RESUMO
Autosomal dominant hereditary spastic paraplegia (AD-HSP) is a genetically heterogeneous neurodegenerative disorder characterized by progressive spasticity of the lower limbs. Among the four loci causing AD-HSP identified so far, the SPG4 locus at chromosome 2p2-1p22 has been shown to account for 40-50% of all AD-HSP families. Using a positional cloning strategy based on obtaining sequence of the entire SPG4 interval, we identified a candidate gene encoding a new member of the AAA protein family, which we named spastin. Sequence analysis of this gene in seven SPG4-linked pedigrees revealed several DNA modifications, including missense, nonsense and splice-site mutations. Both SPG4 and its mouse orthologue were shown to be expressed early and ubiquitously in fetal and adult tissues. The sequence homologies and putative subcellular localization of spastin suggest that this ATPase is involved in the assembly or function of nuclear protein complexes.
Assuntos
Adenosina Trifosfatases/genética , Mutação , Paraplegia Espástica Hereditária/genética , Adenosina Trifosfatases/química , Adenosina Trifosfatases/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Sequência de Bases , Células Cultivadas , Clonagem Molecular , Análise Mutacional de DNA , Éxons/genética , Etiquetas de Sequências Expressas , Humanos , Íntrons/genética , Camundongos , Mitocôndrias Musculares/metabolismo , Dados de Sequência Molecular , Fosforilação Oxidativa , RNA Mensageiro/análise , RNA Mensageiro/genética , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Paraplegia Espástica Hereditária/enzimologia , Paraplegia Espástica Hereditária/metabolismo , Paraplegia Espástica Hereditária/patologia , EspastinaRESUMO
Rickettsia conorii, the aetiological agent of Mediterranean spotted fever, is an intracellular bacterium transmitted by ticks. Preliminary analyses of the nearly complete genome sequence of R. conorii have revealed 44 occurrences of a previously undescribed palindromic repeat (150 base pairs long) throughout the genome. Unexpectedly, this repeat was found inserted in-frame within 19 different R. conorii open reading frames likely to encode functional proteins. We found the same repeat in proteins of other Rickettsia species. The finding of a mobile element inserted in many unrelated genes suggests the potential role of selfish DNA in the creation of new protein sequences.
Assuntos
Proteínas de Bactérias/genética , DNA Bacteriano/genética , Sequências Repetitivas Dispersas , Fases de Leitura Aberta/genética , RNA Mensageiro/genética , Rickettsia conorii/genética , Rickettsia/genética , Proteínas de Bactérias/química , Sequência de Bases , Sequência Conservada , Evolução Molecular , Genoma Bacteriano , Dados de Sequência Molecular , Mutagênese Insercional , Conformação de Ácido Nucleico , Biossíntese de Proteínas , Conformação Proteica , Estrutura Secundária de Proteína , RNA Bacteriano/química , RNA Bacteriano/genética , RNA Bacteriano/metabolismo , RNA Mensageiro/química , RNA Mensageiro/metabolismoAssuntos
Proteínas de Helminto/genética , Doenças das Plantas/parasitologia , Solanum lycopersicum/parasitologia , Tylenchoidea/genética , Animais , Inativação Gênica , Proteínas de Helminto/metabolismo , Interferência de RNA , Tylenchoidea/classificação , Tylenchoidea/isolamento & purificação , Tylenchoidea/metabolismoRESUMO
The genome of the diploid hemiascomycetous yeast Candida tropicalis, an opportunistic human pathogen and an important organism for industrial applications, was explored by the analysis of 2541 Random Sequenced Tags (RSTs) covering about 20% of its genome. Comparison of these sequences with Saccharomyces cerevisiae and other species permitted the identification and the analysis of a total of more than 1000 novel genetic elements of C. tropicalis. Moreover, the present study confirms that in C. tropicalis, the rare CUG codon is read as a serine and not a leucine. The sequences have been deposited at EMBL with the accession numbers AL438875-AL441602.
Assuntos
Candida/genética , Genoma Fúngico , Ascomicetos/genética , Códon , Elementos de DNA Transponíveis , DNA Mitocondrial , DNA Ribossômico , Proteínas Fúngicas/genética , Código Genético , Íntrons , Dados de Sequência Molecular , Família Multigênica , Análise de Sequência de DNA , Spliceossomos/genéticaRESUMO
Saccharomyces bayanus var. uvarum investigated here is the species closest to Saccharomyces cerevisiae. Random sequence tags (RSTs) allowed us to identify homologues to 2789 open reading frames (ORFs) in S. cerevisiae, ORFs duplicated in S. uvarum but not in S. cerevisiae, centromeres, tRNAs, homologues of Ty1/2 and Ty4 retrotransposons, and a complete rDNA repeat. Only 13 RSTs seem to be homologous to sequences in other organisms but not in S. cerevisiae. As the synteny between the two species is very high, cases in which synteny is lost suggest special mechanisms of genome evolution. The corresponding RSTs revealed that S. uvarum can exist without any S. cerevisiae DNA introgression. Accession numbers are from AL397139 to AL402278 in the EMBL databank.
Assuntos
Ordem dos Genes , Genoma Fúngico , Saccharomyces/genética , Ascomicetos/genética , Centrômero , Cromossomos Fúngicos , Mapeamento de Sequências Contíguas , Dados de Sequência Molecular , Retroelementos/genética , Saccharomyces cerevisiae/genética , Análise de Sequência de DNARESUMO
Random sequence tags were obtained from a genomic DNA library of Saccharomyces exiguus. The mitochondrial genome appeared to be at least 25.7 kb in size, with a different organization compared to Saccharomyces cerevisiae. An unusual putative 953 bp long terminal repeated element associated to Ty3 was found. A set of 1451 genes was identified homologous to S. cerevisiae open reading frames. Only five genes were identified outside the S. cerevisiae taxon, confirming that S. exiguus is phylogenetically closely related to S. cerevisiae. Unexpectedly, numerous duplicated genes were found whereas they are unique in S. cerevisiae. The sequences are deposited at EMBL under the accession numbers: AL407377-AL409955.
Assuntos
Genoma Fúngico , Saccharomyces/genética , Ascomicetos/genética , Elementos de DNA Transponíveis , DNA Mitocondrial , DNA Ribossômico , Dosagem de Genes , Duplicação Gênica , Ordem dos Genes , Genes Fúngicos , Genômica/métodos , Dados de Sequência Molecular , Alinhamento de SequênciaRESUMO
The genome of Saccharomyces servazzii was analyzed with 2570 random sequence tags totalling 2.3 Mb. BLASTX comparisons revealed a minimum of 1420 putative open reading frames with significant homology to Saccharomyces cerevisiae (58% aa identity on average), two with Schizosaccharomyces pombe and one with a human protein, confirming that S. servazzii is closely related to S. cerevisiae. About 25% of the S. servazzii genes were identified, assuming that the gene complement is identical in both yeasts. S. servazzii carries very few transposable elements related to Ty elements in S. cerevisiae. Most of the mitochondrial genes were identified in eight contigs altogether spanning 25 kb for a predicted size of 29 kb. A significant match with the Kluyveromyces lactis linear DNA plasmid pGKL-1 encoded RF4 killer protein suggests that a related plasmid exists in S. servazzii. The sequences have been deposited with EMBL under the accession numbers AL402279-AL404848.
Assuntos
Genoma Fúngico , Saccharomyces/genética , Ascomicetos/genética , DNA Mitocondrial , DNA Ribossômico , Proteínas Fúngicas/classificação , Proteínas Fúngicas/genética , Duplicação Gênica , Humanos , Íntrons , Dados de Sequência Molecular , Proteínas Nucleares/genética , Plasmídeos/genética , Retroelementos , Saccharomyces cerevisiae/genética , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Spliceossomos/genéticaRESUMO
The genome of Saccharomyces kluyveri was explored through 2528 random sequence tags with an average length of 981 bp. The complete nuclear ribosomal DNA unit was found to be 8656 bp in length. Sequences homologous to retroelements of the gypsy and copia types were identified as well as numerous solo long terminal repeats. We identified at least 1406 genes homologous to Saccharomyces cerevisiae open reading frames, with on average 58.1% and 72.4% amino acid identity and similarity, respectively. In addition, by comparison with completely sequenced genomes and the SwissProt database, we found 27 novel S. kluyveri genes. Most of these genes belong to pathways or have functions absent from S. cerevisiae, such as the catabolic pathway of purines or pyrimidines, melibiose fermentation, sorbitol utilization, or degradation of pollutants. The sequences are deposited in EMBL under the accession numbers AL404849-AL407376.
Assuntos
Genoma Fúngico , Saccharomyces/genética , Ascomicetos/genética , Proteínas Fúngicas/classificação , Proteínas Fúngicas/genética , Dados de Sequência Molecular , Fases de Leitura Aberta , RNA de Transferência/genética , Sequências Repetitivas de Ácido NucleicoRESUMO
A genomic exploration of Kluyveromyces thermotolerans was performed by random sequence tag (RST) analysis. We sequenced 2653 RSTs corresponding to inserts sequenced from both ends. We performed a systematic comparison with a complete set of proteins from Saccharomyces cerevisiae, other completely sequenced genomes and SwissProt. We identified six mitochondrial genes and 1358-1496 nuclear genes by comparison with S. cerevisiae. In addition, 25 genes were identified by comparison with other organisms. This corresponds to about 24% of the estimated gene content of this organism. A lower level of conservation is observed with orthologues to genes of S. cerevisiae previously classified as orphans. Gene order was found to be conserved between S. cerevisiae and K. thermotolerans in 56.5% of studied cases.
Assuntos
Genoma Fúngico , Kluyveromyces/genética , Sequência de Aminoácidos , Ascomicetos/genética , Mapeamento Cromossômico , Cromossomos Fúngicos , DNA Mitocondrial , DNA Ribossômico , Bases de Dados Factuais , Proteínas Fúngicas/classificação , Proteínas Fúngicas/genética , Ordem dos Genes , Código Genético , Dados de Sequência Molecular , RNA de Transferência/genética , Saccharomyces cerevisiae/genética , Homologia de Sequência de AminoácidosRESUMO
As part of the comparative genomics project 'GENOLEVURES', we studied the Kluyveromyces marxianus var. marxianus strain CBS712 using a partial random sequencing strategy. With a 0.2 x genome equivalent coverage, we identified ca. 1300 novel genes encoding proteins, some containing spliceosomal introns with consensus splice sites identical to those of Saccharomyces cerevisiae, 28 tRNA genes, the whole rDNA repeat, and retrotransposons of the Ty1/2 family of S. cerevisiae with diverged Long Terminal Repeats. Functional classification of the K. marxianus genes, as well as the analysis of the paralogous gene families revealed few differences with respect to S. cerevisiae. Only 42 K. marxianus identified genes are without detectable homolog in the baker's yeast. However, we identified several genetic rearrangements between these two yeast species.
Assuntos
Mapeamento Cromossômico , Genoma Fúngico , Kluyveromyces/genética , Ascomicetos/genética , Sequência de Bases , Cromossomos Fúngicos , Códon , Sequência Conservada , Mapeamento de Sequências Contíguas , DNA Mitocondrial , DNA Ribossômico , Proteínas Fúngicas/classificação , Proteínas Fúngicas/genética , Código Genético , Íntrons , Família Multigênica , Proteínas Nucleares/genética , Fases de Leitura Aberta , RNA de Transferência , Retroelementos , SpliceossomosRESUMO
As part of a comparative genomics project on 13 hemiascomycetous yeasts, the Pichia angusta type strain was studied using a partial random sequencing strategy. With coverage of 0.5 genome equivalents, about 2500 novel protein-coding genes were identified, probably corresponding to more than half of the P. angusta protein-coding genes, 6% of which do not have homologs in Saccharomyces cerevisiae. Some of them contain one or two introns, on average three times shorter than those in S. cerevisiae. We also identified 28 tRNA genes, a few retrotransposons similar to Ty5 of S. cerevisiae, solo long terminal repeats, the whole ribosomal DNA cluster, and segments of mitochondrial DNA. The P. angusta sequences were deposited in EMBL under the accession numbers AL430961 to AL436044.
Assuntos
Genoma Fúngico , Pichia/genética , Ascomicetos/genética , Replicação do DNA/genética , Elementos de DNA Transponíveis , DNA Mitocondrial , DNA Ribossômico , Proteínas Fúngicas/genética , Íntrons , Dados de Sequência Molecular , Família Multigênica , Plasmídeos/genética , RNA de Transferência/genética , Saccharomyces cerevisiae/genética , SpliceossomosRESUMO
By analyzing 2830 random sequence tags (RSTs), totalling 2.7 Mb, we explored the genome of the marine, osmo- and halotolerant yeast, Debaryomyces hansenii. A contig 29 kb in length harbors the entire mitochondrial genome. The genes encoding Cox1, Cox2, Cox3, Cob, Atp6, Atp8, Atp9, several subunits of the NADH dehydrogenase complex 1 and 11 tRNAs were unambiguously identified. An equivalent number of putative transposable elements compared to Saccharomyces cerevisiae were detected, the majority of which are more related to higher eukaryote copia elements. BLASTX comparisons of RSTs with databases revealed at least 1119 putative open reading frames with homology to S. cerevisiae and 49 to other genomes. Specific functions, including transport of metabolites, are clearly over-represented in D. hansenii compared to S. cerevisiae, consistent with the observed difference in physiology of the two species. The sequences have been deposited with EMBL under the accession numbers AL436045-AL438874.
Assuntos
Ascomicetos/genética , Proteínas Fúngicas/genética , Genoma Fúngico , Elementos de DNA Transponíveis , DNA Mitocondrial , DNA Ribossômico , Proteínas Fúngicas/classificação , Duplicação Gênica , Dados de Sequência Molecular , Proteínas Nucleares/genética , RNA de Transferência , Saccharomyces cerevisiae/genéticaRESUMO
A total of 4940 random sequence tags of the dimorphic yeast Yarrowia lipolytica, totalling 4.9 Mb, were analyzed. BLASTX comparisons revealed at least 1229 novel Y. lipolytica genes 1083 genes having homology with Saccharomyces cerevisiae genes and 146 with genes from various other genomes. This confirms the rapid sequence evolution assumed for Y. lipolytica. Functional analysis of newly discovered genes revealed that several enzymatic activities were increased compared to S. cerevisiae, in particular, transport activities, ion homeostasis, and various metabolism pathways. Most of the mitochondrial genes were identified in contigs spanning more than 47 kb. Matches to retrotransposons were observed, including a S. cerevisiae Ty3 and a LINE element. The sequences have been deposited with EMBL under the accession numbers AL409956-AL414895.
Assuntos
Genoma Fúngico , Leveduras/genética , Elementos de DNA Transponíveis , DNA Mitocondrial , DNA Ribossômico , Proteínas Fúngicas/classificação , Proteínas Fúngicas/genética , Duplicação Gênica , Dados de Sequência Molecular , Saccharomyces cerevisiae/genética , Homologia de Sequência de AminoácidosRESUMO
The generation of sequencing data for the hemiascomycetous yeast random sequence tag project was performed using the procedures established at GENOSCOPE. These procedures include a series of protocols for the sequencing reactions, using infra-red labelled primers, performed on both ends of the plasmid inserts in the same reaction tube, and their analysis on automated DNA sequencers. They also include a package of computer programs aimed at detecting potential assignation errors, selecting good quality sequences and estimating their useful length.
Assuntos
Ascomicetos/genética , Biologia Computacional/métodos , Genoma Fúngico , Análise de Sequência de DNA/métodos , Pichia/genéticaRESUMO
This paper reports the genomic analysis of strain CBS732 of Zygosaccharomyces rouxii, a homothallic diploid yeast. We explored the sequences of 4934 random sequencing tags of about 1 kb in size and compared them to the Saccharomyces cerevisiae gene products. Approximately 2250 nuclear genes, 57 tRNAs, the rDNA locus, the endogenous pSR1 plasmid and 15 mitochondrial genes were identified. According to 18S and 25S rRNA cladograms and to synteny analysis, Z. rouxii could be placed among the S. cerevisiae sensu lato yeasts.
Assuntos
Proteínas Fúngicas/genética , Genoma Fúngico , Zygosaccharomyces/genética , Ascomicetos/genética , Cromossomos Fúngicos , Elementos de DNA Transponíveis , DNA Mitocondrial , DNA Ribossômico , Dados de Sequência Molecular , Proteínas Nucleares/genética , Plasmídeos , RNA de Transferência/genética , Saccharomyces cerevisiae/genética , Análise de Sequência de DNA/métodosRESUMO
This paper reports the genomic analysis of the strain CBS7064 of Pichia sorbitophila, a homothallic diploid yeast. We sequenced 4829 random sequence tags of about 1 kb and compared them to the Saccharomyces cerevisiae gene products. Approximately 1300 nuclear genes, 22 tRNAs, the rDNA locus, and six mitochondrial genes have been identified. The analysis of the rDNA genes has permitted to classify this organism close to the Candida species. Accession numbers from AL414896 to AL419724 at EMBL databank.
Assuntos
Genoma Fúngico , Pichia/genética , Ascomicetos/genética , Elementos de DNA Transponíveis , DNA Mitocondrial , DNA Ribossômico , Proteínas Fúngicas/genética , Dados de Sequência Molecular , Proteínas Nucleares/genética , Filogenia , RNA de Transferência , Saccharomyces cerevisiae , Análise de Sequência de DNA , Homologia de Sequência de AminoácidosRESUMO
Random sequencing of the Kluyveromyces lactis genome allowed the identification of 2235-2601 open reading frames (ORFs) homologous to S. cerevisiae ORFs, 51 ORFs which were homologous to genes from other species, 64 tRNAs, the complete rDNA repeat, and a few Ty1- and Ty2-like sequences. In addition, the complete sequence of plasmid pKD1 and a large coverage of the mitochondrial genome were obtained. The global distribution into general functional categories found in Saccharomyces cerevisiae and as defined by MIPS is well conserved in K. lactis. However, detailed examination of certain subcategories revealed a small excess of genes involved in amino acid metabolism in K. lactis. The sequences are deposited at EMBL under the accession numbers AL424881-AL430960.
Assuntos
Genoma Fúngico , Kluyveromyces/genética , Ascomicetos/genética , Centrômero/genética , Cromossomos Fúngicos , Elementos de DNA Transponíveis , DNA Mitocondrial , DNA Ribossômico , Proteínas Fúngicas/genética , Dosagem de Genes , Ordem dos Genes , Dados de Sequência Molecular , Fases de Leitura Aberta , Plasmídeos/genética , RNA de Transferência/genética , Saccharomyces cerevisiae/genética , Homologia de Sequência de AminoácidosRESUMO
The identification of molecular evolutionary mechanisms in eukaryotes is approached by a comparative genomics study of a homogeneous group of species classified as Hemiascomycetes. This group includes Saccharomyces cerevisiae, the first eukaryotic genome entirely sequenced, back in 1996. A random sequencing analysis has been performed on 13 different species sharing a small genome size and a low frequency of introns. Detailed information is provided in the 20 following papers. Additional tables available on websites describe the ca. 20000 newly identified genes. This wealth of data, so far unique among eukaryotes, allowed us to examine the conservation of chromosome maps, to identify the 'yeast-specific' genes, and to review the distribution of gene families into functional classes. This project conducted by a network of seven French laboratories has been designated 'Génolevures'.
Assuntos
Ascomicetos/genética , Evolução Molecular , Genoma Fúngico , Filogenia , Ascomicetos/fisiologia , Genômica/métodos , Dados de Sequência Molecular , RNA Ribossômico , Análise de Sequência de DNARESUMO
We have analyzed the evolution of chromosome maps of Hemiascomycetes by comparing gene order and orientation of the 13 yeast species partially sequenced in this program with the genome map of Saccharomyces cerevisiae. From the analysis of nearly 8000 situations in which two distinct genes having homologs in S. cerevisiae could be identified on the sequenced inserts of another yeast species, we have quantified the loss of synteny, the frequency of single gene deletion and the occurrence of gene inversion. Traces of ancestral duplications in the genome of S. cerevisiae could be identified from the comparison with the other species that do not entirely coincide with those identified from the comparison of S. cerevisiae with itself. From such duplications and from the correlation observed between gene inversion and loss of synteny, a model is proposed for the molecular evolution of Hemiascomycetes. This model, which can possibly be extended to other eukaryotes, is based on the reiteration of events of duplication of chromosome segments, creating transient merodiploids that are subsequently resolved by single gene deletion events.
Assuntos
Ascomicetos/genética , Mapeamento Cromossômico/métodos , Cromossomos Fúngicos , Ordem dos Genes , Genômica/métodos , Biologia Computacional/métodos , Deleção de Genes , Duplicação Gênica , Saccharomyces cerevisiae/genéticaRESUMO
Comparisons of the 6213 predicted Saccharomyces cerevisiae open reading frame (ORF) products with sequences from organisms of other biological phyla differentiate genes commonly conserved in evolution from 'maverick' genes which have no homologue in phyla other than the Ascomycetes. We show that a majority of the 'maverick' genes have homologues among other yeast species and thus define a set of 1892 genes that, from sequence comparisons, appear 'Ascomycetes-specific'. We estimate, retrospectively, that the S. cerevisiae genome contains 5651 actual protein-coding genes, 50 of which were identified for the first time in this work, and that the present public databases contain 612 predicted ORFs that are not real genes. Interestingly, the sequences of the 'Ascomycetes-specific' genes tend to diverge more rapidly in evolution than that of other genes. Half of the 'Ascomycetes-specific' genes are functionally characterized in S. cerevisiae, and a few functional categories are over-represented in them.