RESUMEN
We have traced the evolution patterns of 2480 transmembrane transporters from five complete genome sequences spanning the entire Hemiascomycete phylum: Saccharomyces cerevisiae, Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, and Yarrowia lipolytica. The use of nonambiguous functional and phylogenetic criteria derived from the TCDB classification system has allowed the identification within the Hemiascomycete phylum of 97 small phylogenetic transporter subfamilies comprising a total of 355 transporters submitted to four distinct evolution patterns named "ubiquitous," "species specific," "phylum gains and losses," or "homoplasic." This analysis identifies the transporters that contribute to the emergence of species during the evolution of the Hemiascomycete phylum and may aid in establishing novel phylogenetic criteria for species classification.
Asunto(s)
Ascomicetos/genética , Proteínas Portadoras/genética , Proteínas Portadoras/metabolismo , Evolución Molecular , Candida albicans/genética , Candida albicans/metabolismo , Candida glabrata , Genoma Fúngico , Kluyveromyces/genética , Kluyveromyces/metabolismo , Proteínas de Transporte de Membrana/genética , Proteínas de Transporte de Membrana/metabolismo , Mitocondrias/metabolismo , Familia de Multigenes , Proteoma , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Especificidad de la Especie , Yarrowia/genética , Yarrowia/metabolismoRESUMEN
We have found an extremely large ribonuclease P (RNase P) RNA (RPR1) in the human pathogen Candida glabrata and verified that this molecule is expressed and present in the active enzyme complex of this hemiascomycete yeast. A structural alignment of the C. glabrata sequence with 36 other hemiascomycete RNase P RNAs (abbreviated as P RNAs) allows us to characterize the types of insertions. In addition, 15 P RNA sequences were newly characterized by searching in the recently sequenced genomes Candida albicans, C. glabrata, Debaryomyces hansenii, Eremothecium gossypii, Kluyveromyces lactis, Kluyveromyces waltii, Naumovia castellii, Saccharomyces kudriavzevii, Saccharomyces mikatae, and Yarrowia lipolytica; and by PCR amplification for other Candida species (Candida guilliermondii, Candida krusei, Candida parapsilosis, Candida stellatoidea, and Candida tropicalis). The phylogenetic comparative analysis identifies a hemiascomycete secondary structure consensus that presents a conserved core in all species with variable insertions or deletions. The most significant variability is found in C. glabrata P RNA in which three insertions exceeding in total 700 nt are present in the Specificity domain. This P RNA is more than twice the length of any other homologous P RNAs known in the three domains of life and is eight times the size of the smallest. RNase P RNA, therefore, represents one of the most diversified noncoding RNAs in terms of size variation and structural diversity.
Asunto(s)
Candida glabrata/enzimología , Candida glabrata/metabolismo , ARN de Hongos/química , Ribonucleasa P/química , Ascomicetos/clasificación , Ascomicetos/genética , Secuencia de Bases , Candida glabrata/química , Candida glabrata/genética , Secuencia Conservada , ADN de Hongos , Bases de Datos Genéticas , Genes Fúngicos , Variación Genética , Genoma Fúngico , Modelos Químicos , Datos de Secuencia Molecular , Mutación , Conformación de Ácido Nucleico , Filogenia , ARN de Hongos/genética , ARN de Hongos/aislamiento & purificación , ARN de Hongos/metabolismo , Ribonucleasa P/genética , Ribonucleasa P/metabolismo , Homología de Secuencia de Ácido NucleicoRESUMEN
A comparative analysis among Saccharomyces cerevisiae and the other four yeasts Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, and Yarrowia lipolytica is presented. The broad evolutionary range spanned by the organisms allows to quantitatively demonstrate novel evolutionary effects in protein complexes. The evolution rates within cliques of interlinked proteins are found to bear strong multipoint correlations, witnessing a cooperative coevolution of complex subunits. The coevolution is found to be largely independent of the tendency of the subunits to have similar abundances.