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Item Rice PROTEIN L-ISOASPARTYL METHYLTRANSFERASES provides tolerance against sheath blight disease and repairs ALDH and PBZ1(Nature Publishing Group, 2026) Gautam, Shikha; Kamble, Nitin Uttam; Achary, Rakesh Kumar; Chandan, Ravindra Kumar; Varshney, Vishal; Hazra, Abhijit; Laha, Saroj; Mahawar, Shivangi; Mehandiratta, Sohela; Singh, Sarvanand; Jha, Gopaljee; Majee, ManojProtein L-isoaspartyl methyltransferase (PIMT) regulates key seed traits and abiotic stress tolerance in plants by repairing isoaspartyl (isoAsp) damaged proteins. However, whether PIMT-mediated repair is induced and is required during biotic stress tolerance remains unknown. Using rice lines with OsPIMT overexpression, RNAi-mediated suppression, and genome editing, we show that PIMT enhances tolerance to sheath blight (ShB) caused by Rhizoctonia solani. OsPIMT restricts fungal penetration and colonization of rice sheaths. Co-immunoprecipitation coupled with LC-MS/MS identify various proteins including antioxidant proteins, aldehyde dehydrogenases (ALDH) and pathogenesis-related protein 10 (PBZ1), that undergo isoAsp modification during R. solani infection and interact with PIMT. We show that OsALDH and OsPBZ1 exhibit intrinsic antifungal activity against R. solani, but isoAsp modification impairs their activity, making PIMT mediated repair important. Further, OsALDH enhances tolerance to R. solani by inhibiting lipid peroxidation and ROS homeostasis in rice and fungus. Overall, our study reveals that PIMT enhances ShB tolerance through the repair of isoAsp-damaged proteins important for disease tolerance.Item Molecular intricacies of modulating seed dormancy through CRISPR/Cas9 technology(Oxford University Press, 2026) Gautam, Shikha; Kamble, Nitin Uttam; Majee, ManojThe processes of seed development, maturation, and dormancy acquisition are complex and tightly regulated, and play a critical role in plant survival and propagation. Over the past decades, significant advances have been made in elucidating the molecular mechanisms that govern these intricate processes. The interplay among hormone signaling, epigenetic regulation, reactive oxygen species (ROS), and environmental cues has been recognized as central to determining seed fate. Despite these advancements, many molecular components remain to be fully discovered. Recent developments in CRISPR-based gene-editing technologies have provided promising tools for the precise regulation of seed dormancy without compromising other seed traits. Although CRISPR has been effectively utilized to modify genes controlling physiological characteristics in a wide range of crops, its application in regulating dormancy remains at an early stage. This review synthesizes current knowledge on the molecular and genetic mechanisms controlling seed maturation, dormancy acquisition and germination, with particular emphasis on emerging CRISPR-based strategies. Realizing this potential, however, requires a deeper understanding of the complex regulatory networks orchestrating seed dormancy acquisition and germination. Identifying optimal gene targets and refining editing strategies will be crucial for developing reliable and sustainable dormancy-control systems. Therefore, we highlight key gene targets, summarize their functional relevance, and discuss how genome editing could be leveraged to fine-tune dormancy and germination behaviour. The studies discussed herein underscore the transformative potential of CRISPR/Cas9 and related genome-editing platforms in advancing seed biology and crop improvement, paving the way for next-generation seed technologies.Item Molecular timekeepers: the curious alliance of redox, repair, and protective proteins in preserving seed longevity(Springer Nature Publishing AG, 2026) Das, Arup; Majee, ManojSeed longevity-the ability of seeds to remain viable over time-is an evolutionary masterpiece, ensuring plant survival across generations and in the face of environmental variability. Desiccation-tolerant (orthodox) seeds, representative of most crop species, possess the ability to survive programmed drying during maturation, thereby entering a metabolically inactive state. This anhydrobiotic state serves to prolong embryo viability and shield against adverse environmental conditions. While programmed drying is essential for seed preservation, it can result in oxidative and macromolecular damage, which is exacerbated by fluctuations in temperature and humidity during storage. Consequently, this cumulative damage to deoxyribonucleic acid, proteins, and cellular structures can jeopardize seed viability if not adequately repaired. Seed longevity is therefore dependent not merely on passive resistance by molecular stabilizers but on an active repair mechanism that is initiated upon rehydration. The interplay between redox homeostasis, damage repair, and cellular protective proteins forms the cornerstone of seed longevity, helping seeds retain their ability to germinate. This review delves into the converging roles of redox homeostasis, repair, and protective proteins in governing the longevity of seeds. By unraveling how these components cooperate and communicate, we gain deeper insights into the natural strategies that seeds employ to delay aging. Exploring the molecular underpinnings of seed longevity offers substantial novel genetic targets for developing crops with improved resistance to evolving climates and provides crucial insights for the conservation of plant germplasm.Item Cellular responses in the pigeonpea wild relative Cajanus platycarpus to Helicoverpa armigera herbivory: The role of methionine sulfoxide reductase B1 (CpMSRB1) in enhanced defense(American Phytopathological Society, 2025) Rathinam, Maniraj; Dokka, Narasimham; Senthil, Kameshwaran; Mahawar, Shivangi; Tyagi, Shaily; Rengarajan, Dineshkumar; Vijayaraghavareddy, Preethi; Iyyappan, Yuvaraj; YB, Basavaraj; Reddy, Sandeep; T, Vinutha; G, Rama Prashat; Sinha, Subodh Kumar; Dash, Prasanta K.; Sreeman, Sheshshayee; Majee, Manoj; Sreevathsa, RohiniUnderstanding key cellular mechanisms leading to improved defense against various stressors is essential for cultivating robust nutritious crops capable of flourishing in diverse environments. We present an in-depth characterization of the defense response in the pigeonpea wild relative Cajanus platycarpus to herbivory by pod borer Helicoverpa armigera. To fight the attacking pest, C. platycarpus strategically activated non-enzymatic reactive oxygen species (ROS) scavengers and unleashed methionine sulfoxide reductases to safeguard the integrity of methionine residues. We unveiled for the first time physical interaction between CpMSRB1 and chorismate mutase (CpCM1.1), a pivotal player in the phenylpropanoid pathway. This association fueled the synthesis of phenylpropanoids and enhanced ROS scavenging crucial for repelling herbivores. Repairing CpCM1.1 also boosted salicylic acid production, coordinating defense signaling with jasmonic acid. Additionally, heterologous expression of CpMSRB1 in tomato improved defense against herbivory by enhanced ROS scavenging and polyphenol production. This study demonstrates the role of CpMSRB1 in protecting a major enzyme in the shikimate pathway, reinforcing defense against H. armigera.Item The rice heat shock transcription factor OsHSFC1b increases seed weight, size, and vigor, but its function is disrupted by isoaspartyl modification(John Wiley & Sons, 2025) Achary, Rakesh Kumar; Kamble, Nitin Uttam; Gautam, Shikha; Hazra, Abhijit; Varshney, Vishal; Mahawar, Shivangi; Laha, Saroj; Majee, ManojPlant optimizes seed size, weight, vigor, and various other features during seed development, which are important not only for their successful propagation and establishment but also for effective agriculture. Despite several studies conducted, understanding how plants coordinate the regulatory mechanisms to achieve optimal seed size, weight, and vigor remains elusive. Here, our study reveals the role of rice heat shock transcription factor OsHSFC1b in modulating various seed attributes. We observe that OsHSFC1b expression increases during the later stage of seed development and is primarily localized in the embryo. We found that hsfc1b genome-edited lines exhibit compromised seed size, weight, and vigor, while overexpression lines exhibit increased seed size, weight, and vigor compared with the wild-type seeds. Our study further reveals that OsHSFC1b improves seed vigor by activating HSPs and RFO biosynthetic genes involved in protection mechanisms, while also mediating seed size and weight by modulating auxin biosynthesis, endosperm development, and seed filling. We found that upon ageing and stressful environments, OsHSFC1b undergoes isoaspartyl modification that negatively impacts its biological function in seeds. Our MS/MS analyses confirm that asparagine residues near the DNA-binding domain and nuclear localization sequence of OsHSFC1b undergo isoaspartyl modification that adversely affects OsHSFC1b's transactivation activity. However, PROTEIN L-ISOASPARTYL METHYLTRANSFERASE interacts and repairs this isoaspartate-mediated damage, and restores the function of OsHSFC1b. Taken together, our study uncovers how isoaspartyl modification affects the transactivation ability of OsHSFC1b, yet the intervention of PIMT not only repairs this damage but also elevates agronomically important seed traits.Item PROTEIN L-ISOASPARTYL METHYLTRANSFERASE protects enolase dysfunction by repairing isoaspartyl-induced damage and is positively implicated in agronomically important seed traits(John Wiley & Sons, 2024) Kamble, Nitin Uttam; Ghosh, Shraboni; Petla, Bhanu Prakash; Achary, Rakesh Kumar; Gautam, Shikha; Rao, Venkateswara; Salvi, Prafull; Hazra, Abhijit; Varshney, Vishal; Majee, ManojThe protein-repairing enzyme (PRE) PROTEIN L-ISOASPARTYL METHYLTRANSFERASE (PIMT) influences seed vigor by repairing isoaspartyl-mediated protein damage in seeds. However, PIMTs function in other seed traits, and the mechanisms by which PIMT affects such seed traits are still poorly understood. Herein, through molecular, biochemical, and genetic studies using overexpression and RNAi lines in Oryza sativa and Arabidopsis thaliana, we demonstrate that PIMT not only affects seed vigor but also affects seed size and weight by modulating enolase (ENO) activity. We have identified ENO2, a glycolytic enzyme, as a PIMT interacting protein through Y2H cDNA library screening, and this interaction was further validated by BiFC and co-immunoprecipitation assay. We show that mutation or suppression of ENO2 expression results in reduced seed vigor, seed size, and weight. We also proved that ENO2 undergoes isoAsp modification that affects its activity in both in vivo and in vitro conditions. Further, using MS/MS analyses, amino acid residues that undergo isoAsp modification in ENO2 were identified. We also demonstrate that PIMT repairs such isoAsp modification in ENO2 protein, protecting its vital cellular functions during seed maturation and storage, and plays a vital role in regulating seed size, weight, and seed vigor. Taken together, our study identified ENO2 as a novel substrate of PIMT, and both ENO2 and PIMT in turn implicate in agronomically important seed traits.Item Seed's Awakening: Unveiling the MKK3-MPK7-ERF4 module in dormancy-to-germination transition(Elsevier B.V., 2023) Varshney, Vishal; Majee, ManojSeed dormancy is nature's strategic pause in the plant life cycle, a purposeful interlude during which a seed, poised on the cusp of potential growth, bides its time in a state of quiescence. This period of dormancy is a crucial adaptation, allowing the seed to withstand unfavorable environmental conditions and synchronize germination with optimal circumstances for growth and survival (Née et al., 2017). Dormancy is orchestrated by a complex interplay of genetic, physiological, and environmental factors, including phytohormones like abscisic acid (ABA) and gibberellins (GA), as well as specific regulators like DELAY OF GERMINATION1 (DOG1) and others (Née et al., 2017; Liu et al., 2020)Item The Arabidopsis F-box protein SKP1-INTERACTING PARTNER 31 modulates seed maturation and seed vigor by targeting JASMONATE ZIM DOMAIN proteins independently of jasmonic acid-isoleucine(Oxford University Press, 2023) Varshney, Vishal; Hazra, Abhijit; Rao, Venkateswara; Ghosh, Shraboni; Kamble, Nitin Uttam; Achary, Rakesh Kumar; Gautam, Shikha; Majee, ManojF-box proteins have diverse functions in eukaryotic organisms, including plants, mainly targeting proteins for 26S proteasomal degradation. Here, we demonstrate the role of the F-box protein SKP1-INTERACTING PARTNER 31 (SKIP31) from Arabidopsis (Arabidopsis thaliana) in regulating late seed maturation events, seed vigor, and viability through biochemical and genetic studies using skip31 mutants and different transgenic lines. We show that SKIP31 is predominantly expressed in seeds and that SKIP31 interacts with JASMONATE ZIM DOMAIN (JAZ) proteins, key repressors in jasmonate (JA) signaling, directing their ubiquitination for proteasomal degradation independently of coronatine/jasmonic acid-isoleucine (JA-Ile), in contrast to CORONATINE INSENSITIVE 1, which sends JAZs for degradation in a coronatine/JA-Ile dependent manner. Moreover, JAZ proteins interact with the transcription factor ABSCISIC ACID-INSENSITIVE 5 (ABI5) and repress its transcriptional activity, which in turn directly or indirectly represses the expression of downstream genes involved in the accumulation of LATE EMBRYOGENESIS ABUNDANT proteins, protective metabolites, storage compounds, and abscisic acid biosynthesis. However, SKIP31 targets JAZ proteins, deregulates ABI5 activity, and positively regulates seed maturation and consequently seed vigor. Furthermore, ABI5 positively influences SKIP31 expression, while JAZ proteins repress ABI5-mediated transactivation of SKIP31 and exert feedback regulation. Taken together, our findings reveal the role of the SKIP31-JAZ-ABI5 module in seed maturation and consequently, establishment of seed vigor.Item CONSTANS, a key-player connecting day length to seed size(Elsevier B.V., 2023) Achary, Rakesh Kumar; Majee, ManojPlants sense oscillation in the day length as a reliable seasonal cue to drive optimal vegetative and reproductive growth. A recent study by Yu et al. has revealed how day length regulates seed size through CONSTANS. The CONSTANS-APETALA2 module enables plants to optimize their reproductive growth based on their photoperiod response type.Item Seed germination variability: Why do genetically identical seeds not germinate at the same time?(Oxford University Press, 2023) Sharma, Eshan; Majee, ManojFor survival in the wild environment, plants prefer a bet-hedging strategy where individual variation is high and also produce a range of phenotypes. When faced with unpredictable environmental conditions, fluctuation in seed behaviour is a beneficial trait that allows the survival of plants, particularly if seedlings from early germinated seeds don't survive. However, this is not a desired trait when agriculture is concerned, where a set of uniformly grown seedlings are required. Even though variability in seed behaviour is unavoidable, over the centuries, humans might have selected seeds with minimum variability for agricultural use. In the model plant Arabidopsis, non-stratified seeds even in the same silique germinate variably. How this variability is manifested from genes to a physiological outcome and what molecular mechanism of bet-hedging facilitates this diversity remains elusive. Will the reintroduction of valuable wild alleles in domesticated crops contribute to this variability between individual seeds by promotion of bet-hedging? Recent advances have shed light on possible molecular pathways of germination that are impacted at the level of single seeds and single cells. Here, we review the hormonal, molecular and cellular mechanisms that may impact the germination outcome of individual genetically identical seeds.