Structural engineering of the active site of diguanylate cyclase (GGDEF) domains to produce new second messengers

• Grant number: 15/13318-4
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: October 01, 2015
• End date: November 30, 2020
• Field of knowledge: Biological Sciences - Biochemistry - Chemistry of Macromolecules
• Principal Investigator: Shaker Chuck Farah
• Grantee: Santiago Justo Arevalo
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 11/07777-5 - Cyclic di-GMP signaling and the Type IV macromolecule secretion system in Xanthomonas citri, AP.TEM

Abstract

The cyclic nucleotides are important second messengers involved in several pathways including bacterial virulence, biofilm formation and immune evasion. They can be divided into two main groups: the cyclic nucleotides (cAMP and cGMP) and the cyclic dinucleotides: c-di-GMP, c-di-AMP and cGAMP. The control of cellular levels is mediated through protein domains that synthesize and others that degrade these molecules and their downstream effects are mediated by several receptors in the cell. GGDEF domains are responsible for the condensation of two GTP molecules to produce c-di-GMP. This domain is ubiquitous in the prokaryote kingdom and, although it has only one described enzymatic function, the diversity of its sequences raise the possibility that other enzymatic functions may yet be discovered. The high resolution structure of the canonical GGDEF protein PleD from Caulobacter crescentus and the available database of protein sequences with GGDEF domains, allows us to test the hypothesis that certain structural changes introduced by changing specific aminoacids would produce GGDEF domains that recognize other nucleotide substrates or can retain nucleotide binding with loss of enzymatic activity. The main goal of this work is to test these hypotheses, first by introducing specific point mutations in PleD, thereby creating enzymes that synthesize new dinucleotide molecules, and then searching if these or similar enzyme variants occur naturally in the large database of over 42 thousand GGDEF domains annotated so far. Finally we will use the phytopathogen Xanthomonas citri to test the activities of these new molecules in vivo. (AU)

Scientific publications

(5)

(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)

JUSTO AREVALO, SANTIAGO; ZAPATA SIFUENTES, DANIELA; HUALLPA, CESAR J.; LANDA BIANCHI, GIANFRANCO; CASTILLO CHAVEZ, ADRIANA; GARAVITO-SALINI CASAS, ROMINA; URIBE CALAMPA, CARMEN SOFIA; UCEDA-CAMPOS, GUILLERMO; PINEDA CHAVARRIA, ROBERTO. Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. SCIENTIFIC REPORTS, v. 11, n. 1, SEP 7 2021. (15/13318-4)

JUSTO AREVALO, SANTIAGO; ZAPATA SIFUENTES, DANIELA; CUBA PORTOCARRERO, ANDREA; BRESCIA REATEGUI, MICHELLA; MONGE PIMENTEL, CLAUDIA; FARAGE MARTINS, LAYLA; MARQUES PIERRY, PAULO; MORAIS PIROUPO, CARLOS; GUERRA SANTA CRUZ, ALCIDES; QUINONES AGUILAR, MAURO; et al. Genomic Characterization of Bacillus safensis Isolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD. Applied and Environmental Microbiology, v. 88, n. 14, p. 14-pg., 2022-06-28. (17/17303-7, 15/13318-4)

JUSTO AREVALO, SANTIAGO; URIBE CALAMPA, CARMEN SOFIA; JIMENEZ SILVA, CINTHY; QUINONES AGUILAR, MAURO; BOUCKAERT, REMCO; REBELLO PINHO, JOAO RENATO. Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru. NATURE COMMUNICATIONS, v. 14, n. 1, p. 13-pg., 2023-06-15. (15/13318-4, 22/00943-1)

JUSTO AREVALO, SANTIAGO; ZAPATA SIFUENTES, DANIELA; HUALLPA, CESAR J.; LANDA BIANCHI, GIANFRANCO; CASTILLO CHAVEZ, ADRIANA; GARAVITO-SALINI CASAS, ROMINA; UCEDA-CAMPOS, GUILLERMO; PINEDA CHAVARRIA, ROBERTO. Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. FRONTIERS IN MICROBIOLOGY, v. 12, FEB 17 2021. (15/13318-4)

AREVALO, SANTIAGO JUSTO; CASTILLO-CHAVEZ, ADRIANA; CALAMPA, CARMEN SOFIA URIBE; SIFUENTES, DANIELA ZAPATA; HUALLPA, CESAR J.; BIANCHI, GIANFRANCO LANDA; CASAS, ROMINA GARAVITO-SALINI; AGUILAR, MAURO QUINONES; CHAVARRIA, ROBERTO PINEDA. What do we know about the function of SARS-CoV-2 proteins?. FRONTIERS IN IMMUNOLOGY, v. 14, p. 14-pg., 2023-09-18. (15/13318-4, 22/00943-1)