YIP4B_ARATH
ID YIP4B_ARATH Reviewed; 280 AA.
AC Q93VH1; A0A178V3Z0;
DT 07-OCT-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Protein YIP4b {ECO:0000303|PubMed:23832588};
DE AltName: Full=YPT/RAB GTPase-interacting protein 4b {ECO:0000303|PubMed:23832588};
DE Short=YIP4b {ECO:0000303|PubMed:23832588};
GN Name=YIP4B {ECO:0000303|PubMed:23832588};
GN Synonyms=YIP2 {ECO:0000303|PubMed:23832588};
GN OrderedLocusNames=At4g30260 {ECO:0000312|Araport:AT4G30260};
GN ORFNames=F9N11.110 {ECO:0000312|EMBL:AEE85744.1};
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 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 [2]
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 [3]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, SUBUNIT, AND
RP INTERACTION WITH YIP4A AND ECH.
RC STRAIN=cv. Columbia;
RX PubMed=23832588; DOI=10.1105/tpc.113.112482;
RA Gendre D., McFarlane H.E., Johnson E., Mouille G., Sjoedin A., Oh J.,
RA Levesque-Tremblay G., Watanabe Y., Samuels L., Bhalerao R.P.;
RT "Trans-Golgi network localized ECHIDNA/Ypt interacting protein complex is
RT required for the secretion of cell wall polysaccharides in Arabidopsis.";
RL Plant Cell 25:2633-2646(2013).
RN [4]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND DEVELOPMENTAL
RP STAGE.
RC STRAIN=cv. Columbia;
RX PubMed=30770391; DOI=10.1242/dev.168559;
RA Gendre D., Baral A., Dang X., Esnay N., Boutte Y., Stanislas T., Vain T.,
RA Claverol S., Gustavsson A., Lin D., Grebe M., Bhalerao R.P.;
RT "Rho-of-plant activated root hair formation requires Arabidopsis YIP4a/b
RT gene function.";
RL Development 146:0-0(2019).
CC -!- FUNCTION: Together with YIP4A, involved in the regulation of cell
CC elongation during root and hypocotyl growth (PubMed:23832588). YIP4A
CC and YIP4B are central trafficking components in Rho-of-plant (ROPs,
CC e.g. ARAC4/ROP2, ARAC5/ROP4 and ARAC3/ROP6) small GTPases-dependent
CC root hair formation, thus contributing to activation and plasma
CC membrane accumulation of ROPs during hair initiation (PubMed:30770391).
CC The ECH/YIP4 complex is involved in the modulation of the trans-Golgi
CC network (TGN)-mediated trafficking of some proteins and cell wall
CC components (e.g. pectin and hemicellulose) to the cell wall in dark-
CC grown hypocotyls and in secretory cells of the seed coat
CC (PubMed:23832588). {ECO:0000269|PubMed:23832588,
CC ECO:0000269|PubMed:30770391}.
CC -!- SUBUNIT: Homodimer and heterodimer with YIP4A (PubMed:23832588).
CC Component of a trans-Golgi network (TGN)-localized ECH/YIP4 complex
CC made of ECH, YIP4A and YIP4B (PubMed:23832588). Interacts directly with
CC ECH (PubMed:23832588). {ECO:0000269|PubMed:23832588}.
CC -!- INTERACTION:
CC Q93VH1; Q8GWB3: At3g05280/T12H1_25; NbExp=3; IntAct=EBI-4430553, EBI-4425753;
CC -!- SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network membrane
CC {ECO:0000269|PubMed:23832588}; Multi-pass membrane protein
CC {ECO:0000255}.
CC -!- TISSUE SPECIFICITY: Expressed in developing root hair cells.
CC {ECO:0000269|PubMed:30770391}.
CC -!- DEVELOPMENTAL STAGE: Ubiquitous expression in elongating root hair and
CC non-hair cells prior to hair formation. {ECO:0000269|PubMed:30770391}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype (PubMed:23832588). The
CC double mutant yip4a yip4b exhibits disturbed trans-Golgi network (TGN)-
CC Golgi association and cell elongation defects leading to reduced roots
CC and hypocotyls growth associated with an abnormal cell wall composition
CC and a mislocalization of trans-Golgi network (TGN)-localized proteins
CC SYP61 and VHA-a1 (PubMed:23832588, PubMed:30770391). The double mutant
CC yip4a yip4b has also a reduced number of root trichoblasts displaying
CC Rho-of-plant (ROPs e.g. ARAC4/ROP2, ARAC5/ROP4 and ARAC3/ROP6) patches
CC and leading to an almost complete absence of root hairs
CC (PubMed:30770391). {ECO:0000269|PubMed:23832588,
CC ECO:0000269|PubMed:30770391}.
CC -!- SIMILARITY: Belongs to the YIP1 family. {ECO:0000305}.
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DR EMBL; CP002687; AEE85744.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM67107.1; -; Genomic_DNA.
DR EMBL; AY045675; AAK74033.1; -; mRNA.
DR EMBL; AY056083; AAL06971.1; -; mRNA.
DR EMBL; AY093179; AAM13178.1; -; mRNA.
DR RefSeq; NP_001320089.1; NM_001342003.1.
DR RefSeq; NP_567843.1; NM_119172.4.
DR AlphaFoldDB; Q93VH1; -.
DR IntAct; Q93VH1; 6.
DR STRING; 3702.AT4G30260.1; -.
DR PaxDb; Q93VH1; -.
DR PRIDE; Q93VH1; -.
DR ProteomicsDB; 185664; -.
DR EnsemblPlants; AT4G30260.1; AT4G30260.1; AT4G30260.
DR EnsemblPlants; AT4G30260.3; AT4G30260.3; AT4G30260.
DR GeneID; 829149; -.
DR Gramene; AT4G30260.1; AT4G30260.1; AT4G30260.
DR Gramene; AT4G30260.3; AT4G30260.3; AT4G30260.
DR KEGG; ath:AT4G30260; -.
DR Araport; AT4G30260; -.
DR TAIR; locus:2128926; AT4G30260.
DR HOGENOM; CLU_059592_2_1_1; -.
DR OMA; CVMPLTV; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q93VH1; baseline and differential.
DR GO; GO:0005768; C:endosome; HDA:TAIR.
DR GO; GO:0005794; C:Golgi apparatus; HDA:TAIR.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0005802; C:trans-Golgi network; IDA:TAIR.
DR GO; GO:0032588; C:trans-Golgi network membrane; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0006888; P:endoplasmic reticulum to Golgi vesicle-mediated transport; IEA:InterPro.
DR GO; GO:0045489; P:pectin biosynthetic process; IMP:UniProtKB.
DR GO; GO:0099402; P:plant organ development; IMP:UniProtKB.
DR GO; GO:0052324; P:plant-type cell wall cellulose biosynthetic process; IMP:UniProtKB.
DR GO; GO:0015774; P:polysaccharide transport; IGI:TAIR.
DR GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR GO; GO:0051223; P:regulation of protein transport; IMP:UniProtKB.
DR GO; GO:0048364; P:root development; IMP:UniProtKB.
DR GO; GO:0048766; P:root hair initiation; IMP:UniProtKB.
DR GO; GO:0009826; P:unidimensional cell growth; IMP:UniProtKB.
DR InterPro; IPR045231; Yip1/4-like.
DR InterPro; IPR006977; Yip1_dom.
DR PANTHER; PTHR21236; PTHR21236; 1.
DR Pfam; PF04893; Yip1; 1.
PE 1: Evidence at protein level;
KW Cell wall biogenesis/degradation; Golgi apparatus; Membrane;
KW Protein transport; Reference proteome; Transmembrane; Transmembrane helix;
KW Transport.
FT CHAIN 1..280
FT /note="Protein YIP4b"
FT /id="PRO_0000450870"
FT TOPO_DOM 1..146
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 147..167
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 168..171
FT /note="Lumenal"
FT /evidence="ECO:0000305"
FT TRANSMEM 172..192
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 193..213
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 214..230
FT /note="Lumenal"
FT /evidence="ECO:0000305"
FT TRANSMEM 231..251
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 252..258
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 259..279
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 280
FT /note="Lumenal"
FT /evidence="ECO:0000305"
FT REGION 1..106
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..32
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 49..74
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 90..106
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 280 AA; 30220 MW; BB77E23AC2715D7B CRC64;
MSHNDTIPLY QSSQSDIDEI ENMMNDSFQS GPGTVLPARP PSPIRPSIPV SSSPFVQSNL
PPLPPSSSSS TQKVMPVPAP PPLPSAGNEG NKSIGGSGFG SPPNTLTEPV WDTVKRDLSR
IVSNLKLVVF PNPYREDPGK ALRDWDLWGP FFFIVFLGLT LSWSASVKKS EVFAVAFALL
AAGAVILTLN VLLLGGHIIF FQSLSLLGYC LFPLDVGAVI CMLKDNVILK MVVVSVTLAW
SSWAAYPFMS AAVNPRRKAL ALYPVFLMYV SVGFLIIAIN
