PD338_ARATH
ID PD338_ARATH Reviewed; 500 AA.
AC Q9M9H4; K7YLJ7; Q56XP0;
DT 13-NOV-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 25-MAY-2022, entry version 137.
DE RecName: Full=Protein PIGMENT DEFECTIVE 338, chloroplastic {ECO:0000303|PubMed:21139083};
DE AltName: Full=Protein PETB/PETD STABILIZING FACTOR {ECO:0000303|PubMed:30962391};
DE AltName: Full=Protein PHOTOSYSTEM BIOGENESIS REGULATOR 1 {ECO:0000303|PubMed:27462450};
DE AltName: Full=Protein rbcL RNA S1-binding domain {ECO:0000303|PubMed:24053212};
DE Flags: Precursor;
GN Name=PDE338 {ECO:0000303|PubMed:21139083};
GN Synonyms=BSF {ECO:0000303|PubMed:30962391},
GN PBR1 {ECO:0000303|PubMed:27462450}, RLSB {ECO:0000303|PubMed:24053212};
GN OrderedLocusNames=At1g71720 {ECO:0000312|Araport:AT1G71720};
GN ORFNames=F14O23.10 {ECO:0000312|EMBL:AAF43225.1};
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 [MRNA] (ISOFORM 2), FUNCTION, DISRUPTION PHENOTYPE,
RP SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=24053212; DOI=10.1186/1471-2229-13-138;
RA Bowman S.M., Patel M., Yerramsetty P., Mure C.M., Zielinski A.M.,
RA Bruenn J.A., Berry J.O.;
RT "A novel RNA binding protein affects rbcL gene expression and is specific
RT to bundle sheath chloroplasts in C4 plants.";
RL BMC Plant Biol. 13:138-138(2013).
RN [2]
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 [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;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION [LARGE SCALE ANALYSIS], AND DISRUPTION PHENOTYPE [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=21139083; DOI=10.1104/pp.110.168120;
RA Bryant N., Lloyd J., Sweeney C., Myouga F., Meinke D.;
RT "Identification of nuclear genes encoding chloroplast-localized proteins
RT required for embryo development in Arabidopsis.";
RL Plant Physiol. 155:1678-1689(2011).
RN [6]
RP GENE FAMILY.
RX PubMed=27356975; DOI=10.1186/s12862-016-0713-1;
RA Yerramsetty P., Stata M., Siford R., Sage T.L., Sage R.F., Wong G.K.-S.,
RA Albert V.A., Berry J.O.;
RT "Evolution of RLSB, a nuclear-encoded S1 domain RNA binding protein
RT associated with post-transcriptional regulation of plastid-encoded rbcL
RT mRNA in vascular plants.";
RL BMC Evol. Biol. 16:141-141(2016).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INDUCTION BY LIGHT.
RX PubMed=27462450; DOI=10.1038/celldisc.2016.3;
RA Yang X.-F., Wang Y.-T., Chen S.-T., Li J.-K., Shen H.-T., Guo F.-Q.;
RT "PBR1 selectively controls biogenesis of photosynthetic complexes by
RT modulating translation of the large chloroplast gene Ycf1 in Arabidopsis.";
RL Cell Discov. 2:16003-16003(2016).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH CRP1 AND PRFB3, TISSUE
RP SPECIFICITY, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=30962391; DOI=10.1105/tpc.18.00946;
RA Jiang J., Chai X., Manavski N., Williams-Carrier R., He B., Brachmann A.,
RA Ji D., Ouyang M., Liu Y., Barkan A., Meurer J., Zhang L., Chi W.;
RT "An RNA Chaperone-Like Protein Plays Critical Roles in Chloroplast mRNA
RT Stability and Translation in Arabidopsis and Maize.";
RL Plant Cell 31:1308-1327(2019).
CC -!- FUNCTION: RNA-binding protein that acts as an RNA chaperone to remodel
CC RNA structure and activates their translation (PubMed:30962391).
CC Required for seed pigmentation (PubMed:21139083). Necessary for
CC chloroplast development and subsequent photosynthetic electron flow, as
CC well as for non-photochemical quenching (NPQ) (PubMed:27462450).
CC Rubisco regulatory factor which regulates the concerted biogenesis of
CC NDH, PSI (including PsaA, PsaB, PsaD, PsaF, PsaL, PsaG, PsaK and NdhH)
CC and Cytb(6)f (including PetA, PetB, PetC and PetD) complexes
CC (PubMed:24053212, PubMed:27462450, PubMed:30962391). Binds specifically
CC to and involved in the post-transcriptional regulation of plastid-
CC encoded mRNAs (e.g. rbcL, petA, petB, petD and Ycf1), thus modulating
CC expression, cellular localization/compartmentalization, and
CC photosynthetic function (PubMed:24053212, PubMed:27462450,
CC PubMed:30962391). {ECO:0000269|PubMed:21139083,
CC ECO:0000269|PubMed:24053212, ECO:0000269|PubMed:27462450,
CC ECO:0000269|PubMed:30962391}.
CC -!- SUBUNIT: Interacts with CRP1 and PRFB3. {ECO:0000269|PubMed:30962391}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:24053212, ECO:0000269|PubMed:30962391}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9M9H4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9M9H4-2; Sequence=VSP_060396;
CC -!- TISSUE SPECIFICITY: Present in leaves (at protein level)
CC (PubMed:30962391). Confined to leaf chlorenchyma cells
CC (PubMed:24053212). {ECO:0000269|PubMed:24053212,
CC ECO:0000269|PubMed:30962391}.
CC -!- INDUCTION: By light. {ECO:0000269|PubMed:27462450}.
CC -!- DISRUPTION PHENOTYPE: Pigment defective seeds (PubMed:21139083).
CC Virescent/yellow leaves leading to pale-green seedlings, due to reduced
CC photosynthetic function and disruption of associated signaling
CC networks, later associated with impaired photoautotrophy
CC (PubMed:24053212, PubMed:27462450, PubMed:30962391). Abnormal
CC chloroplast development with disrupted granum-stroma thylakoid
CC membranes and disrupted photosynthetic electron flow (PubMed:27462450).
CC Reduced accumulation of rbcL mRNA and less production of Rubisco large
CC subunit (LSU) (PubMed:24053212). Impaired biogenesis of NDH, PSI
CC (including PsaA, PsaB, PsaD, PsaF, PsaL, PsaG, PsaK and NdhH) and
CC Cytb(6)f (including PetA, PetB, PetC and PetD) complexes; this
CC phenotypes are reversed by Ycf1 overexpression (PubMed:27462450,
CC PubMed:30962391). Inhibited induction of non-photochemical quenching
CC (NPQ) (PubMed:27462450). Structural changes to target RNAs
CC (PubMed:30962391). {ECO:0000269|PubMed:21139083,
CC ECO:0000269|PubMed:24053212, ECO:0000269|PubMed:27462450,
CC ECO:0000269|PubMed:30962391}.
CC -!- SIMILARITY: Belongs to the bacterial ribosomal protein bS1 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAD95265.1; Type=Frameshift; Evidence={ECO:0000305};
CC -!- WEB RESOURCE: Name=Seed defective Arabidopsis mutants;
CC URL="http://seedgenes.org/MutantList";
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DR EMBL; JX843767; AFX82591.1; -; mRNA.
DR EMBL; AC012654; AAF43225.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE35223.1; -; Genomic_DNA.
DR EMBL; AK221633; BAD95265.1; ALT_FRAME; mRNA.
DR PIR; E96739; E96739.
DR RefSeq; NP_177317.2; NM_105830.4. [Q9M9H4-1]
DR AlphaFoldDB; Q9M9H4; -.
DR SMR; Q9M9H4; -.
DR STRING; 3702.AT1G71720.1; -.
DR iPTMnet; Q9M9H4; -.
DR PaxDb; Q9M9H4; -.
DR PRIDE; Q9M9H4; -.
DR ProteomicsDB; 179181; -. [Q9M9H4-1]
DR EnsemblPlants; AT1G71720.1; AT1G71720.1; AT1G71720. [Q9M9H4-1]
DR GeneID; 843502; -.
DR Gramene; AT1G71720.1; AT1G71720.1; AT1G71720. [Q9M9H4-1]
DR KEGG; ath:AT1G71720; -.
DR Araport; AT1G71720; -.
DR TAIR; locus:2013051; AT1G71720.
DR eggNOG; ENOG502QTBZ; Eukaryota.
DR HOGENOM; CLU_026267_0_0_1; -.
DR InParanoid; Q9M9H4; -.
DR OMA; MVRGKMG; -.
DR OrthoDB; 913895at2759; -.
DR PRO; PR:Q9M9H4; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9M9H4; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0009536; C:plastid; IDA:TAIR.
DR GO; GO:0034336; F:misfolded RNA binding; IDA:TAIR.
DR GO; GO:0003729; F:mRNA binding; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0140691; F:RNA folding chaperone; IDA:TAIR.
DR GO; GO:0010196; P:nonphotochemical quenching; IMP:UniProtKB.
DR GO; GO:0009657; P:plastid organization; IMP:TAIR.
DR GO; GO:0032544; P:plastid translation; IMP:TAIR.
DR GO; GO:0045727; P:positive regulation of translation; IDA:UniProtKB.
DR GO; GO:0009416; P:response to light stimulus; IEP:UniProtKB.
DR GO; GO:0043489; P:RNA stabilization; IMP:UniProtKB.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR022967; S1_dom.
DR InterPro; IPR003029; S1_domain.
DR Pfam; PF00575; S1; 1.
DR SMART; SM00316; S1; 3.
DR SUPFAM; SSF50249; SSF50249; 3.
DR PROSITE; PS50126; S1; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; Chloroplast; Plastid; Reference proteome; Repeat;
KW Transit peptide.
FT TRANSIT 1..63
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 64..500
FT /note="Protein PIGMENT DEFECTIVE 338, chloroplastic"
FT /evidence="ECO:0000255"
FT /id="PRO_0000448439"
FT DOMAIN 156..265
FT /note="S1 motif 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00180"
FT DOMAIN 283..351
FT /note="S1 motif 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00180"
FT DOMAIN 362..431
FT /note="S1 motif 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00180"
FT VAR_SEQ 315..327
FT /note="Missing (in isoform 2)"
FT /id="VSP_060396"
SQ SEQUENCE 500 AA; 56326 MW; 97892391C7C902B2 CRC64;
MQTLLCQPCK SLPILTASSS SSLIRSSGDV RECIDFRASE KVSKFQFHVT LSPFAFRGFS
ICREFAVRGA YGIRFCSRED VSGVGNGGIV AEEEIELLNK PNPLPKSENE ESGKADDDAI
LEPFLKFFKP EEEGEGIESE VSDETDRVSV EYYDPKPGDF VVGVVVSGNE NKLDVNIGAD
MLGTMLTKEI LPLYDKELDY LLCDLKYDAE EFLVNGKMGI VKDDDEGVEI AEFARQGRPV
VEIGTVVFAE VLGRTLSGRP LLSSRRYFRR IAWHRVRQIK QLNEPIEVKI TEWNTGGLLT
RIEGLRAFIP KQELVKKVNT FTELKENVGR RFLVQITRLN EDKNDLILSE KVAWEKLYLR
EGTLLEGTVV KILPYGAQVK LGDSSRSGLL HISNITRRRI GSVSDVLQVD ESVKVLVVKS
LFPDKISLSI ADLESEPGLF ISDREKVFTE AEEMAKKYRE KMPLVATSPI SDRPPITSSF
PQGKDEEIYA NWEWFKFESQ
