal genes of the classic Bacillus subtilis supraoperon. Extensive comparative analysis of the member genes of both the Bacillus and Pseudomonas supraoperons from organisms represented in the entire database revealed unmistakable organizational conservation of these genes across wide phylogenetic boundaries, although considerable gene shuffling was apparent. The persistence of aroE-aroB, hisHb-tyrA-aroF, and cmk-rpsA throughout both the gram-negative and gram-positive assemblages of bacteria, but the absence in Archaea, suggests an ancestral gene organization that occurred in bacteria after the separation of the bacterial and archaeal domains. In gram-negative bacteria,the hisHb-tyrAc-aroF grouping may have been expanded (as with the Pseudomonas supraoperon) and then subsequently collapsed (as with the Escherichia serC-aroF supraoperon) via gene shuffling that is herein equated with gene fusion events.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1999.4.5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21380070","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":"Wolbachia: why these bacteria are important to genome research.","authors":"S L O'Neill","doi":"10.1089/omi.1.1999.4.159","DOIUrl":"https://doi.org/10.1089/omi.1.1999.4.159","url":null,"abstract":"","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1999.4.159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21446712","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 Genomes Conference IV: sequencing, functional characterization and comparative genomics. Chantilly, Virginia, USA. February 12-15, 2000. Abstracts.","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21583190","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":"Physical map and gene survey of the Ochrobactrum anthropi genome using bacterial artificial chromosome contigs.","authors":"J P Tomkins,&nbsp;H Miller-Smith,&nbsp;M Sasinowski,&nbsp;S Choi,&nbsp;H Sasinowska,&nbsp;M F Verce,&nbsp;D L Freedman,&nbsp;R A Dean,&nbsp;R A Wing","doi":"10.1089/omi.1.1999.4.203","DOIUrl":"https://doi.org/10.1089/omi.1.1999.4.203","url":null,"abstract":"<p><p>Bacterial artificial chromosome (BAC) clones are effective mapping and sequencing reagents for use with a wide variety of small and large genomes. This report describes research aimed at determining the genome structure of Ochrobactrum anthropi, an opportunistic human pathogen that has potential applications in biodegradation of hazardous organic compounds. A BAC library for O. anthropi was constructed that provides a 70-fold genome coverage based on an estimated genome size of 4.8 Mb. The library contains 3072 clones with an average insert size of 112 kb. High-density colony filters of the library were made, and a physical map of the genome was constructed using a hybridization without replacement strategy. In addition, 1536 BAC clones were fingerprinted with HindIII and analyzed using IMAGE and Fingerprint Contig software (FPC, Sanger Centre, U.K.). The FPC results supported the hybridization data, resulting in the formation of two major contigs representing the two major replicons of the O. anthropi genome. After determining a reduced tiling path, 138 BAC ends from the reduced tile were sequenced for a preliminary gene survey. A search of the public databases with the BLASTX algorithm resulted in 77 strong hits (E-value < 0.001), of which 89% showed similarity to a wide variety of prokaryotic genes. These results provide a contig-based physical map to assist the cloning of important genomic regions and the potential sequencing of the O. anthropi genome.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1999.4.203","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21446717","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":"Molecular cloning of the dnaK gene region from Bacillus sphaericus in the context of genomic comparisons.","authors":"S Ahmad,&nbsp;A Selvapandiyan,&nbsp;M Gasbarri,&nbsp;R K Bhatnagar","doi":"10.1089/omi.1.1999.4.47","DOIUrl":"https://doi.org/10.1089/omi.1.1999.4.47","url":null,"abstract":"<p><p>The dnaK gene region of Bacillus sphaericus was cloned as a 3.8 kb HindIII fragment and an overlapping 1.7 kb EcoRI fragment by using an internal B. sphaericus specific dnaK gene probe generated by polymerase chain reaction (PCR). Complete DNA sequencing of the two fragments revealed three complete open reading frames (ORFs). These ORFs exhibited a high degree of identity to the grpE dnaK, and dnaJ heat shock genes from other gram-positive bacteria. The order of the genes was found to be grpE-dnaK-dnaJ. Additionally, the 5'-end and 3'-end contained amino acid sequences that were homologous to the C-terminal sequence of the hrcA gene and the N-terminal sequence of ORF35 (yqeT), respectively, from Bacillus subtilis. The entire hrcA gene from B. sphaericus was then isolated by high-fidelity PCR and completely sequenced. A transcription stop site is located between the dnaK and dnaJ genes but not after the dnaJ gene. Consistent with this observation, the dnaJ gene is immediately followed by an ORF that shows a high degree of identity to ORF35 from B. subtilis, Staphylococcus aureus, and Clostridium acetobutylicum. The presence of ORF35 is not indicated in other genera representing the gram-positive bacteria. The amino acid sequence of ORF35 exhibited nearly 30% identity with the methyltransferase for large subunit ribosomal protein L11 from gram-negative Proteobacteria and the related protein from cyanobacteria, other gram-negative bacteria, and Archaea, suggesting the presence of the gene for this protein in the common ancestor of Bacteria and Archaea. The absence of the ORF35 gene in Mycobacterium tuberculosis and other gram-positive bacteria indicates that the loss of this gene must have occurred in an ancestor of other gram-positive bacteria following their divergence from the ancestor of Bacillus/Clostridium/staphylococcus lineage.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1999.4.47","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21380072","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":"Phylogenetic analyses of proton-translocating transhydrogenases.","authors":"W K Studley,&nbsp;M Yamaguchi,&nbsp;Y Hatefi,&nbsp;M H Saier","doi":"10.1089/omi.1.1999.4.173","DOIUrl":"https://doi.org/10.1089/omi.1.1999.4.173","url":null,"abstract":"<p><p>The proton-translocating nicotinamide nucleotide transhydrogenases (TH) provide a simple model for understanding chemically coupled transmembrane proton translocation. To further our understanding of TH structure-function relationships, we have identified all sequenced homologous of these vectorial enzymes and have conducted sequence comparison studies. The NAD-binding domains of TH are homologous to bacterial alanine dehydrogenases (ADH) and eukaryotic saccharopine dehydrogenases (SDH) as well as N5(carboxyethyl)-L-ornithine synthase of Lactococcus lactis and dipicolinate synthase of Bacillus subtilis. A multiple alignment, a phylogenetic tree, and two signature sequences for this family, designated the TH-ADH-SDH or TAS superfamily, have been derived. Additionally, the TH family has been characterized. Phylogenetic analyses suggested that these proteins have evolved without inter-system shuffling. However, interdomain splicing-fusion events have occurred during the evolution of several of these systems. Analyses of the multiple alignment for the TH family revealed that domain conservation occurs in the order: NADP-binding domain (domain III) > NAD-binding domain (domain I) > proton-translocating transmembrane domain (domain II). A topologic model for the proton-translocating transmembrane domain consistent with published data is presented, and a possible involvement of specific transmembrane alpha-helical segments in channel formation is suggested.</p>","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1999.4.173","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21446715","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, F. O'Reilly, F. Bolivar, E. Merino","doi":"10.1089/OMI.1.1998.3.243","DOIUrl":"https://doi.org/10.1089/OMI.1.1998.3.243","url":null,"abstract":"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.","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.1.1998.3.243","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60514227","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":"Constructing multigenome views of whole microbial genomes.","authors":"T Gaasterland,&nbsp;M A Ragan","doi":"10.1089/omi.1.1998.3.177","DOIUrl":"https://doi.org/10.1089/omi.1.1998.3.177","url":null,"abstract":"<p><p>We have designed and implemented a system to carry out cross-genome comparisons of open reading frames (ORFs) from multiple genomes. This implementation includes a genome profiling system that allows us to explore pairwise comparisons at different levels of match similarity and ask biologically motivated queries involving number and identity of ORFs, their function, functional category, distribution in genomes or in biological domains, and statistics on their matches and match families. This analysis required precise definition of new classification terms and concepts. We define the terms genomic signature, summary signature, biologic domain signature, domain class, match level, match family, and extended match family, then use these terms to define concepts, including genomically universal proteins and proteins characteristics of sets of genomes. We initiate an analysis based on automated FASTA (Pearson, 1996) comparison of 22,419 conceptually translated protein sequences from nine microbial 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.1.1998.3.177","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20688593","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}