Decay of host mRNAs by virus

Viruses have evolved ways of degrading host mRNAs to favor their survival and maximize expression of their own mRNAs. Inducing cellular mRNAs degradation eventually leads to shutoff of host proteins expression and gives viruses transcripts a competitive edge for access to the cellular translation machinery and counteract the antiviral response.
Most viruses proceed by expressing an endonuclease that cleaves host mRNAs, which are in turn degraded by an host exonuclease, like Xrn1 in mammals .

During the lytic replication cycle of Kaposi's sarcoma-associated herpesvirus (KSHV), SOX protein promotes massive cellular mRNAs decay through an endonucleotic internal cleavage of host mRNAs. The resulting RNA fragments are eliminated by the cellular RNA degradation machinery.

During the lytic replication cycle of Human herpesvirus 1 (HSV-1), VHS protein triggers accelerated degradation of host mRNAs and also seems to relocalize PABP. VHS would specifically target actively translated mRNAs through interactions with host EIF4F components (e.g. EIF4H, EIF4B, EIF4A2) and degrade them by endonucleotic RNA cleavage.

SARS NSP1 binds to 40s ribosomes and induces endonucleotic RNA cleavage of host mRNAs leading to their degradation. The presence of a 5'-end leader sequence protects SARS mRNAs from NSP1 cleavage.

Influenza A virus PA-X protein encoded on segment 3 by ribosomal frameshifting may have a messenger RNA endonuclease activity and play a role in the observed reduced cellular protein synthesis.

Viruses inducing host mRNA decay:

(Sub)Family Virus Viral protein mRNA decay strategy references
Coronaviridae SARS-CoV,bat-Cov ( Betacoronavirus ) NSP1 Endonucleotic mRNAs cleavage
Gammaherpesvirinae HHV-8/KSHV Shutoff alkaline exonuclease Endonucleotic mRNAs cleavage
MHV68 Shutoff alkaline exonuclease Endonucleotic mRNAs cleavage
EBV Shutoff alkaline exonuclease ?
Orthomyxoviridae Influenza A virus PA-X protein Endonucleotic mRNAs cleavage
Alphaherpesvirinae HHV-1 VHS protein Endonucleotic mRNAs cleavage

Matching UniProtKB/Swiss-Prot entries

58 entries grouped by strain (browse by keywords)

2 entries

Bat coronavirus 133/2005 (BtCoV) (BtCoV/133/2005) reference strain

Select_allDeselect_all
R1A_BC133 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...
R1AB_BC133 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...

2 entries

Bat coronavirus HKU4 (BtCoV) (BtCoV/HKU4/2004) reference strain

Select_allDeselect_all
R1AB_BCHK4 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...
R1A_BCHK4 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...

2 entries

Bat coronavirus HKU9 (BtCoV) (BtCoV/HKU9) reference strain

Select_allDeselect_all
R1AB_BCHK9 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...
R1A_BCHK9 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...

2 entries

Human coronavirus OC43 (HCoV-OC43) reference strain

Select_allDeselect_all
R1A_CVHOC Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...
R1AB_CVHOC Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...

2 entries

Murine coronavirus (strain 2) (MHV-2) (Murine hepatitis virus) reference strain

Select_allDeselect_all
R1AB_CVM2 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...
R1A_CVM2 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...

2 entries

Murine coronavirus (strain A59) (MHV-A59) (Murine hepatitis virus) reference strain

Select_allDeselect_all
R1A_CVMA5 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...
R1AB_CVMA5 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...

2 entries

Severe acute respiratory syndrome coronavirus (SARS-CoV) reference strain

Select_allDeselect_all
R1AB_SARS Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...
R1A_SARS Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...

2 entries

Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2) reference strain

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R1AB_SARS2 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...

pdb 5R7Y; 5R7Z; 5R80; 5R81; 5R82; 5R83; 5R84; 5R8T; 5RE4; 5RE5; 5RE6; 5RE7; 5RE8; 5RE9; 5REA; 5REB; 5REC; 5RED; 5REE; 5REF; 5REG; 5REH; 5REI; 5REJ; 5REK; 5REL; 5REM; 5REN; 5REO; 5REP; 5RER; 5RES; 5RET; 5REU; 5REV; 5REW; 5REX; 5REY; 5REZ; 5RF0; 5RF1; 5RF2; 5RF3; 5RF4; 5RF5; 5RF6; 5RF7; 5RF8; 5RF9; 5RFA; 5RFB; 5RFC; 5RFD; 5RFE; 5RFF; 5RFG; 5RFH; 5RFI; 5RFJ; 5RFK; 5RFL; 5RFM; 5RFN; 5RFO; 5RFP; 5RFQ; 5RFR; 5RFS; 5RFT; 5RFU; 5RFV; 5RFW; 5RFX; 5RFY; 5RFZ; 5RG0; 5RG1; 5RG2; 5RG3; 5RGG; 5RGH; 5RGI; 5RGJ; 5RGK; 5RGL; 5RGM; 5RGN; 5RGO; 5RGP; 5RGQ; 5RGR; 5RGS; 5RGT; 5RGU; 5RGV; 5RGW; 5RGX; 5RGY; 5RGZ; 5RH0; 5RH1; 5RH2; 5RH3; 5RH4; 5RH5; 5RH6; 5RH7; 5RH8; 5RH9; 5RHA; 5RHB; 5RHC; 5RHD; 5RHE; 5RHF; 5RL6; 5RL7; 5RL8; 5RL9; 5RLB; 5RLC; 5RLD; 5RLE; 5RLF; 5RLG; 5RLH; 5RLI; 5RLJ; 5RLK; 5RLL; 5RLM; 5RLN; 5RLO; 5RLP; 5RLQ; 5RLR; 5RLS; 5RLT; 5RLU; 5RLV; 5RLW; 5RLY; 5RLZ; 5RM0; 5RM1; 5RM2; 5RM3; 5RM4; 5RM5; 5RM6; 5RM7; 5RM8; 5RM9; 5RMA; 5RMB; 5RMC; 5RMD; 5RME; 5RMF; 5RMG; 5RMH; 5RMI; 5RMJ; 5RMK; 5RML; 5RMM; 6LU7; 6LZE; 6M03; 6M0K; 6M2N; 6M2Q; 6M71; 6VWW; 6VXS; 6W01; 6W02; 6W4B; 6W4H; 6W61; 6W63; 6W6Y; 6W75; 6W9C; 6W9Q; 6WC1; 6WCF; 6WEN; 6WEY; 6WIQ; 6WJT; 6WKQ; 6WKS; 6WLC; 6WNP; 6WOJ; 6WQ3; 6WQD; 6WQF; 6WRH; 6WRZ; 6WTC; 6WTJ; 6WTK; 6WTM; 6WTT; 6WUU; 6WVN; 6WX4; 6WXC; 6WXD; 6WZU; 6X1B; 6X4I; 6XA4; 6XA9; 6XAA; 6XB0; 6XB1; 6XB2; 6XBG; 6XBH; 6XBI; 6XCH; 6XDH; 6XFN; 6XG3; 6XHM; 6XHU; 6XIP; 6XKF; 6XKH; 6XKM; 6XMK; 6XOA; 6XQS; 6XQT; 6XQU; 6XR3; 6Y2E; 6Y2F; 6Y2G; 6Y84; 6YB7; 6YNQ; 6YT8; 6YVA; 6YVF; 6YWK; 6YWL; 6YWM; 6YYT; 6YZ1; 6YZ6; 6Z2E; 6ZCT; 6ZLW; 6ZM7; 6ZME; 6ZMI; 6ZMO; 6ZMT; 6ZN5; 6ZOJ; 6ZOK; 6ZON; 6ZP4; 6ZPE; 6ZRT; 6ZRU; 6ZSL; 7AKU; 7BQ7; 7BQY; 7BRO; 7BRP; 7BTF; 7BUY; 7BV1; 7BV2; 7BZF; 7C2I; 7C2J; 7C2K; 7C2Q; 7C2Y; 7C6S; 7C6U; 7C7P; 7C8B; 7C8R; 7C8T; 7C8U; 7CBT; 7CJD; 7CJM; 7CMD; 7COM; 7CWB; 7CWC; 7CX9; 7D1M; 7D1O; 7JFQ; 7JHE; 7JIB; 7JKV; 7JME; 7JOY; 7JP1; 7JPE; 7JR3; 7JR4; 7JU7; 7JUN; 7JVZ; 7JYC; 7JYY; 7JZ0; 7K1L; 7K1O; 7K3N; 7K3T; 7K40; 7K5I; 7K6D; 7K6E; 7K7P; 7K9P; 7KAG; 7KFI; 7KFJ; 7KG3; 7KHP

R1A_SARS2 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Host translation inhibitor nsp1 ...

1 entry

Alcelaphine herpesvirus 1 (strain C500) (AlHV-1) (Malignant catarrhal fever virus) reference strain

AN_ALHV1 Shutoff alkaline exonuclease (SOX) (EC 3.1.-.-)

1 entry

Bat coronavirus HKU5 (BtCoV) (BtCoV/HKU5/2004) reference strain

R1AB_BCHK5 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...

1 entry

Epstein-Barr virus (strain AG876) (HHV-4) (Human herpesvirus 4) reference strain

AN_EBVA8 Shutoff alkaline exonuclease (SOX) (EC 3.1.-.-)

1 entry

Epstein-Barr virus (strain B95-8) (HHV-4) (Human herpesvirus 4) reference strain

AN_EBVB9 Shutoff alkaline exonuclease (SOX) (EC 3.1.-.-)

1 entry

Equine herpesvirus 1 (strain Ab4p) (EHV-1) (Equine abortion virus) reference strain

SHUT_EHV1B Virion host shutoff protein (Vhs) (EC 3.1.27.-)

1 entry

Equine herpesvirus 2 (strain 86/87) (EHV-2) reference strain

AN_EHV2 Shutoff alkaline exonuclease (SOX) (EC 3.1.-.-)

1 entry

Gallid herpesvirus 2 (strain Chicken/Md5/ATCC VR-987) (GaHV-2) (Marek's disease herpesvirus type 1) reference strain

SHUT_GAHVM Virion host shutoff protein (Vhs) (EC 3.1.27.-)

1 entry

Human herpesvirus 1 (strain 17) (HHV-1) (Human herpes simplex virus 1) reference strain

SHUT_HHV11 Virion host shutoff protein (Vhs) (EC 3.1.27.-)

1 entry

Human herpesvirus 2 (strain HG52) (HHV-2) (Human herpes simplex virus 2) reference strain

SHUT_HHV2H Virion host shutoff protein (Vhs) (EC 3.1.27.-)

1 entry

Human herpesvirus 8 type P (isolate GK18) (HHV-8) (Kaposi's sarcoma-associated herpesvirus) reference strain

AN_HHV8P Shutoff alkaline exonuclease (SOX) (EC 3.1.-.-)

1 entry

Psittacid herpesvirus 1 (isolate Amazon parrot/-/97-0001/1997) (PsHV-1) (Pacheco's disease virus) reference strain

SHUT_PSHV1 Virion host shutoff protein (Vhs) (EC 3.1.27.-)

1 entry

Varicella-zoster virus (strain Dumas) (HHV-3) (Human herpesvirus 3) reference strain

SHUT_VZVD Virion host shutoff protein (Vhs) (EC 3.1.27.-)

2 entries

Bat coronavirus 279/2005 (BtCoV) (BtCoV/279/2005)

Select_allDeselect_all
R1A_BC279 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...
R1AB_BC279 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...

2 entries

Bat coronavirus HKU3 (BtCoV) (SARS-like coronavirus HKU3)

Select_allDeselect_all
R1AB_BCHK3 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...
R1A_BCHK3 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...

2 entries

Bat coronavirus Rp3/2004 (BtCoV/Rp3/2004) (SARS-like coronavirus Rp3)

Select_allDeselect_all
R1A_BCRP3 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...
R1AB_BCRP3 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...

2 entries

Bovine coronavirus (strain 98TXSF-110-ENT) (BCoV-ENT) (BCV)

Select_allDeselect_all
R1AB_CVBEN Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...
R1A_CVBEN Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...

2 entries

Bovine coronavirus (strain 98TXSF-110-LUN) (BCoV-LUN) (BCV)

Select_allDeselect_all
R1AB_CVBLU Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...
R1A_CVBLU Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...

2 entries

Bovine coronavirus (strain Mebus) (BCoV) (BCV)

Select_allDeselect_all
R1A_CVBM Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...
R1AB_CVBM Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...

2 entries

Bovine coronavirus (strain Quebec) (BCoV) (BCV)

Select_allDeselect_all
R1A_CVBQ Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...
R1AB_CVBQ Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...

2 entries

Human coronavirus HKU1 (isolate N1) (HCoV-HKU1)

Select_allDeselect_all
R1AB_CVHN1 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...
R1A_CVHN1 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...

2 entries

Human coronavirus HKU1 (isolate N2) (HCoV-HKU1)

Select_allDeselect_all
R1A_CVHN2 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...
R1AB_CVHN2 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...

2 entries

Human coronavirus HKU1 (isolate N5) (HCoV-HKU1)

Select_allDeselect_all
R1A_CVHN5 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...
R1AB_CVHN5 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...

2 entries

Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012) (MERS-CoV) (Betacoronavirus England 1)

Select_allDeselect_all
R1AB_MERS1 Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...
R1A_MERS1 Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Host translation inhibitor nsp1 ...

2 entries

Murine coronavirus (strain JHM) (MHV-JHM) (Murine hepatitis virus)

Select_allDeselect_all
R1AB_CVMJH Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor ...
R1A_CVMJH Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [Cleaved into: Non-structural protein 1 (nsp1) ...

1 entry

Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4)

AN_EBVG Shutoff alkaline exonuclease (SOX) (EC 3.1.-.-)

1 entry

Equine herpesvirus 1 (strain V592) (EHV-1) (Equine abortion virus)

SHUT_EHV1V Virion host shutoff protein (Vhs) (EC 3.1.27.-)

1 entry

Human herpesvirus 1 (strain KOS) (HHV-1) (Human herpes simplex virus 1)

SHUT_HHV1K Virion host shutoff protein (Vhs) (EC 3.1.27.-)

1 entry

Human herpesvirus 2 (strain 333) (HHV-2) (Human herpes simplex virus 2)

SHUT_HHV23 Virion host shutoff protein (Vhs) (EC 3.1.27.-)

1 entry

Human herpesvirus 2 (strain G) (HHV-2) (Human herpes simplex virus 2)

SHUT_HHV2G Virion host shutoff protein (Vhs) (EC 3.1.27.-)

1 entry

Suid herpesvirus 1 (strain Kaplan) (SuHV-1) (Pseudorabies virus (strain Kaplan))

SHUT_SUHVK Virion host shutoff protein (Vhs) (EC 3.1.27.-)