Arabidopsis <i>RecQl4A</i> suppresses homologous recombination and modulates DNA damage responses

Bagherieh‐Najjar, Mohammad B.; Vries, O.; Hille, Jacques; Dijkwel, Paul P.

doi:10.1111/j.1365-313x.2005.02501.x

Cited by 52 publications

(63 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition to recA, other nuclear-encoded genes are involved in DNA repair (29,30), and their expression has been shown in plastids (31). For example, mutation of recQ14A resulted in increased homologous recombination and genomic rearrangements in Arabidopsis nuclear genomes (32). The presence and function of rec-genes in highly rearranged plastid genomes has not been tested, and mutations in organellar-targeted genes could result in improper homologous recombination or strand exchange leading to both genome rearrangements and increased substitution rates.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

Guisinger

Kuehl²,

Boore

et al. 2008

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

152

173

View full text Add to dashboard Cite

Angiosperm plastid genomes are generally conserved in gene content and order with rates of nucleotide substitutions for protein-coding genes lower than for nuclear protein-coding genes. A few groups have experienced genomic change, and extreme changes in gene content and order are found within the flowering plant family Geraniaceae. The complete plastid genome sequence of Pelargonium X hortorum (Geraniaceae) reveals the largest and most rearranged plastid genome identified to date. Highly elevated rates of sequence evolution in Geraniaceae mitochondrial genomes have been reported, but rates in Geraniaceae plastid genomes have not been characterized. Analysis of nucleotide substitution rates for 72 plastid genes for 47 angiosperm taxa, including nine Geraniaceae, show that values of dN are highly accelerated in ribosomal protein and RNA polymerase genes throughout the family. Furthermore, dN/dS is significantly elevated in the same two classes of plastid genes as well as in ATPase genes. A relatively high dN/dS ratio could be interpreted as evidence of two phenomena, namely positive or relaxed selection, neither of which is consistent with our current understanding of plastid genome evolution in photosynthetic plants. These analyses are the first to use protein-coding sequences from complete plastid genomes to characterize rates and patterns of sequence evolution for a broad sampling of photosynthetic angiosperms, and they reveal unprecedented accumulation of nucleotide substitutions in Geraniaceae. To explain these remarkable substitution patterns in the highly rearranged Geraniaceae plastid genomes, we propose a model of aberrant DNA repair coupled with altered gene expression.comparative genomics ͉ genome evolution ͉ plastid genome A ngiosperm plastid genomes are generally highly conserved in gene order, gene content, and organization (1). Whereas the rates of nucleotide substitutions are highly variable in protein-coding genes of angiosperm nuclear genomes, rates in plastid genes are generally lower (2). Rates of nonsynonomous substitutions (dN), those that cause an amino acid change, are substantially lower than rates of synonymous substitutions (dS), those that do not cause an amino acid change. Aside from a recent report describing elevated dN for a single gene in Oenothera and lineages within Caryophyllaceae (3), plastid genes of photosynthetic plants are under strong purifying selection and the rapid accumulation of either dN or dS has not been described.The plastid genomes of nonphotosynthetic plants reveal accelerated rates of nucleotide substitutions in many proteincoding genes; furthermore, these genomes exhibit extensive gene loss and genome rearrangement (4-6). However, analyses involving either few genes or few taxa for photosynthetic angiosperm plastid genomes generally reveal that modest rate variation is locus-and lineage-specific. A few groups of angiosperms have experienced lineage-specific rate variation, including the lineages leading to the grasses (7), pea (2), Gnetum (8), and Welwitschia...

show abstract

Section: Discussionmentioning

confidence: 99%

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

Guisinger

Kuehl²,

Boore

et al. 2008

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

152

173

View full text Add to dashboard Cite

show abstract

“…Activated by ATR, the mammalian RecQ family member Bloom syndrome protein and the structure-specific nuclease Mus81 were found to be compulsory for the active formation of temporal DSBs that might be required for the resumption of replication or the resolution of stalled forks (Shimura et al, 2008). In Arabidopsis, some of the six RecQ-like helicases were found to modulate genome integrity (Bagherieh-Najjar et al, 2005;Hartung et al, 2007). Plants (Friesner et al, 2005;Vespa et al, 2005) and mammalian cells Baltimore, 2000, 2003) lacking ATR were reported to exhibit genome instabilities, checkpoint deficiencies, and futile cell cycle regulation.…”

Section: A Tight Control Of Dna Replication Ensures the Preservation mentioning

confidence: 99%

Replication Stress Leads to Genome Instabilities inArabidopsisDNA Polymerase Δ Mutants

et al. 2009

View full text Add to dashboard Cite

Impeded DNA replication or a deficiency of its control may critically threaten the genetic information of cells, possibly resulting in genome alterations, such as gross chromosomal translocations, microsatellite instabilities, or increased rates of homologous recombination (HR). We examined an Arabidopsis thaliana line derived from a forward genetic screen, which exhibits an elevated frequency of somatic HR. These HR events originate from replication stress in endoreduplicating cells caused by reduced expression of the gene coding for the catalytic subunit of the DNA polymerase d (POLd1). The analysis of recombination types induced by diverse alleles of pold1 and by replication inhibitors allows the conclusion that two not mutually exclusive mechanisms lead to the generation of recombinogenic breaks at replication forks. In plants with weak pold1 alleles, we observe genome instabilities predominantly at sites with inverted repeats, suggesting the formation and processing of aberrant secondary DNA structures as a result of the accumulation of unreplicated DNA. Stalled and collapsed replication forks account for the more drastic enhancement of HR in plants with strong pold1 mutant alleles. Our data suggest that efficient progression of DNA replication, foremost on the lagging strand, relies on the physiological level of the polymerase d complex and that even a minor disturbance of the replication process critically threatens genomic integrity of Arabidopsis cells.

show abstract

“…Both genes are also derived from a recent duplication. Whereas RECQ4a is required for repairing DNA damage induced by MMS and MMC, no sensitivity could be detected for the recq4b mutants (Bagherieh-Najjar et al, 2005;Hartung et al, 2007). In addition, in the fission yeast (Schizosaccharomyces pombe) two RAD54 homologs, RHP54 and TID1, which also belong to the SNF2 family, exist.…”

Section: Atrad5 Is Involved In Dsb-induced Hr In Somatic Cellsmentioning

confidence: 99%

A Homolog ofScRAD5Is Involved in DNA Repair and Homologous Recombination in Arabidopsis

et al. 2008

View full text Add to dashboard Cite

Rad5 is the key component in the Rad5-dependent error-free branch of postreplication repair in yeast (Saccharomyces cerevisiae). Rad5 is a member of the Snf2 ATPase/helicase family, possessing as a characteristic feature, a RING-finger domain embedded in the Snf2-helicase domain and a HIRAN domain. Yeast mutants are sensitive to DNA-damaging agents and reveal differences in homologous recombination. By sequence comparisons we were able to identify two homologs (AtRAD5a and AtRAD5b) in the Arabidopsis thaliana genome, sharing about 30% identity and 45% similarity to yeast Rad5. AtRad5a and AtRad5b have the same kind of domain organization with a higher degree of similarity to each other than to ScRad5. Surprisingly, both genes differ in function: whereas two independent mutants of Atrad5a are hypersensitive to the cross-linking agents mitomycin C and cis-platin and to a lesser extent to the methylating agent, methyl methane sulfonate, the Atrad5b mutants did not exhibit any sensitivity to all DNA-damaging agents tested. An Atrad5a/Atrad5b double mutant resembles the sensitivity phenotype of the Atrad5a single mutants. Moreover, in contrast to Atrad5b, the two Atrad5a mutants are deficient in homologous recombination after treatment with the double-strand break-inducing agent bleomycin. Our results suggest that the RAD5-dependent error-free branch of postreplication repair is conserved between yeast and plants, and that AtRad5a might be functionally homologous to ScRad5.

show abstract

Arabidopsis RecQl4A suppresses homologous recombination and modulates DNA damage responses

Cited by 52 publications

References 65 publications

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

Replication Stress Leads to Genome Instabilities inArabidopsisDNA Polymerase Δ Mutants

A Homolog ofScRAD5Is Involved in DNA Repair and Homologous Recombination in Arabidopsis

Contact Info

Product

Resources

About