RESUMEN
We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. The genome of M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcina spp. in the region proximal to the origin of replication, with interspecies gene similarities as high as 95%. However, it is disordered and marked by increased transposase frequency and decreased gene synteny and gene density in the distal semigenome. Of the 3,680 open reading frames (ORFs) in M. barkeri, 746 had homologs with better than 80% identity to both M. acetivorans and M. mazei, while 128 nonhypothetical ORFs were unique (nonorthologous) among these species, including a complete formate dehydrogenase operon, genes required for N-acetylmuramic acid synthesis, a 14-gene gas vesicle cluster, and a bacterial-like P450-specific ferredoxin reductase cluster not previously observed or characterized for this genus. A cryptic 36-kbp plasmid sequence that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143-nucleotide motif was detected in M. barkeri. Three-way comparison of these genomes reveals differing mechanisms for the accrual of changes. Elongation of the relatively large M. acetivorans genome is the result of uniformly distributed multiple gene scale insertions and duplications, while the M. barkeri genome is characterized by localized inversions associated with the loss of gene content. In contrast, the short M. mazei genome most closely approximates the putative ancestral organizational state of these species.
Asunto(s)
Genoma Arqueal , Methanosarcina barkeri/genética , Ferredoxinas/metabolismo , Formiato Deshidrogenasas , Reordenamiento Génico , Familia de Multigenes , Sistemas de Lectura Abierta , Oxidorreductasas/genética , Plásmidos/genética , Proteínas/genética , Origen de Réplica/genética , Homología de Secuencia de Ácido NucleicoRESUMEN
BACKGROUND: Translation initiation in eukaryotes involves the recruitment of mRNA to the ribosome which is controlled by the translation factor eIF4E. eIF4E binds to the 5'-m7Gppp cap-structure of mRNA. Three dimensional structures of eIF4Es bound to cap-analogues resemble 'cupped-hands' in which the cap-structure is sandwiched between two conserved Trp residues (Trp-56 and Trp-102 of H. sapiens eIF4E). A third conserved Trp residue (Trp-166 of H. sapiens eIF4E) recognizes the 7-methyl moiety of the cap-structure. Assessment of GenBank NR and dbEST databases reveals that many organisms encode a number of proteins with homology to eIF4E. Little is understood about the relationships of these structurally related proteins to each other. RESULTS: By combining sequence data deposited in the Genbank databases, we have identified sequences encoding 411 eIF4E-family members from 230 species. These sequences have been deposited into an internet-accessible database designed for sequence comparisons of eIF4E-family members. Most members can be grouped into one of three classes. Class I members carry Trp residues equivalent to Trp-43 and Trp-56 of H. sapiens eIF4E and appear to be present in all eukaryotes. Class II members, possess Trp-->Tyr/Phe/Leu and Trp-->Tyr/Phe substitutions relative to Trp-43 and Trp-56 of H. sapiens eIF4E, and can be identified in Metazoa, Viridiplantae, and Fungi. Class III members possess a Trp residue equivalent to Trp-43 of H. sapiens eIF4E but carry a Trp-->Cys/Tyr substitution relative to Trp-56 of H. sapiens eIF4E, and can be identified in Coelomata and Cnidaria. Some eIF4E-family members from Protista show extension or compaction relative to prototypical eIF4E-family members. CONCLUSION: The expansion of sequenced cDNAs and genomic DNAs from all eukaryotic kingdoms has revealed a variety of proteins related in structure to eIF4E. Evolutionarily it seems that a single early eIF4E gene has undergone multiple gene duplications generating multiple structural classes, such that it is no longer possible to predict function from the primary amino acid sequence of an eIF4E-family member. The variety of eIF4E-family members provides a source of alternatives on the eIF4E structural theme that will benefit structure/function analyses and therapeutic drug design.
Asunto(s)
Factor 4E Eucariótico de Iniciación/genética , Evolución Molecular , Secuencia de Aminoácidos , Animales , Secuencia Conservada , Cisteína/química , ADN/química , ADN Complementario/metabolismo , Diseño de Fármacos , Genes MHC Clase II , Humanos , Leucina/química , Datos de Secuencia Molecular , Familia de Multigenes , Filogenia , Biosíntesis de Proteínas , Estructura Terciaria de Proteína , Caperuzas de ARN , Análisis de Secuencia de ADN , Homología de Secuencia de Aminoácido , Relación Estructura-Actividad , Triptófano/químicaRESUMEN
Group II chaperonins belong to the Hsp60 family occurring in archaea and eukaryotes. The archaeal chaperonins build the thermosome, which is similar to the eukaryotic CCT (chaperonin-containing TCP-1). Eukaryotes have eight subunits, and up until now, it was thought that archaea had between one and three subunits, depending on the species. We now report two novel subunits, termed Hsp60-4 and Hsp60-5, in the archaeon Methanosarcina acetivorans, which also has Hsp60-1, Hsp60-2, and Hsp60-3 with orthologs in Methanosarcinae. Hsp60-4 and Hsp60-5 occur only in M. acetivorans, which makes this organism unique in that it has the highest number of chaperonin subunits ever described for an archaeon. Evolutionary analysis suggests that either Hsp60-4 or Hsp60-5 paralogs have arisen by gene duplication with vastly increased accepted substitution rates or that they represent ancestral types found only in this species.
Asunto(s)
Chaperonina 60/genética , Chaperoninas/genética , Evolución Molecular , Methanosarcina/genética , Filogenia , Secuencia de Aminoácidos , Biología Computacional , Bases de Datos de Ácidos Nucleicos , Funciones de Verosimilitud , Modelos Genéticos , Datos de Secuencia Molecular , Conformación Proteica , Alineación de Secuencia , Especificidad de la EspecieRESUMEN
Pyrococcus species are hyperthermophilic members of the order Thermococcales, with optimal growth temperatures approaching 100 degrees C. All species grow heterotrophically and produce H2 or, in the presence of elemental sulfur (S(o)), H2S. Pyrococcus woesei and P. furiosus were isolated from marine sediments at the same Vulcano Island beach site and share many morphological and physiological characteristics. We report here that the rDNA operons of these strains have identical sequences, including their intergenic spacer regions and part of the 23S rRNA. Both species grow rapidly and produce H2 in the presence of 0.1% maltose and 10-100 microM sodium tungstate in S(o)-free medium. However, P. woesei shows more extensive autolysis than P. furiosus in the stationary phase. Pyrococcus furiosus and P. woesei share three closely related families of insertion sequences (ISs). A Southern blot performed with IS probes showed extensive colinearity between the genomes of P. woesei and P. furiosus. Cloning and sequencing of ISs that were in different contexts in P. woesei and P. furiosus revealed that the napA gene in P. woesei is disrupted by a type III IS element, whereas in P. furiosus, this gene is intact. A type I IS element, closely linked to the napA gene, was observed in the same context in both P. furiosus and P. woesei genomes. Our results suggest that the IS elements are implicated in genomic rearrangements and reshuffling in these closely related strains. We propose to rename P. woesei a subspecies of P. furiosus based on their identical rDNA operon sequences, many common IS elements that are shared genomic markers, and the observation that all P. woesei nucleotide sequences deposited in GenBank to date are > 99% identical to P. furiosus sequences.