ISE2_ARATH
ID ISE2_ARATH Reviewed; 1171 AA.
AC B9DFG3; O04538; Q94EZ6;
DT 15-JUN-2010, integrated into UniProtKB/Swiss-Prot.
DT 15-JUN-2010, sequence version 2.
DT 03-AUG-2022, entry version 92.
DE RecName: Full=DExH-box ATP-dependent RNA helicase DExH15 chloroplastic {ECO:0000305};
DE EC=3.6.4.13;
DE AltName: Full=ATP-dependent RNA helicase ISE2;
DE AltName: Full=Protein EMBRYO DEFECTIVE 25;
DE AltName: Full=Protein INCREASED SIZE EXCLUSION LIMIT 2;
DE AltName: Full=Protein PIGMENT DEFECTIVE 317;
DE Flags: Precursor;
GN Name=ISE2; Synonyms=EMB25, PDE317; OrderedLocusNames=At1g70070;
GN ORFNames=F20P5.20;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-916.
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 FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=11779812; DOI=10.1093/genetics/159.4.1751;
RA McElver J., Tzafrir I., Aux G., Rogers R., Ashby C., Smith K., Thomas C.,
RA Schetter A., Zhou Q., Cushman M.A., Tossberg J., Nickle T., Levin J.Z.,
RA Law M., Meinke D., Patton D.;
RT "Insertional mutagenesis of genes required for seed development in
RT Arabidopsis thaliana.";
RL Genetics 159:1751-1763(2001).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=11874921; DOI=10.1242/dev.129.5.1261;
RA Kim I., Hempel F.D., Sha K., Pfluger J., Zambryski P.C.;
RT "Identification of a developmental transition in plasmodesmatal function
RT during embryogenesis in Arabidopsis thaliana.";
RL Development 129:1261-1272(2002).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF ASP-275.
RX PubMed=17601829; DOI=10.1105/tpc.106.045666;
RA Kobayashi K., Otegui M.S., Krishnakumar S., Mindrinos M., Zambryski P.;
RT "INCREASED SIZE EXCLUSION LIMIT 2 encodes a putative DEVH box RNA helicase
RT involved in plasmodesmata function during Arabidopsis embryogenesis.";
RL Plant Cell 19:1885-1897(2007).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=18431481; DOI=10.1371/journal.pone.0001994;
RA Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O., Sun Q.,
RA van Wijk K.J.;
RT "Sorting signals, N-terminal modifications and abundance of the chloroplast
RT proteome.";
RL PLoS ONE 3:E1994-E1994(2008).
RN [9]
RP REVIEW.
RX PubMed=20541498; DOI=10.1016/j.cub.2010.03.047;
RA Lee D.K., Sieburth L.E.;
RT "Plasmodesmata formation: poking holes in walls with ise.";
RL Curr. Biol. 20:R488-R490(2010).
RN [10]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=20434343; DOI=10.1016/j.cub.2010.03.064;
RA Burch-Smith T.-M., Zambryski P.C.;
RT "Loss of INCREASED SIZE EXCLUSION LIMIT (ISE)1 or ISE2 increases the
RT formation of secondary plasmodesmata.";
RL Curr. Biol. 20:989-993(2010).
RN [11]
RP SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=22106293; DOI=10.1073/pnas.1117226108;
RA Burch-Smith T.M., Brunkard J.O., Choi Y.G., Zambryski P.C.;
RT "Organelle-nucleus cross-talk regulates plant intercellular communication
RT via plasmodesmata.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:E1451-E1460(2011).
RN [12]
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 [13]
RP SUBCELLULAR LOCATION, AND FUNCTION.
RX PubMed=26147377; DOI=10.1111/pce.12603;
RA Carlotto N., Wirth S., Furman N., Ferreyra Solari N., Ariel F., Crespi M.,
RA Kobayashi K.;
RT "The chloroplastic DEVH-box RNA helicase INCREASED SIZE EXCLUSION LIMIT 2
RT involved in plasmodesmata regulation is required for group II intron
RT splicing.";
RL Plant Cell Environ. 39:165-173(2016).
CC -!- FUNCTION: RNA helicase involved in group II intron splicing
CC (PubMed:26147377). Essential protein required during embryogenesis.
CC Involved in post-transcriptional gene silencing. Modulates the
CC determination of cell fate. Necessary for normal plasmodesmata (PD)
CC development and aperture regulation. {ECO:0000269|PubMed:11779812,
CC ECO:0000269|PubMed:11874921, ECO:0000269|PubMed:17601829,
CC ECO:0000269|PubMed:20434343, ECO:0000269|PubMed:26147377}.
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 -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:18431481, ECO:0000269|PubMed:22106293,
CC ECO:0000269|PubMed:26147377}. Cytoplasmic granule
CC {ECO:0000269|PubMed:17601829}. Note=Localizes to granule-like
CC structures, probably stress granules (SGs), which number increases upon
CC stress. {ECO:0000269|PubMed:17601829}.
CC -!- DISRUPTION PHENOTYPE: Embryogenesis arrested at cotyledon stage.
CC Altered size exclusion limit of PD; abnormally maintained dilated PD at
CC the torpedo stage, and increased formation of secondary branched PD.
CC Chlorosis. Altered plastid development. {ECO:0000269|PubMed:11779812,
CC ECO:0000269|PubMed:11874921, ECO:0000269|PubMed:20434343,
CC ECO:0000269|PubMed:22106293}.
CC -!- SIMILARITY: Belongs to the DExH box helicase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB61106.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC002062; AAB61106.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE35013.1; -; Genomic_DNA.
DR EMBL; AK316759; BAH19480.1; -; mRNA.
DR EMBL; AF387007; AAK62452.1; -; mRNA.
DR PIR; D96723; D96723.
DR RefSeq; NP_177164.1; NM_105675.2.
DR AlphaFoldDB; B9DFG3; -.
DR SMR; B9DFG3; -.
DR BioGRID; 28564; 4.
DR STRING; 3702.AT1G70070.1; -.
DR iPTMnet; B9DFG3; -.
DR PaxDb; B9DFG3; -.
DR PRIDE; B9DFG3; -.
DR ProteomicsDB; 228858; -.
DR EnsemblPlants; AT1G70070.1; AT1G70070.1; AT1G70070.
DR GeneID; 843343; -.
DR Gramene; AT1G70070.1; AT1G70070.1; AT1G70070.
DR KEGG; ath:AT1G70070; -.
DR Araport; AT1G70070; -.
DR TAIR; locus:2020573; AT1G70070.
DR eggNOG; KOG0947; Eukaryota.
DR HOGENOM; CLU_002902_4_0_1; -.
DR InParanoid; B9DFG3; -.
DR OMA; GHLPFLC; -.
DR OrthoDB; 176060at2759; -.
DR PhylomeDB; B9DFG3; -.
DR BRENDA; 3.6.4.13; 399.
DR PRO; PR:B9DFG3; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; B9DFG3; baseline and differential.
DR Genevisible; B9DFG3; AT.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0010494; C:cytoplasmic stress granule; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
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; IDA:UniProtKB.
DR GO; GO:0003724; F:RNA helicase activity; ISS:TAIR.
DR GO; GO:1901259; P:chloroplast rRNA processing; IMP:CACAO.
DR GO; GO:0016554; P:cytidine to uridine editing; IMP:CACAO.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0031047; P:gene silencing by RNA; IEA:UniProtKB-KW.
DR GO; GO:0000373; P:Group II intron splicing; IMP:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IMP:UniProtKB.
DR GO; GO:0010497; P:plasmodesmata-mediated intercellular transport; IMP:TAIR.
DR GO; GO:0016441; P:post-transcriptional gene silencing; IMP:TAIR.
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; IPR012961; Ski2_C.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF08148; DSHCT; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM01142; DSHCT; 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.
PE 1: Evidence at protein level;
KW ATP-binding; Chloroplast; Helicase; Hydrolase; mRNA processing;
KW mRNA splicing; Nucleotide-binding; Plastid; Reference proteome;
KW RNA-binding; RNA-mediated gene silencing; Transit peptide.
FT TRANSIT 1..58
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 59..1171
FT /note="DExH-box ATP-dependent RNA helicase DExH15
FT chloroplastic"
FT /id="PRO_0000395028"
FT DOMAIN 163..327
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 424..620
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 53..111
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 275..278
FT /note="DEVH box"
FT /evidence="ECO:0000305"
FT COMPBIAS 62..109
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 176..183
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MUTAGEN 275
FT /note="D->N: In emb25, ise2-2; embryo development arrested
FT at cotyledon stage, abnormal PD regulation end
FT development."
FT /evidence="ECO:0000269|PubMed:17601829"
FT CONFLICT 234
FT /note="A -> D (in Ref. 4; AAK62452)"
FT /evidence="ECO:0000305"
FT CONFLICT 395
FT /note="D -> N (in Ref. 3; BAH19480)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1171 AA; 132437 MW; 34668CF0D4A03EFB CRC64;
MNTLPVVSLT ASSSFKFFHF PSLHRSLSHS PNFSFTKSLI LNPNHLSFKS TLNSLSPSQS
QLYEEEDDEE EEEEDEDDDD EAADEYDNIS DEIRNSDDDD DDEETEFSVD LPTESARERV
EFRWQRVEKL RSLVRDFGVE MIDIDELISI YDFRIDKFQR LAIEAFLRGS SVVVSAPTSS
GKTLIAEAAA VSTVAKGRRL FYTTPLKALS NQKFREFRET FGDDNVGLLT GDSAINKDAQ
IVIMTTEILR NMLYQSVGMA SSGTGLFHVD AIVLDEVHYL SDISRGTVWE EIVIYCPKEV
QLICLSATVA NPDELAGWIG EIHGKTELVT STRRPVPLTW YFSTKHSLLP LLDEKGINVN
RKLSLNYLQL SASEARFRDD DDGYRKRRSK KRGGDTSYNN LVNVTDYPLS KNEINKIRRS
QVPQISDTLW HLQGKNMLPA IWFIFNRRGC DAAVQYVENF QLLDDCEKSE VELALKKFRV
LYPDAVRESA EKGLLRGIAA HHAGCLPLWK SFIEELFQRG LVKVVFATET LAAGINMPAR
TAVISSLSKK AGNERIELGP NELYQMAGRA GRRGIDEKGY TVLVQTAFEG AEECCKLVFA
GVKPLVSQFT ASYGMVLNLV AGSKVTRKSS GTEAGKVLQA GRSLEEAKKL VEKSFGNYVS
SNVTVAAKQE LAEIDNKIEI LSSEISDEAI DKKSRKLLSA RDYKEITVLK EELREEKRKR
AEQRRRMELE RFLALKPLLK GMEEGNLPFI CLEFKDSEGR EQSVPAVYLG HIDSFQGSKL
QKMMSLDESF ALNLIEDELA ADEPGKPNVK PSYYVALGSD NSWYLFTEKW VRTVYRTGFP
NIALALGDAL PREIMKNLLD KADMQWDKLA ESELGSLWRL EGSLETWSWS LNVPVLSSLS
DEDEVLHMSE EYDNAAQKYK EQRSKISRLK KKMSRSEGFR EYKKILENAN LTVEKMKRLK
ARSRRLINRL EQIEPSGWKD FMRISNVIHE SRALDINTHL IFPLGETAAA IRGENELWLA
MVLRNKALVD LKPPQLAGVC ASLVSEGIKV RPWRDNNYIY EPSDTVVDMV NFLEDQRSSL
IKLQEKHEVM IPCCLDVQFS GMVEAWASGL SWKEMMMECA MDEGDLARLL RRTIDLLAQI
PKLPDIDPVL QRSAAAAADI MDRPPISELA G
