ORF3b

ORF3b
Identifiers
OrganismSARS-CoV
SymbolORF3b
UniProtP59633
Search for
StructuresSwiss-model
DomainsInterPro
ORF3b
Identifiers
OrganismSARS-CoV-2
SymbolORF3b
UniProtP0DTF1
Search for
StructuresSwiss-model
DomainsInterPro

ORF3b is a gene found in coronaviruses of the subgenus Sarbecovirus, encoding a short non-structural protein. It is present in both SARS-CoV (which causes the disease SARS) and SARS-CoV-2 (which causes COVID-19), though the protein product has very different lengths in the two viruses. The encoded protein is significantly shorter in SARS-CoV-2, at only 22 amino acid residues compared to 153–155 in SARS-CoV.[1][2] Both the longer SARS-CoV and shorter SARS-CoV-2 proteins have been reported as interferon antagonists.[2] It is unclear whether the SARS-CoV-2 gene expresses a functional protein.[3]

Nomenclature

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There has been significant confusion in the scientific literature around the nomenclature used for the accessory proteins of SARS-CoV-2, especially several overlapping genes with ORF3a.[1] Due to differences in the genomes of SARS-CoV and SARS-CoV-2, two distinct open reading frames (ORFs) in the SARS-CoV-2 genome have been referred to as "ORF3b". In SARS-CoV, ORF3b is a gene of 155 codons. In SARS-CoV-2, the homologous region of the genome includes several stop codons in the same reading frame, resulting in a truncated gene of 22 codons. As a result, some papers have used the term "ORF3b" to refer to a later ORF with 57 codons.[1] Exacerbating the confusion, both the 57-codon protein product[4] and the 22-codon protein product[2] have been described to have similar effects as interferon antagonists.[1] In addition, the putative product of yet a third ORF of 41 codons has at least once been described as "3b protein".[5][1] Numerous publications on SARS-CoV-2 refer ambiguously to "ORF3b".[1]

The recommended nomenclature for SARS-CoV-2 uses the term ORF3b for the 22-codon gene homologous to the 5' end of ORF3b in SARS-CoV. The term ORF3c is used for the 41-codon gene and the term ORF3d is used for the 57-codon gene.[1]

Comparative genomics

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Like other genes encoding accessory proteins, ORF3b is located in the genome near the genes encoding viral structural proteins. It is one of several overlapping genes in this region of the genome, overlapping ORF3a and, in SARS-CoV, the E gene encoding the envelope protein.[1] Its length varies significantly, from 22 amino acids in SARS-CoV-2 to around 155 residues in SARS-CoV,[1] with other related bat coronaviruses exhibiting intermediate truncations of varying lengths.[6][7] It is the only ORF in the Sarbecovirus subgenus with significant length variations among known related viruses.[2] Its sequence is not well conserved within the SARSr-CoV species.[3]

Expression and localization

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In SARS-CoV, the ORF3b protein is translated through an internal ribosome entry site (IRES).[8] It has a nuclear localization signal at the C-terminus and has been localized to the nucleolus and mitochondria.[8] It is not essential for viral replication.[8]

In SARS-CoV-2, it is unclear if ORF3b is functional. Proteomics studies, RNA sequencing of subgenomic RNA, ribosome profiling, and comparative genomics have all been used to examine the functional gene content of SARS-CoV-2 and found little evidence that ORF3b expresses a functional protein.[3] The SARS-CoV-2 protein has been reported to localize primarily to the cytosol when expressed in cell culture.[2] Truncated forms of the protein from bat coronaviruses are also reportedly cytosolic, likely due to loss of the C-terminal nuclear localization sequence.[7]

Function

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Cell growth

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In SARS-CoV, ORF3b has been reported to induce G0/G1 cell cycle arrest and apoptosis when studied in cell culture.[8][9]

Interferon antagonist

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In SARS-CoV, ORF3b has been described as an interferon antagonist, suppressing the type I interferon response through inhibition of IRF3.[8] Studies of the truncated SARS-CoV-2 ORF3b protein in cell culture suggest it is a more potent interferon antagonist than the SARS-CoV protein, which may be related to its length and to differences in subcellular localization.[2]

Effect on AP-1

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In SARS-CoV, ORF3b protein reportedly activates the transcription factor AP-1 through the JNK and ERK signaling pathways.[10][8]

References

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  1. ^ a b c d e f g h i Jungreis I, Nelson CW, Ardern Z, Finkel Y, Krogan NJ, Sato K, et al. (June 2021). "Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution". Virology. 558: 145–151. doi:10.1016/j.virol.2021.02.013. hdl:1721.1/130363. PMC 7967279. PMID 33774510.
  2. ^ a b c d e f Konno Y, Kimura I, Uriu K, Fukushi M, Irie T, Koyanagi Y, et al. (September 2020). "SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant". Cell Reports. 32 (12): 108185. doi:10.1016/j.celrep.2020.108185. PMC 7473339. PMID 32941788.
  3. ^ a b c Jungreis I, Sealfon R, Kellis M (May 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. hdl:1721.1/130581. PMC 8113528. PMID 33976134.
  4. ^ Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. (February 2020). "Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding". Lancet. 395 (10224): 565–574. doi:10.1016/S0140-6736(20)30251-8. PMC 7159086. PMID 32007145.
  5. ^ Pavesi A (July 2020). "New insights into the evolutionary features of viral overlapping genes by discriminant analysis". Virology. 546: 51–66. doi:10.1016/j.virol.2020.03.007. PMC 7157939. PMID 32452417.
  6. ^ Hu B, Zeng LP, Yang XL, Ge XY, Zhang W, Li B, et al. (November 2017). "Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus". PLOS Pathogens. 13 (11): e1006698. doi:10.1371/journal.ppat.1006698. PMC 5708621. PMID 29190287.
  7. ^ a b Zhou P, Li H, Wang H, Wang LF, Shi Z (February 2012). "Bat severe acute respiratory syndrome-like coronavirus ORF3b homologues display different interferon antagonist activities". The Journal of General Virology. 93 (Pt 2): 275–281. doi:10.1099/vir.0.033589-0. PMID 22012463.
  8. ^ a b c d e f Liu DX, Fung TS, Chong KK, Shukla A, Hilgenfeld R (September 2014). "Accessory proteins of SARS-CoV and other coronaviruses". Antiviral Research. 109: 97–109. doi:10.1016/j.antiviral.2014.06.013. PMC 7113789. PMID 24995382.
  9. ^ Yuan X, Shan Y, Zhao Z, Chen J, Cong Y (August 2005). "G0/G1 arrest and apoptosis induced by SARS-CoV 3b protein in transfected cells". Virology Journal. 2 (66): 66. doi:10.1186/1743-422X-2-66. PMC 1190220. PMID 16107218.
  10. ^ Varshney B, Lal SK (June 2011). "SARS-CoV accessory protein 3b induces AP-1 transcriptional activity through activation of JNK and ERK pathways". Biochemistry. 50 (24): 5419–5425. doi:10.1021/bi200303r. PMID 21561061.
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