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Warren ME, Pickett BE, Adams BJ, Villalva C, Applegate A, Robison RA. Comparative sequence analysis elucidates the evolutionary patterns of Yersinia pestis in New Mexico over thirty-two years. PeerJ 2023; 11:e16007. [PMID: 37780382 PMCID: PMC10541020 DOI: 10.7717/peerj.16007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/09/2023] [Indexed: 10/03/2023] Open
Abstract
Background Yersinia pestis, a Gram-negative bacterium, is the causative agent of plague. Y. pestis is a zoonotic pathogen that occasionally infects humans and became endemic in the western United States after spreading from California in 1899. Methods To better understand evolutionary patterns in Y. pestis from the southwestern United States, we sequenced and analyzed 22 novel genomes from New Mexico. Analytical methods included, assembly, multiple sequences alignment, phylogenetic tree reconstruction, genotype-phenotype correlation, and selection pressure. Results We identified four genes, including Yscp and locus tag YPO3944, which contained codons undergoing negative selection. We also observed 42 nucleotide sites displaying a statistically significant skew in the observed residue distribution based on the year of isolation. Overall, the three genes with the most statistically significant variations that associated with metadata for these isolates were sapA, fliC, and argD. Phylogenetic analyses point to a single introduction of Y. pestis into the United States with two subsequent, independent movements into New Mexico. Taken together, these analyses shed light on the evolutionary history of this pathogen in the southwestern US over a focused time range and confirm a single origin and introduction into North America.
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Affiliation(s)
- Mary E. Warren
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Byron J. Adams
- Department of Biology, Brigham Young University, Provo, UT, United States
- Monte L. Bean Life Science Museum, Provo, UT, United States
| | - Crystal Villalva
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Alyssa Applegate
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Richard A. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
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2
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Fan Y, Li P, Zhu D, Zhao C, Jiao J, Ji X, Du X. Effects of ESA_00986 Gene on Adhesion/Invasion and Virulence of Cronobacter sakazakii and Its Molecular Mechanism. Foods 2023; 12:2572. [PMID: 37444309 DOI: 10.3390/foods12132572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Cronobacter sakazakii is an opportunistic Gram-negative pathogen that has been identified as a causative agent of severe foodborne infections with a higher risk of mortality in neonates, premature infants, the elderly, and immunocompromised populations. The specific pathogenesis mechanisms of C. sakazakii, such as adhesion and colonization, remain unclear. Previously, we conducted comparative proteomic studies on the two strains with the stronger and weaker infection ability, respectively, and found an interesting protein, ESA_00986, which was more highly expressed in the strain with the stronger ability. This unknown protein, predicted to be a type of invasitin related to invasion, may be a critical factor contributing to its virulence. This study aimed to elucidate the precise roles of the ESA_00986 gene in C. sakazakii by generating gene knockout mutants and complementary strains. The mutant and complementary strains were assessed for their biofilm formation, mobility, cell adhesion and invasion, and virulence in a rat model. Compared with the wild-type strain, the mutant strain exhibited a decrease in motility, whereas the complementary strain showed comparable motility to the wild-type. The biofilm-forming ability of the mutant was weakened, and the mutant also exhibited attenuated adhesion to/invasion of intestinal epithelial cells (HCT-8, HICE-6) and virulence in a rat model. This indicated that ESA_00986 plays a positive role in adhesion/invasion and virulence. This study proves that the ESA_00986 gene encodes a novel virulence factor and advances our understanding of the pathogenic mechanism of C. sakazakii.
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Affiliation(s)
- Yufei Fan
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ping Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Dongdong Zhu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chumin Zhao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jingbo Jiao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xuemeng Ji
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Xinjun Du
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
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3
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Characterization of novel nuclease and protease activities among Leptospiral immunoglobulin-like proteins. Arch Biochem Biophys 2022; 727:109349. [PMID: 35820644 DOI: 10.1016/j.abb.2022.109349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/01/2022] [Accepted: 07/03/2022] [Indexed: 11/24/2022]
Abstract
Bacterial immunoglobulin-like (BIg) domain containing proteins play a variety of biological functions. Leptospiral Immunoglobulin-like (Lig) proteins are well-known virulence factors located on the surface of the pathogenic Leptospira that act during adhesion, invasion, and immune evasion. The Lig proteins have many roles and have been designated as multifaceted proteins. However, the hydrolyzing function of Lig proteins is not yet investigated in detail. Here, we report novel in-vitro nuclease and protease activities in the Ig-like domain of LigA protein. All Ig-like domains were able to cleave DNA in the presence of a divalent ion, but not RNA. Site-directed mutagenesis revealed Mg+2 binding residues in the Ig-like domain of LigA7. The basis of novel nuclease activity may be associated with protein adopting different conformation in the presence of divalent ions and substrate as investigated by change of intrinsic fluorescence. The docking of a stretch of double-strand DNA shows the binding on the positive surface of the protein. In addition, the protein is also observed to cleave a general protease substrate, β-casein, in our experimental condition. Our results proposed that the novel functions may be associated with neutrophil extracellular Trap (NET) evasion. Overall this study enhances the basic knowledge of non-nuclease proteins involved in the DNA cleavage activity and makes the foundation to explore its in-vivo activity in pathogenic Leptospira and other pathogens as well. Moreover, this information may be utilized to develop preventive strategies to interfere with Leptospira immune evasion.
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4
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Deletion of Yersinia pestis ail causes temperature sensitive pleiotropic effects including cell lysis that are suppressed by carbon source, cations, or loss of phospholipase A activity. J Bacteriol 2021; 203:e0036121. [PMID: 34398663 PMCID: PMC8508112 DOI: 10.1128/jb.00361-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Maintenance of phospholipid (PL) and lipopoly- or lipooligo-saccharide (LPS or LOS) asymmetry in the outer membrane (OM) of Gram-negative bacteria is essential but poorly understood. The Yersinia pestis OM Ail protein was required to maintain lipid homeostasis and cell integrity at elevated temperature (37° C). Loss of this protein had pleiotropic effects. A Y. pestis Δail mutant and KIM6+ wild- type were systematically compared for (i) growth requirements at 37° C, (ii) cell structure, (iii) antibiotic and detergent sensitivity, (iv) proteins released into supernates, (v) induction of the heat shock response, and (vi) physiological and genetic suppressors that restored the wild- type phenotype. The Δail mutant grew normally at 28° C but lysed at 37° C when it entered stationary phase as shown by cell count, SDS-PAGE of cell supernatants, and electron microscopy. Immuno-fluorescent microscopy showed that the Δail mutant did not assemble Caf1 capsule. Expression of heat shock promoters rpoE or rpoH fused to a lux operon reporter were not induced when the Δail mutant was shifted from the 28° C to 37° C (p<0.001 and p<0.01 respectively). Mutant lysis was suppressed by addition of 11 mM glucose, 22 or 44 mM glycerol, 2.5 mM Ca2+, or 2.5 mM Mg2+ to the growth medium, or by a mutation in the phospholipase A gene (pldA::miniTn5, ΔpldA, or PldAS164A). A model, accounting for the temperature-sensitive lysis of the Δail mutant and the Ail-dependent stabilization of the OM tetraacylated LOS at 37°C is presented. IMPORTANCE The Gram-negative pathogen, Yersinia pestis, transitions between a flea vector (ambient temperature) and a mammalian host (37° C). In response to 37° C, Y. pestis modifies its outer membrane (OM) by reducing the fatty acid content in lipid A, changing the outer leaflet from being predominantly hexaacylated to being predominantly tetraacylated. It also increases the Ail concentration, so it becomes the most prominent OM protein. Both measures are needed for Y. pestis to evade the host innate immune response. Deletion of ail destabilizes the OM at 37° C causing the cells to lyse. These results show that a protein is essential for maintaining lipid asymmetry and lipid homeostasis in the bacterial OM.
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Campuzano O, Sanchez-Molero O, Fernandez A, Mademont-Soler I, Coll M, Perez-Serra A, Mates J, Del Olmo B, Pico F, Nogue-Navarro L, Sarquella-Brugada G, Iglesias A, Cesar S, Carro E, Borondo JC, Brugada J, Castellà J, Medallo J, Brugada R. Sudden Arrhythmic Death During Exercise: A Post-Mortem Genetic Analysis. Sports Med 2018; 47:2101-2115. [PMID: 28255936 DOI: 10.1007/s40279-017-0705-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Sudden cardiac death is a natural and unexpected death that occurs within 1 h of the first symptom. Most sudden cardiac deaths occur during exercise, mostly as a result of myocardial infarction. After autopsy, some cases, especially in the young, are diagnosed as cardiomyopathies or remain without a conclusive cause of death. In both situations, genetic alterations may explain the arrhythmia. OBJECTIVE Our aim was to identify a genetic predisposition to sudden cardiac death in a cohort of post-mortem cases of individuals who died during exercise, with a structurally normal heart, and were classified as arrhythmogenic death. METHODS We analyzed a cohort of 52 post-mortem samples from individuals <50 years old who had a negative autopsy. Next-generation sequencing technology was used to screen genes associated with sudden cardiac death. RESULTS Our cohort showed a male prevalence (12:1). Half of the deaths occurred in individuals 41-50 years of age. Running was the most common exercise activity during the fatal event, accounting for 46.15% of cases. Genetic analysis identified 83 rare variants in 37 samples (71.15% of all samples). Of all rare variants, 36.14% were classified as deleterious, being present in 53.84% of all cases. CONCLUSIONS A comprehensive analysis of sudden cardiac death-related genes in individuals who died suddenly while exercising enabled the identification of potentially causative variants. However, many genetic variants remain of indeterminate significance, thus further work is needed before clinical translation. Nonetheless, comprehensive genetic analysis of individuals who died during exercise enables the detection of potentially causative variants and helps to identify at-risk relatives.
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Affiliation(s)
- Oscar Campuzano
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain.,Medical Science Department, School of Medicine, University of Girona, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Olallo Sanchez-Molero
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Anna Fernandez
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Irene Mademont-Soler
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Monica Coll
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Alexandra Perez-Serra
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Jesus Mates
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Bernat Del Olmo
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Ferran Pico
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Laia Nogue-Navarro
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
| | | | - Anna Iglesias
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Sergi Cesar
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Esther Carro
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Juan Carlos Borondo
- Histopathology Unit, Instituto Nacional Toxicología y Ciencias Forenses (INTCF), Barcelona, Spain
| | - Josep Brugada
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Josep Castellà
- Forensic Pathology Service, Institut de Medicina Legal i Ciències Forenses de Catalunya (IMLCFC), Barcelona, Spain
| | - Jordi Medallo
- Forensic Pathology Service, Institut de Medicina Legal i Ciències Forenses de Catalunya (IMLCFC), Barcelona, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain. .,Medical Science Department, School of Medicine, University of Girona, Girona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain. .,Cardiology Service, Hospital Josep Trueta, Girona, Spain.
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6
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Perkowski EF, Zulauf KE, Weerakoon D, Hayden JD, Ioerger TR, Oreper D, Gomez SM, Sacchettini JC, Braunstein M. The EXIT Strategy: an Approach for Identifying Bacterial Proteins Exported during Host Infection. mBio 2017; 8:e00333-17. [PMID: 28442606 PMCID: PMC5405230 DOI: 10.1128/mbio.00333-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 04/04/2017] [Indexed: 12/12/2022] Open
Abstract
Exported proteins of bacterial pathogens function both in essential physiological processes and in virulence. Past efforts to identify exported proteins were limited by the use of bacteria growing under laboratory (in vitro) conditions. Thus, exported proteins that are exported only or preferentially in the context of infection may be overlooked. To solve this problem, we developed a genome-wide method, named EXIT (exported in vivotechnology), to identify proteins that are exported by bacteria during infection and applied it to Mycobacterium tuberculosis during murine infection. Our studies validate the power of EXIT to identify proteins exported during infection on an unprecedented scale (593 proteins) and to reveal in vivo induced exported proteins (i.e., proteins exported significantly more during in vivo infection than in vitro). Our EXIT data also provide an unmatched resource for mapping the topology of M. tuberculosis membrane proteins. As a new approach for identifying exported proteins, EXIT has potential applicability to other pathogens and experimental conditions.IMPORTANCE There is long-standing interest in identifying exported proteins of bacteria as they play critical roles in physiology and virulence and are commonly immunogenic antigens and targets of antibiotics. While significant effort has been made to identify the bacterial proteins that are exported beyond the cytoplasm to the membrane, cell wall, or host environment, current methods to identify exported proteins are limited by their use of bacteria growing under laboratory (in vitro) conditions. Because in vitro conditions do not mimic the complexity of the host environment, critical exported proteins that are preferentially exported in the context of infection may be overlooked. We developed a novel method to identify proteins that are exported by bacteria during host infection and applied it to identify Mycobacterium tuberculosis proteins exported in a mouse model of tuberculosis.
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Affiliation(s)
- E F Perkowski
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - K E Zulauf
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - D Weerakoon
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - J D Hayden
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - T R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, USA
| | - D Oreper
- Joint Department of Biomedical Engineering at UNC-Chapel Hill and NC State University, Chapel Hill, North Carolina, USA
| | - S M Gomez
- Joint Department of Biomedical Engineering at UNC-Chapel Hill and NC State University, Chapel Hill, North Carolina, USA
| | - J C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - M Braunstein
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
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7
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Yasuike M, Nishiki I, Iwasaki Y, Nakamura Y, Fujiwara A, Shimahara Y, Kamaishi T, Yoshida T, Nagai S, Kobayashi T, Katoh M. Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species. PLoS One 2017; 12:e0173198. [PMID: 28257489 PMCID: PMC5336288 DOI: 10.1371/journal.pone.0173198] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/16/2017] [Indexed: 01/15/2023] Open
Abstract
Nocardiosis caused by Nocardia seriolae is one of the major threats in the aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S. dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1 predicted genes, we found orthologs of virulence factors of pathogenic mycobacteria and human clinical Nocardia isolates involved in host cell invasion, modulation of phagocyte function and survival inside the macrophages. The virulence factor candidates provide an essential basis for understanding their pathogenic mechanisms at the molecular level by the fish nocardiosis research community in future studies. We also found many potential antibiotic resistance genes on the N. seriolae UTF1 chromosome. Comparative analysis with the four existing complete genomes, N. farcinica IFM 10152, N. brasiliensis HUJEG-1 and N. cyriacigeorgica GUH-2 and N. nova SH22a, revealed that 2,745 orthologous genes were present in all five Nocardia genomes (core genes) and 1,982 genes were unique to N. seriolae UTF1. In particular, the N. seriolae UTF1 genome contains a greater number of mobile elements and genes of unknown function that comprise the differences in structure and gene content from the other Nocardia genomes. In addition, a lot of the N. seriolae UTF1-specific genes were assigned to the ABC transport system. Because of limited resources in ocean environments, these N. seriolae UTF1 specific ABC transporters might facilitate adaptation strategies essential for marine environment survival. Thus, the availability of the complete N. seriolae UTF1 genome sequence will provide a valuable resource for comparative genomic studies of N. seriolae isolates, as well as provide new insights into the ecological and functional diversity of the genus Nocardia.
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Affiliation(s)
- Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
- * E-mail: (AF); (MY)
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
- * E-mail: (AF); (MY)
| | - Yoshiko Shimahara
- Research Center of Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Saiki, Oita, Japan
| | - Takashi Kamaishi
- Fisheries Agency, Ministry of Agriculture, Forestry and Fisheries, Chiyoda-ku, Tokyo, Japan
| | | | - Satoshi Nagai
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Takanori Kobayashi
- Headquarters, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Masaya Katoh
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
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8
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Chauhan N, Wrobel A, Skurnik M, Leo JC. Yersinia adhesins: An arsenal for infection. Proteomics Clin Appl 2016; 10:949-963. [PMID: 27068449 DOI: 10.1002/prca.201600012] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/14/2016] [Accepted: 04/06/2016] [Indexed: 11/09/2022]
Abstract
The Yersiniae are a group of Gram-negative coccobacilli inhabiting a wide range of habitats. The genus harbors three recognized human pathogens: Y. enterocolitica and Y. pseudotuberculosis, which both cause gastrointestinal disease, and Y. pestis, the causative agent of plague. These three organisms have served as models for a number of aspects of infection biology, including adhesion, immune evasion, evolution of pathogenic traits, and retracing the course of ancient pandemics. The virulence of the pathogenic Yersiniae is heavily dependent on a number of adhesin molecules. Some of these, such as the Yersinia adhesin A and invasin of the enteropathogenic species, and the pH 6 antigen of Y. pestis, have been extensively studied. However, genomic sequencing has uncovered a host of other adhesins present in these organisms, the functions of which are only starting to be investigated. Here, we review the current state of knowledge on the adhesin molecules present in the Yersiniae, and their functions and putative roles in the infection process.
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Affiliation(s)
- Nandini Chauhan
- Evolution and Genetics, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Agnieszka Wrobel
- Evolution and Genetics, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland.,Central Hospital Laboratory Diagnostics, Helsinki University, Helsinki, Finland
| | - Jack C Leo
- Evolution and Genetics, Department of Biosciences, University of Oslo, Oslo, Norway.
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9
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Pilatti L, Boldrin de Paiva J, Rojas TCG, Leite JL, Conceição RA, Nakazato G, Dias da Silveira W. The virulence factor ychO has a pleiotropic action in an Avian Pathogenic Escherichia coli (APEC) strain. BMC Microbiol 2016; 16:35. [PMID: 26965678 PMCID: PMC4787180 DOI: 10.1186/s12866-016-0654-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 03/02/2016] [Indexed: 02/04/2023] Open
Abstract
Background Avian pathogenic Escherichia coli strains cause extraintestinal diseases in birds, leading to substantial economic losses to the poultry industry worldwide. Bacteria that invade cells can overcome the host humoral immune response, resulting in a higher pathogenicity potential. Invasins are members of a large family of outer membrane proteins that allow pathogen invasion into host cells by interacting with specific receptors on the cell surface. Results An in silico analysis of the genome of a septicemic APEC strain (SEPT362) demonstrated the presence of a putative invasin homologous to the ychO gene from E. coli str. K-12 substr. MG1655. In vitro and in vivo assays comparing a mutant strain carrying a null mutation of this gene, a complemented strain, and its counterpart wild-type strain showed that ychO plays a role in the pathogenicity of APEC strain SEPT362. In vitro assays demonstrated that the mutant strain exhibited significant decreases in bacterial adhesiveness and invasiveness in chicken cells and biofilm formation. In vivo assay indicated a decrease in pathogenicity of the mutant strain. Moreover, transcriptome analysis demonstrated that the ychO deletion affected the expression of 426 genes. Among the altered genes, 93.66 % were downregulated in the mutant, including membrane proteins and metabolism genes. Conclusion The results led us to propose that gene ychO contributes to the pathogenicity of APEC strain SEPT362 influencing, in a pleiotropic manner, many biological characteristics, such as adhesion and invasion of in vitro cultured cells, biofilm formation and motility, which could be due to the possible membrane location of this protein. All of these results suggest that the absence of gene ychO would influence the virulence of the APEC strain herein studied.
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Affiliation(s)
- Livia Pilatti
- Department of Genetics, Evolution and Bioagents, Institute of Biology (P.O.Box: 6109), State University of Campinas - UNICAMP (ZIP Code 13083-970), Campinas, São Paulo, Brazil
| | - Jacqueline Boldrin de Paiva
- Department of Genetics, Evolution and Bioagents, Institute of Biology (P.O.Box: 6109), State University of Campinas - UNICAMP (ZIP Code 13083-970), Campinas, São Paulo, Brazil
| | - Thaís Cabrera Galvão Rojas
- Department of Genetics, Evolution and Bioagents, Institute of Biology (P.O.Box: 6109), State University of Campinas - UNICAMP (ZIP Code 13083-970), Campinas, São Paulo, Brazil
| | - Janaína Luisa Leite
- Department of Genetics, Evolution and Bioagents, Institute of Biology (P.O.Box: 6109), State University of Campinas - UNICAMP (ZIP Code 13083-970), Campinas, São Paulo, Brazil
| | - Rogério Arcuri Conceição
- Department of Genetics, Evolution and Bioagents, Institute of Biology (P.O.Box: 6109), State University of Campinas - UNICAMP (ZIP Code 13083-970), Campinas, São Paulo, Brazil
| | - Gerson Nakazato
- Department of Microbiology, Center of Biological Sciences, State University of Londrina (UEL), Londrina, Paraná, Brazil
| | - Wanderley Dias da Silveira
- Department of Genetics, Evolution and Bioagents, Institute of Biology (P.O.Box: 6109), State University of Campinas - UNICAMP (ZIP Code 13083-970), Campinas, São Paulo, Brazil.
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Chen S, Thompson KM, Francis MS. Environmental Regulation of Yersinia Pathophysiology. Front Cell Infect Microbiol 2016; 6:25. [PMID: 26973818 PMCID: PMC4773443 DOI: 10.3389/fcimb.2016.00025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/15/2016] [Indexed: 12/26/2022] Open
Abstract
Hallmarks of Yersinia pathogenesis include the ability to form biofilms on surfaces, the ability to establish close contact with eukaryotic target cells and the ability to hijack eukaryotic cell signaling and take over control of strategic cellular processes. Many of these virulence traits are already well-described. However, of equal importance is knowledge of both confined and global regulatory networks that collaborate together to dictate spatial and temporal control of virulence gene expression. This review has the purpose to incorporate historical observations with new discoveries to provide molecular insight into how some of these regulatory mechanisms respond rapidly to environmental flux to govern tight control of virulence gene expression by pathogenic Yersinia.
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Affiliation(s)
- Shiyun Chen
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, China
| | - Karl M Thompson
- Department of Microbiology, College of Medicine, Howard University Washington, DC, USA
| | - Matthew S Francis
- Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden; Department of Molecular Biology, Umeå UniversityUmeå, Sweden
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Leo JC, Oberhettinger P, Schütz M, Linke D. The inverse autotransporter family: intimin, invasin and related proteins. Int J Med Microbiol 2014; 305:276-82. [PMID: 25596886 DOI: 10.1016/j.ijmm.2014.12.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Intimin and invasin are adhesins and central virulence factors of attaching and effacing bacteria, such as enterohaemorrhagic Escherichia coli, and enteropathogenic Yersiniae, respectively. These proteins are prototypes of a large family of adhesins distributed widely in Gram-negative bacteria. It is now evident that this protein family represents a previously unrecognized autotransporter secretion system, termed type Ve secretion. In contrast to classical autotransport, where the transmembrane β-barrel domain or translocation unit is C-terminal to the extracellular region or passenger domain, type Ve-secreted proteins have an inverted topology with the passenger domain C-terminal to the translocation unit; hence the term inverse autotransporter. This minireview covers the recent advances in elucidating the structure and biogenesis of inverse autotransporters.
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Affiliation(s)
- Jack C Leo
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Philipp Oberhettinger
- Interfaculty Institute for Microbiology and Infection Medicine, University Clinics Tübingen, 72076 Tübingen, Germany
| | - Monika Schütz
- Interfaculty Institute for Microbiology and Infection Medicine, University Clinics Tübingen, 72076 Tübingen, Germany
| | - Dirk Linke
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway; Max Planck Institute for Developmental Biology, Department of Protein Evolution, 72076 Tübingen, Germany.
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12
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Abstract
Streptococcus agalactiae (group B Streptococcus [GBS]) is a leading cause of neonatal sepsis and meningitis, peripartum infections in women, and invasive infections in chronically ill or elderly individuals. GBS can be isolated from the gastrointestinal or genital tracts of up to 30% of healthy adults, and infection is thought to arise from invasion from a colonized mucosal site. Accordingly, bacterial surface components that mediate attachment of GBS to host cells or the extracellular matrix represent key factors in the colonization and infection of the human host. We identified a conserved GBS gene of unknown function that was predicted to encode a cell wall-anchored surface protein. Deletion of the gene and a cotranscribed upstream open reading frame (ORF) in GBS strain 515 reduced bacterial adherence to VK2 vaginal epithelial cells in vitro and reduced GBS binding to fibronectin-coated microtiter wells. Expression of the gene product in Lactococcus lactis conferred the ability to adhere to VK2 cells, to fibronectin and laminin, and to fibronectin-coated ME-180 cervical epithelial cells. Expression of the recombinant protein in L. lactis also markedly increased biofilm formation. The adherence function of the protein, named bacterial surface adhesin of GBS (BsaB), depended both on a central BID1 domain found in bacterial intimin-like proteins and on the C-terminal portion of the BsaB protein. Expression of BsaB in GBS, like that of several other adhesins, was regulated by the CsrRS two-component system. We conclude that BsaB represents a newly identified adhesin that participates in GBS attachment to epithelial cells and the extracellular matrix.
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13
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Vera-Cabrera L, Ortiz-Lopez R, Elizondo-Gonzalez R, Ocampo-Candiani J. Complete genome sequence analysis of Nocardia brasiliensis HUJEG-1 reveals a saprobic lifestyle and the genes needed for human pathogenesis. PLoS One 2013; 8:e65425. [PMID: 23755230 PMCID: PMC3670865 DOI: 10.1371/journal.pone.0065425] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 04/24/2013] [Indexed: 01/17/2023] Open
Abstract
Nocardia brasiliensis is an important etiologic agent of mycetoma. These bacteria live as a saprobe in soil or organic material and enter the tissue via minor trauma. Mycetoma is characterized by tumefaction and the production of fistula and abscesses, with no spontaneous cure. By using mass sequencing, we determined the complete genomic nucleotide sequence of the bacteria. According to our data, the genome is a circular chromosome 9,436,348-bp long with 68% G+C content that encodes 8,414 proteins. We observed orthologs for virulence factors, a higher number of genes involved in lipid biosynthesis and catabolism, and gene clusters for the synthesis of bioactive compounds, such as antibiotics, terpenes, and polyketides. An in silico analysis of the sequence supports the conclusion that the bacteria acquired diverse genes by horizontal transfer from other soil bacteria, even from eukaryotic organisms. The genome composition reflects the evolution of bacteria via the acquisition of a large amount of DNA, which allows it to survive in new ecological niches, including humans.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Chromosome Mapping
- Chromosomes, Bacterial/chemistry
- Chromosomes, Bacterial/metabolism
- DNA Transposable Elements
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Gene Expression Regulation, Bacterial
- Gene Transfer, Horizontal
- Genome, Bacterial
- Humans
- Metabolic Networks and Pathways/genetics
- Molecular Sequence Annotation
- Mycetoma/microbiology
- Mycetoma/pathology
- Nocardia/drug effects
- Nocardia/genetics
- Nocardia/metabolism
- Nocardia/pathogenicity
- Nocardia Infections/microbiology
- Nocardia Infections/pathology
- Sequence Analysis, DNA
- Soil Microbiology
- Virulence Factors/genetics
- Virulence Factors/metabolism
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Affiliation(s)
- Lucio Vera-Cabrera
- Laboratorio Interdisciplinario de Investigación Dermatológica, Servicio de Dermatología, Hospital Universitario, UANL, Monterrey, NL, México.
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Physiological levels of glucose induce membrane vesicle secretion and affect the lipid and protein composition of Yersinia pestis cell surfaces. Appl Environ Microbiol 2013; 79:4509-14. [PMID: 23686263 DOI: 10.1128/aem.00675-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yersinia pestis grown with physiologic glucose increased cell autoaggregation and deposition of extracellular material, including membrane vesicles. Membranes were characterized, and glucose had significant effects on protein, lipid, and carbohydrate profiles. These effects were independent of temperature and the biofilm-related locus pgm and were not observed in Yersinia pseudotuberculosis.
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