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Castillo-Zeledón A, Rivas-Solano O, Villalta-Romero F, Gómez-Espinoza O, Moreno E, Chaves-Olarte E, Guzmán-Verri C. The Brucella abortus two-component system response regulator BvrR binds to three DNA regulatory boxes in the upstream region of omp25. Front Microbiol 2023; 14:1241143. [PMID: 37779712 PMCID: PMC10538546 DOI: 10.3389/fmicb.2023.1241143] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/15/2023] [Indexed: 10/03/2023] Open
Abstract
Brucella abortus is a facultative extracellular-intracellular bacterial zoonotic pathogen worldwide. It is also a major cause of abortion in bovines, generating economic losses. The two-component regulatory system BvrR/BvrS modulates the expression of genes required to transition from extracellular to intracellular lifestyles. However, few regulatory regions of BvrR direct target genes have been studied. In this study, we characterized the regulatory region of omp25, a gene encoding an outer membrane protein that is positively regulated by TCS BvrR/BvrS. By omp25-lacZ reporter fusions and β-galactosidase activity assays, we found that the region between-262 and + 127 is necessary for transcriptional activity, particularly a 111-bp long fragment located from-262 to -152. In addition, we demonstrated the binding of P-BvrR to three sites within the -140 to +1 region. Two of these sites were delimited between -18 to +1 and - 99 to -76 by DNase I footprinting and called DNA regulatory boxes 1 and 2, respectively. The third binding site (box 3) was delimited from -140 to -122 by combining EMSA and fluorescence anisotropy results. A molecular docking analysis with HDOCK predicted BvrR-DNA interactions between 11, 13, and 12 amino acid residue-nucleotide pairs in boxes 1, 2, and 3, respectively. A manual sequence alignment of the three regulatory boxes revealed the presence of inverted and non-inverted repeats of five to eight nucleotides, partially matching DNA binding motifs previously described for BvrR. We propose that P-BvrR binds directly to up to three regulatory boxes and probably interacts with other transcription factors to regulate omp25 expression. This gene regulation model could apply to other BvrR target genes and to orthologs of the TCS BvrR/BvrS and Omp25 in phylogenetically closed Rhizobiales.
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Affiliation(s)
- Amanda Castillo-Zeledón
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - Olga Rivas-Solano
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Campus Tecnológico Central Cartago, Cartago, Costa Rica
| | - Fabián Villalta-Romero
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Campus Tecnológico Central Cartago, Cartago, Costa Rica
| | - Olman Gómez-Espinoza
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Campus Tecnológico Central Cartago, Cartago, Costa Rica
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
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Castillo-Zeledón A, Ruiz-Villalobos N, Altamirano-Silva P, Chacón-Díaz C, Barquero-Calvo E, Chaves-Olarte E, Guzmán-Verri C. A Sinorhizobium meliloti and Agrobacterium tumefaciens ExoR ortholog is not crucial for Brucella abortus virulence. PLoS One 2021; 16:e0254568. [PMID: 34388167 PMCID: PMC8362948 DOI: 10.1371/journal.pone.0254568] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/29/2021] [Indexed: 11/19/2022] Open
Abstract
Brucella is a facultative extracellular-intracellular pathogen that belongs to the Alphaproteobacteria class. Precise sensing of environmental changes and a proper response mediated by a gene expression regulatory network are essential for this pathogen to survive. The plant-related Alphaproteobacteria Sinorhizobium meliloti and Agrobacterium tumefaciens also alternate from a free to a host-associated life, where a regulatory invasion switch is needed for this transition. This switch is composed of a two-component regulatory system (TCS) and a global inhibitor, ExoR. In B. abortus, the BvrR/BvrS TCS is essential for intracellular survival. However, the presence of a TCS inhibitor, such as ExoR, in Brucella is still unknown. In this work, we identified a genomic sequence similar to S. meliloti exoR in the B. abortus 2308W genome, constructed an exoR mutant strain, and performed its characterization through ex vivo and in vivo assays. Our findings indicate that ExoR is related to the BvrR phosphorylation state, and is related to the expression of known BvrR/BrvS gene targets, such as virB8, vjbR, and omp25 when grown in rich medium or starving conditions. Despite this, the exoR mutant strain showed no significant differences as compared to the wild-type strain, related to resistance to polymyxin B or human non-immune serum, intracellular replication, or infectivity in a mice model. ExoR in B. abortus is related to BvrR/BvrS as observed in other Rhizobiales; however, its function seems different from that observed for its orthologs described in A. tumefaciens and S. meliloti.
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Affiliation(s)
- Amanda Castillo-Zeledón
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - Nazareth Ruiz-Villalobos
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - Pamela Altamirano-Silva
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Carlos Chacón-Díaz
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Elías Barquero-Calvo
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
- * E-mail:
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Suárez-Esquivel M, Baker KS, Ruiz-Villalobos N, Hernández-Mora G, Barquero-Calvo E, González-Barrientos R, Castillo-Zeledón A, Jiménez-Rojas C, Chacón-Díaz C, Cloeckaert A, Chaves-Olarte E, Thomson NR, Moreno E, Guzmán-Verri C. Brucella Genetic Variability in Wildlife Marine Mammals Populations Relates to Host Preference and Ocean Distribution. Genome Biol Evol 2017; 9:1901-1912. [PMID: 28854602 PMCID: PMC5554395 DOI: 10.1093/gbe/evx137] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2017] [Indexed: 12/31/2022] Open
Abstract
Intracellular bacterial pathogens probably arose when their ancestor adapted from a free-living environment to an intracellular one, leading to clonal bacteria with smaller genomes and less sources of genetic plasticity. Still, this plasticity is needed to respond to the challenges posed by the host. Members of the Brucella genus are facultative-extracellular intracellular bacteria responsible for causing brucellosis in a variety of mammals. The various species keep different host preferences, virulence, and zoonotic potential despite having 97-99% similarity at genome level. Here, we describe elements of genetic variation in Brucella ceti isolated from wildlife dolphins inhabiting the Pacific Ocean and the Mediterranean Sea. Comparison with isolates obtained from marine mammals from the Atlantic Ocean and the broader Brucella genus showed distinctive traits according to oceanic distribution and preferred host. Marine mammal isolates display genetic variability, represented by an important number of IS711 elements as well as specific IS711 and SNPs genomic distribution clustering patterns. Extensive pseudogenization was found among isolates from marine mammals as compared with terrestrial ones, causing degradation in pathways related to energy, transport of metabolites, and regulation/transcription. Brucella ceti isolates infecting particularly dolphin hosts, showed further degradation of metabolite transport pathways as well as pathways related to cell wall/membrane/envelope biogenesis and motility. Thus, gene loss through pseudogenization is a source of genetic variation in Brucella, which in turn, relates to adaptation to different hosts. This is relevant to understand the natural history of bacterial diseases, their zoonotic potential, and the impact of human interventions such as domestication.
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Affiliation(s)
- Marcela Suárez-Esquivel
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Kate S. Baker
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Institute for Integrative Biology, University of Liverpool, United Kingdom
| | - Nazareth Ruiz-Villalobos
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Gabriela Hernández-Mora
- Servicio Nacional de Salud Animal, Ministerio de Agricultura y Ganadería, Heredia, Costa Rica
| | - Elías Barquero-Calvo
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | | | - Amanda Castillo-Zeledón
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - César Jiménez-Rojas
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Carlos Chacón-Díaz
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Axel Cloeckaert
- ISP, INRA, Université François Rabelais de Tours, UMR 1282, Nouzilly, France
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | | | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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Suárez-Esquivel M, Ruiz-Villalobos N, Castillo-Zeledón A, Jiménez-Rojas C, Roop Ii RM, Comerci DJ, Barquero-Calvo E, Chacón-Díaz C, Caswell CC, Baker KS, Chaves-Olarte E, Thomson NR, Moreno E, Letesson JJ, De Bolle X, Guzmán-Verri C. Brucella abortus Strain 2308 Wisconsin Genome: Importance of the Definition of Reference Strains. Front Microbiol 2016; 7:1557. [PMID: 27746773 PMCID: PMC5041503 DOI: 10.3389/fmicb.2016.01557] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 07/24/2016] [Accepted: 09/16/2016] [Indexed: 12/25/2022] Open
Abstract
Brucellosis is a bacterial infectious disease affecting a wide range of mammals and a neglected zoonosis caused by species of the genetically homogenous genus Brucella. As in most studies on bacterial diseases, research in brucellosis is carried out by using reference strains as canonical models to understand the mechanisms underlying host pathogen interactions. We performed whole genome sequencing analysis of the reference strain B. abortus 2308 routinely used in our laboratory, including manual curated annotation accessible as an editable version through a link at https://en.wikipedia.org/wiki/Brucella#Genomics. Comparison of this genome with two publically available 2308 genomes showed significant differences, particularly indels related to insertional elements, suggesting variability related to the transposition of these elements within the same strain. Considering the outcome of high resolution genomic techniques in the bacteriology field, the conventional concept of strain definition needs to be revised.
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Affiliation(s)
- Marcela Suárez-Esquivel
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica Heredia, Costa Rica
| | - Nazareth Ruiz-Villalobos
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica Heredia, Costa Rica
| | - Amanda Castillo-Zeledón
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica Heredia, Costa Rica
| | - César Jiménez-Rojas
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica Heredia, Costa Rica
| | - R Martin Roop Ii
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University Greenville, NC, USA
| | - Diego J Comerci
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde", Instituto Tecnológico de Chascomús, Universidad Nacional de San Martín, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión Nacional de Energía Atómica, Grupo Pecuario, Centro Atómico Ezeiza Buenos Aires, Argentina
| | - Elías Barquero-Calvo
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica San José, Costa Rica
| | - Carlos Chacón-Díaz
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa RicaHeredia, Costa Rica; Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa RicaSan José, Costa Rica
| | - Clayton C Caswell
- Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech Blacksburg, VA, USA
| | - Kate S Baker
- Wellcome Trust Sanger InstituteHinxton, UK; Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of LiverpoolLiverpool, UK
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica San José, Costa Rica
| | - Nicholas R Thomson
- Wellcome Trust Sanger InstituteHinxton, UK; The London School of Hygiene and Tropical MedicineLondon, UK
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa RicaHeredia, Costa Rica; Instituto Clodomiro Picado, Universidad de Costa RicaSan José, Costa Rica
| | - Jean J Letesson
- Unité de Recherche en Biologie des Microorganismes, Université de Namur Namur Belgium
| | - Xavier De Bolle
- Unité de Recherche en Biologie des Microorganismes, Université de Namur Namur Belgium
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa RicaHeredia, Costa Rica; Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa RicaSan José, Costa Rica
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