LIDB1_CAEEL
ID LIDB1_CAEEL Reviewed; 592 AA.
AC G5EEL0; Q8I4H8; Q8IU51;
DT 07-OCT-2020, integrated into UniProtKB/Swiss-Prot.
DT 14-DEC-2011, sequence version 1.
DT 03-AUG-2022, entry version 91.
DE RecName: Full=LIM domain-binding protein 1 {ECO:0000312|WormBase:F58A3.1a};
GN Name=ldb-1 {ECO:0000312|WormBase:F58A3.1a};
GN ORFNames=F58A3.1 {ECO:0000312|WormBase:F58A3.1a};
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239 {ECO:0000312|Proteomes:UP000001940};
RN [1] {ECO:0000312|EMBL:AAB38366.1, ECO:0000312|EMBL:AAB38367.1}
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND B).
RC STRAIN=Bristol N2 {ECO:0000312|EMBL:AAB38366.1};
RA Hobert O., Kohara Y., Ruvkun G.;
RL Submitted (NOV-1996) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000312|Proteomes:UP000001940}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2 {ECO:0000312|Proteomes:UP000001940};
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [3] {ECO:0000305}
RP FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=10993673; DOI=10.1006/dbio.2000.9846;
RA Cassata G., Roehrig S., Kuhn F., Hauri H.P., Baumeister R., Buerglin T.R.;
RT "The Caenorhabditis elegans Ldb/NLI/Clim orthologue ldb-1 is required for
RT neuronal function.";
RL Dev. Biol. 226:45-56(2000).
RN [4] {ECO:0000305}
RP FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=12736204; DOI=10.1242/dev.00500;
RA Gupta B.P., Wang M., Sternberg P.W.;
RT "The C. elegans LIM homeobox gene lin-11 specifies multiple cell fates
RT during vulval development.";
RL Development 130:2589-2601(2003).
RN [5] {ECO:0000305}
RP FUNCTION.
RX PubMed=21115607; DOI=10.1242/dev.055350;
RA Zheng Q., Schaefer A.M., Nonet M.L.;
RT "Regulation of C. elegans presynaptic differentiation and neurite branching
RT via a novel signaling pathway initiated by SAM-10.";
RL Development 138:87-96(2011).
RN [6] {ECO:0000305}
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH BLMP-1.
RX PubMed=32417234; DOI=10.1016/j.bbagrm.2020.194577;
RA Fong H.T., Hagen T., Inoue T.;
RT "LDB1 and the SWI/SNF complex participate in both transcriptional
RT activation and repression by Caenorhabditis elegans BLIMP1/PRDM1.";
RL Biochim. Biophys. Acta 1863:194577-194577(2020).
CC -!- FUNCTION: Binds to the LIM domain of LIM domain-containing
CC transcription factors (PubMed:10993673). Required for the blmp-1-
CC mediated transcriptional activation or repression of several hypodermal
CC genes, such as bed-3 (PubMed:32417234). Regulates sam-10 nuclear
CC localization in PLM neurons (PubMed:21115607). Has a role in synaptic
CC differentiation of PLM mechanosensory neurons (PubMed:21115607).
CC Involved in gonadogenesis (PubMed:12736204).
CC {ECO:0000269|PubMed:10993673, ECO:0000269|PubMed:12736204,
CC ECO:0000269|PubMed:21115607, ECO:0000269|PubMed:32417234}.
CC -!- SUBUNIT: Interacts with blmp-1. {ECO:0000269|PubMed:32417234}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=a {ECO:0000312|WormBase:F58A3.1a};
CC IsoId=G5EEL0-1; Sequence=Displayed;
CC Name=b {ECO:0000312|WormBase:F58A3.1b};
CC IsoId=G5EEL0-2; Sequence=VSP_060758;
CC -!- TISSUE SPECIFICITY: Expressed in all neurons and some other tissues of
CC the adult, including vulval muscle, and, in males, all the neurons of
CC the tail region (PubMed:10993673). Expressed in vulval cells
CC (PubMed:12736204, PubMed:10993673). {ECO:0000269|PubMed:10993673,
CC ECO:0000269|PubMed:12736204}.
CC -!- DEVELOPMENTAL STAGE: First expressed widely in 200- to 260-minute-old
CC embryo, except in hyp-7 cells (PubMed:10993673). Expression becomes
CC more restricted to the anterior, ventral, and posterior part in the
CC comma stage embryo (PubMed:10993673). Expressed in all neurons and some
CC other tissues of the larva (PubMed:10993673). Expressed in primary
CC vulval cells during the L4 larval stage (PubMed:12736204).
CC {ECO:0000269|PubMed:10993673, ECO:0000269|PubMed:12736204}.
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown causes mechanosensory
CC defects and uncoordination in L1 and L2 larval stage animals;
CC phenotypes become weaker in later stages and eventually disappear in
CC young adults (PubMed:10993673). RNAi-mediated knockdown causes defects
CC in vulval morphology and gonad arms (PubMed:12736204). RNAi-mediated
CC knockdown reduces the level of bed-3 and col-124 mRNAs and increases
CC the level of lin-29 mRNA (PubMed:32417234).
CC {ECO:0000269|PubMed:10993673, ECO:0000269|PubMed:12736204,
CC ECO:0000269|PubMed:32417234}.
CC -!- SIMILARITY: Belongs to the LDB family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB38367.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; U80220; AAB38366.1; -; mRNA.
DR EMBL; U80221; AAB38367.1; ALT_INIT; mRNA.
DR EMBL; BX284606; CAB02669.1; -; Genomic_DNA.
DR EMBL; BX284606; CAB02672.1; -; Genomic_DNA.
DR PIR; T22885; T22885.
DR PIR; T22888; T22888.
DR RefSeq; NP_509845.1; NM_077444.3. [G5EEL0-2]
DR RefSeq; NP_509846.1; NM_077445.4.
DR AlphaFoldDB; G5EEL0; -.
DR SMR; G5EEL0; -.
DR PeptideAtlas; G5EEL0; -.
DR EnsemblMetazoa; F58A3.1a.1; F58A3.1a.1; WBGene00002261. [G5EEL0-1]
DR EnsemblMetazoa; F58A3.1a.2; F58A3.1a.2; WBGene00002261. [G5EEL0-1]
DR EnsemblMetazoa; F58A3.1b.1; F58A3.1b.1; WBGene00002261. [G5EEL0-2]
DR EnsemblMetazoa; F58A3.1b.2; F58A3.1b.2; WBGene00002261. [G5EEL0-2]
DR GeneID; 181292; -.
DR UCSC; F58A3.1c; c. elegans.
DR CTD; 181292; -.
DR WormBase; F58A3.1a; CE11350; WBGene00002261; ldb-1.
DR WormBase; F58A3.1b; CE11352; WBGene00002261; ldb-1.
DR HOGENOM; CLU_434933_0_0_1; -.
DR OrthoDB; 849287at2759; -.
DR SignaLink; G5EEL0; -.
DR Proteomes; UP000001940; Chromosome X.
DR Bgee; WBGene00002261; Expressed in pharyngeal muscle cell (C elegans) and 4 other tissues.
DR ExpressionAtlas; G5EEL0; baseline and differential.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005667; C:transcription regulator complex; IBA:GO_Central.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IDA:WormBase.
DR GO; GO:0140297; F:DNA-binding transcription factor binding; IPI:UniProtKB.
DR GO; GO:0030274; F:LIM domain binding; IPI:WormBase.
DR GO; GO:0040011; P:locomotion; IMP:WormBase.
DR GO; GO:0007638; P:mechanosensory behavior; IMP:WormBase.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:UniProtKB.
DR GO; GO:0007399; P:nervous system development; IBA:GO_Central.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:UniProtKB.
DR GO; GO:0040026; P:positive regulation of vulval development; IMP:UniProtKB.
DR GO; GO:0034504; P:protein localization to nucleus; IMP:WormBase.
DR GO; GO:0007416; P:synapse assembly; IMP:WormBase.
DR GO; GO:0040025; P:vulval development; IMP:WormBase.
DR InterPro; IPR041363; LID.
DR InterPro; IPR029005; LIM-bd/SEUSS.
DR PANTHER; PTHR10378; PTHR10378; 1.
DR Pfam; PF17916; LID; 1.
DR Pfam; PF01803; LIM_bind; 1.
DR PROSITE; PS51957; LID; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Reference proteome.
FT CHAIN 1..592
FT /note="LIM domain-binding protein 1"
FT /id="PRO_0000451156"
FT DOMAIN 378..417
FT /note="LIM interaction domain (LID)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01302"
FT REGION 14..41
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 305..368
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 437..458
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 559..592
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 27..41
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 348..368
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 572..586
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 2..44
FT /note="YGHHPDYGYGNYGHPPPFAGPESSNSHYGMPPSQGTNSQNNMM -> FHRPP
FT SARPPLNHVDQLKSLQATALGKPG (in isoform b)"
FT /evidence="ECO:0000305"
FT /id="VSP_060758"
SQ SEQUENCE 592 AA; 66338 MW; 930CA0DC499BBE5E CRC64;
MYGHHPDYGY GNYGHPPPFA GPESSNSHYG MPPSQGTNSQ NNMMMRSQAT EPQPIGNTVS
PLEFRIHDMN RRLYIFSSTG VSENDQQQWW DAFSHEFFDD DCKLWFVIGS EPVAFASRER
YIINRQFIPK FFRSIFDSGM RELQYVLRGP SRECTLANGS QAYENENVLQ ITRYDQSSQF
EVNTEGKLYV EFAPFDEVMN YRIKAWTLEL KRSNEFVYNQ NTADYRVEAQ NPEQENKPRM
GFFKSTFNLM TMLKILDPMQ SIMSSAKSAP AITPREVMKR TLFQHHQVRQ QNMRQQQLNQ
QMMIPAPEPE KPKPARKRQR KPAANPRGSK KATAAAAAAA AAATNGVPPT VPTASPANNQ
QFPPNPMTSQ FQQMSYPDVM VVGEPSMMGS EFGENDERTI SRVENSQYDP NAMQMQSLGQ
GPNSSMNING RNMMNQHHPG MQPPPGQQHM PPHSMGSQMP TSMHNPMHMP PGSMQGHGGM
PPMPSTMANQ MPPPNLPPHT MSNQMPNSRM PPMQGQMPPS GMPGQMSNPN MMGSGMPPMS
MSSQMPGSMS NPMPNQMPGG MQMNQMPPPN YSQYTGGPPP QWPPPNSAMI TG
