PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Spipo14G0021700

Organism

Spirodela polyrhiza

Taxonomic ID

29656

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Alismatales; Araceae; Lemnoideae; Spirodela

Family

bHLH

Protein Properties

Length: 390aa MW: 44074.8 Da PI: 10.0011

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Spipo14G0021700	genome	MIPS/IBIS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	26.3	1.4e-08	77	106	2	30
HHHHHHHHHHHHHHHHHHHHHHHCTSCC.C CS HLH 2 rrahnerErrRRdriNsafeeLrellPk.a 30 r++h +Er+RR+++N+ ++ L++l+P Spipo14G0021700 77 RMSHITVERNRRKQMNEHLSVLKSLMPCfY 106 89*************************844 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	2.91E-8	74	109	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	10.086	75	145	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	3.5E-7	76	106	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	7.1E-6	77	106	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	4.89E-5	77	109	No hit	No description
SuperFamily	SSF88946	2.98E-30	109	223	IPR013325	RNA polymerase sigma factor, region 2
Gene3D	G3DSA:1.10.10.10	1.0E-4	113	144	IPR011991	Winged helix-turn-helix DNA-binding domain
Gene3D	G3DSA:1.10.601.10	2.1E-27	145	223	No hit	No description
TIGRFAMs	TIGR02937	2.1E-24	152	377	IPR014284	RNA polymerase sigma-70 like domain
Pfam	PF04542	2.4E-12	156	222	IPR007627	RNA polymerase sigma-70 region 2
PRINTS	PR00046	9.4E-14	183	196	IPR000943	RNA polymerase sigma-70
PRINTS	PR00046	9.4E-14	207	215	IPR000943	RNA polymerase sigma-70
Gene3D	G3DSA:1.10.10.10	6.1E-9	230	280	IPR011991	Winged helix-turn-helix DNA-binding domain
SuperFamily	SSF88659	5.67E-9	231	295	IPR013324	RNA polymerase sigma factor, region 3/4
Pfam	PF04539	3.5E-14	240	304	IPR007624	RNA polymerase sigma-70 region 3
SuperFamily	SSF88659	8.04E-18	315	387	IPR013324	RNA polymerase sigma factor, region 3/4
Gene3D	G3DSA:1.10.10.10	4.1E-21	320	388	IPR011991	Winged helix-turn-helix DNA-binding domain
Pfam	PF04545	6.6E-14	324	377	IPR007630	RNA polymerase sigma-70 region 4
PRINTS	PR00046	9.4E-14	328	340	IPR000943	RNA polymerase sigma-70
PRINTS	PR00046	9.4E-14	349	364	IPR000943	RNA polymerase sigma-70
PRINTS	PR00046	9.4E-14	364	375	IPR000943	RNA polymerase sigma-70

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006352	Biological Process	DNA-templated transcription, initiation
GO:0009658	Biological Process	chloroplast organization
GO:0010114	Biological Process	response to red light
GO:0010207	Biological Process	photosystem II assembly
GO:0010218	Biological Process	response to far red light
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0071483	Biological Process	cellular response to blue light
GO:0005739	Cellular Component	mitochondrion
GO:0009507	Cellular Component	chloroplast
GO:0001053	Molecular Function	plastid sigma factor activity
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0003899	Molecular Function	DNA-directed RNA polymerase activity
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 390 aa Download sequence Send to blast
MDDSQALSDL FDGSENLFSM LESLEDPRGS LLSPLEEVFS PRGSSTAELE APASRKRMRM 60 GEYAAAAVAV AGEGQVRMSH ITVERNRRKQ MNEHLSVLKS LMPCFYVKRA TLAVKDTLCV 120 DLGREPTDGE LASAINMNVQ QLRRHLEVGH AARNKLIKHN LRLVLFAINK YYHEIANGQK 180 FQDLCQAGVK GLITAIDRFE PKRGFRLSTY ALFWIRHAII RSMTISSFAR VPFGIESVRQ 240 EIQRAKLELT FELKREPTEE EIVSRVGISP DRYNDVLRAS KPVISLNARH ATTQEEFIKG 300 IADVDSVGDR RRQPALLRLA LDDVLDSLKP KESLVIRQRY GLDGKGDRTL GEIAGNLNIS 360 REMVRKHEVK ALMKLKHPAR VDYLRRYIV*

Sequence ? help Back to Top

Protein Sequence Length: 390 aa Download sequence Send to blast

MDDSQALSDL FDGSENLFSM LESLEDPRGS LLSPLEEVFS PRGSSTAELE APASRKRMRM  60
GEYAAAAVAV AGEGQVRMSH ITVERNRRKQ MNEHLSVLKS LMPCFYVKRA TLAVKDTLCV  120
DLGREPTDGE LASAINMNVQ QLRRHLEVGH AARNKLIKHN LRLVLFAINK YYHEIANGQK  180
FQDLCQAGVK GLITAIDRFE PKRGFRLSTY ALFWIRHAII RSMTISSFAR VPFGIESVRQ  240
EIQRAKLELT FELKREPTEE EIVSRVGISP DRYNDVLRAS KPVISLNARH ATTQEEFIKG  300
IADVDSVGDR RRQPALLRLA LDDVLDSLKP KESLVIRQRY GLDGKGDRTL GEIAGNLNIS  360
REMVRKHEVK ALMKLKHPAR VDYLRRYIV*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5vt0_L	2e-37	138	388	267	521	RNA polymerase sigma factor RpoD
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	76	87	RMSHITVERNRR

Functional Description ? help Back to Top
Source	Description
UniProt	Essential protein. Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites (e.g. psbA and psbD) and are then released. Essential for blue light-mediated transcription of psbD, which encodes the photosystem II reaction center protein D2. Plays a role in reproduction. Required during female gametophyte development (PubMed:21123745). {ECO:0000269\|PubMed:12805603, ECO:0000269\|PubMed:14976253, ECO:0000269\|PubMed:18532976, ECO:0000269\|PubMed:21123745}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Induced by blue light illumination (470 nm), especially after dark adaptation. Induction is mediated through both cryptochrome 1 and cryptochrome 2 at lower light intensities and mainly through cryptochrome 1 at higher light intensities. {ECO:0000269\|PubMed:10946105, ECO:0000269\|PubMed:11959137, ECO:0000269\|PubMed:14976253, ECO:0000269\|PubMed:18532976}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009410848.1	1e-166	PREDICTED: RNA polymerase sigma factor sigE, chloroplastic/mitochondrial
Swissprot	Q9ZNX9	1e-154	SIGE_ARATH; RNA polymerase sigma factor sigE, chloroplastic/mitochondrial
TrEMBL	A0A1D1YA77	1e-179	A0A1D1YA77_9ARAE; RNA polymerase sigma factor rpoD (Fragment)
STRING	GSMUA_Achr7P24590_001	1e-165	(Musa acuminata)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G53210.1	3e-16	bHLH family protein

Link Out ? help Back to Top
Phytozome	Spipo14G0021700

Publications ? help Back to Top
Hakimi MA,Privat I,Valay JG,Lerbs-Mache S Evolutionary conservation of C-terminal domains of primary sigma(70)-type transcription factors between plants and bacteria. J. Biol. Chem., 2000. 275(13): p. 9215-21 [PMID:10734058] Allison LA The role of sigma factors in plastid transcription. Biochimie, 2000 Jun-Jul. 82(6-7): p. 537-48 [PMID:10946105] Fujiwara M,Nagashima A,Kanamaru K,Tanaka K,Takahashi H Three new nuclear genes, sigD, sigE and sigF, encoding putative plastid RNA polymerase sigma factors in Aarabidopsis thaliana. FEBS Lett., 2000. 481(1): p. 47-52 [PMID:10984613] Tsunoyama Y,Morikawa K,Shiina T,Toyoshima Y Blue light specific and differential expression of a plastid sigma factor, Sig5 in Arabidopsis thaliana. FEBS Lett., 2002. 516(1-3): p. 225-8 [PMID:11959137] Yao J,Roy-Chowdhury S,Allison LA AtSig5 is an essential nucleus-encoded Arabidopsis sigma-like factor. Plant Physiol., 2003. 132(2): p. 739-47 [PMID:12805603] Kubis S, et al. The Arabidopsis ppi1 mutant is specifically defective in the expression, chloroplast import, and accumulation of photosynthetic proteins. Plant Cell, 2003. 15(8): p. 1859-71 [PMID:12897258] Tsunoyama Y, et al. Blue light-induced transcription of plastid-encoded psbD gene is mediated by a nuclear-encoded transcription initiation factor, AtSig5. Proc. Natl. Acad. Sci. U.S.A., 2004. 101(9): p. 3304-9 [PMID:14976253] Ishizaki Y, et al. A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons. Plant J., 2005. 42(2): p. 133-44 [PMID:15807777] Schweer J,Loschelder H,Link G A promoter switch that can rescue a plant sigma factor mutant. FEBS Lett., 2006. 580(28-29): p. 6617-22 [PMID:17118361] Onda Y,Yagi Y,Saito Y,Takenaka N,Toyoshima Y Light induction of Arabidopsis SIG1 and SIG5 transcripts in mature leaves: differential roles of cryptochrome 1 and cryptochrome 2 and dual function of SIG5 in the recognition of plastid promoters. Plant J., 2008. 55(6): p. 968-78 [PMID:18532976] Yu F, et al. ANK6, a mitochondrial ankyrin repeat protein, is required for male-female gamete recognition in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A., 2010. 107(51): p. 22332-7 [PMID:21123745] Bryant N,Lloyd J,Sweeney C,Myouga F,Meinke D Identification of nuclear genes encoding chloroplast-localized proteins required for embryo development in Arabidopsis. Plant Physiol., 2011. 155(4): p. 1678-89 [PMID:21139083] Davey MP, et al. The UV-B photoreceptor UVR8 promotes photosynthetic efficiency in Arabidopsis thaliana exposed to elevated levels of UV-B. Photosyn. Res., 2012. 114(2): p. 121-31 [PMID:23161229] Noordally ZB, et al. Circadian control of chloroplast transcription by a nuclear-encoded timing signal. Science, 2013. 339(6125): p. 1316-9 [PMID:23493713] Börner T,Aleynikova AY,Zubo YO,Kusnetsov VV Chloroplast RNA polymerases: Role in chloroplast biogenesis. Biochim. Biophys. Acta, 2015. 1847(9): p. 761-9 [PMID:25680513] Yamburenko MV,Zubo YO,Börner T Abscisic acid affects transcription of chloroplast genes via protein phosphatase 2C-dependent activation of nuclear genes: repression by guanosine-3'-5'-bisdiphosphate and activation by sigma factor 5. Plant J., 2015. 82(6): p. 1030-41 [PMID:25976841] Xiao D, et al. SENESCENCE-SUPPRESSED PROTEIN PHOSPHATASE Directly Interacts with the Cytoplasmic Domain of SENESCENCE-ASSOCIATED RECEPTOR-LIKE KINASE and Negatively Regulates Leaf Senescence in Arabidopsis. Plant Physiol., 2015. 169(2): p. 1275-91 [PMID:26304848] Mellenthin M,Ellersiek U,Börger A,Baier M Expression of the Arabidopsis Sigma Factor SIG5 Is Photoreceptor and Photosynthesis Controlled. Plants (Basel), 2014. 3(3): p. 359-91 [PMID:27135509] Belbin FE, et al. Integration of light and circadian signals that regulate chloroplast transcription by a nuclear-encoded sigma factor. New Phytol., 2017. 213(2): p. 727-738 [PMID:27716936] Zhao P, et al. ATHB17 enhances stress tolerance by coordinating photosynthesis associated nuclear gene and ATSIG5 expression in response to abiotic stress. Sci Rep, 2017. 7: p. 45492 [PMID:28358040]