The first plant acyl-CoA-binding protein structures: the close homologues OsACBP1 and OsACBP2 from rice

The apo-acyl coenzyme A binding protein of Leishmania major forms a unique 'AXXA' motif mediated dimer

Acyl-Coenzyme A binding domain containing proteins (ACBDs) are ubiquitous in nearly all eukaryotes. They can exist as a free protein, or a domain of a large, multidomain, multifunctional protein. Besides modularity, ACBDs also display multiplicity. The same organism may have multiple ACBDs, differing in sequence and organization. By virtue of this diversity, ACBDs perform functions ranging from transport, synthesis, trafficking, signal transduction, transcription, and gene regulation. In plants and some microorganisms, these ACBDs are designated ACBPs (acyl-CoA binding proteins). The simplest ACBD/ACBP is a small, ∼10 kDa, soluble protein, comprising the acyl-CoA binding (ACB) domain. Most of these small ACBDs exist as monomers, while a few show a tendency to oligomerize. In sync with those studies, we report the crystal structure of two ACBDs from Leishmania major, named ACBP103, and ACBP96 based on the number of residues present. Interestingly, ACBP103 crystallized as a monomer and a dimer under different crystallization conditions. Careful examination of the dimer disclosed an exposed 'AXXA' motif in the helix I of the two ACBP103 monomers, aligned in a head-to-tail arrangement in the dimer. Glutaraldehyde cross-linking studies confirm that apo-ACBP103 can self-associate in solution. Isothermal titration calorimetry studies further show that ACBP103 can bind ligands ranging from C8 - to C20-CoA, and the data could be best fit to a 'two sets of sites'/sequential binding site model. Taken together, our studies show that Leishmania major ACBP103 can self-associate in the apo-form through a unique dimerization motif, an interaction that may play an important role in its function.

Interaction of Soybean (Glycine max (L.) Merr.) Class II ACBPs with MPK2 and SAPK2 Kinases: New Insights into the Regulatory Mechanisms of Plant ACBPs

Plant acyl-CoA-binding proteins (ACBPs) function in plant development and stress responses, with some ACBPs interacting with protein partners. This study tested the interaction between two Class II GmACBPs (Glycine max ACBPs) and seven kinases, using yeast two-hybrid (Y2H) assays and bimolecular fluorescence complementation (BiFC). The results revealed that both GmACBP3.1 and GmACBP4.1 interact with two soybean kinases, a mitogen-activated protein kinase MPK2, and a serine/threonine-protein kinase SAPK2, highlighting the significance of the ankyrin-repeat (ANK) domain in facilitating protein-protein interactions. Moreover, an in vitro kinase assay and subsequent Phos-tag SDS-PAGE determined that GmMPK2 and GmSAPK2 possess the ability to phosphorylate Class II GmACBPs. Additionally, the kinase-specific phosphosites for Class II GmACBPs were predicted using databases. The HDOCK server was also utilized to predict the binding models of Class II GmACBPs with these two kinases, and the results indicated that the affected residues were located in the ANK region of Class II GmACBPs in both docking models, aligning with the findings of the Y2H and BiFC experiments. This is the first report describing the interaction between Class II GmACBPs and kinases, suggesting that Class II GmACBPs have potential as phospho-proteins that impact signaling pathways.

Mapping of a QTL associated with sucrose content in peanut kernels using BSA-seq

As an important factor affecting the edible quality of peanut kernels, sucrose content is a complex quantitative trait regulated by multiple factors. In this study, an F₂ segregating population and a recombinant inbred line (RIL) population, derived from a cross between the high sucrose content variety Jihuatian 1 and the low sucrose content line PI478819, were used as materials to map a quantitative trait locus (QTL) associated with sucrose content in peanut kernels. Four QTLs were initially located on chromosomes A03 and A06 based on BSA-seq technology, and multiple kompetitive allele-specific PCR markers were developed based on single-nucleotide polymorphisms (SNPs) in the intervals. The markers were genotyped in the RIL population and finely mapped to a stable QTL, qSUCA06, located on chromosome A06 within a 0.29-Mb physical genomic interval (112367085-112662675 bp), which accounted for 31.95%-41.05% of the phenotypic variance explained. SNP and insertion/deletion annotations were performed on genes in the candidate interval, and having screened out those genes with mutations in exons, candidate genes were verified by qRT-PCR. The results revealed that Arahy.Y2LWD9 may be the main gene regulating sucrose content. The QTL identified in this study will not only contribute to marker-assisted breeding for improvement of peanut sucrose content but also paves the way for identifying gene function.

Features and Possible Applications of Plant Lipid-Binding and Transfer Proteins

In plants, lipid trafficking within and inside the cell is carried out by lipid-binding and transfer proteins. Ligands for these proteins are building and signaling lipid molecules, secondary metabolites with different biological activities due to which they perform diverse functions in plants. Many different classes of such lipid-binding and transfer proteins have been found, but the most common and represented in plants are lipid transfer proteins (LTPs), pathogenesis-related class 10 (PR-10) proteins, acyl-CoA-binding proteins (ACBPs), and puroindolines (PINs). A low degree of amino acid sequence homology but similar spatial structures containing an internal hydrophobic cavity are common features of these classes of proteins. In this review, we summarize the latest known data on the features of these protein classes with particular focus on their ability to bind and transfer lipid ligands. We analyzed the structural features of these proteins, the diversity of their possible ligands, the key amino acids participating in ligand binding, the currently known mechanisms of ligand binding and transferring, as well as prospects for possible application.

Roles of acyl-CoA-binding proteins in plant reproduction

Acyl-CoA-binding proteins (ACBPs) constitute a well-conserved family of proteins in eukaryotes that are important in stress responses and development. Past studies have shown that ACBPs are involved in maintaining, transporting and protecting acyl-CoA esters during lipid biosynthesis in plants, mammals, and yeast. ACBPs show differential expression and various binding affinities for acyl-CoA esters. Hence, ACBPs can play a crucial part in maintaining lipid homeostasis. This review summarizes the functions of ACBPs during the stages of reproduction in plants and other organisms. A comprehensive understanding on the roles of ACBPs during plant reproduction may lead to opportunities in crop improvement in agriculture.

Oxylipin signaling in salt-stressed soybean is modulated by ligand-dependent interaction of Class II acyl-CoA-binding proteins with lipoxygenase

Plant lipoxygenases (LOXs) oxygenate linoleic and linolenic acids, creating hydroperoxy derivatives, and from these, jasmonates and other oxylipins are derived. Despite the importance of oxylipin signaling, its activation mechanism remains largely unknown. Here, we show that soybean ACYL-COA-BINDING PROTEIN3 (ACBP3) and ACBP4, two Class II acyl-CoA-binding proteins, suppressed activity of the vegetative LOX homolog VLXB by sequestering it at the endoplasmic reticulum. The ACBP4-VLXB interaction was facilitated by linoleoyl-CoA and linolenoyl-CoA, which competed with phosphatidic acid (PA) for ACBP4 binding. In salt-stressed roots, alternative splicing produced ACBP variants incapable of VLXB interaction. Overexpression of the variants enhanced LOX activity and salt tolerance in Arabidopsis and soybean hairy roots, whereas overexpressors of the native forms exhibited reciprocal phenotypes. Consistently, the differential alternative splicing pattern in two soybean genotypes coincided with their difference in salt-induced lipid peroxidation. Salt-treated soybean roots were enriched in C32:0-PA species that showed high affinity to Class II ACBPs. We conclude that PA signaling and alternative splicing suppress ligand-dependent interaction of Class II ACBPs with VLXB, thereby triggering lipid peroxidation during salt stress. Hence, our findings unveil a dual mechanism that initiates the onset of oxylipin signaling in the salinity response.

Investigations of Lipid Binding to Acyl-CoA-Binding Proteins (ACBP) Using Isothermal Titration Calorimetry (ITC)

Isothermal titration calorimetry (ITC) is a quantitative, biophysical method to investigate intermolecular binding between biomolecules by directly measuring the heat exchange in the binding reaction. The assay is carried out in solution when the molecules interact in vitro. This allows to determine values for binding affinity (K_d), binding stoichiometry (n), as well as changes in Gibbs free energy (ΔG), entropy (ΔS), and enthalpy (ΔH). This method also addresses the kinetics of enzymatic reactions for a substrate during conversion to a product. ITC has been used to study the interactions between proteins and ligands such as those of acyl-CoA-binding proteins (ACBPs) and acyl-CoA thioesters or ACBPs with protein partners. ITC has also been used in investigating interactions between antiserum and antigen, as well as those involving RNA and DNA and other macromolecules. We describe the methods used to isolate and purify a recombinant rice ACBP (OsACBP) for ITC. To study OsACBP binding to long-chain acyl-CoA thioesters, a microcalorimeter was used at 30 °C, and the ligand (acyl-CoA thioesters or a protein partner in the first cell), was mixed with the ACBP protein solution in a second cell, for more than 40 min comprising 20 injections. Subsequently, the binding parameters including the heat-release data were analyzed and various thermodynamic parameters were calculated.

In silico Analysis of Acyl-CoA-Binding Protein Expression in Soybean

Plant acyl-CoA-binding proteins (ACBPs) form a highly conserved protein family that binds to acyl-CoA esters as well as other lipid and protein interactors to function in developmental and stress responses. This protein family had been extensively studied in non-leguminous species such as Arabidopsis thaliana (thale cress), Oryza sativa (rice), and Brassica napus (oilseed rape). However, the characterization of soybean (Glycine max) ACBPs, designated GmACBPs, has remained unreported although this legume is a globally important crop cultivated for its high oil and protein content, and plays a significant role in the food and chemical industries. In this study, 11 members of the GmACBP family from four classes, comprising Class I (small), Class II (ankyrin repeats), Class III (large), and Class IV (kelch motif), were identified. For each class, more than one copy occurred and their domain architecture including the acyl-CoA-binding domain was compared with Arabidopsis and rice. The expression profile, tertiary structure and subcellular localization of each GmACBP were predicted, and the similarities and differences between GmACBPs and other plant ACBPs were deduced. A potential role for some Class III GmACBPs in nodulation, not previously encountered in non-leguminous ACBPs, has emerged. Interestingly, the sole member of Class III ACBP in each of non-leguminous Arabidopsis and rice had been previously identified in plant-pathogen interactions. As plant ACBPs are known to play important roles in development and responses to abiotic and biotic stresses, the in silico expression profiles on GmACBPs, gathered from data mining of RNA-sequencing and microarray analyses, will lay the foundation for future studies in their applications in biotechnology.

RICE ACYL-COA-BINDING PROTEIN6 Affects Acyl-CoA Homeostasis and Growth in Rice

BACKGROUNDS

Acyl-coenzyme A (CoA) esters are important intermediates in lipid metabolism with regulatory properties. Acyl-CoA-binding proteins bind and transport acyl-CoAs to fulfill these functions. RICE ACYL-COA-BINDING PROTEIN6 (OsACBP6) is currently the only one peroxisome-localized plant ACBP that has been proposed to be involved in β-oxidation in transgenic Arabidopsis. The role of the peroxisomal ACBP (OsACBP6) in rice (Oryza sativa) was investigated.

RESULTS

Here, we report on the function of OsACBP6 in rice. The osacbp6 mutant showed diminished growth with reduction in root meristem activity and leaf growth. Acyl-CoA profiling and lipidomic analysis revealed an increase in acyl-CoA content and a slight triacylglycerol accumulation caused by the loss of OsACBP6. Comparative transcriptomic analysis discerned the biological processes arising from the loss of OsACBP6. Reduced response to oxidative stress was represented by a decline in gene expression of a group of peroxidases and peroxidase activities. An elevation in hydrogen peroxide was observed in both roots and shoots/leaves of osacbp6. Taken together, loss of OsACBP6 not only resulted in a disruption of the acyl-CoA homeostasis but also peroxidase-dependent reactive oxygen species (ROS) homeostasis. In contrast, osacbp6-complemented transgenic rice displayed similar phenotype to the wild type rice, supporting a role for OsACBP6 in the maintenance of the acyl-CoA pool and ROS homeostasis. Furthermore, quantification of plant hormones supported the findings observed in the transcriptome and an increase in jasmonic acid level occurred in osacbp6.

CONCLUSIONS

In summary, OsACBP6 appears to be required for the efficient utilization of acyl-CoAs. Disruption of OsACBP6 compromises growth and led to provoked defense response, suggesting a correlation of enhanced acyl-CoAs content with defense responses.

Crystal structure of the rice acyl-CoA-binding protein OsACBP2 in complex with C18:3-CoA reveals a novel pattern of binding to acyl-CoA esters

Acyl-CoA-binding proteins (ACBPs) are a family of proteins that bind acyl-CoA esters at a conserved acyl-CoA-binding domain. ACBPs maintain intracellular acyl-CoA pools to regulate lipid metabolism. Here, we report on the structure of rice OsACBP2 in complex with C18:3-CoA ester. The residues Y33, K34 and K56 of OsACBP2 play a crucial role in binding the CoA group, while residues N23, L27, K52 and Y55 in one molecule of OsACBP2 cooperate with L27, L28, A59 and A62 from another anchoring the fatty acyl group. Multiangle light scattering assays indicate that OsACBP2 binds C18:3-CoA as a monomer. The first complex structure of a plant ACBP binding with C18:3-CoA is therefore presented, providing a novel model for the interaction between an acyl-CoA ester and the acyl-CoA-binding domain(s).

The overexpression of OsACBP5 protects transgenic rice against necrotrophic, hemibiotrophic and biotrophic pathogens

The most devastating diseases in rice (Oryza sativa) are sheath blight caused by the fungal necrotroph Rhizoctonia solani, rice blast by hemibiotrophic fungus Magnaporthe oryzae, and leaf blight by bacterial biotroph Xanthomonas oryzae (Xoo). It has been reported that the Class III acyl-CoA-binding proteins (ACBPs) such as those from dicots (Arabidopsis and grapevine) play a role in defence against biotrophic pathogens. Of the six Arabidopsis (Arabidopsis thaliana) ACBPs, AtACBP3 conferred protection in transgenic Arabidopsis against Pseudomonas syringae, but not the necrotrophic fungus, Botrytis cinerea. Similar to Arabidopsis, rice possesses six ACBPs, designated OsACBPs. The aims of this study were to test whether OsACBP5, the homologue of AtACBP3, can confer resistance against representative necrotrophic, hemibiotrophic and biotrophic phytopathogens and to understand the mechanisms in protection. Herein, when OsACBP5 was overexpressed in rice, the OsACBP5-overexpressing (OsACBP5-OE) lines exhibited enhanced disease resistance against representative necrotrophic (R. solani & Cercospora oryzae), hemibiotrophic (M. oryzae & Fusarium graminearum) and biotrophic (Xoo) phytopathogens. Progeny from a cross between OsACBP5-OE9 and the jasmonate (JA)-signalling deficient mutant were more susceptible than the wild type to infection by the necrotroph R. solani. In contrast, progeny from a cross between OsACBP5-OE9 and the salicylic acid (SA)-signalling deficient mutant was more susceptible to infection by the hemibiotroph M. oryzae and biotroph Xoo. Hence, enhanced resistance of OsACBP5-OEs against representative necrotrophs appears to be JA-dependent whilst that to (hemi)biotrophs is SA-mediated.

Advances in Understanding the Acyl-CoA-Binding Protein in Plants, Mammals, Yeast, and Filamentous Fungi

Acyl-CoA-binding protein (ACBP) is an important protein with a size of about 10 kDa. It has a high binding affinity for C12-C22 acyl-CoA esters and participates in lipid metabolism. ACBP and its family of proteins have been found in all eukaryotes and some prokaryotes. Studies have described the function and structure of ACBP family proteins in mammals (such as humans and mice), plants (such as Oryza sativa, Arabidopsis thaliana, and Hevea brasiliensis) and yeast. However, little information on the structure and function of the proteins in filamentous fungi has been reported. This article concentrates on recent advances in the research of the ACBP family proteins in plants and mammals, especially in yeast, filamentous fungi (such as Monascus ruber and Aspergillus oryzae), and fungal pathogens (Aspergillus flavus, Cryptococcus neoformans). Furthermore, we discuss some problems in the field, summarize the binding characteristics of the ACBP family proteins in filamentous fungi and yeast, and consider the future of ACBP development.

The overexpression of rice ACYL-CoA-BINDING PROTEIN2 increases grain size and bran oil content in transgenic rice

As Oryza sativa (rice) seeds represent food for over three billion people worldwide, the identification of genes that enhance grain size and composition is much desired. Past reports have indicated that Arabidopsis thaliana acyl-CoA-binding proteins (ACBPs) are important in seed development but did not affect seed size. Herein, rice OsACBP2 was demonstrated not only to play a role in seed development and germination, but also to influence grain size. OsACBP2 mRNA accumulated in embryos and endosperm of germinating seeds in qRT-PCR analysis, while β-glucuronidase (GUS) assays on OsACBP2pro::GUS rice transformants showed GUS expression in embryos, as well as the scutellum and aleurone layer of germinating seeds. Deletion analysis of the OsACBP2 5'-flanking region revealed five copies of the seed cis-element, Skn-I-like motif (-1486/-1482, -956/-952, -939/-935, -826/-822, and -766/-762), and the removal of any adversely affected expression in seeds, thereby providing a molecular basis for OsACBP2 expression in seeds. When OsACBP2 function was investigated using osacbp2 mutants and transgenic rice overexpressing OsACBP2 (OsACBP2-OE), osacbp2 was retarded in germination, while OsACBP2-OEs performed better than the wild-type and vector-transformed controls, in germination, seedling growth, grain size and grain weight. Transmission electron microscopy of OsACBP2-OE mature seeds revealed an accumulation of oil bodies in the scutellum cells, while confocal laser scanning microscopy indicated oil accumulation in OsACBP2-OE aleurone tissues. Correspondingly, OsACBP2-OE seeds showed gain in triacylglycerols and long-chain fatty acids over the vector-transformed control. As dietary rice bran contains beneficial bioactive components, OsACBP2 appears to be a promising candidate for enriching seed nutritional value.

Arabidopsis acyl-CoA-binding proteins regulate the synthesis of lipid signals

Plant lipid signals are crucial developmental modulators and stress response mediators. A family of acyl-CoA-binding proteins (ACBPs) participates in the lipid trafficking of these signals. Isoform-specific functions can arise from differences in their subcellular distribution, tissue-specificity, stress-responsiveness, and ligand selectivity. In lipid-mediated cell signaling, plant ACBPs are not merely transporters but are also important regulators via their interaction with lipid-metabolic enzymes and precursor lipids. In this Insight, the regulatory roles of plant ACBPs in the synthesis of various signaling lipids, including phosphatidic acid, sterols, oxylipins, and sphingolipids, are reviewed. We focus on the functional significance of these lipid signals in plant development and stress responses with an overview of recent work using reverse genetics and transgenic Arabidopsis.

Cellular Organization and Regulation of Plant Glycerolipid Metabolism

Great strides have been made in understanding how membranes and lipid droplets are formed and maintained in land plants, yet much more is to be learned given the complexity of plant lipid metabolism. A complicating factor is the multi-organellar presence of biosynthetic enzymes and unique compositional requirements of different membrane systems. This necessitates a rich network of transporters and transport mechanisms that supply fatty acids, membrane lipids and storage lipids to their final cellular destination. Though we know a large number of the biosynthetic enzymes involved in lipid biosynthesis and a few transport proteins, the regulatory mechanisms, in particular, coordinating expression and/or activity of the majority remain yet to be described. Plants undergoing stress alter their membranes' compositions, and lipids such as phosphatidic acid have been implicated in stress signaling. Additionally, lipid metabolism in chloroplasts supplies precursors for jasmonic acid (JA) biosynthesis, and perturbations in lipid homeostasis has consequences on JA signaling. In this review, several aspects of plant lipid metabolism are discussed that are currently under investigation: cellular transport of lipids, regulation of lipid biosynthesis, roles of lipids in stress signaling, and lastly the structural and oligomeric states of lipid enzymes.

A structural perspective of plant antimicrobial peptides

Among the numerous strategies plants have developed to fend off enemy attack, antimicrobial peptides (AMPs) stand out as one of the most prominent defensive barriers that grant direct and durable resistance against a wide range of pests and pathogens. These small proteins are characterized by a compact structure and an overall positive charge. AMPs have an ancient origin and widespread occurrence in the plant kingdom but show an unusually high degree of variation in their amino acid sequences. Interestingly, there is a strikingly conserved topology among the plant AMP families, suggesting that the defensive properties of these peptides are not determined by their primary sequences but rather by their tridimensional structure. To explore and expand this idea, we here discuss the role of AMPs for plant defense from a structural perspective. We show how specific structural properties, such as length, charge, hydrophobicity, polar angle and conformation, are essential for plant AMPs to act as a chemical shield that hinders enemy attack. Knowledge on the topology of these peptides is facilitating the isolation, classification and even structural redesign of AMPs, thus allowing scientists to develop new peptides with multiple agronomical and pharmacological potential.

Functional and Structural Diversity of Acyl-coA Binding Proteins in Oil Crops

Diversities in structure and function of ACBP were discussed in this review. ACBP are important proteins that could transport newly synthesized fatty acid, activated into -coA, from plastid to endoplasmic reticulum, where oil in the form of triacylglycerol occurs. ACBP were detected in various animal and plants species, which indicated their importance in biological function. In fact, involvement of ACBP in important process such as lipid metabolism, regulation of enzyme and gene expression, and in response to plant stresses has been proven in several studies. In this review, findings on ACBP of 11 well-known oil crops were reviewed to comprehend diversity, comparative analyses on ACBP structure were made, and link between structure and function, tissue expression and subcellular location of ACBP were also observed. Incomplete reports in some species were mentioned, which might be encouraging to start or to perform deeper studies. Similar characteristics were found in paralogs ACBP, and orthologs ACBP had different functions, despite the high identity in amino acid sequence. At the end, it is confirmed that ortholog proteins could not necessarily display the same function, even from closely related species.