DNA double-strand break repair machinery in Penaeid crustaceans: A focus on the Non-Homologous End-Joining pathway.

Abstract

DNA double-strand breaks (DSBs) are repaired through three major pathways: Non-Homologous End-Joining (NHEJ), Microhomology-Mediated End-Joining (MMEJ), and Homology-Directed Repair (HDR), each requiring a specific set of diverse proteins. Such pathways and their proteins have been studied in model organisms, including arthropods; however, DSB repair pathways are scarcely described in Crustacea, a taxon that includes the commercially valuable penaeid shrimps (Crustacea: Decapoda: Penaeidae). In this work, transcriptome and proteome databases of Penaeus vannamei and other Crustacea species were scrutinized for each protein of the NHEJ pathway. The structural and functional attributes of such proteins in penaeids were determined using bioinformatics. Additionally, the expression of the NHEJ-related Ku70, Ku80, DNA-PKcs, DNA ligase 4 (Lig4), and HDR- and MMEJ-related protein transcripts were assessed in P. vannamei gills, midgut gland, hemocytes, and muscle by RT-PCR. DSB repair protein transcripts were found expressed in the four assayed tissues, particularly in the gills and midgut gland. Among DSB repair proteins, all the analyzed transcripts of proteins related to the NHEJ pathway were present in gills. To the best of our knowledge, this is the first report on the expression of DSB repair proteins in Decapoda. Together, proteomic, transcriptomic, and expression data suggest the functionality of NHEJ, HDR, and MMEJ pathways in P. vannamei and other decapods. The information presented here contributes to understanding the response to DSB breaks in shrimps, describing possible outcomes in oxidative stress studies and also in the designing of gene editing strategies, which have not been developed in Penaeidae.