PUB1_MEDTR
ID PUB1_MEDTR Reviewed; 694 AA.
AC E4NKF8; A0A0C3XRJ4; G7K272;
DT 08-JUN-2016, integrated into UniProtKB/Swiss-Prot.
DT 08-FEB-2011, sequence version 1.
DT 25-MAY-2022, entry version 50.
DE RecName: Full=U-box domain-containing protein 1 {ECO:0000303|PubMed:20971894};
DE EC=2.3.2.27 {ECO:0000269|PubMed:20971894};
DE AltName: Full=Plant U-box protein 1 {ECO:0000303|PubMed:20971894};
DE Short=MtPUB1 {ECO:0000303|PubMed:20971894};
DE AltName: Full=RING-type E3 ubiquitin transferase PUB1 {ECO:0000305};
GN Name=PUB1 {ECO:0000303|PubMed:20971894};
GN OrderedLocusNames=MTR_5g083030 {ECO:0000312|EMBL:AES99632.2};
OS Medicago truncatula (Barrel medic) (Medicago tribuloides).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; Hologalegina; IRL clade; Trifolieae; Medicago.
OX NCBI_TaxID=3880 {ECO:0000312|EMBL:DAA33939.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF
RP TRP-326, PATHWAY, INTERACTION WITH LYK3, SUBCELLULAR LOCATION, TISSUE
RP SPECIFICITY, DEVELOPMENTAL STAGE, INDUCTION BY NOD FACTORS, AND
RP PHOSPHORYLATION BY LYK3.
RC STRAIN=cv. Jemalong A17;
RX PubMed=20971894; DOI=10.1105/tpc.110.075861;
RA Mbengue M., Camut S., de Carvalho-Niebel F., Deslandes L., Froidure S.,
RA Klaus-Heisen D., Moreau S., Rivas S., Timmers T., Herve C., Cullimore J.,
RA Lefebvre B.;
RT "The Medicago truncatula E3 ubiquitin ligase PUB1 interacts with the LYK3
RT symbiotic receptor and negatively regulates infection and nodulation.";
RL Plant Cell 22:3474-3488(2010).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Jemalong A17;
RX PubMed=22089132; DOI=10.1038/nature10625;
RA Young N.D., Debelle F., Oldroyd G.E.D., Geurts R., Cannon S.B.,
RA Udvardi M.K., Benedito V.A., Mayer K.F.X., Gouzy J., Schoof H.,
RA Van de Peer Y., Proost S., Cook D.R., Meyers B.C., Spannagl M., Cheung F.,
RA De Mita S., Krishnakumar V., Gundlach H., Zhou S., Mudge J., Bharti A.K.,
RA Murray J.D., Naoumkina M.A., Rosen B., Silverstein K.A.T., Tang H.,
RA Rombauts S., Zhao P.X., Zhou P., Barbe V., Bardou P., Bechner M.,
RA Bellec A., Berger A., Berges H., Bidwell S., Bisseling T., Choisne N.,
RA Couloux A., Denny R., Deshpande S., Dai X., Doyle J.J., Dudez A.-M.,
RA Farmer A.D., Fouteau S., Franken C., Gibelin C., Gish J., Goldstein S.,
RA Gonzalez A.J., Green P.J., Hallab A., Hartog M., Hua A., Humphray S.J.,
RA Jeong D.-H., Jing Y., Jocker A., Kenton S.M., Kim D.-J., Klee K., Lai H.,
RA Lang C., Lin S., Macmil S.L., Magdelenat G., Matthews L., McCorrison J.,
RA Monaghan E.L., Mun J.-H., Najar F.Z., Nicholson C., Noirot C.,
RA O'Bleness M., Paule C.R., Poulain J., Prion F., Qin B., Qu C., Retzel E.F.,
RA Riddle C., Sallet E., Samain S., Samson N., Sanders I., Saurat O.,
RA Scarpelli C., Schiex T., Segurens B., Severin A.J., Sherrier D.J., Shi R.,
RA Sims S., Singer S.R., Sinharoy S., Sterck L., Viollet A., Wang B.-B.,
RA Wang K., Wang M., Wang X., Warfsmann J., Weissenbach J., White D.D.,
RA White J.D., Wiley G.B., Wincker P., Xing Y., Yang L., Yao Z., Ying F.,
RA Zhai J., Zhou L., Zuber A., Denarie J., Dixon R.A., May G.D.,
RA Schwartz D.C., Rogers J., Quetier F., Town C.D., Roe B.A.;
RT "The Medicago genome provides insight into the evolution of rhizobial
RT symbioses.";
RL Nature 480:520-524(2011).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Jemalong A17;
RX PubMed=24767513; DOI=10.1186/1471-2164-15-312;
RA Tang H., Krishnakumar V., Bidwell S., Rosen B., Chan A., Zhou S.,
RA Gentzbittel L., Childs K.L., Yandell M., Gundlach H., Mayer K.F.,
RA Schwartz D.C., Town C.D.;
RT "An improved genome release (version Mt4.0) for the model legume Medicago
RT truncatula.";
RL BMC Genomics 15:312-312(2014).
RN [4]
RP FUNCTION, MUTAGENESIS OF ASP-308, INTERACTION WITH NORK/DMI2,
RP PHOSPHORYLATION AT NORK/DMI2, INDUCTION BY RHIZOPHAGUS IRREGULARIS, TISSUE
RP SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX PubMed=26839127; DOI=10.1104/pp.15.01694;
RA Vernie T., Camut S., Camps C., Rembliere C., de Carvalho-Niebel F.,
RA Mbengue M., Timmers T., Gasciolli V., Thompson R.D., Lesignor C.,
RA Lefebvre B., Cullimore J.V., Herve C.;
RT "PUB1 interacts with the receptor kinase DMI2 and negatively regulates
RT rhizobial and arbuscular mycorrhizal symbioses through its ubiquitination
RT activity in Medicago truncatula.";
RL Plant Physiol. 170:2312-2324(2016).
CC -!- FUNCTION: Exhibits U-box-dependent E3 ubiquitin ligase activity in
CC vitro (PubMed:20971894, PubMed:26839127). Negatively modulates
CC successive stages of infection and development of rhizobial (e.g.
CC Sinorhizobium meliloti) and arbuscular mycorrhizal fungi (AM, e.g.
CC Rhizophagus irregularis) symbioses, in an ubiquitin ligase activity-
CC dependent manner (PubMed:26839127). Negative regulator of the LYK3
CC signaling pathway leading to nitrogen-fixing symbiosis (eg. infection
CC and nodulation) by rhizobia. May be involved in the discrimination of
CC rhizobium strains producing variant Nod factors (PubMed:20971894).
CC {ECO:0000269|PubMed:20971894, ECO:0000269|PubMed:26839127}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC EC=2.3.2.27; Evidence={ECO:0000269|PubMed:20971894};
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC {ECO:0000269|PubMed:20971894}.
CC -!- SUBUNIT: Interacts with LYK3 (PubMed:20971894). Binds to NORK/DMI2
CC (PubMed:26839127). {ECO:0000269|PubMed:20971894,
CC ECO:0000269|PubMed:26839127}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:20971894}.
CC -!- TISSUE SPECIFICITY: Present ubiquitously at very low levels during
CC nonsymbiotic growth. Accumulates in roots and nodules during symbiotic
CC growth with rhizobia and mycorrhiza. {ECO:0000269|PubMed:20971894,
CC ECO:0000269|PubMed:26839127}.
CC -!- DEVELOPMENTAL STAGE: Expressed specifically in symbiotic conditions
CC with S.meliloti, especially in cortical cells in close contact with
CC rhizobial infections. Accumulates in nodule primordia. In young
CC nodules, confined to the apical regions. In mature nodules, present in
CC a broad apical region encompassing the pre-infection, infection, and
CC early nitrogen fixation zones (PubMed:20971894). Expressed at all
CC stages of arbuscular mycorrhizal (AM) fungal infection in epidermal and
CC cortical infected cells, and in cells in their close vicinity. Two
CC weeks after inoculation with R.irregularis, confined to localized areas
CC associated with the presence of the fungus. Later expressed in
CC epidermal cells directly associated with visible hyphopodia forming on
CC the root surface, and in a few restricted outer cortical cells in the
CC immediate vicinity. In fully colonized roots, observed in infected
CC outer cortical cells and in surrounding cells. Also detected both
CC inside and in the vicinity of inner cortical cells containing
CC arbuscules (PubMed:26839127). {ECO:0000269|PubMed:20971894,
CC ECO:0000269|PubMed:26839127}.
CC -!- INDUCTION: Induced by S.meliloti Nod factors. Strongly induced in roots
CC during nodulation and to a lesser extent following mycorrhization
CC (PubMed:20971894). Activated during successive stages of root
CC colonization by R.irregularis (PubMed:26839127).
CC {ECO:0000269|PubMed:20971894, ECO:0000269|PubMed:26839127}.
CC -!- PTM: Phosphorylated by LYK3 in vitro (PubMed:20971894). Phosphorylated
CC by NORK/DMI2 (PubMed:26839127). {ECO:0000269|PubMed:20971894,
CC ECO:0000269|PubMed:26839127}.
CC -!- DISRUPTION PHENOTYPE: Increased nodulation in plants infected by
CC S.meliloti expressing modified inefficient Nod factors (e.g. nodF nodL)
CC or in the mutant lyk3-4 infected by wild-type S.meliloti.
CC {ECO:0000269|PubMed:20971894}.
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DR EMBL; BK007068; DAA33939.1; -; mRNA.
DR EMBL; CM001221; AES99632.2; -; Genomic_DNA.
DR RefSeq; XP_003616674.2; XM_003616626.2.
DR AlphaFoldDB; E4NKF8; -.
DR SMR; E4NKF8; -.
DR STRING; 3880.AES99632; -.
DR PRIDE; E4NKF8; -.
DR EnsemblPlants; AES99632; AES99632; MTR_5g083030.
DR GeneID; 11430446; -.
DR Gramene; AES99632; AES99632; MTR_5g083030.
DR KEGG; mtr:MTR_5g083030; -.
DR eggNOG; KOG0167; Eukaryota.
DR HOGENOM; CLU_006348_5_1_1; -.
DR OrthoDB; 584068at2759; -.
DR UniPathway; UPA00143; -.
DR Proteomes; UP000002051; Chromosome 5.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; IDA:UniProtKB.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IDA:UniProtKB.
DR GO; GO:0036377; P:arbuscular mycorrhizal association; IMP:UniProtKB.
DR GO; GO:0009877; P:nodulation; IMP:UniProtKB.
DR GO; GO:0002237; P:response to molecule of bacterial origin; IEP:UniProtKB.
DR GO; GO:0009609; P:response to symbiotic bacterium; IEP:UniProtKB.
DR GO; GO:0009610; P:response to symbiotic fungus; IDA:UniProtKB.
DR CDD; cd16664; RING-Ubox_PUB; 1.
DR Gene3D; 1.25.10.10; -; 2.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR011989; ARM-like.
DR InterPro; IPR016024; ARM-type_fold.
DR InterPro; IPR000225; Armadillo.
DR InterPro; IPR045210; RING-Ubox_PUB.
DR InterPro; IPR003613; Ubox_domain.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF00514; Arm; 1.
DR Pfam; PF04564; U-box; 1.
DR SMART; SM00185; ARM; 5.
DR SMART; SM00504; Ubox; 1.
DR SUPFAM; SSF48371; SSF48371; 1.
DR PROSITE; PS50176; ARM_REPEAT; 2.
DR PROSITE; PS51698; U_BOX; 1.
PE 1: Evidence at protein level;
KW Cell membrane; Membrane; Nodulation; Phosphoprotein; Reference proteome;
KW Repeat; Transferase; Ubl conjugation pathway.
FT CHAIN 1..694
FT /note="U-box domain-containing protein 1"
FT /id="PRO_0000436504"
FT DOMAIN 292..366
FT /note="U-box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01034"
FT REPEAT 392..432
FT /note="ARM 1"
FT /evidence="ECO:0000255"
FT REPEAT 435..474
FT /note="ARM 2"
FT /evidence="ECO:0000255"
FT REPEAT 476..516
FT /note="ARM 3"
FT /evidence="ECO:0000255"
FT REPEAT 519..558
FT /note="ARM 4"
FT /evidence="ECO:0000255"
FT REPEAT 560..599
FT /note="ARM 5"
FT /evidence="ECO:0000255"
FT REPEAT 601..641
FT /note="ARM 6"
FT /evidence="ECO:0000255"
FT REPEAT 646..685
FT /note="ARM 7"
FT /evidence="ECO:0000255"
FT MUTAGEN 308
FT /note="D->N: In pub1-1; abolished E3 ubiquitin ligase
FT activity and slight reduction of the total root length.
FT Increased and faster fungal colonization by R.irregularis."
FT /evidence="ECO:0000269|PubMed:26839127"
FT MUTAGEN 326
FT /note="W->A: Abolished E3 ubiquitin ligase activity."
FT /evidence="ECO:0000269|PubMed:20971894"
SQ SEQUENCE 694 AA; 76929 MW; 913995A6A1323D00 CRC64;
MNDPRSKMMI SPGLLPTESL LDSLILISNE VSSMQKFPLV QIKNVSSMIR RIKLLSSLFE
EIQESDSPLP PSSILCFIEI FSVITRVKVL IQECTDGSSL WSLIQLDFIS NQFFVLVKEM
GRALDILPLN LLNVAQDIKE QVDLLHKQSK RVELELFIDP REVQRRENLF EVMSKNCLQN
KKTNNNKGFI DFVKVEEIMC SIGLRTLSDY VEEISKLEVE AQNQAGTGGL IVVSNINNLM
SLVSYTKSMV FRNDGESEEC KPISMFLYNK SKIHDNDSSS SSSFSQSMMT VNIPDEFRCP
ISLDLMRDPV IVSSGHTYDR ISIAEWINSG HHTCPKSGQR LIHTALIPNY ALKSLVHQWC
YENNVKMNEA ITKNNNSSSK RHKNENAIDH ISENKASKDA VKMTAEFLVG KLATGSTDIQ
RQSAYEIRLL AKTGMDNRRI IAEVGAIPFL VTLLVSKDSR IQEHVVTALF NLSIYDNNKI
LIMAAGAIDN IVEVLEFGKT MEARENAAAA IYSLSMIDDC KVQIGASSRA IPALVGLLKE
GTIIGKRDAA TALFNLAVYN PNKLSIVKSG AVTLLVELLM DDKAGITDDS LAVLAVLLGC
SEGLEEIKNS KSLVPLLIDL LRFGSVKGKE NSITLLLGLC KEEGELVAMR LLANPRSIPS
LQSLAADGSL RARRKADALL RLLNRCCSQP HHSL
