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
BACKGROUND: Any DNA sequence is a result of compromise between the selection and mutation pressures exerted on it during evolution. It is difficult to estimate the relative influence of each of these pressures on the rate of accumulation of substitutions. However, it is important to discriminate between the effect of mutations, and the effect of selection, when studying the phylogenic relations between taxa. RESULTS: We have tested in computer simulations, and analytically, the available substitution matrices for many genomes, and we have found that DNA strands in equilibrium under mutational pressure have unique feature: the fraction of each type of nucleotide is linearly dependent on the time needed for substitution of half of nucleotides of a given type, with a correlation coefficient close to 1. Substitution matrices found for sequences under selection pressure do not have this property. A substitution matrix for the leading strand of the Borrelia burgdorferi genome, having reached equilibrium in computer simulation, gives a DNA sequence with nucleotide composition and asymmetry corresponding precisely to the third positions in codons of protein coding genes located on the leading strand. CONCLUSIONS: Parameters of mutational pressure allow us to count DNA composition in equilibrium with this mutational pressure. Comparing any real DNA sequence with the sequence in equilibrium it is possible to estimate the distance between these sequences, which could be used as a measure of the selection pressure. Furthermore, the parameters of the mutational pressure enable direct estimation of the relative mutation rates in any DNA sequence in the studied genome.
Asunto(s)
ADN Bacteriano/genética , Mutagénesis , Nucleótidos/metabolismo , Composición de Base/genética , Borrelia burgdorferi/genética , Inversión Cromosómica , Codón/genética , Simulación por Computador , ADN Bacteriano/química , ADN Intergénico/genética , Evolución Molecular , Genes Bacterianos/genética , Genoma Bacteriano , Modelos GenéticosRESUMEN
The mode of replication and organisation of bacterial genomes impose asymmetry on their nucleotide composition. The asymmetry is seen in coding and non-coding sequences and is reflected in the amino acid composition of proteins. The mechanisms generating asymmetry include: unequal mutation rates connected with replication and transcription, selection forces positioning genes and signal sequences nonrandomly in the genome, and protein coding constraints on coding sequences. There are different methods of visualising and measuring the asymmetry. Some of them can assess the contribution of individual mechanisms to the observed asymmetry and those have been described in greater detail. Asymmetric mutational and selection pressures differentiate the rates of evolution of genes on leading and lagging strands. The genes relocated to the opposite strand have to adapt to a different mutational pressure or are eliminated. Translocations from leading to lagging strands are more often selected against than from lagging to leading strands. Comparison of intergenic sequences that have lost the coding function to the original genes enables finding the frequencies of the twelve substitution rates in sequences free from selection. In the absence of selection, the half-time of substitution of a given type of nucleotide is linearly correlated with the fraction of that nucleotide in the sequence.
RESUMEN
The potential of herbaceous weeds commonly growing in or adjacent to cucurbit crops to serve as alternate hosts and overwintering reservoirs of Erwinia tracheiphila, a causal agent of cucurbit wilt, was investigated. Methods for isolation, maintenance, long-term storage, and detection of E. tracheiphila from infected plants were developed. E. tracheiphila was consistently detected by enzyme-linked immunosorbent assay (ELISA) and reisolated from infected, susceptible, cucurbit species. When six common herbaceous weed species were inoculated, E. tracheiphila was detected in 49% (combined species) of the plants by ELISA 3 weeks after inoculation. However, we were unable to reisolate E. tracheiphila from these plants by standard techniques. Immunoaffinity isolation with a sensitivity of 2 CFU per sample also failed to recover E. tracheiphila from weed species. Comparisons of cucumber and goldenrod inoculated with live or formaldehyde-killed E. tracheiphila indicated that immunoassays could detect nonviable E. tracheiphila systemically spread in plants 3 weeks post-inoculation. In these tests, the pathogen was reisolated only from cucumber plants inoculated with live E. tracheiphila. Although we could reproduce serological evidence of E. tracheiphila antigen in the weeds investigated, our results do not support the hypothesis that E. tracheiphila can infect, survive in, or overwinter in the weed species tested.
