Systems investigation of SmAP1-mediated regulation of transposase-encoding transcripts in Halobacterium salinarum NRC-1

Author(s)

Alan Péricles Rodrigues Lorenzetti

• Document type: Doctoral Thesis
• Press: Ribeirão Preto.
• Institution: Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI)
• Defense date: 2021-07-29

Examining board members

Tie Koide; João Carlos Setubal; Beny Spira; Alessandro de Mello Varani

• Advisor: Tie Koide; Ricardo Zorzetto Nicoliello Vencio

Abstract

The Sm RNA chaperones are ubiquitous proteins in the three domains of life. Although their role has been well characterized in Eukarya and Bacteria, just a few studies investigated their function in Archaea. In Bacteria, this protein acts in post-transcriptional regulation, binding to messenger RNAs and modulating their translation. Recent studies have shown that IS200/IS605 transposase-encoding RNAs are targets of the mechanism mentioned above in Salmonella enterica. Considering the vast number of transposase-encoding RNAs in Halobacterium salinarum NRC-1, our model organism, we decided to check for the existence of a similar phenomenon. For that, we analyzed SmAP1 RNA coimmunoprecipitation sequencing data and determined the functional impact of this protein by evaluating global RNA differential expression and long-read-based transposition quantification of a null mutant. We also detected transposition and protein levels in standard growth conditions. Our results point out that transposase-encoding transcripts are more prone to bind SmAP1 than transcripts encoding other classes of proteins and are subject to altered stability when this chaperone is absent. Its absence also carries out the perturbation of transposition levels, especially of elements comprising the ISH3 family. Moreover, we detected high levels of IS200/IS605 transcripts but low levels of their protein products, suggesting that SmAP1, alongside antisense RNAs and other features, can have a role in their translational modulation. For the first time, we revealed that SmAP1 might be capable of acting in the post-transcriptional regulation of transposase-encoding RNAs in Archaea, contributing to the insufficient knowledge we currently have about this chaperone in the third domain of life. (AU)

• FAPESP's process: 17/03052-2 - Non-coding RNAs derived from insertion sequences in the halophilic archaeon Halobacterium salinarum NRC-1
• Grantee: Alan Péricles Rodrigues Lorenzetti
• Support Opportunities: Scholarships in Brazil - Doctorate