Functional divergence in the Arabidopsis LOB-domain gene family

Mangeon, Amanda; Lin, Wan-ching; Springer, Patricia S.

doi:10.4161/psb.22320

Cited by 16 publications

(8 citation statements)

References 43 publications

(64 reference statements)

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“…In Arabidopsis , similar expression divergence is also observed for class IA-2 LBD genes. For example, AtLBD6/AS2 is specifically expressed in the adaxial side of leaves [ 3 ], while AtLBD10 is only detected in the pollen grains, and AtLBD36 is expressed in a variety of tissues, including leaf vasculature, flower organs and seeds [ 26 , 27 ]. These observations suggest alteration of expression level and tissue specificity occurred during LBD genes evolution.…”

Section: Resultsmentioning

confidence: 99%

Decipher the ancestry of the plant-specific LBD gene family

Kong

Jing

et al. 2017

BMC Genomics

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Background Lateral Organ Boundaries Domain (LBD) genes arise from charophyte algae and evolve essential functions in land plants in regulating organ development and secondary metabolism. Although diverse plant species have been investigated to construct the phylogeny of LBD gene family, a detailed and reliable ancestry that characterizes their evolutionary patterns has not been revealed.ResultsWe develop an improved bioinformatic method that allows robust detection of 431 LBD genes in 11 high-quality land plant genomes. Phylogenetic analysis classifies the LBD genes into six subfamilies which support the existence of 7 ancient gene lineages. Phylogenetic relationship and gene collinearity are combined to retrace 11 ancestor genes for seed plants and 18 ancestor genes for angiosperms, which improves the resolution of LBD gene ancestry. The ancient gene lineages are strictly preserved in current plant genomes, including the previously controversial class IB gene in Selaginella moellendorphii, suggesting extreme reluctance of LBD genes to be lost during evolution. Meanwhile, whole-genome and dispersed gene duplications substantially expand LBD gene family in angiosperms, and elaborate functions of LBD genes through frequent expression pattern change and protein sequence variation.ConclusionsThrough phylogenetic and gene collinearity analyses, we retrace the landscape of LBD gene ancestry which lays foundation for elucidating evolutionary diversification of LBD genes in land plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3264-3) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Decipher the ancestry of the plant-specific LBD gene family

Kong

Jing

et al. 2017

BMC Genomics

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“…The phylogenetic analysis ( Fig. 1) revealed that the LBDs could be divided into two main clades corresponding to class I and II of Arabidopsis as defined by Mangeon et al (2012). There were 330 and 59 LBD genes involved in class I and II of the fore mentioned cotton species.…”

Section: Phylogenetic Analysis Of the Cotton Lbd Gene Familymentioning

confidence: 99%

Comprehensive characterization and gene expression patterns of LBD gene family in Gossypium

Xie

Cheng

et al. 2020

Planta

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“…Recent studies have expanded their functional diversity beyond the definition of lateral organ boundaries. The LBD family proteins also play pivotal roles in pollen development (9,10), vascular differentiation (11), nitrogen metabolism (12), plant regeneration (13,14), photomorphogenesis (15), disease susceptibility (16,17), and some specific developmental processes in wood and grass species (18,19).…”

Section: Lateral Organ Boundaries Domain (Lbd) Proteins a Family Of mentioning

confidence: 99%

Structural analysis reveals a “molecular calipers” mechanism for a LATERAL ORGAN BOUNDARIES DOMAIN transcription factor protein from wheat

Chen

Xiao

Réty

et al. 2019

Journal of Biological Chemistry

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LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a family of plant-specific transcription factors harboring a conserved Lateral Organ Boundaries (LOB) domain, are regulators of plant organ development. Recent studies haveunraveled additional pivotal roles of the LBD protein family beyond defining lateral organ boundaries, such as pollen development and nitrogen metabolism. The structural basis for the molecular network of LBD-dependent processes remains to be deciphered. Here, we solved the first structure of the homodimeric LOB domain of Ramosa2 from wheat (TtRa2LD) to 1.9 Å resolution. Our crystal structure reveals structural features shared with other zinc-finger transcriptional factors, as well as some features unique to LBD proteins. Formation of the TtRa2LD homodimer relied on hydrophobic interactions of its coiled-coil motifs. Several specific motifs/domains of the LBD protein were also involved in maintaining its overall conformation. The intricate assembly within and between the monomers determined the precise spatial configuration of the two zinc fingers that recognize palindromic DNA sequences. Biochemical, molecular modeling, and small-angle X-ray scattering experiments indicated that dimerization is important for cooperative DNA binding and discrimination of palindromic DNA through a molecular calipers mechanism. Along with previously published data, this study enables us to establish an atomic-scale mechanistic model for LBD proteins as transcriptional regulators in plants.

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Functional divergence in the Arabidopsis LOB-domain gene family

Cited by 16 publications

References 43 publications

Decipher the ancestry of the plant-specific LBD gene family

Decipher the ancestry of the plant-specific LBD gene family

Comprehensive characterization and gene expression patterns of LBD gene family in Gossypium

Structural analysis reveals a “molecular calipers” mechanism for a LATERAL ORGAN BOUNDARIES DOMAIN transcription factor protein from wheat

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