RH2_ARATH
ID RH2_ARATH Reviewed; 408 AA.
AC Q94A52; Q9ZS14;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Eukaryotic initiation factor 4A-III homolog {ECO:0000305};
DE Short=AteIF4AIII {ECO:0000305};
DE Short=eIF-4A-III {ECO:0000305};
DE Short=eIF4A-III {ECO:0000303|PubMed:19435936};
DE EC=3.6.4.13 {ECO:0000305};
DE AltName: Full=DEAD-box ATP-dependent RNA helicase 2 {ECO:0000303|PubMed:17168887};
DE Short=AtRH02 {ECO:0000303|PubMed:17168887};
GN Name=EIF4A3 {ECO:0000303|PubMed:19435936};
GN Synonyms=RH2 {ECO:0000303|PubMed:24743583};
GN OrderedLocusNames=At3g19760 {ECO:0000312|Araport:AT3G19760};
GN ORFNames=MMB12.25 {ECO:0000312|EMBL:BAB02563.1}, MMB12.4;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=9862990; DOI=10.1093/nar/27.2.628;
RA Aubourg S., Kreis M., Lecharny A.;
RT "The DEAD box RNA helicase family in Arabidopsis thaliana.";
RL Nucleic Acids Res. 27:628-636(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=17168887; DOI=10.1111/j.1467-7652.2004.00084.x;
RA Mingam A., Toffano-Nioche C., Brunaud V., Boudet N., Kreis M., Lecharny A.;
RT "DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link
RT between quantitative expression, gene structure and evolution of a family
RT of genes.";
RL Plant Biotechnol. J. 2:401-415(2004).
RN [6]
RP INTERACTION WITH ALY4, AND SUBCELLULAR LOCATION.
RX PubMed=19435936; DOI=10.1105/tpc.108.060434;
RA Koroleva O.A., Calder G., Pendle A.F., Kim S.H., Lewandowska D.,
RA Simpson C.G., Jones I.M., Brown J.W.S., Shaw P.J.;
RT "Dynamic behavior of Arabidopsis eIF4A-III, putative core protein of exon
RT junction complex: fast relocation to nucleolus and splicing speckles under
RT hypoxia.";
RL Plant Cell 21:1592-1606(2009).
RN [7]
RP GENE FAMILY.
RX PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA Xu R., Zhang S., Huang J., Zheng C.;
RT "Genome-wide comparative in silico analysis of the RNA helicase gene family
RT in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT sativa.";
RL PLoS ONE 8:E78982-E78982(2013).
RN [8]
RP FUNCTION.
RX PubMed=24743583; DOI=10.1371/journal.ppat.1004051;
RA Kovalev N., Nagy P.D.;
RT "The expanding functions of cellular helicases: the tombusvirus RNA
RT replication enhancer co-opts the plant eIF4AIII-like AtRH2 and the DDX5-
RT like AtRH5 DEAD-box RNA helicases to promote viral asymmetric RNA
RT replication.";
RL PLoS Pathog. 10:E1004051-E1004051(2014).
RN [9]
RP INTERACTION WITH CPL1/FRY2, SUBCELLULAR LOCATION, PHOSPHORYLATION AT
RP SER-100 AND SER-101, AND MUTAGENESIS OF SER-100 AND SER-101.
RX PubMed=26887918; DOI=10.1105/tpc.15.00771;
RA Cui P., Chen T., Qin T., Ding F., Wang Z., Chen H., Xiong L.;
RT "The RNA polymerase II C-terminal domain phosphatase-like protein
RT FIERY2/CPL1 interacts with eIF4AIII and is essential for nonsense-mediated
RT mrna decay in Arabidopsis.";
RL Plant Cell 28:770-785(2016).
RN [10]
RP FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=26883227; DOI=10.1007/s00299-016-1947-5;
RA Pascuan C., Frare R., Alleva K., Ayub N.D., Soto G.;
RT "mRNA biogenesis-related helicase eIF4AIII from Arabidopsis thaliana is an
RT important factor for abiotic stress adaptation.";
RL Plant Cell Rep. 35:1205-1208(2016).
RN [11]
RP INTERACTION WITH MAGO.
RX PubMed=26867216; DOI=10.1371/journal.pone.0148200;
RA Cilano K., Mazanek Z., Khan M., Metcalfe S., Zhang X.N.;
RT "A new mutation, hap1-2, reveals a C terminal domain function in AtMago
RT protein and its biological effects in male gametophyte development in
RT Arabidopsis thaliana.";
RL PLoS ONE 11:E0148200-E0148200(2016).
CC -!- FUNCTION: ATP-dependent RNA helicase. Core component of the splicing-
CC dependent multiprotein exon junction complex (EJC) deposited at splice
CC junctions on mRNAs. The EJC is a dynamic structure consisting of core
CC proteins and several peripheral nuclear and cytoplasmic associated
CC factors that join the complex only transiently either during EJC
CC assembly or during subsequent mRNA metabolism. The EJC marks the
CC position of the exon-exon junction in the mature mRNA for the gene
CC expression machinery and the core components remain bound to spliced
CC mRNAs throughout all stages of mRNA metabolism thereby influencing
CC downstream processes including nuclear mRNA export, subcellular mRNA
CC localization, translation efficiency and nonsense-mediated mRNA decay
CC (NMD). Its RNA-dependent ATPase and RNA-helicase activities are induced
CC by MLN51/CASC3, but abolished in presence of the MAGO-Y14 heterodimer,
CC thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable
CC conformation. The inhibition of ATPase activity by the MAGO-Y14
CC heterodimer increases the RNA-binding affinity of the EJC (By
CC similarity). Plays a role in abiotic stress adaptation. Can regulate
CC abiotic stress resistance partially via the control of acetoacetyl-CoA
CC thiolase 2 (AC Q8S4Y1) expression (PubMed:26883227).
CC {ECO:0000250|UniProtKB:P38919, ECO:0000269|PubMed:26883227}.
CC -!- FUNCTION: (Microbial infection) Functions as host RNA helicase that is
CC co-opted by the tombusvirus (TBSV) RNA replication enhancer to greatly
CC enhance tombusvirus replication. Interacts with the viral minus-strand
CC RNA and the replication proteins within the viral replicase.
CC {ECO:0000269|PubMed:24743583}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC Evidence={ECO:0000305};
CC -!- SUBUNIT: Interacts with ALY4 (PubMed:19435936). Interacts with MAGO
CC (PubMed:26867216). Interacts with CPL1/FRY2 (PubMed:26887918).
CC {ECO:0000269|PubMed:19435936, ECO:0000269|PubMed:26867216,
CC ECO:0000269|PubMed:26887918}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:19435936}. Nucleus, nucleolus
CC {ECO:0000269|PubMed:19435936}. Nucleus speckle
CC {ECO:0000269|PubMed:19435936}. Nucleus {ECO:0000269|PubMed:26887918}.
CC Cytoplasm {ECO:0000269|PubMed:26887918}. Note=Hypoxia causes transition
CC from diffuse nucleoplasmic localization to accumulation in speckles in
CC nuclei of root cells (PubMed:19435936). Localized to the nucleus when
CC hypophosphorylated. Hyperphosphorylation of EIF4A3 increases its
CC cytoplasmic localization (PubMed:26887918). Nucleocytoplasmic shuttling
CC protein. Travels to the cytoplasm as part of the exon junction complex
CC (EJC) bound to mRNA (By similarity). {ECO:0000250|UniProtKB:P38919,
CC ECO:0000269|PubMed:19435936, ECO:0000269|PubMed:26887918}.
CC -!- INDUCTION: Induced by cold and heat stresses.
CC {ECO:0000269|PubMed:26883227}.
CC -!- DOMAIN: The Q motif is unique to and characteristic of the DEAD box
CC family of RNA helicases and controls ATP binding and hydrolysis.
CC {ECO:0000305}.
CC -!- PTM: Phosphorylated at Ser-100 and Ser-101. Phosphorylation status of
CC Ser-100 and Ser-101 largely determines the subcellular localization of
CC EIF4A3. {ECO:0000269|PubMed:26887918}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions, but mutant seedlings show increased sensitivity to cold and
CC heat stresses. {ECO:0000269|PubMed:24743583}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX48/FAL1
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB02563.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAA09195.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AJ010456; CAA09195.1; ALT_FRAME; mRNA.
DR EMBL; AP000417; BAB02563.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002686; AEE76283.1; -; Genomic_DNA.
DR EMBL; AY050367; AAK91384.1; -; mRNA.
DR EMBL; BT002207; AAN72219.1; -; mRNA.
DR PIR; T51737; T51737.
DR RefSeq; NP_188610.1; NM_112866.4.
DR AlphaFoldDB; Q94A52; -.
DR SMR; Q94A52; -.
DR BioGRID; 6845; 13.
DR IntAct; Q94A52; 2.
DR MINT; Q94A52; -.
DR STRING; 3702.AT3G19760.1; -.
DR iPTMnet; Q94A52; -.
DR PaxDb; Q94A52; -.
DR PRIDE; Q94A52; -.
DR ProteomicsDB; 236248; -.
DR EnsemblPlants; AT3G19760.1; AT3G19760.1; AT3G19760.
DR GeneID; 821513; -.
DR Gramene; AT3G19760.1; AT3G19760.1; AT3G19760.
DR KEGG; ath:AT3G19760; -.
DR Araport; AT3G19760; -.
DR TAIR; locus:2091191; AT3G19760.
DR eggNOG; KOG0328; Eukaryota.
DR HOGENOM; CLU_003041_1_0_1; -.
DR InParanoid; Q94A52; -.
DR OMA; FGCQALV; -.
DR OrthoDB; 726081at2759; -.
DR PhylomeDB; Q94A52; -.
DR PRO; PR:Q94A52; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q94A52; baseline and differential.
DR Genevisible; Q94A52; AT.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0035145; C:exon-exon junction complex; IDA:TAIR.
DR GO; GO:0016607; C:nuclear speck; IDA:TAIR.
DR GO; GO:0005730; C:nucleolus; IDA:TAIR.
DR GO; GO:0005654; C:nucleoplasm; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IBA:GO_Central.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
DR GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR GO; GO:0001666; P:response to hypoxia; IDA:TAIR.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; Helicase; Hydrolase; mRNA processing;
KW mRNA splicing; mRNA transport; Nonsense-mediated mRNA decay;
KW Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome;
KW RNA-binding; Stress response; Translation regulation; Transport.
FT CHAIN 1..408
FT /note="Eukaryotic initiation factor 4A-III homolog"
FT /id="PRO_0000239144"
FT DOMAIN 66..236
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 247..408
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..20
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 35..63
FT /note="Q motif"
FT MOTIF 184..187
FT /note="DEAD box"
FT BINDING 79..86
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 100
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:26887918"
FT MOD_RES 101
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:26887918"
FT MUTAGEN 100
FT /note="S->D: Increases cytoplasmic localization; when
FT associated with D-101."
FT /evidence="ECO:0000269|PubMed:26887918"
FT MUTAGEN 101
FT /note="S->D: Increases cytoplasmic localization; when
FT associated with D-100."
FT /evidence="ECO:0000269|PubMed:26887918"
FT CONFLICT 114
FT /note="E -> G (in Ref. 4; AAK91384/AAN72219)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 408 AA; 45845 MW; 4BD11BBA58BAA0D9 CRC64;
MATANPGRGG GRRGGGAMDD DKLVFETTDG IEPITSFNDM GIKEDVLRGV YEYGFEKPSA
IQQRAVMPIL QGRDVIAQAQ SGTGKTSMIA LSVCQVVDTS SREVQALILS PTRELATQTE
KTIQAIGLHA NIQAHACIGG NSVGEDIRKL EHGVHVVSGT PGRVCDMIKR RSLRTRAIKL
LILDESDEML SRGFKDQIYD VYRYLPPDLQ VCLVSATLPH EILEMTSKFM TEPVKILVKR
DELTLEGIKQ FFVAVEKEEW KFDTLCDLYD TLTITQAVIF CNTKRKVDYL SEKMRSHNFT
VSSMHGDMPQ KERDAIMNEF RSGDSRVLIT TDVWARGIDV QQVSLVINYD LPNNRELYIH
RIGRSGRFGR KGVAINFVKS DDIKILRDIE QYYSTQIDEM PMNVADLI
