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Vinces TC, de Souza AS, Carvalho CF, Visnardi AB, Teixeira RD, Llontop EE, Bismara BAP, Vicente EJ, Pereira JO, de Souza RF, Yonamine M, Marana SR, Farah CS, Guzzo CR. Monomeric Esterase: Insights into Cooperative Behavior, Hysteresis/Allokairy. Biochemistry 2024; 63:1178-1193. [PMID: 38669355 DOI: 10.1021/acs.biochem.3c00668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Herein, we present a novel esterase enzyme, Ade1, isolated from a metagenomic library of Amazonian dark earths soils, demonstrating its broad substrate promiscuity by hydrolyzing ester bonds linked to aliphatic groups. The three-dimensional structure of the enzyme was solved in the presence and absence of substrate (tributyrin), revealing its classification within the α/β-hydrolase superfamily. Despite being a monomeric enzyme, enzymatic assays reveal a cooperative behavior with a sigmoidal profile (initial velocities vs substrate concentrations). Our investigation brings to light the allokairy/hysteresis behavior of Ade1, as evidenced by a transient burst profile during the hydrolysis of substrates such as p-nitrophenyl butyrate and p-nitrophenyl octanoate. Crystal structures of Ade1, coupled with molecular dynamics simulations, unveil the existence of multiple conformational structures within a single molecular state (E̅1). Notably, substrate binding induces a loop closure that traps the substrate in the catalytic site. Upon product release, the cap domain opens simultaneously with structural changes, transitioning the enzyme to a new molecular state (E̅2). This study advances our understanding of hysteresis/allokairy mechanisms, a temporal regulation that appears more pervasive than previously acknowledged and extends its presence to metabolic enzymes. These findings also hold potential implications for addressing human diseases associated with metabolic dysregulation.
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Affiliation(s)
- Tania Churasacari Vinces
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Cecília F Carvalho
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Aline Biazola Visnardi
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Raphael D Teixeira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Edgar E Llontop
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Beatriz Aparecida Passos Bismara
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Elisabete J Vicente
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - José O Pereira
- Biotechnology Group, Federal University of Amazonas, Amazonas CEP 69077-000, Brazil
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Mauricio Yonamine
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Sandro Roberto Marana
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Chuck Shaker Farah
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Cristiane R Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
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2
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Oka GU, Souza DP, Sgro GG, Guzzo CR, Dunger G, Farah CS. Xanthomonas immunity proteins protect against the cis-toxic effects of their cognate T4SS effectors. EMBO Rep 2024; 25:1436-1452. [PMID: 38332152 PMCID: PMC10933484 DOI: 10.1038/s44319-024-00060-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 02/10/2024] Open
Abstract
Many bacteria kill rival species by translocating toxic effectors into target cells. Effectors are often encoded along with cognate immunity proteins that could (i) protect against "friendly-fire" (trans-intoxication) from neighboring sister cells and/or (ii) protect against internal cis-intoxication (suicide). Here, we distinguish between these two mechanisms in the case of the bactericidal Xanthomonas citri Type IV Secretion System (X-T4SS). We use a set of X. citri mutants lacking multiple effector/immunity protein (X-Tfe/X-Tfi) pairs to show that X-Tfis are not absolutely required to protect against trans-intoxication by wild-type cells. Our investigation then focused on the in vivo function of the lysozyme-like effector X-TfeXAC2609 and its cognate immunity protein X-TfiXAC2610. In the absence of X-TfiXAC2610, we observe X-TfeXAC2609-dependent and X-T4SS-independent accumulation of damage in the X. citri cell envelope, cell death, and inhibition of biofilm formation. While immunity proteins in other systems have been shown to protect against attacks by sister cells (trans-intoxication), this is an example of an antibacterial secretion system in which the immunity proteins are dedicated to protecting cells against cis-intoxication.
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Affiliation(s)
- Gabriel U Oka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Structure and Function of Bacterial Nanomachines, Institut Européen de Chimie et Biologie-CNRS, UMR 5234 Microbiologie Fondamentale et Pathogénicité University of Bordeaux, Pessac, France
| | - Diorge P Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Germán G Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Cristiane R Guzzo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - German Dunger
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Instituto de Ciencias Agropecuarias del Litoral (ICiAgro Litoral), Universidad Nacional del Litoral, CONICET, Facultad de Ciencias Agrarias, Esperanza, Argentina
| | - Chuck S Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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El Omari K, Duman R, Mykhaylyk V, Orr CM, Latimer-Smith M, Winter G, Grama V, Qu F, Bountra K, Kwong HS, Romano M, Reis RI, Vogeley L, Vecchia L, Owen CD, Wittmann S, Renner M, Senda M, Matsugaki N, Kawano Y, Bowden TA, Moraes I, Grimes JM, Mancini EJ, Walsh MA, Guzzo CR, Owens RJ, Jones EY, Brown DG, Stuart DI, Beis K, Wagner A. Experimental phasing opportunities for macromolecular crystallography at very long wavelengths. Commun Chem 2023; 6:219. [PMID: 37828292 PMCID: PMC10570326 DOI: 10.1038/s42004-023-01014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing.
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Affiliation(s)
- Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Christian M Orr
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | | | - Graeme Winter
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Vinay Grama
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Feng Qu
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Kiran Bountra
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Hok Sau Kwong
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Maria Romano
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Institute of Biostructures and Bioimaging, IBB, CNR, 80131, Naples, Italy
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Rosana I Reis
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Lutz Vogeley
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Luca Vecchia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - C David Owen
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford, UK
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Max Renner
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Naohiro Matsugaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Erika J Mancini
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Martin A Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Cristiane R Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Raymond J Owens
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - David G Brown
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
| | - Dave I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Konstantinos Beis
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK.
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4
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Fanelli C, Francini ALR, Celestrino GA, Teles F, Barbosa AP, Noda P, Iannuzzi LR, Guzzo CR, Ornellas FM, Noronha IL. Tamoxifen associated to the conservative CKD treatment promoted additional antifibrotic effects on experimental hypertensive nephrosclerosis. Sci Rep 2023; 13:13985. [PMID: 37633958 PMCID: PMC10460450 DOI: 10.1038/s41598-023-39299-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/22/2023] [Indexed: 08/28/2023] Open
Abstract
CKD progression depends on the activation of an intricate set of hemodynamic and inflammatory mechanisms, promoting renal leukocyte infiltration, inflammation and fibrosis, leading to renal function loss. There are currently no specific drugs to detain renal fibrogenesis, which is a common end-point for different nephropathies. Clinical therapy for CKD is mostly based on the management of hypertension and proteinuria, partially achieved with renin-angiotensin-aldosterone system (RAAS) blockers, and the control of inflammation by immunosuppressive drugs. The aim of the present study was to verify if the administration of tamoxifen (TAM), an estrogen receptor modulator, clinically employed in the treatment of breast cancer and predicted to exert antifibrotic effects, would promote additional benefits when associated to a currently used therapeutic scheme for the conservative management of experimental CKD. Wistar rats underwent the NAME model of hypertensive nephrosclerosis, obtained by daily oral administration of a nitric oxide synthesis inhibitor, associated to dietary sodium overload. The therapeutic association of TAM to losartan (LOS), and mofetil mycophenolate (MMF) effectively reduced the severe hypertension, marked albuminuria and glomerular damage exhibited by NAME animals. Moreover, the association also succeeded in limiting renal inflammation in this model, and promoted further reduction of ECM interstitial accumulation and renal fibrosis, compared to the monotherapies. According to our results, the association of TAM to the currently used conservative treatment of CKD added significant antifibrotic effects both in vivo and in vitro, and may represent an alternative to slow the progression of chronic nephropathy.
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Affiliation(s)
- Camilla Fanelli
- Laboratory of Cellular, Genetic, and Molecular Nephrology, Renal Division, University of São Paulo Medical School, São Paulo - SP, Brazil.
| | - Ana L R Francini
- Laboratory of Cellular, Genetic, and Molecular Nephrology, Renal Division, University of São Paulo Medical School, São Paulo - SP, Brazil
| | - Giovanna A Celestrino
- Laboratory of Cellular, Genetic, and Molecular Nephrology, Renal Division, University of São Paulo Medical School, São Paulo - SP, Brazil
| | - Flávio Teles
- Faculty of Medicine, Federal University of Alagoas, Av. Lourival Melo Mota, S/N Tabuleiro do Martins, Maceió - AL, 57072-900, Brazil
| | - Ana P Barbosa
- Institute of Biomedical Sciences, University of São Paulo, São Paulo - SP, Brazil
| | - Paloma Noda
- Laboratory of Cellular, Genetic, and Molecular Nephrology, Renal Division, University of São Paulo Medical School, São Paulo - SP, Brazil
| | - Leandro R Iannuzzi
- Laboratory of Cellular, Genetic, and Molecular Nephrology, Renal Division, University of São Paulo Medical School, São Paulo - SP, Brazil
| | - Cristiane R Guzzo
- Institute of Biomedical Sciences, University of São Paulo, São Paulo - SP, Brazil
| | - Felipe M Ornellas
- Laboratory of Cellular, Genetic, and Molecular Nephrology, Renal Division, University of São Paulo Medical School, São Paulo - SP, Brazil
| | - Irene L Noronha
- Laboratory of Cellular, Genetic, and Molecular Nephrology, Renal Division, University of São Paulo Medical School, São Paulo - SP, Brazil
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5
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Rosa IF, Peçanha APB, Carvalho TRB, Alexandre LS, Ferreira VG, Doretto LB, Souza BM, Nakajima RT, da Silva P, Barbosa AP, Gomes-de-Pontes L, Bomfim CG, Machado-Santelli GM, Condino-Neto A, Guzzo CR, Peron JPS, Andrade-Silva M, Câmara NOS, Garnique AMB, Medeiros RJ, Ferraris FK, Barcellos LJG, Correia-Junior JD, Galindo-Villegas J, Machado MFR, Castoldi A, Oliveira SL, Costa CC, Belo MAA, Galdino G, Sgro GG, Bueno NF, Eto SF, Veras FP, Fernandes BHV, Sanches PRS, Cilli EM, Malafaia G, Nóbrega RH, Garcez AS, Carrilho E, Charlie-Silva I. Photobiomodulation Reduces the Cytokine Storm Syndrome Associated with COVID-19 in the Zebrafish Model. Int J Mol Sci 2023; 24:ijms24076104. [PMID: 37047078 PMCID: PMC10094635 DOI: 10.3390/ijms24076104] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
Although the exact mechanism of the pathogenesis of coronavirus SARS-CoV-2 (COVID-19) is not fully understood, oxidative stress and the release of pro-inflammatory cytokines have been highlighted as playing a vital role in the pathogenesis of the disease. In this sense, alternative treatments are needed to reduce the level of inflammation caused by COVID-19. Therefore, this study aimed to investigate the potential effect of red photobiomodulation (PBM) as an attractive therapy to downregulate the cytokine storm caused by COVID-19 in a zebrafish model. RT-qPCR analyses and protein-protein interaction prediction among SARS-CoV-2 and Danio rerio proteins showed that recombinant Spike protein (rSpike) was responsible for generating systemic inflammatory processes with significantly increased levels of pro-inflammatory (il1b, il6, tnfa, and nfkbiab), oxidative stress (romo1) and energy metabolism (slc2a1a and coa1) mRNA markers, with a pattern similar to those observed in COVID-19 cases in humans. On the other hand, PBM treatment was able to decrease the mRNA levels of these pro-inflammatory and oxidative stress markers compared with rSpike in various tissues, promoting an anti-inflammatory response. Conversely, PBM promotes cellular and tissue repair of injured tissues and significantly increases the survival rate of rSpike-inoculated individuals. Additionally, metabolomics analysis showed that the most-impacted metabolic pathways between PBM and the rSpike treated groups were related to steroid metabolism, immune system, and lipid metabolism. Together, our findings suggest that the inflammatory process is an incisive feature of COVID-19 and red PBM can be used as a novel therapeutic agent for COVID-19 by regulating the inflammatory response. Nevertheless, the need for more clinical trials remains, and there is a significant gap to overcome before clinical trials can commence.
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Affiliation(s)
- Ivana F Rosa
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 01049-010, Brazil
| | - Ana P B Peçanha
- Department of Orthodontics, São Leopoldo Mandic College, Campinas 13045-755, Brazil
| | - Tábata R B Carvalho
- Department of Orthodontics, São Leopoldo Mandic College, Campinas 13045-755, Brazil
| | - Leonardo S Alexandre
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos 13566-590, Brazil
- The National Institute of Science and Technology in Bioanalyses, INCTBio, Campinas 13083-970, Brazil
| | - Vinícius G Ferreira
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos 13566-590, Brazil
- The National Institute of Science and Technology in Bioanalyses, INCTBio, Campinas 13083-970, Brazil
| | - Lucas B Doretto
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 01049-010, Brazil
| | - Beatriz M Souza
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 01049-010, Brazil
| | - Rafael T Nakajima
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 01049-010, Brazil
| | - Patrick da Silva
- Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo 05508-220, Brazil
| | - Ana P Barbosa
- Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo 05508-220, Brazil
| | - Leticia Gomes-de-Pontes
- Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo 05508-220, Brazil
| | - Camila G Bomfim
- Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo 05508-220, Brazil
| | | | - Antonio Condino-Neto
- Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo 05508-220, Brazil
| | - Cristiane R Guzzo
- Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo 05508-220, Brazil
| | - Jean P S Peron
- Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo 05508-220, Brazil
| | - Magaiver Andrade-Silva
- Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo 05508-220, Brazil
| | - Niels O S Câmara
- Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo 05508-220, Brazil
| | - Anali M B Garnique
- Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo 05508-220, Brazil
| | | | | | - Leonardo J G Barcellos
- Laboratório de Fisiologia de Peixes, Programa de Pós-Graduação em Bioexperimentação, Escola de Ciências Agrárias, Inovação e Negócios, Universidade de Passo Fundo, Passo Fundo 99052-900, Brazil
| | - Jose D Correia-Junior
- Institute of Biomedical Sciences, Federal University Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Jorge Galindo-Villegas
- Department of Genomics, Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Mônica F R Machado
- Biological Sciences Special Academic Unit, Federal University of Jatai, Jatai 75804-020, Brazil
| | - Angela Castoldi
- Keizo Asami Institute, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Susana L Oliveira
- School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal 14884-900, Brazil
| | - Camila C Costa
- School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal 14884-900, Brazil
| | - Marco A A Belo
- School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal 14884-900, Brazil
| | - Giovane Galdino
- Institute of Motricity Sciences, Department of Physical Therapy, Federal University of Alfenas, Alfenas 37133-840, Brazil
| | - Germán G Sgro
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo 14040-900, Brazil
| | - Natalia F Bueno
- Integrated Structural Biology Platform, Carlos Chagas Institute, FIOCRUZ Paraná, Curitiba 81310-020, Brazil
| | - Silas F Eto
- Center of Innovation and Development, Laboratory of Development and Innovation Butantan Institute, São Paulo 69310-000, Brazil
| | - Flávio P Veras
- Faculty of Medicine, University of São Paulo (USP), Ribeirão Preto 14040-900, Brazil
| | - Bianca H V Fernandes
- Laboratory of Genetic and Sanitary Control, Technical Board of Support for Teaching and Research, Faculty of Medicine, University of Sao Paulo, São Paulo 01246-903, Brazil
| | - Paulo R S Sanches
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara 14800-060, Brazil
| | - Eduardo M Cilli
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara 14800-060, Brazil
| | - Guilherme Malafaia
- Laboratory of Toxicology Applied to the Environment, Goiano Federal Institute, Urutaí Campus, Urutaí 75790-000, Brazil
| | - Rafael H Nóbrega
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 01049-010, Brazil
| | - Aguinaldo S Garcez
- Department of Orthodontics, São Leopoldo Mandic College, Campinas 13045-755, Brazil
| | - Emanuel Carrilho
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos 13566-590, Brazil
- The National Institute of Science and Technology in Bioanalyses, INCTBio, Campinas 13083-970, Brazil
| | - Ives Charlie-Silva
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara 14800-060, Brazil
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6
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Silva EKVB, Bomfim CG, Barbosa AP, Noda P, Noronha IL, Fernandes BHV, Machado RRG, Durigon EL, Catanozi S, Rodrigues LG, Pieroni F, Lima SG, Teodoro WR, Queiroz ZAJ, Silveira LKR, Charlie-Silva I, Capelozzi VL, Guzzo CR, Fanelli C. Immunization with SARS-CoV-2 Nucleocapsid protein triggers a pulmonary immune response in rats. PLoS One 2022; 17:e0268434. [PMID: 35609032 PMCID: PMC9129034 DOI: 10.1371/journal.pone.0268434] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 04/29/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 pandemic have been affecting millions of people worldwide, since the beginning of 2020. COVID-19 can cause a wide range of clinical symptoms, which varies from asymptomatic presentation to severe respiratory insufficiency, exacerbation of immune response, disseminated microthrombosis and multiple organ failure, which may lead to dead. Due to the rapid spread of SARS-CoV-2, the development of vaccines to minimize COVID-19 severity in the world population is imperious. One of the employed techniques to produce vaccines against emerging viruses is the synthesis of recombinant proteins, which can be used as immunizing agents. Based on the exposed, the aim of the present study was to verify the systemic and immunological effects of IM administration of recombinant Nucleocapsid protein (NP), derived from SARS-CoV-2 and produced by this research group, in 2 different strains of rats (Rattus norvegicus); Wistar and Lewis. For this purpose, experimental animals received 4 injections of NP, once a week, and were submitted to biochemical and histological analysis. Our results showed that NP inoculations were safe for the animals, which presented no clinical symptoms of worrying side effects, nor laboratorial alterations in the main biochemical and histological parameters, suggesting the absence of toxicity induced by NP. Moreover, NP injections successfully triggered the production of specific anti-SARS-CoV-2 IgG antibodies by both Wistar and Lewis rats, showing the sensitization to have been well sufficient for the immunization of these strains of rats. Additionally, we observed the local lung activation of the Bronchus-Associated Lymphoid Tissue (BALT) of rats in the NP groups, suggesting that NP elicits specific lung immune response. Although pre-clinical and clinical studies are still required, our data support the recombinant NP produced by this research group as a potential immunizing agent for massive vaccination, and may represent advantages upon other recombinant proteins, since it seems to induce specific pulmonary protection.
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Affiliation(s)
- Everidiene K. V. B. Silva
- Renal Division, Department of Clinical Medicine, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Camila G. Bomfim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana P. Barbosa
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paloma Noda
- Renal Division, Department of Clinical Medicine, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Irene L. Noronha
- Renal Division, Department of Clinical Medicine, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Bianca H. V. Fernandes
- Laboratório de Controle Genético e Sanitário, Diretoria Técnica de Apoio ao Ensino e Pesquisa, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | - Rafael R. G. Machado
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Edison L. Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sergio Catanozi
- Laboratorio de Lipides (LIM-10), Hospital das Clinicas (HCFMUSP) da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Letícia G. Rodrigues
- Laboratorio de Lipides (LIM-10), Hospital das Clinicas (HCFMUSP) da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Sérgio G. Lima
- Labinbraz Comercial Ltda. - Wiener lab, Sao Paulo, Brazil
| | - Walcy R. Teodoro
- Rheumatology Division of the Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo - SP, Sao Paulo, Brazil
| | - Zelita A. J. Queiroz
- Rheumatology Division of the Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo - SP, Sao Paulo, Brazil
| | - Lizandre K. R. Silveira
- Rheumatology Division of the Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo - SP, Sao Paulo, Brazil
| | - Ives Charlie-Silva
- Department of Pharmacology, Institute of Biomedical Sciences, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Vera L. Capelozzi
- Rheumatology Division of the Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo - SP, Sao Paulo, Brazil
| | - Cristiane R. Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Camilla Fanelli
- Renal Division, Department of Clinical Medicine, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- * E-mail:
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7
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Ventura Fernandes BH, Feitosa NM, Barbosa AP, Bomfim CG, Garnique AMB, Rosa IF, Rodrigues MS, Doretto LB, Costa DF, Camargo-Dos-Santos B, Franco GA, Neto JF, Lunardi JS, Bellot MS, Alves NPC, Costa CC, Aracati MF, Rodrigues LF, Costa CC, Cirilo RH, Colagrande RM, Gomes FIF, Nakajima RT, Belo MAA, Giaquinto PC, de Oliveira SL, Eto SF, Fernandes DC, Manrique WG, Conde G, Rosales RRC, Todeschini I, Rivero I, Llontop E, Sgro GG, Oka GU, Bueno NF, Ferraris FK, de Magalhães MTQ, Medeiros RJ, Mendonça-Gomes JM, Junqueira MS, Conceição K, Pontes LGD, Condino-Neto A, Perez AC, Barcellos LJG, Júnior JDC, Dorlass EG, Camara NOS, Durigon EL, Cunha FQ, Nóbrega RH, Machado-Santelli GM, Farah CS, Veras FP, Galindo-Villegas J, Costa-Lotufo LV, Cunha TM, Chammas R, Carvalho LR, Guzzo CR, Malafaia G, Charlie-Silva I. Toxicity of spike fragments SARS-CoV-2 S protein for zebrafish: A tool to study its hazardous for human health? Sci Total Environ 2022; 813:152345. [PMID: 34942250 PMCID: PMC8688160 DOI: 10.1016/j.scitotenv.2021.152345] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/17/2021] [Accepted: 12/08/2021] [Indexed: 05/19/2023]
Abstract
Despite the significant increase in the generation of SARS-CoV-2 contaminated domestic and hospital wastewater, little is known about the ecotoxicological effects of the virus or its structural components in freshwater vertebrates. In this context, this study evaluated the deleterious effects caused by SARS-CoV-2 Spike protein on the health of Danio rerio, zebrafish. We demonstrated, for the first time, that zebrafish injected with fragment 16 to 165 (rSpike), which corresponds to the N-terminal portion of the protein, presented mortalities and adverse effects on liver, kidney, ovary and brain tissues. The conserved genetic homology between zebrafish and humans might be one of the reasons for the intense toxic effects followed inflammatory reaction from the immune system of zebrafish to rSpike which provoked damage to organs in a similar pattern as happen in severe cases of COVID-19 in humans, and, resulted in 78,6% of survival rate in female adults during the first seven days. The application of spike protein in zebrafish was highly toxic that is suitable for future studies to gather valuable information about ecotoxicological impacts, as well as vaccine responses and therapeutic approaches in human medicine. Therefore, besides representing an important tool to assess the harmful effects of SARS-CoV-2 in the aquatic environment, we present the zebrafish as an animal model for translational COVID-19 research.
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Affiliation(s)
- Bianca H Ventura Fernandes
- Laboratório de Controle Genético e Sanitário, Diretoria Técnica de Apoio ao Ensino e Pesquisa, Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - Natália Martins Feitosa
- Laboratório Integrado de Biociências Translacionais (LIBT), Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro (UFRJ), Macaé, RJ, Brazil
| | - Ana Paula Barbosa
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Camila Gasque Bomfim
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Anali M B Garnique
- Department of Cell Biology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Ivana F Rosa
- Reproductive and Molecular Biology Group, Department of Morphology, Institute of Biosciences, Sao Paulo State University, Botucatu, São Paulo, Brazil
| | - Maira S Rodrigues
- Reproductive and Molecular Biology Group, Department of Morphology, Institute of Biosciences, Sao Paulo State University, Botucatu, São Paulo, Brazil
| | - Lucas B Doretto
- Reproductive and Molecular Biology Group, Department of Morphology, Institute of Biosciences, Sao Paulo State University, Botucatu, São Paulo, Brazil
| | - Daniel F Costa
- Reproductive and Molecular Biology Group, Department of Morphology, Institute of Biosciences, Sao Paulo State University, Botucatu, São Paulo, Brazil
| | - Bruno Camargo-Dos-Santos
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University, SP, Brazil
| | - Gabrielli A Franco
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University, SP, Brazil
| | - João Favero Neto
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University, SP, Brazil
| | - Juliana Sartori Lunardi
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University, SP, Brazil
| | - Marina Sanson Bellot
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University, SP, Brazil
| | - Nina Pacheco Capelini Alves
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University, SP, Brazil
| | - Camila C Costa
- Department of Preventive Veterinary Medicine, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Mayumi F Aracati
- Department of Preventive Veterinary Medicine, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Letícia F Rodrigues
- Department of Preventive Veterinary Medicine, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Camila C Costa
- Department of Preventive Veterinary Medicine, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Rafaela Hemily Cirilo
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University, SP, Brazil
| | - Raul Marcelino Colagrande
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University, SP, Brazil
| | - Francisco I F Gomes
- Department of Pharmacology, Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of São Paulo, Brazil
| | - Rafael T Nakajima
- Reproductive and Molecular Biology Group, Department of Morphology, Institute of Biosciences, Sao Paulo State University, Botucatu, São Paulo, Brazil
| | | | - Percília Cardoso Giaquinto
- Universidade Estadual Paulista Júlio de Mesquita Filho, Instituto de Biociências - Departamento de Fisiologia, São Paulo, Brazil
| | | | - Silas Fernandes Eto
- Postgraduate Program in Health Sciences, PROCISA, Federal University of Roraima, Brazil
| | | | - Wilson G Manrique
- Aquaculture Health Research and Extension Group, GRUPESA, Aquaculture Health Laboratory, LABSA, Department of Veterinary Medicine, Federal University of Rondônia, Rolim de Moura campus, Rondônia, Brazil
| | - Gabriel Conde
- Department of Preventive Veterinary Medicine, São Paulo State University, Jaboticabal, Brazil
| | - Roberta R C Rosales
- Department of Cell and Molecular Biology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Iris Todeschini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - Ilo Rivero
- Pontifícia Universidade Católica de Minas Gerais, Brazil
| | - Edgar Llontop
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - Germán G Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil; Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Gabriel Umaji Oka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | | | - Fausto K Ferraris
- Department of Pharmacology and Toxicology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
| | - Mariana T Q de Magalhães
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Renata J Medeiros
- Laboratory of Physiology, INCQS/Fiocruz Zebrafish Facility, Departament of Pharmacology and Toxicology, National Institute for Quality Control in Health, Brasil
| | - Juliana M Mendonça-Gomes
- Transplantation Immunobiology Lab, Department of Immunology, Institute of Biomedical Sciences, Universidade de Sao Paulo, Brazil
| | - Mara Souza Junqueira
- Center for Translational Research in Oncology, Cancer Institute of the State of Sao Paulo, Faculty of Medicine, University of São Paulo, Sao Paulo, Brazil
| | - Kátia Conceição
- Laboratory of Peptide Biochemistry, Federal University of São Paulo, Brazil
| | - Leticia Gomes de Pontes
- Laboratory of Human Immunology, Department Immunology, Institute Biomedical Sciences, University São Paulo, Sao Paulo, Brazil
| | - Antonio Condino-Neto
- Laboratory of Human Immunology, Department Immunology, Institute Biomedical Sciences, University São Paulo, Sao Paulo, Brazil
| | - Andrea C Perez
- Department of Pharmacology, Universidade Federal de Minas Gerais, Brazil
| | - Leonardo J G Barcellos
- Graduate Program of Pharmacology, Federal University of Santa Maria, Brazil; Laboratory of Fish Physiology, Graduate Program of Bioexperimentation and of Environmental Sciences, University of Passo Fundo, Brazil
| | - José Dias Correa Júnior
- Laboratório do Estudo da Interação Químico Biológica e da Reprodução Animal, LIQBRA, Bloco O3,174, Brazil; Departamento de Morfologia Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Erick Gustavo Dorlass
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Niels O S Camara
- Transplantation Immunobiology Lab, Department of Immunology, Institute of Biomedical Sciences, Universidade de Sao Paulo, Brazil
| | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Fernando Q Cunha
- Department of Pharmacology, Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Rafael H Nóbrega
- Reproductive and Molecular Biology Group, Department of Morphology, Institute of Biosciences, Sao Paulo State University, Botucatu, São Paulo, Brazil
| | - Glaucia M Machado-Santelli
- Department of Cell Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Chuck S Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - Flavio P Veras
- Center of Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil; Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | | | - Letícia V Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, Universidade de São Paulo, Brazil
| | - Thiago M Cunha
- Center of Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil; Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Roger Chammas
- Centro de Investigação Translacional em Oncologia, Instituto do Câncer do Estado de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - Luciani R Carvalho
- Disciplina de Endocrinologia do Departamento de Clinica Medica e Laboratório de Hormônios e Genética Molecular, LIM 42, Brazil
| | - Cristiane R Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Guilherme Malafaia
- Biological Research Laboratory, Goiano Federal Institute, Urutaí Campus, Brazil.
| | - Ives Charlie-Silva
- Department of Pharmacology, Institute of Biomedical Sciences, Universidade de São Paulo, Brazil.
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Llontop EE, Cenens W, Favaro DC, Sgro GG, Salinas RK, Guzzo CR, Farah CS. The PilB-PilZ-FimX regulatory complex of the Type IV pilus from Xanthomonas citri. PLoS Pathog 2021; 17:e1009808. [PMID: 34398935 PMCID: PMC8389850 DOI: 10.1371/journal.ppat.1009808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 08/26/2021] [Accepted: 07/17/2021] [Indexed: 11/19/2022] Open
Abstract
Type IV pili (T4P) are thin and flexible filaments found on the surface of a wide range of Gram-negative bacteria that undergo cycles of extension and retraction and participate in a variety of important functions related to lifestyle, defense and pathogenesis. During pilus extensions, the PilB ATPase energizes the polymerization of pilin monomers from the inner membrane. In Xanthomonas citri, two cytosolic proteins, PilZ and the c-di-GMP receptor FimX, are involved in the regulation of T4P biogenesis through interactions with PilB. In vivo fluorescence microscopy studies show that PilB, PilZ and FimX all colocalize to the leading poles of X. citri cells during twitching motility and that this colocalization is dependent on the presence of all three proteins. We demonstrate that full-length PilB, PilZ and FimX can interact to form a stable complex as can PilB N-terminal, PilZ and FimX C-terminal fragments. We present the crystal structures of two binary complexes: i) that of the PilB N-terminal domain, encompassing sub-domains ND0 and ND1, bound to PilZ and ii) PilZ bound to the FimX EAL domain within a larger fragment containing both GGDEF and EAL domains. Evaluation of PilZ interactions with PilB and the FimX EAL domain in these and previously published structures, in conjunction with mutagenesis studies and functional assays, allow us to propose an internally consistent model for the PilB-PilZ-FimX complex and its interactions with the PilM-PilN complex in the context of the inner membrane platform of the X. citri Type IV pilus.
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Affiliation(s)
- Edgar E. Llontop
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - William Cenens
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Denize C. Favaro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Química Orgânica, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Germán G. Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Roberto K. Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Cristiane R. Guzzo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Chuck S. Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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9
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Teixeira RD, Guzzo CR, Arévalo SJ, Andrade MO, Abrahão J, de Souza RF, Farah CS. A bipartite periplasmic receptor-diguanylate cyclase pair (XAC2383-XAC2382) in the bacterium Xanthomonas citri. J Biol Chem 2018; 293:10767-10781. [PMID: 29728456 DOI: 10.1074/jbc.ra118.003475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 04/27/2018] [Indexed: 11/06/2022] Open
Abstract
The second messenger cyclic diguanylate monophosphate (c-di-GMP) is a central regulator of bacterial lifestyle, controlling several behaviors, including the switch between sessile and motile states. The c-di-GMP levels are controlled by the interplay between diguanylate cyclases (DGCs) and phosphodiesterases, which synthesize and hydrolyze this second messenger, respectively. These enzymes often contain additional domains that regulate activity via binding of small molecules, covalent modification, or protein-protein interactions. A major challenge remains to understand how DGC activity is regulated by these additional domains or interaction partners in specific signaling pathways. Here, we identified a pair of co-transcribed genes (xac2382 and xac2383) in the phytopathogenic, Gram-negative bacterium Xanthomonas citri subsp. citri (Xac), whose mutations resulted in opposing motility phenotypes. We show that the periplasmic cache domain of XAC2382, a membrane-associated DGC, interacts with XAC2383, a periplasmic binding protein, and we provide evidence that this interaction regulates XAC2382 DGC activity. Moreover, we solved the crystal structure of XAC2383 with different ligands, indicating a preference for negatively charged phosphate-containing compounds. We propose that XAC2383 acts as a periplasmic sensor that, upon binding its ligand, inhibits the DGC activity of XAC2382. Of note, we also found that this previously uncharacterized signal transduction system is present in several other bacterial phyla, including Gram-positive bacteria. Phylogenetic analysis of homologs of the XAC2382-XAC2383 pair supports several independent origins that created new combinations of XAC2382 homologs with a conserved periplasmic cache domain with different cytoplasmic output module architectures.
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Affiliation(s)
- Raphael D Teixeira
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000
| | - Cristiane R Guzzo
- the Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-900, and
| | - Santiago Justo Arévalo
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000
| | - Maxuel O Andrade
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000
| | - Josielle Abrahão
- the Departamento de Química Orgânica, Instituto de Química, Universidade de Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Robson F de Souza
- the Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-900, and
| | - Chuck S Farah
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000,
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10
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Lorenzon-Ojea AR, Guzzo CR, Kapidzic M, Fisher SJ, Bevilacqua E. Stromal Cell-Derived Factor 2: A Novel Protein that Interferes in Endoplasmic Reticulum Stress Pathway in Human Placental Cells. Biol Reprod 2016; 95:41. [PMID: 27335075 PMCID: PMC5029474 DOI: 10.1095/biolreprod.115.138164] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/02/2016] [Indexed: 12/24/2022] Open
Abstract
Endoplasmic reticulum (ER) stress results from changes in ER homeostasis and folding of proteins. ER stress initiates cellular adaptive mechanisms to rescue cell homeostasis or, if that does not work, to elicit apoptosis. We have previously shown that mouse SDF2 is sublocalized in the ER, is ubiquitously expressed, and shows strong similarities with stromal cell-derived factor (SDF) 2L1 and SDF2-like from Arabidopsis, ER proteins involved in chaperone network and protein folding. Thus, we hypothesized that SDF2 plays a role in the ER stress and unfolded protein response. In this study, we investigated the possible role of SDF2 in the human placenta. Expression of SDF2 was present throughout gestation and was expressed by several cell types. Second-trimester cytotrophoblast cells (CTBs) in the differentiation process, monitored through chorionic gonadotropin production, showed upregulation of SDF2 protein. SDF2 expression, however, was significantly diminished in placentas from neonates small for gestational age and in hypoxic in vitro conditions (P ≤ 0.001, 2% O2), suggesting a link with cellular stress. ER stress-induced cells-CTB and BeWo-also showed SDF2 downregulation in different time points, emphasizing this relationship. SDF2 downregulation was also followed by an increase in binding immunoglobulin protein (BiP) expression, an ER protein-associated chaperone acting as a sensor for misfolded proteins and an ER stress cell survival marker. In line with this, SDF2 siRNA resulted in significant anticipation of BiP expression. Downregulation of SDF2 also interfered with C/EBP homologous protein expression, one of the highest inducible genes during ER stress. These findings suggest that SDF2 may be an important regulatory factor by which trophoblast cells can control cell survival under ER stress. In conclusion, this study identifies a novel factor with the ability to interfere with ER stress proteins, which may contribute to the understanding of ER stress associated with placental-related diseases of pregnancy.
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Affiliation(s)
- Aline R Lorenzon-Ojea
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil Department of Obstetrics, Gynecology & Reproductive Sciences, School of Medicine, University of California San Francisco, San Francisco, California
| | - Cristiane R Guzzo
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mirhan Kapidzic
- Department of Obstetrics, Gynecology & Reproductive Sciences, School of Medicine, University of California San Francisco, San Francisco, California
| | - Susan J Fisher
- Department of Obstetrics, Gynecology & Reproductive Sciences, School of Medicine, University of California San Francisco, San Francisco, California
| | - Estela Bevilacqua
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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11
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Dunger G, Llontop E, Guzzo CR, Farah CS. The Xanthomonas type IV pilus. Curr Opin Microbiol 2016; 30:88-97. [PMID: 26874963 DOI: 10.1016/j.mib.2016.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/14/2016] [Accepted: 01/17/2016] [Indexed: 02/07/2023]
Abstract
Type IV pili, a special class of bacterial surface filaments, are key behavioral mediators for many important human pathogens. However, we know very little about the role of these structures in the lifestyles of plant-associated bacteria. Over the past few years, several groups studying the extensive genus of Xanthomonas spp. have gained insights into the roles of played by type IV pili in bacteria-host interactions and pathogenesis, motility, biofilm formation, and interactions with bacteriophages. Protein-protein interaction studies have identified T4P regulators and these, along with structural studies, have begun to reveal some of the possible molecular mechanisms that may control the extension/retraction cycles of these dynamic filaments.
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Affiliation(s)
- German Dunger
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP 05508-000, Brazil
| | - Edgar Llontop
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP 05508-000, Brazil
| | - Cristiane R Guzzo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, SP CEP 05508-900, Brazil
| | - Chuck S Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP 05508-000, Brazil.
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12
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Lopes-Kulishev CO, Alves IR, Valencia EY, Pidhirnyj MI, Fernández-Silva FS, Rodrigues TR, Guzzo CR, Galhardo RS. Functional characterization of two SOS-regulated genes involved in mitomycin C resistance in Caulobacter crescentus. DNA Repair (Amst) 2015; 33:78-89. [DOI: 10.1016/j.dnarep.2015.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 06/24/2015] [Accepted: 06/26/2015] [Indexed: 10/23/2022]
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13
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Dunger G, Guzzo CR, Andrade MO, Jones JB, Farah CS. Xanthomonas citri subsp. citri type IV Pilus is required for twitching motility, biofilm development, and adherence. Mol Plant Microbe Interact 2014; 27:1132-47. [PMID: 25180689 DOI: 10.1094/mpmi-06-14-0184-r] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Bacterial type IV pili (T4P) are long, flexible surface filaments that consist of helical polymers of mostly pilin subunits. Cycles of polymerization, attachment, and depolymerization mediate several pilus-dependent bacterial behaviors, including twitching motility, surface adhesion, pathogenicity, natural transformation, escape from immune system defense mechanisms, and biofilm formation. The Xanthomonas citri subsp. citri strain 306 genome codes for a large set of genes involved in T4P biogenesis and regulation and includes several pilin homologs. We show that X. citri subsp. citri can exhibit twitching motility in a manner similar to that observed in other bacteria such as Pseudomonas aeruginosa and Xylella fastidiosa and that this motility is abolished in Xanthomonas citri subsp. citri knockout strains in the genes coding for the major pilin subunit PilAXAC3241, the ATPases PilBXAC3239 and PilTXAC2924, and the T4P biogenesis regulators PilZXAC1133 and FimXXAC2398. Microscopy analyses were performed to compare patterns of bacterial migration in the wild-type and knockout strains and we observed that the formation of mushroom-like structures in X. citri subsp. citri biofilm requires a functional T4P. Finally, infection of X. citri subsp. citri cells by the bacteriophage (ΦXacm4-11 is T4P dependent. The results of this study improve our understanding of how T4P influence Xanthomonas motility, biofilm formation, and susceptibility to phage infection.
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14
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Lorenzon-Ojea AR, Caldeira W, Ribeiro AF, Fisher SJ, Guzzo CR, Bevilacqua E. Stromal cell derived factor-2 (Sdf2): A novel protein expressed in mouse. Int J Biochem Cell Biol 2014; 53:262-70. [DOI: 10.1016/j.biocel.2014.05.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 05/01/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
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15
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Lorenzon AR, Guzzo CR, Farah CS, Fisher SJ, Bevilacqua E. Stromal cell derived factor 2: new insights of function. Placenta 2013. [DOI: 10.1016/j.placenta.2013.06.294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Guzzo CR, Dunger G, Salinas RK, Farah CS. Structure of the PilZ-FimXEAL-c-di-GMP Complex Responsible for the Regulation of Bacterial Type IV Pilus Biogenesis. J Mol Biol 2013; 425:2174-97. [PMID: 23507310 DOI: 10.1016/j.jmb.2013.03.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 03/02/2013] [Accepted: 03/11/2013] [Indexed: 10/27/2022]
Abstract
Signal transduction pathways mediated by cyclic-bis(3'→5')-dimeric GMP (c-di-GMP) control many important and complex behaviors in bacteria. C-di-GMP is synthesized through the action of GGDEF domains that possess diguanylate cyclase activity and is degraded by EAL or HD-GYP domains with phosphodiesterase activity. There is mounting evidence that some important c-di-GMP-mediated pathways require protein-protein interactions between members of the GGDEF, EAL, HD-GYP and PilZ protein domain families. For example, interactions have been observed between PilZ and the EAL domain from FimX of Xanthomonas citri (Xac). FimX and PilZ are involved in the regulation of type IV pilus biogenesis via interactions of the latter with the hexameric PilB ATPase associated with the bacterial inner membrane. Here, we present the crystal structure of the ternary complex made up of PilZ, the FimX EAL domain (FimXEAL) and c-di-GMP. PilZ interacts principally with the lobe region and the N-terminal linker helix of the FimXEAL. These interactions involve a hydrophobic surface made up of amino acids conserved in a non-canonical family of PilZ domains that lack intrinsic c-di-GMP binding ability and strand complementation that joins β-sheets from both proteins. Interestingly, the c-di-GMP binds to isolated FimXEAL and to the PilZ-FimXEAL complex in a novel conformation encountered in c-di-GMP-protein complexes in which one of the two glycosidic bonds is in a rare syn conformation while the other adopts the more common anti conformation. The structure points to a means by which c-di-GMP and PilZ binding could be coupled to FimX and PilB conformational states.
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Affiliation(s)
- Cristiane R Guzzo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, São Paulo SP 05508-000, Brazil; Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo SP 05508-900, Brazil
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17
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Beton D, Guzzo CR, Ribeiro AF, Farah CS, Terra WR. The 3D structure and function of digestive cathepsin L-like proteinases of Tenebrio molitor larval midgut. Insect Biochem Mol Biol 2012; 42:655-664. [PMID: 22659439 DOI: 10.1016/j.ibmb.2012.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 06/01/2023]
Abstract
Cathepsin L-like proteinases (CAL) are major digestive proteinases in the beetle Tenebrio molitor. Procathepsin Ls 2 (pCAL2) and 3 (pCAL3) were expressed as recombinant proteins in Escherichia coli, purified and activated under acidic conditions. Immunoblot analyses of different T. molitor larval tissues demonstrated that a polyclonal antibody to pCAL3 recognized pCAL3 and cathepsin L 3 (CAL3) only in the anterior two-thirds of midgut tissue and midgut luminal contents of T. molitor larvae. Furthermore, immunocytolocalization data indicated that pCAL3 occurs in secretory vesicles and microvilli in anterior midgut. Therefore CAL3, like cathepsin L 2 (CAL2), is a digestive enzyme secreted by T. molitor anterior midgut. CAL3 hydrolyses Z-FR-MCA and Z-RR-MCA (typical cathepsin substrates), whereas CAL2 hydrolyses only Z-FR-MCA. Active site mutants (pCAL2C25S and pCAL3C26S) were constructed by replacing the catalytic cysteine with serine to prevent autocatalytic processing. Recombinant pCAL2 and pCAL3 mutants (pCAL2C25S and pCAL3C26S) were prepared, crystallized and their 3D structures determined at 1.85 and 2.1 Å, respectively. While the overall structure of these enzymes is similar to other members of the papain superfamily, structural differences in the S2 subsite explain their substrate specificities. The data also supported models for CAL trafficking to lysosomes and to secretory vesicles to be discharged into midgut contents.
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Affiliation(s)
- Daniela Beton
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, C. P. 26077, 05513-970 São Paulo, Brazil
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18
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Guzzo CR, Salinas RK, Andrade MO, Farah CS. PILZ protein structure and interactions with PILB and the FIMX EAL domain: implications for control of type IV pilus biogenesis. J Mol Biol 2009; 393:848-66. [PMID: 19646999 DOI: 10.1016/j.jmb.2009.07.065] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 07/20/2009] [Accepted: 07/21/2009] [Indexed: 11/18/2022]
Abstract
The PilZ protein was originally identified as necessary for type IV pilus (T4P) biogenesis. Since then, a large and diverse family of bacterial PilZ homology domains have been identified, some of which have been implicated in signaling pathways that control important processes, including motility, virulence and biofilm formation. Furthermore, many PilZ homology domains, though not PilZ itself, have been shown to bind the important bacterial second messenger bis(3'-->5')cyclic diGMP (c-diGMP). The crystal structures of the PilZ orthologs from Xanthomonas axonopodis pv citri (PilZ(XAC1133), this work) and from Xanthomonas campestris pv campestris (XC1028) present significant structural differences to other PilZ homologs that explain its failure to bind c-diGMP. NMR analysis of PilZ(XAC1133) shows that these structural differences are maintained in solution. In spite of their emerging importance in bacterial signaling, the means by which PilZ proteins regulate specific processes is not clear. In this study, we show that PilZ(XAC1133) binds to PilB, an ATPase required for T4P polymerization, and to the EAL domain of FimX(XAC2398), which regulates T4P biogenesis and localization in other bacterial species. These interactions were confirmed in NMR, two-hybrid and far-Western blot assays and are the first interactions observed between any PilZ domain and a target protein. While we were unable to detect phosphodiesterase activity for FimX(XAC2398)in vitro, we show that it binds c-diGMP both in the presence and in the absence of PilZ(XAC1133). Site-directed mutagenesis studies for conserved and exposed residues suggest that PilZ(XAC1133) interactions with FimX(XAC2398) and PilB(XAC3239) are mediated through a hydrophobic surface and an unstructured C-terminal extension conserved only in PilZ orthologs. The FimX-PilZ-PilB interactions involve a full set of "degenerate" GGDEF, EAL and PilZ domains and provide the first evidence of the means by which PilZ orthologs and FimX interact directly with the TP4 machinery.
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Affiliation(s)
- Cristiane R Guzzo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CEP 05508-000, SP, Brazil
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Hauk P, Guzzo CR, Ho PL, Farah CS. Crystallization and preliminary X-ray analysis of LipL32 from Leptospira interrogans serovar Copenhageni. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:307-9. [PMID: 19255491 PMCID: PMC2650462 DOI: 10.1107/s1744309109005533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 02/16/2009] [Indexed: 11/10/2022]
Abstract
LipL32 is a major surface protein that is expressed during infection by pathogenic Leptospira. Here, the crystallization of recombinant LipL32(21-272), which corresponds to the mature LipL32 protein minus its N-terminal lipid-anchored cysteine residue, is described. Selenomethionine-labelled LipL32(21-272) crystals diffracted to 2.25 A resolution at a synchrotron source. The space group was P3(1)21 or P3(2)21 and the unit-cell parameters were a = b = 126.7, c = 96.0 A.
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Affiliation(s)
- Pricila Hauk
- Centro de Biotecnologia, Instituto Butantan, 05503-900 São Paulo-SP, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia USP/IPT/Instituto Butantan, Instituto de Ciências Biomédicas da USP, 05508-900 São Paulo-SP, Brazil
| | - Cristiane R. Guzzo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo-SP, Brazil
| | - Paulo L. Ho
- Centro de Biotecnologia, Instituto Butantan, 05503-900 São Paulo-SP, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia USP/IPT/Instituto Butantan, Instituto de Ciências Biomédicas da USP, 05508-900 São Paulo-SP, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo-SP, Brazil
| | - Chuck S. Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo-SP, Brazil
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20
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Guzzo CR, Farah CS. Expression, crystallization and preliminary crystallographic analysis of PilZ(XAC1133) from Xanthomonas axonopodis pv. citri. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:304-6. [PMID: 19255490 DOI: 10.1107/s1744309109005545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 02/16/2009] [Indexed: 11/10/2022]
Abstract
Proteins containing PilZ domains are widespread in Gram-negative bacteria and have recently been shown to be involved in the control of biofilm formation, adherence, aggregation, virulence-factor production and motility. Furthermore, some PilZ domains have recently been shown to bind the second messenger bis(3'-->5')cyclic diGMP. Here, the cloning, expression, purification and crystallization of PilZ(XAC1133), a protein consisting of a single PilZ domain from Xanthomonas axonopodis pv. citri, is reported. The closest PilZ(XAC1133) homologues in Pseudomonas aeruginosa and Neisseria meningitidis control type IV pilus function. Recombinant PilZ(XAC1133) containing selenomethionine was crystallized in space group P6(1). The unit-cell parameters were a = 62.125, b = 62.125, c = 83.543 A. These crystals diffracted to 1.85 A resolution and a MAD data set was collected at a synchrotron source. The calculated Matthews coefficient suggested the presence of two PilZ(XAC1133) molecules in the asymmetric unit.
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Affiliation(s)
- Cristiane R Guzzo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
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21
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Guzzo CR, Nagem RAP, Barbosa JARG, Farah CS. Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif. Proteins 2007; 69:644-51. [PMID: 17623842 DOI: 10.1002/prot.21556] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The YaeQ family of proteins are found in many Gram-negative and a few Gram-positive bacteria. We have determined the first structure of a member of the YaeQ family by X-ray crystallography. Comparisons with other structures indicate that YaeQ represents a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif found in type II endonucleases and enzymes involved in DNA replication, repair, and recombination. We show that catalytically important residues in the PD-(D/E)XK nuclease superfamily are spatially conserved in YaeQ and other highly conserved YaeQ residues may be poised to interact with nucleic acid structures.
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Affiliation(s)
- Cristiane R Guzzo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes 748, São Paulo, SP, CEP 05508-000, Brazil
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Andrade MO, Alegria MC, Guzzo CR, Docena C, Rosa MCP, Ramos CHI, Farah CS. The HD-GYP domain of RpfG mediates a direct linkage between the Rpf quorum-sensing pathway and a subset of diguanylate cyclase proteins in the phytopathogen Xanthomonas axonopodis pv citri. Mol Microbiol 2007; 62:537-51. [PMID: 17020586 DOI: 10.1111/j.1365-2958.2006.05386.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacteria use extracellular levels of small diffusible autoinducers to estimate local cell-density (quorum-sensing) and to regulate complex physiological processes. The quorum-sensing signal transduction pathway of Xanthomonas spp. phytopathogens has special features that distinguish it from that of other pathogens. This pathway consists of RpfF, necessary for the production of the unique autoinducer 'diffusible signalling factor' (DSF), and RpfC and RpfG, a two-component system necessary for the DSF-dependent production of extracellular pathogenicity factors and cellular dispersion. Yeast two-hybrid and direct in vitro assays were used to identify interactions involving the Rpf group of proteins. We show that RpfC, a protein consisting of N-terminal transmembrane, histidine kinase, response-regulator and C-terminal histidine phosphotransfer domains interacts with both RpfG, a protein consisting of an N-terminal response regulator domain and a C-terminal HD-GYP domain, and with RpfF. We also show that RpfC interacts with the only known homologue of 'conditioned medium factor', which is involved in quorum-sensing in Dictyostelium discoideum under conditions of nutritional stress. Furthermore, RpfCG is shown to interact with a second two-component system made up of NtrB and NtrC homologues. Finally we show that the recently characterized HD-GYP phosphodiesterase domain of RpfG interacts directly with diguanylate cyclase GGDEF domain-containing proteins coded by the Xanthomonas axonopodis pv. citri genome, which in other bacteria produce cyclic diGMP, an important second messenger involved in the regulation of complex bacterial processes including biofilm production, virulence and motility. These results demonstrate a direct physical linkage between quorum-sensing and cyclic diGMP signalling pathways in bacteria.
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Affiliation(s)
- Maxuel O Andrade
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, CEP 05599-970 São Paulo, SP, Brazil
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Guzzo CR, Silva LR, Galvão-Botton LMP, Barbosa JARG, Farah CS. Expression, crystallization and preliminary crystallographic analysis of SufE (XAC2355) from Xanthomonas axonopodis pv. citri. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:268-70. [PMID: 16511319 PMCID: PMC2197171 DOI: 10.1107/s1744309106004945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Accepted: 02/09/2006] [Indexed: 11/10/2022]
Abstract
Xanthomonas axonopodis pv. citri (Xac) SufE (XAC2355) is a member of a family of bacterial proteins that are conserved in several pathogens and phytopathogens. The Escherichia coli suf operon is involved in iron-sulfur cluster biosynthesis under iron-limitation and stress conditions. It has recently been demonstrated that SufE and SufS form a novel two-component cysteine desulfarase in which SufS catalyses the conversion of L-cysteine to L-alanine, forming a protein-bound persulfide intermediate. The S atom is then transferred to SufE, from which it is subsequently transferred to target molecules or reduced to sulfide in solution. Here, the cloning, expression, crystallization and phase determination of Xac SufE crystals are described. Recombinant SufE was crystallized in space group P2(1)2(1)2(1) and diffracted to 1.9 A resolution at a synchrotron source. The unit-cell parameters are a = 45.837, b = 58.507, c = 98.951 A, alpha = beta = gamma = 90 degrees. The calculated Matthews coefficient indicated the presence of two molecules in the asymmetric unit. Phasing was performed by molecular-replacement using E. coli SufE as a model (PDB code 1mzg) and an interpretable map was obtained.
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Affiliation(s)
- Cristiane R. Guzzo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil
| | - Lucicleide R. Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil
| | - Leonor M. P. Galvão-Botton
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil
| | | | - Chuck S. Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil
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24
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Guzzo CR, Nagem RAP, Galvão-Botton LMP, Guimarães BG, Medrano FJ, Barbosa JARG, Farah CS. Expression, purification, crystallization and preliminary X-ray analysis of YaeQ (XAC2396) from Xanthomonas axonopodis pv. citri. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:493-5. [PMID: 16511077 PMCID: PMC1952311 DOI: 10.1107/s1744309105010985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Accepted: 04/07/2005] [Indexed: 11/10/2022]
Abstract
Xanthomonas axonopodis pv. citri YaeQ (XAC2396) is a member of a family of bacterial proteins conserved in several Gram-negative pathogens. Here, the cloning, expression, purification and crystallization of the 182-residue (20.6 kDa) YaeQ protein are described. Recombinant YaeQ containing selenomethionine was crystallized in space group P2(1) and crystals diffracted to 1.9 A resolution at a synchrotron source. The unit-cell parameters are a = 39.75, b = 91.88, c = 48.03 A, beta = 108.37 degrees. The calculated Matthews coefficient suggests the presence of two YaeQ molecules in the asymmetric unit. Initial experimental phases were calculated by the multiple-wavelength anomalous dispersion technique and an interpretable electron-density map was obtained.
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Affiliation(s)
- Cristiane R. Guzzo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil
| | - Ronaldo A. P. Nagem
- Instituto de Física de São Carlos, Universidade de São Paulo, CEP 13560-970, São Carlos, SP, Brazil
| | - Leonor M. P. Galvão-Botton
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil
| | - Beatriz G. Guimarães
- Centro de Biologia Molecular Estrutural, Laboratório Nacional de Luz Síncrotron, CEP 13084-971, Campinas, SP, Brazil
| | - Francisco J. Medrano
- Centro de Biologia Molecular Estrutural, Laboratório Nacional de Luz Síncrotron, CEP 13084-971, Campinas, SP, Brazil
| | - João A. R. G. Barbosa
- Centro de Biologia Molecular Estrutural, Laboratório Nacional de Luz Síncrotron, CEP 13084-971, Campinas, SP, Brazil
| | - Chuck S. Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil
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Abstract
We applied a high-throughput strategy for the screening of targets for structural proteomics of Xanthomonas axonopodis pv citri. This strategy is based on the rapid (1)H-(15)N HSQC NMR analysis of bacterial lysates containing selectively (15)N-labelled heterologous proteins. Our analysis permitted us to classify the 19 soluble candidates in terms of 'foldedness', that is, the extent to which they present a well-folded solution structure, as reflected by the quality of their NMR spectra. This classification allowed us to define a priority list to be used as a guide to select protein candidates for further structural studies.
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Affiliation(s)
- Leonor M P Galvão-Botton
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CEP 05508-900, SP, São Paulo, Brazil
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