Detection of Insertion Sequence-encoded transposases using proteome data

• Grant number: 19/13440-5
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: October 18, 2019
• End date: October 17, 2020
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Tie Koide
• Grantee: Alan Péricles Rodrigues Lorenzetti
• Supervisor: Nitin Surendranatha Baliga
• Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Institution abroad: Institute for Systems Biology, United States
• Associated to the scholarship: 17/03052-2 - Non-coding RNAs derived from insertion sequences in the halophilic archaeon Halobacterium salinarum NRC-1, BP.DR

Abstract

Our main project has the purpose of identifying the components of insertion sequence regulation in Halobacterium salinarum, primarily those acting on the post-transcriptional level. We successfully identified several transposase-encoding mRNAs binding to the LSm protein, which can repress or induce translation by changing the way ribosome couple with transcripts. We evaluated insertion sequence mobilization after removing LSm protein from the system and detected differences when comparing the null mutant to control strain. This experiment unveiled active insertion sequences that could be explored in depth, but currently we only have genome and transcriptome data. In this project, we propose the integration of proteome data to our findings to better characterize the mobilome scenario in H. salinarum. We intend to check which insertion sequences produce proteins, and correlate their amounts with the identified active elements. Furthermore, we expect to analyze data of H. salinarum grown on different conditions to check whether the transposases are responsive to environmental changes. During the execution of this project, we expect benefits for the main project and for the student professional development.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

DE ARAUJO, HUGO L.; MARTINS, BIANCA P.; VICENTE, ALEXANDRE M.; LORENZETTI, ALAN P. R.; KOIDE, TIE; MARQUES, V, MARILIS. Cold Regulation of Genes Encoding Ion Transport Systems in the Oligotrophic Bacterium Caulobacter crescentus. MICROBIOLOGY SPECTRUM, v. 9, n. 1, SEP 2021. (19/08514-0, 18/17309-8, 19/13440-5, 14/13552-4, 17/03052-2)

LORENZETTI, ALAN P. R.; KUSEBAUCH, ULRIKE; ZARAMELA, LIVIA S.; WU, WEI-JU; DE ALMEIDA, JOAO P. P.; TURKARSLAN, SERDAR; L. G. DE LOMANA, ADRIAN; GOMES-FILHO, JOSE V.; VENCIO, RICARDO Z. N.; MORITZ, ROBERT L.; et al. A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon. MSYSTEMS, v. 8, n. 2, p. 22-pg., 2023-03-13. (17/03052-2, 15/21038-1, 11/07487-7, 19/13440-5, 13/21522-5, 09/09532-0)

DE LOMANA, ADRIAN LOPEZ GARCIA; KUSEBAUCH, ULRIKE; RAMAN, ARJUN, V; PAN, MIN; TURKARSLAN, SERDAR; LORENZETTI, ALAN P. R.; MORITZ, ROBERT L.; BALIGA, NITIN S.. Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum. MSYSTEMS, v. 5, n. 4, p. 18-pg., 2020-07-01. (17/03052-2, 19/13440-5)