LIN29_CAEEL
ID LIN29_CAEEL Reviewed; 459 AA.
AC G5EGB2; E6N0V9; G5EGU6;
DT 02-JUN-2021, integrated into UniProtKB/Swiss-Prot.
DT 14-DEC-2011, sequence version 1.
DT 03-AUG-2022, entry version 95.
DE RecName: Full=Zinc finger transcription factor lin-29 {ECO:0000305};
DE AltName: Full=abnormal cell lineage 29 {ECO:0000312|WormBase:W03C9.4a};
GN Name=lin-29 {ECO:0000312|WormBase:W03C9.4a};
GN Synonyms=lin-29b {ECO:0000303|PubMed:7671813};
GN ORFNames=W03C9.4 {ECO:0000312|WormBase:W03C9.4a};
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:AAC37255.1}
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A), FUNCTION, DEVELOPMENTAL STAGE
RP (ISOFORMS A AND C), AND MUTAGENESIS OF 294-ARG--TYR-459.
RC STRAIN=Bristol N2 {ECO:0000312|EMBL:AAC37255.1};
RX PubMed=7671813; DOI=10.1242/dev.121.8.2491;
RA Rougvie A.E., Ambros V.;
RT "The heterochronic gene lin-29 encodes a zinc finger protein that controls
RT a terminal differentiation event in Caenorhabditis elegans.";
RL Development 121:2491-2500(1995).
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 SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX PubMed=8756296; DOI=10.1242/dev.122.8.2517;
RA Bettinger J.C., Lee K., Rougvie A.E.;
RT "Stage-specific accumulation of the terminal differentiation factor LIN-29
RT during Caenorhabditis elegans development.";
RL Development 122:2517-2527(1996).
RN [4] {ECO:0000305}
RP FUNCTION, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, AND MUTAGENESIS OF
RP 144-GLN--TYR-459.
RX PubMed=9334281; DOI=10.1242/dev.124.21.4333;
RA Bettinger J.C., Euling S., Rougvie A.E.;
RT "The terminal differentiation factor LIN-29 is required for proper vulval
RT morphogenesis and egg laying in Caenorhabditis elegans.";
RL Development 124:4333-4342(1997).
RN [5] {ECO:0000305}
RP FUNCTION, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, AND MUTAGENESIS OF
RP 294-ARG--TYR-459.
RX PubMed=9986728; DOI=10.1006/dbio.1998.9063;
RA Euling S., Bettinger J.C., Rougvie A.E.;
RT "The LIN-29 transcription factor is required for proper morphogenesis of
RT the Caenorhabditis elegans male tail.";
RL Dev. Biol. 206:142-156(1999).
RN [6] {ECO:0000305}
RP FUNCTION, AND MUTAGENESIS OF CYS-182.
RX PubMed=11114514; DOI=10.1016/s0960-9822(00)00827-7;
RA Newman A.P., Inoue T., Wang M., Sternberg P.W.;
RT "The Caenorhabditis elegans heterochronic gene lin-29 coordinates the
RT vulval-uterine-epidermal connections.";
RL Curr. Biol. 10:1479-1488(2000).
RN [7] {ECO:0000305}
RP FUNCTION, AND INTERACTION WITH MAB-10.
RX PubMed=21862562; DOI=10.1242/dev.065417;
RA Harris D.T., Horvitz H.R.;
RT "MAB-10/NAB acts with LIN-29/EGR to regulate terminal differentiation and
RT the transition from larva to adult in C. elegans.";
RL Development 138:4051-4062(2011).
RN [8] {ECO:0000305}
RP FUNCTION.
RX PubMed=25905672; DOI=10.7554/elife.06967;
RA Narasimhan K., Lambert S.A., Yang A.W., Riddell J., Mnaimneh S., Zheng H.,
RA Albu M., Najafabadi H.S., Reece-Hoyes J.S., Fuxman Bass J.I., Walhout A.J.,
RA Weirauch M.T., Hughes T.R.;
RT "Mapping and analysis of Caenorhabditis elegans transcription factor
RT sequence specificities.";
RL Elife 4:0-0(2015).
RN [9] {ECO:0000305}
RP FUNCTION, DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RX PubMed=27401555; DOI=10.1101/gad.283895.116;
RA Dowen R.H., Breen P.C., Tullius T., Conery A.L., Ruvkun G.;
RT "A microRNA program in the C. elegans hypodermis couples to intestinal
RT mTORC2/PQM-1 signaling to modulate fat transport.";
RL Genes Dev. 30:1515-1528(2016).
RN [10] {ECO:0000305}
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=29604168; DOI=10.1002/dvg.23106;
RA Abete-Luzi P., Eisenmann D.M.;
RT "Regulation of C. elegans L4 cuticle collagen genes by the heterochronic
RT protein LIN-29.";
RL Genesis 56:0-0(2018).
RN [11] {ECO:0000305}
RP FUNCTION, FUNCTION (ISOFORM C), SUBCELLULAR LOCATION, AND DEVELOPMENTAL
RP STAGE (ISOFORM C).
RX PubMed=32223899; DOI=10.7554/elife.53387;
RA Azzi C., Aeschimann F., Neagu A., Grosshans H.;
RT "A branched heterochronic pathway directs juvenile-to-adult transition
RT through two LIN-29 isoforms.";
RL Elife 9:0-0(2020).
RN [12] {ECO:0000305}
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=31974205; DOI=10.1534/genetics.119.302860;
RA Abete-Luzi P., Fukushige T., Yun S., Krause M.W., Eisenmann D.M.;
RT "New Roles for the Heterochronic Transcription Factor LIN-29 in Cuticle
RT Maintenance and Lipid Metabolism at the Larval-to-Adult Transition in
RT Caenorhabditis elegans.";
RL Genetics 214:669-690(2020).
CC -!- FUNCTION: Transcription factor which regulates the expression of
CC various genes, including those involved in cuticle synthesis and
CC maintenance, such as collagens, and in lipid metabolism
CC (PubMed:7671813, PubMed:29604168, PubMed:31974205, PubMed:27401555).
CC Binds to promoter regions of genes, at 5'-[(T/G)TTTTTT(A/T/C/G)]-3'
CC consensus sequences (PubMed:29604168, PubMed:25905672). Heterochronic
CC protein which controls the choice of stage specific cell fates,
CC including at the juvenile to adult transition (PubMed:7671813,
CC PubMed:32223899). Promotes differentiation, together with
CC transcriptional cofactor mab-10, perhaps as part of a transcriptional
CC complex (PubMed:21862562). Required for vulval morphogenesis and egg
CC laying; perhaps by acting in a subset of the lateral seam cells
CC (PubMed:9334281). Involved in the exit of seam cells from the cell
CC cycle (PubMed:32223899). Required for specification of uterine pi-cell
CC fate, acting upstream of lin-12 Notch signaling, perhaps via
CC maintenance of lag-2 expression in the anchor cell (AC)
CC (PubMed:11114514). Involved in morphogenesis of the specialized male
CC tail used in mating (PubMed:9986728). Acts cell non-autonomously from
CC the hypodermis to regulate expression of genes in the intestine,
CC including genes involved in lipid metabolism (PubMed:31974205,
CC PubMed:27401555). May regulate vitellogenesis via the mTORC2 signaling
CC mediated pathway, independently of daf-16 (PubMed:27401555). May
CC promote nuclear accumulation of mab-10 in seam cells post-
CC transcriptionally (PubMed:21862562). Dispensable for seam cell fusion
CC (PubMed:32223899). {ECO:0000269|PubMed:11114514,
CC ECO:0000269|PubMed:21862562, ECO:0000269|PubMed:25905672,
CC ECO:0000269|PubMed:27401555, ECO:0000269|PubMed:29604168,
CC ECO:0000269|PubMed:31974205, ECO:0000269|PubMed:32223899,
CC ECO:0000269|PubMed:7671813, ECO:0000269|PubMed:9334281,
CC ECO:0000269|PubMed:9986728}.
CC -!- FUNCTION: [Isoform c]: Required for seam cell fusion.
CC {ECO:0000269|PubMed:32223899}.
CC -!- SUBUNIT: Interacts (via C-terminus) with transcription cofactor mab-10.
CC {ECO:0000269|PubMed:21862562}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:32223899,
CC ECO:0000269|PubMed:8756296, ECO:0000269|PubMed:9334281,
CC ECO:0000269|PubMed:9986728}. Note=Accumulates in nuclei of hypodermal
CC cells in a temporally restricted fashion, beginning during the larval
CC L4 stage. {ECO:0000269|PubMed:8756296}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=a {ECO:0000312|WormBase:W03C9.4a};
CC IsoId=G5EGB2-1; Sequence=Displayed;
CC Name=b {ECO:0000312|WormBase:W03C9.4b};
CC IsoId=G5EGB2-2; Sequence=VSP_061058;
CC Name=c {ECO:0000312|WormBase:W03C9.4c};
CC IsoId=G5EGB2-3; Sequence=VSP_061057;
CC -!- TISSUE SPECIFICITY: Expressed in lateral hypodermal seam cells (at
CC protein level). {ECO:0000269|PubMed:8756296}.
CC -!- DEVELOPMENTAL STAGE: Expressed in all larval stages, increasing in
CC level from L1 to L4 and then diminishing in younger and older adults
CC (PubMed:7671813). Expressed in hermaphrodite lateral hypodermal seam
CC cells during the larval L3- to L4-molt stage and into adulthood (at
CC protein level) (PubMed:8756296). Expressed in the hypodermal cells of
CC the head (hyp1-hyp6), tail (hyp8-hyp12), and the large hypodermal
CC syncytium covering most of the animal (hyp7) (at protein level)
CC (PubMed:8756296, PubMed:27401555). Also expressed in some non-
CC hypodermal cells during stages L2 to L4 (at protein level)
CC (PubMed:8756296, PubMed:9334281). Expressed in the anchor cell
CC beginning at the L2 molt or early L3 stage (PubMed:9334281). Male-
CC specific expression in the linker cell (LC), positioned at the tip of
CC the growing end of the gonad at stage L3 (at protein level). Male-
CC specific expression in ventral cord neurons from late L3 stage (at
CC protein level) (PubMed:9986728). {ECO:0000269|PubMed:27401555,
CC ECO:0000269|PubMed:7671813, ECO:0000269|PubMed:8756296,
CC ECO:0000269|PubMed:9334281, ECO:0000269|PubMed:9986728}.
CC -!- DEVELOPMENTAL STAGE: [Isoform c]: Expressed in all larval stages,
CC increasing in level from L2 to L4 and then diminishing in younger and
CC older adults (PubMed:7671813). Expressed at low level in lateral seam
CC cells in larval L3 stage and up-regulated during L4, including in the
CC major hypodermal syncytium hyp7 (PubMed:32223899).
CC {ECO:0000269|PubMed:32223899, ECO:0000269|PubMed:7671813}.
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown abolished expression of
CC collagen col-38 at mid-to-late larval stage L4 (PubMed:29604168).
CC Knockdown, whether untargeted, or hypodermis-specific, represses
CC intestinal genes involved in fatty acid metabolism and beta-oxidation
CC in the L4 larval stage (PubMed:31974205). Drastically reduces
CC expression of the vitellogenin genes (PubMed:27401555). Knockdown
CC causes transcription factor pqm-1 to accumulate in the intestinal
CC nuclei at adulthood, but has no effect on daf-16 localization
CC (PubMed:27401555). {ECO:0000269|PubMed:27401555,
CC ECO:0000269|PubMed:29604168, ECO:0000269|PubMed:31974205}.
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DR EMBL; L39212; AAC37255.1; -; mRNA.
DR EMBL; BX284602; CAB60308.2; -; Genomic_DNA.
DR EMBL; BX284602; CAN99713.1; -; Genomic_DNA.
DR EMBL; BX284602; CBY85351.1; -; Genomic_DNA.
DR RefSeq; NP_001122649.1; NM_001129177.1. [G5EGB2-2]
DR RefSeq; NP_001254324.1; NM_001267395.1. [G5EGB2-3]
DR RefSeq; NP_496545.1; NM_064144.5. [G5EGB2-1]
DR AlphaFoldDB; G5EGB2; -.
DR SMR; G5EGB2; -.
DR IntAct; G5EGB2; 1.
DR STRING; 6239.W03C9.4a; -.
DR PaxDb; G5EGB2; -.
DR EnsemblMetazoa; W03C9.4a.1; W03C9.4a.1; WBGene00003015. [G5EGB2-1]
DR EnsemblMetazoa; W03C9.4b.1; W03C9.4b.1; WBGene00003015. [G5EGB2-2]
DR EnsemblMetazoa; W03C9.4c.1; W03C9.4c.1; WBGene00003015. [G5EGB2-3]
DR GeneID; 174830; -.
DR KEGG; cel:CELE_W03C9.4; -.
DR CTD; 174830; -.
DR WormBase; W03C9.4a; CE28257; WBGene00003015; lin-29.
DR WormBase; W03C9.4b; CE41270; WBGene00003015; lin-29.
DR WormBase; W03C9.4c; CE45652; WBGene00003015; lin-29.
DR eggNOG; KOG1721; Eukaryota.
DR GeneTree; ENSGT00940000174257; -.
DR HOGENOM; CLU_043863_0_0_1; -.
DR InParanoid; G5EGB2; -.
DR OMA; TKHADRS; -.
DR OrthoDB; 1318335at2759; -.
DR PhylomeDB; G5EGB2; -.
DR Proteomes; UP000001940; Chromosome II.
DR Bgee; WBGene00003015; Expressed in larva and 3 other tissues.
DR ExpressionAtlas; G5EGB2; baseline and differential.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0001228; F:DNA-binding transcription activator activity, RNA polymerase II-specific; IMP:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IMP:UniProtKB.
DR GO; GO:0000977; F:RNA polymerase II transcription regulatory region sequence-specific DNA binding; IDA:WormBase.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:UniProtKB.
DR GO; GO:0001708; P:cell fate specification; IMP:UniProtKB.
DR GO; GO:0140253; P:cell-cell fusion; IMP:UniProtKB.
DR GO; GO:0044255; P:cellular lipid metabolic process; IMP:UniProtKB.
DR GO; GO:0032964; P:collagen biosynthetic process; IMP:UniProtKB.
DR GO; GO:0042335; P:cuticle development; IMP:UniProtKB.
DR GO; GO:0035017; P:cuticle pattern formation; IMP:UniProtKB.
DR GO; GO:0010458; P:exit from mitosis; IMP:UniProtKB.
DR GO; GO:0048808; P:male genitalia morphogenesis; IMP:UniProtKB.
DR GO; GO:0022404; P:molting cycle process; IMP:UniProtKB.
DR GO; GO:0061067; P:negative regulation of dauer larval development; IMP:WormBase.
DR GO; GO:0010628; P:positive regulation of gene expression; IMP:UniProtKB.
DR GO; GO:1903188; P:positive regulation of vitellogenesis; IMP:UniProtKB.
DR GO; GO:0010623; P:programmed cell death involved in cell development; IGI:UniProtKB.
DR GO; GO:0110011; P:regulation of basement membrane organization; IMP:UniProtKB.
DR GO; GO:0040034; P:regulation of development, heterochronic; IMP:WormBase.
DR GO; GO:0090444; P:regulation of nematode larval development, heterochronic; IMP:UniProtKB.
DR GO; GO:0008593; P:regulation of Notch signaling pathway; IMP:UniProtKB.
DR GO; GO:0043067; P:regulation of programmed cell death; IMP:WormBase.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IMP:UniProtKB.
DR GO; GO:0040028; P:regulation of vulval development; IMP:UniProtKB.
DR InterPro; IPR036236; Znf_C2H2_sf.
DR InterPro; IPR013087; Znf_C2H2_type.
DR Pfam; PF00096; zf-C2H2; 4.
DR SMART; SM00355; ZnF_C2H2; 5.
DR SUPFAM; SSF57667; SSF57667; 3.
DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 5.
DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 5.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA-binding; Metal-binding; Nucleus;
KW Reference proteome; Repeat; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..459
FT /note="Zinc finger transcription factor lin-29"
FT /id="PRO_0000452803"
FT ZN_FING 151..173
FT /note="C2H2-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 180..202
FT /note="C2H2-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 208..232
FT /note="C2H2-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 238..260
FT /note="C2H2-type 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 269..291
FT /note="C2H2-type 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT REGION 1..73
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 390..406
FT /note="Interacts with mab-10"
FT /evidence="ECO:0000269|PubMed:21862562"
FT REGION 423..459
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 1..142
FT /note="Missing (in isoform c)"
FT /evidence="ECO:0000305"
FT /id="VSP_061057"
FT VAR_SEQ 37..41
FT /note="FKVSV -> L (in isoform b)"
FT /evidence="ECO:0000305"
FT /id="VSP_061058"
FT MUTAGEN 144..459
FT /note="Missing: In ga94; displays vulval defects and are
FT unable to lay eggs, but still executes lateral hypodermal
FT terminal differentiation."
FT /evidence="ECO:0000269|PubMed:9334281"
FT MUTAGEN 182
FT /note="C->Y: In sy292; egg-laying defective. Fails to
FT specify uterine pi-cell fate, has an abnormal uterine-
FT vulval connection and vulval gene expression patterns are
FT altered."
FT /evidence="ECO:0000269|PubMed:11114514"
FT MUTAGEN 294..459
FT /note="Missing: In n546; fails to execute adult-specific
FT terminal differentiation at the larval L4 molt and instead
FT reiterates larval differentiation program. On a him-5
FT mutant background, males failed to mate with unc-13
FT hermaphrodites. Males have shortened spicules, male-
FT specific mating structures. Males also exhibit delayed ray
FT formation and gonad migration defects. Up-regulates nhr-23
FT and nhr-25 about 12-fold relative to the wild type in adult
FT hermaphrodites."
FT /evidence="ECO:0000269|PubMed:7671813,
FT ECO:0000269|PubMed:9986728"
SQ SEQUENCE 459 AA; 50177 MW; E48DFFA50437E78F CRC64;
MDQTVLDSAF NSPVDSGIAG TTTGSGSTTH FGVGTNFKVS VRSSSRSTDG TDSTDGANSD
NVTGSTGSTP AHHSITNLNM ALSQHSIDSA TAASSTNPFP HFNQADLLNF HQNSLLPHHM
FSQFGRYPQF EQKPDVGVLQ QQMQMREAKP YKCTQCVKAF ANSSYLSQHM RIHLGIKPFG
PCNYCGKKFT QLSHLQQHIR THTGEKPYKC KFTGCDKAFS QLSNLQSHSR CHQTDKPFKC
NSCYKCFTDE QSLLDHIPKH KESKHLKIHI CPFCGKSYTQ QTYLQKHMTK HADRSKASNF
GNDVVPADPF DPSLLSWNPM QGMGDNAHDS SSFNISSLTD QFAANTMIGS QSTNYNPAFQ
NSAFSQLFNI RNNRYLSEYP TSTKNGERAP GFNMITPLEN IQRYNGSSSS ATAVVTATGS
AVVSSTPSST SSSSAGSSSS QGGVFNPQSL INNMKNHSY
