Terminology

DNA Glycosylase

DNA glycosylases are a family of enzymes involved in base excision repair

Base excision repair is the mechanism by which damaged bases in DNA are removed and replaced. DNA glycosylases catalyze the first step of this process. They remove the damaged nitrogenous base while leaving the sugar-phosphate backbone intact, creating an apurinic/apyrimidinic site, commonly referred to as an AP site. This is accomplished by flipping the damaged base out of the double helix followed by cleavage of the N-glycosidic bond.

DNA AP lyase Apurinic/Apyrimidinic Lyase

An enzyme that catalyzes the cleavage of the C-O-P bond 3' from the apurinic or apyrimidinic site in DNA via β-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.

In the 1970s, this class of enzyme was found to repair at apurinic or apyrimidinic DNA sites in E. coli and in mammalian cells. This enzyme is part of a family of lyases that cleave carbon-oxygen bonds.

The major active enzyme of this class in bacteria, and specifically, E. coli is endonuclease type III

Recalcitrant Seeds

Are those that cannot withstand desiccation, presenting significant challenges for long-term storage, often requiring cryopreservation in liquid nitrogen.

Orthodox Seeds

Produced by a wide range of plant species, possess desiccation tolerance and are readily stored through conventional freezing.

Research Articles

DNA Double Strand Break Repair Is Important for the Longevity of Primed Seeds Waterworth et al. 2025 Research Article

"Several crop species, including high value vegetable seeds, are routinely improved by priming, a pre‐germinative seed treatment in which controlled hydration increases the speed of germination and enhances field emergence (Heydecker et al. 1973)."

"Seeds of [Wild Type] and DNA repair mutant lines were primed for 48h with −0.75MPa PEG6000 before drying."

"The transcriptional DNA damage response is activated early in Arabidopsis seed germination, around the re-initiation of cellular metabolism upon rehydration and peaks at 6h (Waterworth et al. 2010)."

"Priming was able to partially reverse this ageing‐related profile, such that the subsequent imbibition of primed seeds resulted in gene expression profiles similar to those of high quality, unaged seed lots."

"Priming significantly activated the transcriptional response to chromosomal breaks and, in lig6lig4 mutant seed, greatly exacerbated programmed cell death."

"These results revealed that DSB repair is an important factor in promoting longevity of primed seed, further supported by the improved longevity of primed seeds with enhanced expression of LIG6."

"Collectively our findings establish the genetic requirement for LIG6 in longevity of primed seed and indicate that the reduced longevity of primed seeds is mitigated by DSB repair activities."

Seed DNA damage responses promote germination and growth in Arabidopsis thaliana Waterworth et al. 2022 Research Article

"Collectively, these results indicate that high levels of DNA damage incurred in seeds are countered by low cell cycle activity, cell cycle checkpoints, and DNA repair, promoting successful seedling establishment."

The importance of safeguarding genome integrity in germination and seed longevity Waterworth et al. 2015 Research Article

What was this book about?

Seed Longevity—The Evolution of Knowledge and a Conceptual Framework Nadarajan et al. 2023 Research Article

What was this book about?

WHIRLY proteins maintain seed longevity by effects on seed oxygen signalling during imbibition Taylor et al. 2023 Research Article

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DNA damage checkpoint kinase ATM regulates germination and maintains genome stability in seeds Waterworth et al. 2016 Research Article

This researches how ATM regulates genome stability and delays germination during repair. It does not look at seed longevity itself.

"Mechanistically, ATM functions through control of DNA replication in imbibing seeds."

"We demonstrate that double-strand breaks (DSBs) are rate-limiting for germination. We identify that desiccation tolerant seeds exhibit a striking transcriptional DSB damage response during germination, indicative of high levels of genotoxic stress, which is induced following maturation drying and quiescence."

"In response to aging, ATM delays germination, whereas atm mutant seeds germinate with extensive chromosomal abnormalities."

"In response to genotoxic stresses, these checkpoint kinases activate DNA repair factors, delay or halt cell cycle progression, and promote endocycles or programmed cell death (1–4)."

The nuclear protein Poly(ADP-ribose) polymerase 3 (AtPARP3) is required for seed storability in Arabidopsis thaliana Rissel et al. 2014 Research Article

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Arabidopsis TAF1 is an MRE11-interacting protein required for resistance to genotoxic stress and viability of the male gametophyte Waterworth et al. 2015 Research Article

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Overexpression of AtOGG1, a DNA glycosylase/AP lyase, enhances seed longevity and abiotic stress tolerance in Arabidopsis Chen et al. 2012 Research Article

"Overexpression of AtOGG1 in Arabidopsis enhanced seed resistance to controlled deterioration treatment."

"In addition, the content of 8-hydroxy-2# deoxyguanosine (8-oxo-dG) in transgenic seeds was reduced compared to wild-type seeds, indicating a DNA damage repair function of AtOGG1 in vivo."

A plant DNA ligase is an important determinant of seed longevity Waterworth et al. 2010 Research Article

"Here, phenotypic analysis of atlig6 mutant plants reveals that this DNA ligase plays important roles in seed germination and seed longevity, particularly under genotoxic stress conditions. "

"Likewise, the delayed germination observed in atlig4 mutants, together with the rapid DNA damage transcriptional response detected in imbibing seeds, suggests that double-strand breaks (DSBs) and their associated repair pathways influence germination performance. "

"Overall, these findings highlight significant roles for DNA ligases in maintaining seed vigor and viability during storage under suboptimal conditions, such as those commonly encountered in developing regions."

"This DSB-induced DNA damage response resulted in the significant upregulation of transcripts within 3 h of imbibition (Figure 8a)", with peaks around 6 hours.

Morphological and Physiological Framework Underlying Plant Longevity in Arabidopsis thaliana Wang et al. 2020 Research Article

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Review Articles

Good for background information and broad concepts.

Review Articles

WHIRLY protein functions in plants Taylor et al. 2021 Review Article

"The WHY1 and WHY2 proteins function as transcription factors in the nucleus regulating phytohormone synthesis and associated growth and stress responses, as well as fulfilling crucial roles in DNA and RNA metabolism in plastids and mitochondria."

"WHY1, WHY2 (and WHY3 proteins in Arabidopsis) maintain organelle genome stability and serve as auxiliary factors for homologous recombination and double-strand break repair."

Unraveling the Mechanistic Basis for Control of Seed Longevity Tan et al. 2025 Review Article

"Genes involved in regulating seed longevity in Arabidopsis."

Terminology

Seed Dormancy

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Seed Longevity

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Seed Germination

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Seed Quality

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Seed Viability

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Research

Questions

Has Arabidopsis plant seeds

• How old is the mustard seed?

• Ways to extend the shelf life w/ nutrients w/o inducing germination?

• Scarring/light on germination rates?

Articles

Enhancing seed quality and viability by suppressing phospholipase D in Arabidopsis X et al. XXXX Article

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Arabidopsis Aspartic Protease ASPG1 Affects Seed Dormancy, Seed Longevity and Seed Germination X et al. XXXX Article

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Evaluating the EPPO method for seed longevity analyses in Arabidopsis X et al. XXXX Article

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Receptor-like kinase HAESA-like 1 positively regulates seed longevity in Arabidopsis X et al. XXXX Article

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E3 ligase ATL5 positively regulates seed longevity by mediating the degradation of ABT1 in Arabidopsis X et al. XXXX Article

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Seed longevity is controlled by metacaspases X et al. XXXX Article

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