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Yan X, Chen X, Zhang X, Qureshi A, Wang Y, Tang X, Hu T, Zhuang H, Ran X, Ma G, Luo P, Shen L. Proteomic analysis of the effects of Dictyophora polysaccharide on arsenic-induced hepatotoxicity in rats. Exp Mol Pathol 2024; 138:104910. [PMID: 38876078 DOI: 10.1016/j.yexmp.2024.104910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/21/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
Arsenic (As) is a highly toxic environmental toxicant and a known human carcinogen. Long-term exposure to As can cause liver injury. Dictyophora polysaccharide (DIP) is a biologically active natural compound found in the Dictyophora with excellent antioxidation, anti-inflammation, and immune protection properties. In this study, the Sprague-Dawley (SD) rat model of As toxicity was established using a feeding method, followed by DIP treatment in rats with As-induced liver injury. The molecular mechanisms of As toxicity to the rat liver and the protective effect of DIP were investigated by proteomic studies. The results showed that 172, 328 and 191 differentially expressed proteins (DEPs) were identified between the As-exposed rats versus control rats (As/Ctrl), DIP treated rats versus As-exposed rats (DIP+As/As), and DIP treated rats versus control rats (DIP+As /Ctrl), respectively. Among them, the expression of 90 DEPs in the As/Ctrl groups was reversed by DIP treatment. As exposure caused dysregulation of metabolic pathways, mitochondria, oxidative stress, and apoptosis-related proteins in the rat liver. However, DIP treatment changed or restored the levels of these proteins, which attenuated the damage to the livers of rats caused by As exposure. The results provide new insights into the mechanisms of liver injury induced by As exposure and the treatment of DIP in As poisoning.
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Affiliation(s)
- Xi Yan
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, PR China
| | - Xiaolu Chen
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, PR China
| | - Xinglai Zhang
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, PR China
| | - Ayesha Qureshi
- College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Yi Wang
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, PR China
| | - Xiaoxiao Tang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Ting Hu
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, PR China
| | - Hongbin Zhuang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Xiaoqian Ran
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, PR China
| | - Guanwei Ma
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, PR China
| | - Peng Luo
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, PR China.
| | - Liming Shen
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, PR China; College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, PR China.
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Matczak S, Bouchez V, Leroux P, Douché T, Collinet N, Landier A, Gianetto QG, Guillot S, Chamot-Rooke J, Hasan M, Matondo M, Brisse S, Toubiana J. Biological differences between FIM2 and FIM3 fimbriae of Bordetella pertussis: not just the serotype. Microbes Infect 2023; 25:105152. [PMID: 37245862 DOI: 10.1016/j.micinf.2023.105152] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 05/30/2023]
Abstract
INTRODUCTION Bordetella pertussis still circulates worldwide despite vaccination. Fimbriae are components of some acellular pertussis vaccines. Population fluctuations of B. pertussis fimbrial serotypes (FIM2 and FIM3) are observed, and fim3 alleles (fim3-1 [clade 1] and fim3-2 [clade 2]) mark a major phylogenetic subdivision of B. pertussis. OBJECTIVES To compare microbiological characteristics and expressed protein profiles between fimbrial serotypes FIM2 and FIM3 and genomic clades. METHODS A total of 19 isolates were selected. Absolute protein abundance of the main virulence factors, autoagglutination and biofilm formation, bacterial survival in whole blood, induced blood cell cytokine secretion, and global proteome profiles were assessed. RESULTS Compared to FIM3, FIM2 isolates produced more fimbriae, less cellular pertussis toxin subunit 1 and more biofilm, but auto-agglutinated less. FIM2 isolates had a lower survival rate in cord blood, but induced higher levels of IL-4, IL-8 and IL-1β secretion. Global proteome comparisons uncovered 15 differentially produced proteins between FIM2 and FIM3 isolates, involved in adhesion and metabolism of metals. FIM3 isolates of clade 2 produced more FIM3 and more biofilm compared to clade 1. CONCLUSION FIM serotype and fim3 clades are associated with proteomic and other biological differences, which may have implications on pathogenesis and epidemiological emergence.
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Affiliation(s)
- Soraya Matczak
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Valérie Bouchez
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 28, Rue Du Docteur Roux, 75015, Paris, France; National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Pauline Leroux
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Thibaut Douché
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology Unit, 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Nils Collinet
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Annie Landier
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 28, Rue Du Docteur Roux, 75015, Paris, France; National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology Unit, 28, Rue Du Docteur Roux, 75015, Paris, France; Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Sophie Guillot
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 28, Rue Du Docteur Roux, 75015, Paris, France; National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Julia Chamot-Rooke
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology Unit, 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Milena Hasan
- Institut Pasteur, Université Paris Cité, Cytometry and Biomarkers Unit of Technology and Service (CB UTechS), 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology Unit, 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 28, Rue Du Docteur Roux, 75015, Paris, France; National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, 28, Rue Du Docteur Roux, 75015, Paris, France
| | - Julie Toubiana
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 28, Rue Du Docteur Roux, 75015, Paris, France; National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, 28, Rue Du Docteur Roux, 75015, Paris, France; Department of General Pediatrics and Pediatric Infectious Diseases, Hôpital Necker-Enfants Malades, APHP, Université Paris Cité, 149, Rue de Sèvres, 75015, Paris, France.
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Suyama H, Luu LDW, Zhong L, Raftery MJ, Lan R. Integrating proteomic data with metabolic modeling provides insight into key pathways of Bordetella pertussis biofilms. Front Microbiol 2023; 14:1169870. [PMID: 37601354 PMCID: PMC10435875 DOI: 10.3389/fmicb.2023.1169870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
Pertussis, commonly known as whooping cough is a severe respiratory disease caused by the bacterium, Bordetella pertussis. Despite widespread vaccination, pertussis resurgence has been observed globally. The development of the current acellular vaccine (ACV) has been based on planktonic studies. However, recent studies have shown that B. pertussis readily forms biofilms. A better understanding of B. pertussis biofilms is important for developing novel vaccines that can target all aspects of B. pertussis infection. This study compared the proteomic expression of biofilm and planktonic B. pertussis cells to identify key changes between the conditions. Major differences were identified in virulence factors including an upregulation of toxins (adenylate cyclase toxin and dermonecrotic toxin) and downregulation of pertactin and type III secretion system proteins in biofilm cells. To further dissect metabolic pathways that are altered during the biofilm lifestyle, the proteomic data was then incorporated into a genome scale metabolic model using the Integrative Metabolic Analysis Tool (iMAT). The generated models predicted that planktonic cells utilised the glyoxylate shunt while biofilm cells completed the full tricarboxylic acid cycle. Differences in processing aspartate, arginine and alanine were identified as well as unique export of valine out of biofilm cells which may have a role in inter-bacterial communication and regulation. Finally, increased polyhydroxybutyrate accumulation and superoxide dismutase activity in biofilm cells may contribute to increased persistence during infection. Taken together, this study modeled major proteomic and metabolic changes that occur in biofilm cells which helps lay the groundwork for further understanding B. pertussis pathogenesis.
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Affiliation(s)
- Hiroki Suyama
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Xu Z, Hu D, Luu LDW, Octavia S, Keil AD, Sintchenko V, Tanaka MM, Mooi FR, Robson J, Lan R. Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis. Emerg Microbes Infect 2022; 11:1460-1473. [PMID: 35543519 PMCID: PMC9176669 DOI: 10.1080/22221751.2022.2077129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Whooping cough (pertussis) is a highly contagious respiratory disease caused by the bacterium Bordetella pertussis. Despite high vaccine coverage, pertussis has re-emerged in many countries including Australia and caused two large epidemics in Australia since 2007. Here, we undertook a genomic and phylogeographic study of 385 Australian B. pertussis isolates collected from 2008 to 2017. The Australian B. pertussis population was found to be composed of mostly ptxP3 strains carrying different fim3 alleles, with ptxP3-fim3A genotype expanding far more than ptxP3-fim3B. Within the former, there were six co-circulating epidemic lineages (EL1 to EL6). The multiple ELs emerged, expanded, and then declined at different time points over the two epidemics. In population genetics terms, both hard and soft selective sweeps through vaccine selection pressures have determined the population dynamics of Australian B. pertussis. Relative risk estimation suggests that once a new B. pertussis lineage emerged, it was more likely to spread locally within the first 1.5 years. However, after 1.5 years, any new lineage was likely to expand to a wider region. Phylogenetic analysis revealed the expansion of ptxP3 strains was also associated with replacement of the type III secretion system allele bscI1 with bscI3. bscI3 is associated with decreased T3SS secretion and may allow B. pertussis to reduce immune recognition. This study advanced our understanding of the epidemic population structure and spatial and temporal dynamics of B. pertussis in a highly immunized population.
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Affiliation(s)
- Zheng Xu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Dalong Hu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Anthony D Keil
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth Children's Hospital, Perth, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, NSW Health Pathology and Westmead Hospital, Sydney, Australia.,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Frits R Mooi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Jenny Robson
- Sullivan Nicolaides Pathology, Queensland, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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Blancá B, Hayes JA, Surmann K, Hugo V, Hentschker C, Lamberti Y, Völker U, Rodriguez ME. Bordetella pertussis outer membrane vesicles as virulence factor vehicles that influence bacterial interaction with macrophages. Pathog Dis 2022; 80:6655986. [PMID: 35927587 DOI: 10.1093/femspd/ftac031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 01/18/2023] Open
Abstract
Gram-negative pathogenic bacteria constitutively shed outer membrane vesicles (OMVs) which play a significant role in the host-pathogen interaction, eventually determining the outcome of the infection. We previously found that Bordetella pertussis, the etiological agent of whooping cough, survives the innate interaction with human macrophages remaining alive inside these immune cells. Adenylate cyclase (CyaA), one of the main toxins of this pathogen, was found involved in the modulation of the macrophage defense response, eventually promoting bacterial survival within the cells. We here investigated whether B. pertussis OMVs, loaded with most of the bacterial toxins and CyaA among them, modulate the macrophage response to the bacterial infection. We observed that the pre-incubation of macrophages with OMVs led to a decreased macrophage defense response to the encounter with the bacteria, in a CyaA dependent way. Our results suggest that CyaA delivered by B. pertussis OMVs dampens macrophages protective function by decreasing phagocytosis and the bactericidal capability of these host cells. By increasing the chances of bacterial survival to the innate encounter with the macrophages, B. pertussis OMVs might play a relevant role in the course of infection, promoting bacterial persistence within the host and eventually, shaping the whole infection process.
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Affiliation(s)
- Bruno Blancá
- CINDEFI (UNLP CONICET La Plata), School of Sciences, La Plata National University, La Plata, Argentina
| | - Jimena Alvarez Hayes
- CINDEFI (UNLP CONICET La Plata), School of Sciences, La Plata National University, La Plata, Argentina
| | - Kristin Surmann
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Valdez Hugo
- CINDEFI (UNLP CONICET La Plata), School of Sciences, La Plata National University, La Plata, Argentina
| | - Christian Hentschker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Yanina Lamberti
- CINDEFI (UNLP CONICET La Plata), School of Sciences, La Plata National University, La Plata, Argentina
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - María Eugenia Rodriguez
- CINDEFI (UNLP CONICET La Plata), School of Sciences, La Plata National University, La Plata, Argentina
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Comparative proteomic analysis of Leptospira interrogans serogroup Icterohaemorrhagiae human vaccine strain and epidemic isolate from China. Arch Microbiol 2022; 204:460. [DOI: 10.1007/s00203-022-02987-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 11/02/2022]
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Modulation of Inflammatory Signaling Molecules in Bordetella pertussis Antigen-Challenged Human Monocytes in Presence of Adrenergic Agonists. Vaccines (Basel) 2022; 10:vaccines10020321. [PMID: 35214778 PMCID: PMC8879854 DOI: 10.3390/vaccines10020321] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 11/20/2022] Open
Abstract
BscF is a type III secretion system (T3SS) needle protein from Bordetella pertussis and has previously been shown to induce a sufficient Th1 and Th17 response in human monocytes and mice as a prerequisite for long-lasting protective immunity against pertussis infection. In our current study, we aim to compare the modulation of inflammatory signaling molecules as a direct measure of the immune response to the B. pertussis antigens BscF and Tdap in the presence or absence of the adrenergic receptor agonists phenylephrine (PE) or isoproterenol (ISO) to observe differences that may contribute to the diminished protective immunity of the current acellular pertussis (aP) vaccine, Tdap. Stimulation of human monocyte THP-1 cells with LPS, BscF, and Tdap induced a robust elevation of CCL20, CXCL10, PGE2, and PGF2α among most chemokine and prostanoid members when compared with the control treatment. Treatment with the adrenergic agonist PE or ISO significantly enhanced the BscF- and Tdap-stimulated modulation of CCL20 and CXCL10 but not PGE2 and PGF2α, suggesting that adrenergic modulation of pertussis antigen responses might be a new therapeutic strategy to improve the longevity of pertussis immunity. Stimulation of THP-1 cells with BscF alone initiated significant expression of CXCL10 and PGF2α but not when Tdap was used, suggesting that BscF might be an important pertussis antigen for next-generation pertussis vaccines or when combined with the current aP vaccine. Our data offer opportunities for designing new therapeutic approaches against pertussis infection.
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8
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Luu LDW, Zhong L, Kaur S, Raftery MJ, Lan R. Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence. Front Cell Infect Microbiol 2021; 11:660280. [PMID: 33928046 PMCID: PMC8076611 DOI: 10.3389/fcimb.2021.660280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/17/2021] [Indexed: 11/13/2022] Open
Abstract
The Bordetella genus is divided into two groups: classical and non-classical. Bordetella pertussis, Bordetella bronchiseptica and Bordetella parapertussis are known as classical bordetellae, a group of important human pathogens causing whooping cough or whooping cough-like disease and hypothesized to have evolved from environmental non-classical bordetellae. Bordetella infections have increased globally driving the need to better understand these pathogens for the development of new treatments and vaccines. One unexplored component in Bordetella is the role of serine, threonine and tyrosine phosphorylation. Therefore, this study characterized the phosphoproteome of classical bordetellae and examined its potential role in Bordetella biology and virulence. Applying strict identification of localization criteria, this study identified 70 unique phosphorylated proteins in the classical bordetellae group with a high degree of conservation. Phosphorylation was a key regulator of Bordetella metabolism with proteins involved in gluconeogenesis, TCA cycle, amino acid and nucleotide synthesis significantly enriched. Three key virulence pathways were also phosphorylated including type III secretion system, alcaligin synthesis and the BvgAS master transcriptional regulatory system for virulence genes in Bordetella. Seven new phosphosites were identified in BvgA with 6 located in the DNA binding domain. Of the 7, 4 were not present in non-classical bordetellae. This suggests that serine/threonine phosphorylation may play an important role in stabilizing/destabilizing BvgA binding to DNA for fine-tuning of virulence gene expression and that BvgA phosphorylation may be an important factor separating classical from non-classical bordetellae. This study provides the first insight into the phosphoproteome of classical Bordetella species and the role that Ser/Thr/Tyr phosphorylation may play in Bordetella biology and virulence.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Shropshire H, Jones RA, Aguilo-Ferretjans MM, Scanlan DJ, Chen Y. Proteomics insights into the Burkholderia cenocepacia phosphorus stress response. Environ Microbiol 2021; 23:5069-5086. [PMID: 33684254 DOI: 10.1111/1462-2920.15451] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/02/2021] [Indexed: 11/26/2022]
Abstract
The Burkholderia cepacia complex is a group of Burkholderia species that are opportunistic pathogens causing high mortality rates in patients with cystic fibrosis. An environmental stress often encountered by these soil-dwelling and pathogenic bacteria is phosphorus limitation, an essential element for cellular processes. Here, we describe cellular and extracellular proteins differentially regulated between phosphate-deplete (0 mM, no added phosphate) and phosphate-replete (1 mM) growth conditions using a comparative proteomics (LC-MS/MS) approach. We observed a total of 128 and 65 unique proteins were downregulated and upregulated respectively, in the B. cenocepacia proteome. Of those downregulated proteins, many have functions in amino acid transport/metabolism. We have identified 24 upregulated proteins that are directly/indirectly involved in inorganic phosphate or organic phosphorus acquisition. Also, proteins involved in virulence and antimicrobial resistance were differentially regulated, suggesting B. cenocepacia experiences a dramatic shift in metabolism under these stress conditions. Overall, this study provides a baseline for further research into the biology of Burkholderia in response to phosphorus stress.
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Affiliation(s)
- Holly Shropshire
- BBSRC Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry, CV4 7AL, UK.,School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Rebekah A Jones
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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10
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Xie L, Zhao Y, Duan J, Fan S, Shu L, Liu H, Wang Y, Xu Y, Li Y. Integrated Proteomics and Metabolomics Reveal the Mechanism of Nephrotoxicity Induced by Triptolide. Chem Res Toxicol 2020; 33:1897-1906. [PMID: 32519852 DOI: 10.1021/acs.chemrestox.0c00091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Triptolide (TP), the main active ingredient of Tripterygium wilfordii Hook F., has great potential in the treatment of autoimmune diseases. However, it has been found that the side effects of TP involve multiple organs and systems, of which the most serious side effects relate to the kidney. The mechanism of nephrotoxicity caused by TP requires further investigation. In the present study, we integrated proteomic and metabolomic methods to identify proteins and small molecule metabolites associated with TP-induced nephrotoxicity. There was a significant difference (p value <0.05) in the expression changes of 357 proteins for quantitative proteomics. In addition, high resolution metabolomic data showed significant changes in the levels of 9 metabolites, including hypoxanthine, PC(22:0/18:4), sphingosine, phenylalanine, etc. Finally, based on the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database for network analysis, it was determined that the 7 differentially expressed proteins were highly correlated with these 9 metabolites. Enrichment analysis revealed that the metabolic pathways involved purine and pyrimidine metabolism, glycerol and phospholipid metabolism, sphingolipid metabolism, and amino acid metabolism. The key target proteins were verified by Western blot technology, and the mechanism of TP-induced nephrotoxicity was further elucidated to provide a basis for safe and rational application.
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Affiliation(s)
- Lijuan Xie
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Yiwei Zhao
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Jingyi Duan
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Simiao Fan
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Lexin Shu
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Hui Liu
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Yuming Wang
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Yanyan Xu
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
| | - Yubo Li
- Tianjin University of Traditional Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin 301600, China
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Safarchi A, Octavia S, Nikbin VS, Lotfi MN, Zahraei SM, Tay CY, Lamichhane B, Shahcheraghi F, Lan R. Genomic epidemiology of Iranian Bordetella pertussis: 50 years after the implementation of whole cell vaccine. Emerg Microbes Infect 2020; 8:1416-1427. [PMID: 31543006 PMCID: PMC6764348 DOI: 10.1080/22221751.2019.1665479] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Pertussis caused by Bordetella pertussis, remains a public health problem worldwide, despite high vaccine coverage in infants and children in many countries. Iran has been using whole cell vaccine for the last 50 years with more than 95% vaccination rate since 1988 and has experienced pertussis resurgence in recent years. Here, we sequenced 55 B. pertussis isolates mostly collected from three provinces with the highest number of pertussis cases in Iran, including Tehran, Mazandaran, and Eastern-Azarbayjan from the period of 2008-2016. Most isolates carried ptxP3/prn2 alleles (42/55, 76%), the same genotype as isolates circulating in acellular vaccine-administrating countries. The second most frequent genotype was ptxP3/prn9 (8/55, 14%). Only three isolates (5%) were ptxP1. Phylogenetic analysis showed that Iranian ptxP3 isolates can be divided into eight clades (Clades 1-8) with no temporal association. Most of the isolates from Tehran grouped together as one distinctive clade (Clade 8) with six unique single nucleotide polymorphisms (SNPs). In addition, the prn9 isolates were grouped together as Clade 5 with 12 clade-supporting SNPs. No pertactin deficient isolates were found among the 55 Iranian isolates. Our findings suggest that there is an ongoing adaptation and evolution of B. pertussis regardless of the types of vaccine used.
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Affiliation(s)
- Azadeh Safarchi
- Pertussis Reference Laboratory, Department of Bacteriology, Pasteur Institute of Iran , Tehran , Islamic Republic of Iran.,School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney , Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney , Australia
| | - Vajihe Sadat Nikbin
- Pertussis Reference Laboratory, Department of Bacteriology, Pasteur Institute of Iran , Tehran , Islamic Republic of Iran
| | - Masoumeh Nakhost Lotfi
- Pertussis Reference Laboratory, Department of Bacteriology, Pasteur Institute of Iran , Tehran , Islamic Republic of Iran
| | - Seyed Mohsen Zahraei
- Centre for Communicable Disease Control, Ministry of Health and Medical Education , Tehran , Islamic Republic of Iran
| | - Chin Yen Tay
- Pathology and Laboratory Medicine, University of Western Australia , Perth , Australia
| | - Binit Lamichhane
- Pathology and Laboratory Medicine, University of Western Australia , Perth , Australia
| | - Fereshteh Shahcheraghi
- Pertussis Reference Laboratory, Department of Bacteriology, Pasteur Institute of Iran , Tehran , Islamic Republic of Iran
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney , Australia
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12
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Lin H, Tang D, Xu Y, Zhang R, Ou M, Zheng F, Chen J, Zhang Y, Zou G, Xue W, Zou Y, Dai W, Sui W, Dai Y. Quantitative analysis of protein crotonylation identifies its association with immunoglobulin A nephropathy. Mol Med Rep 2020; 21:1242-1250. [PMID: 32016442 PMCID: PMC7002971 DOI: 10.3892/mmr.2020.10931] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 11/19/2019] [Indexed: 01/31/2023] Open
Abstract
Posttranslational modifications (PTMs) to histones such as lysine crotonylation are classified as epigenetic changes. Lysine crotonylation participates in various cellular processes and occurs in active promoters, directly accelerating transcription. The present study performed a proteomics analysis of crotonylation between healthy controls and patients with immunoglobulin A (IgA) nephropathy using tandem mass spectrometry and high-resolution liquid chromatography. The present results identified 353 crotonylated proteins and 770 modification sites, including 155 upregulated and 198 downregulated crotonylated proteins. In total, seven conserved motifs were identified in the present study. The present bioinformatics analysis results suggested a number of the crotonylated proteins exhibited various subcellular localization patterns, such as in the cytoplasm. Protein domains, including thioredoxin, moesin tail and myosin like IQ motif domains were markedly enriched in crotonylated proteins. Kyoto Encyclopedia of Genes and Genomes and functional enrichment analyses suggested significant enrichment of crotonylated proteins in complement and coagulation cascades, and antigen processing and presentation pathways displaying important relationships with IgA nephropathy. The present results suggested that crotonylation occurred in numerous proteins and may play key regulatory roles in IgA nephropathy.
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Affiliation(s)
- Hua Lin
- Nephrology Department of 924th Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Donge Tang
- Clinical Medical Research Center of The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Yong Xu
- Clinical Medical Research Center of The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Ruohan Zhang
- Nephrology Department of 924th Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Minglin Ou
- Nephrology Department of 924th Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Fengping Zheng
- Clinical Medical Research Center of The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Jiejing Chen
- Nephrology Department of 924th Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Yue Zhang
- Nephrology Department of 924th Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Guimian Zou
- Nephrology Department of 924th Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Wen Xue
- Nephrology Department of 924th Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Yaoshuang Zou
- Nephrology Department of 924th Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX 78712, USA
| | - Weiguo Sui
- Nephrology Department of 924th Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Yong Dai
- Nephrology Department of 924th Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Diseases Research, Guilin, Guangxi 541002, P.R. China
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Luu LDW, Octavia S, Aitken C, Zhong L, Raftery MJ, Sintchenko V, Lan R. Surfaceome analysis of Australian epidemic Bordetella pertussis reveals potential vaccine antigens. Vaccine 2019; 38:539-548. [PMID: 31703933 DOI: 10.1016/j.vaccine.2019.10.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/22/2022]
Abstract
Since acellular vaccines (ACV) were introduced in Australia, epidemic Bordetella pertussis strains changed from single nucleotide polymorphism (SNP) cluster II to SNP cluster I. Our previous proteomic analysis identified potential proteomic adaptations in the whole cell and secretome of SNP cluster I. Additionally, current ACVs were shown to be less efficacious against cluster I in mice models and there is a pressing need to discover new antigens to improve the ACV. One important source of novel antigens is the surfaceome. Therefore, in this study we established surface shaving in B. pertussis to compare the surfaceome of SNP cluster I (L1423) and II (L1191), and identify novel surface antigens for vaccine development. Surface shaving using 1 μg of trypsin for 5 min identified 126 proteins with the most abundant being virulence-associated and known outer membrane proteins. Cell viability counts showed minimal lysis from shaving. The proportion of immunogenic proteins was higher in the surfaceome than in the whole cell and secretome. Key differences in the surfaceome were identified between SNP cluster I and II, consistent with those identified in the whole cell proteome and secretome. These differences include unique transport proteins and decreased immunogenic proteins in L1423, and provides further evidence of proteomic adaptation in SNP cluster I. Finally, a comparison of proteins in each sub-proteome identified 22 common proteins. These included 11 virulence proteins (Prn, PtxA, FhaB, CyaA, TcfA, SphB1, Vag8, BrkA, BopD, Bsp22 and BipA) and 11 housekeeping proteins (TuF, CtpA, TsF, OmpH, GltA, SucC, SucD, FusA, GroEL, BP3330 and BP3561) which were immunogenic, essential and consistently expressed thus demonstrating their potential as future targets. This study established surface shaving in B. pertussis, confirmed key expression differences and identified unknown surface proteins which may be potential vaccine antigens.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Chelsea Aitken
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - Pathology West, Westmead Hospital, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Luu LDW, Octavia S, Zhong L, Raftery MJ, Sintchenko V, Lan R. Comparison of the Whole Cell Proteome and Secretome of Epidemic Bordetella pertussis Strains From the 2008-2012 Australian Epidemic Under Sulfate-Modulating Conditions. Front Microbiol 2018; 9:2851. [PMID: 30538686 PMCID: PMC6277516 DOI: 10.3389/fmicb.2018.02851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 11/06/2018] [Indexed: 01/19/2023] Open
Abstract
Sulfate is an important modulator for virulence factor expression in Bordetella pertussis, the causative organism for whooping cough. During infection, sulfate is released when respiratory epithelial cells are damaged which can affect gene expression. The current predominant strains in Australia are found in single nucleotide polymorphism (SNP) cluster I (ptxP3/prn2). It has been reported that ptxP3 strains have higher mRNA expression of virulence genes than ptxP1 strains under intermediate sulfate-modulating conditions (5 mM MgSO4). Our previous proteomic study compared L1423 (cluster I, ptxP3) and L1191 (cluster II, ptxP1) in Thalen-IJssel (THIJS) media without sulfate modulation and identified an upregulation of transport proteins and a downregulation of immunogenic proteins. To determine whether proteomic differences exist between cluster I and cluster II strains in intermediate modulating conditions, this study compared the whole cell proteome and secretome between L1423 and L1191 grown in THIJS media with 5 mM MgSO4 using iTRAQ and high-resolution multiple reaction monitoring (MRM-hr). Two proteins (BP0200 and BP1175) in the whole cell were upregulated in L1423 [fold change (FC) >1.2, false discovery rate (FDR) <0.05]. In the secretome, four proteins from the type III secretion system (T3SS) effectors were downregulated (FC < 0.8, FDR < 0.05) while six proteins, including two adhesins, pertactin (Prn) and tracheal colonization factor A (TcfA), were upregulated which were consistent with our previous proteomic study. The upregulation of Prn and TcfA in SNP cluster I may result in improved adhesion while the downregulation of the T3SS and other immunogenic proteins may reduce immune recognition, which may contribute to the increased fitness of cluster I B. pertussis strains.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Westmead Hospital, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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15
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Keidel K, Amman F, Bibova I, Drzmisek J, Benes V, Hot D, Vecerek B. Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis. RNA (NEW YORK, N.Y.) 2018; 24:1530-1541. [PMID: 30097543 PMCID: PMC6191719 DOI: 10.1261/rna.067306.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/01/2018] [Indexed: 06/08/2023]
Abstract
Bordetella pertussis is the causative agent of human whooping cough, a highly contagious respiratory disease which despite vaccination programs remains the major cause of infant morbidity and mortality. The requirement of the RNA chaperone Hfq for virulence of B. pertussis suggested that Hfq-dependent small regulatory RNAs are involved in the modulation of gene expression. High-throughput RNA sequencing revealed hundreds of putative noncoding RNAs including the RgtA sRNA. Abundance of RgtA is strongly decreased in the absence of the Hfq protein and its expression is modulated by the activities of the two-component regulatory system BvgAS and another response regulator RisA. Whereas RgtA levels were elevated under modulatory conditions or in the absence of bvg genes, deletion of the risA gene completely abolished RgtA expression. Profiling of the ΔrgtA mutant in the ΔbvgA genetic background identified the BP3831 gene encoding a periplasmic amino acid-binding protein of an ABC transporter as a possible target gene. The results of site-directed mutagenesis and in silico analysis indicate that RgtA base-pairs with the region upstream of the start codon of the BP3831 mRNA and thereby weakens the BP3831 protein production. Furthermore, our data suggest that the function of the BP3831 protein is related to transport of glutamate, an important metabolite in the B. pertussis physiology. We propose that the BvgAS/RisA interplay regulates the expression of RgtA which upon infection, when glutamate might be scarce, attenuates translation of the glutamate transporter and thereby assists in adaptation of the pathogen to other sources of energy.
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Affiliation(s)
- Kristina Keidel
- Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic
| | - Fabian Amman
- Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria
- Department of Chromosome Biology of the University of Vienna, A-1030 Vienna, Austria
| | - Ilona Bibova
- Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic
| | - Jakub Drzmisek
- Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - David Hot
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Branislav Vecerek
- Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic
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