RESUMO
This study describes an algorithm that finds rho-independent transcription terminators in bacterial genomes and evaluates the accuracy of its predictions. The algorithm identifies terminators by searching for a common mRNA motif: a hairpin structure followed by a short uracil-rich region. For each terminator, an energy-scoring function that reflects hairpin stability, and a tail-scoring function based on the number of U nucleotides and their proximity to the stem, are computed. A confidence value can be assigned to each terminator by analyzing candidate terminators found both within and between genes, and taking into account the energy and tail scores. The confidence is an empirical estimate of the probability that the sequence is a true terminator. The algorithm was used to conduct a comprehensive analysis of 12 bacterial genomes to identify likely candidates for rho-independent transcription terminators. Four of these genomes (Deinococcus radiodurans, Escherichia coli, Haemophilus influenzae and Vibrio cholerae) were found to have large numbers of rho-independent terminators. Among the other genomes, most appear to have no transcription terminators of this type, with the exception of Thermotoga maritima. A set of 131 experimentally determined E. coli terminators was used to evaluate the sensitivity of the method, which ranges from 89 % to 98 %, with corresponding false positive rates of 2 % and 18 %.
Assuntos
Algoritmos , Bactérias/genética , Biologia Computacional/métodos , Genoma Bacteriano , Regiões Terminadoras Genéticas/genética , Reações Falso-Positivas , Genes Bacterianos/genética , Conformação de Ácido Nucleico , Estabilidade de RNA , RNA Bacteriano/química , RNA Bacteriano/genética , RNA Bacteriano/metabolismo , RNA Mensageiro/química , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Sensibilidade e Especificidade , TermodinâmicaRESUMO
Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.
