About: Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes

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About: Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes
Creator	Karlin, David Belshaw, Robert Bao, Yiming Blinkova, Olga Pavesi, Angelo Chirico, Nicola Firth, Andrew Vianelli, Alberto
Source	PMC
abstract	Overlapping genes represent a fascinating evolutionary puzzle, since they encode two functionally unrelated proteins from the same DNA sequence. They originate by a mechanism of overprinting, in which point mutations in an existing frame allow the expression (the %22birth%22) of a completely new protein from a second frame. In viruses, in which overlapping genes are abundant, these new proteins often play a critical role in infection, yet they are frequently overlooked during genome annotation. This results in erroneous interpretation of mutational studies and in a significant waste of resources. Therefore, overlapping genes need to be correctly detected, especially since they are now thought to be abundant also in eukaryotes. Developing better detection methods and conducting systematic evolutionary studies require a large, reliable benchmark dataset of known cases. We thus assembled a high-quality dataset of 80 viral overlapping genes whose expression is experimentally proven. Many of them were not present in databases. We found that overall, overlapping genes differ significantly from non-overlapping genes in their nucleotide and amino acid composition. In particular, the proteins they encode are enriched in high-degeneracy amino acids and depleted in low-degeneracy ones, which may alleviate the evolutionary constraints acting on overlapping genes. Principal component analysis revealed that the vast majority of overlapping genes follow a similar composition bias, despite their heterogeneity in length and function. Six proven mammalian overlapping genes also followed this bias. We propose that this apparently near-universal composition bias may either favour the birth of overlapping genes, or/and result from selection pressure acting on them.
has issue date	2018-10-19(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0202513
bibo:pmid	30339683
has license	cc0
sha1sum (hex)	17192bd07c09aa9e70552f7f15f90f0a6b8180c6
schema:url	https://doi.org/10.1371/journal.pone.0202513
resource representing a document's title	Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes
has PubMed Central identifier	PMC6195259
has PubMed identifier	30339683
schema:publication	PLoS One
resource representing a document's body	covid:17192bd07c09aa9e70552f7f15f90f0a6b8180c6#body_text
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