Genome blaze: engineering chilli pepper chloroplasts for sustainable production of capsaicinoids through organellar genome editing M. Bulle, S. Abbagani, A. Raza Plant Biology, 2025 The quest for superior parental lines of chilli pepper, enriched with heightened levels of phytochemicals, such as capsinoids (CATs) and capsaicinoids (CAPs), has recently gained momentum. Plant scientists now pay more attention to generating pepper cultivars that offer both increased yield and richness in these crucial ingredients. Indeed, the average pepper yield per hectare, as well as richness of these ingredients, are affected by multiple environmental stimuli. However, expression of specific genes is crucial to stimulate the CAT and CAP levels in response to environmental conditions. Recently, new technologies, like genome editing using CRISPR/Cas and engineering of chloroplasts, have been tested in chilli pepper. The advances in genome editing tools, such as the prime editor and base editor methods, have tremendous potential for plant organelle genome engineering. In this article, we highlight recent advancements in CRISPR/Cas and plastid engineering within Capsicum, coupled with application of base editing approaches for editing plant organelle DNA. We also assess the challenges and opportunities in the pursuit of commercial and sustainable production of bioactive compounds specific to Capsicum species.
Strategies to develop climate-resilient chili peppers: transcription factor optimization through genome editing Mallesham Bulle, Md. Mezanur Rahman, Md. Robyul Islam, Sadanandam Abbagani Planta, 2025 Chili peppers (Capsicum spp.), a globally significant crop revered for their nutritional, economic, and cultural importance, are increasingly imperiled by the converging burdens of climate-induced abiotic stresses, including drought, heat, and salinity, and relentless biotic assaults from pathogens and insect herbivores. These overlapping stressors not only destabilize yield but also compromise the metabolic intricacy responsible for the accumulation of health-promoting secondary metabolites. Although Capsicum exhibits remarkable genetic and phytochemical diversity, the integrated transcriptional, metabolic, and epigenetic frameworks that underpin its stress resilience remain poorly delineated. This review synthesizes recent advances in decoding core transcription factor families, such as CaNAC, CaWRKY, and CaMYB, that serve as pivotal regulators of osmotic adjustment, reactive oxygen species detoxification, hormonal crosstalk, and secondary metabolite biosynthesis under stress conditions. We further highlight how multi-omics-guided gene discovery, when paired with CRISPR/Cas-mediated genome editing, enables precise reprogramming of key regulatory loci to enhance adaptive responses. Emerging innovations, including base editing, prime editing, and novel nucleases like Cas12a and Cas13d, are expanding the functional genome-editing landscape, while the integration of morphogenic regulators and genotype-independent transformation platforms is beginning to circumvent long-standing obstacles in Capsicum genetic engineering. Lastly, we propose a transformative framework that converges transcription factor modulation, multi-omics strategies, precision phenotyping, and next-generation genome editing to accelerate the development of climate-resilient Capsicum cultivars with optimized metabolic traits. This strategic convergence of molecular insight and biotechnological innovation offers a robust foundation for building next-generation chili pepper varieties capable of withstanding intensifying environmental and pathogenic pressures, ultimately safeguarding yield, nutritional quality, and agricultural sustainability in the face of global climate change.
Past trauma, better future: how stress memory shapes plant adaptation to drought Md. Mezanur Rahman, Sanjida Sultana Keya, Mallesham Bulle, S.M. Ahsan, Md. Abiar Rahman, et al. Functional Plant Biology, 2025 Can plants remember drought? Emerging evidence suggests that prior stress exposure leaves an epigenetic imprint, reprogramming plants for enhanced resilience. However, the stability and functional relevance of drought memory remain unresolved. This review synthesizes recent advances in epigenetic modifications, transcriptional reprogramming, and metabolic priming, critically assessing their roles in plant stress adaptation. DNA methylation dynamically reshapes chromatin landscapes, yet its transient nature questions its long-term inheritance. Histone modifications, particularly H3K9ac and H2Bub1, may encode stress signatures, enabling rapid transcriptional responses, whereas small RNAs fine-tune chromatin states to reinforce memory. Beyond epigenetics, physiological priming, including osmotic adjustments, antioxidant defenses, and hormonal crosstalk, introduces further complexity, yet its evolutionary advantage remains unclear. Root system plasticity may enhance drought resilience, but its metabolic trade-offs and epigenetic underpinnings are largely unexplored. A critical challenge is disentangling stable adaptive mechanisms from transient acclimatory shifts. We propose a framework for evaluating drought memory across temporal and generational scales and highlight the potential of precision genome editing to establish causality. By integrating multi-omics, gene editing, and field-based validation, this review aims to unlock the molecular blueprint of drought memory. Understanding these mechanisms is key to engineering climate-resilient crops, ensuring global food security in an era of increasing environmental uncertainty.
Method for Extending Shelf-Life of Agricultural Produce M BULLE, A KUMARI, KJ GUPTA EP Patent EP3,937,633 , 2026 2026
Advancing chloroplast bioengineering: Innovations, regulatory challenges, and translational pathways for sustainable agriculture M Bulle*, MM Rahman, S Kota, MR Islam, SS Keya, S Abbagani, PB Kirti International Journal of Biological Macromolecules, 150873 , 2026 2026 Citations: 1
Genome blaze: engineering chilli pepper chloroplasts for sustainable production of capsaicinoids through organellar genome editing M Bulle*, S Abbagani, A Raza Plant Biology 27 (7), 1244-1252 , 2025 2025 Citations: 3
Revolutionizing Metabolic Engineering in Cannabis sativa L.: Harnessing the Power of Hairy Root Culture M Injamum-Ul-Hoque, MM Rahman, NC Howlader, S Tavakoli, ... Int.J.Exp.Bot. , 2025 2025
Strategies to develop climate-resilient chili peppers: transcription factor optimization through genome editing M Bulle*, MM Rahman, MR Islam, S Abbagani Planta 262 (2), 1-18 , 2025 2025 Citations: 14
Method for extending shelf-life of agricultural produce JG KAPUGANTI, M BULLE, A KUMARI US Patent 12,310,380 , 2025 2025
Past trauma, better future: How stress memory shapes plant adaptation to drought MM Rahman, S Keya, M Bulle, SM Ahsan, MA Rahman, MS Roni, ... Functional Plant Biology , 2025 2025 Citations: 12
Delivering Genome Editing Reagents Into Plants: Agrobacterium- and Non-Agrobacterium-mediated Approaches M Bulle, K Ghose, H Shinde, A Nadaf, R Deshmukh, G B. Patil Genome Editing for Crop Improvement: Theory and Methodology, 88-118 , 2025 2025 Citations: 1
Thirsty, soaked, and thriving: Maize morpho-physiological and biochemical responses to sequential drought, waterlogging, and re-drying SS Keya, MR Islam, H Pham, MA Rahman, M Bulle, A Patwary, ... Plant Stress 15, 100722 , 2025 2025 Citations: 17
Green vanguards: Harnessing the power of plant antioxidants, signal catalysts, and genetic engineering to combat reactive oxygen species under multiple abiotic stresses MM Rahman, PK Ghosh, M Akter, MM Al Noor, MA Rahman, SS Keya, ... Plant Stress, 100547 , 2024 2024 Citations: 66
Enhancing drought tolerance in chilli pepper through AdDjSKI-mediated modulation of ABA sensitivity, photosynthetic preservation, and ROS scavenging. M Bulle*.,AK Venkatapuram.,M M Rahman.,K A Attia., A A Mohammed.,S Abbagani ... Physiologia Plantarum 176 (3), e14379 , 2024 2024 Citations: 14
Plastid-expressed AdDjSKI enhances photosystem II stability, delays leaf senescence, and increases fruit yield in tomato plants under heat stress M Bulle*, E Devadasi, S Rampuria, R Subramanyam, Kirti P.B. Physiologia Plantarum 176, e14374 , 2024 2024 Citations: 6
CRISPR/Cas9 based genome editing of Phytoene desaturase (PDS) gene in chilli pepper (Capsicum annuum L.) M Bulle*, AK Venkatapuram, S Abbagani, PB Kirti Journal of Genetic Engineering and Biotechnology 22 (2) , 2024 2024 Citations: 29
MetaTopolin-driven breakthrough in lemon beebalm (Monarda citriodora) regeneration: A molecular fidelity study for genome engineering applications Y Sen, V Sharma, S Singh, M Bulle, P Misra, S Kota JOURNAL OF MEDICINAL AND AROMATIC PLANT SCIENCES 46 (3), 123-132 , 2024 2024 Citations: 1
Thanks to Reviewers, The Plant Genome, 2023 AJ Ackerman, A Adak, J Adaskaveg, G Agarwal, J Akhtar, RO Akinwale, ... The Plant Genome , 2024 2024
Chloroplast Genome Engineering: A Plausible Approach to Combat Chili Thrips and Other Agronomic Insect Pests of Crops M Bulle*, V Sheri, M Aileni, B Zhang Plants 12 (19), 3448 , 2023 2023 Citations: 12
Woodfordia fruticosa (L.) Kurz: in vitro biotechnological interventions and perspectives M Aileni, M Bulle*, RN Malavath, S Thurpu, K Bandaram, B Balkampeta, M Marri ... Applied Microbiology and Biotechnology 107, 5855–5871 , 2023 2023 Citations: 7
Method For Extending Shelf-life of Fruits and Vegetables Using Hypoxia Induced Nitric Oxide M BULLE, A KUMARI, K J Gupta IN Patent 201,911,009,428 , 2020 2020
Method for Extending Sheli-life of Agricultural Produce M BULLE,A KUMARI,KJ Gupta WO Patent WO/2020/183,491 , 2020 2020
Nitrogen Metabolism in Plants: Methods and Protocols R Kishorekumar, M Bulle, A Wany, KJ Gupta Humana Press/ Springer , 2020 2020 Citations: 8
MOST CITED SCHOLAR PUBLICATIONS
An overview of important enzymes involved in nitrogen assimilation of plants R Kishorekumar, M Bulle, A Wany, KJ Gupta Methods in Molecular Biology, 1-13 , 2020 2020 Citations: 166
Overexpression of a wheat Na + /H + antiporter gene ( TaNHX2 ) enhances tolerance to salt stress in transgenic tomato plants ( Solanum lycopersicum L.) R Yarra, SJ He, S Abbagani, B Ma, M Bulle, WK Zhang Plant Cell, Tissue and Organ Culture (PCTOC) 111 (1), 49-57 , 2012 2012 Citations: 106
Enhanced salinity stress tolerance in transgenic chilli pepper (Capsicum annuum L.) plants overexpressing the wheat antiporter (TaNHX2) gene M Bulle*, R Yarra, S Abbagani Molecular Breeding 36, 36 , 2016 2016 Citations: 82
Green vanguards: Harnessing the power of plant antioxidants, signal catalysts, and genetic engineering to combat reactive oxygen species under multiple abiotic stresses MM Rahman, PK Ghosh, M Akter, MM Al Noor, MA Rahman, SS Keya, ... Plant Stress, 100547 , 2024 2024 Citations: 66
Current approaches to measure nitric oxide in plants Vishwakarma, A., Wany, A., Pandey, S., Bulle, M*., Kumari, A., Kishorekumar ... Journal of Experimental Botany 70 (17), 4333-4343 , 2019 2019 Citations: 60
Alternative oxidase is an important player in the regulation of nitric oxide levels under normoxic and hypoxic conditions in plants A Kumari, PK Pathak, M Bulle, AU Igamberdiev, KJ Gupta Journal of Experimental Botany 70 (17), 4345–4354 , 2019 2019 Citations: 48
CRISPR/Cas9 based genome editing of Phytoene desaturase (PDS) gene in chilli pepper (Capsicum annuum L.) M Bulle*, AK Venkatapuram, S Abbagani, PB Kirti Journal of Genetic Engineering and Biotechnology 22 (2) , 2024 2024 Citations: 29
Efficient in vitro direct shoot organogenesis from seedling derived split node explants of Maize (Zea mays L.) R Mushke, R Yarra, M Bulle Journal of Genetic Engineering and Biotechnology 14 (1), 49-53 , 2016 2016 Citations: 28
Polyamine induction in postharvest banana fruits in response to NO donor SNP occurs via L–arginine mediated pathway and not via competitive diversion of S adenosyl-L-methionine. Lokesh V, Manjunatha G, Namratha SH, Bulle M, Bijesh P, Gupta KJ, Neelwerne B Antioxidants 8 (9), 358 , 2019 2019 Citations: 26
A rapid and efficient method for in vitro shoot organogenesis and production of transgenic Bacopa monnieri L. mediated by Agrobacterium tumefaciens M Aileni, M Bulle, S Kota, KK Gadidasu, VR Kokkirala, R Yarra, Z Peng, ... In Vitro Cellular & Developmental Biology-Plant 48, 153-159 , 2012 2012 Citations: 21
Thirsty, soaked, and thriving: Maize morpho-physiological and biochemical responses to sequential drought, waterlogging, and re-drying SS Keya, MR Islam, H Pham, MA Rahman, M Bulle, A Patwary, ... Plant Stress 15, 100722 , 2025 2025 Citations: 17
Strategies to develop climate-resilient chili peppers: transcription factor optimization through genome editing M Bulle*, MM Rahman, MR Islam, S Abbagani Planta 262 (2), 1-18 , 2025 2025 Citations: 14
Enhancing drought tolerance in chilli pepper through AdDjSKI-mediated modulation of ABA sensitivity, photosynthetic preservation, and ROS scavenging. M Bulle*.,AK Venkatapuram.,M M Rahman.,K A Attia., A A Mohammed.,S Abbagani ... Physiologia Plantarum 176 (3), e14379 , 2024 2024 Citations: 14
In vitro plantlet regeneration and Agrobacterium tumefaciens -mediated genetic transformation of Indian Kino tree ( Pterocarpus marsupium Roxb.) R Tippani, R Yarra, M Bulle, M Porika, S Abbagani, C Thammidala Acta physiologiae plantarum 35 (12), 3437-3446 , 2013 2013 Citations: 14
An efficient in vitro leaf-based regeneration and evaluation of genetic Fidelity using ISSR markers in Woodfordia fruticosa (L.) Kurz M Bulle, S Kota, D Rathakatla, M Aileni, VR Kokkirala, KK Gadidasu, ... Journal of Herbs, Spices & Medicinal plants 18 (2), 178-190 , 2012 2012 Citations: 14
Past trauma, better future: How stress memory shapes plant adaptation to drought MM Rahman, S Keya, M Bulle, SM Ahsan, MA Rahman, MS Roni, ... Functional Plant Biology , 2025 2025 Citations: 12
Chloroplast Genome Engineering: A Plausible Approach to Combat Chili Thrips and Other Agronomic Insect Pests of Crops M Bulle*, V Sheri, M Aileni, B Zhang Plants 12 (19), 3448 , 2023 2023 Citations: 12
In vitro conservation and genetic homogeneity assessment of Butea monosperma (Lam.) Taub. Var. lutea (Witt.) Maheshwari—A potential pharmaceutical legume tree R Yarra, M Bulle, R Mushke, EN Murthy Journal of Applied Research on Medicinal and Aromatic Plants 3 (4), 195-199 , 2016 2016 Citations: 9
Nitrogen Metabolism in Plants: Methods and Protocols R Kishorekumar, M Bulle, A Wany, KJ Gupta Humana Press/ Springer , 2020 2020 Citations: 8
Woodfordia fruticosa (L.) Kurz: in vitro biotechnological interventions and perspectives M Aileni, M Bulle*, RN Malavath, S Thurpu, K Bandaram, B Balkampeta, M Marri ... Applied Microbiology and Biotechnology 107, 5855–5871 , 2023 2023 Citations: 7
