The dual nature of homologous recombination in plants. Trends Genet

Friedrich Miescher Institute, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.
Trends in Genetics (Impact Factor: 9.92). 04/2005; 21(3):172-81. DOI: 10.1016/j.tig.2005.01.002
Source: PubMed


Homologous recombination creates covalent linkages between DNA in regions of highly similar or identical sequence. Recent results from several laboratories, many of them based on forward and reverse genetics in Arabidopsis, give insights into the mechanisms of the enzymatic machinery and the involvement of chromatin in somatic and meiotic DNA recombination. Also, signaling pathways and interconnections between repair pathways are being discovered. In addition, recent work shows that biotic and abiotic influences from the environment can dramatically affect plant genomes. The resulting changes in the DNA sequence, exerted at the level of somatic or meiotic tissue, might contribute to evolution.

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    • "An intrinsic feature of certain DNA repair 72 pathways is that they are not error-free, leading to potentially transmissible mutational 73 alterations. The error-prone nature of some DNA repair mechanisms, however, increases the 74 genetic diversity and variability of the populations, thus contributing to the evolution of plant 75 genomes (Schuermann et al., 2005). Chemical or radiation-induced mutagenesis has been a 76 powerful tool for creation and improvement of economically important crop varieties (Parry 77 P r o v i s i o n a l et al., 2009; Forster and Shu, 2012). "
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    ABSTRACT: The genomic integrity of every organism is constantly challenged by endogenous and exogenous DNA-damaging factors. Mutagenic agents cause reduced stability of plant genome and have a deleterious effect on development, and in the case of crop species lead to yield reduction. It is crucial for all organisms, including plants, to develop efficient mechanisms for maintenance of the genome integrity. DNA repair processes have been characterized in bacterial, fungal, and mammalian model systems. The description of these processes in plants, in contrast, was initiated relatively recently and has been focused largely on the model plant Arabidopsis thaliana. Consequently, our knowledge about DNA repair in plant genomes - particularly in the genomes of crop plants - is by far more limited. However, the relatively small size of the Arabidopsis genome, its rapid life cycle and availability of various transformation methods make this species an attractive model for the study of eukaryotic DNA repair mechanisms and mutagenesis. Moreover, abnormalities in DNA repair which proved to be lethal for animal models are tolerated in plant genomes, although sensitivity to DNA damaging agents is retained. Due to the high conservation of DNA repair processes and factors mediating them among eukaryotes, genes and proteins that have been identified in model species may serve to identify homologous sequences in other species, including crop plants, in which these mechanisms are poorly understood. Crop breeding programs have provided remarkable advances in food quality and yield over the last century. Although the human population is predicted to "peak" by 2050, further advances in yield will be required to feed this population. Breeding requires genetic diversity. The biological impact of any mutagenic agent used for the creation of genetic diversity depends on the chemical nature of the induced lesions and on the efficiency and accuracy of their repair. More recent targeted mutagenesis procedures also depend on host repair processes, with different pathways yielding different products. Enhanced understanding of DNA repair processes in plants will inform and accelerate the engineering of crop genomes via both traditional and targeted approaches.
    Frontiers in Plant Science 10/2015; 6. DOI:10.3389/fpls.2015.00885 · 3.95 Impact Factor
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    • "This phenomenon is attributed to intrachromosomal recombination between direct and indirect repeats. These two L-type LecRKs fall under the fraction of tandem duplicate genes that exist as a result of intrachromosomal recombination in A. thaliana (Schuermann et al. 2005). Head-tohead orientation of tandem duplicates has been shown to be relevant for gene function. "
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    ABSTRACT: The comparative analysis of plant gene families in a phylogenetic framework has greatly accelerated due to advances in next generation sequencing. In this study, we provide an evolutionary analysis of the L-type lectin receptor kinase and L-type lectin domain proteins (L-type LecRKs and LLPs) that are considered as components in plant immunity, in the plant family Brassicaceae and related outgroups. We combine several lines of evidence provided by sequence homology, HMM-driven protein domain annotation, phylogenetic analysis and gene synteny for large-scale identification of L-type LecRK and LLP genes within nine core-eudicot genomes. We show that both polyploidy and local duplication events (tandem duplication and gene transposition duplication) have played a major role in L-type LecRK and LLP gene family expansion in the Brassicaceae. We also find significant differences in rates of molecular evolution based on the mode of duplication. Additionally, we show that LLPs share a common evolutionary origin with L-type LecRKs and provide a consistent gene family nomenclature. Finally, we demonstrate that the largest and most diverse L-type LecRK clades are lineage-specific. Our evolutionary analyses of these plant immune components provide a framework to support future plant resistance breeding. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    Genome Biology and Evolution 01/2015; 7(3). DOI:10.1093/gbe/evv020 · 4.23 Impact Factor
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    • "This indicates that the HR requirement of NRP1 and NRP2 is H3K56ac independent, which contrasts with the H3K56ac- dependent HR requirement of ASF1 in yeast (Endo et al., 2010). We next investigated the expression of several genes encoding evolutionarily conserved components implicated in DNA repair (Schuermann et al., 2005; Heyer et al., 2010; Knoll and Puchta, 2011). We found that genes involved in HR, including BRCA1 (for BREAST CANCER SUSCEPTIBILITY1), RAD51 (for RADIATION SENSITIVE51), PARP1 (for POLY ADP-RIBOSE POLYMERASE1), RAD54, and PARP2, were upregulated in fas2-4 compared with Col under standard plant growth conditions (Figure 6D). "
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    ABSTRACT: Homologous recombination (HR) is essential for maintaining genome integrity and variability. To orchestrate HR in the context of chromatin is a challenge, both in terms of DNA accessibility and restoration of chromatin organization after DNA repair. Histone chaperones function in nucleosome assembly/disassembly and could play a role in HR. Here, we show that the NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) family histone chaperones are required for somatic HR in Arabidopsis thaliana. Depletion of either the NAP1 group or NAP1-RELATED PROTEIN (NRP) group proteins caused a reduction in HR in plants under normal growth conditions as well as under a wide range of genotoxic or abiotic stresses. This contrasts with the hyperrecombinogenic phenotype caused by the depletion of the CHROMATIN ASSEMBLY FACTOR-1 (CAF-1) histone chaperone. Furthermore, we show that the hyperrecombinogenic phenotype caused by CAF-1 depletion relies on NRP1 and NRP2, but the telomere shortening phenotype does not. Our analysis of DNA lesions, H3K56 acetylation, and expression of DNA repair genes argues for a role of NAP1 family histone chaperones in nucleosome disassembly/reassembly during HR. Our study highlights distinct functions for different families of histone chaperones in the maintenance of genome stability and establishes a crucial function for NAP1 family histone chaperones in somatic HR.
    The Plant Cell 04/2012; 24(4):1437-47. DOI:10.1105/tpc.112.096792 · 9.34 Impact Factor
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