Evidence of translation efficiency adaptation of the coding regions of the bacteriophage lambda.
Deciphering the way gene expression regulatory aspects are encoded in viral genomes is a challenging mission with ramifications related to all biomedical disciplines. Here, we aimed to understand how the evolution shapes the bacteriophage lambda genes by performing a high resolution analysis of ribosomal profiling data and gene expression related synonymous/silent information encoded in bacteriophage coding regions.We demonstrated evidence of selection for distinct compositions of synonymous codons in early and late viral genes related to the adaptation of translation efficiency to different bacteriophage developmental stages. Specifically, we showed that evolution of viral coding regions is driven, among others, by selection for codons with higher decoding rates; during the initial/progressive stages of infection the decoding rates in early/late genes were found to be superior to those in late/early genes, respectively. Moreover, we argued that selection for translation efficiency could be partially explained by adaptation to Escherichia coli tRNA pool and the fact that it can change during the bacteriophage life cycle.An analysis of additional aspects related to the expression of viral genes, such as mRNA folding and more complex/longer regulatory signals in the coding regions, is also reported. The reported conclusions are likely to be relevant also to additional viruses.
Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv 69978, Israel.|SynVaccine Ltd Ramat Hachayal, Tel Aviv 6971039, Israel.
Eli
E
Goz
Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv 69978, Israel.
Oriah
O
Mioduser
Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv 69978, Israel.
Alon
A
Diament
Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv 69978, Israel.|SynVaccine Ltd Ramat Hachayal, Tel Aviv 6971039, Israel.|Sagol School of Neuroscience, Tel-Aviv University, Ramat Aviv 69978, Israel.
Tamir
T
Tuller
D000220:Adaptation, Biological; D010582:Bacteriophage lambda / Q000235:genetics* / Q000254:growth & development; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism / Q000821:virology; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D015967:Gene Expression Regulation, Viral; D005814:Genes, Viral; D014176:Protein Biosynthesis; D012329:RNA, Bacterial / Q000378:metabolism; D012343:RNA, Transfer / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism
D012329:RNA, Bacterial; D012343:RNA, Transfer
bacteriophage fitness; bacteriophage genome; coding regions evolution; decoding rates; ribosomes and tRNAs