RESUMEN
We have elaborated a method which has allowed us to estimate the direction of translocation of orthologs which have changed, during the phylogeny, their positions on chromosome in respect to the leading or lagging role of DNA strands. We have shown that the relative number of translocations which have switched positions of genes from the leading to the lagging DNA strand is lower than the number of translocations which have transferred genes from the lagging strand to the leading strand of prokaryotic genomes. This paradox could be explained by assuming that the stronger mutation pressure and selection after inversion preferentially eliminate genes transferred from the leading to the lagging DNA strand.
Asunto(s)
Borrelia burgdorferi/genética , Chlamydia trachomatis/genética , Chlamydophila pneumoniae/genética , Inversión Cromosómica , ADN Bacteriano/genética , Genes Bacterianos , Selección Genética , Treponema pallidum/genética , Cromosomas Bacterianos , Evolución MolecularRESUMEN
One of the main causes of bacterial chromosome asymmetry is replication-associated mutational pressure. Different rates of nucleotide substitution accumulation on leading and lagging strands implicate qualitative and quantitative differences in the accumulation of mutations in protein coding sequences lying on different DNA strands. We show that the divergence rate of orthologs situated on leading strands is lower than the divergence rate of those situated on lagging strands. The ratio of the mutation accumulation rate for sequences lying on lagging strands to that of sequences lying on leading strands is rather stable and time-independent. The divergence rate of sequences which changed their positions, with respect to the direction of replication fork movement, is not stable-sequences which have recently changed their positions are the most prone to mutation accumulation. This effect may influence estimations of evolutionary distances between species and the topology of phylogenetic trees.
Asunto(s)
Replicación del ADN/genética , ADN Bacteriano/biosíntesis , ADN Bacteriano/genética , Evolución Molecular , Genes Bacterianos/genética , Mutagénesis/genética , Sustitución de Aminoácidos/genética , Cromosomas Bacterianos/genética , ADN de Cadena Simple/biosíntesis , ADN de Cadena Simple/genética , CinéticaRESUMEN
Compositional bias of yeast chromosomes was analysed using detrended DNA walks. Unlike eubacterial chromosomes, the yeast chromosomes did not show the specific asymmetry correlated with origin and terminus of replication. It is probably a result of a relative excess of autonomously replicating sequences (ARS) and of random choice of these sequences in each replication cycle. Nevertheless, the last ARS from both ends of chromosomes are responsible for unidirectional replication of subtelomeric sequences with pre-established leading/lagging roles of DNA strands. In these sequences a specific asymmetry is observed, resembling the asymmetry introduced by replication-associated mutational pressure into eubacterial chromosomes.
Asunto(s)
Replicación del ADN , Saccharomyces cerevisiae/genética , Animales , Grupo Borrelia Burgdorferi/genética , Huella de ADN , Mutación , Replicón , Telómero/genéticaRESUMEN
In a recent paper we have estimated the total number of protein coding open reading frames (ORFs) in the Saccharomyces cerevisiae genome, based on their properties, at about 4800. This number is much smaller than the 5800-6000 which is widely accepted. In this paper we analyse differences between the set of ORFs with known phenotypes annotated in the Munich Information Centre for Protein Sequences (MIPS) database and ORFs for which the probability of coding, counted by us, is very low. We have found that many of the latter ORFs have properties of antisense sequences of coding ORFs, which suggests that they could have been generated by duplication of coding sequences. Since coding sequences generate ORFs inside themselves, with especially high frequency in the antisense sequences, we have looked for homology between known proteins and hypothetical polypeptides generated by ORFs under consideration in all the six phases. For many ORFs we have found paralogues and orthologues in phases different than the phase which had been assumed in the MIPS database as coding.
Asunto(s)
Genoma Fúngico , Sistemas de Lectura Abierta , Saccharomyces cerevisiae/genética , Algoritmos , Bases de Datos Factuales , Evolución Molecular , Código GenéticoRESUMEN
At the end of 1996 we approximated the total number of protein coding ORFs in the Saccharomyces cerevisiae genome, based on their properties, as 4700-4800. The number is much smaller than the 5800 which is widely accepted. According to our calculations, there remain about 200-300 orphans-ORFs without known function or homology to already discovered genes, which is only about 5% of the total number of genes. Our results would be questionable if the analysed set of known genes was not a statistically representative sample of the whole set of protein coding genes in the S. cerevisiae genome. Therefore, we repeated our estimation using recently updated databases. In the course of the last 18 months, previously unknown functions of about 500 genes have been found. We have used these to check our method, former results and conclusions. Our previous estimation of the total number of coding ORFs was confirmed.
Asunto(s)
Genoma Fúngico , Sistemas de Lectura Abierta/genética , Saccharomyces cerevisiae/genética , Codón/genética , Codón/fisiología , ADN de Hongos/química , Bases de Datos Factuales , Sistemas de Lectura Abierta/fisiología , Saccharomyces cerevisiae/químicaRESUMEN
We have performed detrended DNA walks on whole prokaryotic genomes, on noncoding sequences and, separately, on each position in codons of coding sequences. Our method enables us to distinguish between the mutational pressure associated with replication and the mutational pressure associated with transcription and other mechanisms that introduce asymmetry into prokaryotic chromosomes. In many prokaryotic genomes, each component of mutational pressure affects coding sequences not only in silent positions but also in positions in which changes cause amino acid substitutions in coded proteins. Asymmetry in the silent positions of codons differentiates the rate of translation of mRNA produced from leading and lagging strands. Asymmetry in the amino acid composition of proteins resulting from replication-associated mutational pressure also corresponds to leading and lagging roles of DNA strands, whereas asymmetry connected with transcription and coding function corresponds to the distance of genes from the origin or terminus of chromosome replication.