Hairpin Opening and Overhang Processing by an Artemis/DNA-Dependent Protein Kinase Complex in Nonhomologous End Joining and V(D)J Recombination

Cloning and characterization of the

Cation transport is a critical process in all organisms and is essential for mineral nutrition, ion stress tolerance, and signal transduction. Transporters that are members of the Ca(2+)/cation antiporter (CaCA) superfamily are involved in the transport of Ca(2+) and/or other cations using the counter exchange of another ion such as H(+) or Na(+). The CaCA superfamily has been previously divided into five transporter families: the YRBG, Na(+)/Ca(2+) exchanger (NCX), Na(+)/Ca(2+), K(+) exchanger (NCKX), H(+)/cation exchanger (CAX), and cation/Ca(2+) exchanger (CCX) families, which include the well-characterized NCX and CAX transporters. To examine the evolution of CaCA transporters within higher plants and the green plant lineage, CaCA genes were identified from the genomes of sequenced flowering plants, a bryophyte, lycophyte, and freshwater and marine algae, and compared with those from non-plant species. We found evidence of the expansion and increased diversity of flowering plant genes within the CAX and CCX families. Genes related to the NCX family are present in land plant though they encode distinct MHX homologs which probably have an altered transport function. In contrast, the NCX and NCKX genes which are absent in land plants have been retained in many species of algae, especially the marine algae, indicating that these organisms may share "animal-like" characteristics of Ca(2+) homeostasis and signaling. A group of genes encoding novel CAX-like proteins containing an EF-hand domain were identified from plants and selected algae but appeared to be lacking in any other species. Lack of functional data for most of the CaCA proteins make it impossible to reliably predict substrate specificity and function for many of the groups or individual proteins. The abundance and diversity of CaCA genes throughout all branches of life indicates the importance of this class of cation transporter, and that many transporters with novel functions are waiting to be discovered.

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Protein Phylogenetic Analysis of Ca2+/cation Antiporters and Insights into their Evolution in Plants

Germination vigor is driven by the ability of the plant embryo, embedded within the seed, to resume its metabolic activity in a coordinated and sequential manner. Studies using “-omics” approaches support the finding that a main contributor of seed germination success is the quality of the messenger RNAs stored during embryo maturation on the mother plant. In addition, proteostasis and DNA integrity play a major role in the germination phenotype. Because of its pivotal role in cell metabolism and its close relationships with hormone signaling pathways regulating seed germination, the sulfur amino acid metabolism pathway represents a key biochemical determinant of the commitment of the seed to initiate its development toward germination. This review highlights that germination vigor depends on multiple biochemical and molecular variables. Their characterization is expected to deliver new markers of seed quality that can be used in breeding programs and/or in biotechnological approaches to improve crop yields.

https://www.uv.mx/personal/tcarmona/files/2010/08/Rajjou-et-al-2012.pdf

Seed Germination and Vigor

Rapid seed germination and stand establishment are critical factors to crop production under salt‐stress conditions. In many crop species, seed germination and early seedling growth are the most sensitive stages to salinity stress. Salinity may delay the onset, reduce the rate, and increase the dispersion of germination events, leading to reductions in plant growth and final crop yield. The adverse effects of salt‐stress can be alleviated by various measures, including seed priming (a.k.a. pre‐sowing seed treatment). The general purpose of seed priming is to partially hydrate the seed to a point where germination processes are begun but not completed. Most priming treatments involve imbibing seed with restricted amounts of water to allow sufficient hydration and advancement of metabolic processes but preventing germination or loss of desiccation tolerance. Treated seeds are usually redried before use, but they would exhibit rapid germination when re‐imbibed under normal or stress conditions. Various seed priming techniques have been developed, including hydropriming (soaking in water), halopriming (soaking in inorganic salt solutions), osmopriming (soaking in solutions of different organic osmotica), thermopriming (treatment of seed with low or high temperatures), solid matrix priming (treatment of seed with solid matrices), and biopriming (hydration using biological compounds). Each treatment has advantages and disadvantages and may have varying effects depending upon plant species, stage of plant development, concentration/dose of priming agent, and incubation period. In this article, we review, evaluate, and compare effects of various methods of seed priming in improving germination of different plant species under saline and non‐saline conditions. We also discuss the known metabolic and ultra‐structural changes that occur during seed priming and subsequent germination. To maximize the utility of various seed priming techniques, factors affecting their efficiency must be examined and potential benefits and drawbacks determined. For example, quality of the seed before treatment, concentration/dose of priming agent, time period for priming, and storage quality of the seed following priming treatment must be carefully determined. Furthermore, such assessments must be based on large‐scale experiments if seed priming is to be used for large‐scale field planting. A better understanding of the metabolic events that take place in the seed during priming and subsequent germination will improve the effective application of this technology. The incorporation of advanced molecular biology techniques in seed research is vital to the understanding and integration of multiple metabolic processes that can lead to enhanced seed germination, and consequently to improved stand establishment and crop yield under saline and non‐saline conditions.

Pre‐Sowing Seed Treatment—A Shotgun Approach to Improve Germination, Plant Growth, and Crop Yield Under Saline and Non‐Saline Conditions

As obligate phototrophs, plants harness energy from sunlight to split water, producing oxygen and reducing power. This lifestyle exposes plants to particularly high levels of genotoxic stress that threatens genomic integrity, leading to mutation, developmental arrest and cell death. Plants, which with algae are the only photosynthetic eukaryotes, have evolved very effective pathways for DNA damage signalling and repair, and this review summarises our current understanding of these processes in the responses of plants to genotoxic stress. We also identify how the use of new and emerging technologies can complement established physiological and ecological studies to progress the application of this knowledge in biotechnology.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2005.01548.x

DNA repair mechanisms in plants: crucial sensors and effectors for the maintenance of genome integrity.

Biochemical Changes During Osmopriming of Leek Seeds

DNA damage threatens the integrity of the genome and has potentially lethal consequences for the organism. Plant DNA is under continuous assault from endogenous and environmental factors and effective detection and repair of DNA damage are essential to ensure the stability of the genome. One of the most cytotoxic forms of DNA damage are DNA double-strand breaks (DSBs) which fragment chromosomes. Failure to repair DSBs results in loss of large amounts of genetic information which, following cell division, severely compromises daughter cells that receive fragmented chromosomes. This review will survey recent advances in our understanding of plant responses to chromosomal breaks, including the sources of DNA damage, the detection and signalling of DSBs, mechanisms of DSB repair, the role of chromatin structure in repair, DNA damage signalling and the link between plant recombination pathways and transgene integration. These mechanisms are of critical importance for maintenance of plant genome stability and integrity under stress conditions and provide potential targets for the improvement of crop plants both for stress resistance and for increased precision in the generation of genetically improved varieties.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2011.03926.x

Repairing breaks in the plant genome: the importance of keeping it together

DNA repair is important for maintaining genome integrity. In plants, DNA damage accumulated in the embryo of seeds is repaired early in imbibition, and is important for germination performance and seed longevity. An essential step in most repair pathways is the DNA ligase-mediated rejoining of single- and double-strand breaks. Eukaryotes possess multiple DNA ligase enzymes, each having distinct roles in cellular metabolism. Here, we report the characterization of DNA LIGASE VI, which is only found in plant species. The primary structure of this ligase shows a unique N-terminal region that contains a β-CASP motif, which is found in a number of repair proteins, including the DNA double-strand break (DSB) repair factor Artemis. Phenotypic analysis revealed a delay in the germination of atlig6 mutants compared with wild-type lines, and this delay becomes markedly exacerbated in the presence of the genotoxin menadione. Arabidopsis atlig6 and atlig6 atlig4 mutants display significant hypersensitivity to controlled seed ageing, resulting in delayed germination and reduced seed viability relative to wild-type lines. In addition, atlig6 and atlig6 atlig4 mutants display increased sensitivity to low-temperature stress, resulting in delayed germination and reduced seedling vigour upon transfer to standard growth conditions. Seeds display a rapid transcriptional DNA DSB response, which is activated in the earliest stages of water imbibition, providing evidence for the accumulation of cytotoxic DSBs in the quiescent seed. These results implicate AtLIG6 and AtLIG4 as major determinants of Arabidopsis seed quality and longevity.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2010.04285.x

A plant DNA ligase is an important determinant of seed longevity.

Seeds are important to agriculture and conservation of plant biodiversity. In agriculture, seed germination performance is an important determinant of crop yield, in particular under adverse climatic conditions. Deterioration in seed quality is associated with the accumulation of cellular damage to macromolecules including lipids, protein, and DNA. Mechanisms that mitigate the deleterious cellular damage incurred in the quiescent state and in cycles of desiccation-hydration are crucial for the maintenance of seed viability and germination vigour. In early-imbibing seeds, damage to the embryo genome must be repaired prior to initiation of cell division to minimize growth inhibition and mutation of genetic information. Here we review recent advances that have established molecular links between genome integrity and seed quality. These studies identified that maintenance of genome integrity is particularly important to the seed stage of the plant lifecycle, revealing new insight into the physiological roles of plant DNA repair and recombination mechanisms. The high conservation of DNA repair and recombination factors across plant species underlines their potential as promising targets for the improvement of crop performance and development of molecular markers for prediction of seed vigour.

Clifford M. Bray

Papers

DNA repair mechanisms in plants: crucial sensors and effectors for the maintenance of genome integrity.

Biochemical Changes During Osmopriming of Leek Seeds

Repairing breaks in the plant genome: the importance of keeping it together

A plant DNA ligase is an important determinant of seed longevity.

The importance of safeguarding genome integrity in germination and seed longevity