Biology of Bacteria and Bacteriophages Research Center

• Grant number: 21/10577-0
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• Start date: May 01, 2023
• End date: April 30, 2028
• Field of knowledge: Biological Sciences - Biochemistry - Biochemistry of Microorganisms
• Principal Investigator: Shaker Chuck Farah
• Grantee: Shaker Chuck Farah
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Pesquisadores principais: Aline Maria da Silva ; Beny Spira ; Cristiane Rodrigues Guzzo Carvalho ; Cristina Elisa Alvarez Martinez ; Henrique Ferreira ; João Carlos Setubal ; Marcelo Brocchi ; Marcio Vinicius Bertacine Dias ; Marilis Do Valle Marques ; Regina Lúcia Baldini ; Roberto Kopke Salinas ; Rodrigo da Silva Galhardo ; Sandro Roberto Marana
• Associated researchers: Cristiane Rodrigues Guzzo Carvalho ; Cristina Elisa Alvarez Martinez ; Frederico José Gueiros Filho ; Germán Gustavo Sgro ; João Carlos Setubal ; José Freire da Silva Neto ; Julio Cezar Franco de Oliveira ; Leonardo Talachia Rosa ; Marcio Vinicius Bertacine Dias ; Marco Aurélio Takita ; Rita de Cássia Café Ferreira ; Robson Francisco de Souza ; Rodrigo da Silva Galhardo ; Ronaldo Bento Quaggio
• Associated research grant(s): 24/09645-9 - Integration of Experimental and in silico Methods in the Study of Antimicrobials Mechanisms Resistance in Mycobacterium tuberculosis, AP.R SPRINT; 24/02235-0 - Study of the NlpC_P60-like enzymes for the development of novel antimycobacterial agents, AP.R; 23/15471-0 - Multi-user equipment approved in grant 2021/10577-0: BMG Labtech Clariostar multimode microplate reader, AP.EMU; 23/12177-4 - Multi-user equipment approved in grant 2021/10577-0: circular dichroism spectrophotometers JASCO, model J-1500, AP.EMU; 23/12239-0 - Multi-user equipment approved in grant 2021/10577-0: PEAQ-ITC (Isothermal Calorimeter), AP.EMU
• Associated scholarship(s): 25/03800-5 - Characterization of Salmonella enterica Typhimurium mutant strains for bacterial chromosome associated proteins., BP.MS; 25/00779-5 - Evaluating regulatory proteins as drug targets for controlling the growth of Salmonella enterica, BP.PD; 25/02990-5 - Study of the association of tailoring enzymes with secondary metabolite production enzymes, and construction of predictors of products and loci biosynthetic., BP.DD; + associated scholarships 25/06208-0 - Development and implementation of the educational project MicroMath, BP.IC; 24/16330-4 - Structural and functional studies of key enzymes involved in the apramycin biosynthesis., BP.DD; 25/03876-1 - Characterization of the X-TfeXAC3266/X-TfiXAC3267 nuclease/inhibitor complex associated with the Xanthomonas citri type IV secretion system, BP.IC; 24/21568-0 - Structural study of glycosyltransferases dependent on P450-type helper proteins involved in the biosynthesis of macrolide antibiotics, BP.DD; 25/06226-8 - Development and implementation of distributed bioinformatics pipelines for hybrid and distributed HPC environments, BP.TT; 25/04443-1 - Xanthomonadales bacteriofages and the search for Crispr-Cas3 inhibitors, BP.DR; 25/03250-5 - Global transcriptome analysis of the tripartite interaction between X. citri, one of its lytic bacteriophage and the citrus host, BP.PD; 25/04946-3 - Structural and functional studies of proteins from integrative conjugative elements, BP.DR; 25/05809-0 - Implementation of the computational infrastructure for cryoelectron microscopy, BP.TT; 24/23910-7 - Heterogeneity in ¿-lactam resistance confered by a mobile element, BP.MS; 25/00760-2 - Outer membrane vesicles carrying violacein and their antibacterial activity to Staphylococcus aureus, BP.IC; 25/02200-4 - Differential gene expression of Pseudomonas aeruginosa using a transcriptomic approach, BP.TT; 25/02846-1 - Analysis of co-evolutionary adaptations in bacteriophages infecting Pseudomonas aeruginosa and Klebsiella pneumoniae strains, BP.PD; 25/03197-7 - Classification and annotation of Metagenome-Assembled Genomes, BP.IC; 24/22312-9 - ANALYSIS OF TRANSCRIPTIONAL PROFILES OF Xanthomonas citri pv. citri IN CONDITIONS RELEVANT TO PLANT INFECTION, BP.DR; 24/23478-8 - Role of the RppH and NudC orthologs in RNA homeostasis in Caulobacter, BP.MS; 24/21751-9 - Integrated analysis of genomic and pangenome diversity of bacterial genera present in metagenomic data, BP.IC; 24/23287-8 - Structure and function of iterative polyketide synthases (iPKSs) and hybrid systems of iPKS and Nonribosomal peptide synthases (iPKS-NRPSs) involved in antibiotic biosynthesis, BP.PD; 25/00091-3 - Phenotypic and molecular characterization of Acinetobacter baumannii clinical isolates, BP.IC; 24/14407-0 - Investigation of the potential of viral depolymerases for use in alternative treatment of infections caused by Klebsiella pneumoniae, BP.IC; 24/20406-6 - Studying the role of sRNAs in post-transcriptional regulation of stress response in Caulobacter., BP.PD; 24/15711-4 - Identification of compounds that interact with the ClpC1 enzyme of the ClpP1P2C1 protein complex of Mycobacterium tuberculosis by fragment screening, BP.IC; 24/19817-1 - Study of the mechanism of action and resistance to pyrazinamide in Mycobacterium tuberculosis, BP.IC; 24/17666-6 - Structural and molecular investigation of the type IV secretion systems of Gram-positive bacteria, BP.DD; 24/04962-6 - Inhibition of dihydrofolate reductase from Mycobacterium tuberculosis and pathogenic fungi by antimicrobials identified by Fragment-Based Drug Discovery, BP.DR; 24/10763-6 - Structural study by electron cryomicroscopy of the MotA/MotB flagellar stator of Leptospira interrogans, BP.DD; 24/12387-1 - Development of a system for the identification and characterization of peptides associated with the adsorption of Xanthomonas citri bacteriophages, BP.DR; 24/01729-9 - Development and application of a computational tool for surveys of bacterial species using metagenomics datasets, BP.DD; 24/14262-1 - Public outreach and science communication of CEPID B3, BP.JC; 24/13851-3 - Evaluation of phage depolymerases against Xanthomonas citri subsp. citri, BP.IC; 24/10539-9 - Characterization of the nucleoprotein complex interconnecting the divisome and the terminal replication region of the Xanthomonas citri chromosome, BP.DR; 24/16116-2 - Screening for molecules that inhibit widespread bacterial transcription factors, BP.IC; 24/09014-9 - STUDY OF THE REGULATION OF EXPRESSION OF ACONITASE AND THE EFFECT OF ITS LIGATION TO THE RNA DEGRADOSOME IN CAULOBACTER CRESCENTUS, BP.MS; 24/12945-4 - Expanding the host range of lytic bacteriophages through recombination and selection, BP.DR; 23/08535-2 - Construction of "Artilysins" for the control of Xanthomonas citri subsp. citri, BP.PD; 23/03213-7 - Salmonella enterica and Membrane Vesicles (MVs) in Vaccine Development, BP.DR; 24/03230-1 - Characterization of FAN1 DNA repair pathway in Pseudomonas aeruginosa, BP.DD; 23/16089-2 - Cryo-EM study of the adsorption of a type IV pilus-specific bacteriophage to its receptor, BP.PD; 24/06039-0 - Exploring biotechnological applications of bacteria-killing type IV secretion systems., BP.PD; 24/05782-1 - Implementation of bioinformatic tools and pipelines for analyses of phage and bacterial genomes and their interactions., BP.TT; 23/17618-9 - Xanthomonas citri R-bodies: expression and structural characterization, BP.IC; 24/01290-7 - Characterization of the stress response by alternative sigma factors in Xanthomonas citri, BP.PD; 24/03640-5 - Intersection between stress responses in bacteria, BP.PD; 24/03217-5 - Structural studies of the inner membrane subunits of the Xanthomonas citri Type IV Secretion System using NMR spectroscopy and cryoelectron microscopy, BP.PD; 24/03134-2 - A novel domain and the new signaling pathway of DgcP in Pseudomonas aeruginosa, BP.DD; 23/13894-1 - CryoEM study of the adsorption of a phage to a type IV pilus, BP.DD; 24/02648-2 - Development and implementation of the educational project MicroMath, BP.IC; 24/01159-8 - Uncovering bacterial-phage interplay by monitoring transcriptomic changes during phage infection., BP.MS; 23/13202-2 - Characterization of Xanthomas citri bacteriophage, BP.IC; 23/13291-5 - Determining the intrinsic levels of ppGpp across a species and its influence on growth rate and tolerance to antibiotics, BP.DD; 23/05679-3 - Characterization of xac4136 gene as a putative Type VI Secretion System effector in Xanthomonas citri, BP.MS; 23/14021-1 - Phage endolysins (ELs) as antimicrobial agents to Gram-negative bacteria, BP.PD; 23/12063-9 - Dissemination of concepts in microbiology: Impact assessment on basic education., BP.IC; 23/09812-0 - Study of the action of Pseudomonas aeruginosa secretion systems and their effectors in co-cultures with Aspergillus fumigatus, BP.IC; 23/10731-4 - Implementation of computational infrastructure for NMR spectroscopy, BP.TT; 23/11219-5 - Development and implementation of the educational project MicroMath, BP.IC; 23/06554-0 - Identification of compounds that interact with DNA gyrase from Mycobacterium tuberculosis through fragment screening, BP.IC; 23/06833-6 - Evaluating the role of aconitase in the regulation of FeS synthesis genes in Caulobacter, BP.IC; 23/06724-2 - Isolation of Pseudomonas aeruginosa lytic bacteriophages from various natural sources, BP.IC; 23/06729-4 - Training of Pseudomonas aeruginosa lytic bacteriophages to overcome bacterial resistance, BP.IC; 17/23627-0 - Determination of the structural bases of Biosynthetic formation of heterocyclic rings in ionophores polyethers, BP.PD - associated scholarships

Abstract

The CEPID B3 is a network with research hubs based in São Paulo (IQ-USP, ICB-USP), Campinas (IB-UNICAMP, IAC), Ribeirão Preto (FCFRP-USP, FMRP-USP) and Rio Claro (UNESP) that will collaborate to carry out cutting edge basic research into molecular mechanisms that are of prime importance to understand bacterial reproduction, multicellular behavior, competition, colonization and interactions with their eukaryotic hosts and bacteriophages. The acquired knowledge will be used in the search and development of new chemical and biological inhibitors of bacterial growth. (AU)

Scientific publications

(22)

(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)

DOS SANTOS, NAARA M.; PICINATO, BEATRIZ A.; SANTOS, LUCAS S.; DE ARAUJO, HUGO L.; BALAN, ANDREA; KOIDE, TIE; MARQUES, MARILIS V.. Mapping the IscR regulon sheds light on the regulation of iron homeostasis in Caulobacter. FRONTIERS IN MICROBIOLOGY, v. 15, p. 18-pg., 2024-09-30. (21/10577-0, 22/00308-4, 20/10171-0, 22/06360-8, 18/17309-8)

DE ALMEIDA, MICHELLE TEIXEIRA; BARBOSA, ANA PAULA; BOMFIM, CAMILA GASQUE; VISNARDI, ALINE BIAZOLA; VINCES, TANIA CHURASACARI; CERONI, ALEXANDRE; DURIGON, EDISON LUIZ; GUZZO, CRISTIANE RODRIGUES. Obtaining a high titer of polyclonal antibodies from rats to the SARS-CoV-2 nucleocapsid protein and its N- and C-terminal domains for diagnostic test development. JOURNAL OF IMMUNOLOGICAL METHODS, v. 522, p. 9-pg., 2023-09-27. (21/10577-0, 19/21739-0, 22/08730-7, 20/14914-8, 19/00195-2, 16/09047-8, 20/04680-0)

CHAGAS, RAFAEL S.; MARANA, SANDRO R.. Tris inhibits a GH1 β-glucosidase by a linear mixed inhibition mechanism. PLoS One, v. 20, n. 3, p. 11-pg., 2025-03-25. (21/10577-0, 21/03967-6)

BATISTA, BIANCA B.; DE LIMA, VINICIUS M.; WILL, W. RYAN; FANG, FERRIC C.; DA SILVA NETO, JOSE F.. A cytochrome bd repressed by a MarR family regulator confers resistance to metals, nitric oxide, sulfide, and cyanide in Chromobacterium violaceum. Applied and Environmental Microbiology, v. 91, n. 2, p. 15-pg., 2025-01-24. (18/19058-2, 20/15268-2, 21/10577-0, 21/09170-2, 21/06894-0, 18/01388-6)

ZAMUNER, CAIO FELIPE CAVICCHIA; CARHUARICRA-HUAMAN, DENNIS; RAGUPATHY, ROOBINIDEVI; REDFERN, JAMES; RODRIGUEZ-CUEVA, CARMEN L.; BEHLAU, FRANKLIN; ENRIGHT, MARK C.; FERREIRA, HENRIQUE; SETUBAL, JOAO C.. Evolution and spread of Xanthomonas citri subsp. citri in the São Paulo, Brazil, citrus belt inferred from 758 novel genomes. MICROBIAL GENOMICS, v. 11, n. 1, p. 14-pg., 2025-01-01. (21/10577-0, 17/50454-9, 18/21164-5, 19/05497-7, 14/50880-0)

VISNARDI, ALINE BIAZOLA; RIBEIRO, RODOLFO ALVARENGA; DE SOUZA, ANACLETO SILVA; VINCES, TANIA GERALDINE CHURASACARI; LLONTOP, EDGAR E.; FERRARI, ANIELLE SALVIANO DE ALMEIDA; HENRIQUE, PEDRO ANTONIO FRANCA; VALDIVIESO, DANIELA; SANCHEZ-LIMACHE, DANIEL ENRIQUE; SILVA, GABRIELA ROBERTO; et al. Insertion of a Divergent GAF-like Domain Defines a Novel Family of YcgR Homologues That Bind c-di-GMP in Leptospirales. ACS OMEGA, v. 10, n. 4, p. 19-pg., 2025-01-21. (20/04680-0, 19/00195-2, 21/05262-0, 21/00070-5, 21/10577-0, 17/17303-7, 23/10432-7, 17/06394-1, 16/09047-8, 23/18211-0, 22/08730-7)

VINCES, TANIA CHURASACARI; DE SOUZA, ANACLETO SILVA; CARVALHO, CECILIA F.; VISNARDI, ALINE BIAZOLA; TEIXEIRA, RAPHAEL D.; LLONTOP, EDGAR E.; BISMARA, BEATRIZ APARECIDA PASSOS; VICENTE, ELISABETE J.; PEREIRA, JOSE O.; DE SOUZA, ROBSON FRANCISCO; et al. Monomeric Esterase: Insights into Cooperative Behavior, Hysteresis/Allokairy. BIOCHEMISTRY, v. 63, n. 9, p. 16-pg., 2024-04-26. (21/10577-0, 19/12234-2, 22/08730-7, 21/05262-0, 19/00195-2, 17/17303-7, 20/04680-0)

OKA, GABRIEL U.; SOUZA, DIORGE P.; SGRO, GERMAN G.; GUZZO, CRISTIANE R.; DUNGER, GERMAN; FARAH, CHUCK S.. Xanthomonas immunity proteins protect against the cis-toxic effects of their cognate T4SS effectors. EMBO REPORTS, v. 25, n. 3, p. 17-pg., 2024-03-12. (18/09277-9, 11/22571-4, 21/10577-0, 17/17303-7, 14/04294-1)

MARTINS, LAYLA FARAGE; DOS SANTOS JUNIOR, ARIOSVALDO PEREIRA; NICASTRO, GIANLUCCA GONCALVES; SCHEUNEMANN, GABY; ANGELI, CLAUDIA BLANES; ROSSI, FERNANDO PACHECO NOBRE; QUAGGIO, RONALDO BENTO; PALMISANO, GIUSEPPE; SGRO, GERMAN GUSTAVO; ISHIDA, KELLY; et al. Phages ZC01 and ZC03 require type-IV pilus for Pseudomonas aeruginosa infection and have a potential for therapeutic applications. MICROBIOLOGY SPECTRUM, v. N/A, p. 17-pg., 2024-10-29. (21/10577-0, 20/04923-0, 18/18257-1, 18/15549-1, 22/11334-6)

DE SOUZA, ANACLETO SILVA; DE SOUZA, ROBSON FRANCISCO; GUZZO, CRISTIANE RODRIGUES. Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). Journal of Computer-Aided Molecular Design, v. 37, n. 12, p. 22-pg., 2023-10-04. (21/10577-0, 19/00195-2, 21/00070-5, 16/09047-8, 20/04680-0)

SILVA, CATHARINA DOS SANTOS; DIAS, MARCIO VINICIUS BERTACINE. The multiple roles of the NlpC_P60 peptidase family in mycobacteria - an underexplored target for antimicrobial drug discovery. FEBS Letters, v. N/A, p. 19-pg., 2025-03-03. (24/02235-0, 22/12234-5, 20/03850-9, 16/18721-4, 21/10577-0, 24/15878-6)

VALENCIA, ESTELA YNES; NUNES, VIVIANE ABREU; CHAMBERGO, FELIPE S.; SPIRA, BENY. ADP-MoA-Pa: a platform for screening antibiotic activity and their mechanism of action in Pseudomonas aeruginosa. Journal of Applied Microbiology, v. 136, n. 3, p. 10-pg., 2025-03-19. (21/10577-0, 23/04848-6, 24/02524-1)

ADRIANI, PATRICIA P.; LOPES, LUCIANA B.; DE OLIVEIRA, GABRIEL S.; NUNES, JESSICA R.; SALATA, GIOVANNA C.; FERNANDES, MYRIAN T. P.; REIGADO, GUSTAVO RONCOLI; CAMARENA, DENISSE ESTHER MALLAUPOMA; MARIA-ENGLER, SILVYA S.; DIAS, MARCIO V. B.; et al. PEP-1 fused to glutathione peroxidase from Trichoderma reesei: a safe and effective antioxidant active ingredient for cutaneous applications. JOURNAL OF DRUG DELIVERY SCIENCE AND TECHNOLOGY, v. 110, p. 11-pg., 2025-08-01. (20/00030-0, 21/10577-0, 17/25705-8, 17/04926-6, 24/03868-6, 21/09105-6, 17/23627-0, 22/12234-5, 19/26048-6, 18/13877-1)

KIRKMAN, TIM; SILVA, CATHARINA DOS SANTOS; TOSIN, MANUELA; DIAS, MARCIO VINICIUS BERTACINE BERTACINE. How to Find a Fragment: Methods for Screening and Validation in Fragment-Based Drug Discovery. CHEMMEDCHEM, v. N/A, p. 15-pg., 2024-11-04. (21/10577-0, 22/12234-5)

DE OLIVEIRA, GABRIEL S.; BURY, PRISCILA DOS S.; HUANG, FANGLU; LI, YUAN; DE ARAUJO, NATALIA C.; ZHOU, JIAHAI; SUN, YUHUI; LEEPER, FINIAN J.; LEADLAY, PETER F.; DIAS, MARCIO V. B.. Structural and Functional Basis of GenB2 Isomerase Activity from Gentamicin Biosynthesis. ACS Chemical Biology, v. 19, n. 9, p. 10-pg., 2024-08-29. (14/07843-6, 10/15971-3, 15/09188-8, 21/10577-0, 18/00351-1, 17/23627-0, 22/12234-5)

DE ARAUJO, HUGO L.; PICINATO, BEATRIZ A.; LORENZETTI, ALAN P. R.; MUTHUNAYAKE, NISANSALA S.; RATHNAYAKA-MUDIYANSELAGE, I. W.; DOS SANTOS, NAARA M.; SCHRADER, JARED; KOIDE, TIE; MARQUES, MARILIS V.. The DEAD-box RNA helicase RhlB is required for efficient RNA processing at low temperature in Caulobacter. MICROBIOLOGY SPECTRUM, v. 11, n. 6, p. 20-pg., 2023-10-18. (21/10577-0, 17/03052-2, 19/08514-0, 22/00308-4, 22/06360-8, 18/17309-8)

DOS SANTOS, HADASSA CRISTHINA DE AZEVEDO SOARES; ARMELLINI, BARBARA RODRIGUES CINTRA; NAVES, GIOVANNA LELLO; BUERIS, VANESSA; MORENO, ANA CAROLINA RAMOS; FERREIRA, RITA DE CASSIA CAFE. Using "Adopt a Bacterium" as an e-learning tool for simultaneously teaching microbiology to different health-related university courses. FEMS Microbiology Letters, v. 371, p. 8-pg., 2024-05-28. (21/10577-0)

JORGE, GENESY PEREZ; GONTIJO, MARCO; FLORO E SILVA, MARINA; GOES, ISABELLA CAROLINA RODRIGUES DOS SANTOS; JAIMES-FLOREZ, YESSICA PAOLA; COSER, LILIAN DE OLIVEIRA; ROCHA, FRANCISCA JANAINA SOARES; GIORGIO, SELMA; BROCCHI, MARCELO. Attenuated mutants of Salmonella enterica Typhimurium mediate melanoma regression via an immune response. Experimental Biology and Medicine, v. 249, p. 19-pg., 2024-06-21. (19/17091-5, 21/10577-0, 21/00465-0, 22/11399-0, 20/01535-9)

DE ALMEIDA, MICHELLE TEIXEIRA; MERIGHI, DAVI GABRIEL SALUSTIANO; VISNARDI, ALINE BIAZOLA; GONCALVES, CAUE AUGUSTO BONETO; AMORIM, VITOR MARTINS DE FREITAS; FERRARI, ANIELLE SALVIANO DE ALMEIDA; DE SOUZA, ANACLETO SILVA; GUZZO, CRISTIANE RODRIGUES. Latin America's Dengue Outbreak Poses a Global Health Threat. Viruses-Basel, v. 17, n. 1, p. 32-pg., 2025-01-01. (23/13894-1, 21/05262-0, 21/10577-0, 23/18211-0, 22/08730-7, 23/07366-2)

AMORIM, VITOR MARTINS DE FREITAS; SOARES, EDUARDO PEREIRA; FERRARI, ANIELLE SALVIANO DE ALMEIDA; MERIGHI, DAVI GABRIEL SALUSTIANO; DE SOUZA, ROBSON FRANCISCO; GUZZO, CRISTIANE RODRIGUES; DE SOUZA, ANACLETO SILVA. 3-Chymotrypsin-like Protease (3CLpro) of SARS-CoV-2: Validation as a Molecular Target, Proposal of a Novel Catalytic Mechanism, and Inhibitors in Preclinical and Clinical Trials. Viruses-Basel, v. 16, n. 6, p. 22-pg., 2024-06-01. (21/10577-0, 22/08730-7, 19/00195-2, 21/00070-5, 23/13894-1, 16/09047-8, 20/04680-0)

DORR, NATALIA CAROLINA DREBES; ALVAREZ-MARTINEZ, CRISTINA ELISA. Predator-prey interplay When chemical conversation turns deadly. CELL HOST & MICROBE, v. 33, n. 5, p. 4-pg., 2025-05-14. (21/10577-0, 22/15160-2, 22/06555-3)

GOZZI, ISABELLE CAROLINA COTRIM; ROSA, BRUNA GENNARI; MEDEIROS, ISADORA; SILVA, BEATRIZ DINAT LABONE; RODRIGUES, GIOVANNA MATOS; YOSHIHARA, FERNANDA AYUMI NAGAY; CUSTODIO, GIOVANNA TRESSO; DE LUCENA, JOSE RICARDO FERREIRA; BARONI, LARA NARDI; MORENO, ANA CAROLINA RAMOS; et al. The adoption of a superhero bacteria: Escherichia coli and its adventures in microbiology education. FEMS Microbiology Letters, v. 372, p. 8-pg., 2025-01-01. (21/10577-0)