RDRP_RCNMV
ID RDRP_RCNMV Reviewed; 767 AA.
AC P22956; P22957; Q86156; Q86157;
DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1991, sequence version 2.
DT 29-SEP-2021, entry version 97.
DE RecName: Full=RNA-directed RNA polymerase;
DE EC=2.7.7.48;
DE AltName: Full=Protein p88;
GN ORFNames=ORF1;
OS Red clover necrotic mosaic virus (RCNMV).
OC Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Tolucaviricetes;
OC Tolivirales; Tombusviridae; Regressovirinae; Dianthovirus.
OX NCBI_TaxID=12267;
OH NCBI_TaxID=3879; Medicago sativa (Alfalfa).
OH NCBI_TaxID=47083; Melilotus officinalis (Yellow sweet clover) (Trifolium officinale).
OH NCBI_TaxID=57577; Trifolium pratense (Red clover).
OH NCBI_TaxID=3899; Trifolium repens (Creeping white clover).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RC STRAIN=Australian;
RX PubMed=2763465; DOI=10.1016/0042-6822(89)90624-7;
RA Xiong Z., Lommel S.A.;
RT "The complete nucleotide sequence and genome organization of red clover
RT necrotic mosaic virus RNA-1.";
RL Virology 171:543-554(1989).
RN [2]
RP SEQUENCE REVISION.
RA Xiong Z., Lommel S.A.;
RL Submitted (MAY-2015) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP RIBOSOMAL FRAMESHIFT.
RX PubMed=8438566; DOI=10.1006/viro.1993.1117;
RA Xiong Z., Kim K.H., Kendall T.L., Lommel S.A.;
RT "Synthesis of the putative red clover necrotic mosaic virus RNA polymerase
RT by ribosomal frameshifting in vitro.";
RL Virology 193:213-221(1993).
RN [4]
RP SUBCELLULAR LOCATION.
RX PubMed=15016550; DOI=10.1016/j.virol.2003.12.006;
RA Turner K.A., Sit T.L., Callaway A.S., Allen N.S., Lommel S.A.;
RT "Red clover necrotic mosaic virus replication proteins accumulate at the
RT endoplasmic reticulum.";
RL Virology 320:276-290(2004).
RN [5]
RP FUNCTION.
RX PubMed=16096641; DOI=10.1038/sj.emboj.7600776;
RA Takeda A., Tsukuda M., Mizumoto H., Okamoto K., Kaido M., Mise K.,
RA Okuno T.;
RT "A plant RNA virus suppresses RNA silencing through viral RNA
RT replication.";
RL EMBO J. 24:3147-3157(2005).
RN [6]
RP SUBUNIT, AND FUNCTION.
RX PubMed=20375154; DOI=10.1128/jvi.00054-10;
RA Mine A., Takeda A., Taniguchi T., Taniguchi H., Kaido M., Mise K.,
RA Okuno T.;
RT "Identification and characterization of the 480-kilodalton template-
RT specific RNA-dependent RNA polymerase complex of red clover necrotic mosaic
RT virus.";
RL J. Virol. 84:6070-6081(2010).
RN [7]
RP SUBUNIT, AND FUNCTION.
RX PubMed=20828775; DOI=10.1016/j.virol.2010.07.038;
RA Mine A., Hyodo K., Takeda A., Kaido M., Mise K., Okuno T.;
RT "Interactions between p27 and p88 replicase proteins of Red clover necrotic
RT mosaic virus play an essential role in viral RNA replication and
RT suppression of RNA silencing via the 480-kDa viral replicase complex
RT assembly.";
RL Virology 407:213-224(2010).
RN [8]
RP FUNCTION, RNA-BINDING, AND MUTAGENESIS OF ARG-164; HIS-179 AND HIS-180.
RX PubMed=21440279; DOI=10.1016/j.virol.2011.02.017;
RA Hyodo K., Mine A., Iwakawa H.O., Kaido M., Mise K., Okuno T.;
RT "Identification of amino acids in auxiliary replicase protein p27 critical
RT for its RNA-binding activity and the assembly of the replicase complex in
RT Red clover necrotic mosaic virus.";
RL Virology 413:300-309(2011).
RN [9]
RP FUNCTION, AND RNA-BINDING.
RX PubMed=20980498; DOI=10.1128/jvi.01754-10;
RA Iwakawa H.O., Mine A., Hyodo K., An M., Kaido M., Mise K., Okuno T.;
RT "Template recognition mechanisms by replicase proteins differ between
RT bipartite positive-strand genomic RNAs of a plant virus.";
RL J. Virol. 85:497-509(2011).
RN [10]
RP FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF TRP-38; PHE-41; PHE-45;
RP PHE-46 AND LEU-48.
RX PubMed=22898643; DOI=10.1016/j.virol.2012.07.017;
RA Kusumanegara K., Mine A., Hyodo K., Kaido M., Mise K., Okuno T.;
RT "Identification of domains in p27 auxiliary replicase protein essential for
RT its association with the endoplasmic reticulum membranes in Red clover
RT necrotic mosaic virus.";
RL Virology 433:131-141(2012).
RN [11]
RP FUNCTION, INTERACTION WITH HOST ARF1, AND SUBCELLULAR LOCATION.
RX PubMed=23097452; DOI=10.1128/jvi.02383-12;
RA Hyodo K., Mine A., Taniguchi T., Kaido M., Mise K., Taniguchi H., Okuno T.;
RT "ADP ribosylation factor 1 plays an essential role in the replication of a
RT plant RNA virus.";
RL J. Virol. 87:163-176(2013).
RN [12]
RP FUNCTION, INTERACTION WITH HOST NBRBOHB, AND SUBCELLULAR LOCATION.
RX PubMed=28154139; DOI=10.1073/pnas.1610212114;
RA Hyodo K., Hashimoto K., Kuchitsu K., Suzuki N., Okuno T.;
RT "Harnessing host ROS-generating machinery for the robust genome replication
RT of a plant RNA virus.";
RL Proc. Natl. Acad. Sci. U.S.A. 114:E1282-E1290(2017).
RN [13]
RP FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH HOST NBRACK1.
RX PubMed=30169907; DOI=10.1111/nph.15412;
RA Hyodo K., Suzuki N., Okuno T.;
RT "Hijacking a host scaffold protein, RACK1, for replication of a plant RNA
RT virus.";
RL New Phytol. 221:935-945(2019).
CC -!- FUNCTION: RNA-dependent RNA polymerase, made of isoforms p88 and p27,
CC plays an essential role in the replication of the bipartite viral
CC genome composed of RNA-1 and RNA-2. Replicase proteins p88 and p27
CC interact together and selectively recruit viral replication templates
CC as well as other essential components into intracellular membranes for
CC the assembly of the 480 kDa viral replicase complex. Mechanistically,
CC isoform protein p27 binds to the Y-shaped RNA element (YRE) located in
CC the 3' UTR of RNA2 via a direct RNA-protein interaction and to RNA1 in
CC a translation-coupled manner. This RNA-binding activity allows RNA2
CC recruitment to host membranes. The viral replicase complex synthesizes
CC the dsRNA genome from the genomic ssRNA(+). It recognizes internal
CC subgenomic promoters on the negative-sense RNA to transcribe the 3' co-
CC terminal subgenomic RNAs that will generate the capsid and movement
CC proteins. In addition, the viral replication process requires the
CC trigger of an intracellular ROS burst mediated by p27 recruitment of
CC the host ROS-generating machinery. The viral replicase complex also
CC acts as a suppressor of RNA-mediated gene silencing, known as post-
CC transcriptional gene silencing (PTGS), a mechanism of plant viral
CC defense that limits the accumulation of viral RNAs.
CC {ECO:0000269|PubMed:20375154, ECO:0000269|PubMed:20828775,
CC ECO:0000269|PubMed:20980498, ECO:0000269|PubMed:21440279,
CC ECO:0000269|PubMed:22898643, ECO:0000269|PubMed:23097452,
CC ECO:0000269|PubMed:30169907}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC EC=2.7.7.48; Evidence={ECO:0000255|PROSITE-ProRule:PRU00539};
CC -!- SUBUNIT: [RNA-directed RNA polymerase]: Interacts with protein p27 (via
CC C-terminus) (PubMed:15016550, PubMed:20375154).
CC {ECO:0000269|PubMed:15016550, ECO:0000269|PubMed:20375154}.
CC -!- SUBUNIT: [Isoform protein p27]: Forms homooligomers (PubMed:15016550,
CC PubMed:20375154). interacts with host NbRACK1; this interaction is
CC required for efficient viral replication (PubMed:30169907). interacts
CC with host NbRBOHB; this interaction triggers an intracellular ROS
CC burst, important for viral replication (PubMed:28154139). Interacts
CC with host ARF1; this interaction is required for the assembly of the
CC viral replicase complex (PubMed:23097452).
CC {ECO:0000269|PubMed:15016550, ECO:0000269|PubMed:23097452,
CC ECO:0000269|PubMed:28154139, ECO:0000269|PubMed:30169907}.
CC -!- SUBCELLULAR LOCATION: [Isoform RNA-directed RNA polymerase p88]: Host
CC endoplasmic reticulum membrane {ECO:0000269|PubMed:15016550,
CC ECO:0000269|PubMed:23097452}.
CC -!- SUBCELLULAR LOCATION: [Isoform protein p27]: Host endoplasmic reticulum
CC membrane {ECO:0000269|PubMed:15016550, ECO:0000269|PubMed:22898643,
CC ECO:0000269|PubMed:23097452, ECO:0000269|PubMed:28154139,
CC ECO:0000269|PubMed:30169907}. Note=Associates with intracellular
CC membranes via membrane-association domain in the N-terminal region.
CC Membrane association is essential for RNA replication complex
CC formation. {ECO:0000269|PubMed:22898643}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Ribosomal frameshifting; Named isoforms=2;
CC Name=RNA-directed RNA polymerase p88; Synonyms=88 kDa protein;
CC IsoId=P22956-1; Sequence=Displayed;
CC Name=protein p27;
CC IsoId=P22956-2; Sequence=VSP_032886;
CC -!- MISCELLANEOUS: [Isoform RNA-directed RNA polymerase p88]: Produced by
CC ribosomal frameshifting between codons 236 and 237.
CC -!- MISCELLANEOUS: [Isoform protein p27]: Produced by conventional
CC translation. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the tombusviridae RNA polymerase family.
CC {ECO:0000305}.
CC -!- CAUTION: The 57-kDa protein cited in PubMed:2763465 has only been seen
CC in vitro and is likely not expressed in vivo. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB02541.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; J04357; AAB02539.1; -; Genomic_RNA.
DR EMBL; J04357; AAB02540.2; -; Genomic_RNA.
DR EMBL; J04357; AAB02541.1; ALT_SEQ; Genomic_RNA.
DR PIR; T10779; B43684.
DR RefSeq; NP_620523.2; NC_003756.1. [P22956-1]
DR RefSeq; NP_620524.1; NC_003756.1. [P22956-2]
DR RefSeq; NP_620525.1; NC_003756.1.
DR GeneID; 956630; -.
DR GeneID; 956631; -.
DR GeneID; 956632; -.
DR KEGG; vg:956630; -.
DR KEGG; vg:956631; -.
DR KEGG; vg:956632; -.
DR Proteomes; UP000008651; Genome.
DR GO; GO:0044167; C:host cell endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR Gene3D; 3.30.70.270; -; 1.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR InterPro; IPR007094; RNA-dir_pol_PSvirus.
DR InterPro; IPR002166; RNA_pol_HCV.
DR Pfam; PF00998; RdRP_3; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS50507; RDRP_SSRNA_POS; 1.
PE 1: Evidence at protein level;
KW Host endoplasmic reticulum; Host membrane; Membrane; Nucleotide-binding;
KW Nucleotidyltransferase; Reference proteome; Ribosomal frameshifting;
KW RNA-directed RNA polymerase; Suppressor of RNA silencing; Transferase;
KW Viral RNA replication.
FT CHAIN 1..767
FT /note="RNA-directed RNA polymerase"
FT /id="PRO_0000040206"
FT DOMAIN 463..580
FT /note="RdRp catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT VAR_SEQ 237..767
FT /note="Missing (in isoform protein p27)"
FT /evidence="ECO:0000305"
FT /id="VSP_032886"
FT MUTAGEN 38
FT /note="W->A: Complete loss of RNA replication and membrane
FT association."
FT /evidence="ECO:0000269|PubMed:22898643"
FT MUTAGEN 41
FT /note="F->A: Complete loss of RNA replication and membrane
FT association."
FT /evidence="ECO:0000269|PubMed:22898643"
FT MUTAGEN 45
FT /note="F->A: Complete loss of RNA replication."
FT /evidence="ECO:0000269|PubMed:22898643"
FT MUTAGEN 46
FT /note="F->A: Complete loss of RNA replication."
FT /evidence="ECO:0000269|PubMed:22898643"
FT MUTAGEN 48
FT /note="L->A: Complete loss of RNA replication."
FT /evidence="ECO:0000269|PubMed:22898643"
FT MUTAGEN 164
FT /note="R->A: Complete loss of binding to the Y-shaped RNA
FT element (YRE)."
FT /evidence="ECO:0000269|PubMed:21440279"
FT MUTAGEN 179
FT /note="H->A: More than 90% loss of binding to the Y-shaped
FT RNA element (YRE)."
FT /evidence="ECO:0000269|PubMed:21440279"
FT MUTAGEN 180
FT /note="H->A: More than 90% loss of binding to the Y-shaped
FT RNA element (YRE)."
FT /evidence="ECO:0000269|PubMed:21440279"
FT CONFLICT 237
FT /note="Missing (in Ref. 1; AAB02540)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 767 AA; 87544 MW; 3515C03BFF4F7A1B CRC64;
MGFINLSLFD VDKLMVWVSK FNPGKILSAI CNLGIDCWNR FRKWFFGLNF DAHMWAVDAF
IPLMPHYTEQ MERVVDDFCS ETPESKLEDC LELDTSVNEF FDEEVYKKDE EGVMKLQRSA
ARKHIKRVRP GMMQAAIKAV ETRIRNRHTI FGDDMGKVDE AAVRATASDI CGEFKINEHH
TNALVYAAAY LAMTPDQRSI DSVKLAYNPK SQARRTLVSA IRENKAVAGF KSLEDFLGGP
LSFPVEDAPY PILGIPEIRV AEKRASRVMK SKRVVGLPAV SAGLKVCVHQ TSLHNMIVSL
ERRVFRVKNS AGELVVPPKP IQNAFDSISY FREEWLRKLS HKGQILKSSL ADVVACYSSE
KRKLYQKAAD SLEKKPVQWR DSKVQAFIKV EKLECDTKDP VPRTIQPRSK RYNLAIGQYL
RLNEKKMLDS IDDVFKEKTV LSGLDNRAQG RAIAHKWRKY QNPIGIGLDA SRFDQHCSVD
ALKFEQTFYK ACFPGDQQLE TLLKWQLSNT GSALLPTGEL VRYRTKGCRM SGDINTGLGN
KILMCSMVHA FLKETGVRAS LANNGDDCVL FCEKGDYEQI NRNLEQWFLC RGFEMTVEKP
VDVLEKVAFC RSQPVCIATQ WAMVRQLGSL SRDCFSTQDW LNPKTFKDAM NALGQCNGII
NDGVPIHMAQ AKLMHRIGGN RKFNLDALHK QMEYSWRDRL GKRTNLLWSE VEDATRLSYF
RAFGIEPYIQ RIVEEYFSQV EITCEGRSTN VLPTHYSRIH KDLIKAR
