1
|
Wang LX, Ji CH, Ning CC, Liu YC, Li ZY, Sun YQ, Xia XZ, Cai XP, Meng QL, Qiao J. A Regulatory sRNA rli41 is Implicated in Cell Adhesion, Invasion and Pathogenicity in Listeria monocytogenes. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
|
2
|
Studies on host-foodborne bacteria in intestinal three-dimensional cell culture model indicate possible mechanisms of interaction. World J Microbiol Biotechnol 2021; 37:31. [PMID: 33458785 DOI: 10.1007/s11274-021-02996-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/05/2021] [Indexed: 01/09/2023]
Abstract
Spheroids of intestinal cells (Caco-2) were used to evaluate the adhesion/invasion ability of Listeria monocytogenes (pathogen) and Lactobacillus sakei 1 (potential probiotic). Besides, transcriptomic analyses of Caco-2 cells in three dimensional cultures were done, with the aim of revealing possible host-foodborne bacteria interactions. Result of adhesion assay for L. monocytogenes in Caco-2 spheroids was 22.86 ± 0.33%, but it was stimulated in acidic pH (4.5) and by the presence of 2% sucrose (respectively, 32.56 ± 1.35% and 33.25 ± 1.26%). Conversely, the invasion rate of L. monocytogenes was lower at pH 4.5, in comparison with non-stressed controls (18.89 ± 1.05% and 58.65 ± 0.30%, respectively). L. sakei 1 adhered to Caco-2 tridimensional cell culture (27.30 ± 2.64%), with no invasiveness. There were 19 and 21 genes down and upregulated, respectively, in tridimensional Caco-2 cells, upon infection with L. monocytogenes, which involved immunity, apoptosis; cytoprotective responses, cell signalling-regulatory pathways. It was evidenced despite activation or deactivation of several pathways in intestinal cells to counteract infection, the pathogen was able to hijack many host defense mechanisms. On the other hand, the probiotic candidate L. sakei 1 was correlated with decreased transcription of two genes in Caco-2 cells, though it stimulated the expression of 14 others, with diverse roles in immunity, apoptosis, cytoprotective response and cell signalling-regulatory pathways. Our data suggest the use of tridimensional cell culture to mimic the intestinal epithelium is a good model for gathering broad information on the putative mechanisms of interaction between host and bacteria of importance for food safety, which can serve as a basis for further in-depth investigation.
Collapse
|
3
|
Li M, Chen WD, Wang YD. The roles of the gut microbiota-miRNA interaction in the host pathophysiology. Mol Med 2020; 26:101. [PMID: 33160314 PMCID: PMC7648389 DOI: 10.1186/s10020-020-00234-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/26/2020] [Indexed: 12/20/2022] Open
Abstract
The gut microbiota regulates the biological processes of organisms acting like ‘another’ genome, affecting the health and disease of the host. MicroRNAs, as important physiological regulators, have been found to be involved in health and disease. Recently, the gut microbiota has been reported to affect host health by regulating host miRNAs. For example, Fusobacterium nucleatum could aggravate chemoresistance of colorectal cancer by decreasing the expression of miR-18a* and miR-4802. What’s more, miRNAs can shape the gut microbiota composition, ultimately affecting the host's physiology and disease. miR-515-5p and miR-1226-5p could promote the growth of Fusobacterium nucleatum (Fn) and Escherichia coli (E.coli), which have been reported to drive colorectal cancer. Here, we will review current findings of the interactions between the gut microbiota and microRNAs and discuss how the gut microbiota–microRNA interactions affect host pathophysiology including intestinal, neurological, cardiovascular, and immune health and diseases.
Collapse
Affiliation(s)
- Meihong Li
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Wei-Dong Chen
- Key Laboratory of Molecular Pathology, School of Basic Medical Science, Inner Mongolia Medical University, Hohhot, Inner Mongolia, People's Republic of China. .,Key Laboratory of Receptors-Mediated Gene Regulation and Drug Discovery, The People's Hospital of Hebi, School of Medicine, Henan University, Henan, People's Republic of China.
| | - Yan-Dong Wang
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People's Republic of China.
| |
Collapse
|
4
|
Behrouzi A, Mazaheri H, Falsafi S, Tavassol ZH, Moshiri A, Siadat SD. Intestinal effect of the probiotic Escherichia coli strain Nissle 1917 and its OMV. J Diabetes Metab Disord 2020; 19:597-604. [PMID: 32550212 DOI: 10.1007/s40200-020-00511-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 02/26/2020] [Indexed: 12/15/2022]
Abstract
Several investigations have been conducted during the past years to examine the correlation between dysbiosis and both intestinal and extra-intestinal diseases such as inflammatory bowel disease (IBD) and ulcerative colitis (UC). E. coli Nissle 1917 (EcN) is a nonpathogenic gram-negative strain utilized in numerous gastrointestinal issues, consisting of diarrhea, uncomplicated diverticular malady, IBD and specifically UC. Many investigations have been done to examine the capability of assertive bacteria, inclusive of commensal and probiotic strains to enhance IBD in clinical testing. Bacterial secreted factors have been investigated to detect the EcN agents that facilitate the regulation of tight junction. These agents candiffuse smoothly through the mucin layer before reaching intestinal epithelial cells. Outer membrane vesicles (OMVs) are known as intercellular communicasomes as they facilitate the distal transfer of active compounds between cells. A few investigations have detailed immune-modulatory attributes for EcN through various systems that could be liable for its clinical viability in IBD. Today, the function of gut microbiota extracellular vesicles in health and disease has become a focus of attention as they serve as vehicles for the transmission of microorganisms to distal tissues of many bacterial effectors.
Collapse
Affiliation(s)
- Ava Behrouzi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Hoora Mazaheri
- Department of Molecular Biology, Pasteur Institute of Iran , Tehran, Iran
| | - Sarvenaz Falsafi
- Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Science, Islamic Azad University, Tehran, Iran
| | - Zahra Hoseini Tavassol
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Arfa Moshiri
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
5
|
Abstract
Bacteria participate in a wide diversity of symbiotic associations with eukaryotic hosts that require precise interactions for bacterial recognition and persistence. Most commonly, host-associated bacteria interfere with host gene expression to modulate the immune response to the infection. However, many of these bacteria also interfere with host cellular differentiation pathways to create a hospitable niche, resulting in the formation of novel cell types, tissues, and organs. In both of these situations, bacterial symbionts must interact with eukaryotic regulatory pathways. Here, we detail what is known about how bacterial symbionts, from pathogens to mutualists, control host cellular differentiation across the central dogma, from epigenetic chromatin modifications, to transcription and mRNA processing, to translation and protein modifications. We identify four main trends from this survey. First, mechanisms for controlling host gene expression appear to evolve from symbionts co-opting cross-talk between host signaling pathways. Second, symbiont regulatory capacity is constrained by the processes that drive reductive genome evolution in host-associated bacteria. Third, the regulatory mechanisms symbionts exhibit correlate with the cost/benefit nature of the association. And, fourth, symbiont mechanisms for interacting with host genetic regulatory elements are not bound by native bacterial capabilities. Using this knowledge, we explore how the ubiquitous intracellular Wolbachia symbiont of arthropods and nematodes may modulate host cellular differentiation to manipulate host reproduction. Our survey of the literature on how infection alters gene expression in Wolbachia and its hosts revealed that, despite their intermediate-sized genomes, different strains appear capable of a wide diversity of regulatory manipulations. Given this and Wolbachia's diversity of phenotypes and eukaryotic-like proteins, we expect that many symbiont-induced host differentiation mechanisms will be discovered in this system.
Collapse
Affiliation(s)
- Shelbi L Russell
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
| | | |
Collapse
|
6
|
Pang X, Jia Z, Lu J, Zhang S, Zhang C, Zhang M, Lv J. A new method for quantitative detection of Lactobacillus casei based on casx gene and its application. BMC Biotechnol 2019; 19:87. [PMID: 31823776 PMCID: PMC6902566 DOI: 10.1186/s12896-019-0587-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023] Open
Abstract
Background The traditional method of bacterial identification based on 16S rRNA is a widely used and very effective detection method, but this method still has some deficiencies, especially in the identification of closely related strains. A high homology with little differences is mostly observed in the 16S sequence of closely related bacteria, which results in difficulty to distinguish them by 16S rRNA-based detection method. In order to develop a rapid and accurate method of bacterial identification, we studied the possibility of identifying bacteria with other characteristic fragments without the use of 16S rRNA as detection targets. Results We analyzed the potential of using cas (CRISPR-associated proteins) gene as a target for bacteria detection. We found that certain fragment located in the casx gene was species-specific and could be used as a specific target gene. Based on these fragments, we established a TaqMan MGB Real-time PCR method for detecting bacteria. We found that the method used in this study had the advantages of high sensitivity and good specificity. Conclusions The casx gene-based method of bacterial identification could be used as a supplement to the conventional 16 s rRNA-based detection method. This method has an advantage over the 16 s rRNA-based detection method in distinguishing the genetic relationship between closely-related bacteria, such as subgroup bacteria, and can be used as a supplement to the 16 s rRNA-based detection method.
Collapse
Affiliation(s)
- Xiaoyang Pang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing, 100048, China.,Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Ziyang Jia
- Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Jing Lu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Shuwen Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Cai Zhang
- Laboratory of Environment and Livestock Products, Henan University of Science and Technology, Luoyang, 471023, China
| | - Min Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing, 100048, China.
| | - Jiaping Lv
- Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing, 100193, China.
| |
Collapse
|
7
|
Hu Y, Zhang L, Wang X, Sun F, Kong X, Dong H, Xu H. Two virulent sRNAs identified by genomic sequencing target the type III secretion system in rice bacterial blight pathogen. BMC PLANT BIOLOGY 2018; 18:237. [PMID: 30326834 PMCID: PMC6192180 DOI: 10.1186/s12870-018-1470-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 10/05/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Small non-coding RNA (sRNA) short sequences regulate various biological processes in all organisms, including bacteria that are animal or plant pathogens. Virulent or pathogenicity-associated sRNAs have been increasingly elucidated in animal pathogens but little is known about similar category of sRNAs in plant-pathogenic bacteria. This is particularly true regarding rice bacterial blight pathogen Xanthomonas oryzae pathovar oryzae (Xoo) as studies on the virulent role of Xoo sRNAs is very limited at present. RESULTS The number and genomic distribution of sRNAs in Xoo were determined by bioinformatics analysis based on high throughput sequencing (sRNA-Seq) of the bacterial cultures from virulence-inducing and standard growth media, respectively. A total of 601 sRNAs were identified in the Xoo genome and ten virulent sRNA candidates were screened out based on significant differences of their expression levels between the culture conditions. In addition, trans3287 and trans3288 were also selected as candidates due to high expression levels in both media. The differential expression of 12 sRNAs evidenced by the sRNA-Seq data was confirmed by a convincing quantitative method. Based on genetic analysis of Xoo ΔsRNA mutants generated by deletion of the 12 single sRNAs, trans217 and trans3287 were characterized as virulent sRNAs. They are essential not only for the formation of bacterial blight in a susceptible rice variety Nipponbare but also for the induction of hypersensitive response (HR) in nonhost plant tobacco. Xoo Δtrans217 and Δtrans3287 mutants fail to induce bacterial blight in Nipponbare and also fail to induce the HR in tobacco, whereas, genetic complementation restores both mutants to the wild type in the virulent performance and HR induction. Similar effects of gene knockout and complementation were found in the expression of hrpG and hrpX genes, which encode regulatory proteins of the type III secretion system. Consistently, secretion of a type III effector, PthXo1, is blocked in Δtrans217 or Δtrans3287 bacterial cultures but retrieved by genetic complementation to both mutants. CONCLUSIONS The genetic analysis characterizes trans217 and trans3287 as pathogenicity-associated sRNAs essential for the bacterial virulence on the susceptible rice variety and for the HR elicitation in the nonhost plant. The molecular evidence suggests that both virulent sRNAs regulate the bacterial virulence by targeting the type III secretion system.
Collapse
Affiliation(s)
- Yiqun Hu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province China
| | - Liyuan Zhang
- State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 Jiangsu Province China
| | - Xuan Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province China
| | - Fengli Sun
- State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 Jiangsu Province China
- Current Address: Rural Work Bureau of Zhangpu Town, Suzhou, 215300 Jiangsu Province China
| | - Xiangxin Kong
- State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 Jiangsu Province China
| | - Hansong Dong
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province China
| | - Heng Xu
- State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 Jiangsu Province China
| |
Collapse
|
8
|
Cheah HL, Raabe CA, Lee LP, Rozhdestvensky TS, Citartan M, Ahmed SA, Tang TH. Bacterial regulatory RNAs: complexity, function, and putative drug targeting. Crit Rev Biochem Mol Biol 2018; 53:335-355. [PMID: 29793351 DOI: 10.1080/10409238.2018.1473330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, RNA-deep sequencing has uncovered copious non-protein coding RNAs (npcRNAs) in bacteria. Many of them are key players in the regulation of gene expression, taking part in various regulatory circuits, such as metabolic responses to different environmental stresses, virulence, antibiotic resistance, and host-pathogen interactions. This has contributed to the high adaptability of bacteria to changing or even hostile environments. Their mechanisms include the regulation of transcriptional termination, modulation of translation, and alteration of messenger RNA (mRNA) stability, as well as protein sequestration. Here, the mechanisms of gene expression by regulatory bacterial npcRNAs are comprehensively reviewed and supplemented with well-characterized examples. This class of molecules and their mechanisms of action might be useful targets for the development of novel antibiotics.
Collapse
Affiliation(s)
- Hong-Leong Cheah
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Carsten A Raabe
- b Institute of Experimental Pathology, Centre for Molecular Biology of Inflammation , University of Münster , Münster , Germany.,c Brandenburg Medical School (MHB) , Neuruppin , Germany.,d Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation , University of Münster , Münster , Germany
| | - Li-Pin Lee
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Timofey S Rozhdestvensky
- e Medical Faculty, Transgenic Mouse and Genome Engineering Model Core Facility (TRAM) , University of Münster , Münster , Germany
| | - Marimuthu Citartan
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Siti Aminah Ahmed
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Thean-Hock Tang
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| |
Collapse
|
9
|
MicroRNA-146a Deficiency Protects against Listeria monocytogenes Infection by Modulating the Gut Microbiota. Int J Mol Sci 2018; 19:ijms19040993. [PMID: 29587465 PMCID: PMC5979314 DOI: 10.3390/ijms19040993] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/15/2018] [Accepted: 03/24/2018] [Indexed: 12/21/2022] Open
Abstract
The gut microbiota and microRNAs play important roles in the defense against infection. However, the role of miR-146a in L. monocytogenes infection and gut microbiota remains unclear. We tried to determine whether miR-146a controlled L. monocytogenes infection by regulating the gut microbiota. Wild-type and miR-146a-deficient mice or macrophages were used to characterize the impact of miR-146a on animal survival, cell death, bacterial clearance, and gut microbiota following L. monocytogenes challenge. We found that L. monocytogenes infection induced miR-146a expression both in vitro and in vivo. When compared to wild-type mice, miR-146a-deficient mice were more resistant to L. monocytogenes infection. MiR-146a deficiency in macrophages resulted in reduced invasion and intracellular survival of L. monocytogenes. High-throughput sequencing of 16S rRNA revealed that the gut microbiota composition differed between miR-146a-deficient and wild-type mice. Relative to wild-type mice, miR-146a-deficient mice had decreased levels of the Proteobacteria phylum, Prevotellaceae family, and Parasutterella genus, and significantly increased short-chain fatty acid producing bacteria, including the genera Alistipes, Blautia, Coprococcus_1, and Ruminococcus_1. Wild-type mice co-housed with miR-146a-deficient mice had increased resistance to L. monocytogenes, indicating that miR-146a deficiency guides the gut microbiota to alleviate infection. Together, these results suggest that miR-146a deficiency protects against L. monocytogenes infection by regulating the gut microbiota.
Collapse
|
10
|
Cerutti F, Mallet L, Painset A, Hoede C, Moisan A, Bécavin C, Duval M, Dussurget O, Cossart P, Gaspin C, Chiapello H. Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria. BMC Genomics 2017; 18:882. [PMID: 29145803 PMCID: PMC5689173 DOI: 10.1186/s12864-017-4242-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/29/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. RESULTS We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes. We applied this approach on 79 complete genomes of the Listeria genus and identified fifty-two accessory sRNAs, of which most were present in the Listeria common ancestor and lost during Listeria evolution. We detected significant coevolution between 23 sRNA and 52 coding genes and inferred the Listeria sRNA-coding genes coevolution network. We characterized a main hub of 12 sRNAs that coevolved with genes encoding cell wall proteins and virulence factors. Among them, an sRNA specific to L. monocytogenes species, rli133, coevolved with genes involved either in pathogenicity or in interaction with host cells, possibly acting as a direct negative post-transcriptional regulation. CONCLUSIONS Our approach allowed the identification of candidate sRNAs potentially involved in pathogenicity and host interaction, consistent with recent findings on known pathogenicity actors. We highlight four sRNAs coevolving with seven internalin genes, some of which being important virulence factors in Listeria.
Collapse
Affiliation(s)
- Franck Cerutti
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Ludovic Mallet
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Anaïs Painset
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France.,Present address: Public Health England, 61 Colindale Avenue, London, NW9 5EQ, England
| | - Claire Hoede
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Annick Moisan
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Christophe Bécavin
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France.,Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | - Mélodie Duval
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France
| | - Olivier Dussurget
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, F-75013, Paris, France
| | - Pascale Cossart
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France
| | - Christine Gaspin
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Hélène Chiapello
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France.
| |
Collapse
|
11
|
Tronnet S, Garcie C, Brachmann AO, Piel J, Oswald E, Martin P. High iron supply inhibits the synthesis of the genotoxin colibactin by pathogenic Escherichia coli through a non-canonical Fur/RyhB-mediated pathway. Pathog Dis 2017. [DOI: 10.1093/femspd/ftx066] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Sophie Tronnet
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31024 Toulouse, France
- Université Toulouse III Paul Sabatier, 31000 Toulouse, France
| | - Christophe Garcie
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31024 Toulouse, France
- Université Toulouse III Paul Sabatier, 31000 Toulouse, France
- CHU Toulouse, Service de Bactériologie-Hygiène, 31000 Toulouse, France
| | - Alexander O. Brachmann
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH), 8093 Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH), 8093 Zurich, Switzerland
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31024 Toulouse, France
- Université Toulouse III Paul Sabatier, 31000 Toulouse, France
- CHU Toulouse, Service de Bactériologie-Hygiène, 31000 Toulouse, France
| | - Patricia Martin
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31024 Toulouse, France
- Université Toulouse III Paul Sabatier, 31000 Toulouse, France
- CHU Toulouse, Service de Bactériologie-Hygiène, 31000 Toulouse, France
| |
Collapse
|
12
|
Rolhion N, Cossart P. How the study of Listeria monocytogenes has led to new concepts in biology. Future Microbiol 2017; 12:621-638. [PMID: 28604108 DOI: 10.2217/fmb-2016-0221] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The opportunistic intracellular bacterial pathogen Listeria monocytogenes has in 30 years emerged as an exceptional bacterial model system in infection biology. Research on this bacterium has provided considerable insight into how pathogenic bacteria adapt to mammalian hosts, invade eukaryotic cells, move intracellularly, interfere with host cell functions and disseminate within tissues. It also contributed to unveil features of normal host cell pathways and unsuspected functions of previously known cellular proteins. This review provides an updated overview of our knowledge on this pathogen. In many examples, findings on L. monocytogenes provided the basis for new concepts in bacterial regulation, cell biology and infection processes.
Collapse
Affiliation(s)
- Nathalie Rolhion
- Département de Biologie Cellulaire et Infection, Unité des Interactions Bactéries-Cellules, Institut Pasteur, F-75015 Paris, France.,INSERM, U604, F-75015 Paris, France.,INRA, Unité sous-contrat 2020, F-75015 Paris, France
| | - Pascale Cossart
- Département de Biologie Cellulaire et Infection, Unité des Interactions Bactéries-Cellules, Institut Pasteur, F-75015 Paris, France.,INSERM, U604, F-75015 Paris, France.,INRA, Unité sous-contrat 2020, F-75015 Paris, France
| |
Collapse
|
13
|
Duval M, Cossart P, Lebreton A. Mammalian microRNAs and long noncoding RNAs in the host-bacterial pathogen crosstalk. Semin Cell Dev Biol 2017; 65:11-19. [PMID: 27381344 PMCID: PMC7089780 DOI: 10.1016/j.semcdb.2016.06.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/30/2016] [Accepted: 06/01/2016] [Indexed: 12/20/2022]
Abstract
Gene expression regulation is a critical question in host-pathogen interactions, and RNAs act as key players in this process. In this review, we focus on the mammalian RNA response to bacterial infection, with a special interest on microRNAs and long non-coding RNAs. We discuss the role of cellular miRNAs in immunity, the implication of circulating miRNAs as well as the influence of the microbiome on the miRNA response. We also review how pathogens counteract the host miRNA expression. Interestingly, bacterial non-coding RNAs regulate host gene expression and conversely eukaryotic miRNAs may regulate bacterial gene expression. Overall, the characterization of RNA regulatory networks represents an emerging theme in the field of host pathogen interactions.
Collapse
Affiliation(s)
- Mélodie Duval
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, USC2020, 75015 Paris, France
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, USC2020, 75015 Paris, France.
| | - Alice Lebreton
- École Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'École Normale Supérieure (IBENS), Équipe Infection et Devenir de l'ARN, 75005 Paris, France; INRA, IBENS, 75005 Paris, France.
| |
Collapse
|
14
|
Quereda JJ, García-Del Portillo F, Pucciarelli MG. Listeria monocytogenes remodels the cell surface in the blood-stage. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:641-648. [PMID: 27085096 DOI: 10.1111/1758-2229.12416] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
After crossing the intestinal barrier, the bacterial pathogen Listeria monocytogenes disseminates via the blood to the liver, spleen, brain and placenta. Transcriptomic studies have shown that L. monocytogenes changes expression of many genes during this blood-stage. However, no comparable data at the protein level are known. As main interactors with the environment, we focused in surface proteins produced by L. monocytogenes in an ex vivo bovine blood model. Bacteria exposed to blood alter selectively the amount of several surface proteins compared with bacteria grown in laboratory media. Increased levels were detected for Lmo0514 and Internalin A, two surface proteins covalently bound to peptidoglycan, and the moonlighting protein alcohol-acetaldehyde dehydrogenase, also known as Lap for 'Listeria adhesion protein'. Lmo0514, induced by L. monocytogenes inside epithelial cells, is required for survival in plasma and for virulence in mice at early infection stages. Lmo0514 is also important to cope with low pH stress. By contrast, L. monocytogenes down-regulates other surface proteins following exposure to blood and plasma such as Internalin I. These data provide evidence for remodelling of the L. monocytogenes cell surface during the blood-stage, which it could facilitate pathogen dissemination to deep organs.
Collapse
Affiliation(s)
- Juan J Quereda
- Laboratory of Intracellular Bacterial Pathogens, Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Francisco García-Del Portillo
- Laboratory of Intracellular Bacterial Pathogens, Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - M Graciela Pucciarelli
- Laboratory of Intracellular Bacterial Pathogens, Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- Centro de Biología Molecular 'Severo Ochoa' (CBMSO-CSIC), Departamento de Biología Molecular, Universidad Autónoma de Madrid, Spain
| |
Collapse
|
15
|
Koeppen K, Hampton TH, Jarek M, Scharfe M, Gerber SA, Mielcarz DW, Demers EG, Dolben EL, Hammond JH, Hogan DA, Stanton BA. A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles. PLoS Pathog 2016; 12:e1005672. [PMID: 27295279 PMCID: PMC4905634 DOI: 10.1371/journal.ppat.1005672] [Citation(s) in RCA: 304] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 05/10/2016] [Indexed: 12/20/2022] Open
Abstract
Bacterial outer membrane vesicle (OMV)-mediated delivery of proteins to host cells is an important mechanism of host-pathogen communication. Emerging evidence suggests that OMVs contain differentially packaged short RNAs (sRNAs) with the potential to target host mRNA function and/or stability. In this study, we used RNA-Seq to characterize differentially packaged sRNAs in Pseudomonas aeruginosa OMVs, and to show transfer of OMV sRNAs to human airway cells. We selected one sRNA for further study based on its stable secondary structure and predicted mRNA targets. Our candidate sRNA (sRNA52320), a fragment of a P. aeruginosa methionine tRNA, was abundant in OMVs and reduced LPS-induced as well as OMV-induced IL-8 secretion by cultured primary human airway epithelial cells. We also showed that sRNA52320 attenuated OMV-induced KC cytokine secretion and neutrophil infiltration in mouse lung. Collectively, these findings are consistent with the hypothesis that sRNA52320 in OMVs is a novel mechanism of host-pathogen interaction whereby P. aeruginosa reduces the host immune response. Pseudomonas aeruginosa is a gram-negative, opportunistic pathogen that accounts for about 10% of all hospital-acquired infections in the US and primarily infects immunocompromised hosts, including patients with chronic obstructive pulmonary disease and cystic fibrosis. Gram-negative bacteria like P. aeruginosa produce outer membrane vesicles (OMVs), which constitute an important mechanism for host colonization. In this study we demonstrate a novel mechanism of pathogen-host interaction that attenuates the innate immune response in human airway epithelial cells and in mouse lung through a regulatory sRNA contained inside OMVs secreted by P. aeruginosa.
Collapse
Affiliation(s)
- Katja Koeppen
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail:
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Michael Jarek
- Genome Analytics Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
| | - Maren Scharfe
- Genome Analytics Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
| | - Scott A. Gerber
- Departments of Genetics and Biochemistry, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Norris Cotton Cancer Center, Lebanon, New Hampshire, United States of America
| | - Daniel W. Mielcarz
- Norris Cotton Cancer Center, Lebanon, New Hampshire, United States of America
| | - Elora G. Demers
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Emily L. Dolben
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - John H. Hammond
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Bruce A. Stanton
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| |
Collapse
|
16
|
Abstract
The model opportunistic pathogen Listeria monocytogenes has been the object of extensive research, aiming at understanding its ability to colonize diverse environmental niches and animal hosts. Bacterial transcriptomes in various conditions reflect this efficient adaptability. We review here our current knowledge of the mechanisms allowing L. monocytogenes to respond to environmental changes and trigger pathogenicity, with a special focus on RNA-mediated control of gene expression. We highlight how these studies have brought novel concepts in prokaryotic gene regulation, such as the ‘excludon’ where the 5′-UTR of a messenger also acts as an antisense regulator of an operon transcribed in opposite orientation, or the notion that riboswitches can regulate non-coding RNAs to integrate complex metabolic stimuli into regulatory networks. Overall, the Listeria model exemplifies that fine RNA tuners act together with master regulatory proteins to orchestrate appropriate transcriptional programmes.
Collapse
Affiliation(s)
- Alice Lebreton
- a École Normale Supérieure , PSL Research University, CNRS, Inserm, Institut de Biologie de l'École Normale Supérieure (IBENS), Équipe Infection et Devenir de l'ARN , Paris , France.,b INRA, IBENS , Paris , France
| | - Pascale Cossart
- c Institut Pasteur, Unité des Interactions Bactéries-Cellules , Paris , France.,d Inserm , Paris , France.,e INRA, USC2020 , Paris , France
| |
Collapse
|
17
|
Ting K, Aitken KJ, Penna F, Samiei AN, Sidler M, Jiang JX, Ibrahim F, Tolg C, Delgado-Olguin P, Rosenblum N, Bägli DJ. Uropathogenic E. coli (UPEC) Infection Induces Proliferation through Enhancer of Zeste Homologue 2 (EZH2). PLoS One 2016; 11:e0149118. [PMID: 26964089 PMCID: PMC4786126 DOI: 10.1371/journal.pone.0149118] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/27/2016] [Indexed: 01/13/2023] Open
Abstract
Host-pathogen interactions can induce epigenetic changes in the host directly, as well as indirectly through secreted factors. Previously, uropathogenic Escherichia coli (UPEC) was shown to increase DNA methyltransferase activity and expression, which was associated with methylation-dependent alterations in the urothelial expression of CDKN2A. Here, we showed that paracrine factors from infected cells alter expression of another epigenetic writer, EZH2, coordinate with proliferation. Urothelial cells were inoculated with UPEC, UPEC derivatives, or vehicle (mock infection) at low moi, washed, then maintained in media with Gentamycin. Urothelial conditioned media (CM) and extracellular vesicles (EV) were isolated after the inoculations and used to treat naïve urothelial cells. EZH2 increased with UPEC infection, inoculation-induced CM, and inoculation-induced EV vs. parallel stimulation derived from mock-inoculated urothelial cells. We found that infection also increased proliferation at one day post-infection, which was blocked by the EZH2 inhibitor UNC1999. Inhibition of demethylation at H3K27me3 had the opposite effect and augmented proliferation. CONCLUSION: Uropathogen-induced paracrine factors act epigenetically by altering expression of EZH2, which plays a key role in early host cell proliferative responses to infection.
Collapse
Affiliation(s)
- Kenneth Ting
- Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Karen J. Aitken
- Developmental and Stem Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Urology Division, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
- * E-mail:
| | - Frank Penna
- Urology Division, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alaleh Najdi Samiei
- Developmental and Stem Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Martin Sidler
- Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Urology Division, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jia-Xin Jiang
- Developmental and Stem Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fadi Ibrahim
- Developmental and Stem Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Cornelia Tolg
- Developmental and Stem Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Paul Delgado-Olguin
- Developmental and Stem Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Physiology and Experimental Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Norman Rosenblum
- Developmental and Stem Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Nephrology Division, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Darius J. Bägli
- Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Urology Division, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| |
Collapse
|