RESUMO
In prokaryotes, Shine-Dalgarno (SD) sequences, nucleotides upstream from start codons on messenger RNAs (mRNAs) that are complementary to ribosomal RNA (rRNA), facilitate the initiation of protein synthesis. The location of SD sequences relative to start codons and the stability of the hybridization between the mRNA and the rRNA correlate with the rate of synthesis. Thus, accurate characterization of SD sequences enhances our understanding of how an organism's transcriptome relates to its cellular proteome. We implemented the Individual Nearest Neighbor Hydrogen Bond model for oligo-oligo hybridization and created a new metric, relative spacing (RS), to identify both the location and the hybridization potential of SD sequences by simulating the binding between mRNAs and single-stranded 16S rRNA 3' tails. In 18 prokaryote genomes, we identified 2,420 genes out of 58,550 where the strongest binding in the translation initiation region included the start codon, deviating from the expected location for the SD sequence of five to ten bases upstream. We designated these as RS+1 genes. Additional analysis uncovered an unusual bias of the start codon in that the majority of the RS+1 genes used GUG, not AUG. Furthermore, of the 624 RS+1 genes whose SD sequence was associated with a free energy release of less than -8.4 kcal/mol (strong RS+1 genes), 384 were within 12 nucleotides upstream of in-frame initiation codons. The most likely explanation for the unexpected location of the SD sequence for these 384 genes is mis-annotation of the start codon. In this way, the new RS metric provides an improved method for gene sequence annotation. The remaining strong RS+1 genes appear to have their SD sequences in an unexpected location that includes the start codon. Thus, our RS metric provides a new way to explore the role of rRNA-mRNA nucleotide hybridization in translation initiation.
Assuntos
Códon de Iniciação/genética , Biologia Computacional , Regulação Bacteriana da Expressão Gênica/genética , Genoma Bacteriano/genética , Iniciação Traducional da Cadeia Peptídica/genética , Sequência de Bases , Escherichia coli/genética , Ligação de Hidrogênio , Modelos Genéticos , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Ribossômico/genética , RNA Ribossômico/metabolismo , Projetos de PesquisaRESUMO
The free energy released during the interaction of the 16S rRNA tail with the mRNA sequence during translation contains a weak sinusoidal pattern of frequency 1/3 cycles/nucleotide. We hypothesize that this signal encodes information related to the maintenance of reading frame during elongation. In the case of the well-studied +1 frameshifter, prfB in E. coli, we have observed a direct relationship between cumulative signal phase and reading frame. Based on this observation, we have developed a model that indicates how likely it is for the ribosome to stay in frame throughout the process of elongation. We validate this model by analyzing verified coding sequences in E. coli.
Assuntos
Proteínas de Escherichia coli/fisiologia , Fases de Leitura Aberta , Fatores de Terminação de Peptídeos/fisiologia , RNA Ribossômico 16S/química , Ribossomos/fisiologia , Algoritmos , Códon , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Mutação da Fase de Leitura , Modelos Genéticos , Modelos Estatísticos , Modelos Teóricos , Hibridização de Ácido Nucleico , Fatores de Terminação de Peptídeos/metabolismo , RNA Mensageiro/metabolismo , Ribossomos/genética , Processamento de Sinais Assistido por Computador , SoftwareRESUMO
Two methods, power spectrum density analysis (PSD) and synchronization signal approximation, were investigated to determine if underlying periodic, free energy signals could be detected for the individual genes in this paper. These signals could be revealed assuming Watson-Crick type hybridization between the eight, 3'-terminal nucleotides of the 18S rRNA and pre- and mature-mRNA sequences in Saccharomyces cerevisiae in a manner similar to that used to analyze coding region sequences in prokaryotic genes. Using PSD, a periodic signal could only be detected in 35 of 106 genes tested; using the synchronization signal approximation, 91 of 106 genes showed linearly increasing magnitude and phase, characteristics consistent with the presence of an underlying periodic signal with an assumed frequency of one-third. The majority of introns did not show magnitude and phase behavior consistent with an underlying non-periodic signal. The periodicity property for the free energy on the protein-coding regions can contribute to finding the approximate boundaries of the exons (protein coding regions) and the introns, which provides a foundation for future studies in identifying the exact positions of the splice sites, especially for the higher eukaryotic genes.
Assuntos
Genoma Fúngico , Saccharomyces cerevisiae/genética , Regiões 3' não Traduzidas/genética , DNA Fúngico/genética , Código Genético , Íntrons/genética , Hibridização de Ácido Nucleico , RNA Fúngico/genética , RNA Mensageiro/genética , RNA Ribossômico/genética , RNA Ribossômico 18S/genética , TermodinâmicaRESUMO
This work reports on a novel signal processing method that can be applied to analysis of genetic sequences in prokaryotes to identify their translational characteristics. The methodology involves computation of a signal based on free-energy score of the interaction between the 3' tail end of the 16S rRNA and the mRNA sequence of interest. We find that in the coding region of prokaryotes this signal is has a strong harmonic corresponding to every 3/sup rd/ base position. Noncoding regions appears not have such a signal. We discuss the methodology in detail and we demonstrate its ability to clearly recognize a) the coding region of a single prokaryotic gene, and b) special characteristics of the gene, such as frameshifts. We use E. Coli K-12 genes to illustrate the findings.