Systems biology of the extremophile Halobacterium salinarum: role of the non-coding RNAs in the global gene regulatory network model

• Grant number: 09/09532-0
• Support Opportunities: Research Grants - Young Investigators Grants
• Start date: July 01, 2010
• End date: June 30, 2015
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Tie Koide
• Grantee: Tie Koide
• Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• City of the host institution: Ribeirão Preto
• Associated researchers: Ricardo Zorzetto Nicoliello Vêncio
• Associated scholarship(s): 14/24087-0 - Validation of small peptides expression in Halobacterium salinarum using chromosomal tagging, BP.IC; 13/23712-6 - Identification of small proteins and peptides in extremophile Halobacterium salinarum: discriminating of non-coding RNAs and small ORFs, BP.PD; 13/04125-2 - New genetic tools for Archaea: functional characterization and modeling of the non-coding RNA regulatory network of Halobacterium salinarum, BP.PD; + associated scholarships 12/12734-6 - Bioinformatics applied to Halobacterium salinarum RNA Structurome investigation, BP.PD; 12/02896-9 - Prediction of RNA-Protein Interactions by an Ensemble Approach, BP.DR; 11/14455-4 - RNA-seq: segmentation and modeling of the signal, BP.DD; 11/07487-7 - Identification and characterization of Lsm-binding non-coding RNAs in the extremophile Halobacterium salinarum, BP.DR; 10/10195-5 - Characterization of the non-coding RNAs in the extremophile Halobacterium salinarum, BP.PD - associated scholarships

Abstract

Systems approaches have been developed in the post-genomic era to have a global understanding of the cell. In this framework, the use of computational, mathematical and statistical tools, together with new technologies in biology allow the development of global models with predictive power. These global models usually take into account mRNA and protein levels. However, there is an increasingly important category of regulatory molecules that are not considered in these models: the non-coding RNAs (ncRNAs). To identify the influence of these molecules in the global gene regulatory network, we propose the study of ncRNAs in Halobacterium salinarum, a model extremophile in systems biology. Top-down and bottom-up approaches will be combined, together with bioinformatics tools to characterize these molecules and their role in gene regulation. The characterization of the global regulatory networks in this organism will contribute to the development of technologies to reengineering and potential applications in biotechnology. (AU)

Scientific publications

(4)

(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)

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)

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)

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)

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)