CRISPR-CAS type IVB in Rhodococcus sp. strain ADH, an actinobacterial antarctic isolate

NAPOLITANO N.; QUIROGA C.; MAC CORMACK WP; LOPEZ JL

Bogota

Congreso; Second ISME Latin American Congress; 2021

Universidad de los Andes Facultad de Ciencias

Virus‐host co‐evolution is a topic of special scientific interest. Antarctica is a poorly explored extreme environment and the study of extremophilic organisms is of interest at both basic and applied scientific levels. Our work studies the virus‐host co‐evolution of Rhodococcus sp. strain ADH (NZ_LJIS00000000.1) and a parasitizing prophage. In silico analysis of the ADH genome, using ACLAME Prophinder, revealed the existence of a prophage on contig 10 (accession LJIS01000120.1, 227198bp). In parallel, a CRISPR‐Cas type IVB system was detected on contig 38 (access LJIS01000092.1, 54009bp) of the ADH genome (congruent with previous work). Our objective question was, what is the degree of conservation of the type IVB CRISPR‐Cas system in actinobacteria?Previous work determined that the phosphoadenosine phosphosulfate reductase (CysH) gene is a marker for the CRISPR‐Cas IVB operon. Blastp analysis of the Joint Genome Institute database showed 139 CysH homologues in actinobacterial scaffolds. These genes were found to be associated with other components of the cas operon of the IVB system but not with CRISPR sequences (analysis performed using CRISPRCasTyper). In addition, the organisation of the cas‐IVB operon in actinobacteria showed the csf2 gene to be ubiquitous.Phylogenetic reconstruction of CysH showed the formation of 14 clades (≥ 91% bootstrap) and of csf2 (PHYML) 14 clades (≥ 82% bootstrap). Both topologies were shown to be partially congruent (Tanglegram, Dendroscope).Synthesizing: a) the cas‐IVB operon in actinobacteria presented 11 rearrangements in 139 genomes analyzed; b) the molecular phylogeny of the cysH and csf2 genes showed great diversity and c) the comparison of those molecular phylogenies suggests that both vertical and horizontal transmission of both genes would be possible in the cas‐IVB operon of actinobacteria. Finally, our results suggest that IVB‐type systems are poorly conserved among the actinobacteria studied.