ORF10
From Wikipedia the free encyclopedia
| Orf10 protein, SARS-CoV-2 | |
|---|---|
| Identifiers | |
| Symbol | Orf10_SARS-CoV-2 |
| InterPro | IPR044342 |
ORF10 is an open reading frame (ORF) found in the genome of the SARS-CoV-2 coronavirus. It is 38 codons long.[1] It is not conserved in all Sarbecoviruses (including SARS-CoV). In studies prompted by the COVID-19 pandemic, ORF10 attracted research interest as one of two viral accessory protein genes not conserved between SARS-CoV and SARS-CoV-2[2] and was initially described as a protein-coding gene likely under positive selection.[3] However, although it is sometimes included in lists of SARS-CoV-2 accessory genes, experimental and bioinformatics evidence suggests ORF10 is likely not a functional protein-coding gene.[4]
Properties[edit]
ORF10 is located downstream of the N gene, which encodes coronavirus nucleocapsid protein. It is the annotated open reading frame furthest to the 3' end of the genome. It encodes a 38-amino acid hypothetical protein.[1]
Expression and function[edit]
It is unlikely that ORF10 is translated under natural conditions, since subgenomic RNA containing the ORF10 region is not detected, though there is some ribosome footprinting signal.[5] When experimentally overexpressed, the ORF10 protein has been reported to interact with ZYG11B and its cullin-RING ligase protein complex.[6] However, this interaction has been shown to be dispensable in in vitro studies of the viral life cycle.[7]
Evolution[edit]
Some studies of SARS-CoV-2 genomes have described ORF10 as likely to be functional and under positive selection.[3] However, premature stop codons have been identified in SARS-CoV-2 variants[8] and in many Sarbecovirus sequences, suggesting that the putative protein product is not essential for viral replication.[4] Loss of ORF10 has also shown no effect on replication under experimental conditions in vitro.[8] It has been suggested through bioinformatics analysis that apparent sequence conservation in SARS-CoV-2 ORF10 may not be due to a protein-coding function, but instead due to conserved RNA secondary structure in the region.[4] The conserved region, which extends beyond ORF10 itself, overlaps with the coronavirus 3' UTR pseudoknot region, a secondary structure known to be involved in genome replication.[4]
References[edit]
- ^ a b Redondo, Natalia; Zaldívar-López, Sara; Garrido, Juan J.; Montoya, Maria (7 July 2021). "SARS-CoV-2 Accessory Proteins in Viral Pathogenesis: Knowns and Unknowns". Frontiers in Immunology. 12: 708264. doi:10.3389/fimmu.2021.708264. PMC 8293742. PMID 34305949.
- ^ Xu, Jiabao; Zhao, Shizhe; Teng, Tieshan; Abdalla, Abualgasim Elgaili; Zhu, Wan; Xie, Longxiang; Wang, Yunlong; Guo, Xiangqian (22 February 2020). "Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV". Viruses. 12 (2): 244. doi:10.3390/v12020244. PMC 7077191. PMID 32098422.
- ^ a b Cagliani, Rachele; Forni, Diego; Clerici, Mario; Sironi, Manuela (September 2020). "Coding potential and sequence conservation of SARS-CoV-2 and related animal viruses". Infection, Genetics and Evolution. 83: 104353. doi:10.1016/j.meegid.2020.104353. PMC 7199688. PMID 32387562.
- ^ a b c d Jungreis, Irwin; Sealfon, Rachel; Kellis, Manolis (December 2021). "SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes". Nature Communications. 12 (1): 2642. Bibcode:2021NatCo..12.2642J. doi:10.1038/s41467-021-22905-7. PMC 8113528. PMID 33976134.
- ^ Finkel, Yaara; Mizrahi, Orel; Nachshon, Aharon; Weingarten-Gabbay, Shira; Morgenstern, David; Yahalom-Ronen, Yfat; Tamir, Hadas; Achdout, Hagit; Stein, Dana; Israeli, Ofir; Beth-Din, Adi; Melamed, Sharon; Weiss, Shay; Israely, Tomer; Paran, Nir; Schwartz, Michal; Stern-Ginossar, Noam (7 January 2021). "The coding capacity of SARS-CoV-2". Nature. 589 (7840): 125–130. Bibcode:2021Natur.589..125F. doi:10.1038/s41586-020-2739-1. PMID 32906143. S2CID 221624633.
- ^ Gordon, David E.; et al. (16 July 2020). "A SARS-CoV-2 protein interaction map reveals targets for drug repurposing". Nature. 583 (7816): 459–468. Bibcode:2020Natur.583..459G. doi:10.1038/s41586-020-2286-9. PMC 7431030. PMID 32353859.
- ^ Mena, Elijah L.; Donahue, Callie J.; Vaites, Laura Pontano; Li, Jie; Rona, Gergely; O’Leary, Colin; Lignitto, Luca; Miwatani-Minter, Bearach; Paulo, Joao A.; Dhabaria, Avantika; Ueberheide, Beatrix; Gygi, Steven P.; Pagano, Michele; Harper, J. Wade; Davey, Robert A.; Elledge, Stephen J. (27 April 2021). "ORF10–Cullin-2–ZYG11B complex is not required for SARS-CoV-2 infection". Proceedings of the National Academy of Sciences. 118 (17): e2023157118. Bibcode:2021PNAS..11823157M. doi:10.1073/pnas.2023157118. PMC 8092598. PMID 33827988.
- ^ a b Pancer, Katarzyna; Milewska, Aleksandra; Owczarek, Katarzyna; Dabrowska, Agnieszka; Kowalski, Michał; Łabaj, Paweł P.; Branicki, Wojciech; Sanak, Marek; Pyrc, Krzysztof (10 December 2020). "The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans". PLOS Pathogens. 16 (12): e1008959. doi:10.1371/journal.ppat.1008959. PMC 7755277. PMID 33301543.
