The lipid‐binding START domain regulates the dimerization of ATML1 via modulating the ZIP motif activity in Arabidopsis thaliana

Accumulation of the stress hormone abscisic acid (ABA) in response to drought and low water-potential controls many downstream acclimation mechanisms. However, mechanisms controlling ABA accumulation itself are less known. There was a 10-fold range of variation in ABA levels among nearly 300 Arabidopsis thaliana accessions exposed to the same low water-potential severity. Genome-wide association analysis (GWAS) identified genomic regions containing clusters of ABA-associated SNPs. Candidate genes within these regions included few genes with known stress or ABA-related function. The GWAS data were used to guide reverse genetic analysis, which found effectors of ABA accumulation. These included plasma-membrane–localized signaling proteins such as receptor-like kinases, aspartic protease, a putative lipid-binding START domain protein, and other membrane proteins of unknown function as well as a RING U-box protein and possible effect of tonoplast transport on ABA accumulation. Putative loss-of-function polymorphisms within the START domain protein were associated with climate factors at accession sites of origin, indicating its potential involvement in drought adaptation. Overall, using ABA accumulation as a basis for a combined GWAS–reverse genetic strategy revealed the broad natural variation in low-water-potential–induced ABA accumulation and was successful in identifying genes that affect ABA levels and may act in upstream drought-related sensing and signaling mechanisms. ABA effector loci were identified even when each one was of incremental effect, consistent with control of ABA accumulation being distributed among the many branches of ABA metabolism or mediated by genes with partially redundant function.

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Arabidopsis thaliana calcium-dependent lipid-binding protein (AtCLB): a novel repressor of abiotic stress response

Journal of Experimental Botany ◽

10.1093/jxb/erq468 ◽

2011 ◽

Vol 62 (8) ◽

pp. 2679-2689 ◽

Cited By ~ 46

Author(s):

Kanishka de Silva ◽

Bozena Laska ◽

Christopher Brown ◽

Heike Winter Sederoff ◽

Mariya Khodakovskaya

Keyword(s):

Arabidopsis Thaliana ◽

Abiotic Stress ◽

Stress Response ◽

Binding Protein ◽

Lipid Binding ◽

Abiotic Stress Response ◽

Lipid Binding Protein ◽

Calcium Dependent

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StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication

Frontiers in Genetics ◽

10.3389/fgene.2021.737194 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sanjeet Kumar Mahtha ◽

Ravi Kiran Purama ◽

Gitanjali Yadav

Keyword(s):

Lipid Binding ◽

Chromosomal Mapping ◽

Specific Substrate ◽

Limited Information ◽

Lipid Transfer ◽

Rice Varieties ◽

Selection Pressures ◽

Preferential Expression ◽

Start Domain ◽

Rice Domestication

The StAR-related lipid transfer (START) domain containing proteins or START proteins, encoded by a plant amplified family of evolutionary conserved genes, play important roles in lipid binding, transport, signaling, and modulation of transcriptional activity in the plant kingdom, but there is limited information on their evolution, duplication, and associated sub- or neo-functionalization. Here we perform a comprehensive investigation of this family across the rice pangenome, using 10 wild and cultivated varieties. Conservation of START domains across all 10 rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication and domain structure patterns. Analysis of synteny highlights a preponderance of segmental and dispersed duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization amongst genes family members in terms of preferential expression across various developmental stages and anatomical parts, such as flowering. Ka/Ks ratios confirmed strong negative/purifying selection on START family evolution, implying that ontogeny recapitulated selection pressures during rice domestication. Our findings provide evidence for high conservation of START genes across rice varieties in numbers, as well as in their stringent regulation of Ka/Ks ratio, and showed strong functional dependency of plants on START proteins for their growth and reproductive development. We believe that our findings advance the limited knowledge about plant START domain diversity and evolution, and pave the way for more detailed assessment of individual structural classes of START proteins among plants and their domain specific substrate preferences, to complement existing studies in animals and yeast.

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Identification of novel candidate phosphatidic acid-binding proteins involved in the salt-stress response of Arabidopsis thaliana roots

Biochemical Journal ◽

10.1042/bj20121639 ◽

2013 ◽

Vol 450 (3) ◽

pp. 573-581 ◽

Cited By ~ 78

Author(s):

Fionn McLoughlin ◽

Steven A. Arisz ◽

Henk L. Dekker ◽

Gertjan Kramer ◽

Chris G. de Koster ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Salt Stress ◽

Phosphatidic Acid ◽

Stress Responses ◽

Ribosomal Proteins ◽

Binding Proteins ◽

Affinity Purification ◽

Lipid Binding ◽

Biotic And Abiotic Stress ◽

Salt Stress Response

PA (phosphatidic acid) is a lipid second messenger involved in an array of processes occurring during a plant's life cycle. These include development, metabolism, and both biotic and abiotic stress responses. PA levels increase in response to salt, but little is known about its function in the earliest responses to salt stress. In the present study we have combined an approach to isolate peripheral membrane proteins of Arabidopsis thaliana roots with lipid-affinity purification, to identify putative proteins that interact with PA and are recruited to the membrane in response to salt stress. Of the 42 putative PA-binding proteins identified by MS, a set of eight new candidate PA-binding proteins accumulated at the membrane fraction after 7 min of salt stress. Among these were CHC (clathrin heavy chain) isoforms, ANTH (AP180 N-terminal homology) domain clathrin-assembly proteins, a putative regulator of potassium transport, two ribosomal proteins, GAPDH (glyceraldehyde 3-phosphate dehydrogenase) and a PI (phosphatidylinositol) 4-kinase. PA binding and salt-induced membrane recruitment of GAPDH and CHC were confirmed by Western blot analysis of the cellular fractions. In conclusion, the approach of the present study is an effective way to isolate biologically relevant lipid-binding proteins and provides new leads in the study of PA-mediated salt-stress responses in roots.

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AtVPS34, a phosphatidylinositol 3-kinase of Arabidopsis thaliana, is an essential protein with homology to a calcium-dependent lipid binding domain.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.91.24.11398 ◽

1994 ◽

Vol 91 (24) ◽

pp. 11398-11402 ◽

Cited By ~ 115

Author(s):

P. Welters ◽

K. Takegawa ◽

S. D. Emr ◽

M. J. Chrispeels

Keyword(s):

Arabidopsis Thaliana ◽

Lipid Binding ◽

Binding Domain ◽

Phosphatidylinositol 3 Kinase ◽

Essential Protein ◽

Calcium Dependent ◽

Phosphatidylinositol 3

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Arabidopsis PROTODERMAL FACTOR2 binds lysophosphatidylcholines and transcriptionally regulates phospholipid metabolism

10.1101/2021.10.20.465175 ◽

2021 ◽

Author(s):

Izabela Wojciechowska ◽

Thiya Mukherjee ◽

Patrick Knox-Brown ◽

Xueyun Hu ◽

Aashima Khosla ◽

...

Keyword(s):

Target Genes ◽

Affinity Purification ◽

Regulatory Protein ◽

Lipid Binding ◽

Epidermal Differentiation ◽

In Vitro Assays ◽

Dependent Manner ◽

Lipid Transfer ◽

Start Domain

Plant homeodomain leucine-zipper IV (HD-Zip IV) transcription factors (TFs) contain an evolutionarily conserved steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain. The START domain is required for TF activity; however, its presumed role as a lipid sensor is not well understood. Here we used tandem affinity purification from Arabidopsis cell cultures to demonstrate that PROTODERMAL FACTOR2 (PDF2), a representative family member which controls epidermal differentiation, recruits lysophosphatidylcholines in a START-dependent manner. In vitro assays with recombinant protein verified that a missense mutation in a predicted ligand contact site reduces lysophospholipid binding. We additionally uncovered that PDF2 controls the expression of phospholipid-related target genes by binding to a palindromic octamer with consensus to a phosphate (Pi) response element. Phospholipid homeostasis and elongation growth were altered in pdf2 mutants according to Pi availability. Cycloheximide chase experiments further revealed a role for START in maintaining protein levels, and Pi limitation resulted in enhanced protein destabilization, suggesting a mechanism by which lipid binding controls TF activity. We propose that the START domain serves as a molecular sensor for membrane phospholipid status in the epidermis. Overall our data provide insights towards understanding how the lipid metabolome integrates Pi availability with gene expression.

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Human COQ10A and COQ10B are distinct lipid-binding START domain proteins required for coenzyme Q function

The Journal of Lipid Research ◽

10.1194/jlr.m093534 ◽

2019 ◽

Vol 60 (7) ◽

pp. 1293-1310 ◽

Cited By ~ 11

Author(s):

Hui S. Tsui ◽

Nguyen V. B. Pham ◽

Brendan R. Amer ◽

Michelle C. Bradley ◽

Jason E. Gosschalk ◽

...

Keyword(s):

Coenzyme Q ◽

Lipid Binding ◽

Start Domain ◽

Q Function

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Identification of lipids and lipid-binding proteins in phloem exudates from Arabidopsis thaliana

Journal of Experimental Botany ◽

10.1093/jxb/ers028 ◽

2012 ◽

Vol 63 (10) ◽

pp. 3603-3616 ◽

Cited By ~ 59

Author(s):

Brandon S. Guelette ◽

Urs F. Benning ◽

Susanne Hoffmann-Benning

Keyword(s):

Arabidopsis Thaliana ◽

Binding Proteins ◽

Lipid Binding ◽

Lipid Binding Proteins

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Ceramides mediate positional signals in Arabidopsis thaliana protoderm differentiation

Development ◽

10.1242/dev.194969 ◽

2021 ◽

Vol 148 (2) ◽

pp. dev194969

Author(s):

Kenji Nagata ◽

Toshiki Ishikawa ◽

Maki Kawai-Yamada ◽

Taku Takahashi ◽

Mitsutomo Abe

Keyword(s):

Arabidopsis Thaliana ◽

Cell Fate ◽

Cell Types ◽

Specific Protein ◽

Lipid Binding ◽

Lateral Root Development ◽

The People ◽

Distinct Cell ◽

Cell Type Specific ◽

Multicellular Organisms

ABSTRACTThe differentiation of distinct cell types in appropriate patterns is a fundamental process in the development of multicellular organisms. In Arabidopsis thaliana, protoderm/epidermis differentiates as a single cell layer at the outermost position. However, little is known about the molecular nature of the positional signals that achieve correct epidermal cell differentiation. Here, we propose that very-long-chain fatty acid-containing ceramides (VLCFA-Cers) mediate positional signals by stimulating the function of ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1), a master regulator of protoderm/epidermis differentiation, during lateral root development. We show that VLCFA-Cers, which are synthesized predominantly in the outermost cells, bind to the lipid-binding domain of ATML1. Importantly, this cell type-specific protein-lipid association alters the activity of ATML1 protein and consequently restricts its expression to the protoderm/epidermis through a transcriptional feedback loop. Furthermore, establishment of a compartment, enriched with VLCFA-containing sphingolipids, at the outer lateral membrane facing the external environment may function as a determinant of protodermal cell fate. Taken together, our results indicate that VLCFA-Cers play a pivotal role in directing protoderm/epidermis differentiation by mediating positional signals to ATML1.This article has an associated ‘The people behind the papers’ interview.

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