Constitutive over-expression of rice chymotrypsin protease inhibitor gene OCPI2 results in enhanced growth, salinity and osmotic stress tolerance of the transgenic Arabidopsis plants

The Dual Role of Antimicrobial Proteins and Peptides: Exploring Their Direct Impact and Plant Defense-Enhancing Abilities

Plants face numerous environmental stresses that hinder their growth and productivity, including biotic agents, such as herbivores and parasitic microorganisms, as well as abiotic factors, such as cold, drought, salinity, and high temperature. To counter these challenges, plants have developed a range of defense strategies. Among these, plant antimicrobial proteins and peptides (APPs) have emerged as a promising solution. Due to their broad-spectrum activity, structural stability, and diverse mechanisms of action, APPs serve as powerful tools to complement and enhance conventional agricultural methods, significantly boosting plant defense and productivity. This review focuses on different studies on APPs, emphasizing their crucial role in combating plant pathogens and enhancing plant resilience against both biotic and abiotic stresses. Beginning with in vitro studies, we explore how APPs combat various plant pathogens. We then delve into the defense mechanisms triggered by APPs against biotic stress, showcasing their effectiveness against bacterial and fungal diseases. Additionally, we highlight the role of APPs in mitigating the abiotic challenges associated with climatic change. Finally, we discuss the current applications of APPs in agriculture, emphasizing their potential for sustainable agricultural practices and the need for future research in this area.

Polysome-bound mRNAs and translational mechanisms regulate drought tolerance in rice

Plants evolved several acquired tolerance traits for drought stress adaptation to maintain the cellular homeostasis. Drought stress at the anthesis stage in rice affects productivity due to the inefficiency of protein synthesis machinery. The effect of translational mechanisms on different pathways involved in cellular tolerance plays an important role. We report differential responses of translation-associated mechanisms in rice using polysome bound mRNA sequencing at anthesis stage drought stress in resistant Apo and sensitive IR64 genotypes. Apo maintained higher polysomes with 60 S-to-40 S and polysome-to-monosome ratios which directly correlate with protein levels under stress. IR64 has less protein levels under stress due to defective translation machinery and reduced water potential. Many polysome-bound long non-coding RNAs (lncRNA) were identified in both genotypes under drought, influencing translation. Apo had higher levels of N6-Methyladenosine (m6A) mRNA modifications that contributed for sustained translation. Translation machinery in Apo could maintain higher levels of photosynthetic machinery-associated proteins in drought stress, which maintain gas exchange, photosynthesis and yield under stress. The protein stability and ribosome biogenesis mechanisms favoured improved translation in Apo. The phytohormone signalling and transcriptional responses were severely affected in IR64. Our results demonstrate that, the higher translation ability of Apo favours maintenance of photosynthesis and physiological responses that are required for drought stress adaptation.

Protease inhibitor ASP enhances freezing tolerance by inhibiting protein degradation in kumquat

Cold acclimation is a complex biological process leading to the development of freezing tolerance in plants. In this study, we demonstrated that cold-induced expression of protease inhibitor FmASP in a Citrus-relative species kumquat [Fortunella margarita (Lour.) Swingle] contributes to its freezing tolerance by minimizing protein degradation. Firstly, we found that only cold-acclimated kumquat plants, despite extensive leaf cellular damage during freezing, were able to resume their normal growth upon stress relief. To dissect the impact of cold acclimation on this anti-freezing performance, we conducted protein abundance assays and quantitative proteomic analysis of kumquat leaves subjected to cold acclimation (4°C), freezing treatment (-10°C) and post-freezing recovery (25°C). FmASP (Against Serine Protease) and several non-specific proteases were identified as differentially expressed proteins induced by cold acclimation and associated with stable protein abundance throughout the course of low-temperature treatment. FmASP was further characterized as a robust inhibitor of multiple proteases. In addition, heterogeneous expression of FmASP in Arabidopsis confirmed its positive role in freezing tolerance. Finally, we proposed a working model of FmASP and illustrated how this extracellular-localized protease inhibitor protects proteins from degradation, thereby maintaining essential cellular function for post-freezing recovery. These findings revealed the important role of protease inhibition in freezing response and provide insights on how this role may help develop new strategies to enhance plant freezing tolerance.

The roles of plant proteases and protease inhibitors in drought response: a review

Upon exposure to drought, plants undergo complex signal transduction events with concomitant changes in the expression of genes, proteins and metabolites. For example, proteomics studies continue to identify multitudes of drought-responsive proteins with diverse roles in drought adaptation. Among these are protein degradation processes that activate enzymes and signalling peptides, recycle nitrogen sources, and maintain protein turnover and homeostasis under stressful environments. Here, we review the differential expression and functional activities of plant protease and protease inhibitor proteins under drought stress, mainly focusing on comparative studies involving genotypes of contrasting drought phenotypes. We further explore studies of transgenic plants either overexpressing or repressing proteases or their inhibitors under drought conditions and discuss the potential roles of these transgenes in drought response. Overall, the review highlights the integral role of protein degradation during plant survival under water deficits, irrespective of the genotypes' level of drought resilience. However, drought-sensitive genotypes exhibit higher proteolytic activities, while drought-tolerant genotypes tend to protect proteins from degradation by expressing more protease inhibitors. In addition, transgenic plant biology studies implicate proteases and protease inhibitors in various other physiological functions under drought stress. These include the regulation of stomatal closure, maintenance of relative water content, phytohormonal signalling systems including abscisic acid (ABA) signalling, and the induction of ABA-related stress genes, all of which are essential for maintaining cellular homeostasis under water deficits. Therefore, more validation studies are required to explore the various functions of proteases and their inhibitors under water limitation and their contributions towards drought adaptation.

Aspartic protease inhibitor enhances resistance to potato virus Y and A in transgenic potato plants

BACKGROUND

Viruses are the major threat to commercial potato (Solanum tuberosum) production worldwide. Because viral genomes only encode a small number of proteins, all stages of viral infection rely on interactions between viral proteins and host factors. Previously, we presented a list of the most important candidate genes involved in potato plants' defense response to viruses that are significantly activated in resistant cultivars. Isolated from this list, Aspartic Protease Inhibitor 5 (API5) is a critical host regulatory component of plant defense responses against pathogens. The purpose of this study is to determine the role of StAPI5 in defense of potato against potato virus Y and potato virus A, as well as its ability to confer virus resistance in a transgenic susceptible cultivar of potato (Desiree). Potato plants were transformed with Agrobacterium tumefaciens via a construct encoding the potato StAPI5 gene under the control of the Cauliflower mosaic virus (CaMV) 35S promoter.

RESULTS

Transgenic plants overexpressing StAPI5 exhibited comparable virus resistance to non-transgenic control plants, indicating that StAPI5 functions in gene regulation during virus resistance. The endogenous StAPI5 and CaMV 35S promoter regions shared nine transcription factor binding sites. Additionally, the net photosynthetic rate, stomatal conductivity, and maximum photochemical efficiency of photosystem II were significantly higher in virus-infected transgenic plants than in wild-type plants.

CONCLUSION

Overall, these findings indicate that StAPI5 may be a viable candidate gene for engineering plant disease resistance to viruses that inhibit disease development.

RING Zinc Finger Proteins in Plant Abiotic Stress Tolerance

RING zinc finger proteins have a conserved RING domain, mainly function as E3 ubiquitin ligases, and play important roles in plant growth, development, and the responses to abiotic stresses such as drought, salt, temperature, reactive oxygen species, and harmful metals. RING zinc finger proteins act in abiotic stress responses mainly by modifying and degrading stress-related proteins. Here, we review the latest progress in research on RING zinc finger proteins, including their structural characteristics, classification, subcellular localization, and physiological functions, with an emphasis on abiotic stress tolerance. Under abiotic stress, RING zinc finger proteins on the plasma membrane may function as sensors or abscisic acid (ABA) receptors in abiotic stress signaling. Some RING zinc finger proteins accumulate in the nucleus may act like transcription factors to regulate the expression of downstream abiotic stress marker genes through direct or indirect ways. Most RING zinc finger proteins usually accumulate in the cytoplasm or nucleus and act as E3 ubiquitin ligases in the abiotic stress response through ABA, mitogen-activated protein kinase (MAPK), and ethylene signaling pathways. We also highlight areas where further research on RING zinc finger proteins in plants is needed.

Identification of Key Genes in 'Luang Pratahn', Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks

Salinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critical genes. The transcriptomes of 'Luang Pratahn' rice, a local Thai rice variety with high salt tolerance, were used as a model for analyzing and identifying the key genes responsible for salt-stress tolerance. Based on 3' Tag-Seq data from the time course of salt-stress treatment, weighted gene co-expression network analysis was used to identify key genes in gene modules. We obtained 1,386 significantly differentially expressed genes in eight modules. Among them, six modules indicated a significant correlation within 6, 12, or 48h after salt stress. Functional and pathway enrichment analysis was performed on the co-expressed genes of interesting modules to reveal which genes were mainly enriched within important functions for salt-stress responses. To identify the key genes in salt-stress responses, we considered the two-state co-expression networks, normal growth conditions, and salt stress to investigate which genes were less important in a normal situation but gained more impact under stress. We identified key genes for the response to biotic and abiotic stimuli and tolerance to salt stress. Thus, these novel genes may play important roles in salinity tolerance and serve as potential biomarkers to improve salt tolerance cultivars.

Modulation of Abiotic Stress Responses in Rice by E3-Ubiquitin Ligases: A Promising Way to Develop Stress-Tolerant Crops

Plants are unable to physically escape environmental constraints and have, therefore, evolved a range of molecular and physiological mechanisms to maximize survival in an ever-changing environment. Among these, the post-translational modification of ubiquitination has emerged as an important mechanism to understand and improve the stress response. The ubiquitination of a given protein can change its abundance (through degradation), alter its localization, or even modulate its activity. Hence, ubiquitination increases the plasticity of the plant proteome in response to different environmental cues and can contribute to improve stress tolerance. Although ubiquitination is mediated by different enzymes, in this review, we focus on the importance of E3-ubiquitin ligases, which interact with the target proteins and are, therefore, highly associated with the mechanism specificity. We discuss their involvement in abiotic stress response and place them as putative candidates for ubiquitination-based development of stress-tolerant crops. This review covers recent developments in this field using rice as a reference for crops, highlighting the questions still unanswered.

AtHsc70-1 negatively regulates the basal heat tolerance in Arabidopsis thaliana through affecting the activity of HsfAs and Hsp101

Heat shock protein 70 (Hsp70) chaperones are highly conserved and essential proteins with diverse cellular functions, including plant abiotic stress tolerance. Hsp70 proteins have been linked with basal heat tolerance in plants. Hsp101 likewise is an important chaperone protein that plays a critical role in heat tolerance in plants. We observed that Arabidopsis hsc70-1 mutant seedlings show elevated basal heat tolerance compared with wild-type. Over-expression of Hsc70-1 resulted in increased heat sensitivity. Hsp101 transcript and protein levels were increased during non-heat stress (HS) and post-HS conditions in hsc70-1 mutant seedlings. In contrast, Hsp101 was repressed in Hsc70-1 over-expressing plants after post-HS conditions. Hsc70-1 showed physical interaction with HsfA1d and HsfA1e protein in the cytosol under non-HS conditions. In transient reporter gene analysis, HsfA1d, HsfA1e and HsfA2 showed transcriptional response on the Hsp101 promoter. HsfA1d and HsfA2 transcripts were at higher levels in hsc70-1 mutant compared with wild-type. We provide genetic evidence that Hsc70-1 is a negative regulator affecting HsfA1d/A1e/A2 activators, which in turn regulate Hsp101 expression and basal thermotolerance.

Investigating the role of Bowman-Birk serine protease inhibitor in Arabidopsis plants under drought stress

Serine protease inhibitors (SPIs) play an important role in cell survival, development and host defense. In plants, serine protease inhibitors such as the Kunitz-type inhibitor (KTI) and the Bowman-Birk inhibitor (BBI) have been shown to be induced in response to abiotic stress such as salinity and drought resulting in tolerance to these stresses. In this study, Arabidopsis thaliana (T3) plants overexpressing the BBI gene from maize were generated and subjected to drought stress in order to study the role of BBI protease inhibitor in drought tolerance. Drought treatment of four-week-old Arabidopsis plants was performed by withholding water from plants for nine days and harvested plant material was used for physiological and biochemical analysis. The transgenic lines exhibited normal growth after nine days of drought as compared to the wild-type. The results also showed a higher leaf relative water content (RWC) in transgenic lines when compared to the wild-type (WT), with line 2 having the highest RWC of 72% and the WT having the lowest RWC of 32%. Trypsin-inhibitor activity indicated that the total protein of the positive transgenic plants had stronger protease inhibitory activity than the wild-type. Transgenic lines overexpressing BBI also showed reduced lipid peroxidation (MDA content) as well as enhanced activity of antioxidants glutathione-s-transferase (GST) and ascorbate peroxidase (APX). These results suggest that BBI protease inhibitor leads to drought tolerance associated with reduction in drought-induced oxidative stress.

Cpn60β4 protein regulates growth and developmental cycling and has bearing on flowering time in Arabidopsis thaliana plants

Chloroplastic Cpn60 proteins are type I chaperonins comprising of Cpn60α and Cpn60β subunits. Arabidopsis genome contains six entries in Cpn60 family, out of which two are for Cpn60α subunit and four for Cpn60β subunit. We noted that the cpn60β4 knockout mutant plants (T-DNA insertion salk_064887 line) differed from the wild type Col-0 plants in the developmental programming. cpn60β4 mutant plants showed early seed germination. Radical emergence, hypocotyl emergence and cotyledons opening were faster in cpn60β4 mutant plants than WT. Importantly, cpn60β4 mutant plants showed early-flowering phenotype. The number of flowers and siliques as well as weight of the seeds were higher in cpn60β4 mutant plants as compared to Col-0 plants. These effects were reverted to wild type like growth and developmental patterns when genomic fragment of Arabidopsis encompassing Cpn60β4 gene was complemented in the mutant background. The overexpression of Cpn60β4 gene using CaMV35 promoter in wild type background (OE-Cpn60β4) delayed the floral transition as against wild type plants. The plastid division were affected in cpn60β4 mutant plants compared to Col-0. The results of this study suggest that Cpn60β4 plays important role(s) in chloroplast development and is a key factor in plant growth, development and flowering in Arabidopsis.

Evaluation of Glycosyl-Hydrolases, Phosphatases, Esterases and Proteases as Potential Biomarker for NaCl-Stress Tolerance in Solanum lycopersicum L. Varieties

Salinity stress limited the production in over 30% of irrigated crops and 7% of dryland agriculture worldwide. The objective was to evaluate the effects of NaCl-stress on the enzymatic activity in tomato. Two experiments were carried out in germination and early vegetative growth stages. The activity of proline and peroxidase of eight varieties (Missouri, Yaqui, Vita, Feroz, Rio Grande, Tropic, Ace, and Floradade) submitted to NaCl concentrations (0, 50, 100, 150 and 200 mM de NaCl) and the semi-quantitative activity of 19 enzymes APY ZYM® were measured under a completely randomized design with four replications. Data were analyzed using univariate-multivariate analysis of variance, Tukey's HSD (p = 0.05), canonical discriminant and cluster analysis. The results showed significant differences between varieties and NaCl in proline content. Proline increased as the NaCl concentration increased. Peroxidase did no show significant differences. Eight enzymes were included within the model to properly classify the varieties and NaCl. In shoots, varieties and NaCl showed that enzymatic activity was higher in the order of alkaline-phosphatase > leucine arylamidase > acid phosphatase > naphthol-AS-BI-phosphohydrolase > n-acetyl-β-glucosaminidase > β-galactosidase, while in roots was higher in the order of alkaline-phosphatase > naphthol-AS-BI-phosphohydrolase > acid phosphatase > n-acetyl-β-glucosaminidase. Acid and alkali phosphatase, lipase, esterase, β-galactosidase, and trypsin can be a potential biomarker for NaCl-stress tolerance in tomato.

OsDSSR1, a novel small peptide, enhances drought tolerance in transgenic rice

Small signaling peptides play important roles in plant development and responses to abiotic and biotic stresses. We have identified a novel small peptide gene in rice, OsDSSR1, which is expressed mainly in the root, stem, node, leaf, and panicle. OsDSSR1 expression is also induced by drought, salinity, ABA, and H₂O₂ treatment. OsDSSR1 is localized in the nucleus and cytoplasm. Transgenic plants overexpressing OsDSSR1 exhibited enhanced drought stress tolerance and decreased ABA sensitivity as compared to the wild type. Overexpression of OsDSSR1 promoted the accumulation of compatible osmolytes, such as free proline and soluble sugars. OsDSSR1-overexpressing plants displayed enhanced OsSodCc2 and OscAPX expression and superoxide dismutase and ascorbate peroxidase activities under drought stress. RNA-sequencing data revealed that the expression of 72 abiotic stress-responsive genes was significantly altered in homozygous transgenic plants. These stress-responsive candidate genes will aid in expanding our understanding of the mechanisms by which small peptides mediate tolerance in crop species.

The microtubule-associated RING finger protein 1 (OsMAR1) acts as a negative regulator for salt-stress response through the regulation of OCPI2 (O. sativa chymotrypsin protease inhibitor 2)

Our results suggest that a rice E3 ligase, OsMAR1, physically interacts with a cytosolic protein OCPI2 and may play an important role under salinity stress. Salt is an important abiotic stressor that negatively affects plant growth phases and alters development. Herein, we found that a rice gene, OsMAR1 (Oryza sativa microtubule-associated RING finger protein 1), encoding the RING E3 ligase was highly expressed in response to high salinity, water deficit, and ABA treatment. Fluorescence signals of its recombinant proteins were clearly associated with the microtubules in rice protoplasts. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) showed that OsMAR1 interacted with a cytosolic protein OCPI2 (O. sativa chymotrypsin protease inhibitor 2) and led to its degradation via the 26S proteasome. Heterogeneous overexpression of OsMAR1 in Arabidopsis showed retarded root growth compared with that of control plants, and then led to hypersensitivity phenotypes under high salinity stress. Taken together, OsMAR1 negatively regulates the salt-stress response via the regulation of the OCPI2 protein in rice.

Overexpression of the aphid-induced serine protease inhibitor CI2c gene in barley affects the generalist green peach aphid, not the specialist bird cherry-oat aphid

Aphids are serious pests in crop plants. In an effort to identify plant genes controlling resistance against aphids, we have here studied a protease inhibitor, CI2c in barley (Hordeum vulgare L.). The CI2c gene was earlier shown to be upregulated by herbivory of the bird cherry-oat aphid (Rhopalosiphum padi L.) in barley genotypes with moderate resistance against this aphid, but not in susceptible lines. We hypothesized that CI2c contributes to the resistance. To test this idea, cDNA encoding CI2c was overexpressed in barley and bioassays were carried out with R. padi. For comparison, tests were carried out with the green peach aphid (Myzus persicae Sulzer), for which barley is a poor host. The performance of R. padi was not different on the CI2c-overexpressing lines in comparison to controls in test monitoring behavior and fecundity. M. persicae preference was affected as shown in the choice test, this species moved away from control plants, but remained on the CI2c-overexpressing lines. R. padi-induced responses related to defense were repressed in the overexpressing lines as compared to in control plants or the moderately resistant genotypes. A putative susceptibility gene, coding for a β-1,3-glucanase was more strongly induced by aphids in one of the CI2c-overexpressing lines. The results indicate that the CI2c inhibitor in overexpressing lines affects aphid-induced responses by suppressing defense. This is of little consequence to the specialist R.padi, but causes lower non-host resistance towards the generalist M. persicae in barley.

Arabidopsis CBL interacting protein kinase 3 interacts with ABR1, an APETALA2 domain transcription factor, to regulate ABA responses

Calcium (Ca²⁺) plays a vital role as a second messenger in several signaling pathways in plants. The calcineurin B-like proteins (CBLs) represent a family of plant calcium-binding proteins that function in propagating Ca²⁺ signals by interacting with CBL interacting protein kinases (CIPKs). Phosphorylation of CBL by CIPK is essential for the module to display full activity towards its target protein. Previous genetic analysis showed that the function of CBL9-CIPK3 module was implicated in negatively regulating seed germination and early development. In the present study, we have biochemically investigated the interaction of CBL9-CIPK3 module and our findings show that CBL9 is phosphorylated by CIPK3. Moreover, Abscisic acid repressor 1 (ABR1) is identified as the downstream target of CIPK3 and CIPK3-ABR1 function to regulate ABA responses during seed germination. Our study also indicates that the role of ABR1 is not limited to seed germination but it also regulates the ABA dependent processes in the adult stage of plant development. Combining our results, we conclude that the CBL9-CIPK3-ABR1 pathway functions to regulate seed germination and ABA dependent physiological processes in Arabidopsis.

Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India

Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.

Genome interrogation for novel salinity tolerant Arabidopsis mutants

Soil salinity is becoming an increasingly large problem in agriculture. In this study, we have investigated whether a capacity to withstand salinity can be induced in the salinity sensitive plant species Arabidopsis thaliana, and whether it can be maintained in subsequent generations. To this end, we have used zinc finger artificial transcription factor (ZF-ATFs) mediated genome interrogation. Already within a relatively small collection Arabidopsis lines expressing ZF-ATFs, we found 41 lines that were tolerant to 100 mM NaCl. Furthermore, ZF-ATF encoding gene constructs rescued from the most strongly salinity tolerant lines were indeed found to act as dominant and heritable agents for salinity tolerance. Altogether, our data provide evidence that a silent capacity to withstand normally lethal levels of salinity exists in Arabidopsis and can be evoked relatively easily by in trans acting transcription factors like ZF-ATFs.

Constitutive over-expression of rice ClpD1 protein enhances tolerance to salt and desiccation stresses in transgenic Arabidopsis plants

Caseinolytic proteases (Clps) perform the important role of removing protein aggregates from cells, which can otherwise prove to be highly toxic. ClpD system is a two-component protease complex composed of a regulatory ATPase module ClpD and a proteolytic component ClpP. Under desiccation stress condition, rice ClpD1 (OsClpD1) gene encoding for the regulatory subunit, was represented by four variant transcripts differing mainly in the expanse of their N-terminal amino acids. These transcripts were expressed in a differential manner in response to salt, mannitol and polyethylene glycol stresses in rice. Purified OsClpD1.3 protein exhibited intrinsic chaperone activity, shown using citrate synthase as substrate. Arabidopsis (Col-0) plants over-expressing OsClpD1.3 open reading frame downstream to CaMV35S promoter (ClpD1.3 plants) showed higher tolerance to salt and desiccation stresses as compared to wild type plants. ClpD1.3 seedlings also showed enhanced growth during the early stages of seed germination under unstressed, control conditions. The free proline levels and starch breakdown activities were higher in the ClpD1.3 seedlings as compared to the wild type Arabidopsis seedlings. It thus emerges that increasing the potential of ClpD1 chaperoning activity may be of advantage in protection against abiotic stresses.