Sweet potato SPAP1 is a typical aspartic protease and participates in ethephon-mediated leaf senescence

Genome-wide identification and expression patterns of the aspartic protease gene family in Epimedium pubescens

BACKGROUND

Aspartic proteases (APs), proteolytic enzymes involved in protein maturation, degradation, and signaling, are found in various organisms. The plant Epimedium pubescens is known for its pharmacologically active flavonoids and its use in traditional Chinese medicine. Despite this, to date, the AP gene family in this species has not been functionally analyzed. This study aimed to uncover the roles of AP genes in E. pubescens (EpAPs), focusing in particular on their involvement in light stress responses.

RESULTS

Genome-wide analysis identified and characterized a total of 103 EpAPs, which were categorized into four phylogenetic groups and revealed conserved motifs crucial for their catalytic function. Structural analysis highlighted the diversity of intron-exon arrangements and the predominant role of tandem duplication in gene expansion. Promoter analysis showed an enrichment of light-responsive elements, indicating potential involvement in light stress responses. Tissue-specific expression patterns revealed specialized roles in various organs, whereas several EpAPs exhibited stage-specific expression during the formation of abscission zones. The analysis of protein-protein interactions identified links to reproductive development, programmed cell death, and stress responses. Under light stress, selected AP genes exhibited dynamic changes in expression, with some showing transient upregulation or recovery phases, which suggests their involvement in short-term adaptation or sustained light stress responses.

CONCLUSIONS

This study provides the first comprehensive analysis of AP genes in E. pubescens, highlighting their potential roles in development and stress adaptation. The presence of light-responsive elements and changes in expression under light stress suggest that AP genes may serve as key regulators of environmental responses in this species. Further validation studies could inform strategies to improve light stress resistance in shade-adapted plants.

Aspartic proteases gene family: Identification and expression profiles during stem vascular development in tobacco

Aspartic proteases (APs) constitute a large family in plants and are widely involved in diverse biological processes, like chloroplast metabolism, biotic and abiotic stress responses, and reproductive development. In this study, we focused on overall analysis of the APs genes in tobacco. Our analysis included the phylogeny and cis-elements in the cell wall-associated promoters of these genes. To characterize the expression patterns of APs genes in stem vascular development. The tissue expression analysis showed that NtAED3-like was preferentially expressed in the differentiating xylem and phloem cells of the vascular system. Based on histochemical staining analysis showed that the NtAED3-like gene was specifically expressed in stem vascular tissue, root vascular tissue, and petiole vascular tissue. The TdT-mediated dUTP nick-end labeling (TUNEL) assay illustrated a delayed progression of programmed cell death (PCD) within the xylem of the ko-ntaed3a-like mutant, relative to the wild type. The mutant ko-ntaed3a-like exhibited a phenotype of thinning stem circumference and changed in xylem structure and lignin content. In addition, the two-dimension heteronuclear single quantum coherent nuclear magnetic resonance (2D-HSQC) analysis of three milled wood lignins (MWLs) showed that the content of β-O-4 connection in ko-ntaed3a-like decreased slightly compared with wild type. In conclusion, this study provides our understanding of the regulation of vascular tissue development by the NtAED3-like gene in tobacco and provides a better basis for determining the molecular mechanism of the aspartic protease in secondary cell wall (SCW) development.

Genome and GWAS analysis identified genes significantly related to phenotypic state of Rhododendron bark

As an important horticultural plant, Rhododendron is often used in urban greening and landscape design. However, factors such as the high rate of genetic recombination, frequent outcrossing in the wild, weak linkage disequilibrium, and the susceptibility of gene expression to environmental factors limit further exploration of functional genes related to important horticultural traits, and make the breeding of new varieties require a longer time. Therefore, we choose bark as the target trait which is not easily affected by environmental factors, but also has ornamental properties. Genome-wide association study (GWAS) of Rhododendron delavayi (30 samples), R. irroratum (30 samples) and their F1 generation R. agastum (200 samples) was conducted on the roughness of bark phenotypes. Finally, we obtained 2416.31 Gbp of clean data and identified 5 328 800 high-quality SNPs. According to the P-value and the degree of linkage disequilibrium of SNPs, we further identified 4 out of 11 candidate genes that affect bark roughness. The results of gene differential expression analysis further indicated that the expression levels of Rhdel02G0243600 and Rhdel08G0220700 in different bark phenotypes were significantly different. Our study identified functional genes that influence important horticultural traits of Rhododendron, and illustrated the powerful utility and great potential of GWAS in understanding and exploiting wild germplasm genetic resources of Rhododendron.

Aspartyl proteases identified as candidate genes of a fiber length QTL, qFLD05, that regulates fiber length in cotton (Gossypium hirsutum L.)

KEY MESSAGE

GhAP genes were identified as the candidates involved in cotton fiber length under the scope of fine mapping a stable fiber length QTL, qFLD05. Moreover, the transcription factor GhWRKY40 positively regulated GhAP3 to decrease fiber length. Fiber length (FL) is an economically important fiber quality trait. Although several genes controlling cotton fiber development have been identified, our understanding of this process remains limited. In this study, an FL QTL (qFLD05) was fine-mapped to a 216.9-kb interval using a secondary F2:3 population derived from the upland hybrid cultivar Ji1518. This mapped genomic segment included 15 coding genes, four of which were annotated as aspartyl proteases (GhAP1-GhAP4). GhAPs were identified as candidates for qFLD05 as the sequence variations in GhAPs were associated with FL deviations in the mapping population, and functional validation of GhAP3 and GhAP4 indicated a longer FL following decreases in their expression levels through virus-induced gene silencing (VIGS). Subsequently, the potential involvement of GhWRKY40 in the regulatory network was revealed: GhWRKY40 positively regulated GhAP3's expression according to transcriptional profiling, VIGS, yeast one-hybrid assays and dual-luciferase experiments. Furthermore, alterations in the expression of the eight previously reported cotton FL-responsive genes from the above three VIGS lines (GhAP3, GhAP4 and GhWRKY40) implied that MYB5_A12 was involved in the GhWRKY40-GhAP network. In short, we unveiled the unprecedented FL regulation roles of GhAPs in cotton, which was possibly further regulated by GhWRKY40. These findings will reveal the genetic basis of FL development associated with qFLD05 and be beneficial for the marker-assisted selection of long-staple cotton.

Transcriptional and post-transcriptional regulation of ethylene biosynthesis by exogenous acetylsalicylic acid in kiwifruit

Levels of ethylene, implicated in the induction of fruit ripening in a diverse array of plants, are influenced by genetic and environmental factors, such as other plant hormones. Among these, salicylic acid (SA) and its derivative, acetylsalicylic acid (ASA), have been demonstrated to inhibit ethylene biosynthesis in fruit, yet the underlying regulatory mechanisms remain elusive. Here, we showed that treatment with exogenous ASA dramatically reduced ethylene production, as well as activities of ACC synthase (ACS) and ACC oxidase (ACO), in kiwifruit tissues. Comparative transcriptome analysis indicated the differential expression of ethylene biosynthetic genes (AdACS1/2 and AdACO5). A screen of transcription factors indicated that AdERF105L and AdWRKY29 were ASA-responsive regulators of AdACS1/2 and AdACO5, respectively. In addition to these genes, AdACS3 and AdACO3 were abundantly expressed in both ASA-treated and control tissues. AdACS3 protein was phosphorylated and stabilized by AdMPK16, a mitogen-activated protein kinase, while AdACO3 activity was enhanced by AdAP, an aspartic peptidase. Exogenous ASA downregulated AdMPK16 and AdAP, thereby influencing ethylene biosynthesis at a post-transcriptional level. These findings led us to propose a multidimensional system for inhibition of ethylene biosynthesis by ASA, inducing differential expression of some ethylene biosynthesis genes, as well as differential effects on protein activity on other targets.

Thinopyrum intermedium TiAP1 interacts with a chitin deacetylase from Blumeria graminis f. sp. tritici and increases the resistance to Bgt in wheat

The biotrophic fungal pathogen Blumeria graminis f. sp. tritici (Bgt) is a crucial factor causing reduction in global wheat production. Wild wheat relatives, for example Thinopyrum intermedium, is one of the wild-used parents in wheat disease-resistant breeding. From T. intermedium line, we identified the aspartic protease gene, TiAP1, which is involved in resistance against Bgt. TiAP1 is a secreted protein that accumulates in large amounts at the infection sites of Bgt and extends to the intercellular space. Yeast two-hybrid, luciferase complementation imaging and bimolecular florescent complimentary analysis showed that TiAP1 interacted with the chitin deacetylase (BgtCDA1) of Bgt. The yeast expression, purification and in vitro test confirmed the chitin deacetylase activity of BgtCDA1. The bombardment and VIGS-mediated host-induced gene silencing showed that BgtCDA1 promotes the invasion of Bgt. Transcriptome analysis showed the cell wall xylan metabolism, lignin biosynthesis-related and defence genes involved in the signal transduction were up-regulated in the transgenic TiAP1 wheat induced by Bgt. The TiAP1 in wheat may inactivate the deacetylation function of BgtCDA1, cause chitin oligomers expose to wheat chitin receptor, then trigger the wheat immune response to inhibit the growth and penetration of Bgt, and thereby enhance the resistance of wheat to pathogens.

Molecular mechanisms of mesocotyl elongation induced by brassinosteroid in maize under deep-seeding stress by RNA-sequencing, microstructure observation, and physiological metabolism

Deep-seeding is an important way to improve maize drought resistance, mesocotyl elongation can significantly enhance its seedling germination. To improve our understanding of transcription-mediated maize mesocotyl elongation under deep-seeding stress. RNA-sequencing was used to identify differentially expressed genes (DEGs) in both deep-seeding tolerant W64A and intolerant K12 mesocotyls following culture for 10 days after 2.0 mg·L^-1 24-epibrassinolide (EBR) induced stress at the depths of 3 and 20 cm. Phenotypically, the mesocotyl length of both maize significantly increased under 20 cm stress and in the presence of EBR. Microstructure observations revealed that the mesocotyls underwent programmed cell death under deep-seeding stress, which was alleviated by EBR. This was found to be regulated by multiple DEGs encoding cysteine protease/senescence-specific cysteine protease, aspartic protease family protein, phospholipase D, etc. and transcription factors (TFs; MYB, NAC). Additionally, some DEGs associated with cell wall components, i.e., cellulose synthase/cellulose synthase like protein (CESA/CSL), fasciclin-like arabinogalactan (APG), leucine-rich repeat protein (LRR) and lignin biosynthesis enzymes including phenylalanine ammonia-lyase, S-adenosyl-L-methionine-dependent methyltransferases, 4-coumarate-CoA ligase, cinnamoyl CoA reductase, cinnamyl alcohol dehydrogenase, catalase, peroxiredoxin/peroxidase were found to control cell wall sclerosis. Moreover, in auxin, ethylene, brassinosteriod, cytokinin, zeatin, abscisic acid, gibberellin, jasmonic acid, and salicylic acid signaling transduction pathways, the corresponding DEGs were activated/inhibited by TFs (ARF, BZR1/2, B-ARR, A-ARR, MYC2, ABF, TGA) and synthesis of phytohormones-related metabolites. These findings provide information on the molecular mechanisms controlling maize deep-seeding tolerance and will aid in the breeding of deep-seeding maize varieties.

Defense and Offense Strategies: The Role of Aspartic Proteases in Plant-Pathogen Interactions

Plant aspartic proteases (APs; E.C.3.4.23) are a group of proteolytic enzymes widely distributed among different species characterized by the conserved sequence Asp-Gly-Thr at the active site. With a broad spectrum of biological roles, plant APs are suggested to undergo functional specialization and to be crucial in developmental processes, such as in both biotic and abiotic stress responses. Over the last decade, an increasing number of publications highlighted the APs' involvement in plant defense responses against a diversity of stresses. In contrast, few studies regarding pathogen-secreted APs and AP inhibitors have been published so far. In this review, we provide a comprehensive picture of aspartic proteases from plant and pathogenic origins, focusing on their relevance and participation in defense and offense strategies in plant-pathogen interactions.

Roles of Plant-Specific Inserts in Plant Defense

Ubiquitously expressed in plants, the plant-specific insert (PSI) of typical plant aspartic proteases (tpAPs) has been associated with plant development, stress response, and defense processes against invading pathogens. Despite sharing high sequence identity, structural studies revealed possible different mechanisms of action among species. The PSI induces signaling pathways of defense hormones in vivo and demonstrates broad-spectrum activity against phytopathogens in vitro. Recent characterization of the PSI-tpAP relationship uncovered novel, nonconventional intracellular protein transport pathways and improved tpAP production yields for industrial applications. In spite of research to date, relatively little is known about the structure-function relationships of PSIs. A comprehensive understanding of their biological roles may benefit plant protection strategies against virulent phytopathogens.

Atypical and nucellin-like aspartic proteases: emerging players in plant developmental processes and stress responses

Members of the pepsin-like family (A1) of aspartic proteases (APs) are widely distributed in plants. A large number of genes encoding putative A1 APs are found in different plant genomes, the vast majority of which exhibit distinct features when compared with the so-called typical APs (and, therefore, grouped as atypical and nucellin-like APs). These features include the absence of the plant-specific insert; an unusually high number of cysteine residues; the nature of the amino acids preceding the first catalytic aspartate; and unexpected localizations. The over-representation of atypical and nucellin-like APs in plants is suggestive of greater diversification of protein functions and a more regulatory role for these APs, as compared with the housekeeping function generally attributed to typical APs. New functions have been uncovered for non-typical APs, with proposed roles in biotic and abiotic stress responses, chloroplast metabolism, and reproductive development, clearly suggesting functional specialization and tight regulation of activity. Furthermore, unusual enzymatic properties have also been documented for some of these proteases. Here, we give an overview of the current knowledge on the distinctive features and functions of both atypical and nucellin-like APs, and discuss this emerging pattern of functional complexity and specialization among plant pepsin-like proteases.

Root Proteomics Reveals the Effects of Wood Vinegar on Wheat Growth and Subsequent Tolerance to Drought Stress

Wood vinegar (WV) or pyroligneous acid (PA) is a reddish-brown liquid created during the dry distillation of biomass, a process called pyrolysis. WV contains important biologically active components, which can enhance plant growth and tolerance to drought stress. However, its mechanism of action remains unknown. Our results after presoaking wheat seeds with various concentrations of WV indicate that a 1:900 WV concentration can significantly enhance growth. To investigate the response of wheat roots to drought stress, we compared quantitative proteomic profiles in the roots of wheat plants grown from seeds either presoaked (treatment) or non-presoaked (control) with WV. Our results indicated that the abscisic acid (ABA) content of wheat roots in the WV treatment was significantly increased. Reactive oxygen species (ROS) and malonaldehyde (MDA) levels roots were significantly lower than in the control treatment under drought stress, while the activity of major antioxidant enzymes was significantly increased. Two-dimensional electrophoresis (2D-PAGE) identified 138 differentially accumulated protein (DAP) spots representing 103 unique protein species responding to drought stress in wheat roots of the control and WV-treated groups. These DAPs are mostly involved in the stress response, carbohydrate metabolism, protein metabolism, and secondary metabolism. Proteome profiles showed the DAPs involved in carbohydrate metabolism, stress response, and secondary metabolism had increased accumulation in roots of the WV-treated groups. These findings suggest that the roots from wheat seeds presoaked with WV can initiate an early defense mechanism to mitigate drought stress. These results provide an explanation of how WV enhances the tolerance of wheat plants to drought stress.

Quantitative analysis of the grain amyloplast proteome reveals differences in metabolism between two wheat cultivars at two stages of grain development

Background

Wheat (Triticum aestivum L.) is one of the world’s most important grain crops. The amyloplast, a specialized organelle, is the major site for starch synthesis and storage in wheat grain. Understanding the metabolism in amyloplast during grain development in wheat cultivars with different quality traits will provide useful information for potential yield and quality improvement.

Results

Two wheat cultivars, ZM366 and YM49–198 that differ in kernel hardness and starch characteristics, were used to examine the metabolic changes in amyloplasts at 10 and 15 days after anthesis (DAA) using label-free-based proteome analysis. We identified 523 differentially expressed proteins (DEPs) between 10 DAA and 15 DAA, and 229 DEPs between ZM366 and YM49–198. These DEPs mainly participate in eight biochemical processes: carbohydrate metabolism, nitrogen metabolism, stress/defense, transport, energetics-related, signal transduction, protein synthesis/assembly/degradation, and nucleic acid-related processes. Among these proteins, the DEPs showing higher expression levels at 10 DAA are mainly involved in carbohydrate metabolism, stress/defense, and nucleic acid related processes, whereas DEPs with higher expression levels at 15 DAA are mainly carbohydrate metabolism, energetics-related, and transport-related proteins. Among the DEPs between the two cultivars, ZM366 had more up-regulated proteins than YM49–198, and these are mainly involved in carbohydrate metabolism, nucleic acid-related processes, and transport.

Conclusions

The results of our study indicate that wheat grain amyloplast has the broad metabolic capability. The DEPs involved in carbohydrate metabolism, nucleic acids, stress/defense, and transport processes, with grain development and cultivar differences, are possibly responsible for different grain characteristics, especially with respect to yield and quality-related traits.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5174-z) contains supplementary material, which is available to authorized users.

iTRAQ-based quantitative proteomic analysis reveals dynamic changes during daylily flower senescence

Sugar-related metabolic biological processes and metabolic pathways as well as invertase, protease, and ribosomal proteins may be critical regulators controlling the circadian rhythm and ephemeral properties of daylily flowers. Daylily is a familiar perennial flower. The daylily flower opens at dawn and withers away at night. Flower longevity in almost all daylily varieties from opening to fading is less than 24 h. In the past decades, the physiological changes and genetic responses to senescence in daylily flowers have been reported. However, the main metabolic pathways and biological processes involved in daylily flower senescence and the proteins involved in premature senility of daylily flowers are poorly understood. Herein, we identified differences between the proteomes of four developmental stages (s1-s4) of daylily flowers using iTRAQ-based quantitative proteomic methods. A total of 445 proteins (containing at least two unique peptides) were identified, and differentially expressed proteins (upregulation ≥ 1.5 or downregulation ≤ 0.67, P value ≤ 0.05) were detected between these stages in the following numbers: 58 (s2/s1), 59 (s3/s1), 31 (s3/s2), 64 (s4/s1), 52 (s4/s2), and 29 (s4/s3). Protein functions and classifications were analyzed based on GO, KEGG, and COG, and expressive hierarchical cluster analysis and functional enrichment analysis for differentially expressed proteins were carried out. A comparison of the late stages (s3 and s4) with the early stage (s1) revealed that the sugar (hexose, monosaccharide, and glucose) metabolic process GO category was the most enriched, and sugar (galactose, pentose, starch, and sucrose) metabolism pathways constituted the most enriched KEGG category. Finally, the potential research value of invertase, protease, and ribosomal proteins for revealing the mechanism underlying the circadian rhythm and ephemeral properties of daylily flowers are discussed. These data and analyses provide new insight into the senescence mechanism of daylily flowers.

Indispensable Role of Proteases in Plant Innate Immunity

Plant defense is achieved mainly through the induction of microbe-associated molecular patterns (MAMP)-triggered immunity (MTI), effector-triggered immunity (ETI), systemic acquired resistance (SAR), induced systemic resistance (ISR), and RNA silencing. Plant immunity is a highly complex phenomenon with its own unique features that have emerged as a result of the arms race between plants and pathogens. However, the regulation of these processes is the same for all living organisms, including plants, and is controlled by proteases. Different families of plant proteases are involved in every type of immunity: some of the proteases that are covered in this review participate in MTI, affecting stomatal closure and callose deposition. A large number of proteases act in the apoplast, contributing to ETI by managing extracellular defense. A vast majority of the endogenous proteases discussed in this review are associated with the programmed cell death (PCD) of the infected cells and exhibit caspase-like activities. The synthesis of signal molecules, such as salicylic acid, jasmonic acid, and ethylene, and their signaling pathways, are regulated by endogenous proteases that affect the induction of pathogenesis-related genes and SAR or ISR establishment. A number of proteases are associated with herbivore defense. In this review, we summarize the data concerning identified plant endogenous proteases, their effect on plant-pathogen interactions, their subcellular localization, and their functional properties, if available, and we attribute a role in the different types and stages of innate immunity for each of the proteases covered.

Protein Structure Insights into the Bilayer Interactions of the Saposin-Like Domain of Solanum tuberosum Aspartic Protease

Many plant aspartic proteases contain a saposin-like domain whose principal functions are intracellular sorting and host defence. Its structure is characterised by helical segments cross-linked by three highly conserved cystines. The present study on the saposin-like domain of Solanum tuberosum aspartic protease revealed that acidification from inactive to active conditions causes dimerisation and a strand-to-helix secondary structure transition independent of bilayer interaction. Bilayer fusion was shown to occur under reducing conditions yielding a faster shift to larger vesicle sizes relative to native conditions, implying that a lower level structural motif might be bilayer-active. Characterisation of peptide sequences based on the domain’s secondary structural regions showed helix-3 to be active (~4% of the full domain’s activity), and mutation of its sole positively charged residue resulted in loss of activity and disordering of structure. Also, the peptides’ respective circular dichroism spectra suggested that native folding within the full domain is dependent on surrounding structure. Overall, the present study reveals that the aspartic protease saposin-like domain active structure is an open saposin fold dimer whose formation is pH-dependent, and that a bilayer-active motif shared among non-saposin membrane-active proteins including certain plant defence proteins is nested within an overall structure essential for native functionality.

Trends and Prospects of Plant Proteases in Therapeutics

The main function of proteases in any living organism is the cleavage of proteins resulting in the degradation of damaged, misfolded and potentially harmful proteins and therefore providing the cell with amino acids essential for the synthesis of new proteins. Besides this main function, proteases may play an important role as signal molecules and participate in numerous protein cascades to maintain the vital processes of an organism. Plant proteases are no exception to this rule. Moreover, in contrast to humanencoded enzymes, many plant proteases possess exceptional features such as higher stability, unique substrate specificity and a wide pH range for enzymatic activity. These valuable features make plant-derived proteolytic enzymes suitable for many biomedical applications, and furthermore, the plants can serve as factories for protein production. Plant proteases are already applied in the treatment of several pathological conditions in the human organism. Some of the enzymes possess antitumour, antibacterial and antifungal activity. The collagenolytic activity of plant proteases determines important medical applications such as the healing of wounds and burn debridement. Plant proteases may affect blood coagulation processes and can be applied in the treatment of digestive disorders. The present review summarizes recent advances and possible applications for plant proteases in biomedicine, and proposes further development of plant-derived proteolytic enzymes in the biotechnology and pharmaceutical industries.

Similarities between plant traits based on their connection to underlying gene functions

Understanding of phenotypes and their genetic basis is a major focus in current plant biology. Large amounts of phenotype data are being generated, both for macroscopic phenotypes such as size or yield, and for molecular phenotypes such as expression levels and metabolite levels. More insight in the underlying genetic and molecular mechanisms that influence phenotypes will enable a better understanding of how various phenotypes are related to each other. This will be a major step forward in understanding plant biology, with immediate value for plant breeding and academic plant research. Currently the genetic basis of most phenotypes remains however to be discovered, and the relatedness of different traits is unclear. We here present a novel approach to connect phenotypes to underlying biological processes and molecular functions. These connections define similarities between different types of phenotypes. The approach starts by using Quantitative Trait Locus (QTL) data, which are abundantly available for many phenotypes of interest. Overrepresentation analysis of gene functions based on Gene Ontology term enrichment across multiple QTL regions for a given phenotype, be it macroscopic or molecular, results in a small set of biological processes and molecular functions for each phenotype. Subsequently, similarity between different phenotypes can be defined in terms of these gene functions. Using publicly available rice data as example, a close relationship with defined molecular phenotypes is demonstrated for many macroscopic phenotypes. This includes for example a link between 'leaf senescence' and 'aspartic acid', as well as between 'days to maturity' and 'choline'. Relationships between macroscopic and molecular phenotypes may result in more efficient marker-assisted breeding and are likely to direct future research aimed at a better understanding of plant phenotypes.