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

AT2G42430.1

Common Name

ASL18, LBD16, MHK10.15

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

LBD

Protein Properties

Length: 245aa MW: 26465.4 Da PI: 7.865

Description

lateral organ boundaries-domain 16

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT2G42430.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	122	3.1e-38	15	115	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelall 97 +C aCk+lrrkCa+dC++apyf +eq +++fa++hk+FGasnv+kll ++p ++r +a+ +++yeA+ar++dPvyG+v++i++lqqq++ l++++ ++ AT2G42430.1 15 PCGACKFLRRKCASDCIFAPYFSSEQgAARFAAIHKVFGASNVSKLLLNVPIHDRCEAVVTIAYEAQARLHDPVYGCVSHIFALQQQVAFLQSQVMQM 112 7*********************9989****************************************************************9999 PP DUF260 98 kee 100 k++ AT2G42430.1 113 KAQ 115 887 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.866	14	116	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	4.2E-37	15	113	IPR004883	Lateral organ boundaries, LOB

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010311	Biological Process	lateral root formation
GO:0005634	Cellular Component	nucleus

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009025	anatomy	vascular leaf

Sequence ? help Back to Top
Protein Sequence Length: 245 aa Download sequence Send to blast
MASSGNGTTA GTGSPCGACK FLRRKCASDC IFAPYFSSEQ GAARFAAIHK VFGASNVSKL 60 LLNVPIHDRC EAVVTIAYEA QARLHDPVYG CVSHIFALQQ QVAFLQSQVM QMKAQIAGHQ 120 TSAAGDLRHS SESTNQFMTW QQTSVSPIGS AYSTPYNHHQ PYYGHVNPNN PVSPQSSLEE 180 SFSNTSSDVT TTANVRETHH QTGGGVYGHD GIGFHEGYPN KKRSVSYCSS DLGELQALAL 240 RMMKN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	4e-37	8	109	4	104	LOB family transfactor Ramosa2.1
5ly0_B	4e-37	8	109	4	104	LOB family transfactor Ramosa2.1
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.13375	0.0	root

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	265856_at	0.0
Expression Atlas	AT2G42430	-
AtGenExpress	AT2G42430	-
ATTED-II	AT2G42430	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: During lateral root formation, expressed in the lateral root primordia, and the developing, emerged, and mature lateral roots. {ECO:0000269\|PubMed:19717544}.
Uniprot	TISSUE SPECIFICITY: Expressed in roots and faintly in shoots. {ECO:0000269\|PubMed:12068116}.

Functional Description ? help Back to Top
Source	Description
TAIR	LOB-domain protein gene LBD16. This gene contains one auxin-responsive element (AuxRE).
UniProt	Transcriptional activator (PubMed:19717544, PubMed:22974309). Involved in lateral root formation. Regulated by the transcriptional activators ARF7 and ARF19 (PubMed:17259263). Functions in the initiation and emergence of lateral roots, in conjunction with LBD18, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269\|PubMed:17259263, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:22974309, ECO:0000269\|PubMed:23749813, ECO:0000269\|PubMed:26059335}.

Function -- GeneRIF ? help Back to Top
LBD16 and LBD18 might function in a combinatorial manner in lateral root formation. [PMID: 19717544] Results indicate that the localized activity of LBD16/ASL18 and its related LBD/ASLs is involved in the symmetry breaking of lateral root (LR) founder cells for LR initiation, a key step for constructing the plant root system. [PMID: 22278921] Data show that overexpression of each of the LBD genes promotes callus formation in the absence of exogenous phytohormones, while suppression of LBD function inhibits the callus induction process. [PMID: 22508267] LBD16, LBD29, and LBD18 are involved in cell cycle progression of the pericycle in response to auxin. [PMID: 22699776] PUCHI co-acts with LBD16 and LBD18 to control lateral root primordium development and lateral root emergence. [PMID: 23749813] LBD16 is a key molecular player in the xylem pole pericycle cells during giant cells and gall development. [PMID: 24803293] Results suggest that Lateral Organ Boundaries Domain16 and 18 (LBD16 and LBD18) are important regulators of lateral root (LR) initiation and development downstream of AUXIN1 (AUX1) and LIKE-AUXIN3 (LAX3) auxin influx carriers. [PMID: 26059335] Data show that the conserved Leu or valine residues in the coiled-coil motif are critical for the dimerization of LBD16 or LBD18 transcription factors. [PMID: 28336771] conserved Leu or Val residues in the coiled-coil motifs of LBD16 and LBD18 are critical for their dimerization as well as the transcriptional regulation to display their biological functions. [PMID: 29227192] These findings define the AtbZIP59-LBD complex as a critical regulator of auxin-induced cell fate change during callus formation, which provides a new insight into the molecular regulation of plant regeneration and possible developmental programs. [PMID: 29358751] the WOX11-LBD16 pathway promotes pluripotency acquisition in callus cells. [PMID: 29361138] acts downstream of ARF7 and ARF19 in formation of adventitious roots [PMID: 30704405]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00309	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT2G42430.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. {ECO:0000269\|PubMed:15659631, ECO:0000269\|PubMed:17259263, ECO:0000269\|PubMed:23749813}.

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

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT1G19220 (A), AT5G20730 (A)

Regulation -- Hormone ? help Back to Top
Source	Hormone
AHD	auxin

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT2G42430, AT2G45420

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Reduced number of lateral roots. {ECO:0000269\|PubMed:19717544}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT2G42430

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB473851	0.0	AB473851.1 Arabidopsis thaliana ASL18 mRNA for ASYMMETRIC LEAVES2-like 18 protein, complete cds.
GenBank	AF345339	0.0	AF345339.1 Arabidopsis thaliana MHK10.15/At2g42430 mRNA, complete cds.
GenBank	AF410334	0.0	AF410334.1 Arabidopsis thaliana At2g42430/MHK10.15 mRNA, complete cds.
GenBank	AF447890	0.0	AF447890.1 Arabidopsis thaliana LOB DOMAIN 16 (LBD16) mRNA, complete cds.
GenBank	BT000866	0.0	BT000866.1 Arabidopsis thaliana At2g42430/MHK10.15 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_565973.1	0.0	lateral organ boundaries-domain 16
Swissprot	Q9SLB7	0.0	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	A0A178VSA2	0.0	A0A178VSA2_ARATH; LBD16
STRING	AT2G42430.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM108	28	359
Representative plant	OGRP405	15	100

Link Out ? help Back to Top
Phytozome	AT2G42430.1
Entrez Gene	818843
iHOP	AT2G42430
wikigenes	AT2G42430

Publications ? help Back to Top
Iwakawa H, et al. The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana, required for formation of a symmetric flat leaf lamina, encodes a member of a novel family of proteins characterized by cysteine repeats and a leucine zipper. Plant Cell Physiol., 2002. 43(5): p. 467-78 [PMID:12040093] Shuai B,Reynaga-Peña CG,Springer PS The lateral organ boundaries gene defines a novel, plant-specific gene family. Plant Physiol., 2002. 129(2): p. 747-61 [PMID:12068116] Xiao YL,Malik M,Whitelaw CA,Town CD Cloning and sequencing of cDNAs for hypothetical genes from chromosome 2 of Arabidopsis. Plant Physiol., 2002. 130(4): p. 2118-28 [PMID:12481096] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Goda H, et al. Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis. Plant Physiol., 2004. 134(4): p. 1555-73 [PMID:15047898] Okushima Y, et al. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell, 2005. 17(2): p. 444-63 [PMID:15659631] Laplaze L, et al. GAL4-GFP enhancer trap lines for genetic manipulation of lateral root development in Arabidopsis thaliana. J. Exp. Bot., 2005. 56(419): p. 2433-42 [PMID:16043452] Okushima Y,Fukaki H,Onoda M,Theologis A,Tasaka M ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis. Plant Cell, 2007. 19(1): p. 118-30 [PMID:17259263] Matsumura Y,Iwakawa H,Machida Y,Machida C Characterization of genes in the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) family in Arabidopsis thaliana, and functional and molecular comparisons between AS2 and other family members. Plant J., 2009. 58(3): p. 525-37 [PMID:19154202] Lee HW,Kim NY,Lee DJ,Kim J LBD18/ASL20 regulates lateral root formation in combination with LBD16/ASL18 downstream of ARF7 and ARF19 in Arabidopsis. Plant Physiol., 2009. 151(3): p. 1377-89 [PMID:19717544] Ikeyama Y,Tasaka M,Fukaki H RLF, a cytochrome b(5)-like heme/steroid binding domain protein, controls lateral root formation independently of ARF7/19-mediated auxin signaling in Arabidopsis thaliana. Plant J., 2010. 62(5): p. 865-75 [PMID:20230485] Goh T,Joi S,Mimura T,Fukaki H The establishment of asymmetry in Arabidopsis lateral root founder cells is regulated by LBD16/ASL18 and related LBD/ASL proteins. Development, 2012. 139(5): p. 883-93 [PMID:22278921] Fan M,Xu C,Xu K,Hu Y LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration. Cell Res., 2012. 22(7): p. 1169-80 [PMID:22508267] Kim MJ,Kim J Identification of nuclear localization signal in ASYMMETRIC LEAVES2-LIKE18/LATERAL ORGAN BOUNDARIES DOMAIN16 (ASL18/LBD16) from Arabidopsis. J. Plant Physiol., 2012. 169(12): p. 1221-6 [PMID:22591857] Feng Z,Zhu J,Du X,Cui X Effects of three auxin-inducible LBD members on lateral root formation in Arabidopsis thaliana. Planta, 2012. 236(4): p. 1227-37 [PMID:22699776] Lee HW,Kim MJ,Kim NY,Lee SH,Kim J LBD18 acts as a transcriptional activator that directly binds to the EXPANSIN14 promoter in promoting lateral root emergence of Arabidopsis. Plant J., 2013. 73(2): p. 212-24 [PMID:22974309] M Role of a respiratory burst oxidase of Lepidium sativum (cress) seedlings in root development and auxin signalling. J. Exp. Bot., 2012. 63(18): p. 6325-34 [PMID:23095998] Kim J,Lee HW Direct activation of EXPANSIN14 by LBD18 in the gene regulatory network of lateral root formation in Arabidopsis. Plant Signal Behav, 2013. 8(2): p. e22979 [PMID:23299420] Lee HW,Kim MJ,Park MY,Han KH,Kim J The conserved proline residue in the LOB domain of LBD18 is critical for DNA-binding and biological function. Mol Plant, 2013. 6(5): p. 1722-5 [PMID:23430048] Kang NY,Lee HW,Kim J The AP2/EREBP gene PUCHI Co-Acts with LBD16/ASL18 and LBD18/ASL20 downstream of ARF7 and ARF19 to regulate lateral root development in Arabidopsis. Plant Cell Physiol., 2013. 54(8): p. 1326-34 [PMID:23749813] Bargmann BO,Birnbaum KD,Brenner ED An undergraduate study of two transcription factors that promote lateral root formation. Biochem Mol Biol Educ, 2014 May-Jun. 42(3): p. 237-45 [PMID:24615800] Cabrera J, et al. A role for LATERAL ORGAN BOUNDARIES-DOMAIN 16 during the interaction Arabidopsis-Meloidogyne spp. provides a molecular link between lateral root and root-knot nematode feeding site development. New Phytol., 2014. 203(2): p. 632-45 [PMID:24803293] Cabrera J,Fenoll C,Escobar C Genes co-regulated with LBD16 in nematode feeding sites inferred from in silico analysis show similarities to regulatory circuits mediated by the auxin/cytokinin balance in Arabidopsis. Plant Signal Behav, 2015. 10(3): p. e990825 [PMID:25664644] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Lee HW,Cho C,Kim J Lateral Organ Boundaries Domain16 and 18 Act Downstream of the AUXIN1 and LIKE-AUXIN3 Auxin Influx Carriers to Control Lateral Root Development in Arabidopsis. Plant Physiol., 2015. 168(4): p. 1792-806 [PMID:26059335] Lee HW, et al. Dimerization in LBD16 and LBD18 Transcription Factors Is Critical for Lateral Root Formation. Plant Physiol., 2017. 174(1): p. 301-311 [PMID:28336771] Olmo R, et al. Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program? Front Plant Sci, 2017. 8: p. 875 [PMID:28603536] Lee K,Seo PJ High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis. Planta, 2017. 246(4): p. 797-802 [PMID:28766014] Jeon E, et al. LBD14/ASL17 Positively Regulates Lateral Root Formation and is Involved in ABA Response for Root Architecture in Arabidopsis. Plant Cell Physiol., 2017. 58(12): p. 2190-2201 [PMID:29040694] Pandey SK,Kim J Coiled-coil motif in LBD16 and LBD18 transcription factors are critical for dimerization and biological function in arabidopsis. Plant Signal Behav, 2018. 13(1): p. e1411450 [PMID:29227192] Xu C, et al. Control of auxin-induced callus formation by bZIP59-LBD complex in Arabidopsis regeneration. Nat Plants, 2018. 4(2): p. 108-115 [PMID:29358751] Liu J, et al. The WOX11-LBD16 Pathway Promotes Pluripotency Acquisition in Callus Cells During De Novo Shoot Regeneration in Tissue Culture. Plant Cell Physiol., 2018. 59(4): p. 734-743 [PMID:29361138] Lee HW, et al. LBD16 and LBD18 acting downstream of ARF7 and ARF19 are involved in adventitious root formation in Arabidopsis. BMC Plant Biol., 2019. 19(1): p. 46 [PMID:30704405]