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Ambush hypothesis revisited: Evidences for phylogenetic trends

Paper ID Volume ID Publish Year Pages File Format Full-Text
15385 1408 2009 6 PDF Available
Ambush hypothesis revisited: Evidences for phylogenetic trends

Recoding events occur in competition with standard readout of the transcript, and are site-specific. Recoding is the reprogramming of mRNA translation by localized alterations in the standard translational rules. Frame-shifting is one class of recoding and defined as protein translations that start not at the first, but either at the second (+1 frame-shift) or the third (−1 frame-shift) nucleotide of the codon. Coding sequences lack stop codons, but frame-shifted sequences contain many stop codons, termed off-frame stops or hidden stops. These hidden stops terminate frame-shifted translation, potentially decreasing energy, and resource waste on non-functional proteins. Our results support this putative ancient adaptive event for the selection of codons that can be part of hidden stop codons. All taxonomic groups represent positive correlation between codon usage frequencies and contribution of codons to hidden stops in off-frame context. Our analysis on nuclear and mitochondrial genomic data revealed phylogenomic selection of ambush mechanism. Strongest impact of this event was found in viruses and bacteria. It has been suggested that this mechanism has occurred and been utilized in the early stages of evolution.

Ambush hypothesis; Frame-shifting; Hidden stops; Codon usage; Phylogenetic trends
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Ambush hypothesis revisited: Evidences for phylogenetic trends
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 33, Issue 3, June 2009, Pages 239–244
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Physical Sciences and Engineering Chemical Engineering Bioengineering