New genetic tools for Archaea: functional characterization and modeling of the non-coding RNA regulatory network of Halobacterium salinarum

• Grant number: 13/04125-2
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: June 01, 2013
• End date: February 02, 2015
• Field of knowledge: Biological Sciences - Microbiology - Biology and Physiology of Microorganisms
• Principal Investigator: Tie Koide
• Grantee: Rafael Silva Rocha
• 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

Organisms from the Archaea domain are excellent models to investigate the different strategies used by living cells to thrive in extreme niches. The current proposal has as the main goal the investigation of the gene regulatory network of the model organism Halobacterium salinarum NRC-1. First, a new set of modular genetic tools will be developed to improve the capability to genetically manipulate this organism. Second, the regulatory role and the molecular mechanism of action of new non-coding RNAs (ncRNAs) will be investigated in H. salinarum. Finally, the newly in vivo generated information will be integrated with pre-existing knowledge in order to implement a computational model of the regulatory network in H. salinarum taking into account the interplay of both general transcriptional factors (GTFs) and ncRNAs. This integrative approach attempts to get insight into the molecular mechanisms used by this organism to adapt to environmental signals. The model predictions will be validated in vivo using pre-existing and newly implemented genetic tools. The expected results from this project would allow enhancing our knowledge about the adaptation mechanism used by this organism to thrive under hash environments, with high relevance for new biotechnological applications.

Scientific publications

(9)

(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; DE LORENZO, VICTOR. The pWW0 plasmid imposes a stochastic expression regime to the chromosomal ortho pathway for benzoate metabolism in Pseudomonas putida. FEMS Microbiology Letters, v. 356, n. 2, p. 8-pg., 2014-07-01. (13/04125-2)

GUAZZARONI, MARIA-EUGENIA; SILVA-ROCHA, RAFAEL; WARD, RICHARD JOHN. Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening. MICROBIAL BIOTECHNOLOGY, v. 8, n. 1, p. 52-64, JAN 2015. (13/04125-2, 10/18850-2)

SILVA-ROCHA, RAFAEL; DE LORENZO, VICTOR. The pWW0 plasmid imposes a stochastic expression regime to the chromosomal ortho pathway for benzoate metabolism in Pseudomonas putida. FEMS Microbiology Letters, v. 356, n. 2, SI, p. 176-183, JUL 2014. (13/04125-2)

GUAZZARONI, MARIA-EUGENIA; SILVA-ROCHA, RAFAEL. Expanding the Logic of Bacterial Promoters Using Engineered Overlapping Operators for Global Regulators. ACS SYNTHETIC BIOLOGY, v. 3, n. 9, p. 666-675, SEP 2014. (13/04125-2)

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)

CAMPOS ANTONIETO, AMANDA CRISTINA; CASTRO, LILIAN DOS SANTOS; SILVA-ROCHA, RAFAEL; PERSINOTI, GABRIELA FELIX; SILVA, ROBERTO NASCIMENTO. Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis. Fungal Genetics and Biology, v. 73, p. 93-103, DEC 2014. (13/04125-2, 10/15683-8)

SILVA-ROCHA, RAFAEL; CASTRO, LILIAN DOS SANTOS; CAMPOS ANTONIERO, AMANDA CRISTINA; GUAZZARONI, MARIA-EUGENIA; PERSINOTI, GABRIELA FELIX; SILVA, ROBERTO NASCIMENTO. Deciphering the Cis-Regulatory Elements for XYR1 and CRE1 Regulators in Trichoderma reesei. PLoS One, v. 9, n. 6, JUN 18 2014. (13/04125-2)

NIKEL, PABLO IVAN; SILVA-ROCHA, RAFAEL; BENEDETTI, ILARIA; DE LORENZO, VICTOR. The private life of environmental bacteria: pollutant biodegradation at the single cell level. ENVIRONMENTAL MICROBIOLOGY, v. 16, n. 3, p. 628-642, MAR 2014. (13/04125-2)

GUAZZARONI, MARIA-EUGENIA; SILVA-ROCHA, RAFAEL; WARD, RICHARD JOHN. Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening. MICROBIAL BIOTECHNOLOGY, v. 8, n. 1, p. 13-pg., 2015-01-01. (13/04125-2, 10/18850-2)