Development of a computational tool for searching and strength prediction of bacterial promoters for applications in synthetic biology

• Grant number: 17/04217-5
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: June 01, 2017
• End date: May 31, 2019
• Field of knowledge: Biological Sciences - Microbiology - Biology and Physiology of Microorganisms
• Principal Investigator: Rafael Silva Rocha
• Grantee: Murilo Henrique Anzolini Cassiano
• 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

Abstract

Genes are not expressed all the time, they have to be regulated and a critical step of this regulation is transcription initiation. Bacteria possess a cellular machinery to regulate transcription that synthetic biology compare to a true decision-making program. The players of this process are the RNA polymerase, transcription factors (that stimulate or inhibit transcription), DNA intrinsic sequences called as promoters (which are related to the frequency of transcriptional activity), and the sigma factors, which recognize these promoter sequences on DNA. The current project aims the development of a computational tool that integrate several parameters to search and predict strength of bacterial promoters. The promoter specificity offers transcription fine-tuning and this, in turn, could be used in many applications. Several approaches had been described in literature, both experimental and computational ones. The approach of this project will be to gather in a computational platform sequence characteristics of bacterial promoter from previous works and use then to construct a predictive model that will be validated using synthetic promoters. (AU)

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)

CAMPOS ANTONIETO, AMANDA CRISTINA; VIEIRA NOGUEIRA, KAROLINE MARIA; DE PAULA, RENATO GRACIANO; NORA, LUFSA CZAMANSKI; ANZOLINI CASSIANO, MURILO HENRIQUE; GUAZZARONI, MARIA-EUGENIA; ALMEIDA, FAUSTO; DA SILVA, THIAGO APARECIDO; RIES, LAURE NICOLAS ANNICK; DE ASSIS, LEANDRO JOSE; et al. A Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in Trichoderma reesei. MSYSTEMS, v. 4, n. 4, JUL-AUG 2019. (16/23233-9, 16/03322-7, 15/04309-1, 17/04217-5, 16/03763-3, 18/03766-8, 15/09553-8, 12/22921-8)

MARTINS-SANTANA, LEONARDO; NORA, LUISA C.; SANCHES-MEDEIROS, ANANDA; LOVATE, GABRIEL L.; CASSIANO, MURILO H. A.; SILVA-ROCHA, RAFAEL. Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production. FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY, v. 6, OCT 3 2018. (15/22386-3, 17/17924-1, 16/11093-8, 17/04217-5, 16/03763-3, 12/22921-8)