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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.
07-NOV-2018, entry version 147.
RecName: Full=Protein lin-28 {ECO:0000305};
AltName: Full=Abnormal cell lineage protein 28 {ECO:0000312|WormBase:F02E9.2a};
Name=lin-28 {ECO:0000312|WormBase:F02E9.2a};
ORFNames=F02E9.2 {ECO:0000312|WormBase:F02E9.2a};
Caenorhabditis elegans.
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Rhabditina; Rhabditomorpha; 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].
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).
[21]
FUNCTION, PROTEOLYTIC CLEAVAGE, AND MUTAGENESIS OF 2-SER--ASN-32;
ASP-31 AND ASN-32.
PubMed=28602583; DOI=10.1016/j.devcel.2017.05.013;
Weaver B.P., Weaver Y.M., Mitani S., Han M.;
"Coupled Caspase and N-End Rule Ligase Activities Allow Recognition
and Degradation of Pluripotency Factor LIN-28 during Non-Apoptotic
Development.";
Dev. Cell 41:665-673(2017).
-!- FUNCTION: Heterochronic protein which controls the choice of stage
specific cell fates (PubMed:9054503, PubMed:6494891,
PubMed:2702689, PubMed:2628162, PubMed:1916265, PubMed:7671811,
PubMed:8625405, PubMed:8756295, PubMed:8756296, PubMed:9477318,
PubMed:9649524, PubMed:10706289, PubMed:12871707, PubMed:15073154,
PubMed:16139228). Regulates the timing of the second larval stage
events (L2 events) in the hypodermis (PubMed:2702689,
PubMed:2628162). May negatively regulate the larval to adult
transition via the suppression of the microRNA (miRNA) let-7
during L3 (PubMed:10706289, PubMed:12871707, PubMed:16139228).
Plays a role in the control of seam cell number and vulval
development (PubMed:28602583). {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:28602583, 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 {ECO:0000312|WormBase:F02E9.2a};
IsoId=P92186-1; Sequence=Displayed;
Name=b {ECO:0000312|WormBase:F02E9.2b};
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,
ECO:0000269|PubMed:28602583}.
-!- 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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Distributed under the Creative Commons Attribution (CC BY 4.0) License
-----------------------------------------------------------------------
EMBL; U75912; AAC47476.1; -; mRNA.
EMBL; U75915; AAB49759.1; -; Genomic_DNA.
EMBL; BX284601; CAB61008.1; -; Genomic_DNA.
EMBL; BX284601; 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]
EnsemblMetazoa; F02E9.2b; F02E9.2b; WBGene00003014. [P92186-2]
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; ENSGT00930000150863; -.
HOGENOM; HOG000113330; -.
InParanoid; P92186; -.
KO; K18754; -.
OMA; CPERRRK; -.
OrthoDB; EOG091G0RTY; -.
PhylomeDB; P92186; -.
PRO; PR:P92186; -.
Proteomes; UP000001940; Chromosome I.
Bgee; WBGene00003014; Expressed in 5 organ(s), highest expression level in multi-cellular organism.
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,
ECO:0000269|PubMed:28602583}.
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 2 32 Missing: Constitutively active and
results in reduced lin-28 protein levels.
Rescues the seam cell number and vulval
developmental defects of the lin-28 n719
loss of function mutant.
{ECO:0000269|PubMed:28602583}.
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,
ECO:0000269|PubMed:28602583}.
MUTAGEN 32 32 N->M: Loss of ced-3-mediated cleavage in
vitro. Prevents reduction of lin-28
protein levels in vitro.
{ECO:0000269|PubMed:28602583}.
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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