page_title: Overlapping gene
section_title: Viruses
hierarchical_section_title: Overlapping gene / Taxonomic distribution / Viruses
caption_attribution_description: English: The RNA silencing suppressor p19 from the tomato bushy stunt virus, rendered from PDB ID 1R9F. The protein forms a dimer whose two monomers are shown in blue and green. The dimer forms an interaction surface that binds double-stranded RNAs of 19 to 21 base pairs. Plants use RNA silencing as a defense mechanism against viruses; the p19 protein serves as a viral counter-defense that specifically binds siRNAs and suppresses the silencing machinery. Keqiong Ye, Lucy Malinina &amp; Dinshaw J. Patel. Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature 426, 874-878 (18 December 2003). DOI: 10.1038/nature02213. http://www.nature.com/nature/journal/v426/n6968/full/nature02213.html
context_page_description: An overlapping gene is a gene whose expressible nucleotide sequence partially overlaps with the expressible nucleotide sequence of another gene. In this way, a nucleotide sequence may make a contribution to the function of one or more gene products. Overprinting refers to a type of overlap in which all or part of the sequence of one gene is read in an alternate reading frame from another gene at the same locus. Overprinting has been hypothesized as a mechanism for de novo emergence of new genes from existing sequences, either older genes or previously non-coding regions of the genome. Overprinted genes are particularly common features of the genomic organization of viruses, likely to greatly increase the number of potential expressible genes from a small set of viral genetic information.
context_section_description: The existence of overlapping genes was first identified in viruses; the first DNA genome ever sequenced, of the bacteriophage ΦX174, contained several examples. Overlapping genes are particularly common in viral genomes. 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. 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. Overprinting is a common source of de novo genes in viruses.
  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. In some cases overprinted proteins do have well-defined, but novel, three-dimensional structures; 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.
caption: 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.[19]
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