PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Previous version: v3.0 v4.0

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Cucsa.048600.1

Common Name

Csa_6G526320

Organism

Cucumis sativus

Taxonomic ID

3659

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; Cucumis

Family

LSD

Protein Properties

Length: 172aa MW: 17832.6 Da PI: 8.4422

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cucsa.048600.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	39.9	7.1e-13	7	31	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCr +L YP GA++V+CalC+tV Cucsa.048600.1 7 CSGCRSILLYPGGATNVCCALCNTV 31 ************************9 PP
2	zf-LSD1	47.1	3.9e-15	46	70	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggCrtlL+Y rGA+sVRC++C+tV Cucsa.048600.1 46 CGGCRTLLMYARGATSVRCSCCHTV 70 ************************9 PP
3	zf-LSD1	41.7	1.9e-13	84	108	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Crt+L +P+GApsV+Ca+C+ V Cucsa.048600.1 84 CGNCRTTLVFPYGAPSVKCAICHYV 108 **********************987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	6.3E-12	4	34	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	3.5E-10	7	31	IPR005735	Zinc finger, LSD1-type
SuperFamily	SSF48695	9.84E-5	21	107	IPR011031	Multihaem cytochrome
TIGRFAMs	TIGR01053	5.4E-17	43	72	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	4.9E-13	46	70	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	2.3E-11	81	111	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	8.1E-13	84	108	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: 172 aa Download sequence Send to blast
MQSQLVCSGC RSILLYPGGA TNVCCALCNT VTSVPPPGTD MAQLICGGCR TLLMYARGAT 60 SVRCSCCHTV NLAPATNQVA HVNCGNCRTT LVFPYGAPSV KCAICHYVTN VGISNVRVPI 120 PVHRRNGTIS SGMPPSSSSQ SQTVVVENPM SVDESGKLVS NVVVGVTTDK R*

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	LN681875	4e-53	LN681875.1 Cucumis melo genomic scaffold, anchoredscaffold00007.
GenBank	LN713262	4e-53	LN713262.1 Cucumis melo genomic chromosome, chr_8.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_011658526.1	1e-124	PREDICTED: vacuolar protein sorting-associated protein 2 homolog 2
Swissprot	P94077	1e-70	LSD1_ARATH; Protein LSD1
TrEMBL	A0A0A0KJ18	1e-118	A0A0A0KJ18_CUCSA; Uncharacterized protein
TrEMBL	A0A1S3AZJ7	1e-118	A0A1S3AZJ7_CUCME; protein LSD1
STRING	XP_008439499.1	1e-119	(Cucumis melo)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4027	33	61

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	6e-72	LSD family protein

Link Out ? help Back to Top
Phytozome	Cucsa.048600.1

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] Ren Y, et al. An integrated genetic and cytogenetic map of the cucumber genome. PLoS ONE, 2009. 4(6): p. e5795 [PMID:19495411] Guo S, et al. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics, 2010. 11: p. 384 [PMID:20565788] Li Z, et al. RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics, 2011. 12: p. 540 [PMID:22047402] 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]