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

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.

scholarly journals Comparative genomics of StAR-related lipid transfer (START) domains across wild and cultivated rice

2020 ◽  
Author(s):  
Sanjeet Kumar Mahtha ◽  
Ravi Kiran Purama ◽  
Gitanjali Yadav
Keyword(s):  
Developmental Stages ◽  
Purifying Selection ◽  
Lipid Binding ◽  
Chromosomal Mapping ◽  
Limited Information ◽  
Lipid Transfer ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Preferential Expression ◽  
Conserved Genes

AbstractSTART proteins, encoded by a plant amplified family of evolutionary conserved genes, are known to bind lipids/sterols in mammals. In the plant kingdom, they have been reported in proteins involved in lipid binding, transport, signaling, as well as modulation of transcriptional activity, but there is very limited information on sub-functionalization or evolution of new function within the amplified gene family. Availability of ten fully annotated wild and cultivated rice varieties enables a comprehensive analysis of this family across the rice pangenome, across functional categories, as well as across START sub-families. The presence of START domains in all seven wild and three cultivated rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication analysis and conservation of domain structure. Analysis of synteny highlights a preponderance of segmental and dispersed modes of duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization among START genes family members in terms of preferential expression across various developmental stages and anatomical parts, especially flowering related parts. Importance of this family was further supported by Ka/Ks ratios confirming strong negative/purifying selection, implying that START family duplication is strongly constrained and evolutionarily stable.

scholarly journals Arabidopsis PROTODERMAL FACTOR2 binds lysophosphatidylcholines and transcriptionally regulates phospholipid metabolism

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.

scholarly journals The lipid transfer protein Saposin B does not directly bind CD1d for lipid antigen loading

2019 ◽  
Vol 4 ◽  
pp. 117
Author(s):  
Maria Shamin ◽  
Tomasz H. Benedyk ◽  
Stephen C. Graham ◽  
Janet E. Deane
Keyword(s):  
Lipid Transfer Protein ◽  
Direct Interaction ◽  
Lipid Binding ◽  
Lipid Transfer ◽  
Binding Assays ◽  
Lipid Transfer Proteins ◽  
Lipid Antigens ◽  
Saposin B ◽  
Protein Components ◽  
Lipid Loading

Background: Lipid antigens are presented on the surface of cells by the CD1 family of glycoproteins, which have structural and functional similarity to MHC class I molecules. The hydrophobic lipid antigens are embedded in membranes and inaccessible to the lumenal lipid-binding domain of CD1 molecules. Therefore, CD1 molecules require lipid transfer proteins for lipid loading and editing. CD1d is loaded with lipids in late endocytic compartments, and lipid transfer proteins of the saposin family have been shown to play a crucial role in this process. However, the mechanism by which saposins facilitate lipid binding to CD1 molecules is not known and is thought to involve transient interactions between protein components to ensure CD1-lipid complexes can be efficiently trafficked to the plasma membrane for antigen presentation. Of the four saposin proteins, the importance of Saposin B (SapB) for loading of CD1d is the most well-characterised. However, a direct interaction between CD1d and SapB has yet to be described. Methods: In order to determine how SapB might load lipids onto CD1d, we used purified, recombinant CD1d and SapB and carried out a series of highly sensitive binding assays to monitor direct interactions. We performed equilibrium binding analysis, chemical cross-linking and co-crystallisation experiments, under a range of different conditions. Results: We could not demonstrate a direct interaction between SapB and CD1d using any of these binding assays. Conclusions: This work establishes comprehensively that the role of SapB in lipid loading does not involve direct binding to CD1d. We discuss the implication of this for our understanding of lipid loading of CD1d and propose several factors that may influence this process.

scholarly journals The structure and flexibility analysis of the Arabidopsis Synaptotagmin 1 reveal the basis of its regulation at membrane contact sites

2021 ◽  
Author(s):  
Juan Luis Benavente ◽  
Dritan Siliqi ◽  
Lourdes Infantes ◽  
Laura Lagartera ◽  
Alberto Mills ◽  
...  
Keyword(s):  
Cell Function ◽  
Lipid Extraction ◽  
Membrane Lipid ◽  
Lipid Binding ◽  
Lipid Transfer ◽  
C2 Domains ◽  
Membrane Contact Sites ◽  
Contact Sites ◽  
Cellular Environment ◽  
Synaptotagmin 1

Cell function requires the maintenance of membrane lipid homeostasis as changes in cellular environment unbalance this equilibrium. The non-vesicular lipid transfer at endoplasmic reticulum (ER) and plasma membrane (PM) contact sites (CS) is central to restore it. Extended synaptotagmins (E-Syts) are ER proteins that play a central role in this process as they act as molecular tethers with PM and as lipid transfer proteins between these organelles. E-Syts are constitutively anchored to the ER through an N-terminal hydrophobic segment and bind to the PM via C-terminal C2 domains. In plants, synaptotagmins (SYTs) are orthologous of E-Syts and regulate the ER-PM communication by the activity of their two C2 domains in response to abiotic stresses. We have combined macromolecular crystallography, small-angle X-ray scattering, structural bioinformatics and biochemical data to analyze the regulation of plant synaptotagmin 1 (SYT1). Our data show that the binding of SYT1 to the PM is regulated by the interaction of the first C2 domain through a Ca2+-dependent lipid binding site and by a site for phosphorylated forms of phosphatidylinositol in such a way that two different molecular signals are integrated in response to stress. In addition, our data show that SYT1 is highly flexible by virtue of up to three hinge points, including one that connects the two C2 domains. This feature provides conformational freedom to SYT1 to define a large and complementary interaction surface with the PM. This structural plasticity, in turn, may facilitate lipid extraction, protein loading and subsequent transfer between PM and ER.

scholarly journals Redox proteomics of stomatal immunity reveals role of a lipid transfer protein in plant defense

2020 ◽  
Author(s):  
Kelly M Balmant ◽  
Sheldon R Lawrence ◽  
Benjamin V Duong ◽  
Fanzhao Zhu ◽  
Ning Zhu ◽  
...  
Keyword(s):  
Plant Defense ◽  
Lipid Transfer Protein ◽  
Guard Cells ◽  
Lipid Binding ◽  
Lipid Transfer ◽  
Redox Proteomics ◽  
Transfer Protein ◽  
Redox Responsive ◽  
Redox Sensors ◽  
Thiol Redox

ABSTRACTRedox-based post-translational modifications (PTMs) involving protein cysteine residues as redox sensors are important to various physiological processes. However, little is known about redox-sensitive proteins in guard cells and their functions in stomatal immunity. In this study, we applied an integrative protein labeling method cysTMTRAQ and identified guard cell proteins that were altered by thiol redox PTMs in response to a bacterial flagellin peptide flg22. In total, eight, seven and 20 potential redox-responsive proteins were identified in guard cells treated with flg22 for 15, 30 and 60 min, respectively. The proteins fall into several functional groups including photosynthesis, lipid binding, oxidation-reduction, and defense. Among the proteins, a lipid transfer protein (LTP)-II was confirmed to be redox-responsive and involved in plant resistance to Pseudomonas syringe pv. tomato DC3000. This study not only creates an inventory of potential redox-sensitive proteins in flg22 signal transduction in guard cells, but also highlights the relevance of the lipid transfer protein in plant defense against the bacterial pathogens.Sentence summaryThiol-redox proteomics identified potential redox sensors important in stomatal immunity, and a lipid transfer protein was characterized to function as a redox sensor in plant immune response.

scholarly journals Structural characterization and in vitro lipid binding studies of non-specific lipid transfer protein 1 (nsLTP1) from fennel (Foeniculum vulgare) seeds

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mekdes Megeressa ◽  
Bushra Siraj ◽  
Shamshad Zarina ◽  
Aftab Ahmed
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
3D Structure ◽  
Lipid Binding ◽  
Lipid Transfer ◽  
Binding Studies ◽  
Foeniculum Vulgare ◽  
Complete Amino Acid Sequence ◽  
Specific Lipid

AbstractNon-specific lipid transfer proteins (nsLTPs) are cationic proteins involved in intracellular lipid shuttling in growth and reproduction, as well as in defense against pathogenic microbes. Even though the primary and spatial structures of some nsLTPs from different plants indicate their similar features, they exhibit distinct lipid-binding specificities signifying their various biological roles that dictate further structural study. The present study determined the complete amino acid sequence, in silico 3D structure modeling, and the antiproliferative activity of nsLTP1 from fennel (Foeniculum vulgare) seeds. Fennel is a member of the family Umbelliferae (Apiaceae) native to southern Europe and the Mediterranean region. It is used as a spice medicine and fresh vegetable. Fennel nsLTP1 was purified using the combination of gel filtration and reverse-phase high-performance liquid chromatography (RP-HPLC). Its homogeneity was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. The purified nsLTP1 was treated with 4-vinyl pyridine, and the modified protein was then digested with trypsin. The complete amino acid sequence of nsLTP1 established by intact protein sequence up to 28 residues, overlapping tryptic peptides, and cyanogen bromide (CNBr) peptides. Hence, it is confirmed that fennel nsLTP1 is a 9433 Da single polypeptide chain consisting of 91 amino acids with eight conserved cysteines. Moreover, the 3D structure is predicted to have four α-helices interlinked by three loops and a long C-terminal tail. The lipid-binding property of fennel nsLTP1 is examined in vitro using fluorescent 2-p-toluidinonaphthalene-6-sulfonate (TNS) and validated using a molecular docking study with AutoDock Vina. Both of the binding studies confirmed the order of binding efficiency among the four studied fatty acids linoleic acid > linolenic acid > Stearic acid > Palmitic acid. A preliminary screening of fennel nsLTP1 suppressed the growth of MCF-7 human breast cancer cells in a dose-dependent manner with an IC50 value of 6.98 µM after 48 h treatment.

scholarly journals Identifying Cancer-Relevant Mutations in the DLC START Domain Using Evolutionary and Structure-Function Analyses

2020 ◽  
Vol 21 (21) ◽  
pp. 8175
Author(s):  
Ashton S. Holub ◽  
Renee A. Bouley ◽  
Ruben C. Petreaca ◽  
Aman Y. Husbands
Keyword(s):  
Structure Function ◽  
Rho Gtpases ◽  
Rho Gtpase ◽  
Structural Level ◽  
Lipid Transfer ◽  
Gtp Hydrolysis ◽  
Conserved Residues ◽  
Wide Range ◽  
Bona Fide ◽  
Start Domain

Rho GTPase signaling promotes proliferation, invasion, and metastasis in a broad spectrum of cancers. Rho GTPase activity is regulated by the deleted in liver cancer (DLC) family of bona fide tumor suppressors which directly inactivate Rho GTPases by stimulating GTP hydrolysis. In addition to a RhoGAP domain, DLC proteins contain a StAR-related lipid transfer (START) domain. START domains in other organisms bind hydrophobic small molecules and can regulate interacting partners or co-occurring domains through a variety of mechanisms. In the case of DLC proteins, their START domain appears to contribute to tumor suppressive activity. However, the nature of this START-directed mechanism, as well as the identities of relevant functional residues, remain virtually unknown. Using the Catalogue of Somatic Mutations in Cancer (COSMIC) dataset and evolutionary and structure-function analyses, we identify several conserved residues likely to be required for START-directed regulation of DLC-1 and DLC-2 tumor-suppressive capabilities. This pan-cancer analysis shows that conserved residues of both START domains are highly overrepresented in cancer cells from a wide range tissues. Interestingly, in DLC-1 and DLC-2, three of these residues form multiple interactions at the tertiary structural level. Furthermore, mutation of any of these residues is predicted to disrupt interactions and thus destabilize the START domain. As such, these mutations would not have emerged from traditional hotspot scans of COSMIC. We propose that evolutionary and structure-function analyses are an underutilized strategy which could be used to unmask cancer-relevant mutations within COSMIC. Our data also suggest DLC-1 and DLC-2 as high-priority candidates for development of novel therapeutics that target their START domain.

scholarly journals Lipid binding in rice nonspecific lipid transfer protein-1 complexes fromOryza sativa

2004 ◽  
Vol 13 (9) ◽  
pp. 2304-2315 ◽  
Author(s):  
Hui-Chun Cheng ◽  
Pei-Tsung Cheng ◽  
Peiyu Peng ◽  
Ping-Chiang Lyu ◽  
Yuh-Ju Sun
Keyword(s):  
Lipid Transfer Protein ◽  
Lipid Binding ◽  
Lipid Transfer ◽  
Transfer Protein ◽  
Nonspecific Lipid Transfer Protein
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