RESUMEN
The human genome was analyzed for evidence that genes had been laterally transferred into the genome from prokaryotic organisms. Protein sequence comparisons of the proteomes of human, fruit fly, nematode worm, yeast, mustard weed, eukaryotic parasites, and all completed prokaryote genomes were performed, and all genes shared between human and each of the other groups of organisms were collected. About 40 genes were found to be exclusively shared by humans and bacteria and are candidate examples of horizontal transfer from bacteria to vertebrates. Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation.
Asunto(s)
Evolución Biológica , Transferencia de Gen Horizontal , Genes Bacterianos , Genoma Humano , Animales , Arabidopsis/genética , Bacterias/genética , Caenorhabditis elegans/genética , Biología Computacional , Bases de Datos Factuales , Drosophila melanogaster/genética , Genoma , Humanos , Invertebrados/genética , Parásitos/genética , Filogenia , Plantas/genética , Proteoma , Saccharomyces cerevisiae/genética , Vertebrados/genéticaRESUMEN
The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.
Asunto(s)
Genoma Bacteriano , Análisis de Secuencia de ADN , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/patogenicidad , Antígenos Bacterianos , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/inmunología , Proteínas Bacterianas/metabolismo , Vacunas Bacterianas , Composición de Base , Metabolismo de los Hidratos de Carbono , Proteínas Portadoras/genética , Proteínas Portadoras/metabolismo , Cromosomas Bacterianos/genética , Biología Computacional , Elementos Transponibles de ADN , ADN Bacteriano/química , ADN Bacteriano/genética , Duplicación de Gen , Genes Bacterianos , Hexosaminas/metabolismo , Análisis de Secuencia por Matrices de Oligonucleótidos , Recombinación Genética , Secuencias Repetitivas de Ácidos Nucleicos , Especificidad de la Especie , Streptococcus pneumoniae/inmunología , Streptococcus pneumoniae/metabolismo , Virulencia , Operón de ARNrRESUMEN
The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont Sinorhizobium meliloti suggest a recent evolutionary divergence. Their similarities include metabolic, transport, and regulatory systems that promote survival in the highly competitive rhizosphere; differences are apparent in their genome structure and virulence gene complement. Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles.
Asunto(s)
Agrobacterium tumefaciens/genética , Genoma Bacteriano , Análisis de Secuencia de ADN , Agrobacterium tumefaciens/clasificación , Agrobacterium tumefaciens/patogenicidad , Agrobacterium tumefaciens/fisiología , Adhesión Bacteriana/genética , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas Portadoras/genética , Proteínas Portadoras/metabolismo , Cromosomas Bacterianos/genética , Conjugación Genética , Replicación del ADN , Genes Bacterianos , Genes Reguladores , Proteínas de la Membrana/genética , Proteínas de la Membrana/metabolismo , Datos de Secuencia Molecular , Filogenia , Plantas/microbiología , Plásmidos , Replicón , Rhizobiaceae/genética , Rhizobiaceae/fisiología , Sinorhizobium meliloti/genética , Sinorhizobium meliloti/fisiología , Simbiosis , Virulencia/genéticaRESUMEN
The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.
Asunto(s)
Genoma Bacteriano , Neisseria meningitidis/genética , Neisseria meningitidis/patogenicidad , Análisis de Secuencia de ADN , Variación Antigénica , Antígenos Bacterianos/inmunología , Bacteriemia/microbiología , Cápsulas Bacterianas/genética , Proteínas Bacterianas/genética , Proteínas Bacterianas/fisiología , Elementos Transponibles de ADN , Evolución Molecular , Fimbrias Bacterianas/genética , Humanos , Meningitis Meningocócica/microbiología , Infecciones Meningocócicas/microbiología , Datos de Secuencia Molecular , Mutación , Neisseria meningitidis/clasificación , Neisseria meningitidis/fisiología , Sistemas de Lectura Abierta , Operón , Filogenia , Recombinación Genética , Serotipificación , Transformación Bacteriana , Virulencia/genéticaRESUMEN
The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284, 156 base pairs. Multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of DNA damage were identified. Deinococcus radiodurans represents an organism in which all systems for DNA repair, DNA damage export, desiccation and starvation recovery, and genetic redundancy are present in one cell.
Asunto(s)
Genoma Bacteriano , Cocos Grampositivos/genética , Mapeo Físico de Cromosoma , Análisis de Secuencia de ADN , Proteínas Bacterianas/biosíntesis , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Catalasa/genética , Cromosomas Bacterianos/genética , Daño del ADN , Reparación del ADN/genética , ADN Bacteriano/genética , Metabolismo Energético , Genes Bacterianos , Cocos Grampositivos/química , Cocos Grampositivos/clasificación , Cocos Grampositivos/efectos de la radiación , Datos de Secuencia Molecular , Sistemas de Lectura Abierta , Estrés Oxidativo , Plásmidos , Tolerancia a Radiación , Secuencias Repetitivas de Ácidos Nucleicos , Superóxido Dismutasa/genética , Thermus/química , Thermus/genética , Rayos UltravioletaRESUMEN
The determination and analysis of complete genome sequences has led to the suggestion that horizontal gene transfer may be much more extensive than previously appreciated. Many of these studies, however, rely on evidence that could be generated by forces other than gene transfer including selection, variable evolutionary rates, and biased sampling.
Asunto(s)
Evolución Molecular , Transferencia de Gen Horizontal , Genoma Arqueal , Genoma Bacteriano , Modelos GenéticosRESUMEN
Genome sequence information has continued to accumulate at a spectacular pace during the past year. Details of the sequence and gene content of human chromosome 22 were published. The sequencing and annotation of the first two Arabidopsis thaliana chromosomes was completed. The sequence of chromosome 3 from Plasmodium falciparum, the second sequenced malaria chromosome, was reported, as was that of chromosome 1 from Leishmania major. The complete genomic sequences of five microbes were reported. Approaches to using data from completely sequenced microbial genomes in phylogenetic studies are being explored, as is the application of microarrays to whole genome expression analysis.
Asunto(s)
Genoma Humano , Genoma , Animales , Evolución Molecular , Humanos , FilogeniaRESUMEN
The comprehensive analysis of the genome sequence of the plant Arabidopsis thaliana has been completed recently. The genome sequence and associated analyses provide the foundations for rapid progress in many fields of plant research, such as the exploitation of genetic variation in Arabidopsis ecotypes, the assessment of the transcriptome and proteome, and the association of genome changes at the sequence level with evolutionary processes. Nevertheless, genome sequencing and analysis are only the first steps towards a new plant biology. Much remains to be done to refine the analysis of encoded genes, to define the functions of encoded proteins systematically, and to establish new generations of databases to capture and relate diverse data sets generated in widely distributed laboratories.
Asunto(s)
Arabidopsis/genética , Genoma de Planta , Arabidopsis/metabolismo , Proteínas de Plantas/fisiología , Análisis de Secuencia de ADNAsunto(s)
Adenosina Trifosfatasas , Proteínas Bacterianas/genética , Proteínas de Unión al ADN , Proteínas de Escherichia coli , Escherichia coli/genética , Genoma Bacteriano , Helicobacter pylori/genética , Redes de Comunicación de Computadores , Reparación del ADN , Escherichia coli/ultraestructura , Helicobacter pylori/ultraestructura , Proteína MutS de Unión a los Apareamientos Incorrectos del ADN , Filogenia , Programas InformáticosRESUMEN
The determination and analysis of complete genome sequences have recently enabled many major advances to be made in the area of microbial evolutionary biology. These include the determination of the first genome of a Crenarchaeota, the suggestion that horizontal gene transfer may be the rule rather than the exception, and revelations about how genomes evolve on short timescales.
Asunto(s)
Evolución Molecular , Genética Microbiana/métodos , Genómica , Archaea/genética , Bacterias/genética , Recombinación GenéticaRESUMEN
TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional identification of proteins by sequence homology. We introduce the term 'equivalog' to describe members of a set of homologous proteins that are conserved with respect to function since their last common ancestor. Related proteins are grouped into equivalog families where possible, and otherwise into protein families with other hierarchically defined homology types. TIGRFAMs currently contains over 800 protein families, available for searching or downloading at www.tigr.org/TIGRFAMs. Classification by equivalog family, where achievable, complements classification by orthology, superfamily, domain or motif. It provides the information best suited for automatic assignment of specific functions to proteins from large-scale genome sequencing projects.
Asunto(s)
Bases de Datos Factuales , Proteínas , Internet , Filogenia , Proteínas/genética , Alineación de SecuenciaRESUMEN
Halobacterium species display a variety of responses to light, including phototrophic growth, phototactic behavior, and photoprotective mechanisms. The complete genome sequence of Halobacterium species NRC-1 (Proc Natl Acad Sci USA 97: 12176-12181, 2000), coupled with the availability of a battery of methods for its analysis makes this an ideal model system for studying photobiology among the archaea. Here, we review: (1) the structure of the 2.57 Mbp Halobacterium NRC-1 genome, including a large chromosome, two minichromosomes, and 91 transposable IS elements; (2) the purple membrane regulon, which programs the accumulation of large quantities of the light-driven proton pump, bacteriorhodopsin, and allows for a period of phototrophic growth; (3) components of the sophisticated pathways for color-sensitive phototaxis; (4) the gas vesicle gene cluster, which codes for cell buoyancy organelles; (5) pathways for the production of carotenoid pigments and retinal, (6) processes for the repair of DNA damage; and (7) putative homologs of circadian rhythm regulators. We conclude with a discussion of the power of systems biology for comprehensive understanding of Halobacterium NRC-1 photobiology.
RESUMEN
The complete genome sequence has been reported for 24 microbial organisms. The genome organization and gene content of these organisms has revealed an incredible diversity. Nearly half of the open reading frames identified by these sequencing projects are for potential genes with no known biological function. Efforts to make evolutionary sense and biological sense of the gene content of these organisms have been initiated. The greatest future challenge of genomics will be to determine function for the unknown genes.
Asunto(s)
Bacterias/genética , Genoma Bacteriano , Análisis de Secuencia de ADN , Bacterias/metabolismo , Evolución Molecular , Perfilación de la Expresión Génica , Regulación Bacteriana de la Expresión GénicaRESUMEN
Using RecA as the phylogenetic marker, the relationships of the green sulfur bacterium Chlorobium tepidum and the green non-sulfur bacterium Chloroflexus aurantiacus to other eubacteria were investigated. The recA genes of the two organisms were cloned, and the resulting protein sequences aligned with 86 other eubacterial RecA sequences. Cb. tepidum was placed as the nearest relative to the Cytophaga/Flexibacter/Bacteriodes group, a relationship supported by results obtained with several phylogenetic markers. Cf. aurantiacus was placed near Chlamydia trachomatis and the high-GC Gram-positives; however, this branching pattern was not strongly supported statistically by bootstrap analyses. Possible reasons for this ambiguity are discussed.
Asunto(s)
Chlorobi/genética , Filogenia , Rec A Recombinasas/genética , Secuencia de Aminoácidos , Clonación Molecular , Genes Bacterianos/genética , Datos de Secuencia Molecular , Mapeo Restrictivo , Alineación de Secuencia , Análisis de Secuencia de ADNAsunto(s)
Células Eucariotas/virología , Transferencia de Gen Horizontal , Genoma , Glicosiltransferasas , Proteínas de la Membrana , Transferasas , Vertebrados/virología , Fenómenos Fisiológicos de los Virus , Proteínas de Xenopus , Animales , Replicación del ADN , Genes Virales , Glucuronosiltransferasa/genética , Humanos , Hialuronano Sintasas , Filogenia , Recombinación Genética , Replicación ViralRESUMEN
The ability to recognize and repair abnormal DNA structures is common to all forms of life. Studies in a variety of species have identified an incredible diversity of DNA repair pathways. Documenting and characterizing the similarities and differences in repair between species has important value for understanding the origin and evolution of repair pathways as well as for improving our understanding of phenotypes affected by repair (e.g., mutation rates, lifespan, tumorigenesis, survival in extreme environments). Unfortunately, while repair processes have been studied in quite a few species, the ecological and evolutionary diversity of such studies has been limited. Complete genome sequences can provide potential sources of new information about repair in different species. In this paper, we present a global comparative analysis of DNA repair proteins and processes based upon the analysis of available complete genome sequences. We use a new form of analysis that combines genome sequence information and phylogenetic studies into a composite analysis we refer to as phylogenomics. We use this phylogenomic analysis to study the evolution of repair proteins and processes and to predict the repair phenotypes of those species for which we now know the complete genome sequence.
Asunto(s)
ADN Glicosilasas , ADN Helicasas , ADN Ligasas/genética , Reparación del ADN/genética , Proteínas de Escherichia coli , Genes Bacterianos , Integrasas , Filogenia , Adenosina Trifosfatasas/genética , Alquilación , Proteínas Bacterianas/biosíntesis , Proteínas Bacterianas/genética , Disparidad de Par Base , Daño del ADN , ADN Nucleotidiltransferasas/genética , Replicación del ADN/genética , ADN Bacteriano/metabolismo , Proteínas de Unión al ADN/genética , ADN-Formamidopirimidina Glicosilasa , Desoxirribonucleasa (Dímero de Pirimidina) , Desoxirribonucleasas/genética , Endodesoxirribonucleasas/genética , Células Eucariotas/metabolismo , Exodesoxirribonucleasa V , Exodesoxirribonucleasas/genética , Exonucleasas/genética , Genes p53 , Genoma , Genoma Arqueal , Familia de Multigenes , N-Glicosil Hidrolasas/genética , Proteína Recombinante y Reparadora de ADN Rad52 , Recombinasas , Recombinación Genética , Respuesta SOS en Genética/genética , Serina Endopeptidasas/biosíntesis , Serina Endopeptidasas/genética , Uracil-ADN GlicosidasaAsunto(s)
Genoma Bacteriano , Thermotoga maritima/genética , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Evolución Molecular , Datos de Secuencia Molecular , Sistemas de Lectura Abierta , Filogenia , Análisis de Secuencia de ADN , Homología de Secuencia de Aminoácido , Thermotoga maritima/química , Thermotoga maritima/metabolismoRESUMEN
Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.