Comprehensive Classification of the RNaseH-like domain-containing Proteins in Plants

R-loop is a nucleic acid structure containing an RNA-DNA hybrid and a displaced single-stranded DNA. Recently, accumulated evidences show that R-loops occur frequently in various organisms9 genomes and have crucial physiological functions, including replication, transcription and DNA repair. RNaseH-like superfamily (RNHLS) domain-containing proteins, such as RNase H enzymes, RNase H1 and RNase H2, are important in restricting R-loop levels. However, little is known about other RNHLS proteins and their relationship and function on modulating R-loops, especially in plants. In this study we characterized 6193 RNHLS proteins from 13 representative plant species, and clustered them into 27 clusters, among which reverse transcriptase and exonuclease are the two largest groups. Further we found there are 691 RNHLS proteins in Arabidopsis, and the catalytic alpha helix and beta sheet domain are conserved among them. Interestingly, each of the Arabidopsis RNHLS proteins is combined with other distinctive protein domains. we further found that RNHLS genes are highly expressed in diverse meristems and metabolic tissues. Various RNHLS genes expressed in different tissues grouped together indicate that they work both isolatedly and cooperatively. In summary, we systematically analyzed the RNHL protein in plant and found that there are mainly 27 sub-clusters of them. Most of these proteins are implicated in DNA replication, RNA transcription and nucleic acid degradation. we characterize and classify the RNHLS proteins in plants, which affords new insights on investigation of novel regulatory mechanisms and functions in R-loop biology.