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Smith EA, Miller EA, Weber BP, Munoz Aguayo J, Flores Figueroa C, Huisinga J, Nezworski J, Kromm M, Wileman B, Johnson TJ. Genomic Landscape of Ornithobacterium rhinotracheale in Commercial Turkey Production in the United States. Appl Environ Microbiol 2020; 86:e02874-19. [PMID: 32245763 PMCID: PMC7237767 DOI: 10.1128/aem.02874-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/25/2020] [Indexed: 01/02/2023] Open
Abstract
Ornithobacterium rhinotracheale is a causative agent of respiratory tract infections in avian hosts worldwide but is a particular problem for commercial turkey production. Little is known about the ecologic and evolutionary dynamics of O. rhinotracheale, which makes prevention and control of this pathogen a challenge. The purpose of this study was to gain insight into the genetic relationships between O. rhinotracheale populations through comparative genomics of clinical isolates from different U.S. turkey producers. O. rhinotracheale clinical isolates were collected from four major U.S. turkey producers and several independent turkey growers from the upper Midwest and Southeast, and whole-genome sequencing was performed. Genomes were compared phylogenetically using single nucleotide polymorphism (SNP)-based analysis, and then assembly and annotations were performed to identify genes encoding putative virulence factors and antimicrobial resistance determinants. A pangenome approach was also used to establish a core set of genes consistently present in O. rhinotracheale and to highlight differences in gene content between phylogenetic clades. A total of 1,457 nonrecombinant SNPs were identified from 157 O. rhinotracheale genomes, and four distinct phylogenetic clades were identified. Isolates clustered by company on the phylogenetic tree, however, and each company had isolates in multiple clades with similar collection dates, indicating that there are multiple O. rhinotracheale strains circulating within each of the companies examined. Additionally, several antimicrobial resistance proteins, putative virulence factors, and the pOR1 plasmid were associated with particular clades and multilocus sequence types, which may explain why the same strains seem to have persisted in the same turkey operations for decades.IMPORTANCE The whole-genome approach enhances our understanding of evolutionary relationships between clinical Ornithobacterium rhinotracheale isolates from different commercial turkey producers and allows for identification of genes associated with virulence, antimicrobial resistance, or mobile genetic elements that are often excluded using traditional typing methods. Additionally, differentiating O. rhinotracheale isolates at the whole-genome level may provide insight into selection of the most appropriate autogenous vaccine strain, or groups of strains, for a given population of clinical isolates.
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Affiliation(s)
- Emily A Smith
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
| | - Elizabeth A Miller
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
| | - Bonnie P Weber
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
| | - Jeannette Munoz Aguayo
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
| | | | | | | | | | | | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
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Kim HN, Seok SH, Lee YS, Won HS, Seo MD. Crystal structure and functional characterization of SF216 from Shigella flexneri. FEBS Lett 2017; 591:3692-3703. [PMID: 28983914 DOI: 10.1002/1873-3468.12873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/01/2017] [Accepted: 10/02/2017] [Indexed: 12/18/2022]
Abstract
Shigella flexneri is a Gram-negative anaerobic bacterium that causes highly infectious bacterial dysentery in humans. Here, we solved the crystal structure of SF216, a hypothetical protein from the S. flexneri 5a strain M90T, at 1.7 Å resolution. The crystal structure of SF216 represents a homotrimer stabilized by intersubunit interactions and ion-mediated electrostatic interactions. Each subunit consists of three β-strands and five α-helices with the β-β-β-α-α-α-α-α topology. Based on the structural information, we also demonstrate that SF216 shows weak ribonuclease activity by a fluorescence quenching assay. Furthermore, we identify potential druggable pockets (putative hot spots) on the surface of the SF216 structure by computational mapping.
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Affiliation(s)
- Ha-Neul Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi, Korea.,College of Pharmacy, Ajou University, Suwon, Gyeonggi, Korea
| | | | - Yoo-Sup Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi, Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute and College of Biomedical and Health Science (RIBHS), Konkuk University, Chungju, Chungbuk, Korea
| | - Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi, Korea.,College of Pharmacy, Ajou University, Suwon, Gyeonggi, Korea
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Henrich B, Kretzmer F, Deenen R, Köhrer K. Validation of a novel Mho microarray for a comprehensive characterisation of the Mycoplasma hominis action in HeLa cell infection. PLoS One 2017; 12:e0181383. [PMID: 28753664 PMCID: PMC5533444 DOI: 10.1371/journal.pone.0181383] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/29/2017] [Indexed: 12/30/2022] Open
Abstract
Mycoplasma hominis is the second smallest facultative pathogen of the human urogenital tract. With less than 600 protein-encoding genes, it represents an ideal model organism for the study of host-pathogen interactions. For a comprehensive characterisation of the M. hominis action in infection a customized Mho microarray, which was based on two genome sequences (PG21 and LBD-4), was designed to analyze the dynamics of the mycoplasma transcriptome during infection and validated for M. hominis strain FBG. RNA preparation was evaluated and adapted to ensure the highest recovery of mycoplasmal mRNAs from in vitro HeLa cell infection assays. Following cRNA hybridization, the read-out strategy of the hybridization results was optimized and confirmed by RT-PCR. A statistically robust infection assay with M. hominis strain FBG enabled the identification of differentially regulated key effector molecules such as critical cytoadhesins (4 h post infection (pI)), invasins (48 h pI) and proteins associated with establishing chronic infection of the host (336 h pI). Of the 294 differentially regulated genes (>2-fold) 128 (43.5%) encoded hypothetical proteins, including lipoproteins that seem to play a central role as virulence factors at each stage of infection: P75 as a novel cytoadhesin candidate, which is also differentially upregulated in chronic infection; the MHO_2100 protein, a postulated invasin and the MHO_730-protein, a novel ecto-nuclease and domain of an ABC transporter, the function of which in chronic infection has still to be elucidated. Implementation of the M. hominis microarray strategy led to a comprehensive identification of to date unknown candidates for virulence factors at relevant stages of host cell infection.
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Affiliation(s)
- Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
- * E-mail:
| | - Freya Kretzmer
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
- Biological and Medical Research Centre (BMFZ), Medical Faculty of the Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - René Deenen
- Biological and Medical Research Centre (BMFZ), Medical Faculty of the Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Karl Köhrer
- Biological and Medical Research Centre (BMFZ), Medical Faculty of the Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
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Alencar VC, Jabes DL, Menegidio FB, Sassaki GL, de Souza LR, Puzer L, Meneghetti MCZ, Lima MA, Tersariol ILDS, de Oliveira RC, Nunes LR. Functional and Evolutionary Characterization of a UDP-Xylose Synthase Gene from the Plant Pathogen Xylella fastidiosa, Involved in the Synthesis of Bacterial Lipopolysaccharide. Biochemistry 2017; 56:779-792. [PMID: 28125217 DOI: 10.1021/acs.biochem.6b00886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Xylella fastidiosa is a plant-infecting bacillus, responsible for many important crop diseases, such as Pierce's disease of vineyards, citrus variegated chlorosis, and coffee leaf scorch (CLS), among others. Recent genomic comparisons involving two CLS-related strains, belonging to X. fastidiosa subsp. pauca, revealed that one of them carries a frameshift mutation that inactivates a gene encoding an oxidoreductase of the short-chain dehydrogenase/reductase (SDR) superfamily, which may play important roles in determining structural variations in bacterial glycans and glycoconjugates. However, the exact nature of this SDR has been a matter of controversy, as different annotations of X. fastidiosa genomes have implicated it in distinct reactions. To confirm the nature of this mutated SDR, a comparative analysis was initially performed, suggesting that it belongs to a subgroup of SDR decarboxylases, representing a UDP-xylose synthase (Uxs). Functional assays, using a recombinant derivative of this enzyme, confirmed its nature as XfUxs, and carbohydrate composition analyses, performed with lipopolysaccharide (LPS) molecules obtained from different strains, indicate that inactivation of the X. fastidiosa uxs gene affects the LPS structure among CLS-related X. fastidiosa strains. Finally, a comparative sequence analysis suggests that this mutation is likely to result in a morphological and evolutionary hallmark that differentiates two subgroups of CLS-related strains, which may influence interactions between these bacteria and their plant and/or insect hosts.
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Affiliation(s)
- Valquíria Campos Alencar
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC) , Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes, SP CEP 08780-911, Brazil
| | - Daniela Leite Jabes
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC) , Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes, SP CEP 08780-911, Brazil
| | - Fabiano Bezerra Menegidio
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC) , Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes, SP CEP 08780-911, Brazil
| | - Guilherme Lanzi Sassaki
- Setor de Ciências Biológicas-Departamento de Bioquímica e Biologia Molecular Laboratório de Química de Carboidratos, Universidade Federal do Paraná (UFPR) , Rua Cel. Francisco H. dos Santos, 100, Curitiba, Paraná CEP 81531-980, Brazil
| | - Lucas Rodrigo de Souza
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC) , Rua Santa Adélia, 166, Santo André, SP CEP 09210-170, Brazil
| | - Luciano Puzer
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC) , Rua Santa Adélia, 166, Santo André, SP CEP 09210-170, Brazil
| | - Maria Cecília Zorél Meneghetti
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP) , Rua Três de Maio, Vila Clementino, São Paulo CEP 04044-020, Brazil
| | - Marcelo Andrade Lima
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP) , Rua Três de Maio, Vila Clementino, São Paulo CEP 04044-020, Brazil
| | - Ivarne Luis Dos Santos Tersariol
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP) , Rua Três de Maio, Vila Clementino, São Paulo CEP 04044-020, Brazil
| | - Regina Costa de Oliveira
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC) , Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes, SP CEP 08780-911, Brazil
| | - Luiz R Nunes
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC) , Rua Santa Adélia, 166, Santo André, SP CEP 09210-170, Brazil
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Mendes JS, Santiago AS, Toledo MAS, Horta MAC, de Souza AA, Tasic L, de Souza AP. In vitro Determination of Extracellular Proteins from Xylella fastidiosa. Front Microbiol 2016; 7:2090. [PMID: 28082960 PMCID: PMC5183587 DOI: 10.3389/fmicb.2016.02090] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/09/2016] [Indexed: 12/20/2022] Open
Abstract
The phytopathogen Xylella fastidiosa causes economic losses in important agricultural crops. Xylem vessel occlusion caused by biofilm formation is the major mechanism underlying the pathogenicity of distinct strains of X. fastidiosa. Here, we provide a detailed in vitro characterization of the extracellular proteins of X. fastidiosa. Based on the results, we performed a comparison with a strain J1a12, which cannot induce citrus variegated chlorosis symptoms when inoculated into citrus plants. We then extend this approach to analyze the extracellular proteins of X. fastidiosa in media supplemented with calcium. We verified increases in extracellular proteins concomitant with the days of growth and, consequently, biofilm development (3-30 days). Outer membrane vesicles carrying toxins were identified beginning at 10 days of growth in the 9a5c strain. In addition, a decrease in extracellular proteins in media supplemented with calcium was observed in both strains. Using mass spectrometry, 71 different proteins were identified during 30 days of X. fastidiosa biofilm development, including proteases, quorum-sensing proteins, biofilm formation proteins, hypothetical proteins, phage-related proteins, chaperones, toxins, antitoxins, and extracellular vesicle membrane components.
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Affiliation(s)
- Juliano S. Mendes
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
| | - André S. Santiago
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
| | - Marcelo A. S. Toledo
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
| | - Maria A. C. Horta
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
| | | | - Ljubica Tasic
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual de CampinasCampinas, Brazil
| | - Anete P. de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de CampinasCampinas, Brazil
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