Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans

Abstract

Failure to maintain organelle genome stability has been linked to numerous phenotypes, including variegation and cytosolic male sterility (CMS) in plants, as well as cancer and neurodegenerative diseases in mammals. Here we describe a next-generation sequencing approach that precisely maps and characterizes organelle DNA rearrangements in a single genome-wide experiment. In addition to displaying global portraits of genomic instability, it surprisingly unveiled an abundance of shortrange rearrangements in Arabidopsis thaliana and human organelles. Among these, short-range U-turn-like inversions reach 25% of total rearrangements in wild-type Arabidopsis plastids and 60% in human mitochondria. Furthermore, we show that replication stress correlates with the accumulation of this type of rearrangement, suggesting that U-turn-like rearrangements could be the outcome of a replication-dependent mechanism. We also show that U-turn-like rearrangements are mostly generated using microhomologies and are repressed in plastids by Whirly proteins WHY1 and WHY3. A synergistic interaction is also observed between the genes for the plastid DNA recombinase RECA1 and those encoding plastid Whirly proteins, and the triple mutant why1why3reca1 accumulates almost 60 times the WT levels of U-turn-like rearrangements. We thus propose that the process leading to U-turn-like rearrangements may constitute a RecA-independent mechanism to restart stalled forks. Our results reveal that short-range rearrangements, and especially U-turn-like rearrangements, are a major factor of genomic instability in organelles, and this raises the question of whether they could have been underestimated in diseases associated with mitochondrial dysfunction.

Elevation of Pollen Mitochondrial DNA Copy Number by WHIRLY2: Altered Respiration and Pollen Tube Growth in Arabidopsis

“…These Whirly family proteins share a typical DNA-binding structure (Desveaux et al, 2002) and participate in the maintenance of organellar genomes. Recent work demonstrated that a double knockout of AtWHY1 and AtWHY3 results in chloroplast defects due to illegitimate recombination in the plastid genome (Maréchal et al, 2009;Lepage et al, 2013), and AtWHY1 and AtWHY3 appear to stabilize the plastid genome by repressing short-range rearrangements (Zampini et al, 2015). Structural analysis also indicated that AtWHY2 binding may stabilize mtDNA to favor accurate repair of DNA double-strand breaks (Cappadocia et al, 2010).…”

Spontaneous Chloroplast Mutants Mostly Occur by Replication Slippage and Show a Biased Pattern in the Plastome of Oenothera

“…However, such signatures are not found in the indels identified in this study (Supplemental Data Set 1). Furthermore, no plastome rearrangements suggesting MMBIR repair (Cappadocia et al, 2010) or U-turn-like inversions (Zampini et al, 2015) were found. One possible exception is the large 1364-bp deletion in the mutant V-delta, which is not associated with a repetitive element (Supplemental Figure 6).…”

The RECG1 DNA Translocase Is a Key Factor in Recombination Surveillance, Repair, and Segregation of the Mitochondrial DNA in Arabidopsis

“…In the corresponding mutants, there is reduced repair by homologous recombination and there might be increased illegitimate recombination involving sequence microhomologies (Cappadocia et al, 2010;Parent et al, 2011;Janicka et al, 2012;Miller-Messmer et al, 2012). These illegitimate recombination events are possibly responsible for U-turn genomic inversions that accumulate in plant organelles and also in human mitochondria (Zampini et al, 2015).…”