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Deciphering the architecture/function relationship in complex bacterial promoters through synthetic biology approaches

Grant number: 16/19179-9
Support Opportunities:Scholarships in Brazil - Doctorate
Effective date (Start): May 01, 2017
Effective date (End): November 30, 2020
Field of knowledge:Biological Sciences - Microbiology - Biology and Physiology of Microorganisms
Acordo de Cooperação: Coordination of Improvement of Higher Education Personnel (CAPES)
Principal Investigator:Rafael Silva Rocha
Grantee:Lummy Maria Oliveira Monteiro
Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
Associated research grant:12/22921-8 - Synthetic biology approaches for deciphering the logic of signal integration in complex bacterial promoters, AP.JP
Associated scholarship(s):18/21133-2 - Reconstruction of bacterial regulatory networks in environmental terrestrial samples, BE.EP.DR

Abstract

The regulation of gene expression in prokaryotes has been studied extensively, but the effect of different factors, such as the order of the operator sequences in a promoter remains poorly understood. One possible strategy to unravel the mechanisms of action and architecture/function relationship of bacterial promoters is thought synthetic biology approaches, which in turn, combines biology and engineering to design and build new functions in biological systems. The current project aims to characterize the effect that different transcription factors would have on the final system logic, thus revealing fundamental rules of the architecture/logic relationship in bacterial promoters. Unraveling these rules would help to create a predictive system able to decipher the logic of natural promoters based on the distribution of operators sequences, allowing a significant advance in the understanding of the combinatorial mechanisms of control of gene expression in bacteria, with the potential impact on biotechnological applications on the re-engineering of biological circuits. We expect that the results of this endeavor will contribute not only to a fundamental understanding of the signal integration mechanisms in prokaryotic promoters, but will also produce new rules and methods for the desig and build of standardized, integrated biological systems to accomplish many tasks of biotechnological interest. (AU)

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Scientific publications (8)
(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)
NORA, LUISA CZAMANSKI; WESTMANN, CAUA ANTUNES; MARTINS-SANTANA, LEONARDO; ALVES, LUANA DE FATIMA; OLIVEIRA MONTEIRO, LUMMY MARIA; GUAZZARONI, MARIA-EUGENIA; SILVA-ROCHA, RAFAEL. The art of vector engineering: towards the construction of next-generation genetic tools. MICROBIAL BIOTECHNOLOGY, v. 12, n. 1, p. 125-147, . (16/19179-9, 17/17924-1, 16/06323-4, 16/05472-6, 16/03763-3, 15/04309-1, 12/22921-8)
OLIVEIRA MONTEIRO, LUMMY MARIA; SANCHES-MEDEIROS, ANANDA; WESTMANN, CAUA ANTUNES; SILVA-ROCHA, RAFAEL. Unraveling the Complex Interplay of Fis and IHF Through Synthetic Promoter Engineering. FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY, v. 8, . (18/04810-0, 12/22921-8, 16/05472-6, 16/19179-9, 17/50116-6)
SANCHES-MEDEIROS, ANANDA; OLIVEIRA MONTEIRO, LUMMY MARIA; SILVA-ROCHA, RAFAEL. Calibrating Transcriptional Activity Using Constitutive Synthetic Promoters in Mutants for Global Regulators in Escherichia coli. INTERNATIONAL JOURNAL OF GENOMICS, . (16/19179-9, 15/22386-3, 12/22921-8)
MONTEIRO, LUMMY MARIA OLIVEIRA; SARAIVA, JOAO PEDRO; TOSCAN, RODOLFO BRIZOLA; STADLER, PETER F.; SILVA-ROCHA, RAFAEL; DA ROCHA, ULISSES NUNES. redicTF: prediction of bacterial transcription factors in complex microbial communities using deep learnin. ENVIRONMENTAL MICROBIOME, v. 17, n. 1, . (19/15675-0, 18/21133-2, 16/19179-9)
NORA, LUISA CZAMANSKI; WESTMANN, CAUA ANTUNES; MARTINS-SANTANA, LEONARDO; ALVES, LUANA DE FATIMA; OLIVEIRA MONTEIRO, LUMMY MARIA; GUAZZARONI, MARIA-EUGENIA; SILVA-ROCHA, RAFAEL. The art of vector engineering: towards the construction of next-generation genetic tools. MICROBIAL BIOTECHNOLOGY, v. 12, n. 1, p. 23-pg., . (16/05472-6, 16/06323-4, 17/17924-1, 16/19179-9, 16/03763-3, 12/22921-8, 15/04309-1)
SANCHES-MEDEIROS, ANANDA; OLIVEIRA MONTEIRO, LUMMY MARIA; SILVA-ROCHA, RAFAEL. Calibrating Transcriptional Activity Using Constitutive Synthetic Promoters in Mutants for Global Regulators in Escherichia coli. INTERNATIONAL JOURNAL OF GENOMICS, v. 2018, p. 10-pg., . (16/19179-9, 12/22921-8, 15/22386-3)
OLIVEIRA MONTEIRO, LUMMY MARIA; ARRUDA, LETICIA MAGALHAES; SANCHES-MEDEIROS, ANANDA; MARTINS-SANTANA, LEONARDO; DE FATIMA ALVES, LUANA; DEFELIPE, LUCAS; GUSTAVO TURJANSKI, ADRIAN; GUAZZARONI, MARIA-EUGENIA; DE LORENZO, VICTOR; SILVA-ROCHA, RAFAEL. Reverse Engineering of an Aspirin-Responsive Transcriptional Regulator in Escherichia coli. ACS SYNTHETIC BIOLOGY, v. 8, n. 8, p. 1890-1900, . (16/19179-9, 17/17924-1, 16/06323-4, 18/04810-0, 15/04309-1, 12/22921-8)
OLIVEIRA MONTEIRO, LUMMY MARIA; ARRUDA, LETICIA MAGALHAES; SILVA-ROCHA, RAFAEL. Emergent Properties in Complex Synthetic Bacterial Promoters. ACS SYNTHETIC BIOLOGY, v. 7, n. 2, p. 602-612, . (16/19179-9, 12/22921-8)
Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
MONTEIRO, Lummy Maria Oliveira. Deciphering the architecture/function relationship in complex bacterial promoters through Synthetic Biology approaches. 2020. Doctoral Thesis - Universidade de São Paulo (USP). Faculdade de Medicina de Ribeirão Preto (PCARP/BC) Ribeirão Preto.

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