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Protein lin-28 (Abnormal cell lineage protein 28)

 LIN28_CAEEL             Reviewed;         227 AA.
P92186; Q9U3K6;
17-OCT-2006, integrated into UniProtKB/Swiss-Prot.
01-MAY-1997, sequence version 1.
28-MAR-2018, entry version 144.
RecName: Full=Protein lin-28;
AltName: Full=Abnormal cell lineage protein 28;
Name=lin-28; ORFNames=F02E9.2;
Caenorhabditis elegans.
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
NCBI_TaxID=6239;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM A), FUNCTION,
SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, INDUCTION, AND MUTAGENESIS
OF GLY-55; MET-87; ARG-91; GLY-128 AND PRO-133.
STRAIN=Bristol N2;
PubMed=9054503; DOI=10.1016/S0092-8674(00)81906-6;
Moss E.G., Lee R.C., Ambros V.;
"The cold shock domain protein LIN-28 controls developmental timing in
C. elegans and is regulated by the lin-4 RNA.";
Cell 88:637-646(1997).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND ALTERNATIVE
SPLICING.
STRAIN=Bristol N2;
PubMed=9851916; DOI=10.1126/science.282.5396.2012;
The C. elegans sequencing consortium;
"Genome sequence of the nematode C. elegans: a platform for
investigating biology.";
Science 282:2012-2018(1998).
[3]
FUNCTION.
PubMed=6494891; DOI=10.1126/science.6494891;
Ambros V., Horvitz H.R.;
"Heterochronic mutants of the nematode Caenorhabditis elegans.";
Science 226:409-416(1984).
[4]
FUNCTION.
PubMed=2702689; DOI=10.1016/0092-8674(89)90171-2;
Ambros V.;
"A hierarchy of regulatory genes controls a larva-to-adult
developmental switch in C. elegans.";
Cell 57:49-57(1989).
[5]
FUNCTION.
PubMed=2628162; DOI=10.1101/gad.3.12b.2039;
Liu Z.C., Ambros V.;
"Heterochronic genes control the stage-specific initiation and
expression of the dauer larva developmental program in Caenorhabditis
elegans.";
Genes Dev. 3:2039-2049(1989).
[6]
FUNCTION.
PubMed=1916265; DOI=10.1101/gad.5.10.1825;
Arasu P., Wightman B., Ruvkun G.;
"Temporal regulation of lin-14 by the antagonistic action of two other
heterochronic genes, lin-4 and lin-28.";
Genes Dev. 5:1825-1833(1991).
[7]
FUNCTION.
PubMed=7671811;
Liu Z.C., Kirch S., Ambros V.;
"The Caenorhabditis elegans heterochronic gene pathway controls stage-
specific transcription of collagen genes.";
Development 121:2471-2478(1995).
[8]
FUNCTION.
PubMed=8625405; DOI=10.1016/S0092-8674(00)81045-4;
Euling S., Ambros V.;
"Heterochronic genes control cell cycle progress and developmental
competence of C. elegans vulva precursor cells.";
Cell 84:667-676(1996).
[9]
FUNCTION.
PubMed=8756295;
Euling S., Ambros V.;
"Reversal of cell fate determination in Caenorhabditis elegans vulval
development.";
Development 122:2507-2515(1996).
[10]
FUNCTION.
PubMed=8756296;
Bettinger J.C., Lee K., Rougvie A.E.;
"Stage-specific accumulation of the terminal differentiation factor
LIN-29 during Caenorhabditis elegans development.";
Development 122:2517-2527(1996).
[11]
FUNCTION.
PubMed=9477318;
Antebi A., Culotti J.G., Hedgecock E.M.;
"daf-12 regulates developmental age and the dauer alternative in
Caenorhabditis elegans.";
Development 125:1191-1205(1998).
[12]
FUNCTION.
PubMed=9649524;
Abrahante J.E., Miller E.A., Rougvie A.E.;
"Identification of heterochronic mutants in Caenorhabditis elegans.
Temporal misexpression of a collagen::green fluorescent protein fusion
gene.";
Genetics 149:1335-1351(1998).
[13]
FUNCTION.
PubMed=10706289; DOI=10.1038/35002607;
Reinhart B.J., Slack F.J., Basson M., Pasquinelli A.E.,
Bettinger J.C., Rougvie A.E., Horvitz H.R., Ruvkun G.;
"The 21-nucleotide let-7 RNA regulates developmental timing in
Caenorhabditis elegans.";
Nature 403:901-906(2000).
[14]
DEVELOPMENTAL STAGE, AND INDUCTION.
PubMed=11884032; DOI=10.1006/dbio.2001.0563;
Seggerson K., Tang L., Moss E.G.;
"Two genetic circuits repress the Caenorhabditis elegans heterochronic
gene lin-28 after translation initiation.";
Dev. Biol. 243:215-225(2002).
[15]
FUNCTION.
PubMed=12871707; DOI=10.1016/S0012-1606(03)00202-1;
Johnson S.M., Lin S.-Y., Slack F.J.;
"The time of appearance of the C. elegans let-7 microRNA is
transcriptionally controlled utilizing a temporal regulatory element
in its promoter.";
Dev. Biol. 259:364-379(2003).
[16]
INDUCTION.
PubMed=15380030; DOI=10.1186/1471-213X-4-11;
Liu T., Zimmerman K.K., Patterson G.I.;
"Regulation of signaling genes by TGFbeta during entry into dauer
diapause in C. elegans.";
BMC Dev. Biol. 4:11-11(2004).
[17]
FUNCTION.
PubMed=15073154; DOI=10.1242/dev.01098;
Pepper A.-S., McCane J.E., Kemper K., Yeung D.A., Lee R.C., Ambros V.,
Moss E.G.;
"The C. elegans heterochronic gene lin-46 affects developmental timing
at two larval stages and encodes a relative of the scaffolding protein
gephyrin.";
Development 131:2049-2059(2004).
[18]
DEVELOPMENTAL STAGE, AND INDUCTION.
PubMed=16122423; DOI=10.1016/j.cell.2005.07.031;
Bagga S., Bracht J., Hunter S., Massirer K., Holtz J., Eachus R.,
Pasquinelli A.E.;
"Regulation by let-7 and lin-4 miRNAs results in target mRNA
degradation.";
Cell 122:553-563(2005).
[19]
FUNCTION, AND DEVELOPMENTAL STAGE.
PubMed=16139228; DOI=10.1016/j.devcel.2005.07.009;
Abbott A.L., Alvarez-Saavedra E., Miska E.A., Lau N.C., Bartel D.P.,
Horvitz H.R., Ambros V.;
"The let-7 MicroRNA family members mir-48, mir-84, and mir-241
function together to regulate developmental timing in Caenorhabditis
elegans.";
Dev. Cell 9:403-414(2005).
[20]
PROTEOLYTIC CLEAVAGE, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF ASP-11;
GLU-23; ASP-24 AND ASP-31.
PubMed=25432023; DOI=10.7554/eLife.04265;
Weaver B.P., Zabinsky R., Weaver Y.M., Lee E.S., Xue D., Han M.;
"CED-3 caspase acts with miRNAs to regulate non-apoptotic gene
expression dynamics for robust development in C. elegans.";
Elife 3:E04265-E04265(2014).
-!- FUNCTION: Heterochronic protein which controls the choice of stage
specific cell fates. Regulates the timing of the second larval
stage events (L2 events) in the hypodermis. May negatively
regulate the larval to adult transition via the suppression of the
microRNA (miRNA) let-7 during L3. {ECO:0000269|PubMed:10706289,
ECO:0000269|PubMed:12871707, ECO:0000269|PubMed:15073154,
ECO:0000269|PubMed:16139228, ECO:0000269|PubMed:1916265,
ECO:0000269|PubMed:2628162, ECO:0000269|PubMed:2702689,
ECO:0000269|PubMed:6494891, ECO:0000269|PubMed:7671811,
ECO:0000269|PubMed:8625405, ECO:0000269|PubMed:8756295,
ECO:0000269|PubMed:8756296, ECO:0000269|PubMed:9054503,
ECO:0000269|PubMed:9477318, ECO:0000269|PubMed:9649524}.
-!- INTERACTION:
Q09408:pup-2; NbExp=2; IntAct=EBI-15801711, EBI-15801698;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:9054503}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=a;
IsoId=P92186-1; Sequence=Displayed;
Name=b;
IsoId=P92186-2; Sequence=VSP_021122, VSP_021123;
Note=Gene prediction based on EST data.;
-!- DEVELOPMENTAL STAGE: Expressed at the first larval stage (L1) in
several cell types including hypodermis, muscle, neurons and seam
cells. Down-regulated at L2, and absent from L3 and L4.
{ECO:0000269|PubMed:11884032, ECO:0000269|PubMed:16122423,
ECO:0000269|PubMed:16139228, ECO:0000269|PubMed:9054503}.
-!- INDUCTION: Negatively regulated by the miRNA lin-4 which causes
degradation of the mRNA encoding this protein. This requires a
lin-4 complementary element (LCE) in the 3'-UTR of the mRNA
encoding this protein. Also negatively regulated independent of
lin-4 and this is counteracted by the action of lin-14. Positively
regulated by TGF-beta signaling. {ECO:0000269|PubMed:11884032,
ECO:0000269|PubMed:15380030, ECO:0000269|PubMed:16122423,
ECO:0000269|PubMed:9054503}.
-!- PTM: Cleavage by caspase ced-3 during larval development probably
induces lin-28 degradation. {ECO:0000269|PubMed:25432023}.
-!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown in a ced-3 and ain-1
double mutant background reduces the percentage of animals with
developmental defects including impaired egg-laying and production
of ectopic seam cells. {ECO:0000269|PubMed:25432023}.
-!- SIMILARITY: Belongs to the lin-28 family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; U75912; AAC47476.1; -; mRNA.
EMBL; U75915; AAB49759.1; -; Genomic_DNA.
EMBL; Z81494; CAB61008.1; -; Genomic_DNA.
EMBL; Z81494; CAB61009.1; -; Genomic_DNA.
RefSeq; NP_001021085.1; NM_001025914.4. [P92186-1]
RefSeq; NP_492281.2; NM_059880.5. [P92186-2]
UniGene; Cel.22515; -.
ProteinModelPortal; P92186; -.
SMR; P92186; -.
DIP; DIP-40151N; -.
IntAct; P92186; 4.
STRING; 6239.F02E9.2a; -.
iPTMnet; P92186; -.
EPD; P92186; -.
PaxDb; P92186; -.
PeptideAtlas; P92186; -.
EnsemblMetazoa; F02E9.2a; F02E9.2a; WBGene00003014. [P92186-1]
GeneID; 172626; -.
KEGG; cel:CELE_F02E9.2; -.
UCSC; F02E9.2a; c. elegans. [P92186-1]
CTD; 38639; -.
WormBase; F02E9.2a; CE24879; WBGene00003014; lin-28. [P92186-1]
WormBase; F02E9.2b; CE24880; WBGene00003014; lin-28. [P92186-2]
eggNOG; KOG3070; Eukaryota.
eggNOG; COG1278; LUCA.
GeneTree; ENSGT00880000137959; -.
HOGENOM; HOG000113330; -.
InParanoid; P92186; -.
KO; K18754; -.
OMA; NHIASEC; -.
OrthoDB; EOG091G0RTY; -.
PhylomeDB; P92186; -.
PRO; PR:P92186; -.
Proteomes; UP000001940; Chromosome I.
Bgee; WBGene00003014; -.
GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
GO; GO:0005634; C:nucleus; IDA:WormBase.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:0019899; F:enzyme binding; IPI:WormBase.
GO; GO:0003730; F:mRNA 3'-UTR binding; IDA:WormBase.
GO; GO:0003729; F:mRNA binding; IDA:WormBase.
GO; GO:1990715; F:mRNA CDS binding; IDA:WormBase.
GO; GO:0070883; F:pre-miRNA binding; IPI:WormBase.
GO; GO:0070878; F:primary miRNA binding; IDA:WormBase.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0001708; P:cell fate specification; IMP:UniProtKB.
GO; GO:0007549; P:dosage compensation; IGI:WormBase.
GO; GO:0007275; P:multicellular organism development; IEA:UniProtKB-KW.
GO; GO:2000635; P:negative regulation of primary miRNA processing; IMP:WormBase.
GO; GO:0031054; P:pre-miRNA processing; IDA:WormBase.
GO; GO:0042659; P:regulation of cell fate specification; IGI:UniProtKB.
GO; GO:0040034; P:regulation of development, heterochronic; IMP:WormBase.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:InterPro.
CDD; cd04458; CSP_CDS; 1.
InterPro; IPR011129; CSD.
InterPro; IPR002059; CSP_DNA-bd.
InterPro; IPR012340; NA-bd_OB-fold.
InterPro; IPR001878; Znf_CCHC.
InterPro; IPR036875; Znf_CCHC_sf.
Pfam; PF00313; CSD; 1.
Pfam; PF00098; zf-CCHC; 1.
PRINTS; PR00050; COLDSHOCK.
SMART; SM00357; CSP; 1.
SMART; SM00343; ZnF_C2HC; 2.
SUPFAM; SSF50249; SSF50249; 1.
SUPFAM; SSF57756; SSF57756; 1.
PROSITE; PS51857; CSD_2; 1.
PROSITE; PS50158; ZF_CCHC; 1.
1: Evidence at protein level;
Alternative splicing; Complete proteome; Cytoplasm;
Developmental protein; Metal-binding; Reference proteome; Repeat;
Zinc; Zinc-finger.
CHAIN 1 227 Protein lin-28.
/FTId=PRO_0000253799.
DOMAIN 52 120 CSD.
ZN_FING 143 160 CCHC-type 1. {ECO:0000255|PROSITE-
ProRule:PRU00047}.
ZN_FING 166 183 CCHC-type 2. {ECO:0000255|PROSITE-
ProRule:PRU00047}.
METAL 144 144 Zinc 1. {ECO:0000250}.
METAL 147 147 Zinc 1. {ECO:0000250}.
METAL 153 153 Zinc 1. {ECO:0000250}.
METAL 158 158 Zinc 1. {ECO:0000250}.
METAL 168 168 Zinc 2. {ECO:0000250}.
METAL 171 171 Zinc 2. {ECO:0000250}.
METAL 176 176 Zinc 2. {ECO:0000250}.
METAL 181 181 Zinc 2. {ECO:0000250}.
SITE 31 32 Cleavage; by ced-3.
{ECO:0000269|PubMed:25432023}.
VAR_SEQ 1 16 MSTVVSEGRNDGNNRY -> MIEAALENPVPIKSQL (in
isoform b). {ECO:0000305}.
/FTId=VSP_021122.
VAR_SEQ 17 47 Missing (in isoform b). {ECO:0000305}.
/FTId=VSP_021123.
MUTAGEN 11 11 D->A: Reduced ced-3-mediated cleavage in
vitro. {ECO:0000269|PubMed:25432023}.
MUTAGEN 23 23 E->A: Reduced ced-3-mediated cleavage in
vitro. {ECO:0000269|PubMed:25432023}.
MUTAGEN 24 24 D->A: Reduced ced-3-mediated cleavage in
vitro. {ECO:0000269|PubMed:25432023}.
MUTAGEN 31 31 D->A: Loss of ced-3-mediated cleavage in
vitro. Partially prevents reduction of
lin-28 protein levels in vivo. About 20
percent of mutants fail to reach
adulthood. Defects in alae morphology.
{ECO:0000269|PubMed:25432023}.
MUTAGEN 55 55 G->S: In n1119; loss of function.
{ECO:0000269|PubMed:9054503}.
MUTAGEN 87 87 M->I: In ga73; when associated with Q-91.
{ECO:0000269|PubMed:9054503}.
MUTAGEN 91 91 R->Q: In ga73; when associated with I-87.
{ECO:0000269|PubMed:9054503}.
MUTAGEN 128 128 G->E: In ma157.
{ECO:0000269|PubMed:9054503}.
MUTAGEN 128 128 G->R: In sy283.
{ECO:0000269|PubMed:9054503}.
MUTAGEN 133 133 P->S: In ve9.
{ECO:0000269|PubMed:9054503}.
SEQUENCE 227 AA; 25465 MW; 5E4AE901AD8BAEBC CRC64;
MSTVVSEGRN DGNNRYSPQD EVEDRLPDVV DNRLTENMRV PSFERLPSPT PRYFGSCKWF
NVSKGYGFVI DDITGEDLFV HQSNLNMQGF RSLDEGERVS YYIQERSNGK GREAYAVSGE
VEGQGLKGSR IHPLGRKKAV SLRCFRCGKF ATHKAKSCPN VKTDAKVCYT CGSEEHVSSI
CPERRRKHRP EQVAAEEAEA ARMAAEKSSP TTSDDDIREK NSNSSDE


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