LIRP1_ARATH
ID LIRP1_ARATH Reviewed; 141 AA.
AC Q96500; C0Z293;
DT 22-NOV-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 25-MAY-2022, entry version 135.
DE RecName: Full=Light-regulated protein 1, chloroplastic {ECO:0000303|PubMed:8932388};
DE AltName: Full=Protein CCR-LIKE, chloroplastic {ECO:0000303|PubMed:16055688};
DE Flags: Precursor;
GN Name=LIR1 {ECO:0000303|PubMed:8932388};
GN Synonyms=CCL {ECO:0000303|PubMed:16055688},
GN LRP {ECO:0000303|PubMed:16980540};
GN OrderedLocusNames=At3g26740 {ECO:0000312|Araport:AT3G26740};
GN ORFNames=MLJ15.13 {ECO:0000312|EMBL:BAB01737.1};
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 [GENOMIC DNA / MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=8932388; DOI=10.1093/nar/24.21.4313;
RA Quigley F., Dao P., Cottet A., Mache R.;
RT "Sequence analysis of an 81 kb contig from Arabidopsis thaliana chromosome
RT III.";
RL Nucleic Acids Res. 24:4313-4318(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP INDUCTION.
RC STRAIN=cv. Columbia;
RX PubMed=16055688; DOI=10.1104/pp.105.060368;
RA Lidder P., Gutierrez R.A., Salome P.A., McClung C.R., Green P.J.;
RT "Circadian control of messenger RNA stability. Association with a sequence-
RT specific messenger RNA decay pathway.";
RL Plant Physiol. 138:2374-2385(2005).
RN [8]
RP REPRESSION BY TFP AND W7.
RC STRAIN=cv. Wassilewskija;
RX PubMed=16980540; DOI=10.1105/tpc.106.042713;
RA Kaplan B., Davydov O., Knight H., Galon Y., Knight M.R., Fluhr R.,
RA Fromm H.;
RT "Rapid transcriptome changes induced by cytosolic Ca2+ transients reveal
RT ABRE-related sequences as Ca2+-responsive cis elements in Arabidopsis.";
RL Plant Cell 18:2733-2748(2006).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH LFNR1 AND LFNR2,
RP REPRESSION BY LIGHT, AND DISULFIDE BOND.
RC STRAIN=cv. Columbia;
RX PubMed=26941088; DOI=10.1105/tpc.15.01027;
RA Yang C., Hu H., Ren H., Kong Y., Lin H., Guo J., Wang L., He Y., Ding X.,
RA Grabsztunowicz M., Mulo P., Chen T., Liu Y., Wu Z., Wu Y., Mao C., Wu P.,
RA Mo X.;
RT "LIGHT-INDUCED RICE1 regulates light-dependent attachment of LEAF-TYPE
RT FERREDOXIN-NADP+ OXIDOREDUCTASE to the thylakoid membrane in rice and
RT Arabidopsis.";
RL Plant Cell 28:712-728(2016).
CC -!- FUNCTION: Thylakoid-determinant subunit of high molecular weight LFNRs-
CC containing protein complexes. {ECO:0000269|PubMed:26941088}.
CC -!- SUBUNIT: Component of high molecular weight thylakoid LFNRs-containing
CC protein complexes containing LIR1, LFNR1, LFNR2, TIC62 and TROL
CC proteins. Interacts directly with LFNR1 and LFNR2; LIR1 increases the
CC affinity of LFNR1 and LFNR2 for TIC62 and subsequent thylakoid
CC relocalization. {ECO:0000269|PubMed:26941088}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane
CC {ECO:0000269|PubMed:26941088}; Peripheral membrane protein
CC {ECO:0000269|PubMed:26941088}; Stromal side
CC {ECO:0000269|PubMed:26941088}. Plastid, chloroplast envelope
CC {ECO:0000269|PubMed:26941088}. Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:26941088}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q96500-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q96500-2; Sequence=VSP_059232;
CC -!- INDUCTION: Expression is controlled by light and by a circadian clock.
CC Differentially regulated at the level of mRNA stability at different
CC times of day, being a target of the degradation pathway mediated by the
CC downstream (DST) instability determinant and thus following a circadian
CC clock rhythm with highest levels in early afternoon (PubMed:16055688).
CC Rapidly degraded upon illumination; this degradation coincides with the
CC release of the LFNR from the thylakoid membrane (PubMed:26941088).
CC Repressed by calmodulin (CaM) antagonists such as trifluoperazine (TFP)
CC and N-(6-aminohexyl)-5-chloro-1-naphthelene-sulfonamid-hydrochloride
CC (W7); this repression is alleviated by lanthanum (e.g. LaCl(3))
CC (PubMed:16980540). {ECO:0000269|PubMed:16055688,
CC ECO:0000269|PubMed:16980540, ECO:0000269|PubMed:26941088}.
CC -!- PTM: May form interchain disulfide bonds with LFNR1 and LFNR2.
CC {ECO:0000269|PubMed:26941088}.
CC -!- DISRUPTION PHENOTYPE: Slight increase in nonphotochemical quenching
CC (NPQ). Marked decrease in the accumulation of LFNR1 and LFNR2-
CC containing thylakoid protein complexes. {ECO:0000269|PubMed:26941088}.
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DR EMBL; X97829; CAA66408.1; -; mRNA.
DR EMBL; X98130; CAA66824.1; -; Genomic_DNA.
DR EMBL; AB026648; BAB01737.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE77206.1; -; Genomic_DNA.
DR EMBL; AF375445; AAK53029.1; -; mRNA.
DR EMBL; AF410315; AAK95301.1; -; mRNA.
DR EMBL; AF424610; AAL11604.1; -; mRNA.
DR EMBL; AY060542; AAL31173.1; -; mRNA.
DR EMBL; AK318707; BAH56822.1; -; mRNA.
DR EMBL; AY088085; AAM65631.1; -; mRNA.
DR RefSeq; NP_189308.1; NM_113585.4. [Q96500-1]
DR AlphaFoldDB; Q96500; -.
DR STRING; 3702.AT3G26740.1; -.
DR iPTMnet; Q96500; -.
DR PaxDb; Q96500; -.
DR PRIDE; Q96500; -.
DR ProteomicsDB; 238384; -. [Q96500-1]
DR EnsemblPlants; AT3G26740.1; AT3G26740.1; AT3G26740. [Q96500-1]
DR GeneID; 822286; -.
DR Gramene; AT3G26740.1; AT3G26740.1; AT3G26740. [Q96500-1]
DR KEGG; ath:AT3G26740; -.
DR Araport; AT3G26740; -.
DR TAIR; locus:2090837; AT3G26740.
DR eggNOG; ENOG502S43X; Eukaryota.
DR HOGENOM; CLU_154099_0_0_1; -.
DR InParanoid; Q96500; -.
DR OMA; REYLAYN; -.
DR OrthoDB; 1601928at2759; -.
DR PhylomeDB; Q96500; -.
DR PRO; PR:Q96500; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q96500; baseline and differential.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009941; C:chloroplast envelope; IEA:UniProtKB-SubCell.
DR GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
DR GO; GO:0098807; C:chloroplast thylakoid membrane protein complex; IMP:UniProtKB.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0007623; P:circadian rhythm; IEP:UniProtKB.
DR InterPro; IPR009856; Lir1.
DR PANTHER; PTHR36762; PTHR36762; 1.
DR Pfam; PF07207; Lir1; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chloroplast; Disulfide bond; Membrane; Plastid;
KW Reference proteome; Repeat; Thylakoid; Transit peptide.
FT TRANSIT 1..41
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 42..141
FT /note="Light-regulated protein 1, chloroplastic"
FT /id="PRO_0000442377"
FT REPEAT 67..81
FT /note="1"
FT REPEAT 118..132
FT /note="2"
FT REGION 35..58
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 58..132
FT /note="2 X 15 AA approximate repeats"
FT VAR_SEQ 67..141
FT /note="Missing (in isoform 2)"
FT /id="VSP_059232"
SQ SEQUENCE 141 AA; 15314 MW; AA5481D28D962060 CRC64;
MQGALFIKPT ILLPLPSSVS SPKLTFLLPH ATKASRLSSL RSNNSSSSSS LTSDPNTVDY
NSSILSVFPA EACEVISGYA CSADIYPEVK LDTKPVSRPV ASEPVDREYE EYNSPKTVFR
EEACDDLGGE FCEPDFQKDA N
