DNA recombination in somatic plant cells: mechanisms and evolutionary consequences

Knoll, Alexander; Fauser, Friedrich; Puchta, Holger

doi:10.1007/s10577-014-9415-y

Cited by 88 publications

(79 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In addition, mutants in the plant RAD51 family are well known to be sensitive to DSB‐inducing drugs such as BLM and MMC (Bleuyard et al , 2005; Da Ines et al , 2013b; Wang et al , 2014). Previous studies have shown that NHEJ is the most prominent repair mechanism in plants and hence a role of CDKB1‐CYCB1 complexes in DSB repair might be largely masked by a very efficient execution of NHEJ (Knoll et al , 2014). We therefore asked which role CYCB1‐mediated HR plays in a genetic background in which the NHEJ pathway is severely compromised, that is, in mutants of the DNA binding protein KU70 that is required during NHEJ.…”

Section: Resultsmentioning

confidence: 99%

The plant‐specific CDKB 1‐ CYCB 1 complex mediates homologous recombination repair in Arabidopsis

et al. 2016

View full text Add to dashboard Cite

Upon DNA damage, cyclin‐dependent kinases (CDKs) are typically inhibited to block cell division. In many organisms, however, it has been found that CDK activity is required for DNA repair, especially for homology‐dependent repair (HR), resulting in the conundrum how mitotic arrest and repair can be reconciled. Here, we show that Arabidopsis thaliana solves this dilemma by a division of labor strategy. We identify the plant‐specific B1‐type CDKs (CDKB1s) and the class of B1‐type cyclins (CYCB1s) as major regulators of HR in plants. We find that RADIATION SENSITIVE 51 (RAD51), a core mediator of HR, is a substrate of CDKB1‐CYCB1 complexes. Conversely, mutants in CDKB1 and CYCB1 fail to recruit RAD51 to damaged DNA. CYCB1;1 is specifically activated after DNA damage and we show that this activation is directly controlled by SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a transcription factor that acts similarly to p53 in animals. Thus, while the major mitotic cell‐cycle activity is blocked after DNA damage, CDKB1‐CYCB1 complexes are specifically activated to mediate HR.

show abstract

Section: Resultsmentioning

confidence: 99%

The plant‐specific CDKB 1‐ CYCB 1 complex mediates homologous recombination repair in Arabidopsis

et al. 2016

View full text Add to dashboard Cite

show abstract

“…This finding led to the application of I-SceI as a tool for detailed analysis of genomic changes that might occur due to DSB repair via nonhomologous end-joining (NHEJ) in plants. Thus, it was possible to demonstrate that along with inducing various kinds of deletions (2,3), DSB repair also can be associated with the integration of T-DNA, as well as with the copying of genomic sequences into the break (4,5).…”

mentioning

confidence: 99%

Repair of adjacent single-strand breaks is often accompanied by the formation of tandem sequence duplications in plant genomes

Schiml

Fauser

Puchta

2016

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

Duplication of existing sequences is a major mechanism of genome evolution. It has been previously shown that duplications can occur by replication slippage, unequal sister chromatid exchange, homologous recombination, and aberrant double-strand break-induced synthesis-dependent strand annealing reactions. In a recent study, the abundant presence of short direct repeats was documented by comparative bioinformatics analysis of different rice genomes, and the hypothesis was put forward that such duplications might arise due to the concerted repair of adjacent single-strand breaks (SSBs). Applying the CRISPR/Cas9 technology, we were able to test this hypothesis experimentally in the model plant Arabidopsis thaliana. Using a Cas9 nickase to induce adjacent genomic SSBs in different regions of the genome (genic, intergenic, and heterochromatic) and at different distances (∼20, 50, and 100 bps), we analyzed the repair outcomes by deep sequencing. In addition to deletions, we regularly detected the formation of direct repeats close to the break sites, independent of the genomic context. The formation of these duplications as well as deletions may be associated with the presence of microhomologies. Most interestingly, we found that even the induction of two SSBs on the same DNA strand can cause genome alterations, albeit at a much lower level. Because such a scenario reflects a natural step during nucleotide excision repair, and given that the germline is set aside only late during development in plants, the repair of adjacent SSBs indeed seems to have an important influence on the shaping of plant genomes during evolution. T he opportunity to experimentally investigate the outcome of double-strand break (DSB) repair in eukaryotic organisms was enabled by the use of site-specific endonucleases targeting unique genomic sequences. Early work using the meganuclease I-SceI more than 20 y ago demonstrated that the induction of a DSB leads to enhanced homologous recombination (HR) in multicellular eukaryotes (1). This finding led to the application of I-SceI as a tool for detailed analysis of genomic changes that might occur due to DSB repair via nonhomologous end-joining (NHEJ) in plants. Thus, it was possible to demonstrate that along with inducing various kinds of deletions (2, 3), DSB repair also can be associated with the integration of T-DNA, as well as with the copying of genomic sequences into the break (4, 5).Recently, a novel type of programmable nuclease was introduced by the discovery of the molecular mechanism of the bacterial clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated (Cas) system (6, 7). In this system, the endonuclease Cas9 is guided by two specialized RNAs (CRISPR RNA and transactivating CRISPR RNA) via direct base-pairing to bind and cleave invading harmful DNA. It has been demonstrated in vitro and in vivo that by fusing the two RNAs to a so-called singleguide RNA (sgRNA), the system can serve as a highly efficient and precisely programmable nuclease for genome eng...

show abstract

“…It has to be considered that recent years have displayed a complex network of DNA repair pathways (reviewed in Chapman et al 2012;Knoll et al 2014;Maher et al 2011;Puchta 2005) and several gene products involved in HR in plants have been described with potentially redundant functions and also preferences in meiotic and mitotic cell cycles (Bleuyard et al 2005;Da Ines et al 2013;Wang et al 2014). Therefore, the function of Rad54 in geminivirus replication may be masked by complementation through other HR proteins.…”

Section: Discussionmentioning

confidence: 99%

Rad54 is not essential for any geminiviral replication mode in planta

2014

View full text Add to dashboard Cite

The circular single-stranded DNA of phytopathogenic geminiviruses is propagated by three modes: complementary strand replication (CSR), rolling circle replication (RCR) and recombination-dependent replication (RDR), which need host plant factors to be carried out. In addition to necessary host polymerases, proteins of the homologous recombination repair pathway may be considered essential, since geminiviruses are particularly prone to recombination. Among several others, Rad54 was suggested to be necessary for the RCR of Mungbean yellow mosaic India virus. This enzyme is a double-stranded DNA-dependent ATPase and chromatin remodeller and was found to bind and modulate the viral replication-initiator protein in vitro and in Saccharomyces cerevisiae. In contrast to the previous report, we scrutinized the requirement of Rad54 in planta for two distinct fully infectious geminiviruses with respect to the three replication modes. Euphorbia yellow mosaic virus and Cleome leaf crumple virus were inoculated into Rad54-deficient and wildtype Arabidopsis thaliana plant lines to compare the occurrence of viral DNA forms. Replication intermediates were displayed in the time course of infection by one and two-dimensional agarose gel electrophoresis and Southern hybridization. The experiments showed that Rad54 was neither essential for CSR, RCR nor RDR, and it had no significant influence on virus titers during systemic infection.

show abstract

DNA recombination in somatic plant cells: mechanisms and evolutionary consequences

Cited by 88 publications

References 31 publications

The plant‐specific CDKB 1‐ CYCB 1 complex mediates homologous recombination repair in Arabidopsis

The plant‐specific CDKB 1‐ CYCB 1 complex mediates homologous recombination repair in Arabidopsis

Repair of adjacent single-strand breaks is often accompanied by the formation of tandem sequence duplications in plant genomes

Rad54 is not essential for any geminiviral replication mode in planta

Contact Info

Product

Resources

About