VCL1_ARATH
ID VCL1_ARATH Reviewed; 858 AA.
AC Q93VQ0; B9DFU5; F4IRY5;
DT 19-MAR-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Protein VACUOLELESS1;
DE AltName: Full=Vacuolar protein sorting-associated protein 16 homolog;
GN Name=VCL1; OrderedLocusNames=At2g38020; ORFNames=T8P21.7;
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 1), FUNCTION, DISRUPTION PHENOTYPE,
RP TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX PubMed=11702788; DOI=10.1016/s1534-5807(01)00024-7;
RA Rojo E., Gillmor C.S., Kovaleva V., Somerville C.R., Raikhel N.V.;
RT "VACUOLELESS1 is an essential gene required for vacuole formation and
RT morphogenesis in Arabidopsis.";
RL Dev. Cell 1:303-310(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
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] (ISOFORM 1).
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] OF 309-834 (ISOFORM 2).
RC TISSUE=Root;
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 IDENTIFICATION IN THE C-VSP COMPLEX, TISSUE SPECIFICITY, AND SUBCELLULAR
RP LOCATION.
RX PubMed=12589039; DOI=10.1091/mbc.e02-08-0509;
RA Rojo E., Zouhar J., Kovaleva V., Hong S., Raikhel N.V.;
RT "The AtC-VPS protein complex is localized to the tonoplast and the
RT prevacuolar compartment in arabidopsis.";
RL Mol. Biol. Cell 14:361-369(2003).
RN [7]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=14988481; DOI=10.1104/pp.103.037382;
RA Hicks G.R., Rojo E., Hong S., Carter D.G., Raikhel N.V.;
RT "Geminating pollen has tubular vacuoles, displays highly dynamic vacuole
RT biogenesis, and requires VACUOLESS1 for proper function.";
RL Plant Physiol. 134:1227-1239(2004).
RN [8]
RP SUBUNIT, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=29463724; DOI=10.1073/pnas.1717839115;
RA Takemoto K., Ebine K., Askani J.C., Krueger F., Gonzalez Z.A., Ito E.,
RA Goh T., Schumacher K., Nakano A., Ueda T.;
RT "Distinct sets of tethering complexes, SNARE complexes, and Rab GTPases
RT mediate membrane fusion at the vacuole in Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 115:E2457-E2466(2018).
CC -!- FUNCTION: Required for vacuole biogenesis and vacuole enlargment in
CC dividing and expanding cells. Involved in the docking or fusion of
CC prevacuolar vesicles. Important for the function of both male and
CC female gametophytes, but is not essential for the germination and
CC development of pollen. {ECO:0000269|PubMed:11702788,
CC ECO:0000269|PubMed:14988481}.
CC -!- SUBUNIT: Core component of at least two putative endosomal tethering
CC complexes, the homotypic fusion and vacuole protein sorting (HOPS)
CC complex and the class C core vacuole/endosome tethering (CORVET)
CC complex. Their common core is composed of the class C Vps proteins
CC VPS11, VCL1, VPS18 and VPS33, which in HOPS further associates with
CC VPS39 and VPS41 and in CORVET with VPS3. {ECO:0000269|PubMed:12589039,
CC ECO:0000269|PubMed:29463724}.
CC -!- SUBCELLULAR LOCATION: Vacuole membrane {ECO:0000269|PubMed:12589039};
CC Peripheral membrane protein {ECO:0000269|PubMed:12589039}. Prevacuolar
CC compartment membrane {ECO:0000269|PubMed:12589039}; Peripheral membrane
CC protein {ECO:0000269|PubMed:12589039}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q93VQ0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q93VQ0-2; Sequence=VSP_053914, VSP_053915;
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems, siliques,
CC flowers and mature pollen. {ECO:0000269|PubMed:11702788,
CC ECO:0000269|PubMed:12589039, ECO:0000269|PubMed:14988481}.
CC -!- DEVELOPMENTAL STAGE: Expressed throughout development.
CC {ECO:0000269|PubMed:11702788}.
CC -!- DISRUPTION PHENOTYPE: Absence of vacuoles in the embryo and
CC accumulation of small vesicles and autophagosomes. Embryo lethality at
CC late torpedo stage. {ECO:0000269|PubMed:11702788}.
CC -!- SIMILARITY: Belongs to the VPS16 family. {ECO:0000305}.
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DR EMBL; AF359240; AAK43713.1; -; mRNA.
DR EMBL; CP002685; AEC09479.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC09480.1; -; Genomic_DNA.
DR EMBL; AY048248; AAK82510.1; -; mRNA.
DR EMBL; AY139799; AAM98105.1; -; mRNA.
DR EMBL; AK316906; BAH19612.1; -; mRNA.
DR RefSeq; NP_001078020.1; NM_001084551.1. [Q93VQ0-2]
DR RefSeq; NP_565879.1; NM_129359.4. [Q93VQ0-1]
DR AlphaFoldDB; Q93VQ0; -.
DR SMR; Q93VQ0; -.
DR BioGRID; 3724; 5.
DR STRING; 3702.AT2G38020.1; -.
DR iPTMnet; Q93VQ0; -.
DR PaxDb; Q93VQ0; -.
DR PRIDE; Q93VQ0; -.
DR ProteomicsDB; 242328; -. [Q93VQ0-1]
DR EnsemblPlants; AT2G38020.1; AT2G38020.1; AT2G38020. [Q93VQ0-1]
DR EnsemblPlants; AT2G38020.2; AT2G38020.2; AT2G38020. [Q93VQ0-2]
DR GeneID; 818380; -.
DR Gramene; AT2G38020.1; AT2G38020.1; AT2G38020. [Q93VQ0-1]
DR Gramene; AT2G38020.2; AT2G38020.2; AT2G38020. [Q93VQ0-2]
DR KEGG; ath:AT2G38020; -.
DR Araport; AT2G38020; -.
DR TAIR; locus:2065674; AT2G38020.
DR eggNOG; KOG2280; Eukaryota.
DR InParanoid; Q93VQ0; -.
DR OMA; KIYVHWA; -.
DR OrthoDB; 1258856at2759; -.
DR PhylomeDB; Q93VQ0; -.
DR PRO; PR:Q93VQ0; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q93VQ0; baseline and differential.
DR Genevisible; Q93VQ0; AT.
DR GO; GO:0033263; C:CORVET complex; IDA:UniProtKB.
DR GO; GO:0005783; C:endoplasmic reticulum; HDA:TAIR.
DR GO; GO:0005768; C:endosome; IBA:GO_Central.
DR GO; GO:0030897; C:HOPS complex; IDA:UniProtKB.
DR GO; GO:0009705; C:plant-type vacuole membrane; IDA:TAIR.
DR GO; GO:0032991; C:protein-containing complex; IPI:UniProtKB.
DR GO; GO:0003779; F:actin binding; IBA:GO_Central.
DR GO; GO:0016197; P:endosomal transport; IBA:GO_Central.
DR GO; GO:0006886; P:intracellular protein transport; IEA:InterPro.
DR GO; GO:0045992; P:negative regulation of embryonic development; IMP:UniProtKB.
DR GO; GO:0042144; P:vacuole fusion, non-autophagic; IBA:GO_Central.
DR GO; GO:0007033; P:vacuole organization; IMP:UniProtKB.
DR GO; GO:0051469; P:vesicle fusion with vacuole; IMP:UniProtKB.
DR Gene3D; 1.10.150.780; -; 1.
DR InterPro; IPR016534; VPS16.
DR InterPro; IPR006925; Vps16_C.
DR InterPro; IPR038132; Vps16_C_sf.
DR InterPro; IPR006926; Vps16_N.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR PANTHER; PTHR12811; PTHR12811; 1.
DR Pfam; PF04840; Vps16_C; 1.
DR Pfam; PF04841; Vps16_N; 1.
DR PIRSF; PIRSF007949; VPS16; 1.
DR SUPFAM; SSF50978; SSF50978; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Membrane; Reference proteome; Vacuole.
FT CHAIN 1..858
FT /note="Protein VACUOLELESS1"
FT /id="PRO_0000425970"
FT VAR_SEQ 810..834
FT /note="AYARIGMAKEAADCAAQANDGGELL -> VCPAYKTCTWIIGLDMYKIYRNL
FT LV (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:19423640"
FT /id="VSP_053914"
FT VAR_SEQ 835..858
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:19423640"
FT /id="VSP_053915"
SQ SEQUENCE 858 AA; 96632 MW; 94D8658581CA7023 CRC64;
MANVSVAAEW QLLYDRYYRK PEIYQMKWKH VDLSRNKVAC ASFGGPIAVI RDDSKIVQLY
AESALRKLRI FNSAGILLSE TVWKHPGGRL IGMSWSDDQT LICIVQDGTI YRYNIHAELI
EPNMSMGQEC FEQNVVECVF WGNGVVCLTE GGQLICIFDF KTMKPSKLPD VPGLAEDDLL
QPICLTVREP KYTMSGIAEV LVAVGDDIFV VEEDMVQTIR FDEPSVDDSE MQNDDSGNLI
GVVQKMIVSP NGKFLTLFTH DGRIVVVDME TKQIAIDYSC ESALPPQQMA WCGMDSVLLY
WDEDLMMVGP VGDPVHYFYD EPIILIPECD GVRILSNTNL EFLQRVPDST ESIFKIGSTS
PAALLYDALD HFDRRSAKAD ENLRLIRSSL SEAVESCIDA AGHEFDVTRQ RALLRAASYG
QAFCSNFQRE RVQETCRTLR VLNAVRDPAI GIPLSIQQYK LLTPVVLISR LINANCHLLA
LRISEYLDMN KEVVIMHWAC AKITASPSTP DSHLLEILLD KLQLCKGISY AAVATHADNC
GRRKLAAMLV EHEPRSTKQV PLLLSIGEED TALVKATESG DTDLVYLVIF HIWQKRPPLE
FFAMIQGRVL ARDLFVAYAR CHKHEFLKDF FLSTGQIHEV AFLLWKESWD MGKNPMASKG
SPLHGPRIKL IEKARNLFSQ TKEHTFESKA AEEHAKLLKI QHELEASTKQ AIFVDSSIND
TIRTCIVLGN NRAAIKVKTE FKVSDKRWYW LKAFALATIK DWAALEKFSK EKRPPMGFRP
FVEACIDADE KAEALKYIPK LSDLVERGEA YARIGMAKEA ADCAAQANDG GELLERFRKT
FVQNAIFDTL LMPFQGAS
