Archaeal Ribosomal Operons on Plasmids vs Chromosome: Methylation Survey of Halococcus

Euryarchaeon Halococcus dombrowskii has an unusual genomic architecture with multiple rrn (ribosomal RNA) operons distributed across its chromosome and plasmids. Our previous study on differences between H. dombrowskii’s plasmid and chromosome rrn operon ITS (Internal Transcribed Spacer) sites suggested there could be further quantitative differences among these disparate rrn operon regions. As the rrn operon ITS regions in question occur close to well-characterized tRNA site known to interact with archaeal RNAse, we performed an exploratory methylation survey of H. dombrowskii genome to check for genomic compartment specific rrn operon methylation pattern and site differences. Here, we present a preliminary long-read based direct methylation calling data for H. dombrowskii, describing a genome rich in N4-methylcytosine (4mC) followed by N6-methyladenine (6mA). Initial survey describes a minor methylation site difference between regions in and around chromosomal and plasmid rrn operons that would require further analysis and discussion. We also note a curious lack of N4-methyltransferase annotation for the H. dombrowskii genome, and offer a putative candidate gene for further study based on HMM profiling and sequence homology analysis. We hope to utilize the data and tools we developed for this initial study on follow-up long-read sequencing and direct methylation calling analysis of other Halococcus spp. Additional data would allow us to perform vitally needed comparative genomics analysis, providing us with further fascinating insight into archaeal ribogenesis in genomes with multi-compartment rrn operon placement.