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Overlapping genetic codes for overlapping frameshifted genes in Testudines, and Lepidochelys olivacea as special case

Paper ID Volume ID Publish Year Pages File Format Full-Text
15158 1383 2012 17 PDF Available
Title
Overlapping genetic codes for overlapping frameshifted genes in Testudines, and Lepidochelys olivacea as special case
Abstract

Mitochondrial genes code for additional proteins after +2 frameshifts by reassigning stops to code for amino acids, which defines overlapping genetic codes for overlapping genes. Turtles recode stops UAR → Trp and AGR → Lys (AGR → Gly in the marine Olive Ridley turtle, Lepidochelys olivacea). In Lepidochelys the +2 frameshifted mitochondrial Cytb gene lacks stops, open reading frames from other genes code for unknown proteins, and for regular mitochondrial proteins after frameshifts according to the overlapping genetic code. Lepidochelys’ inversion between proteins coded by regular and overlapping genetic codes substantiates the existence of overlap coding. ND4 differs among Lepidochelys mitochondrial genomes: it is regular in DQ486893; in NC_011516, the open reading frame codes for another protein, the regular ND4 protein is coded by the frameshifted sequence reassigning stops as in other turtles. These systematic patterns are incompatible with Genbank/sequencing errors and DNA decay. Random mixing of synonymous codons, conserving main frame coding properties, shows optimization of natural sequences for overlap coding; Ka/Ks analyses show high positive (directional) selection on overlapping genes. Tests based on circular genetic codes confirm programmed frameshifts in ND3 and ND4l genes, and predicted frameshift sites for overlap coding in Lepidochelys. Chelonian mitochondria adapt for overlapping gene expression: cloverleaf formation by antisense tRNAs with predicted anticodons matching stops coevolves with overlap coding; antisense tRNAs with predicted expanded anticodons (frameshift suppressor tRNAs) associate with frameshift-coding in ND3 and ND4l, a potential regulation of frameshifted overlap coding. Anaeroby perhaps switched between regular and overlap coding genes in Lepidochelys.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► Frameshifted turtle mitochondrial proteins match regular proteins. ► Frameshifted stops are reassigned to amino acids. ► AGR → Gly, Lys (Lepidochelys, other turtles); UAR → Trp. ► Lepidochelys CytB gene: 2 reading frames, for cytochrome B, and an unknown protein.

Keywords
Codon reassignment; tRNA synthetase; Codon usage; Synonymous codon optimization; Homology; Ribosomal frameshift; Termination codon
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Overlapping genetic codes for overlapping frameshifted genes in Testudines, and Lepidochelys olivacea as special case
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 41, December 2012, Pages 18–34
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us