Genome-wide analysis of protein–protein interactions and involvement of viral proteins in SARS-CoV-2 replication

Cell & Bioscience

Table 1 The sequences of SARS-CoV-2 used for interaction analysis

Protein	Coding sequence*	Position in polyprotein*	Protein length	Function described**
Nsp1	266–805	M1-G180	180	Inhibits host gene expression
Nsp2	806–2719	A181-G818	638
Nsp3.1	2720–4966	A819-T1568	749	ADRP, SUD for OGB
Nsp3.2	4967–7105	I1569-T2282	713	PLpro, DU
Nsp3.3	7106–8554	Y2283-G2765	483
Nsp4	8555–10054	K2766-Q3266	500	Membrane rearrangement, essential for viral replication
Nsp5	10055–10972	S3267-Q3572	306	3C-like proteinase
Nsp6	10973–11842	S3573-Q3863	290	TM
Nsp7	11843–12091	S3864-Q3945	81	dsRNA-binding
Nsp8	12092–12685	A3946-Q4144	198	dsRNA-binding & RdRP
Nsp9	12686–13024	N4145-Q4258	113	ssRNA-binding
Nsp10	13025–13441	A4259-Q4398	139	GFL
Nsp12	13442–16236	S4399-Q5331	932	RdRP
Nsp13	16237–18039	A5332-Q5933	601	The helicase enzyme, NTPase
Nsp14	18040–19620	A5934-Q6461	527	ExoN
Nsp15	19621–20658	S6462-Q6808	346	EndoRNase, degrades viral dsRNA
Nsp16	20659–21552	S6809-N7107	298	2ʹ-O-MT
S1	21563–23617	n/a	685	Spike (receptor-binding)
S2	23618–25384	n/a	588	Spike (fusion peptide & TM)
3	25393–26220	n/a	275	TM, ion channel, antagonist of IFN
E	26245–26472	n/a	75	envelope
M	26523–27191	n/a	222	Membrane
6	27202–27387	n/a	61	Viral pathogenesis
7a	27394–27759	n/a	121
7b	27756–27884	n/a	43
8	27894–28259	n/a	121	Disrupts antigen presentation
N	28274–29533	n/a	419	Binds viral RNA, antagonize antiviral RNAi
10	29558–29674	n/a	38

n/a not applied
*The coordinate of the sequence is based on the genome of severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1 (NCBI Reference Sequence: NC_045512.2)
**Abbreviations: ADRP adenosine diphosphate-ribose 1”-phosphatase, SUD SARS Unique Domain, OGB oligo(G)-binding, PLpro papain-like cysteine proteinase, DU deubiquitinating activity, TM transmembrane domain, RdRP RNA-dependent RNA polymerase, GFL growth-factor-like protein, NTPase NTP and RNA 5’ triphosphatase, ExoN 3’ to 5’ exonuclease, 2’-O-MT S-adenosylmethionine-dependent ribose 2’-O-methyltransferase, IFN interferon

ISSN: 2045-3701