The combinatorics of overlapping genes

DOI10.1016/J.JTBI.2016.09.018MaRDI QIDQ2013690zbMATH OpenOpenAlexWikidataFDO

Authors Sophie Lèbre, O. Gascuel

Publication date 9 August 2017

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1602.04971

zbMATH Keywords

genetic codecodon usageamino-acid compositiondouble-coding sequenceslinear and logical constraintsoverlapping gene detectionstop codons

Mathematics Subject Classification ID

Permutations, words, matrices (05A05) Applications of graph theory (05C90) Biochemistry, molecular biology (92C40)

Abstract: Overlapping genes exist in all domains of life and are much more abundant than expected at their first discovery in the late 1970s. Assuming that the reference gene is read in frame +0, an overlapping gene can be encoded in two reading frames in the sense strand, denoted by +1 and +2, and in three reading frames in the opposite strand, denoted by -0, -1 and -2. This motivated numerous researchers to study the constraints induced by the genetic code on the various overlapping frames, mostly based on information theory. Our focus in this paper is on the constraints induced on two overlapping genes in terms of amino acids, as well as polypeptides. We show that simple linear constraints bind the amino acid composition of two proteins encoded by overlapping genes. Novel constraints are revealed when polypeptides are considered, and not just single amino acids. For example, in double-coding sequences with an overlapping reading frame -2, each Tyrosine (denoted as Tyr or Y) in the overlapping frame overlaps a Tyrosine in the reference frame +0 (and reciprocally), whereas specific words (e.g. YY) never occur. We thus distinguish between null constraints (YY = 0 in frame -2) and non-null constraints (Y in frame +0 <=> Y in frame -2). Our equivalence-based constraints are symmetrical and thus enable the characterization of the joint composition of overlapping proteins. We describe several formal frameworks and a graph algorithm to characterize and compute these constraints. These results yield support for understanding the mechanisms and evolution of overlapping genes, and for developing novel overlapping gene detection methods.

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Cites work

• scientific article; zbMATH DE number 3755865 (Why is no real title available?)
• A new 5‐arc‐transitive cubic graph
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Cited in

(8)

• Positions of silent mutations in overlapping genes from different DNA strands
• scientific article; zbMATH DE number 1305428 (Why is no real title available?)
• Two proteins for the price of one: the design of maximally compressed coding sequences
• The Combinatorics of Sequencing the Corn Genome
• A theorem on the genetic code
• Overlapping genes coded in the 3'-to-5'-direction in mitochondrial genes and 3'-to-5' polymerization of non-complementary RNA by an `invertase'
• Overlapping genes in vertebrate genomes
• Overlapping genetic codes for overlapping frameshifted genes in Testudines, and \textit{Lepidochelys olivacea} as special case

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