Q9SP32 (DCL1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Endoribonuclease Dicer homolog 1
EC=3.1.26.-

Alternative name(s):
Dicer-like protein 1
Short name=AtDCL1
Protein ABNORMAL SUSPENSOR 1
Protein CARPEL FACTORY
Protein SHORT INTEGUMENTS 1
Protein SUSPENSOR 1

Gene names

Name:	DCL1
Synonyms:	ASU1, CAF SIN1, SUS1
Ordered Locus Names:	At1g01040
ORF Names:	T25K16.4

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	1909 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Ribonuclease (RNase) III involved in RNA-mediated post-transcriptional gene silencing (PTGS). Functions in the microRNAs (miRNAs) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Functions with DRB1/HYL1 and SERRATE proteins for accurate pri-miRNAs to miRNAs processing. Indirectly involved in the production of trans-acting small interfering RNAs (ta-siRNAs) derived from the TAS1, TAS2 or TAS3 endogenous transcripts by participating in the production of their initiating miRNAs. Involved in the processing of natural siRNAs (nat-siRNAs, derived from cis-natural antisense transcripts) by cleaving 24 nucleotide nat-siRNAs into 21 nucleotide nat-siRNAs. Can produce RDR6-dependent endogenous ta-siRNAs derived from TAS1 and TAS2. Required for the production of 30-40 nucleotide bacterial-induced long siRNAs (lsiRNA). Acts redundantly with DICER-LIKE 3 (DCL3) to promote flowering via repression of FLOWERING LOCUS C (FLC). Represses antiviral RNA silencing through negative regulation of the expression of DCL4 and DCL3. Ref.5 Ref.6 Ref.7 Ref.9 Ref.10 Ref.11 Ref.13
Cofactor	Magnesium or manganese By similarity.
Subunit structure	Interacts (via N-terminus) with DDL. Interacts (via DRBM domains) with DRB1, DRB2 and DRB5. May interact with AGO1 or AGO10 through their common PAZ domains By similarity. Ref.6 Ref.7 Ref.12
Subcellular location	Nucleus. Note: Localizes to nuclear dicing body (also named D body), a nuclear body distributed throughout the nucleoplasm and involved in miRNA processing. Ref.6 Ref.8
Tissue specificity	Highly expressed in flowers and seeds and detected in leaves and stems. Found in ovule integuments, inflorescence and floral meristems, stigma of flowers until just before pollination, vasculature of the funiculus, and embryo. Ref.1 Ref.2
Developmental stage	Detected in the embryo, but not in the suspensor, up to the globular stage. Ref.2
Disruption phenotype	Embryonic lethality in sus-1 mutant. Weaker mutant (caf-1) also exists. Mutant caf-1 produces extra whorls of stamens, indefinite number of carpels and show an absence of axillary inflorescence meristems and abnormally shaped leaves and floral organs. Ref.1 Ref.2
Miscellaneous	Expression in the early embryo is from the maternally contributed genome.
Sequence similarities	Belongs to the helicase family. Dicer subfamily. Contains 1 Dicer dsRNA-binding fold domain. Contains 2 DRBM (double-stranded RNA-binding) domains. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain. Contains 1 PAZ domain. Contains 2 RNase III domains.
Sequence caution	The sequence AAF26461.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	RNA-mediated gene silencing
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Repeat
Ligand	ATP-binding Magnesium Manganese Metal-binding Nucleotide-binding RNA-binding
Molecular function	Endonuclease Helicase Hydrolase Nuclease
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	RNA processing Inferred from electronic annotation. Source: InterPro gene silencing by RNA Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC rRNA catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: InterPro double-stranded RNA binding Inferred from electronic annotation. Source: InterPro helicase activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW ribonuclease III activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
DDL	Q8W4D8	2	EBI-632627,EBI-2015534
DRB1	O04492	3	EBI-632627,EBI-632620

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: Q9SP32-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1909

1909

Endoribonuclease Dicer homolog 1

PRO_0000180472

Regions

Domain

256 – 433

178

Helicase ATP-binding

Domain

651 – 812

162

Helicase C-terminal

Domain

840 – 935

96

Dicer dsRNA-binding fold

Domain

1180 – 1318

139

PAZ

Domain

1342 – 1518

177

RNase III 1

Domain

1559 – 1707

149

RNase III 2

Domain

1733 – 1796

64

DRBM 1

Domain

1831 – 1906

76

DRBM 2

Nucleotide binding

269 – 276

8

ATP Potential

Motif

378 – 381

4

DECH box

Sites

Metal binding

1597

1

Magnesium or manganese By similarity

Metal binding

1693

1

Magnesium or manganese By similarity

Metal binding

1696

1

Magnesium or manganese By similarity

Site

1689

1

Important for activity By similarity

Experimental info

Mutagenesis

395

1

E → K in dcl1-13; early-flowering and decreased number of leaves. Suppresses hyl1 mutant phenotype. Ref.14

Mutagenesis

415

1

P → S in sin1-1; impaired reproductive development. Ref.2

Mutagenesis

431

1

I → K in sin1-2; impaired reproductive development. Ref.2

Mutagenesis

1837 – 1843

7

NDICLRK → IAEIDPG in caf-1; converts the floral meristem to an indeterminate state. Ref.1

Mutagenesis

1844 – 1909

66

Missing in caf-1; converts the floral meristem to an indeterminate state. Ref.1

Sequence conflict

148

1

S → F in AAF03534. Ref.1

Sequence conflict

988

1

Y → H in AAF03534. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

1909

Helix Strand Turn

Details...

Helix

1838 – 1842

5

Beta strand

1849 – 1854

6

Beta strand

1864 – 1869

6

Turn

1873 – 1875

3

Beta strand

1886 – 1888

3

Helix

1889 – 1903

15

Helix

1904 – 1906

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified September 19, 2003. Version 2. Checksum: EAA944F0C0C81D4C	FASTA	1,909	213,574
	10 20 30 40 50 60 MVMEDEPREA TIKPSYWLDA CEDISCDLID DLVSEFDPSS VAVNESTDEN GVINDFFGGI 70 80 90 100 110 120 DHILDSIKNG GGLPNNGVSD TNSQINEVTV TPQVIAKETV KENGLQKNGG KRDEFSKEEG 130 140 150 160 170 180 DKDRKRARVC SYQSERSNLS GRGHVNNSRE GDRFMNRKRT RNWDEAGNNK KKRECNNYRR 190 200 210 220 230 240 DGRDREVRGY WERDKVGSNE LVYRSGTWEA DHERDVKKVS GGNRECDVKA EENKSKPEER 250 260 270 280 290 300 KEKVVEEQAR RYQLDVLEQA KAKNTIAFLE TGAGKTLIAI LLIKSVHKDL MSQNRKMLSV 310 320 330 340 350 360 FLVPKVPLVY QQAEVIRNQT CFQVGHYCGE MGQDFWDSRR WQREFESKQV LVMTAQILLN 370 380 390 400 410 420 ILRHSIIRME TIDLLILDEC HHAVKKHPYS LVMSEFYHTT PKDKRPAIFG MTASPVNLKG 430 440 450 460 470 480 VSSQVDCAIK IRNLETKLDS TVCTIKDRKE LEKHVPMPSE IVVEYDKAAT MWSLHETIKQ 490 500 510 520 530 540 MIAAVEEAAQ ASSRKSKWQF MGARDAGAKD ELRQVYGVSE RTESDGAANL IHKLRAINYT 550 560 570 580 590 600 LAELGQWCAY KVGQSFLSAL QSDERVNFQV DVKFQESYLS EVVSLLQCEL LEGAAAEKVA 610 620 630 640 650 660 AEVGKPENGN AHDEMEEGEL PDDPVVSGGE HVDEVIGAAV ADGKVTPKVQ SLIKLLLKYQ 670 680 690 700 710 720 HTADFRAIVF VERVVAALVL PKVFAELPSL SFIRCASMIG HNNSQEMKSS QMQDTISKFR 730 740 750 760 770 780 DGHVTLLVAT SVAEEGLDIR QCNVVMRFDL AKTVLAYIQS RGRARKPGSD YILMVERGNV 790 800 810 820 830 840 SHAAFLRNAR NSEETLRKEA IERTDLSHLK DTSRLISIDA VPGTVYKVEA TGAMVSLNSA 850 860 870 880 890 900 VGLVHFYCSQ LPGDRYAILR PEFSMEKHEK PGGHTEYSCR LQLPCNAPFE ILEGPVCSSM 910 920 930 940 950 960 RLAQQAVCLA ACKKLHEMGA FTDMLLPDKG SGQDAEKADQ DDEGEPVPGT ARHREFYPEG 970 980 990 1000 1010 1020 VADVLKGEWV SSGKEVCESS KLFHLYMYNV RCVDFGSSKD PFLSEVSEFA ILFGNELDAE 1030 1040 1050 1060 1070 1080 VLSMSMDLYV ARAMITKASL AFKGSLDITE NQLSSLKKFH VRLMSIVLDV DVEPSTTPWD 1090 1100 1110 1120 1130 1140 PAKAYLFVPV TDNTSMEPIK GINWELVEKI TKTTAWDNPL QRARPDVYLG TNERTLGGDR 1150 1160 1170 1180 1190 1200 REYGFGKLRH NIVFGQKSHP TYGIRGAVAS FDVVRASGLL PVRDAFEKEV EEDLSKGKLM 1210 1220 1230 1240 1250 1260 MADGCMVAED LIGKIVTAAH SGKRFYVDSI CYDMSAETSF PRKEGYLGPL EYNTYADYYK 1270 1280 1290 1300 1310 1320 QKYGVDLNCK QQPLIKGRGV SYCKNLLSPR FEQSGESETV LDKTYYVFLP PELCVVHPLS 1330 1340 1350 1360 1370 1380 GSLIRGAQRL PSIMRRVESM LLAVQLKNLI SYPIPTSKIL EALTAASCQE TFCYERAELL 1390 1400 1410 1420 1430 1440 GDAYLKWVVS RFLFLKYPQK HEGQLTRMRQ QMVSNMVLYQ FALVKGLQSY IQADRFAPSR 1450 1460 1470 1480 1490 1500 WSAPGVPPVF DEDTKDGGSS FFDEEQKPVS EENSDVFEDG EMEDGELEGD LSSYRVLSSK 1510 1520 1530 1540 1550 1560 TLADVVEALI GVYYVEGGKI AANHLMKWIG IHVEDDPDEV DGTLKNVNVP ESVLKSIDFV 1570 1580 1590 1600 1610 1620 GLERALKYEF KEKGLLVEAI THASRPSSGV SCYQRLEFVG DAVLDHLITR HLFFTYTSLP 1630 1640 1650 1660 1670 1680 PGRLTDLRAA AVNNENFARV AVKHKLHLYL RHGSSALEKQ IREFVKEVQT ESSKPGFNSF 1690 1700 1710 1720 1730 1740 GLGDCKAPKV LGDIVESIAG AIFLDSGKDT TAAWKVFQPL LQPMVTPETL PMHPVRELQE 1750 1760 1770 1780 1790 1800 RCQQQAEGLE YKASRSGNTA TVEVFIDGVQ VGVAQNPQKK MAQKLAARNA LAALKEKEIA 1810 1820 1830 1840 1850 1860 ESKEKHINNG NAGEDQGENE NGNKKNGHQP FTRQTLNDIC LRKNWPMPSY RCVKEGGPAH 1870 1880 1890 1900 AKRFTFGVRV NTSDRGWTDE CIGEPMPSVK KAKDSAAVLL LELLNKTFS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Disruption of an RNA helicase/RNase III gene in Arabidopsis causes unregulated cell division in floral meristems." Jacobsen S.E., Running M.P., Meyerowitz E.M. Development 126:5231-5243(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, DISRUPTION PHENOTYPE, MUTAGENESIS OF 1837-ASN--LYS-1843 AND 1844-ASN--SER-1909. Strain: cv. Wassilewskija.
[2]	"SHORT INTEGUMENTS1/SUSPENSOR1/CARPEL FACTORY, a Dicer homolog, is a maternal effect gene required for embryo development in Arabidopsis." Golden T.A., Schauer S.E., Lang J.D., Pien S., Mushegian A.R., Grossniklaus U., Meinke D.W., Ray A. Plant Physiol. 130:808-822(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE, MUTAGENESIS OF PRO-415 AND ILE-431. Strain: cv. Landsberg erecta.
[3]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[4]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[5]	"Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs." Gasciolli V., Mallory A.C., Bartel D.P., Vaucheret H. Curr. Biol. 15:1494-1500(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[6]	"Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana." Hiraguri A., Itoh R., Kondo N., Nomura Y., Aizawa D., Murai Y., Koiwa H., Seki M., Shinozaki K., Fukuhara T. Plant Mol. Biol. 57:173-188(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH DRB1; DRB2 AND DRB5.
[7]	"The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis." Kurihara Y., Takashi Y., Watanabe Y. RNA 12:206-212(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH DRB1.
[8]	"Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants." Fang Y., Spector D.L. Curr. Biol. 17:818-823(2007) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[9]	"A novel class of bacteria-induced small RNAs in Arabidopsis." Katiyar-Agarwal S., Gao S., Vivian-Smith A., Jin H. Genes Dev. 21:3123-3134(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[10]	"DICER-LIKE 1 and DICER-LIKE 3 redundantly act to promote flowering via repression of FLOWERING LOCUS C in Arabidopsis thaliana." Schmitz R.J., Hong L., Fitzpatrick K.E., Amasino R.M. Genetics 176:1359-1362(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[11]	"The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1." Dong Z., Han M.-H., Fedoroff N. Proc. Natl. Acad. Sci. U.S.A. 105:9970-9975(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[12]	"The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis." Yu B., Bi L., Zheng B., Ji L., Chevalier D., Agarwal M., Ramachandran V., Li W., Lagrange T., Walker J.C., Chen X. Proc. Natl. Acad. Sci. U.S.A. 105:10073-10078(2008) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH DDL.
[13]	"Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1." Qu F., Ye X., Morris T.J. Proc. Natl. Acad. Sci. U.S.A. 105:14732-14737(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[14]	"A dominant mutation in DCL1 suppresses the hyl1 mutant phenotype by promoting the processing of miRNA." Tagami Y., Motose H., Watanabe Y. RNA 15:450-458(2009) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF GLU-395.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF187317 mRNA. Translation: AAF03534.1.
AF292940 mRNA. Translation: AAG38019.1.
AF292941 Genomic DNA. Translation: AAG38020.1.
AC007323 Genomic DNA. Translation: AAF26461.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE27220.1.

IPI

IPI00541769.

RefSeq

NP_171612.1. NM_099986.3.

UniGene

At.22088.
At.57123.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2LRS	NMR	-	A	1837-1907	[»]

ProteinModelPortal

Q9SP32.

SMR

Q9SP32. Positions 248-816, 835-939, 1295-1440, 1559-1795.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-33454N.

IntAct

Q9SP32. 4 interactions.

Proteomic databases

PaxDb

Q9SP32.

PRIDE

Q9SP32.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT1G01040.1; AT1G01040.1; AT1G01040.

GeneID

839574.

KEGG

ath:AT1G01040.

Organism-specific databases

TAIR

At1g01040.

Phylogenomic databases

eggNOG

COG1111.

HOGENOM

HOG000239675.

InParanoid

Q9SP32.

KO

K11592.

PhylomeDB

Q9SP32.

ProtClustDB

CLSN2682824.

Gene expression databases

ArrayExpress

Q9SP32.

Genevestigator

Q9SP32.

GermOnline

AT1G01040. Arabidopsis thaliana.

Family and domain databases

Gene3D

1.10.1520.10. 3 hits.
3.30.160.20. 2 hits.

InterPro

IPR005034. Dicer_dsRNA_binding_fold.
IPR001159. Ds-RNA-bd.
IPR014720. dsRNA-bd-like_dom.
IPR006935. Helicase/UvrB_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR003100. PAZ.
IPR011907. RNase_III.
IPR000999. RNase_III_dom.
[Graphical view]

Pfam

PF00035. dsrm. 2 hits.
PF03368. dsRNA_bind. 1 hit.
PF00271. Helicase_C. 1 hit.
PF02170. PAZ. 1 hit.
PF04851. ResIII. 1 hit.
PF00636. Ribonuclease_3. 2 hits.
[Graphical view]

SMART

SM00487. DEXDc. 1 hit.
SM00358. DSRM. 2 hits.
SM00490. HELICc. 1 hit.
SM00949. PAZ. 1 hit.
SM00535. RIBOc. 2 hits.
[Graphical view]

SUPFAM

SSF101690. PAZ. 1 hit.
SSF69065. RNase_III. 2 hits.

PROSITE

PS51327. DICER_DSRBF. 1 hit.
PS50137. DS_RBD. 2 hits.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS50821. PAZ. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 2 hits.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DCL1_ARATH

Accession

Primary (citable) accession number: Q9SP32
Secondary accession number(s): Q9FDY6, Q9MAN0

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 19, 2003
Last sequence update:	September 19, 2003
Last modified:	May 1, 2013
This is version 107 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program