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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Available from: Olivier Fritsch, Oct 13, 2015
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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). "
    Frontiers in Plant Science 10/2015; 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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