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

Sp_045440_nhwo.t3

Common Name

SOVF_045440

Organism

Spinacia oleracea

Taxonomic ID

3562

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Chenopodiaceae; Chenopodioideae; Anserineae; Spinacia

Family

LSD

Protein Properties

Length: 174aa MW: 18288.2 Da PI: 8.3241

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sp_045440_nhwo.t3	genome	TBVR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	48.5	1.4e-15	7	31	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCrt+L YPrGAp+VRCa+C+tV Sp_045440_nhwo.t3 7 CNGCRTVLLYPRGAPNVRCAVCNTV 31 ************************9 PP
2	zf-LSD1	34.1	4.5e-11	46	70	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg C+tlL+Y+rGA+sVRC +C+tV Sp_045440_nhwo.t3 46 CGCCHTLLMYTRGATSVRCLCCHTV 70 9***********************9 PP
3	zf-LSD1	44.6	2.4e-14	85	108	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 Cg+C+ +L+YP+GApsV+Ca+C+ Sp_045440_nhwo.t3 85 CGSCQMTLMYPYGAPSVKCAVCQY 108 **********************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	5.8E-15	4	33	IPR005735	Zinc finger, LSD1-type
Gene3D	G3DSA:3.90.10.10	0.001	5	107	No hit	No description
Pfam	PF06943	2.2E-13	7	31	IPR005735	Zinc finger, LSD1-type
SuperFamily	SSF48695	3.98E-5	21	106	IPR011031	Multihaem cytochrome
TIGRFAMs	TIGR01053	2.3E-12	43	72	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	5.7E-10	46	70	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	2.9E-10	83	111	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	5.5E-13	85	109	IPR005735	Zinc finger, LSD1-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000303	Biological Process	response to superoxide
GO:0001666	Biological Process	response to hypoxia
GO:0002240	Biological Process	response to molecule of oomycetes origin
GO:0009626	Biological Process	plant-type hypersensitive response
GO:0009862	Biological Process	systemic acquired resistance, salicylic acid mediated signaling pathway
GO:0010104	Biological Process	regulation of ethylene-activated signaling pathway
GO:0010310	Biological Process	regulation of hydrogen peroxide metabolic process
GO:0010602	Biological Process	regulation of 1-aminocyclopropane-1-carboxylate metabolic process
GO:0010618	Biological Process	aerenchyma formation
GO:0043069	Biological Process	negative regulation of programmed cell death

Sequence ? help Back to Top
Protein Sequence Length: 174 aa Download sequence Send to blast
MQSQLVCNGC RTVLLYPRGA PNVRCAVCNT VTPVQPAGLE MDQIICGCCH TLLMYTRGAT 60 SVRCLCCHTV NLTTPVANQV ATVRCGSCQM TLMYPYGAPS VKCAVCQYIT NVGTANGSLP 120 SSIHRQNGVA TSSSPSPSIP QSPTQTVVVE NPMSFDGSGK LVSNVVVGVT TEKK

Functional Description ? help Back to Top
Source	Description
UniProt	Negative regulator of reactive oxygen-induced cell death, cold stress-induced cell death, pathogen-induced hypersensitive response (HR), basal disease resistance. May be involved in the induction of the copper/zinc superoxide dismutase CSD1 and CSD2 that detoxify accumulating superoxide before the reactive oxygen species (ROS) can trigger a cell death cascade. LSD1 and LOL1 have antagonistic effects on CSD1 and CSD2 accumulation to regulate oxidative stress-induced cell death. Antagonizes the function of BZIP10, a positive regulator of cell death, by interacting in the cytoplasm and preventing its nuclear localization. Controls lysigenous aerenchyma in hypocotyls under root hypoxia. Required for leaf acclimation in response to excess excitation energy. {ECO:0000269\|PubMed:10550898, ECO:0000269\|PubMed:11595797, ECO:0000269\|PubMed:11844114, ECO:0000269\|PubMed:12732715, ECO:0000269\|PubMed:15347794, ECO:0000269\|PubMed:16957775, ECO:0000269\|PubMed:18055613, ECO:0000269\|PubMed:18790826, ECO:0000269\|PubMed:20456049, ECO:0000269\|PubMed:21097903}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By methyl viologen. {ECO:0000269\|PubMed:20456049}.

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_021848768.1	1e-122	protein LSD1 isoform X1
Refseq	XP_021848769.1	1e-122	protein LSD1 isoform X1
Swissprot	P94077	3e-63	LSD1_ARATH; Protein LSD1
TrEMBL	A0A0K9RQL7	1e-121	A0A0K9RQL7_SPIOL; Uncharacterized protein
STRING	XP_010687113.1	1e-100	(Beta vulgaris)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	2e-64	LSD family protein

Publications ? help Back to Top
Spedaletti V, et al. Characterization of a lysine-specific histone demethylase from Arabidopsis thaliana. Biochemistry, 2008. 47(17): p. 4936-47 [PMID:18393445] Szechyńska-Hebda M,Czarnocka W,Hebda M,Bernacki MJ,Karpiński S PAD4, LSD1 and EDS1 regulate drought tolerance, plant biomass production, and cell wall properties. Plant Cell Rep., 2016. 35(3): p. 527-39 [PMID:26754794] Czarnocka W, et al. The dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator. Plant Cell Environ., 2017. 40(11): p. 2644-2662 [PMID:28555890] Bernacki MJ, et al. LSD1-, EDS1- and PAD4-dependent conditional correlation among salicylic acid, hydrogen peroxide, water use efficiency and seed yield in Arabidopsis thaliana. Physiol Plant, 2019. 165(2): p. 369-382 [PMID:30461017]