DUF538 protein super family is predicted to be the potential homologue of bactericidal/permeability-increasing protein in plant system

Genome-wide association mapping combined with gene-based haplotype analysis identify a novel gene for shoot length in rice (Oryza sativa L.)

KEY MESSAGE

Genome-wide association mapping revealed a novel QTL for shoot length across multiple environments. Its causal gene, LOC_Os01g68500, was identified firstly through gene-based haplotype analysis, gene expression and knockout transgenic verification. Strong seedling vigor is an important breeding target for rice varieties used in direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor characterized by rapid growth of seedling, which enhance seedling emergence. Therefore, mining genes for SL and conducting molecular breeding help to develop varieties for direct seeding. However, few QTLs for SL have been fine mapped or cloned so far. In this study, a genome-wide association study of SL was performed in a diverse rice collection consisting of 391 accessions in two years, using phenotypes generated by different cultivation methods according to the production practice, and a total of twenty-four QTLs for SL were identified. Among them, the novel QTL qSL-1f on chromosome 1 could be stably detected across all three cultivation methods in the whole population and indica subpopulation. Through gene-based haplotype analysis of the annotated genes within the putative region of qSL-1f, and validated by gene expression and knockout transgenic experiments, LOC_Os01g68500 (i.e., Os01g0913100 in RAP-DB) was identified as the causal gene for SL, which has a single-base variation (C-to-A transversion) in its CDS region, resulting in the significant difference in SL of rice. LOC_Os01g68500 encodes a DUF538 (Domain of unknown function) containing protein, and the function of DUF538 protein gene on rice seedling growth is firstly reported in this study. These results provide a new clue for exploring the molecular mechanism regulating SL, and promising gene source for the molecular breeding in rice.

Antagonistic Regulation of ABA Responses by Duplicated Tandemly Repeated DUF538 Protein Genes in Arabidopsis

The plant hormone ABA (abscisic acid) regulates plant responses to abiotic stresses by regulating the expression of ABA response genes. However, the functions of a large portion of ABA response genes have remained unclear. We report in this study the identification of ASDs (ABA-inducible signal peptide-containing DUF538 proteins), a subgroup of DUF538 proteins with a signal peptide, as the regulators of plant responses to ABA in Arabidopsis. ASDs are encoded by four closely related DUF538 genes, with ASD1/ASD2 and ASD3/ASD4 being two pairs of duplicated tandemly repeated genes. The quantitative RT-PCR (qRT-PCR) results showed that the expression levels of ASDs increased significantly in response to ABA as well as NaCl and mannitol treatments, with the exception that the expression level of ASD2 remained largely unchanged in response to NaCl treatment. The results of Arabidopsis protoplast transient transfection assays showed that ASDs were localized on the plasma membrane and in the cytosol and nucleus. When recruited to the promoter of the reporter gene via a fused GD domain, ASDs were able to slightly repress the expression of the co-transfected reporter gene. Seed germination and cotyledon greening assays showed that ABA sensitivity was increased in the transgenic plants that were over-expressing ASD1 or ASD3 but decreased in the transgenic plants that were over-expressing ASD2 or ASD4. On the other hand, ABA sensitivity was increased in the CRISPR/Cas9 gene-edited asd2 single mutants but decreased in the asd3 single mutants. A transcriptome analysis showed that differentially expressed genes in the 35S:ASD2 transgenic plant seedlings were enriched in several different processes, including in plant growth and development, the secondary metabolism, and plant hormone signaling. In summary, our results show that ASDs are ABA response genes and that ASDs are involved in the regulation of plant responses to ABA in Arabidopsis; however, ASD1/ASD3 and ASD2/ASD4 have opposite functions.

Unraveling the Diverse Roles of Neglected Genes Containing Domains of Unknown Function (DUFs): Progress and Perspective

Domain of unknown function (DUF) is a general term for many uncharacterized domains with two distinct features: relatively conservative amino acid sequence and unknown function of the domain. In the Pfam 35.0 database, 4795 (24%) gene families belong to the DUF type, yet, their functions remain to be explored. This review summarizes the characteristics of the DUF protein families and their functions in regulating plant growth and development, generating responses to biotic and abiotic stress, and other regulatory roles in plant life. Though very limited information is available about these proteins yet, by taking advantage of emerging omics and bioinformatic tools, functional studies of DUF proteins could be utilized in future molecular studies.

Leaf physiology variations are modulated by natural variations that underlie stomatal morphology in Populus

Stomata are essential for photosynthesis and abiotic stress tolerance. Here, we used multiomics approaches to dissect the genetic architecture and adaptive mechanisms that underlie stomatal morphology in Populus tomentosa juvenile natural population (303 accessions). We detected 46 candidate genes and 15 epistatic gene-pairs, associated with 5 stomatal morphologies and 18 leaf development and photosynthesis traits, through genome-wide association studies. Expression quantitative trait locus mapping revealed that stomata-associated gene loci were significantly associated with the expression of leaf-related genes; selective sweep analysis uncovered significant differentiation in the allele frequencies of genes that underlie stomatal variations. An allelic regulatory network operating under drought stress and adequate precipitation conditions, with three key regulators (DUF538, TRA2 and AbFH2) and eight interacting genes, was identified that might regulate leaf physiology via modulation of stomatal shape and density. Validation of candidate gene variations in drought-tolerant and F₁ hybrid populations of P. tomentosa showed that the DUF538, TRA2 and AbFH2 loci cause functional stabilisation of spatiotemporal regulatory, whose favourable alleles can be faithfully transmitted to offspring. This study provides insights concerning leaf physiology and stress tolerance via the regulation of stomatal determination in perennial plants.

DUF1005 Family Identification, Evolution Analysis in Plants, and Primary Root Elongation Regulation of CiDUF1005 From Caragana intermedia

Proteins with a domain of unknown function (DUF) represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. In particular, members of the DUF1005 family in plants have a 411-amino-acid conserved domain, and this family has not been described previously. In this study, a total of 302 high-confidence DUF1005 family members were identified from 58 plant species, and none were found in the four algae that were selected. Thus, this result showed that DUF1005s might belong to a kind of plant-specific gene family, and this family has not been evolutionarily expanded. Phylogenetic analysis showed that the DUF1005 family genes could be classified into four subgroups in 58 plant species. The earliest group to emerge was Group I, including a total of 100 gene sequences, and this group was present in almost all selected species spanning from mosses to seed plants. Group II and Group III, with 69 and 74 members, respectively, belong to angiosperms. Finally, with 59 members, Group IV was the last batch of genes to emerge, and this group is unique to dicotyledons. Expression pattern analysis of the CiDUF1005, a member of the DUF1005 family from Caragana intermedia, showed that CiDUF1005 genes were differentially regulated under various treatments. Compared to the wild type, transgenic lines with heterologous CiDUF1005 expression in Arabidopsis thaliana had longer primary roots and more lateral roots. These results expanded our knowledge of the evolution of the DUF1005 family in plants and will contribute to elucidating biological functions of the DUF1005 family in the future.

A pair of DUF538 domain-containing proteins modulates plant growth and trichome development through the transcriptional regulation of GLABRA1 in Arabidopsis thaliana

SMALLER TRICHOMES WITH VARIABLE BRANCHES (SVB) is an emerging plant growth regulator in trichome development, endoplasmic reticulum stress response, and phosphoinositide signaling, and belongs to the land plant-specific DUF538 domain-containing protein family. Despite its multifaceted roles, the functions of this protein family are poorly understood in plant growth and development. Here, we report that SVB-like (SVBL), the closest homolog of SVB, modulates plant growth and trichome development with SVB in Arabidopsis thaliana. Although none of the single mutants showed an obvious growth defect, the double mutants of svb svbl exhibited dwarfed plant growth. In trichome development, the defects in svb mutant were greatly enhanced by the additional mutation in SVBL, despite the single knockout of SVBL showing the mild defects. The double mutation reduced the transcript level of one of the central hub genes for trichome development, GLABRA1 (GL1), which in turn affects the other downstream genes, GLABRA2 (GL2), TRANSPARENT TESTA GLABRA2 (TTG2), TRIPTYCHON (TRY), CAPRICE (CPC), and ENHANCER OF TRY AND CPC1 (ETC1). In situ translational reporter assays showed that SVB and SVBL share highly similar localization patterns both at tissue and subcellular levels. The present study suggests that SVB and SVBL play a pivotal role in plant growth and trichome development by affecting a specific subset of known trichome developmental regulators, highlighting the importance of the DUF538 protein family in higher plants.

Bioactive peptides derived from plant origin by-products: Biological activities and techno-functional utilizations in food developments - A review

Agro-industrial by-products containing considerable amounts of protein (10-50%) such as soybean meal, rice bran and coconut pulp are promising bioactive peptide sources with annual disposal rate of 800 million tons in the world. More recently, plant by-products rich in protein content have been studied under various prisms that include recovery techniques, peptide production methods, determination of technological benefits and functional properties, and their applications in foods. The researches in bioactive peptides provide evidence over the techno-functional properties and the health benefits are highly dependent upon their amino acid sequences, molecular weights, conformations and surface properties. Research findings compared bioactive properties of the obtained peptides with respect to their amino acid sequences and also reported that hydrophobic/hydrophilic properties have direct effect on both functional and health effects. In addition, the resultant properties of the peptides could be affected by the conducted extraction method (alkaline, enzymatic, ultrasound assisted, microwave assisted, etc.), extraction solvent, precipitation and purification techniques and even by the final drying process (spray, freeze, vacuum, etc.) which may alter molecular weights, conformations and surface properties. Latest studies have investigated solubility, emulsifying, foaming, water/oil holding capacity and surface properties and also antioxidant, antimicrobial, anticarcinogenic, hypocholesterolemic, antihypertensive, immunomodulatory and opioid activities of bioactive peptides obtained from plant by-products. Moreover, the application of the bioactive peptides into different food formulations has been a recent trend of functional food development. These bioactive peptides' bitter taste and toxicity are possible challenges in some cases that need to be resolved before their wider utilization.

Genome-Wide Mining of Wheat DUF966 Gene Family Provides New Insights Into Salt Stress Responses

Domain of unknown function (DUF) proteins constitute a great deal of families of functionally uncharacterized proteins in eukaryotes. The DUF966 gene family is found in monocotyledons, dicotyledons, mosses, and other species. However, little is known about the functions of DUF966 genes in wheat (Triticum aestivum L.). In this study, we identified and characterized the TaDUF966 gene family members in wheat by in silico analysis. A total of 28 TaDUF966 proteins were identified in wheat. Phylogenetic analysis divided these proteins into two groups (Groups I and II). Proteins in each group showed a highly conserved DUF966 domain and conserved motif distribution, implying their functional conservation. Analysis of gene expression profiling data showed that some TaDUF966 genes were induced by salt stress. We further confirmed the role of TaDUF966-9B in salt stress using virus induced gene silencing (VIGS) assay. Compared with the empty vector control, the TaDUF966-9B knockdown plants exhibited severe leaf curling at 10 days post-inoculation with BSMV under salt stress, suggesting that TaDUF966 genes play a vital role in salt stress tolerance in wheat. Taken together, these results expand our knowledge of the evolution of the DUF966 gene family in wheat and promote the potential application of these genes in wheat genetic improvement.

Pectin methylesterase activity of plant DUF538 protein superfamily

DUF538 (domain of unknown function 538) proteins are known as a group of putative hypothetical proteins in a wide range of plant species. They have been identified from some plants challenged with various environmental stresses. However, a little is known about their functional properties. They have been newly predicted to have binding capacity and esterase-type hydrolytic activity towards bacterial lipopolysaccharides and chlorophyll molecules as carboxylic compounds in plants. In the present study, the binding ability and the methylesterase activity of DUF538 proteins towards pectin molecules were also predicted. Their similarities to pectin methylesterases and their binding ability to pectin molecule were predicted using bioinformatic tools as well as the experimental method. A probable cooperation was speculated between DUF538 and pectin methylesterase protein families in cell wall associated defense responses in plants.

Maize glossy6 is involved in cuticular wax deposition and drought tolerance

Cuticular waxes, long-chain hydrocarbon compounds, form the outermost layer of plant surfaces in most terrestrial plants. The presence of cuticular waxes protects plants from water loss and other environmental stresses. Cloning and characterization of genes involved in the regulation, biosynthesis, and extracellular transport of cuticular waxes onto the surface of epidermal cells have revealed the molecular basis of cuticular wax accumulation. However, intracellular trafficking of synthesized waxes to the plasma membrane for cellular secretion is poorly understood. Here, we characterized a maize glossy (gl6) mutant that exhibited decreased epicuticular wax load, increased cuticle permeability, and reduced seedling drought tolerance relative to wild-type. We combined an RNA-sequencing-based mapping approach (BSR-Seq) and chromosome walking to identify the gl6 candidate gene, which was confirmed via the analysis of multiple independent mutant alleles. The gl6 gene represents a novel maize glossy gene containing a conserved, but uncharacterized, DUF538 domain. This study suggests that the GL6 protein may be involved in the intracellular trafficking of cuticular waxes, opening the door to elucidating the poorly understood process by which cuticular wax is transported from its site of biosynthesis to the plasma membrane.

DUF538 protein superfamily is predicted to be chlorophyll hydrolyzing enzymes in plants

The possible hydrolytic activity towards chlorophyll molecules was predicted for DUF538 protein superfamily in plants. It was examined by using computational as well as experimental tools including in vitro chlorophyll degradation, antioxidant compounds production and in vivo real-time gene expression tests. Comparison of the computational data with the experimental results indicated that DUF538 proteins might be chlorophyll hydrolyzing enzyme (most probably carboxyesterase) which degrade chlorophyll molecules (66 % per 12 hrs) to produce new compounds (1.8 fold per 12 hrs) with antioxidant properties. The relevance of DUF538 gene expression level with the chlorophyll contents (2.8 fold increase per chlorophyll content of 50 %) of the drought-stressed leaves showed that chlorophyll degradation by DUF538 is most probably induced in response to stress stimuli. Despite membranous chlorophyll catabolic pathways, DUF538-dependent reactions is predicted to be occurred in the cytosol of the under stressed plants. We addressed as to whether chlorophyll breakdown to antioxidant compounds by DUF538 is a defense mechanism of plants against stress stimuli, in vivo? This question is going to be investigated in our next research project.

Cell wall proteomic of Brachypodium distachyon grains: A focus on cell wall remodeling proteins

Cell walls play key roles during plant development. Following their deposition into the cell wall, polysaccharides are continually remodeled according to the growth stage and stress environment to accommodate cell growth and differentiation. To date, little is known concerning the enzymes involved in cell wall remodeling, especially in gramineous and particularly in the grain during development. Here, we investigated the cell wall proteome of the grain of Brachypodium distachyon. This plant is a suitable model for temperate cereal crops. Among the 601 proteins identified, 299 were predicted to be secreted. These proteins were distributed into eight functional classes; the class of proteins that act on carbohydrates was the most highly represented. Among these proteins, numerous glycoside hydrolases were found. Expansins and peroxidases, which are assumed to be involved in cell wall polysaccharide remodeling, were also identified. Approximately half of the proteins identified in this study were newly discovered in grain and were not identified in the previous proteome analysis conducted using the culms and leaves of B. distachyon. Therefore, the data obtained from all organs of B. distachyon infer a global cell wall proteome consisting of 460 proteins. At present, this is the most extensive cell wall proteome of a monocot species.