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Yang Y, Xu S, He H, Zhu X, Liu Y, Ai X, Chen Y. Mechanism of sturgeon intestinal inflammation induced by Yersinia ruckeri and the effect of florfenicol intervention. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116138. [PMID: 38394759 DOI: 10.1016/j.ecoenv.2024.116138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024]
Abstract
The mechanism by which Y. ruckeri infection induces enteritis in Chinese sturgeon remains unclear, and the efficacy of drug prevention and control measures is not only poor but also plagued with numerous issues. We conducted transcriptomic and 16 S rRNA sequencing analyses to examine the differences in the intestinal tract of hybrid sturgeon before and after Y. ruckeri infection and florfenicol intervention. Our findings revealed that Y. ruckeri induced the expression of multiple inflammatory factors, including il1β, il6, and various chemokines, as well as casp3, casp8, and multiple tumor necrosis factor family members, resulting in pathological injury to the body. Additionally, at the phylum level, the relative abundance of Firmicutes and Bacteroidota increased, while the abundance of Plesiomonas and Cetobacterium decreased at the genus level, altering the composition of the intestinal flora. Following florfenicol intervention, the expression of multiple apoptosis and inflammation-related genes was down-regulated, promoting tissue repair. However, the flora became further dysregulated, increasing the risk of infection. In conclusion, our analysis of the transcriptome and intestinal microbial composition demonstrated that Y. ruckeri induces intestinal pathological damage by triggering apoptosis and altering the composition of the intestinal microbiota. Florfenicol intervention can repair pathological damage, but it also exacerbates flora imbalance, leading to a higher risk of infection. These findings help elucidate the molecular mechanism of Y. ruckeri-induced enteritis in sturgeon and evaluate the therapeutic effect of drugs on intestinal inflammation in sturgeon.
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Affiliation(s)
- Yibin Yang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou Qiandao Lake Sturgeon Technology Co., Ltd., Hangzhou 311799, China
| | - Shijian Xu
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou Qiandao Lake Sturgeon Technology Co., Ltd., Hangzhou 311799, China.
| | - Hao He
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Xia Zhu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yongtao Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Xiaohui Ai
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Yuhua Chen
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
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Descoeudres N, Jouneau L, Henry C, Gorrichon K, Derré-Bobillot A, Serror P, Gillespie LL, Archambaud C, Pagliuso A, Bierne H. An Immunomodulatory Transcriptional Signature Associated With Persistent Listeria Infection in Hepatocytes. Front Cell Infect Microbiol 2021; 11:761945. [PMID: 34858876 PMCID: PMC8631403 DOI: 10.3389/fcimb.2021.761945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Listeria monocytogenes causes severe foodborne illness in pregnant women and immunocompromised individuals. After the intestinal phase of infection, the liver plays a central role in the clearance of this pathogen through its important functions in immunity. However, recent evidence suggests that during long-term infection of hepatocytes, a subpopulation of Listeria may escape eradication by entering a persistence phase in intracellular vacuoles. Here, we examine whether this long-term infection alters hepatocyte defense pathways, which may be instrumental for bacterial persistence. We first optimized cell models of persistent infection in human hepatocyte cell lines HepG2 and Huh7 and primary mouse hepatocytes (PMH). In these cells, Listeria efficiently entered the persistence phase after three days of infection, while inducing a potent interferon response, of type I in PMH and type III in HepG2, while Huh7 remained unresponsive. RNA-sequencing analysis identified a common signature of long-term Listeria infection characterized by the overexpression of a set of genes involved in antiviral immunity and the under-expression of many acute phase protein (APP) genes, particularly involved in the complement and coagulation systems. Infection also altered the expression of cholesterol metabolism-associated genes in HepG2 and Huh7 cells. The decrease in APP transcripts was correlated with lower protein abundance in the secretome of infected cells, as shown by proteomics, and also occurred in the presence of APP inducers (IL-6 or IL-1β). Collectively, these results reveal that long-term infection with Listeria profoundly deregulates the innate immune functions of hepatocytes, which could generate an environment favorable to the establishment of persistent infection.
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Affiliation(s)
- Natalie Descoeudres
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Céline Henry
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Kevin Gorrichon
- Université Paris-Saclay, Institut de Biologie Intégrative de la Cellule, CEA, CNRS UMR 9198, Université Paris-Sud, Gif-sur-Yvette, France
| | | | - Pascale Serror
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Laura Lee Gillespie
- Terry Fox Cancer Research Laboratories, Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Cristel Archambaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Alessandro Pagliuso
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Hélène Bierne
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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Fuchs S, Kucklick M, Lehmann E, Beckmann A, Wilkens M, Kolte B, Mustafayeva A, Ludwig T, Diwo M, Wissing J, Jänsch L, Ahrens CH, Ignatova Z, Engelmann S. Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach. PLoS Genet 2021; 17:e1009585. [PMID: 34061833 PMCID: PMC8195425 DOI: 10.1371/journal.pgen.1009585] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 06/11/2021] [Accepted: 05/07/2021] [Indexed: 01/08/2023] Open
Abstract
Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results. We used the workflow to identify high quality peptide spectrum matches (PSMs) for small proteins (≤ 100 aa, SP100) in Staphylococcus aureus Newman. Protein extracts from S. aureus were subjected to different experimental workflows for protein digestion and prefractionation and measured with highly sensitive mass spectrometers. In total, 175 proteins with up to 100 aa (SP100) were identified. Out of these 24 (ranging from 9 to 99 aa) were novel and not contained in the used genome annotation.144 SP100 are highly conserved and were found in at least 50% of the publicly available S. aureus genomes, while 127 are additionally conserved in other staphylococci. Almost half of the identified SP100 were basic, suggesting a role in binding to more acidic molecules such as nucleic acids or phospholipids.
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Affiliation(s)
- Stephan Fuchs
- Robert Koch Institute, Methodenentwicklung und Forschungsinfrastruktur (MF), Berlin, Germany
| | - Martin Kucklick
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Erik Lehmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Alexander Beckmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Maya Wilkens
- Robert Koch Institute, Methodenentwicklung und Forschungsinfrastruktur (MF), Berlin, Germany
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Baban Kolte
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Ayten Mustafayeva
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Tobias Ludwig
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Maurice Diwo
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Josef Wissing
- Helmholtz Center for Infection Research GmbH, Cellular Proteomics, Braunschweig, Germany
| | - Lothar Jänsch
- Helmholtz Center for Infection Research GmbH, Cellular Proteomics, Braunschweig, Germany
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Zoya Ignatova
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Susanne Engelmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
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Shao Y, Yin X, Kang D, Shen B, Zhu Z, Li X, Li H, Xie L, Wang G, Liang Y. An integrated strategy for the quantitative analysis of endogenous proteins: A case of gender-dependent expression of P450 enzymes in rat liver microsome. Talanta 2017; 170:514-522. [DOI: 10.1016/j.talanta.2017.04.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/14/2017] [Accepted: 04/21/2017] [Indexed: 12/17/2022]
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