Stress-Responsive Expression, Subcellular Localization and Protein-Protein Interactions of the Rice Metacaspase Family

A novel acidic pH-dependent metacaspase governs defense-response against pathogens in tomato

The importance of metacaspases in programmed cell death and tissue differentiation is known, but their significance in disease stress response, particularly in a crop plant, remained enigmatic. We show the tomato metacaspase expression landscape undergoes differential reprogramming during biotrophic and necrotrophic modes of pathogenesis; also, the metacaspase activity dynamics correlate with the disease progression. These stresses have contrasting effects on the expression pattern of SlMC8, a Type II metacaspase, indicating that SlMC8 is crucial for stress response. In accordance, selected biotic stress-related transcription factors repress SlMC8 promoter activity. Interestingly, SlMC8 exhibits maximum proteolysis at an acidic pH range of 5-6. Molecular dynamics simulation identified the low pH-driven protonation event of Glu246 as critical to stabilize the interaction of SlMC8 with its substrate. Mutagenesis of Glu246 to charge-neutral glutamine suppressed SlMC8's proteolytic activity, corroborating the importance of the amino acid in SlMC8 activation. The glutamic acid residue is found in an equivalent position in metacaspases having acidic pH dependence. SlMC8 overexpression leads to heightened ROS levels, cell death, and tolerance to PstDC3000, and SlMC8 repression reversed the phenomena. However, the overexpression of SlMC8 increases tomato susceptibility to necrotrophic Alternaria solani. We propose that SlMC8 activation due to concurrent changes in cellular pH during infection contributes to the basal resistance of the plant by promoting cell death at the site of infection, and the low pH dependence acts as a guard against unwarranted cell death. Our study confirms the essentiality of a low pH-driven Type II metacaspase in tomato biotic stress-response regulation.

Type II metacaspase mediates light-dependent programmed cell death in Chlamydomonas reinhardtii

Among the crucial processes that preside over the destiny of cells from any type of organism are those involving their self-destruction. This process is well characterized and conceptually logical to understand in multicellular organisms; however, the levels of knowledge and comprehension of its existence are still quite enigmatic in unicellular organisms. We use Chlamydomonas (Chlamydomonas reinhardtii) to lay the foundation for understanding the mechanisms of programmed cell death (PCD) in a unicellular photosynthetic organism. In this paper, we show that while PCD induces the death of a proportion of cells, it allows the survival of the remaining population. A quantitative proteomic analysis aiming at unveiling the proteome of PCD in Chlamydomonas allowed us to identify key proteins that led to the discovery of essential mechanisms. We show that in Chlamydomonas, PCD relies on the light dependence of a photosynthetic organism to generate reactive oxygen species and induce cell death. Finally, we obtained and characterized mutants for the 2 metacaspase genes in Chlamydomonas and showed that a type II metacaspase is essential for PCD execution.

Industrial wastewater irrigation increased higher heavy metals uptake and expansins, metacaspases, and cystatin genes expression in Parthenium and maize

Industrial wastewater irrigation of agricultural crops can cause a lot of environmental and health problems in developing countries due to heavy metals deposition in agricultural soils as well as edible plant consumption by human beings. Therefore, this study was conducted to find out the heavy metals concentration in industrial wastewater and soil irrigated with that wastewater. In addition, the aim was to determine the impact of industrial wastewater irrigation on Parthenium hysterophorus and Zea mays genes involved in growth improvement and inhibition. For this purpose, plant samples from agriculture fields irrigated with wastewater from Hattar Industrial Estate (HIE) of Haripur, Pakistan, and control plants from non-contaminated soil irrigated with tape water were collected after 15 and 45 days of germination. Heavy metals concentration in the collected plant samples, wastewater, and soil was determined. The results revealed that the soil of the sample collection site was predominantly contaminated with Cr, Pb, Ni, Cu, Co, Zn, and Cd up to the concentrations of 38.98, 21.14, 46.01, 155.73, 12.50, 68.50, and 7.01 mg/kg, respectively. The concentrations of these heavy metals were found to surpass the permissible limit in normal agricultural soil. Expansins, cystatins (plant growth enhancers), and metacaspases (plant growth inhibitor) gene expression were studied through reverse transcription polymerase chain reaction. The results showed that the expression of these genes was higher in samples collected from wastewater-irrigated soils as compared to control. The expression of these genes was observed in 45 days old samples, 15 days old samples, and control. Taken together, this study suggests the use of Parthenium and maize for phytoremediation and that they should not be used for eating purposes if irrigated with industrial wastewater.

Integrated Transcriptomic and Proteomic Analyses of Low-Nitrogen-Stress Tolerance and Function Analysis of ZmGST42 Gene in Maize

Maize (Zea mays L.) is one of the major staple crops providing human food, animal feed, and raw material support for biofuel production. For its growth and development, maize requires essential macronutrients. In particular, nitrogen (N) plays an important role in determining the final yield and quality of a maize crop. However, the excessive application of N fertilizer is causing serious pollution of land area and water bodies. Therefore, cultivating high-yield and low-N-tolerant maize varieties is crucial for minimizing the nitrate pollution of land and water bodies. Here, based on the analysis of the maize leaf transcriptome and proteome at the grain filling stage, we identified 3957 differentially expressed genes (DEGs) and 329 differentially abundant proteins (DAPs) from the two maize hybrids contrasting in N stress tolerance (low-N-tolerant XY335 and low-N-sensitive HN138) and screened four sets of low-N-responsive genes and proteins through Venn diagram analysis. We identified 761 DEGs (253 up- and 508 down-regulated) specific to XY335, whereas 259 DEGs (198 up- and 61 down-regulated) were specific to HN138, and 59 DEGs (41 up- and 18 down-regulated) were shared between the two cultivars under low-N-stress conditions. Meanwhile, among the low-N-responsive DAPs, thirty were unique to XY335, thirty were specific to HN138, and three DAPs were shared between the two cultivars under low-N treatment. Key among those genes/proteins were leucine-rich repeat protein, DEAD-box ATP-dependent RNA helicase family proteins, copper transport protein, and photosynthesis-related proteins. These genes/proteins were involved in the MAPK signaling pathway, regulating membrane lipid peroxidation, and photosynthesis. Our results may suggest that XY335 better tolerates low-N stress than HN138, possibly through robust low-N-stress sensing and signaling, amplified protein phosphorylation and stress response, and increased photosynthesis efficiency, as well as the down-regulation of 'lavish' or redundant proteins to minimize N demand. Additionally, we screened glutathione transferase 42 (ZmGST42) and performed physiological and biochemical characterizations of the wild-type (B73) and gst42 mutant at the seedling stage. Resultantly, the wild-type exhibited stronger tolerance to low N than the mutant line. Our findings provide a better understanding of the molecular mechanisms underlying low-N tolerance during the maize grain filling stage and reveal key candidate genes for low-N-tolerance breeding in maize.

Rice FERONIA-LIKE RECEPTOR 3 and 14 affect grain quality by regulating redox homeostasis during endosperm development

Chalky endosperm negatively affects the appearance, milling, and eating qualities of rice (Oryza sativa L.) grains. Here, we report the role of two receptor-like kinases, FERONIA-LIKE RECEPTOR 3 (FLR3) and FERONIA-LIKE RECEPTOR 14 (FLR14), in grain chalkiness and quality. Knockouts of FLR3 and/or FLR14 increased the number of white-core grains caused by aberrant accumulation of storage substances, resulting in poor grain quality. Conversely, the overexpression of FLR3 or FLR14 reduced grain chalkiness and improved grain quality. Transcriptome and metabolome analyses showed that genes and metabolites involved in the oxidative stress response were significantly up-regulated in flr3 and flr14 grains. The content of reactive oxygen species was significantly increased in flr3 and flr14 mutant endosperm but decreased in overexpression lines. This strong oxidative stress response induced the expression of programmed cell death (PCD)-related genes and caspase activity in endosperm, which further accelerated PCD, resulting in grain chalkiness. We also demonstrated that FLR3 and FLR14 reduced grain chalkiness by alleviating heat-induced oxidative stress in rice endosperm. Therefore, we report two positive regulators of grain quality that maintain redox homeostasis in the endosperm, with potential applications in breeding rice for optimal grain quality.

Regulating Death and Disease: Exploring the Roles of Metacaspases in Plants and Fungi

Identified over twenty years ago and distantly related to animal caspases are a group of cysteine proteases known as metacaspases. Throughout the years, much like caspase roles in metazoans, metacaspases have been shown to be involved in regulating cellular death in non-metazoan organisms. Yet, continued research on metacaspases describes these proteins as intricate and multifunctional, displaying striking diversity on distinct biological functions. In this review, we intend to describe the recent advances in our understanding of the divergence of metacaspase functionality in plants and fungi. We will dissect the duality of metacaspase activity in the context of plant-pathogen interactions, providing a unique lens from which to characterize metacaspases in the development, immunity, and stress responses of plants, and the development and virulence of fungi. Furthermore, we explore the evolutionary trajectory of fungal metacaspases to delineate their structure and function. Bridging the gap between metacaspase roles in immunity and pathogenicity of plant-pathogen interactions can enable more effective and targeted phytopathogen control efforts to increase production of globally important food crops. Therefore, the exploitation and manipulation of metacaspases in plants or fungi represent new potential avenues for developing mitigation strategies against plant pathogens.

Comparative analysis of expression profiles of metacaspase (MC) genes between two apple (Malus domestica) cultivars with distinct ripening behavior

The purpose of this research was to determine expression profiles of metacaspase (MC) genes during ripening and senescence of two apple cultivars with distinct ripening behavior. "Golden Delicious" and "Fuji" harvested at commercial maturity were used as materials. Our data revealed that flesh firmness, respiration rate, ethylene production, metacaspase (MC) activity, superoxide anion (O₂ ^•- ) production rate, relative electrical conductivity (REC), hydrogen peroxide (H₂ O₂ ), and malondialdehyde (MDA) contents in "Golden Delicious" were higher than in "Fuji" during ripening. At 35 days, no DNA ladder was observed in both cultivars, and tonoplast disintegration was only observed in "Golden Delicious" by transmission electron microscope (TEM), indicating that programmed cell death (PCD) was initiated earlier in "Golden Delicious" than in "Fuji." A total of 18 MC genes were detected to be expressed in both cultivars. For those genes expressed only in "Golden Delicious," MdMC06, MdMC10, MdMC12, and MdMC21 might play a role in the early stage of ripening, whereas MdMC19 might be associated with the late stage of ripening. MdMC15 was expressed only in "Fuji." The remaining MC genes were differentially expressed in both cultivars during ripening. These results would provide useful information to further underlie the relationships among MC genes, PCD and storability of different apple cultivars. PRACTICAL APPLICATIONS: Apple is one of the most popular fruits in the world. Different apple cultivars vary in their ripening behavior and storability, but the molecular mechanism has not yet been fully elucidated. "Golden Delicious" and "Fuji" are two important apple cultivars worldwide. Our data indicated that PCD was initiated earlier in "Golden delicious" than in "Fuji" during postharvest ripening and senescence. MdMCs showed variable expression patterns in both cultivars during ripening. MdMC15 and MdMC19 might be closely associated with the early stage of PCD. These results would provide useful information to further decode the molecular mechanisms responsible for different storage storability of apple cultivars.

Assessment of Rice Sheath Blight Resistance Including Associations with Plant Architecture, as Revealed by Genome-Wide Association Studies

BACKGROUND

Sheath blight (ShB) disease caused by Rhizoctonia solani Kühn, is one of the most economically damaging rice (Oryza sativa L.) diseases worldwide. There are no known major resistance genes, leaving only partial resistance from small-effect QTL to deploy for cultivar improvement. Many ShB-QTL are associated with plant architectural traits detrimental to yield, including tall plants, late maturity, or open canopy from few or procumbent tillers, which confound detection of physiological resistance.

RESULTS

To identify QTL for ShB resistance, 417 accessions from the Rice Diversity Panel 1 (RDP1), developed for association mapping studies, were evaluated for ShB resistance, plant height and days to heading in inoculated field plots in Arkansas, USA (AR) and Nanning, China (NC). Inoculated greenhouse-grown plants were used to evaluate ShB using a seedling-stage method to eliminate effects from height or maturity, and tiller (TN) and panicle number (PN) per plant. Potted plants were used to evaluate the RDP1 for TN and PN. Genome-wide association (GWA) mapping with over 3.4 million SNPs identified 21 targeted SNP markers associated with ShB which tagged 18 ShB-QTL not associated with undesirable plant architecture traits. Ten SNPs were associated with ShB among accessions of the Indica subspecies, ten among Japonica subspecies accessions, and one among all RDP1 accessions. Across the 18 ShB QTL, only qShB4-1 was not previously reported in biparental mapping studies and qShB9 was not reported in the GWA ShB studies. All 14 PN QTL overlapped with TN QTL, with 15 total TN QTL identified. Allele effects at the five TN QTL co-located with ShB QTL indicated that increased TN does not inevitably increase disease development; in fact, for four ShB QTL that overlapped TN QTL, the alleles increasing resistance were associated with increased TN and PN, suggesting a desirable coupling of alleles at linked genes.

CONCLUSIONS

Nineteen accessions identified as containing the most SNP alleles associated with ShB resistance for each subpopulation were resistant in both AR and NC field trials. Rice breeders can utilize these accessions and SNPs to develop cultivars with enhanced ShB resistance along with increased TN and PN for improved yield potential.

Plant metacaspases: Decoding their dynamics in development and disease

Plant metacaspases were evolved in parallel to well-characterized animal counterpart caspases and retained the similar histidine-cysteine catalytic dyad, leading to functional congruity between these endopeptidases. Although phylogenetic relatedness of the catalytic domain and functional commonality placed these proteases in the caspase family, credible counterarguments predominantly about their distinct substrate specificity raised doubts about the classification. Metacaspases are involved in regulating the PCD during development as well as in senescence. Balancing acts of metacaspase activity also dictate cell fate during defense upon the perception of adverse environmental cues. Accordingly, their activity is tightly regulated, while suppressing spurious activation, by a combination of genetic and post-translational modifications. Structural insights from recent studies provided vital clues on the functionality. This comprehensive review aims to explore the origin of plant metacaspases, and their regulatory and functional diversity in different plants while discussing their analogy to mammalian caspases. Besides, we have presented various modern methodologies for analyzing the proteolytic activity of these indispensable molecules in the healthy or stressed life of a plant. The review would serve as a repository of all the available pieces of evidence indicating metacaspases as the key regulator of PCD across the plant kingdom and highlight the prospect of studying metacaspases for their inclusion in a crop improvement program.

Evolutionary Diversity and Function of Metacaspases in Plants: Similar to but Not Caspases

Caspase is a well-studied metazoan protease involved in programmed cell death and immunity in animals. Obviously, homologues of caspases with evolutionarily similar sequences and functions should exist in plants, and yet, they do not exist in plants. Plants contain structural homologues of caspases called metacaspases, which differ from animal caspases in a rather distinct way. Metacaspases, a family of cysteine proteases, play critical roles in programmed cell death during plant development and defense responses. Plant metacaspases are further subdivided into types I, II, and III. In the type I Arabidopsis MCs, AtMC1 and AtMC2 have similar structures, but antagonistically regulate hypersensitive response cell death upon immune receptor activation. This regulatory action is similar to caspase-1 inhibition by caspase-12 in animals. However, so far very little is known about the biological function of the other plant metacaspases. From the increased availability of genomic data, the number of metacaspases in the genomes of various plant species varies from 1 in green algae to 15 in Glycine max. It is implied that the functions of plant metacaspases will vary due to these diverse evolutions. This review is presented to comparatively analyze the evolution and function of plant metacaspases compared to caspases.

Initiation and Execution of Programmed Cell Death and Regulation of Reactive Oxygen Species in Plants

Programmed cell death (PCD) plays crucial roles in plant development and defence response. Reactive oxygen species (ROS) are produced during normal plant growth, and high ROS concentrations can change the antioxidant status of cells, leading to spontaneous cell death. In addition, ROS function as signalling molecules to improve plant stress tolerance, and they induce PCD under different conditions. This review describes the mechanisms underlying plant PCD, the key functions of mitochondria and chloroplasts in PCD, and the relationship between mitochondria and chloroplasts during PCD. Additionally, the review discusses the factors that regulate PCD. Most importantly, in this review, we summarise the sites of production of ROS and discuss the roles of ROS that not only trigger multiple signalling pathways leading to PCD but also participate in the execution of PCD, highlighting the importance of ROS in PCD.

The potential roles of different metacaspases in maize defense response

Metacaspases (MCs), a class of cysteine-dependent proteases, act as important regulators in plant defense response. In maize genome, there are 11 ZmMCs which have been categorized into two types (type I and II) based on their structural differences. In this study, we investigated the different transcript patterns of 11 ZmMCs in maize defense response mediated by the nucleotide-binding, leucine-rich-repeat protein Rp1-D21. We further predicted that many cis-elements responsive to salicylic acid (SA), methyl jasmonate (MeJA), abscisic acid (ABA) and auxin were identified in the promoter regions of ZmMCs, and several different transcription factors were predicted to bind to their promoters. We analyzed the localization of ZmMCs with previously identified quantitative trait loci (QTLs) in maize disease resistance, and found that all other ZmMCs, except for ZmMC6-8, are co-located with at least one QTL associated with disease resistance to southern leaf blight, northern leaf blight, gray leaf spot or Fusarium ear rot. Based on previous RNA-seq analysis, different ZmMCs display different transcript levels in response to Cochliobolous heterostrophus and Fusarium verticillioides. All the results imply that the members of ZmMCs might have differential functions to different maize diseases. This study lays the basis for further investigating the roles of ZmMCs in maize disease resistance.

Maize metacaspases modulate the defense response mediated by the NLR protein Rp1-D21 likely by affecting its subcellular localization

Plants usually employ resistance (R) genes to defend against the infection of pathogens, and most R genes encode intracellular nucleotide-binding, leucine-rich repeat (NLR) proteins. The recognition between R proteins and their cognate pathogens often triggers a rapid localized cell death at the pathogen infection sites, termed the hypersensitive response (HR). Metacaspases (MCs) belong to a cysteine protease family, structurally related to metazoan caspases. MCs play crucial roles in plant immunity. However, the underlying molecular mechanism and the link between MCs and NLR-mediated HR are not clear. In this study, we systematically investigated the MC gene family in maize and identified 11 ZmMCs belonging to two types. Further functional analysis showed that the type I ZmMC1 and ZmMC2, but not the type II ZmMC9, suppress the HR-inducing activity of the autoactive NLR protein Rp1-D21 and of its N-terminal coiled-coil (CCD21 ) signaling domain when transiently expressed in Nicotiana benthamiana. ZmMC1 and ZmMC2 physically associate with CCD21 in vivo. We further showed that ZmMC1 and ZmMC2, but not ZmMC9, are predominantly localized in a punctate distribution in both N. benthamiana and maize (Zea mays) protoplasts. Furthermore, the co-expression of ZmMC1 and ZmMC2 with Rp1-D21 and CCD21 causes their re-distribution from being uniformly distributed in the nucleocytoplasm to a punctate distribution co-localizing with ZmMC1 and ZmMC2. We reveal a novel role of plant MCs in modulating the NLR-mediated defense response and derive a model to explain it.

Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice

Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies of Oryza sativa, japonica, and indica and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, cis-regulatory elements, expression patterns, and haplotypic variations. Further, the haplotyping study of metacaspase genes was conducted using the whole-genome resequencing data publicly available for 4726 diverse genotype and in-house resequencing data generated for north-east Indian rice lines. Sequence variations observed among wild and cultivated rice species for metacaspase genes were used to understand the duplication and neofunctionalization events. The expression profiles of metacaspase genes were analyzed using RNA-seq transcriptome profiling in rice during different developmental stages and stress conditions. Real-time quantitative PCR analysis of candidate metacaspase genes in rice cultivars Pusa Basmati-1 in response to Magnaporthe oryzae infection indicated a significant role in the disease resistance mechanism. The information provided here will help to understand the evolution of metacaspases and their role under stress conditions in rice.

Programmed cell death (PCD) control in plants: New insights from the Arabidopsis thaliana deathosome

Programmed cell death (PCD) is a genetically controlled process that leads to cell suicide in both eukaryotic and prokaryotic organisms. In plants PCD occurs during development, defence response and when exposed to adverse conditions. PCD acts controlling the number of cells by eliminating damaged, old, or unnecessary cells to maintain cellular homeostasis. Unlike in animals, the knowledge about PCD in plants is limited. The molecular network that controls plant PCD is poorly understood. Here we present a review of the current mechanisms involved with the genetic control of PCD in plants. We also present an updated version of the AtLSD1 deathosome, which was previously proposed as a network controlling HR-mediated cell death in Arabidopsis thaliana. Finally, we discuss the unclear points and open questions related to the AtLSD1 deathosome.

The Mechanosensitive Ion Channel MSL10 Potentiates Responses to Cell Swelling in Arabidopsis Seedlings

The ability to respond to unanticipated increases in volume is a fundamental property of cells, essential for cellular integrity in the face of osmotic challenges. Plants must manage cell swelling during flooding, rehydration, and pathogen invasion-but little is known about the mechanisms by which this occurs. It has been proposed that plant cells could sense and respond to cell swelling through the action of mechanosensitive ion channels. Here, we characterize a new assay to study the effects of cell swelling on Arabidopsis thaliana seedlings and to test the contributions of the mechanosensitive ion channel MscS-like10 (MSL10). The assay incorporates both cell wall softening and hypo-osmotic treatment to induce cell swelling. We show that MSL10 is required for several previously demonstrated responses to hypo-osmotic shock, including a cytoplasmic calcium transient within the first few seconds, accumulation of ROS within the first 30 min, and increased transcript levels of mechano-inducible genes within 60 min. We also show that cell swelling induces programmed cell death within 3 h in a MSL10-dependent manner. Finally, we show that MSL10 is unable to potentiate cell swelling-induced death when phosphomimetic residues are introduced into its soluble N terminus. Thus, MSL10 functions as a phospho-regulated membrane-based sensor that connects the perception of cell swelling to a downstream signaling cascade and programmed cell death.

Identification and characterization of a spotted-leaf mutant spl40 with enhanced bacterial blight resistance in rice

BACKGROUND

Spotted leaf mutants show typical necrotic lesions that appear spontaneously in the absence of any pathogen attack. These mutants are often characterized to exhibit programmed cell death (PCD) and activation of plant defense responses resulting in enhanced disease resistance to multiple pathogens. Here, we reported a novel spotted-leaf mutant, spl40 that showed enhanced disease resistance response.

RESULTS

Initially lesions appeared at leaf tips during seedling stage and gradually covered the whole leaf at the tillering stage. The lesion development was light-dependent. spl40 showed obvious cell death at and around the lesion, and burst of reactive oxygen species (ROS) was accompanied by disturbed ROS scavenging system. Photosynthetic capacity was compromised as evidenced by significant reductions in chlorophyll content, important photosynthesis parameters and downregulated expression of photosynthesis-related genes which ultimately led to poor performance of major agronomic traits. spl40 exhibited enhanced resistance to 14 out of 16 races of bacterial blight pathogen of rice, caused by Xanthomonas oryzae pv. oryzae, most probably though activation of SA and JA signaling pathways, owing to upregulated expression of SA and JA signaling genes, though the exact mechanism remain to be elucidated. The spotted-leaf phenotype was controlled by a novel single recessive nuclear gene. Genetic mapping combined with high throughput sequencing analysis identified Os05G0312000 as the most probable candidate gene. Sequencing of ORF revealed a single SNP change from C to T that resulted in non-synonymous change in amino acid residue from leucine to phenylalanine. Interestingly, the complementation plants did not display lesions before heading but showed lesions at the heading stage and the transgenic T₁ progenies could be classified into 3 categories based on their lesion intensity, indicating the complex genetic nature of the spl40 mutation.

CONCLUSION

The results obtained here clearly show that genes related to defense and PCD were upregulated in accordance with enhanced disease resistance and occurrence of PCD, whereas the photosynthetic capacity and overall ROS homeostasis was compromised in spl40. Our data suggest that a novel spotted-leaf mutant, spl40, would help to elucidate the mechanism behind lesion development involving programmed cell death and associated defense responses.

Biotechnological Potential of LSD1, EDS1, and PAD4 in the Improvement of Crops and Industrial Plants

Lesion Simulating Disease 1 (LSD1), Enhanced Disease Susceptibility (EDS1) and Phytoalexin Deficient 4 (PAD4) were discovered a quarter century ago as regulators of programmed cell death and biotic stress responses in Arabidopsis thaliana. Recent studies have demonstrated that these proteins are also required for acclimation responses to various abiotic stresses, such as high light, UV radiation, drought and cold, and that their function is mediated through secondary messengers, such as salicylic acid (SA), reactive oxygen species (ROS), ethylene (ET) and other signaling molecules. Furthermore, LSD1, EDS1 and PAD4 were recently shown to be involved in the modification of cell walls, and the regulation of seed yield, biomass production and water use efficiency. The function of these proteins was not only demonstrated in model plants, such as Arabidopsis thaliana or Nicotiana benthamiana, but also in the woody plant Populus tremula x tremuloides. In addition, orthologs of LSD1, EDS1, and PAD4 were found in other plant species, including different crop species. In this review, we focus on specific LSD1, EDS1 and PAD4 features that make them potentially important for agricultural and industrial use.

Genome-Wide Identification and Expression Analysis of the Metacaspase Gene Family in Gossypium Species

Metacaspases (MCs) are cysteine proteases that are important for programmed cell death (PCD) in plants. In this study, we identified 89 MC genes in the genomes of four Gossypium species (Gossypium raimondii, Gossypium barbadense, Gossypium hirsutum, and Gossypium arboreum), and classified them as type-I or type-II genes. All of the type-I and type-II MC genes contain a sequence encoding the peptidase C14 domain. During developmentally regulated PCD, type-II MC genes may play an important role related to fiber elongation, while type-I genes may affect the thickening of the secondary wall. Additionally, 13 genes were observed to be differentially expressed between two cotton lines with differing fiber strengths, and four genes (GhMC02, GhMC04, GhMC07, and GhMC08) were predominantly expressed in cotton fibers at 5–30 days post-anthesis (DPA). During environmentally induced PCD, the expression levels of four genes were affected in the root, stem, and leaf tissues within 6 h of an abiotic stress treatment. In general, the MC gene family affects the development of cotton fibers, including fiber elongation and fiber thickening while four prominent fiber- expressed genes were identified. The effects of the abiotic stress and hormone treatments imply that the cotton MC gene family may be important for fiber development. The data presented herein may form the foundation for future investigations of the MC gene family in Gossypium species.

Two grapevine metacaspase genes mediate ETI-like cell death in grapevine defence against infection of Plasmopara viticola

Metacaspase, as hypersensitive response (HR) executors, has been identified in many plant species. Previously, the entire gene family of metacaspase has been uncovered, but there are still questions that remain unclear regarding HR-regulating gene members. In this study, based on metacaspase expression during different grapevine genotypes interacting with Plasmopara viticola, we identified MC2 and MC5 as candidates involved in HR. We overexpressed both metacaspases as GFP fusions in tobacco BY-2 cells to address subcellular localization and cellular functions. We found MC2 located at the ER, while MC5 was nucleocytoplasmic. In these overexpressor lines, cell death elicited by the bacterial protein harpin, is significantly enhanced, indicating MC2 and MC5 mediated defence-related programmed cell death (PCD). This effect was mitigated, when the membrane-located NADPH oxidase was inhibited by the specific inhibitor diphenylene iodonium, or when cells were complemented with methyl jasmonate, a crucial signal of basal immunity. Both findings are consistent with a role of MC2 and MC5 in cell death-related immunity. Using a dual-luciferase reporter system in grapevine cells we demonstrated both MC2 and MC5 promoter alleles from V. rupestris were more responsive to harpin than those from V. vinifera cv 'Müller-Thurgau', while they were not induced by MeJA as signal linked with basal immunity. These findings support a model, where MC2 and MC5 act specifically as executors of the HR.

Involvement of HbMC1-mediated cell death in tapping panel dryness of rubber tree (Hevea brasiliensis)

Tapping panel dryness (TPD) causes a significant reduction in the latex yield of rubber tree (Hevea brasiliensis Muell. Arg.). It is reported that TPD is a typical programmed cell death (PCD) process. Although PCD plays a vital role in TPD occurrence, there is a lack of detailed and systematic study. Metacaspases are key regulators of diverse PCD in plants. Based on our previous result that HbMC1 was associated with TPD, we further elucidate the roles of HbMC1 on rubber tree TPD in this study. HbMC1 was up-regulated by TPD-inducing factors including wounding, ethephon and H2O2. Moreover, the expression level of HbMC1 was increased along with TPD severity in rubber tree, suggesting a positive correlation between HbMC1 expression and TPD severity. To investigate its biological function, HbMC1 was overexpressed in yeast (Saccharomyces cerevisiae) and tobacco (Nicotiana benthamiana). Transgenic yeast and tobacco overexpressing HbMC1 showed growth retardation compared with controls under H2O2-induced oxidative stress. In addition, overexpression of HbMC1 in yeast and tobacco reduced cell survival after high-concentration H2O2 treatment and resulted in enhanced H2O2-induced leaf cell death, respectively. A total of 11 proteins, rbcL, TM9SF2-like, COX3, ATP9, DRP, HbREF/Hevb1, MSSP2-like, SRC2, GATL8, CIPK14-like and STK, were identified and confirmed to interact with HbMC1 by yeast two-hybrid screening and co-transformation in yeast. The 11 proteins mentioned above are associated with many biological processes, including rubber biosynthesis, stress response, autophagy, carbohydrate metabolism, signal transduction, etc. Taken together, our results suggest that HbMC1-mediated PCD plays an important role in rubber tree TPD, and the identified HbMC1-interacting proteins provide valuable information for further understanding the molecular mechanism of HbMC1-mediated TPD in rubber tree.

Metacaspase gene family in Rosaceae genomes: Comparative genomic analysis and their expression during pear pollen tube and fruit development

Metacaspase (MC), which is discovered gene family with distant caspase homologs in plants, fungi, and protozoa, may be involved in programmed cell death (PCD) processes during plant development and respond abiotic and biotic stresses. To reveal the evolutionary relationship of MC gene family in Rosaceae genomes, we identified 8, 7, 8, 12, 12, and 23 MC genes in the genomes of Fragaria vesca, Prunus mume, Prunus persica, Pyrus communis, Pyrus bretschneideri and Malus domestica, respectively. Phylogenetic analysis suggested that the MC genes could be grouped into three clades: Type I*, Type I and Type II, which was supported by gene structure and conserved motif analysis. Microsynteny analysis revealed that MC genes present in the corresponding syntenic blocks of P. communis, P. bretschneideri and M. domestica, and further suggested that large-scale duplication events play an important role in the expansion of MC gene family members in these three genomes than other Rosaceae plants (F. vesca, P. mume and P. persica). RNA-seq data showed the specific expression patterns of PbMC genes in response to drought stress. The expression analysis of MC genes demonstrated that PbMC01 and PbMC03 were able to be detected in all four pear pollen tubes and seven fruit development stages. The current study highlighted the evolutionary relationship and duplication of the MC gene family in these six Rosaceae genomes and provided appropriate candidate genes for further studies in P. bretschneideri.

Genome-wide characterization, molecular evolution and expression profiling of the metacaspases in potato (Solanum tuberosum L.)

Metacaspases are distant relatives of animal caspases found in plants, protozoa and fungi. Some recent studies have demonstrated that metacaspases are involved in regulating the developmental and environmentally induced programmed cell death in plants. In this study, we identified metacaspase gene family in potato (Solanum tuberosum L.) and analyzed their expression pattern in various developmental tissues and stress responses of plants. There were eight metacaspase genes identified in the Peptidase (Cysteine protease) C14 family and based upon sequence alignment and phylogenetic analysis, a systematic nomenclature of potato metacaspases (SotubMCs) has been proposed. Three of the eight candidate genes showing homology with Arabidopsis thaliana type I metacaspase, AtMC1 were given name SotubMC1, SotubMC2 and SotubMC3 as per the degree of relatedness. Similarly, the next three being homologous to A. thaliana type I metacaspase, AtMC3 were named SotubMC4, SotubMC5, and SotubMC6. The remaining two were named SotubMC7 and SotubMC8, showing significant similarity with type II metacaspases of A. thaliana, AtMC4 and AtMC9, respectively. Evolutionary divergence analysis of SotubMCs from its orthologs in seven other members of Solanaceae family as well as with A. thaliana, Vitis vinifera and Oryza sativa was also carried out. The d_N/d_S ratios of the orthologous pairs suggested the SotubMCs were under purifying (negative) selection in course of plant evolution. Splicing patterns of potato metacaspases were also analyzed. Amongst all SotubMCs, SotubMC2, SotubMC4, SotubMC6 and SotubMC7 genes appeared to produce multiple alternative spliced variants of different lengths. Furthermore using protein modeling tools, we have predicted the protein structure of identified metacaspases. The cis-regulatory elements analysis was also performed exhibiting the presence of development, stress and hormones related cis-elements in the promoter regions of the SotubMCs. This indicates that potato metacaspases might be playing important roles in the development, stress and hormone responsive pathways. Moreover, relative expression analysis of identified genes was carried out using qRT-PCR in various developmental tissues that also include stolons and tubers. The eight metacaspases showed differential expression in different tissues. Some of the tissues such as leaf undergoing senescence among different leaf developmental stages (immature, mature and senescent) displayed higher relative expression of some of the metacaspases, implying their involvement in leaf senescence. The expression pattern of SotubMCs under various abiotic, biotic and hormonal stresses was also analysed. The results showed that many members of the potato metacaspase gene family displayed differential expression patterns under various stress conditions. Taken together, the study could provide crucial resources for further investigations to understand the functional roles of the identified metacaspases in potato.

Identification of a Novel Semi-Dominant Spotted-Leaf Mutant with Enhanced Resistance to Xanthomonas oryzae pv. oryzae in Rice

Many spotted-leaf mutants show enhanced disease resistance to multiple pathogen attacks; however, the mechanisms are largely unknown. Here, we reported a novel semi-dominant spotted-leaf mutant 24 (spl24) obtained from an ethyl methane sulfonate (EMS)-induced IR64 mutant bank. spl24 developed tiny brown lesions on the leaf tip and spread down gradually to the leaf base as well as the sheath at the early heading stage. The performances of major agronomic traits such as the plant height, panicle length, number of panicles/plant, and 1000-grain weight were significantly altered in spl24 when compared to the wild-type IR64. Furthermore, spl24 exhibited a premature senescing phenotype with degeneration of nuclear acids, significantly reduced soluble protein content, increased level of malonaldehyde (MDA), and lowered activities of reactive oxygen species (ROS) scavenging enzymes. Disease evaluation indicated that spl24 showed enhanced resistance to multiple races of Xanthomonas oryzae pv. oryzae, the causal pathogen of bacterial leaf blight in rice, with elevated expression of pathogenesis-related genes, salicylic acid (SA) signaling pathway-associated genes revealed by real-time quantitative PCR and high-throughput RNA sequencing analysis. Genetic analysis and gene mapping indicated that the lesion mimic phenotype was controlled by a novel semi-dominant nuclear gene. The mutation, tentatively termed as OsSPL24, was in a 110 kb region flanked by markers Indel-33 and Indel-12 in chromosome 11. Together, our data suggest that spl24 is a novel lesion mimic mutant with enhanced innate immunity and would facilitate the isolation and functional characterization of the target gene.

Genome-wide identification, characterization, and transcriptional analysis of the metacaspase gene family in cucumber (Cucumis sativus)

Metacaspase (MC), a family of caspase-like proteins, plays vital roles in regulating programmed cell death (PCD) during development and in response to stresses in plants. In this study, five MC genes (designated as CsMC1 to CsMC5) were identified in the cucumber (Cucumis sativus) genome. Sequence analysis revealed that CsMC1–CsMC3 belong to type I MC proteins, while CsMC4 and CsMC5 are type II MC proteins. Phylogenetic tree and conserved motif analysis of MC proteins indicated that these proteins can be classified into two groups, which are correlated with the types of these MC proteins. Gene structure analysis demonstrated that type I CsMC genes contain 4–7 introns, while all type II CsMC genes harbor one intron. In addition, many hormone-, stress-, and development-related cis-elements were identified in the promoter regions of CsMC genes. Expression analysis using RNA-seq data revealed that CsMC genes have distinct expression patterns in various tissues and developmental stages. qRT-PCR results showed that the transcript levels of CsMC genes could be regulated by various abiotic stresses such as NaCl, PEG, and cold. These results demonstrate that the cucumber MC gene family may function in tissue development and plant stress responses.

Excessive UDPG resulting from the mutation of UAP1 causes programmed cell death by triggering reactive oxygen species accumulation and caspase-like activity in rice

Lesion mimic mutants are valuable to unravel the mechanisms governing the programmed cell death (PCD) process. Uridine 5'-diphosphoglucose-glucose (UDPG) functions as a signaling molecule activating multiple pathways in animals, but little is known about its function in plants. Two novel allelic mutants of spl29 with typical PCD characters and reduced pollen viability were obtained by ethane methyl sulfonate mutagenesis in rice cv Kitaake. The enzymatic analyses showed that UDP-N-acetylglucosamine pyrophosphorylase 1 (UAP1) irreversibly catalyzed the decomposition of UDPG. Its activity was severely destroyed and caused excessive UDPG accumulation, with the lesion occurrence associated with the enhanced caspase-like activities in spl29-2. At the transcriptional level, several key genes involved in endoplasmic reticulum stress and the unfolded protein response were abnormally expressed. Moreover, exogenous UDPG could aggravate lesion initiation and development in spl29-2. Importantly, exogenous UDPG and its derivative UDP-N-acetylglucosamine could induce reactive oxygen species (ROS) accumulation and lesion mimics in Kitaake seedlings. These results suggest that the excessive accumulation of UDPG, caused by the mutation of UAP1, was a key biochemical event resulting in the lesion mimics in spl29-2. Thus, our findings revealed that UDPG might be an important component involved in ROS accumulation, PCD execution and lesion mimicking in rice, which also provided new clues for investigating the connection between sugar metabolism and PCD process.

LcMCII-1 is involved in the ROS-dependent senescence of the rudimentary leaves of Litchi chinensis

KEY MESSAGE

LcMCII - 1 is a type II metacaspase. Over-expression of LcMCII- 1 in Arabidopsis promoted ROS-dependent and natural senescence. Virus-induced LcMCII- 1 silencing delayed the ROS-dependent senescence of the rudimentary leaves of Litchi chinensis . Litchi is an evergreen woody fruit tree that is widely cultivated in subtropical and tropical regions. Its floral buds are mixed with axillary or apical panicle primordia, leaf primordia and rudimentary leaves. A low spring temperature is vital for litchi production as it promotes the abscission of the rudimentary leaves, which could otherwise prevent panicle development. Hence, climate change could present additional challenges for litchi production. We previously reported that reactive oxygen species (ROS) can substitute low-temperature treatment to induce the senescence of rudimentary leaves. We have now identified from RNA-Seq data a litchi type II metacaspase gene, LcMCII-1, that is responsive to ROS. Silencing LcMCII-1 by virus-induced gene silencing delayed ROS-dependent senescence. The ectopic over-expression of LcMCII-1 in transgenic Arabidopsis promoted ROS-dependent and natural senescence. Consistently, the transient expression of LcMCII-1 in tobacco leaf by agroinfiltration resulted in leaf yellowing. Our findings demonstrate that LcMCII-1 is positively involved in the regulation of rudimentary leaf senescence in litchi and provide a new target for the future molecular breeding of new cultivars that can set fruit in warmer climates.

Plant Proteases Involved in Regulated Cell Death

Each plant genome encodes hundreds of proteolytic enzymes. These enzymes can be divided into five distinct classes: cysteine-, serine-, aspartic-, threonine-, and metalloproteinases. Despite the differences in their structural properties and activities, members of all of these classes in plants are involved in the processes of regulated cell death - a basic feature of eukaryotic organisms. Regulated cell death in plants is an indispensable mechanism supporting plant development, survival, stress responses, and defense against pathogens. This review summarizes recent advances in studies of plant proteolytic enzymes functioning in the initiation and execution of distinct types of regulated cell death.

Genome-wide identification and expression analysis of the metacaspase gene family in Hevea brasiliensis

Metacaspases, a family of cysteine proteases, have been suggested to play important roles in programmed cell death (PCD) during plant development and stress responses. To date, no systematic characterization of this gene family has been reported in rubber tree (Hevea brasiliensis). In the present study, nine metacaspase genes, designated as HbMC1 to HbMC9, were identified from whole-genome sequence of rubber tree. Multiple sequence alignment and phylogenetic analyses suggested that these genes were divided into two types: type I (HbMC1-HBMC7) and type II (HbMC8 and HbMC9). Gene structure analysis demonstrated that type I and type II HbMCs separately contained four and two introns, indicating the conserved exon-intron organization of HbMCs. Quantitative real-time PCR analysis revealed that HbMCs showed distinct expression patterns in different tissues, suggesting the functional diversity of HbMCs in various tissues during development. Most of the HbMCs were regulated by drought, cold, and salt stress, implying their possible functions in regulating abiotic stress-induced cell death. Of the nine HbMCs, HbMC1, HbMC2, HbMC5, and HbMC8 displayed a significantly higher relative transcript accumulation in barks of tapping panel dryness (TPD) trees compared with healthy trees. In addition, the four genes were up-regulated by ethephon (ET) and methyl jasmonate (MeJA), indicating their potential involvement in TPD resulting from ET- or JA-induced PCD. In summary, this work provides valuable information for further functional characterization of HbMC genes in rubber tree.