Transcription is a major driving force for plastid genome instability in Arabidopsis

• Published in: PloS one 2019-04, Vol.14 (4), p.e0214552-e0214552
• Main Authors: Pérez Di Giorgio, Juliana Andrea, Lepage, Étienne, Tremblay-Belzile, Samuel, Truche, Sébastien, Loubert-Hudon, Audrey, Brisson, Normand
• Format: Article
• Language: English
• Subjects: Arabidopsis; Arabidopsis - genetics; Arabidopsis Proteins - genetics; Arabidopsis thaliana; Biochemistry; Biology and Life Sciences; Biosynthesis; Cell Nucleus - metabolism; Chlorophyll - chemistry; Chloroplasts; Chloroplasts - genetics; Chromosomes; Ciprofloxacin; Complementary DNA; Computer and Information Sciences; Deoxyribonucleic acid; DNA; DNA biosynthesis; DNA Damage; DNA Primers - genetics; DNA Repair; DNA Replication; DNA, Plant - genetics; DNA-Binding Proteins - genetics; DNA-Directed DNA Polymerase - genetics; EDTA; Engineering and Technology; Flowers & plants; Gene expression; Gene Expression Regulation, Plant; Genetic aspects; Genome, Chloroplast; Genome, Plant; Genomes; Genomic Instability; Genomics; Hybrids; Instability; Medicine; Mitochondrial DNA; Mutation; Phenotype; Phenotypes; Photosynthesis; Plants, Genetically Modified - genetics; Plastids; Polymerase Chain Reaction; Promoter Regions, Genetic; Proteins; Publishing; R-loops; Recombinases - genetics; Research and Analysis Methods; Ribonuclease; Ribonuclease H1; Ribonucleic acid; Rifampin; Rifampin - pharmacology; RNA; Sequence Analysis, DNA; Stability; Stalling; Transcription (Genetics); Transcription factors; Transcription, Genetic
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0214552

Though it is an essential process, transcription can be a source of genomic instability. For instance, it may generate RNA:DNA hybrids as the nascent transcript hybridizes with the complementary DNA template. These hybrids, called R-loops, act as a major cause of replication fork stalling and DNA breaks. In this study, we show that lowering transcription and R-loop levels in plastids of Arabidopsis thaliana reduces DNA rearrangements and mitigates plastid genome instability phenotypes. This effect can be observed on a genome-wide scale, as the loss of the plastid sigma transcription factor SIG6 prevents DNA rearrangements by favoring conservative repair in the presence of ciprofloxacin-induced DNA damage or in the absence of plastid genome maintenance actors such as WHY1/WHY3, RECA1 and POLIB. Additionally, resolving R-loops by the expression of a plastid-targeted exogenous RNAse H1 produces similar results. We also show that highly-transcribed genes are more susceptible to DNA rearrangements, as increased transcription of the psbD operon by SIG5 correlates with more locus-specific rearrangements. The effect of transcription is not specific to Sigma factors, as decreased global transcription levels by mutation of heat-stress-induced factor HSP21, mutation of nuclear-encoded polymerase RPOTp, or treatment with transcription-inhibitor rifampicin all prevent the formation of plastid genome rearrangements, especially under induced DNA damage conditions.