LIM6_CAEEL
ID LIM6_CAEEL Reviewed; 316 AA.
AC Q21192; G4RV72; Q94157;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 25-JAN-2012, sequence version 4.
DT 03-AUG-2022, entry version 187.
DE RecName: Full=LIM/homeobox protein lim-6 {ECO:0000303|PubMed:10068647};
GN Name=lim-6 {ECO:0000312|WormBase:K03E6.1b};
GN ORFNames=K03E6.1 {ECO:0000312|WormBase:K03E6.1b};
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:AAD12189.1}
RP NUCLEOTIDE SEQUENCE [MRNA] OF 124-224, FUNCTION, AND DEVELOPMENTAL STAGE.
RX PubMed=10068647; DOI=10.1242/dev.126.7.1547;
RA Hobert O., Tessmar K., Ruvkun G.;
RT "The Caenorhabditis elegans lim-6 LIM homeobox gene regulates neurite
RT outgrowth and function of particular GABAergic neurons.";
RL Development 126:1547-1562(1999).
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.
RX PubMed=11287956; DOI=10.1038/35070575;
RA Pierce-Shimomura J.T., Faumont S., Gaston M.R., Pearson B.J., Lockery S.R.;
RT "The homeobox gene lim-6 is required for distinct chemosensory
RT representations in C. elegans.";
RL Nature 410:694-698(2001).
RN [4] {ECO:0000305}
RP FUNCTION, AND DEVELOPMENTAL STAGE.
RX PubMed=12490565; DOI=10.1242/dev.00277;
RA Aurelio O., Boulin T., Hobert O.;
RT "Identification of spatial and temporal cues that regulate postembryonic
RT expression of axon maintenance factors in the C. elegans ventral nerve
RT cord.";
RL Development 130:599-610(2003).
RN [5] {ECO:0000305}
RP FUNCTION.
RX PubMed=14568548; DOI=10.1016/s0012-1606(03)00447-0;
RA Tsalik E.L., Niacaris T., Wenick A.S., Pau K., Avery L., Hobert O.;
RT "LIM homeobox gene-dependent expression of biogenic amine receptors in
RT restricted regions of the C. elegans nervous system.";
RL Dev. Biol. 263:81-102(2003).
RN [6] {ECO:0000305}
RP FUNCTION, AND MUTAGENESIS OF CYS-106.
RX PubMed=21555395; DOI=10.1534/genetics.111.129064;
RA Zhang F., O'Meara M.M., Hobert O.;
RT "A left/right asymmetric neuronal differentiation program is controlled by
RT the Caenorhabditis elegans lsy-27 zinc-finger transcription factor.";
RL Genetics 188:753-759(2011).
RN [7] {ECO:0000305}
RP FUNCTION.
RX PubMed=26949257; DOI=10.7554/elife.12499;
RA Turek M., Besseling J., Spies J.P., Koenig S., Bringmann H.;
RT "Sleep-active neuron specification and sleep induction require FLP-11
RT neuropeptides to systemically induce sleep.";
RL Elife 5:0-0(2016).
CC -!- FUNCTION: Transcription factor (By similarity). Required for the
CC terminal differentiation of sensory- and motor-neurons, especially
CC GABAergic neurons, and for morphological aspects of uterine development
CC (PubMed:10068647). Plays a role in the cell-type-specific regulation of
CC glutamic acid decarboxylase unc-25 (PubMed:10068647). Involved in
CC promoting sleep-like behavioral quiescence, acting by modulating
CC expression of transcription factor aptf-1 in the single sleep-active
CC ring interneuron RIS (PubMed:26949257). Plays a role in regulation of
CC RIS differentiation (PubMed:14568548). Required for the functional
CC asymmetry of the ASER and ASEL chemosensory neuron pair, conferring the
CC ability to discriminate sodium from chloride, perhaps by modulating
CC expression of receptor-type guanylate cyclases, such as gcy-5
CC (PubMed:11287956, PubMed:21555395). Involved in regulating
CC postembryonic axon maintenance in the ventral nerve cord, acting in
CC concert with LIM homeobox protein ceh-14, via modulation of expression
CC of immunoglobulin domain zig genes in the interneuron PVT
CC (PubMed:12490565). May play a role in the functions of the excretory
CC gland cell (PubMed:10068647). {ECO:0000250|UniProtKB:O60663,
CC ECO:0000269|PubMed:10068647, ECO:0000269|PubMed:11287956,
CC ECO:0000269|PubMed:12490565, ECO:0000269|PubMed:14568548,
CC ECO:0000269|PubMed:21555395, ECO:0000269|PubMed:26949257}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00108,
CC ECO:0000255|RuleBase:RU000682}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=b {ECO:0000312|WormBase:K03E6.1b};
CC IsoId=Q21192-1; Sequence=Displayed;
CC Name=a {ECO:0000312|WormBase:K03E6.1a};
CC IsoId=Q21192-2; Sequence=VSP_061398;
CC -!- DEVELOPMENTAL STAGE: Expressed in a restricted set of neurons, and
CC epithelial cells of the uterus and the excretory system, late in
CC embryogenesis at about 300 minutes of development (PubMed:10068647).
CC Expression in neurons continues throughout adulthood (PubMed:10068647).
CC Expressed asymmetrically, only in the left neuron (ASEL), of the ASER
CC and ASEL chemosensory pair (PubMed:10068647). Expressed in the
CC interneuron PVT during embryogenesis (PubMed:12490565).
CC {ECO:0000269|PubMed:10068647, ECO:0000269|PubMed:12490565}.
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DR EMBL; U72347; AAD12189.1; -; mRNA.
DR EMBL; BX284606; CCD62867.1; -; Genomic_DNA.
DR EMBL; BX284606; CCD62868.1; -; Genomic_DNA.
DR RefSeq; NP_001256980.1; NM_001270051.1.
DR AlphaFoldDB; Q21192; -.
DR SMR; Q21192; -.
DR IntAct; Q21192; 1.
DR STRING; 6239.K03E6.1b; -.
DR PaxDb; Q21192; -.
DR EnsemblMetazoa; K03E6.1a.1; K03E6.1a.1; WBGene00002988. [Q21192-2]
DR EnsemblMetazoa; K03E6.1b.1; K03E6.1b.1; WBGene00002988. [Q21192-1]
DR EnsemblMetazoa; K03E6.1b.2; K03E6.1b.2; WBGene00002988. [Q21192-1]
DR GeneID; 180459; -.
DR KEGG; cel:CELE_K03E6.1; -.
DR UCSC; K03E6.1; c. elegans. [Q21192-1]
DR CTD; 180459; -.
DR WormBase; K03E6.1a; CE44857; WBGene00002988; lim-6.
DR WormBase; K03E6.1b; CE45007; WBGene00002988; lim-6.
DR eggNOG; KOG0490; Eukaryota.
DR GeneTree; ENSGT00940000169507; -.
DR HOGENOM; CLU_027802_6_0_1; -.
DR InParanoid; Q21192; -.
DR OMA; RFCARCH; -.
DR OrthoDB; 948890at2759; -.
DR PhylomeDB; Q21192; -.
DR Proteomes; UP000001940; Chromosome X.
DR Bgee; WBGene00002988; Expressed in larva and 3 other tissues.
DR ExpressionAtlas; Q21192; baseline and differential.
DR GO; GO:0005634; C:nucleus; IDA:WormBase.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:WormBase.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000977; F:RNA polymerase II transcription regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0007409; P:axonogenesis; IMP:WormBase.
DR GO; GO:0030421; P:defecation; IMP:WormBase.
DR GO; GO:0060756; P:foraging behavior; IMP:WormBase.
DR GO; GO:0010629; P:negative regulation of gene expression; IMP:UniProtKB.
DR GO; GO:0048666; P:neuron development; IMP:WormBase.
DR GO; GO:0030182; P:neuron differentiation; IBA:GO_Central.
DR GO; GO:0010628; P:positive regulation of gene expression; IMP:UniProtKB.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:WormBase.
DR GO; GO:1904081; P:positive regulation of transcription from RNA polymerase II promoter involved in neuron differentiation; IMP:WormBase.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0061038; P:uterus morphogenesis; IMP:WormBase.
DR CDD; cd00086; homeodomain; 1.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR017970; Homeobox_CS.
DR InterPro; IPR001356; Homeobox_dom.
DR InterPro; IPR001781; Znf_LIM.
DR Pfam; PF00046; Homeodomain; 1.
DR Pfam; PF00412; LIM; 2.
DR SMART; SM00389; HOX; 1.
DR SMART; SM00132; LIM; 2.
DR SUPFAM; SSF46689; SSF46689; 1.
DR PROSITE; PS00027; HOMEOBOX_1; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
DR PROSITE; PS00478; LIM_DOMAIN_1; 2.
DR PROSITE; PS50023; LIM_DOMAIN_2; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA-binding; Homeobox; LIM domain; Metal-binding;
KW Nucleus; Reference proteome; Repeat; Zinc.
FT CHAIN 1..316
FT /note="LIM/homeobox protein lim-6"
FT /id="PRO_0000454830"
FT DOMAIN 40..101
FT /note="LIM zinc-binding 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT DOMAIN 102..163
FT /note="LIM zinc-binding 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT DNA_BIND 186..245
FT /note="Homeobox"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT REGION 244..297
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 244..277
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 281..316
FT /note="NLDADEVETSETSSYTDPIQKLYNMTSSQIYFPYHS -> SKLKRIGIDIGE
FT LWLYKLKSVFQKVRKFVP (in isoform a)"
FT /evidence="ECO:0000305"
FT /id="VSP_061398"
FT MUTAGEN 106
FT /note="C->Y: In ot146; Impairs left/right asymmetric gene
FT expression programs of two gustatory neurons, ASEL and
FT ASER. In particular, markers of ASER cell fate, such as
FT receptor-type guanylate cyclase gcy-5, are gained in ASEL,
FT but ASEL fate markers are unaffected."
FT /evidence="ECO:0000269|PubMed:21555395"
SQ SEQUENCE 316 AA; 36507 MW; E3F2D191978BD50A CRC64;
MERDCDIVDL DQPSLGTVIS IKDGSTPTDI STTSSTTEDK LCSGCGCLIK DRYIYRVMED
SYHESCLRCS CCQLSLSSFK KCFSRHGNIY CEHDHQMLYG KRCRRCMTLL LPTDIVHRVH
FMYYHAQCFS CCSCQRPFNL GDEYHVFDGE VFCRNDYQSI CNFQTISNPD PLMEEVVRSE
IHRKTPKRPR TILNAQQRRQ FKTAFERSSK PSRKVREQLA NETGLSVRVV QVWFQNQRAK
IKKLNKKDSD SGDTFKHGPG SEGRSTEDIR SSDDEEESVI NLDADEVETS ETSSYTDPIQ
KLYNMTSSQI YFPYHS
