Overlapping gene

A cladogram indicating the likely evolutionary trajectory of the gene-dense pX region in human T-lymphotropic virus 1 (HTLV1), a deltaretrovirus associated with blood cancers. This region contains numerous overlapping genes, several of which likely originated de novo through overprinting.[4]

In 1977, Pierre-Paul Grassé proposed that one of the genes in the pair could have originated de novo by mutations to introduce novel ORFs in alternate reading frames; he described the mechanism as overprinting.[15]^:231 It was later substantiated by Susumu Ohno, who identified a candidate gene that may have arisen by this mechanism.[16] Some de novo genes originating in this way may not remain overlapping, but subfunctionalize following gene duplication,[3] contributing to the prevalence of orphan genes. Which member of an overlapping gene pair is younger can be identified bioinformatically either by a more restricted phylogenetic distribution, or by less optimized codon usage.[4][17][18] Younger members of the pair tend to have higher intrinsic structural disorder than older members, but the older members are also more disordered than other proteins, presumably as a way of alleviating the increased evolutionary constraints posed by overlap.[17] Overlaps are more likely to originate in proteins that already have high disorder.[17]

The RNA silencing suppressor p19 from tomato bushy stunt virus, a protein encoded by an overprinted gene. The protein specifically binds siRNAs produced as part of the plant's RNA silencing defense against viruses.[20]

The existence of overlapping genes was first identified in viruses; the first DNA genome ever sequenced, of the bacteriophage ΦX174, contained several examples.[19] Another example is the ORF3d gene in the SARS-CoV 2 virus.[1][21] Overlapping genes are particularly common in viral genomes.[4] Some studies attribute this observation to selective pressure toward small genome sizes mediated by the physical constraints of packaging the genome in a viral capsid, particularly one of icosahedral geometry.[22] However, other studies dispute this conclusion and argue that the distribution of overlaps in viral genomes is more likely to reflect overprinting as the evolutionary origin of overlapping viral genes.[23] Overprinting is a common source of de novo genes in viruses.[18]

Studies of overprinted viral genes suggest that their protein products tend to be accessory proteins which are not essential to viral proliferation, but contribute to pathogenicity. Overprinted proteins often have unusual amino acid distributions and high levels of intrinsic disorder.[24] In some cases overprinted proteins do have well-defined, but novel, three-dimensional structures;[25] one example is the RNA silencing suppressor p19 found in Tombusviruses, which has both a novel protein fold and a novel binding mode in recognizing siRNAs.[18][20][26]

Estimates of gene overlap in bacterial genomes typically find that around one third of bacterial genes are overlapped, though usually only by a few base pairs.[7][27][28] Most studies of overlap in bacterial genomes find evidence that overlap serves a function in gene regulation, permitting the overlapped genes to be transcriptionally and translationally co-regulated.[7][13] In prokaryotic genomes, unidirectional overlaps are most common, possibly due to the tendency of adjacent prokaryotic genes to share orientation.[7][9][6] Among unidirectional overlaps, long overlaps are more commonly read with a one-nucleotide offset in reading frame (i.e., phase 1) and short overlaps are more commonly read in phase 2.[28][29] Long overlaps of greater than 60 base pairs are more common for convergent genes; however, putative long overlaps have very high rates of misannotation.[30] Robustly validated examples of long overlaps in bacterial genomes are rare; in the well-studied model organism Escherichia coli, only four gene pairs are well validated as having long, overprinted overlaps.[31]

Compared to prokaryotic genomes, eukaryotic genomes are often poorly annotated and thus identifying genuine overlaps is relatively challenging.[18] However, examples of validated gene overlaps have been documented in a variety of eukaryotic organisms, including mammals such as mice and humans.[32][33][34][35] Eukaryotes differ from prokaryotes in distribution of overlap types: while unidirectional (i.e., same-strand) overlaps are most common in prokaryotes, opposite or antiparallel-strand overlaps are more common in eukaryotes. Among the opposite-strand overlaps, convergent orientation is most common.[33] Most studies of eukaryotic gene overlap have found that overlapping genes are extensively subject to genomic reorganization even in closely related species, and thus the presence of an overlap is not always well-conserved.[34][36] Overlap with older or less taxonomically restricted genes is also a common feature of genes likely to have originated de novo in a given eukaryotic lineage.[34][37][38]