Abstract
The state of the art in the evolution of plant viruses allows the genetic foundations of antiviral immunity in higher (including the most important crops) plants to be categorized as one of the most pressing issues of genetics and selection. According to the endosymbiotic theory, mitochondria descended from alphaproteobacteria that had been absorbed but not degraded by the host cell. The discovery of CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins), which implement the adaptive immunity function in prokaryotes, raises the question whether such a mechanism of antiviral protection could be caught up by evolution and used by representatives of eukaryotes (in particular, plants). The purpose of this work was to analyze the complete sequences of nuclear, mitochondrial, and chloroplast genomes of Arabidopsis thaliana in order to search for genetic elements similar to those in CRISPR-Cas systems of bacteria and archaea. As a result, in silico methods helped us to detect a locus of regularly intermittent short direct repeats in the mitochondrial genome of A. thaliana ecotypes. The structure of this locus corresponds to the CRISPR locus of the prokaryotic adaptive antiviral immune system. The probable connection between the locus found in the mitochondrial genome of the higher plant and the function of adaptive immunity is indicated by a similarity between the spacer sequences in the CRISPR cassette found and the genome of Cauliflower mosaic virus affecting Arabidopsis plants. Sequences of repeats and spacers of CRISPR cassettes in Arabidopsis C24 and Ler lines are perfectly identical. However, the locations of the CRISPR locus in the mitochondrial genomes of these lines differ significantly. The CRISPR cassette in the Col-0 line was found to be completely broken as a result of four deletions and one insertion. Although cas genes were not detected in the mitochondrial genome of the studied Arabidopsis ecotypes, their presence was detected in the nuclear genome. Both cas genes and numerous CRISPR cassettes were found on all the five chromosomes in the nuclear genome of the Col-0 ecotype. The results suggest the existence of a system of adaptive immunity in plants, which is similar to the CRISPR immunity of bacteria and archaea.
Highlights
The acquisition of alphaproteobacteria as endosymbionts by the archaeal host is unquestionably accepted to be one of the most important events in the nascence of the eukaryotic cell (Archibald, 2015)
Resting on the known evolutionary relationship between mitochondria and bacteria, we searched for elements of the CRISPR-Cas system in the mitochondrial genome of three ecotypes of A. thaliana using approaches and methods of bioinformatics that are widely used in studying CRISPRCas systems of prokaryotes nowadays (Jansen et al, 2002; Makarova et al, 2006, 2015; Grissa et al, 2007; Zhang, Ye, 2017; Couvin et al, 2018)
The context analysis of the complete mitochondrial genome sequence of A. thaliana (C24 and Ler ecotypes) revealed a site whose structure is fully consistent with the organization of CRISPR cassettes of prokaryotic origin
Summary
The acquisition of alphaproteobacteria (which subsequently gave rise to mitochondria) as endosymbionts by the archaeal host is unquestionably accepted to be one of the most important events in the nascence of the eukaryotic cell (Archibald, 2015). The discovery of the CRISPR-Cas adaptive immunity system based on the phenomenon of RNA interference in a significant percentage of bacterial and archaeal species (Jansen et al, 2002; Mojica et al, 2005; Makarova et al, 2006; Barrangou et al, 2007; Lander, 2016) poses the question whether such a protective system may exist in eukaryotic mitochondria, organelles that have an obvious evolutionary relationship with their bacterial ancestors. The mitochondrial genome of higher plants is tightly involved in horizontal gene transfer processes, where it can act as both a donor and an acceptor of the gene (Kleine et al, 2009; Zhao et al, 2018)
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