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Subject: search.filters.subject.DNA repair

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    Molecular timekeepers: the curious alliance of redox, repair, and protective proteins in preserving seed longevity
    (Springer Nature Publishing AG, 2026) Das, Arup; Majee, Manoj
    Seed 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.
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    Branched DNA processing by a thermostable CAS-Cas4 from Thermococcus onnurineus: expanding biochemical landscape of nuclease activity
    (Elsevier B.V., 2025) Jain, Muskan; Pattnayak, Asish Kumar; Aggarwal, Sakshi; Rai, Praveen; Kavya, J.; Chandrayan, Sanjeev; Goel, Manisha; Gaur, Vineet
    The adaptive immune function of CRISPR-Cas systems in bacteria and archaea is mediated through CRISPR-Associated Proteins (Cas). The adaptation module, typically involving Cas1, Cas2, and Cas4, helps integrate viral “spacer” sequences into the host genome. Cas4 proteins are classified into two types based on neighboring genes: CAS-Cas4, flanked by other cas genes, and Solo-Cas4, which exist independently. While CAS-Cas4 proteins are implicated in adaptation, they remain biochemically uncharacterized in archaea, unlike archaeal Solo-Cas4 proteins. This study biochemically characterizes TON_0321, a CAS-Cas4 protein from the Type IV-C CRISPR cassette of Thermococcus onnurineus. TON_0321 exhibits 5′ to 3′ exonuclease activity and unique structure-dependent endonuclease activity, shedding light on CAS-Cas4 functional diversity. A distinct spatial organization of the catalytic site, angled with the positively charged patch on the protein surface, enables TON_0321 to recognize branching points in DNA substrates. Furthermore, this spatial arrangement facilitates cleavage 2 to 3 nucleotides away from the branch point in the 5′ direction, demonstrating structure-specific endonuclease activity.
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    Emerging tools and paradigm shift of gene editing in cereals, fruits, and horticultural crops for enhancing nutritional value and food security
    (John Wiley & Sons, 2021) Tiwari, Manish; Trivedi, Prabodh Kumar; Pandey, Ashutosh
    Gene editing using sequence‐specific nucleases, particularly CRISPR/Cas ribonucleoprotein, has drawn enormous attention in plant research in recent years. Nearly a decade ago, Cas9 protein was initially discovered for a role in adaptive immunity in bacteria. Owing to vast potential, a large number of reports came out in a short span of time, comprising the identification of Cas protein from different bacterial sources, new Cas9 variants with reduced off‐targets, multiplexing, base editing, prime editing, and RNA manipulation in plants. Studies revealed that CRISPR/Cas‐based gene editing can play a major role in ensuring food security via developing resilient commercial crops with improved yield and nutritional value. Use of the CRISPR/Cas9 system for creating mutation in genes and regulatory regions of promoter generated a number of alleles with variable phenotypes, which can serve as an excellent genetic resource in the breeding program. In this review, we provide a recent overview of state‐of‐art discoveries in the CRISPR/Cas system comprised of new Cas proteins, modifications of existing Cas9, refinements in CRISPR/Cas‐induced gene editing, applications, and outcome emphasizing on major cereals and horticultural crops. We also highlight the current global policy framework for the regulation of gene‐edited crops.
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    A combined structural and biochemical approach reveals translocation and stalling of UvrB on the DNA lesion as a mechanism of damage verification in bacterial nucleotide excision repair
    (Elsevier B.V., 2020) Jaciuk, Marcin; Swuec, Paolo; Gaur, Vineet; Kasprzak, Joanna M.; Renault, Ludovic; Dobrychłop, Mateusz; Nirwal, Shivlee; Bujnicki, Janusz M.; Costa, Alessandro; Nowotny, Marcin
    Nucleotide excision repair (NER) is a DNA repair pathway present in all domains of life. In bacteria, UvrA protein localizes the DNA lesion, followed by verification by UvrB helicase and excision by UvrC double nuclease. UvrA senses deformations and flexibility of the DNA duplex without precisely localizing the lesion in the damaged strand, an element essential for proper NER. Using a combination of techniques, we elucidate the mechanism of the damage verification step in bacterial NER. UvrA dimer recruits two UvrB molecules to its two sides. Each of the two UvrB molecules clamps a different DNA strand using its β-hairpin element. Both UvrB molecules then translocate to the lesion, and UvrA dissociates. The UvrB molecule that clamps the damaged strand gets stalled at the lesion to recruit UvrC. This mechanism allows UvrB to verify the DNA damage and identify its precise location triggering subsequent steps in the NER pathway.