Identification and characterization of Lsm-binding non-coding RNAs in the extremophile Halobacterium salinarum

• Grant number: 11/07487-7
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: August 01, 2011
• End date: July 31, 2015
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Tie Koide
• Grantee: Lívia Soares Zaramela
• Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated research grant: 09/09532-0 - Systems biology of the extremophile Halobacterium salinarum: role of the non-coding RNAs in the global gene regulatory network model, AP.JP

Abstract

The main purpose of systems approaches is to understand how a simple genetic change or environmental perturbation affects the behavior of an organism at the molecular level and consequently, determines its phenotype. High-throughput technologies that exploit data from transcriptome, proteome, protein-protein interactions, protein-DNA, protein-RNA, and other technologies, represent powerful tools to achieve this goal. However, each of these individual data sets reflect an incomplete scenario of cellular dynamics. In current predictive models that integrates data from different methodologies, there is an important class of regulators of gene expression that are not contemplated yet: the non-coding RNAs (ncRNAs). Many ncRNAs require interaction with proteins to perform their functions in regulating cellular processes. In bacteria, the protein Hfq is an important partner of ncRNAs in the recognition of the mRNA targets. Proteins similar to the bacterial Hfq such as the Lsm proteins are found in eukaryotes and archaea, suggesting an importance role of these molecules in the process of gene regulation. For this reason, our purpose in this project is to study the ncRNAs that interact with the RNA binding protein Lsm from Halobacterium salinarum, an extremophile model in Systems Biology. For the identification of these ncRNAs, we will perform RIP-ChIP experiments in different stages of the growth curve of H. salinarum. After the identification, a subgroup of ncRNAs will be selected for functional characterization, including the construction of strains overexpressing ncRNAs and the use of bioinformatics tools. The data obtained should help to understand the role of ncRNAs and Lsm protein in global gene regulation. (AU)

Scientific publications

(6)

(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)

TEN-CATEN, FELIPE; VENCIO, RICARDO Z. N.; LORENZETTI, ALAN PERICLES R.; ZARAMELA, LIVIA SOARES; SANTANA, ANA CAROLINA; KOIDE, TIE. Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. RNA BIOLOGY, v. 15, n. 8, p. 1119-1132, 2018. (11/14455-4, 15/21038-1, 17/03052-2, 11/07487-7, 15/12012-9)

GOMES-FILHO, JOSE VICENTE; ZARAMELA, LIVIA SOARES; DA SILVA ITALIANI, VALERIA CRISTINA; BALIGA, NITIN S.; VENCIO, RICARDO Z. N.; KOIDE, TIE. Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea. RNA BIOLOGY, v. 12, n. 5, p. 490-500, MAY 4 2015. (13/21522-5, 10/10195-5, 11/07487-7, 09/09532-0)

COELHO, PRISCILA DE O.; GUARNIER, FLAVIA A.; FIGUEIREDO, LEONARDO BRUNO; ZARAMELA, LIVIA S.; PACINI, ENIO S. A.; GODINHO, ROSELY O.; GOMES, MARCELO D.. Identification of potential target genes associated with the reversion of androgen-dependent skeletal muscle atrophy. Archives of Biochemistry and Biophysics, v. 663, p. 173-182, MAR 15 2019. (15/07019-4, 14/10898-7, 11/07487-7)

ZARAMELA, LIVIA S.; VENCIO, RICARDO Z. N.; TEN-CATEN, FELIPE; BALIGA, NITIN S.; KOIDE, TIE. Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life. PLoS One, v. 9, n. 9, SEP 19 2014. (11/14455-4, 11/07487-7, 09/09532-0)

SILVA-ROCHA, RAFAEL; PONTELLI, MARJORIE CORNEJO; FURTADO, GILVAN PESSOA; ZARAMELA, LIVIA SOARES; KOIDE, TIE. Development of New Modular Genetic Tools for Engineering the Halophilic Archaeon Halobacterium salinarum. PLoS One, v. 10, n. 6, JUN 10 2015. (13/04125-2, 11/07487-7, 13/23712-6, 09/09532-0)

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)