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Goh KJ, Altuvia Y, Argaman L, Raz Y, Bar A, Lithgow T, Margalit H, Gan YH. RIL-seq reveals extensive involvement of small RNAs in virulence and capsule regulation in hypervirulent Klebsiella pneumoniae. Nucleic Acids Res 2024; 52:9119-9138. [PMID: 38804271 PMCID: PMC11347178 DOI: 10.1093/nar/gkae440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 04/29/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) can infect healthy individuals, in contrast to classical strains that commonly cause nosocomial infections. The recent convergence of hypervirulence with carbapenem-resistance in K. pneumoniae can potentially create 'superbugs' that are challenging to treat. Understanding virulence regulation of hvKp is thus critical. Accumulating evidence suggest that posttranscriptional regulation by small RNAs (sRNAs) plays a role in bacterial virulence, but it has hardly been studied in K. pneumoniae. We applied RIL-seq to a prototypical clinical isolate of hvKp to unravel the Hfq-dependent RNA-RNA interaction (RRI) network. The RRI network is dominated by sRNAs, including predicted novel sRNAs, three of which we validated experimentally. We constructed a stringent subnetwork composed of RRIs that involve at least one hvKp virulence-associated gene and identified the capsule gene loci as a hub target where multiple sRNAs interact. We found that the sRNA OmrB suppressed both capsule production and hypermucoviscosity when overexpressed. Furthermore, OmrB base-pairs within kvrA coding region and partially suppresses translation of the capsule regulator KvrA. This agrees with current understanding of capsule as a major virulence and fitness factor. It emphasizes the intricate regulatory control of bacterial phenotypes by sRNAs, particularly of genes critical to bacterial physiology and virulence.
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Affiliation(s)
- Kwok Jian Goh
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yair Raz
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yunn-Hwen Gan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
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2
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Vigoda MB, Argaman L, Kournos M, Margalit H. Unraveling the interplay between a small RNA and RNase E in bacteria. Nucleic Acids Res 2024; 52:8947-8966. [PMID: 39036964 PMCID: PMC11347164 DOI: 10.1093/nar/gkae621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Small RNAs (sRNAs) are major regulators of gene expression in bacteria, exerting their regulation primarily via base pairing with their target transcripts and modulating translation. Accumulating evidence suggest that sRNAs can also affect the stability of their target transcripts by altering their accessibility to endoribonucleases. Yet, the effects of sRNAs on transcript stability and the mechanisms underlying them have not been studied in wide scale. Here we employ large-scale RNA-seq-based methodologies in the model bacterium Escherichia coli to quantitatively study the functional interaction between a sRNA and an endoribonuclease in regulating gene expression, using the well-established sRNA, GcvB, and the major endoribonuclease, RNase E. Studying single and double mutants of gcvB and rne and analysing their RNA-seq results by the Double Mutant Cycle approach, we infer distinct modes of the interplay between GcvB and RNase E. Transcriptome-wide mapping of RNase E cleavage sites provides further support to the results of the RNA-seq analysis, identifying cleavage sites in targets in which the functional interaction between GcvB and RNase E is evident. Together, our results indicate that the most dominant mode of GcvB-RNase E functional interaction is GcvB enhancement of RNase E cleavage, which varies in its magnitude between different targets.
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Affiliation(s)
- Meshi Barsheshet Vigoda
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Mark Kournos
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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3
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Wu K, Lin X, Lu Y, Dong R, Jiang H, Svensson SL, Zheng J, Shen N, Camilli A, Chao Y. RNA interactome of hypervirulent Klebsiella pneumoniae reveals a small RNA inhibitor of capsular mucoviscosity and virulence. Nat Commun 2024; 15:6946. [PMID: 39138169 PMCID: PMC11322559 DOI: 10.1038/s41467-024-51213-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (HvKP) is an emerging bacterial pathogen causing invasive infection in immune-competent humans. The hypervirulence is strongly linked to the overproduction of hypermucoviscous capsule, but the underlying regulatory mechanisms of hypermucoviscosity (HMV) have been elusive, especially at the post-transcriptional level mediated by small noncoding RNAs (sRNAs). Using a recently developed RNA interactome profiling approach iRIL-seq, we interrogate the Hfq-associated sRNA regulatory network and establish an intracellular RNA-RNA interactome in HvKP. Our data reveal numerous interactions between sRNAs and HMV-related mRNAs, and identify a plethora of sRNAs that repress or promote HMV. One of the strongest HMV repressors is ArcZ, which is activated by the catabolite regulator CRP and targets many HMV-related genes including mlaA and fbp. We discover that MlaA and its function in phospholipid transport is crucial for capsule retention and HMV, inactivation of which abolishes Klebsiella virulence in mice. ArcZ overexpression drastically reduces bacterial burden in mice and reduces HMV in multiple hypervirulent and carbapenem-resistant clinical isolates, indicating ArcZ is a potent RNA inhibitor of bacterial pneumonia with therapeutic potential. Our work unravels a novel CRP-ArcZ-MlaA regulatory circuit of HMV and provides mechanistic insights into the posttranscriptional virulence control in a superbug of global concern.
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Affiliation(s)
- Kejing Wu
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Xingyu Lin
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yujie Lu
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Dong
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Hongnian Jiang
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sarah L Svensson
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jiajia Zheng
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Ning Shen
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Yanjie Chao
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of RNA Innovation, Science and Engineering (RISE), Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
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4
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Birk MS, Walch P, Baykara T, Sefried S, Amelang J, Buerova E, Breuer I, Vervoots J, Typas A, Savitski MM, Mateus A, Selkrig J. Salmonella infection impacts host proteome thermal stability. Eur J Cell Biol 2024; 103:151448. [PMID: 39128247 DOI: 10.1016/j.ejcb.2024.151448] [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: 08/21/2023] [Revised: 07/31/2024] [Accepted: 08/03/2024] [Indexed: 08/13/2024] Open
Abstract
Intracellular bacterial pathogens hijack the protein machinery of infected host cells to evade their defenses and cultivate a favorable intracellular niche. The intracellular pathogen Salmonella enterica subsp. Typhimurium (STm) achieves this by injecting a cocktail of effector proteins into host cells that modify the activity of target host proteins. Yet, proteome-wide approaches to systematically map changes in host protein function during infection have remained challenging. Here we adapted a functional proteomics approach - Thermal-Proteome Profiling (TPP) - to systematically assess proteome-wide changes in host protein abundance and thermal stability throughout an STm infection cycle. By comparing macrophages treated with live or heat-killed STm, we observed that most host protein abundance changes occur independently of STm viability. In contrast, a large portion of host protein thermal stability changes were specific to infection with live STm. This included pronounced thermal stability changes in proteins linked to mitochondrial function (Acod1/Irg1, Cox6c, Samm50, Vdac1, and mitochondrial respiratory chain complex proteins), as well as the interferon-inducible protein with tetratricopeptide repeats, Ifit1. Integration of our TPP data with a publicly available STm-host protein-protein interaction database led us to discover that the secreted STm effector kinase, SteC, thermally destabilizes and phosphorylates the ribosomal preservation factor Serbp1. In summary, this work emphasizes the utility of measuring protein thermal stability during infection to accelerate the discovery of novel molecular interactions at the host-pathogen interface.
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Affiliation(s)
- Marlène S Birk
- Institute of Medical Microbiology, RWTH University Hospital, Aachen 52074, Germany
| | - Philipp Walch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Tarik Baykara
- Institute of Medical Microbiology, RWTH University Hospital, Aachen 52074, Germany
| | - Stephanie Sefried
- Institute of Medical Microbiology, RWTH University Hospital, Aachen 52074, Germany
| | - Jan Amelang
- Institute of Biochemistry and Molecular Biology, RWTH University Hospital, Aachen 52074, Germany
| | - Elena Buerova
- Institute of Biochemistry and Molecular Biology, RWTH University Hospital, Aachen 52074, Germany
| | - Ingrid Breuer
- Institute of Medical Microbiology, RWTH University Hospital, Aachen 52074, Germany
| | - Jörg Vervoots
- Institute of Biochemistry and Molecular Biology, RWTH University Hospital, Aachen 52074, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - André Mateus
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany; Department of Chemistry, Umeå University, Umeå 907 36, Sweden; The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå 907 36, Sweden.
| | - Joel Selkrig
- Institute of Medical Microbiology, RWTH University Hospital, Aachen 52074, Germany; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany.
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5
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Jafari SH, Lajevardi ZS, Zamani Fard MM, Jafari A, Naghavi S, Ravaei F, Taghavi SP, Mosadeghi K, Zarepour F, Mahjoubin-Tehran M, Rahimian N, Mirzaei H. Imaging Techniques and Biochemical Biomarkers: New Insights into Diagnosis of Pancreatic Cancer. Cell Biochem Biophys 2024:10.1007/s12013-024-01437-z. [PMID: 39026059 DOI: 10.1007/s12013-024-01437-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
Pancreatic cancer (PaC) incidence is increasing, but our current screening and diagnostic strategies are not very effective. However, screening could be helpful in the case of PaC, as recent evidence shows that the disease progresses gradually. Unfortunately, there is no ideal screening method or program for detecting PaC in its early stages. Conventional imaging techniques, such as abdominal ultrasound, CT, MRI, and EUS, have not been successful in detecting early-stage PaC. On the other hand, biomarkers may be a more effective screening tool for PaC and have greater potential for further evaluation compared to imaging. Recent studies on biomarkers and artificial intelligence (AI)-enhanced imaging have shown promising results in the early diagnosis of PaC. In addition to proteins, non-coding RNAs are also being studied as potential biomarkers for PaC. This review consolidates the current literature on PaC screening modalities to provide an organized framework for future studies. While conventional imaging techniques have not been effective in detecting early-stage PaC, biomarkers and AI-enhanced imaging are promising avenues of research. Further studies on the use of biomarkers, particularly non-coding RNAs, in combination with imaging modalities may improve the accuracy of PaC screening and lead to earlier detection of this deadly disease.
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Affiliation(s)
- Seyed Hamed Jafari
- Medical Imaging Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Radiology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Sadat Lajevardi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammad Masoud Zamani Fard
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Ameneh Jafari
- Chronic Respiratory Diseases Research Center, NRITLD, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soroush Naghavi
- Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Ravaei
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Seyed Pouya Taghavi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Kimia Mosadeghi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Zarepour
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Neda Rahimian
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences (IUMS), Tehran, Iran; Department of Internal Medicine, School of Medicine, Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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6
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Chapagain P, Ali A, Kidane DT, Farone M, Salem M. Characterisation of sRNAs enriched in outer membrane vesicles of pathogenic Flavobacterium psychrophilum causing Bacterial Cold Water Disease in rainbow trout. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e161. [PMID: 38947174 PMCID: PMC11212332 DOI: 10.1002/jex2.161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/15/2024] [Accepted: 05/22/2024] [Indexed: 07/02/2024]
Abstract
Flavobacterium psychrophilum (Fp) causes Bacterial Cold Water Disease in salmonids. During host-pathogen interactions, gram-negative bacteria, such as Fp, release external membrane vesicles (OMVs) harbouring cargos, such as DNA, RNA and virulence factors. This study aimed to characterise the potential role of the OMVs' small RNAs (sRNAs) in the Fp-rainbow trout host-pathogen interactions. sRNAs carried within OMVs were isolated from Fp. RNA-Seq datasets from whole-cell Fp and their isolated OMVs indicated substantial enrichment of specific sRNAs in the OMVs compared to the parent cell. Many of the OMV-packaged sRNAs were located in the pathogenicity islands of Fp. Conservation of sRNAs in 65 strains with variable degrees of virulence was reported. Dual RNA-Seq of host and pathogen transcriptomes on day 5 post-infection of Fp -resistant and -susceptible rainbow trout genetic lines revealed correlated expression of OMV-packaged sRNAs and their predicted host's immune gene targets. In vitro, treatment of the rainbow trout epithelial cell line RTgill-W1 with OMVs showed signs of cytotoxicity accompanied by dynamic changes in the expression of host genes when profiled 24 h following treatment. The OMV-treated cells, similar to the Fp -resistant fish, showed downregulated expression of the suppressor of cytokine signalling 1 (SOCS1) gene, suggesting induction of phagosomal maturation. Other signs of modulating the host gene expression following OMV-treatment include favouring elements from the phagocytic, endocytic and antigen presentation pathways in addition to HSP70, HSP90 and cochaperone proteins, which provide evidence for a potential role of OMVs in boosting the host immune response. In conclusion, the study identified novel microbial targets and inherent characteristics of OMVs that could open up new avenues of treatment and prevention of fish infections.
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Affiliation(s)
- Pratima Chapagain
- Department of Medicine, Division of Diabetes, Endocrinology and MetabolismVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Ali Ali
- Department of Animal and Avian SciencesUniversity of MarylandCollege ParkMarylandUSA
| | - Destaalem T. Kidane
- Department of Biology and Molecular Bioscience ProgramMiddle Tennessee State UniversityMurfreesboroTennesseeUSA
| | - Mary Farone
- Department of Biology and Molecular Bioscience ProgramMiddle Tennessee State UniversityMurfreesboroTennesseeUSA
| | - Mohamed Salem
- Department of Animal and Avian SciencesUniversity of MarylandCollege ParkMarylandUSA
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7
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Meng H, Zhang T, Wang Z, Zhu Y, Yu Y, Chen H, Chen J, Wang F, Yu Y, Hua X, Wang Y. High-Throughput Host-Microbe Single-Cell RNA Sequencing Reveals Ferroptosis-Associated Heterogeneity during Acinetobacter baumannii Infection. Angew Chem Int Ed Engl 2024; 63:e202400538. [PMID: 38419141 DOI: 10.1002/anie.202400538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/02/2024]
Abstract
Interactions between host and bacterial cells are integral to human physiology. The complexity of host-microbe interactions extends to different cell types, spatial aspects, and phenotypic heterogeneity, requiring high-resolution approaches to capture their full complexity. The latest breakthroughs in single-cell RNA sequencing (scRNA-seq) have opened up a new era of studies in host-pathogen interactions. Here, we first report a high-throughput cross-species dual scRNA-seq technology by using random primers to simultaneously capture both eukaryotic and bacterial RNAs (scRandom-seq). Using reference cells, scRandom-seq can detect individual eukaryotic and bacterial cells with high throughput and high specificity. Acinetobacter baumannii (A.b) is a highly opportunistic and nosocomial pathogen that displays resistance to many antibiotics, posing a significant threat to human health, calling for discoveries and treatment. In the A.b infection model, scRandom-seq witnessed polarization of THP-1 derived-macrophages and the intracellular A.b-induced ferroptosis-stress in host cells. The inhibition of ferroptosis by Ferrostatin-1 (Fer-1) resulted in the improvement of cell vitality and resistance to A.b infection, indicating the potential to resist related infections. scRandom-seq provides a high-throughput cross-species dual single-cell RNA profiling tool that will facilitate future discoveries in unraveling the complex interactions of host-microbe interactions in infection systems and tumor micro-environments.
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Affiliation(s)
- Hongen Meng
- Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310030, China
| | - Tianyu Zhang
- Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310030, China
| | - Zhang Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, People's Republic of China
| | - Yuyi Zhu
- M20 Genomics, Hangzhou, 311121, China
| | - Yingying Yu
- The Second Affiliated Hospital, School of Public Health, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Hangfei Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, People's Republic of China
| | - Jiaye Chen
- Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310030, China
| | - Fudi Wang
- The Second Affiliated Hospital, School of Public Health, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, People's Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310016, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, People's Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310016, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Yongcheng Wang
- Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310030, China
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8
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Hu W, Zhai ZY, Huang ZY, Chen ZM, Zhou P, Li XX, Yang GH, Bao CJ, You LJ, Cui XB, Xia GL, Ou Yang MP, Zhang L, Wu WKK, Li LF, Zhang YX, Xiao ZG, Gong W. Dual RNA sequencing of Helicobacter pylori and host cell transcriptomes reveals ontologically distinct host-pathogen interaction. mSystems 2024; 9:e0020624. [PMID: 38514462 PMCID: PMC11019886 DOI: 10.1128/msystems.00206-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Helicobacter pylori is a highly successful pathogen that poses a substantial threat to human health. However, the dynamic interaction between H. pylori and the human gastric epithelium has not been fully investigated. In this study, using dual RNA sequencing technology, we characterized a cytotoxin-associated gene A (cagA)-modulated bacterial adaption strategy by enhancing the expression of ATP-binding cassette transporter-related genes, metQ and HP_0888, upon coculturing with human gastric epithelial cells. We observed a general repression of electron transport-associated genes by cagA, leading to the activation of oxidative phosphorylation. Temporal profiling of host mRNA signatures revealed the downregulation of multiple splicing regulators due to bacterial infection, resulting in aberrant pre-mRNA splicing of functional genes involved in the cell cycle process in response to H. pylori infection. Moreover, we demonstrated a protective effect of gastric H. pylori colonization against chronic dextran sulfate sodium (DSS)-induced colitis. Mechanistically, we identified a cluster of propionic and butyric acid-producing bacteria, Muribaculaceae, selectively enriched in the colons of H. pylori-pre-colonized mice, which may contribute to the restoration of intestinal barrier function damaged by DSS treatment. Collectively, this study presents the first dual-transcriptome analysis of H. pylori during its dynamic interaction with gastric epithelial cells and provides new insights into strategies through which H. pylori promotes infection and pathogenesis in the human gastric epithelium. IMPORTANCE Simultaneous profiling of the dynamic interaction between Helicobacter pylori and the human gastric epithelium represents a novel strategy for identifying regulatory responses that drive pathogenesis. This study presents the first dual-transcriptome analysis of H. pylori when cocultured with gastric epithelial cells, revealing a bacterial adaptation strategy and a general repression of electron transportation-associated genes, both of which were modulated by cytotoxin-associated gene A (cagA). Temporal profiling of host mRNA signatures dissected the aberrant pre-mRNA splicing of functional genes involved in the cell cycle process in response to H. pylori infection. We demonstrated a protective effect of gastric H. pylori colonization against chronic DSS-induced colitis through both in vitro and in vivo experiments. These findings significantly enhance our understanding of how H. pylori promotes infection and pathogenesis in the human gastric epithelium and provide evidence to identify targets for antimicrobial therapies.
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Affiliation(s)
- Wei Hu
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
- The Third School of Clinical Medicine, Southern Medical University, Shenzhen, Guangdong, China
| | - Zhi Yong Zhai
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
- The Third School of Clinical Medicine, Southern Medical University, Shenzhen, Guangdong, China
| | - Zhao Yu Huang
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
- The Third School of Clinical Medicine, Southern Medical University, Shenzhen, Guangdong, China
| | - Ze Min Chen
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Ping Zhou
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
- The Third School of Clinical Medicine, Southern Medical University, Shenzhen, Guangdong, China
| | - Xia Xi Li
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Gen Hua Yang
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Chong Ju Bao
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Li Juan You
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Xiao Bing Cui
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Gui Li Xia
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Mei Ping Ou Yang
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Lin Zhang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - William Ka Kei Wu
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Long Fei Li
- Guangdong Engineering Technology Research Center of Reproductive Immunology for Peri-implantation, Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong, China
| | - Yu Xuan Zhang
- Department of Pharmacology and Therapeutics, King’s College London, London, United Kingdom
| | - Zhan Gang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
- South Sichuan Institute of Translational Medicine, Luzhou, China
- Laboratory of Personalized Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Wei Gong
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
- The Third School of Clinical Medicine, Southern Medical University, Shenzhen, Guangdong, China
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9
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Zhang J, Zhang S, Zhou W, Zhang X, Li G, Li R, Lin X, Chen Z, Liu F, Shen P, Zhou X, Gao Y, Chen Z, Chao Y, Wang C. A widely conserved protein Rof inhibits transcription termination factor Rho and promotes Salmonella virulence program. Nat Commun 2024; 15:3187. [PMID: 38622116 PMCID: PMC11018607 DOI: 10.1038/s41467-024-47438-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024] Open
Abstract
Transcription is crucial for the expression of genetic information and its efficient and accurate termination is required for all living organisms. Rho-dependent termination could rapidly terminate unwanted premature RNAs and play important roles in bacterial adaptation to changing environments. Although Rho has been discovered for about five decades, the regulation mechanisms of Rho-dependent termination are still not fully elucidated. Here we report that Rof is a conserved antiterminator and determine the cryogenic electron microscopy structure of Rho-Rof antitermination complex. Rof binds to the open-ring Rho hexamer and inhibits the initiation of Rho-dependent termination. Rof's N-terminal α-helix undergoes conformational changes upon binding with Rho, and is key in facilitating Rof-Rho interactions. Rof binds to Rho's primary binding site (PBS) and excludes Rho from binding with PBS ligand RNA at the initiation step. Further in vivo analyses in Salmonella Typhimurium show that Rof is required for virulence gene expression and host cell invasion, unveiling a physiological function of Rof and transcription termination in bacterial pathogenesis.
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Affiliation(s)
- Jing Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Shuo Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhou
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xiang Zhang
- The Fifth People's Hospital, Institutes of Biomedical Sciences, School of Public Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Guanjin Li
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruoxuan Li
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xingyu Lin
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziying Chen
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- The Fifth People's Hospital, Institutes of Biomedical Sciences, School of Public Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Fang Liu
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Pan Shen
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xiaogen Zhou
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Yue Gao
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Zhenguo Chen
- The Fifth People's Hospital, Institutes of Biomedical Sciences, School of Public Health, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Yanjie Chao
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
| | - Chengyuan Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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10
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Shen Z, Ke Z, Yang Q, Ghebremichael ST, Li T, Li T, Chen J, Meng X, Xiang H, Li C, Zhou Z, Pan G, Chen P. Transcriptomic changes in the microsporidia proliferation and host responses in congenitally infected embryos and larvae. BMC Genomics 2024; 25:321. [PMID: 38556880 PMCID: PMC10983672 DOI: 10.1186/s12864-024-10236-y] [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: 08/24/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
Congenital infection caused by vertical transmission of microsporidia N. bombycis can result in severe economic losses in the silkworm-rearing industry. Whole-transcriptome analyses have revealed non-coding RNAs and their regulatory networks in N. bombycis infected embryos and larvae. However, transcriptomic changes in the microsporidia proliferation and host responses in congenitally infected embryos and larvae remains unclear. Here, we simultaneously compared the transcriptomes of N. bombycis and its host B. mori embryos of 5-day and larvae of 1-, 5- and 10-day during congenital infection. For the transcriptome of N. bombycis, a comparison of parasite expression patterns between congenital-infected embryos and larva showed most genes related to parasite central carbon metabolism were down-regulated in larvae during infection, whereas the majority of genes involved in parasite proliferation and growth were up-regulated. Interestingly, a large number of distinct or shared differentially expressed genes (DEGs) were revealed by the Venn diagram and heat map, many of them were connected to infection related factors such as Ricin B lectin, spore wall protein, polar tube protein, and polysaccharide deacetylase. For the transcriptome of B. mori infected with N. bombycis, beyond numerous DEGs related to DNA replication and repair, mRNA surveillance pathway, RNA transport, protein biosynthesis, and proteolysis, with the progression of infection, a large number of DEGs related to immune and infection pathways, including phagocytosis, apoptosis, TNF, Toll-like receptor, NF-kappa B, Fc epsilon RI, and some diseases, were successively identified. In contrast, most genes associated with the insulin signaling pathway, 2-oxacarboxylic acid metabolism, amino acid biosynthesis, and lipid metabolisms were up-regulated in larvae compared to those in embryos. Furthermore, dozens of distinct and three shared DEGs that were involved in the epigenetic regulations, such as polycomb, histone-lysine-specific demethylases, and histone-lysine-N-methyltransferases, were identified via the Venn diagram and heat maps. Notably, many DEGs of host and parasite associated with lipid-related metabolisms were verified by RT-qPCR. Taken together, simultaneous transcriptomic analyses of both host and parasite genes lead to a better understanding of changes in the microsporidia proliferation and host responses in embryos and larvae in N. bombycis congenital infection.
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Affiliation(s)
- Zigang Shen
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Tiansheng Street, Chongqing, 400716, China
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400716, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Tiansheng Street, Chongqing, 400716, China
| | - Zhuojun Ke
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400716, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Tiansheng Street, Chongqing, 400716, China
| | - Qiong Yang
- Sericulture and Agri-food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Samson Teweldeberhan Ghebremichael
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400716, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Tiansheng Street, Chongqing, 400716, China
| | - Tangxin Li
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400716, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Tiansheng Street, Chongqing, 400716, China
| | - Tian Li
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400716, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Tiansheng Street, Chongqing, 400716, China
| | - Jie Chen
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400716, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Tiansheng Street, Chongqing, 400716, China
| | - Xianzhi Meng
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400716, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Tiansheng Street, Chongqing, 400716, China
| | - Heng Xiang
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Chunfeng Li
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400716, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Tiansheng Street, Chongqing, 400716, China
| | - Zeyang Zhou
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400716, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Tiansheng Street, Chongqing, 400716, China
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400716, China.
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Tiansheng Street, Chongqing, 400716, China.
| | - Ping Chen
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Tiansheng Street, Chongqing, 400716, China.
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400716, China.
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11
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Bergman S, Andresen L, Kjellin J, Martinez Burgo Y, Geiser P, Baars S, Söderbom F, Sellin ME, Holmqvist E. ProQ-dependent activation of Salmonella virulence genes mediated by post-transcriptional control of PhoP synthesis. mSphere 2024; 9:e0001824. [PMID: 38411119 PMCID: PMC10964419 DOI: 10.1128/msphere.00018-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
Gastrointestinal disease caused by Salmonella enterica is associated with the pathogen's ability to replicate within epithelial cells and macrophages. Upon host cell entry, the bacteria express a type-three secretion system encoded within Salmonella pathogenicity island 2, through which host-manipulating effector proteins are secreted to establish a stable intracellular niche. Transcription of this intracellular virulence program is activated by the PhoPQ two-component system that senses the low pH and the reduced magnesium concentration of host cell vacuoles. In addition to transcriptional control, Salmonella commonly employ RNA-binding proteins (RBPs) and small regulatory RNAs (sRNAs) to regulate gene expression at the post-transcriptional level. ProQ is a globally acting RBP in Salmonella that promotes expression of the intracellular virulence program, but its RNA repertoire has previously been characterized only under standard laboratory growth conditions. Here, we provide a high-resolution ProQ interactome during conditions mimicking the environment of the Salmonella-containing vacuole (SCV), revealing hundreds of previously unknown ProQ binding sites in sRNAs and mRNA 3'UTRs. ProQ positively affected both the levels and the stability of many sRNA ligands, some of which were previously shown to associate with the well-studied and infection-relevant RBP Hfq. We further show that ProQ activates the expression of PhoP at the post-transcriptional level, which, in turn, leads to upregulation of the intracellular virulence program. IMPORTANCE Salmonella enterica is a major pathogen responsible for foodborne gastroenteritis, and a leading model organism for genetic and molecular studies of bacterial virulence mechanisms. One key trait of this pathogen is the ability to survive within infected host cells. During infection, the bacteria employ a type three secretion system that deliver effector proteins to target and manipulate host cell processes. The transcriptional regulation of this virulence program is well understood. By contrast, the factors and mechanisms operating at the post-transcriptional level to control virulence gene expression are less clear. In this study, we have charted the global RNA ligand repertoire of the RNA-binding protein ProQ during in vitro conditions mimicking the host cell environment. This identified hundreds of binding sites and revealed ProQ-dependent stabilization of intracellular-specific small RNAs. Importantly, we show that ProQ post-transcriptionally activates the expression of PhoP, a master transcriptional activator of intracellular virulence in Salmonella.
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Affiliation(s)
- Sofia Bergman
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Liis Andresen
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Jonas Kjellin
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Yolanda Martinez Burgo
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Petra Geiser
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sophie Baars
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Mikael E. Sellin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Erik Holmqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
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12
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Zhang K, Repnik U, Diab N, Friske D, Pütz A, Bachmann AZ, Gubbi NMKP, Hensel M, Förstner KU, Westermann AJ, Dupont A, Hornef MW. Non-professional efferocytosis of Salmonella-infected intestinal epithelial cells in the neonatal host. J Exp Med 2024; 221:e20231237. [PMID: 38305765 PMCID: PMC10837083 DOI: 10.1084/jem.20231237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/04/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
The intestinal epithelium is the first line of defense against enteric pathogens. Removal of infected cells by exfoliation prevents mucosal translocation and systemic infection in the adult host, but is less commonly observed in the neonatal intestine. Instead, here, we describe non-professional efferocytosis of Salmonella-infected enterocytes by neighboring epithelial cells in the neonatal intestine. Intestinal epithelial stem cell organoid cocultures of neonatal and adult cell monolayers with damaged enterocytes replicated this observation, confirmed the age-dependent ability of intestinal epithelial cells for efferocytosis, and identified the involvement of the "eat-me" signals and adaptors phosphatidylserine and C1q as well as the "eat-me" receptors integrin-αv (CD51) and CD36 in cellular uptake. Consistent with this, massive epithelial cell membrane protrusions and CD36 accumulation at the contact site with apoptotic cells were observed in the infected neonatal host in vivo. Efferocytosis of infected small intestinal enterocytes by neighboring epithelial cells may represent a previously unrecognized mechanism of neonatal antimicrobial host defense to maintain barrier integrity.
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Affiliation(s)
- Kaiyi Zhang
- Institute of Medical Microbiology, RWTH Aachen University Hospital , Aachen, Germany
| | - Urska Repnik
- Department of Biology, Central Microscopy Unit, University of Kiel, Kiel, Germany
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Nour Diab
- Institute of Medical Microbiology, RWTH Aachen University Hospital , Aachen, Germany
| | - Daniel Friske
- Institute of Medical Microbiology, RWTH Aachen University Hospital , Aachen, Germany
| | - Andreas Pütz
- Institute of Medical Microbiology, RWTH Aachen University Hospital , Aachen, Germany
| | - Alina Z Bachmann
- Institute of Medical Microbiology, RWTH Aachen University Hospital , Aachen, Germany
| | | | - Michael Hensel
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Konrad U Förstner
- Institute of Molecular Infection Biology, University of Würzburg , Würzburg, Germany
| | - Alexander J Westermann
- Institute of Molecular Infection Biology, University of Würzburg , Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research , Würzburg, Germany
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany
| | - Aline Dupont
- Institute of Medical Microbiology, RWTH Aachen University Hospital , Aachen, Germany
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH Aachen University Hospital , Aachen, Germany
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13
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Warrier I, Perry A, Hubbell SM, Eichelman M, van Opijnen T, Meyer MM. RNA cis-regulators are important for Streptococcus pneumoniae in vivo success. PLoS Genet 2024; 20:e1011188. [PMID: 38442125 PMCID: PMC10942264 DOI: 10.1371/journal.pgen.1011188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/15/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Bacteria have evolved complex transcriptional regulatory networks, as well as many diverse regulatory strategies at the RNA level, to enable more efficient use of metabolic resources and a rapid response to changing conditions. However, most RNA-based regulatory mechanisms are not well conserved across different bacterial species despite controlling genes important for virulence or essential biosynthetic processes. Here, we characterize the activity of, and assess the fitness benefit conferred by, twelve cis-acting regulatory RNAs (including several riboswitches and a T-box), in the opportunistic pathogen Streptococcus pneumoniae TIGR4. By evaluating native locus mutants of each regulator that result in constitutively active or repressed expression, we establish that growth defects in planktonic culture are associated with constitutive repression of gene expression, while constitutive activation of gene expression is rarely deleterious. In contrast, in mouse nasal carriage and pneumonia models, strains with either constitutively active and repressed gene expression are significantly less fit than matched control strains. Furthermore, two RNA-regulated pathways, FMN synthesis/transport and pyrimidine synthesis/transport display exceptional sensitivity to mis-regulation or constitutive gene repression in both planktonic culture and in vivo environments. Thus, despite lack of obvious phenotypes associated with constitutive gene expression in vitro, the fitness benefit conferred on bacteria via fine-tuned metabolic regulation through cis-acting regulatory RNAs is substantial in vivo, and therefore easily sufficient to drive the evolution and maintenance of diverse RNA regulatory mechanisms.
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Affiliation(s)
- Indu Warrier
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Ariana Perry
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Sara M. Hubbell
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Matthew Eichelman
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Boston Children’s Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michelle M. Meyer
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
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14
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Ajam-Hosseini M, Akhoondi F, Parvini F, Fahimi H. Gram-negative bacterial sRNAs encapsulated in OMVs: an emerging class of therapeutic targets in diseases. Front Cell Infect Microbiol 2024; 13:1305510. [PMID: 38983695 PMCID: PMC11232669 DOI: 10.3389/fcimb.2023.1305510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/26/2023] [Indexed: 07/11/2024] Open
Abstract
Small regulatory RNAs (sRNAs) encapsulated in outer membrane vesicles (OMVs) are critical post-transcriptional regulators of gene expression in prokaryotic and eukaryotic organisms. OMVs are small spherical structures released by Gram-negative bacteria that serve as important vehicles for intercellular communication and can also play an important role in bacterial virulence and host-pathogen interactions. These molecules can interact with mRNAs or proteins and affect various cellular functions and physiological processes in the producing bacteria. This review aims to provide insight into the current understanding of sRNA localization to OMVs in Gram-negative bacteria and highlights the identification, characterization and functional implications of these encapsulated sRNAs. By examining the research gaps in this field, we aim to inspire further exploration and progress in investigating the potential therapeutic applications of OMV-encapsulated sRNAs in various diseases.
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Affiliation(s)
- Mobarakeh Ajam-Hosseini
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Akhoondi
- Department of Molecular Biology of The Cell, Faculty of Bioscience, University of Milan, Milan, Italy
| | - Farshid Parvini
- Department of Biology, Faculty of Basic Sciences, Semnan University, Semnan, Iran
| | - Hossein Fahimi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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15
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David C, Czauderna A, Cheng L, Lagune M, Jung HJ, Kim SG, Pamer EG, Prados J, Chen L, Becattini S. Intestinal carbapenem-resistant Klebsiella pneumoniae undergoes complex transcriptional reprogramming following immune activation. Gut Microbes 2024; 16:2340486. [PMID: 38659243 PMCID: PMC11057644 DOI: 10.1080/19490976.2024.2340486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CR-Kp) is a significant threat to public health worldwide. The primary reservoir for CR-Kp is the intestinal tract. There, the bacterium is usually present at low density but can bloom following antibiotic treatment, mostly in hospital settings. The impact of disturbances in the intestinal environment on the fitness, survival, expansion, and drug susceptibility of this pathogen is not well-understood, yet it may be relevant to devise strategies to tackle CR-Kp colonization and infection. Here, we adopted an in vivo model to examine the transcriptional adaptation of a CR-Kp clinical isolate to immune activation in the intestine. We report that as early as 6 hours following host treatment with anti-CD3 antibody, CR-Kp underwent rapid transcriptional changes including downregulation of genes involved in sugar utilization and amino acid biosynthesis and upregulation of genes involved in amino acid uptake and catabolism, antibiotic resistance, and stress response. In agreement with these findings, treatment increased the concentration of oxidative species and amino acids in the mouse intestine. Genes encoding for proteins containing the domain of unknown function (DUF) 1471 were strongly upregulated, however their deletion did not impair CR-Kp fitness in vivo upon immune activation. Transcription factor enrichment analysis identified the global regulator cAMP-Receptor Protein, CRP, as a potential orchestrator of the observed transcriptional signature. In keeping with the recognized role of CRP in regulating utilization of alternative carbon sources, crp deletion in CR-Kp resulted in strongly impaired gut colonization, although this effect was not amplified by immune activation. Thus, following intestinal colonization, which occurs in a CRP-dependent manner, CR-Kp can rapidly respond to immune cues by implementing a well-defined and complex transcriptional program whose direct relevance toward bacterial fitness warrants further investigation. Additional analyses utilizing this model may identify key factors to tackle CR-Kp colonization of the intestine.
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Affiliation(s)
- Clement David
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Aleksander Czauderna
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Liqing Cheng
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marion Lagune
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Hea-Jin Jung
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Sohn G. Kim
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Eric G. Pamer
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Julien Prados
- Bioinformatics Support Platform for data analysis, Faculty of medicine, University of Geneva, Geneva, Switzerland
| | - Liang Chen
- Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Simone Becattini
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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16
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Ali A, Salem M. Methods for Bioinformatic Prediction of Genuine sRNAs from Outer Membrane Vesicles. Methods Mol Biol 2024; 2843:37-54. [PMID: 39141293 DOI: 10.1007/978-1-0716-4055-5_4] [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] [Indexed: 08/15/2024]
Abstract
The molecular pathogenesis of Gram-negative bacteria remains a complex and incompletely understood phenomenon. Various factors are believed to contribute to the pathogenicity of these bacteria. One key mechanism utilized by Gram-negative bacteria is the production of outer membrane vesicles (OMVs), which are small spherical particles derived from the bacterial outer membrane. These OMVs are crucial in delivering virulence factors to the host, facilitating host-pathogen interactions. Within these OMVs, small regulatory RNAs (sRNAs) have been identified as important players in modulating the host immune response. One of the main challenges in studying OMVs and their cargo of sRNAs is the difficulty in isolating and purifying sufficient quantities of OMVs, as well as accurately predicting genuine sRNAs computationally. In this chapter, we present protocols aimed at overcoming these obstacles.
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Affiliation(s)
- Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
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17
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García-Tomsig NI, Lagares A, Becker A, Valverde C, Jiménez-Zurdo JI. An Integrated Affinity Chromatography-Based Approach to Unravel the sRNA Interactome in Nitrogen-Fixing Rhizobia. Methods Mol Biol 2024; 2741:363-380. [PMID: 38217663 DOI: 10.1007/978-1-0716-3565-0_19] [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] [Indexed: 01/15/2024]
Abstract
The activity mechanism and function of bacterial base-pairing small non-coding RNA regulators (sRNAs) are largely shaped by their main interacting cellular partners, i.e., proteins and mRNAs. We describe here an MS2 affinity chromatography-based procedure adapted to unravel the sRNA interactome in nitrogen-fixing legume endosymbiotic bacteria. The method consists of tagging of the bait sRNA at its 5'-end with the MS2 aptamer followed by pulse overexpression and immobilization of the chimeric transcript from cell lysates by an MS2-MBP fusion protein conjugated to an amylose resin. The sRNA-binding proteins and target mRNAs are further profiled by mass spectrometry and RNAseq, respectively.
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Affiliation(s)
- Natalia Isabel García-Tomsig
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Antonio Lagares
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas (LFGBBP), Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Argentina
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas (LFGBBP), Centro de Bioquímica y Microbiología del Suelo (CBMS), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires, Argentina
| | - José Ignacio Jiménez-Zurdo
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
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18
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Yao X, Jing T, Geng Q, Pang M, Zhao X, Li S, Chen D, Ma W. Dual analysis of wild-type and attenuated Orf virus and host cell transcriptomes revealed novel virus-host cell interactions. mSphere 2023; 8:e0039823. [PMID: 37982609 PMCID: PMC10732022 DOI: 10.1128/msphere.00398-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Currently, the only available commercial vaccines for Orf virus (ORFV) are live attenuated vaccines, which present a potential risk of reversion to virulence. Therefore, understanding the pathogenic mechanisms of different virulent strains of ORFV and host immune responses triggered by these viruses is crucial for developing new vaccines and interventions. In this study, we found that the attenuated strain downregulates the host innate immune response and antiviral activity. In addition, we noted that the wild-type strain can induce the immune response pattern centered on interferon-stimulated genes and interferon regulatory factor gene family. We predicted that STAT1 and STAT2 are the main transcription factors upstream of target gene promoters through gene regulatory networks and exert significant regulatory effects on co-expressed genes. Our study elucidated the complex interaction between ORFV strains and host cell immune responses, providing new insights into vaccine research for ORFV.
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Affiliation(s)
- Xiaoting Yao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Tian Jing
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingru Geng
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ming Pang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuanduo Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Shaofei Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Dekun Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Wentao Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
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19
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Pérez-Stuardo D, Frazão M, Ibaceta V, Brianson B, Sánchez E, Rivas-Pardo JA, Vallejos-Vidal E, Reyes-López FE, Toro-Ascuy D, Vidal EA, Reyes-Cerpa S. KLF17 is an important regulatory component of the transcriptomic response of Atlantic salmon macrophages to Piscirickettsia salmonis infection. Front Immunol 2023; 14:1264599. [PMID: 38162669 PMCID: PMC10755876 DOI: 10.3389/fimmu.2023.1264599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/07/2023] [Indexed: 01/03/2024] Open
Abstract
Piscirickettsia salmonis is the most important health problem facing Chilean Aquaculture. Previous reports suggest that P. salmonis can survive in salmonid macrophages by interfering with the host immune response. However, the relevant aspects of the molecular pathogenesis of P. salmonis have been poorly characterized. In this work, we evaluated the transcriptomic changes in macrophage-like cell line SHK-1 infected with P. salmonis at 24- and 48-hours post-infection (hpi) and generated network models of the macrophage response to the infection using co-expression analysis and regulatory transcription factor-target gene information. Transcriptomic analysis showed that 635 genes were differentially expressed after 24- and/or 48-hpi. The pattern of expression of these genes was analyzed by weighted co-expression network analysis (WGCNA), which classified genes into 4 modules of expression, comprising early responses to the bacterium. Induced genes included genes involved in metabolism and cell differentiation, intracellular transportation, and cytoskeleton reorganization, while repressed genes included genes involved in extracellular matrix organization and RNA metabolism. To understand how these expression changes are orchestrated and to pinpoint relevant transcription factors (TFs) controlling the response, we established a curated database of TF-target gene regulatory interactions in Salmo salar, SalSaDB. Using this resource, together with co-expression module data, we generated infection context-specific networks that were analyzed to determine highly connected TF nodes. We found that the most connected TF of the 24- and 48-hpi response networks is KLF17, an ortholog of the KLF4 TF involved in the polarization of macrophages to an M2-phenotype in mammals. Interestingly, while KLF17 is induced by P. salmonis infection, other TFs, such as NOTCH3 and NFATC1, whose orthologs in mammals are related to M1-like macrophages, are repressed. In sum, our results suggest the induction of early regulatory events associated with an M2-like phenotype of macrophages that drives effectors related to the lysosome, RNA metabolism, cytoskeleton organization, and extracellular matrix remodeling. Moreover, the M1-like response seems delayed in generating an effective response, suggesting a polarization towards M2-like macrophages that allows the survival of P. salmonis. This work also contributes to SalSaDB, a curated database of TF-target gene interactions that is freely available for the Atlantic salmon community.
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Affiliation(s)
- Diego Pérez-Stuardo
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Mateus Frazão
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Valentina Ibaceta
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Bernardo Brianson
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Evelyn Sánchez
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo (ANID) Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - J. Andrés Rivas-Pardo
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Eva Vallejos-Vidal
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad De Las Américas, La Florida, Santiago, Chile
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Centro de Nanociencia y Nanotecnología (CEDENNA), Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe E. Reyes-López
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Daniela Toro-Ascuy
- Laboratorio de Virología, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Elena A. Vidal
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo (ANID) Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sebastián Reyes-Cerpa
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
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20
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Liu F, Chen Z, Zhang S, Wu K, Bei C, Wang C, Chao Y. In vivo RNA interactome profiling reveals 3'UTR-processed small RNA targeting a central regulatory hub. Nat Commun 2023; 14:8106. [PMID: 38062076 PMCID: PMC10703908 DOI: 10.1038/s41467-023-43632-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Small noncoding RNAs (sRNAs) are crucial regulators of gene expression in bacteria. Acting in concert with major RNA chaperones such as Hfq or ProQ, sRNAs base-pair with multiple target mRNAs and form large RNA-RNA interaction networks. To systematically investigate the RNA-RNA interactome in living cells, we have developed a streamlined in vivo approach iRIL-seq (intracellular RIL-seq). This generic approach is highly robust, illustrating the dynamic sRNA interactomes in Salmonella enterica across multiple stages of growth. We have identified the OmpD porin mRNA as a central regulatory hub that is targeted by a dozen sRNAs, including FadZ cleaved from the conserved 3'UTR of fadBA mRNA. Both ompD and FadZ are activated by CRP, constituting a type I incoherent feed-forward loop in the fatty acid metabolism pathway. Altogether, we have established an approach to profile RNA-RNA interactomes in live cells, highlighting the complexity of RNA regulatory hubs and RNA networks.
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Affiliation(s)
- Fang Liu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ziying Chen
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center & Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shuo Zhang
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kejing Wu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cheng Bei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
| | - Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China.
| | - Yanjie Chao
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China.
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
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21
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Santana-da-Silva MN, Sena-dos-Santos C, Cáceres-Durán MÁ, de Souza FG, Gobbo AR, Pinto P, Salgado CG, dos Santos SEB. ncRNAs: an unexplored cellular defense mechanism in leprosy. Front Genet 2023; 14:1295586. [PMID: 38116294 PMCID: PMC10729009 DOI: 10.3389/fgene.2023.1295586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
Leprosy is an infectious disease primarily caused by the obligate intracellular parasite Mycobacterium leprae. Although it has been considered eradicated in many countries, leprosy continues to be a health issue in developing nations. Besides the social stigma associated with it, individuals affected by leprosy may experience nerve damage leading to physical disabilities if the disease is not properly treated or early diagnosed. Leprosy is recognized as a complex disease wherein socioenvironmental factors, immune response, and host genetics interact to contribute to its development. Recently, a new field of study called epigenetics has emerged, revealing that the immune response and other mechanisms related to infectious diseases can be influenced by noncoding RNAs. This review aims to summarize the significant advancements concerning non-coding RNAs in leprosy, discussing the key perspectives on this novel approach to comprehending the pathophysiology of the disease and identifying molecular markers. In our view, investigations on non-coding RNAs in leprosy hold promise and warrant increased attention from researches in this field.
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Affiliation(s)
- Mayara Natália Santana-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Imunologia, Seção de Virologia (SAVIR), Instituto Evandro Chagas, Ananindeua, Brazil
| | - Camille Sena-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Miguel Ángel Cáceres-Durán
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Felipe Gouvea de Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Angelica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Sidney Emanuel Batista dos Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
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22
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Kazemi S, Mirzaei R, Karampoor S, Hosseini-Fard SR, Ahmadyousefi Y, Soltanian AR, Keramat F, Saidijam M, Alikhani MY. Circular RNAs in tuberculosis: From mechanism of action to potential diagnostic biomarker. Microb Pathog 2023; 185:106459. [PMID: 37995882 DOI: 10.1016/j.micpath.2023.106459] [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: 05/25/2023] [Revised: 10/01/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tuberculosis), continues to be a major global health concern. Understanding the molecular intricacies of TB pathogenesis is crucial for developing effective diagnostic and therapeutic approaches. Circular RNAs (circRNAs), a class of single-stranded RNA molecules characterized by covalently closed loops, have recently emerged as potential diagnostic biomarkers in various diseases. CircRNAs have been demonstrated to modulate the host's immunological responses against TB, specifically by reducing monocyte apoptosis, augmenting autophagy, and facilitating macrophage polarization. This review comprehensively explores the roles and mechanisms of circRNAs in TB pathogenesis. We also discuss the growing body of evidence supporting their utility as promising diagnostic biomarkers for TB. By bridging the gap between fundamental circRNA biology and TB diagnostics, this review offers insights into the exciting potential of circRNAs in combatting this infectious disease.
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Affiliation(s)
- Sima Kazemi
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Hosseini-Fard
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yaghoub Ahmadyousefi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, Iran; Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ali Reza Soltanian
- Department of Biostatistics and Epidemiology, School of Public Health, Hamadan University of Medical Sciences, Iran
| | - Fariba Keramat
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Massoud Saidijam
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Yousef Alikhani
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, Iran; Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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23
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Torabi S, Seifi S, Geddes-McAlister J, Tenuta A, Wally O, Torkamaneh D, Eskandari M. Soybean-SCN Battle: Novel Insight into Soybean's Defense Strategies against Heterodera glycines. Int J Mol Sci 2023; 24:16232. [PMID: 38003422 PMCID: PMC10671692 DOI: 10.3390/ijms242216232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Soybean cyst nematode (SCN, Heterodera glycines, Ichinohe) poses a significant threat to global soybean production, necessitating a comprehensive understanding of soybean plants' response to SCN to ensure effective management practices. In this study, we conducted dual RNA-seq analysis on SCN-resistant Plant Introduction (PI) 437654, 548402, and 88788 as well as a susceptible line (Lee 74) under exposure to SCN HG type 1.2.5.7. We aimed to elucidate resistant mechanisms in soybean and identify SCN virulence genes contributing to resistance breakdown. Transcriptomic and pathway analyses identified the phenylpropanoid, MAPK signaling, plant hormone signal transduction, and secondary metabolite pathways as key players in resistance mechanisms. Notably, PI 437654 exhibited complete resistance and displayed distinctive gene expression related to cell wall strengthening, oxidative enzymes, ROS scavengers, and Ca2+ sensors governing salicylic acid biosynthesis. Additionally, host studies with varying immunity levels and a susceptible line shed light on SCN pathogenesis and its modulation of virulence genes to evade host immunity. These novel findings provide insights into the molecular mechanisms underlying soybean-SCN interactions and offer potential targets for nematode disease management.
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Affiliation(s)
- Sepideh Torabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Soren Seifi
- Aurora Cannabis Inc., Comox, BC V9M 4A1, Canada;
| | | | - Albert Tenuta
- Ontario Ministry of Agriculture, Food and Rural Affairs, Ridgetown, ON N0P 2C0, Canada;
| | - Owen Wally
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N0R 1G0, Canada;
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada;
| | - Milad Eskandari
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada;
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24
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Liu L, Liu F, Yan Z, Zhou H, Song W. Transcriptome analysis of damage mechanism of Candida utilis under U(VI) stress. MARINE POLLUTION BULLETIN 2023; 196:115650. [PMID: 37839133 DOI: 10.1016/j.marpolbul.2023.115650] [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: 08/20/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/17/2023]
Abstract
Marine radioactive pollution has a great impact on Marine microorganisms, but the damage mechanism by hexavalent uranium (U(VI)) exposure has been rarely known. In this study, Candida utilis (C. utilis) were exposed to U(VI) for 50, 100 and 150 mg/L, and then morphologic change and RNA-Seq in C. utilis were determined. U(VI) exposure significantly induced the changes of morphological characteristics of C. utilis. There were 39 DEGs in the 50 mg/L treated group, including 30 up-regulated genes and 9 down-regulated genes. There were 196 DEGs, 31 up-regulated and 165 down-regulated in the 100 mg/L treated group. The 150 mg/L treated group had 272 DEGs, 74 up-regulated and 198 down-regulated, compared with the control group. The results showed that the number of DEGs increased dose-dependently with U(VI) treatment. The results of this study provide a theoretical basis for the mechanism of radioactive wastewater damage to Marine microorganisms.
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Affiliation(s)
- Lei Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; School of Environment and Chemical Engineering, Anhui Vocational and Technical College, Hefei 230011, PR China
| | - Fang Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Zhuna Yan
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Han Zhou
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Wencheng Song
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, PR China; Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions and School for Radiological and Interdisciplinary Sciences, Soochow University, 215123 Suzhou, PR China.
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25
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Frost LR, Stark R, Anonye BO, MacCreath TO, Ferreira LRP, Unnikrishnan M. Dual RNA-seq identifies genes and pathways modulated during Clostridioides difficile colonization. mSystems 2023; 8:e0055523. [PMID: 37615437 PMCID: PMC10654110 DOI: 10.1128/msystems.00555-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/11/2023] [Indexed: 08/25/2023] Open
Abstract
IMPORTANCE The initial interactions between the colonic epithelium and the bacterium are likely critical in the establishment of Clostridioides difficile infection, one of the major causes of hospital-acquired diarrhea worldwide. Molecular interactions between C. difficile and human gut cells have not been well defined mainly due to the technical challenges of studying cellular host-pathogen interactions with this anaerobe. Here we have examined transcriptional changes occurring in the pathogen and host cells during the initial 24 hours of infection. Our data indicate several changes in metabolic pathways and virulence-associated factors during the initial bacterium-host cell contact and early stages of infection. We describe canonical pathways enriched based on the expression profiles of a dual RNA sequencing in the host and bacterium, and functions of bacterial factors that are modulated during infection. This study thus provides fresh insight into the early C. difficile infection process.
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Affiliation(s)
- Lucy R. Frost
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Richard Stark
- Bioinformatics Research Technology Platform, University of Warwick, Coventry, United Kingdom
| | - Blessing O. Anonye
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Thomas O. MacCreath
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ludmila R. P. Ferreira
- RNA Systems Biology Laboratory (RSBL), Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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26
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Zhou J, Ma H, Zhang L. Mechanisms of Virulence Reprogramming in Bacterial Pathogens. Annu Rev Microbiol 2023; 77:561-581. [PMID: 37406345 DOI: 10.1146/annurev-micro-032521-025954] [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] [Indexed: 07/07/2023]
Abstract
Bacteria are single-celled organisms that carry a comparatively small set of genetic information, typically consisting of a few thousand genes that can be selectively activated or repressed in an energy-efficient manner and transcribed to encode various biological functions in accordance with environmental changes. Research over the last few decades has uncovered various ingenious molecular mechanisms that allow bacterial pathogens to sense and respond to different environmental cues or signals to activate or suppress the expression of specific genes in order to suppress host defenses and establish infections. In the setting of infection, pathogenic bacteria have evolved various intelligent mechanisms to reprogram their virulence to adapt to environmental changes and maintain a dominant advantage over host and microbial competitors in new niches. This review summarizes the bacterial virulence programming mechanisms that enable pathogens to switch from acute to chronic infection, from local to systemic infection, and from infection to colonization. It also discusses the implications of these findings for the development of new strategies to combat bacterial infections.
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Affiliation(s)
- Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
| | - Hongmei Ma
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
| | - Lianhui Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
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Broglia L, Le Rhun A, Charpentier E. Methodologies for bacterial ribonuclease characterization using RNA-seq. FEMS Microbiol Rev 2023; 47:fuad049. [PMID: 37656885 PMCID: PMC10503654 DOI: 10.1093/femsre/fuad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/06/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
Bacteria adjust gene expression at the post-transcriptional level through an intricate network of small regulatory RNAs and RNA-binding proteins, including ribonucleases (RNases). RNases play an essential role in RNA metabolism, regulating RNA stability, decay, and activation. These enzymes exhibit species-specific effects on gene expression, bacterial physiology, and different strategies of target recognition. Recent advances in high-throughput RNA sequencing (RNA-seq) approaches have provided a better understanding of the roles and modes of action of bacterial RNases. Global studies aiming to identify direct targets of RNases have highlighted the diversity of RNase activity and RNA-based mechanisms of gene expression regulation. Here, we review recent RNA-seq approaches used to study bacterial RNases, with a focus on the methods for identifying direct RNase targets.
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Affiliation(s)
- Laura Broglia
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Center for Human Technologies, Istituto Italiano di Tecnologia, 16152 Genova, Italy
| | - Anaïs Le Rhun
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Institute for Biology, Humboldt University, D-10115 Berlin, Germany
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28
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Fels U, Willems P, De Meyer M, Gevaert K, Van Damme P. Shift in vacuolar to cytosolic regime of infecting Salmonella from a dual proteome perspective. PLoS Pathog 2023; 19:e1011183. [PMID: 37535689 PMCID: PMC10426988 DOI: 10.1371/journal.ppat.1011183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 08/15/2023] [Accepted: 06/19/2023] [Indexed: 08/05/2023] Open
Abstract
By applying dual proteome profiling to Salmonella enterica serovar Typhimurium (S. Typhimurium) encounters with its epithelial host (here, S. Typhimurium infected human HeLa cells), a detailed interdependent and holistic proteomic perspective on host-pathogen interactions over the time course of infection was obtained. Data-independent acquisition (DIA)-based proteomics was found to outperform data-dependent acquisition (DDA) workflows, especially in identifying the downregulated bacterial proteome response during infection progression by permitting quantification of low abundant bacterial proteins at early times of infection when bacterial infection load is low. S. Typhimurium invasion and replication specific proteomic signatures in epithelial cells revealed interdependent host/pathogen specific responses besides pointing to putative novel infection markers and signalling responses, including regulated host proteins associated with Salmonella-modified membranes.
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Affiliation(s)
- Ursula Fels
- iRIP unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Patrick Willems
- iRIP unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Margaux De Meyer
- iRIP unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- iRIP unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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29
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Jiao C, Reckstadt C, König F, Homberger C, Yu J, Vogel J, Westermann AJ, Sharma CM, Beisel CL. RNA recording in single bacterial cells using reprogrammed tracrRNAs. Nat Biotechnol 2023; 41:1107-1116. [PMID: 36604543 PMCID: PMC7614944 DOI: 10.1038/s41587-022-01604-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 11/07/2022] [Indexed: 01/07/2023]
Abstract
Capturing an individual cell's transcriptional history is a challenge exacerbated by the functional heterogeneity of cellular communities. Here, we leverage reprogrammed tracrRNAs (Rptrs) to record selected cellular transcripts as stored DNA edits in single living bacterial cells. Rptrs are designed to base pair with sensed transcripts, converting them into guide RNAs. The guide RNAs then direct a Cas9 base editor to target an introduced DNA target. The extent of base editing can then be read in the future by sequencing. We use this approach, called TIGER (transcribed RNAs inferred by genetically encoded records), to record heterologous and endogenous transcripts in individual bacterial cells. TIGER can quantify relative expression, distinguish single-nucleotide differences, record multiple transcripts simultaneously and read out single-cell phenomena. We further apply TIGER to record metabolic bet hedging and antibiotic resistance mobilization in Escherichia coli as well as host cell invasion by Salmonella. Through RNA recording, TIGER connects current cellular states with past transcriptional states to decipher complex cellular responses in single cells.
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Affiliation(s)
- Chunlei Jiao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Claas Reckstadt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Fabian König
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Christina Homberger
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jiaqi Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Cynthia M Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
- Medical Faculty, University of Würzburg, Würzburg, Germany.
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30
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Yan T, Sun M, Su R, Wang X, Lu X, Xiao Y, Deng H, Liu X, Tang W, Zhang G. Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of Indica Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2675. [PMID: 37514289 PMCID: PMC10384097 DOI: 10.3390/plants12142675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/15/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023]
Abstract
Cold stress significantly constrains the growth, development, productivity, and distribution of rice, particularly the indica cultivar, known for its susceptibility to cold, limiting its cultivation to specific regions. This study investigated the genes associated with cold responsiveness in the roots of two indica cultivars, SQSL (cold-tolerant) and XZX45 (cold-susceptible), through transcriptome dynamics analysis during the seedling stage. The analysis identified 8144 and 6427 differentially expressed genes (DEGs) in XZX45 and SQSL, respectively. Among these DEGs, 4672 (G2) were shared by both cultivars, while 3472 DEGs (G1) were specific to XZX45, and 1755 DEGs (G3) were specific to SQSL. Additionally, 572 differentially expressed transcription factors (TFs) from 48 TF families, including WRKY, NAC, bHLH, ERF, bZIP, MYB, C2H2, and GRAS, were identified. Gene Ontology (GO) enrichment analysis revealed significant enrichment of DEGs in the G3 group, particularly in the "response to cold" category, highlighting the crucial role of these specific genes in response to cold stress in SQSL. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated pronounced enrichment of DEGs in the G3 group in metabolic pathways such as "Pyruvate metabolism", "Glycolysis/Gluconeogenesis", and "Starch and sucrose metabolism", contributing to cold tolerance mechanisms in SQSL. Overall, this study provides comprehensive insights into the molecular mechanisms underlying cold responses in the indica cultivar, informing future genetic improvement strategies to enhance cold tolerance in susceptible indica rice cultivars.
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Affiliation(s)
- Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Meng Sun
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Rui Su
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xiaozhong Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xuedan Lu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Wenbang Tang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410128, China
- State Key Laboratory of Hybrid Rice, Changsha 410128, China
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
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31
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Wang X, Wang H, Yi P, Baker C, Casey G, Xie X, Luo H, Cai J, Fan X, Soong L, Hu H, Shi PY, Liang Y, Sun J. Metformin restrains ZIKV replication and alleviates virus-induced inflammatory responses in microglia. Int Immunopharmacol 2023; 121:110512. [PMID: 37343373 DOI: 10.1016/j.intimp.2023.110512] [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: 05/05/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023]
Abstract
The re-emergence of Zika virus (ZIKV) remains a major public health threat that has raised worldwide attention. Accumulating evidence suggests that ZIKV can cause serious pathological changes to the human nervous system, including microcephaly in newborns. Recent studies suggest that metformin, an established treatment for diabetes may play a role in viral infection; however, little is known about the interactions between ZIKV infection and metformin administration. Using fluorescent ZIKV by flow cytometry and immunofluorescence imaging, we found that ZIKV can infect microglia in a dose-dependent manner. Metformin diminished ZIKV replication without the alteration of viral entry and phagocytosis. Our study demonstrated that metformin downregulated ZIKV-induced inflammatory response in microglia in a time- and dose-dependent manner. Our RNA-Seq and qRT-PCR analysis found that type I and III interferons (IFN), such as IFNα2, IFNβ1 and IFNλ3 were upregulated in ZIKV-infected cells by metformin treatment, accompanied with the downregulation of GBP4, OAS1, MX1 and ISG15. Together, our results suggest that metformin-mediated modulation in multiple pathways may attribute to restraining ZIKV infection in microglia, which may provide a potential tool to consider for use in unique clinical circumstances.
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Affiliation(s)
- Xiaofang Wang
- Department of Infectious Disease, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, Hunan 410005, China; Department of Infectious Diseases, Key Laboratory of Viral Hepatitis of Hunan, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Hui Wang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Panpan Yi
- Department of Infectious Diseases, Key Laboratory of Viral Hepatitis of Hunan, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Coleman Baker
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Gonzales Casey
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Huanle Luo
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
| | - Jiyang Cai
- Department of Ophthalmology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xuegong Fan
- Department of Infectious Diseases, Key Laboratory of Viral Hepatitis of Hunan, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lynn Soong
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Haitao Hu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA; Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Yuejin Liang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Jiaren Sun
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA.
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32
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Cao P, Fleming D, Moustafa DA, Dolan SK, Szymanik KH, Redman WK, Ramos A, Diggle FL, Sullivan CS, Goldberg JB, Rumbaugh KP, Whiteley M. A Pseudomonas aeruginosa small RNA regulates chronic and acute infection. Nature 2023; 618:358-364. [PMID: 37225987 PMCID: PMC10247376 DOI: 10.1038/s41586-023-06111-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/21/2023] [Indexed: 05/26/2023]
Abstract
The ability to switch between different lifestyles allows bacterial pathogens to thrive in diverse ecological niches1,2. However, a molecular understanding of their lifestyle changes within the human host is lacking. Here, by directly examining bacterial gene expression in human-derived samples, we discover a gene that orchestrates the transition between chronic and acute infection in the opportunistic pathogen Pseudomonas aeruginosa. The expression level of this gene, here named sicX, is the highest of the P. aeruginosa genes expressed in human chronic wound and cystic fibrosis infections, but it is expressed at extremely low levels during standard laboratory growth. We show that sicX encodes a small RNA that is strongly induced by low-oxygen conditions and post-transcriptionally regulates anaerobic ubiquinone biosynthesis. Deletion of sicX causes P. aeruginosa to switch from a chronic to an acute lifestyle in multiple mammalian models of infection. Notably, sicX is also a biomarker for this chronic-to-acute transition, as it is the most downregulated gene when a chronic infection is dispersed to cause acute septicaemia. This work solves a decades-old question regarding the molecular basis underlying the chronic-to-acute switch in P. aeruginosa and suggests oxygen as a primary environmental driver of acute lethality.
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Affiliation(s)
- Pengbo Cao
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Derek Fleming
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Burn Center of Research Excellence, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dina A Moustafa
- Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, GA, USA
| | - Stephen K Dolan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kayla H Szymanik
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Whitni K Redman
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Burn Center of Research Excellence, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| | - Anayancy Ramos
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Frances L Diggle
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Joanna B Goldberg
- Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, GA, USA
| | - Kendra P Rumbaugh
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Burn Center of Research Excellence, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
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Jung J, Popella L, Do PT, Pfau P, Vogel J, Barquist L. Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server. RNA (NEW YORK, N.Y.) 2023; 29:570-583. [PMID: 36750372 PMCID: PMC10158992 DOI: 10.1261/rna.079263.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 01/10/2023] [Indexed: 05/06/2023]
Abstract
Antisense oligomers (ASOs), such as peptide nucleic acids (PNAs), designed to inhibit the translation of essential bacterial genes, have emerged as attractive sequence- and species-specific programmable RNA antibiotics. Yet, potential drawbacks include unwanted side effects caused by their binding to transcripts other than the intended target. To facilitate the design of PNAs with minimal off-target effects, we developed MASON (make antisense oligomers now), a web server for the design of PNAs that target bacterial mRNAs. MASON generates PNA sequences complementary to the translational start site of a bacterial gene of interest and reports critical sequence attributes and potential off-target sites. We based MASON's off-target predictions on experiments in which we treated Salmonella enterica serovar Typhimurium with a series of 10-mer PNAs derived from a PNA targeting the essential gene acpP but carrying two serial mismatches. Growth inhibition and RNA-sequencing (RNA-seq) data revealed that PNAs with terminal mismatches are still able to target acpP, suggesting wider off-target effects than anticipated. Comparison of these results to an RNA-seq data set from uropathogenic Escherichia coli (UPEC) treated with eleven different PNAs confirmed that our findings are not unique to Salmonella We believe that MASON's off-target assessment will improve the design of specific PNAs and other ASOs.
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Affiliation(s)
- Jakob Jung
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Linda Popella
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Phuong Thao Do
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Patrick Pfau
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
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Fernández-Fernández R, López-Igual R, Casadesús J, Sánchez-Romero MA. Analysis of Salmonella lineage-specific traits upon cell sorting. Front Cell Infect Microbiol 2023; 13:1146070. [PMID: 37065195 PMCID: PMC10090396 DOI: 10.3389/fcimb.2023.1146070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Microbial cell individuality is receiving increasing interest in the scientific community. Individual cells within clonal populations exhibit noticeable phenotypic heterogeneity. The advent of fluorescent protein technology and advances in single-cell analysis has revealed phenotypic cell variant in bacterial populations. This heterogeneity is evident in a wide range of phenotypes, for example, individual cells display variable degrees of gene expression and survival under selective conditions and stresses, and can exhibit differing propensities to host interactions. Last few years, numerous cell sorting approaches have been employed for resolving the properties of bacterial subpopulations. This review provides an overview of applications of cell sorting to analyze Salmonella lineage-specific traits, including bacterial evolution studies, gene expression analysis, response to diverse cellular stresses and characterization of diverse bacterial phenotypic variants.
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Affiliation(s)
- Rocío Fernández-Fernández
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Seville, Spain
| | - Rocío López-Igual
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and C.S.I.C., Seville, Spain
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - María Antonia Sánchez-Romero
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Seville, Spain
- *Correspondence: María Antonia Sánchez-Romero,
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Improved Bacterial Single-Cell RNA-Seq through Automated MATQ-Seq and Cas9-Based Removal of rRNA Reads. mBio 2023; 14:e0355722. [PMID: 36880749 PMCID: PMC10127585 DOI: 10.1128/mbio.03557-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Bulk RNA sequencing technologies have provided invaluable insights into host and bacterial gene expression and associated regulatory networks. Nevertheless, the majority of these approaches report average expression across cell populations, hiding the true underlying expression patterns that are often heterogeneous in nature. Due to technical advances, single-cell transcriptomics in bacteria has recently become reality, allowing exploration of these heterogeneous populations, which are often the result of environmental changes and stressors. In this work, we have improved our previously published bacterial single-cell RNA sequencing (scRNA-seq) protocol that is based on multiple annealing and deoxycytidine (dC) tailing-based quantitative scRNA-seq (MATQ-seq), achieving a higher throughput through the integration of automation. We also selected a more efficient reverse transcriptase, which led to reduced cell loss and higher workflow robustness. Moreover, we successfully implemented a Cas9-based rRNA depletion protocol into the MATQ-seq workflow. Applying our improved protocol on a large set of single Salmonella cells sampled over different growth conditions revealed improved gene coverage and a higher gene detection limit compared to our original protocol and allowed us to detect the expression of small regulatory RNAs, such as GcvB or CsrB at a single-cell level. In addition, we confirmed previously described phenotypic heterogeneity in Salmonella in regard to expression of pathogenicity-associated genes. Overall, the low percentage of cell loss and high gene detection limit makes the improved MATQ-seq protocol particularly well suited for studies with limited input material, such as analysis of small bacterial populations in host niches or intracellular bacteria. IMPORTANCE Gene expression heterogeneity among isogenic bacteria is linked to clinically relevant scenarios, like biofilm formation and antibiotic tolerance. The recent development of bacterial single-cell RNA sequencing (scRNA-seq) enables the study of cell-to-cell variability in bacterial populations and the mechanisms underlying these phenomena. Here, we report a scRNA-seq workflow based on MATQ-seq with increased robustness, reduced cell loss, and improved transcript capture rate and gene coverage. Use of a more efficient reverse transcriptase and the integration of an rRNA depletion step, which can be adapted to other bacterial single-cell workflows, was instrumental for these improvements. Applying the protocol to the foodborne pathogen Salmonella, we confirmed transcriptional heterogeneity across and within different growth phases and demonstrated that our workflow captures small regulatory RNAs at a single-cell level. Due to low cell loss and high transcript capture rates, this protocol is uniquely suited for experimental settings in which the starting material is limited, such as infected tissues.
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36
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Qin G, Ai X, Xu J, Yang Y. Dual RNA-seq of spleens extracted from channel catfish infected with Aeromonas veronii reveals novel insights into host-pathogen interactions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 252:114609. [PMID: 36739739 DOI: 10.1016/j.ecoenv.2023.114609] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Interactions between host and pathogen are involving various dynamic changes in transcript expression and critical for understanding host immunity against infections and its associated pathogenesis. Herein, we established a model of channel catfish infected with Aeromonas veronii. The infected fish had prominent body surface bleeding, and the spleen showed hyperemia and swelling. Then, the spleen of channel catfish infected with A. veronii was analyzed by dual RNA sequencing (RNA-seq), and the transcriptome data were compared with uninfected channel catfish spleen or bacteria cultured in vitro. The transcript expression profile of pathogen-host interaction between A. veronii and channel catfish was successfully studied. During infection, the host was enriched for multiple immune-related signaling pathways, such as the Toll-like receptor signaling pathway, Cytokine-cytokine receptor interaction, and T cell receptor signaling pathway; and significantly upregulated for many innate immune-related genes, including IL-8. At the same time, we found that A. veronii mainly harmed the host spleen through hemolysin. Our current findings are of great significance in clarifying the pathogenesis of channel catfish induced by A. veronii and provide gene targets for developing preventive measures.
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Affiliation(s)
- Gaixiao Qin
- College of Animal Science and Technology, Henan university of animal husbandry and Economy, Zhengzhou 450046, China
| | - Xiaohui Ai
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Jin Xu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Yibin Yang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
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37
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Zaldívar-López S, Herrera-Uribe J, Bautista R, Jiménez Á, Moreno Á, Claros MG, Garrido JJ. Salmonella Typhimurium induces genome-wide expression and phosphorylation changes that modulate immune response, intracellular survival and vesicle transport in infected neutrophils. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 140:104597. [PMID: 36450302 DOI: 10.1016/j.dci.2022.104597] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Salmonella Typhimurium is a food-borne pathogen that causes salmonellosis. When in contact with the host, neutrophils are rapidly recruited to act as first line of defense. To better understand the pathogenesis of this infection, we used an in vitro model of neutrophil infection to perform dual RNA-sequencing (both host and pathogen). In addition, and given that many pathogens interfere with kinase-mediated phosphorylation in host signaling, we performed a phosphoproteomic analysis. The immune response was overall diminished in infected neutrophils, mainly JAK/STAT and toll-like receptor signaling pathways. We found decreased expression of proinflammatory cytokine receptor genes and predicted downregulation of the mitogen-activated protein (MAPK) signaling pathway. Also, Salmonella infection inhibited interferons I and II signaling pathways by upregulation of SOCS3 and subsequent downregulation of STAT1 and STAT2. Additionally, phosphorylation of PSMC2 and PSMC4, proteasome regulatory proteins, was decreased in infected neutrophils. Cell viability and survival was increased by p53 signaling, cell cycle arrest and NFkB-proteasome pathways activation. Combined analysis of RNA-seq and phosphoproteomics also revealed inhibited vesicle transport mechanisms mediated by dynein/dynactin and exocyst complexes, involved in ER-to-Golgi transport and centripetal movement of lysosomes and endosomes. Among the overexpressed virulence genes from Salmonella we found potential effectors responsible of these dysregulations, such as spiC, sopD2, sifA or pipB2, all of them involved in intracellular replication. Our results suggest that Salmonella induces (through overexpression of virulence factors) transcriptional and phosphorylation changes that increases neutrophil survival and shuts down immune response to minimize host response, and impairing intracellular vesicle transport likely to keep nutrients for replication and Salmonella-containing vacuole formation and maintenance.
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Affiliation(s)
- Sara Zaldívar-López
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain.
| | - Juber Herrera-Uribe
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Rocío Bautista
- Plataforma Andaluza de Bioinformática, Universidad de Málaga, Málaga, Spain
| | - Ángeles Jiménez
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Ángela Moreno
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - M Gonzalo Claros
- Plataforma Andaluza de Bioinformática, Universidad de Málaga, Málaga, Spain; Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain
| | - Juan J Garrido
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
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38
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Fan R, Zhou Y, Chen X, Zhong X, He F, Peng W, Li L, Wang X, Xu Y. Porphyromonas gingivalis Outer Membrane Vesicles Promote Apoptosis via msRNA-Regulated DNA Methylation in Periodontitis. Microbiol Spectr 2023; 11:e0328822. [PMID: 36629433 PMCID: PMC9927323 DOI: 10.1128/spectrum.03288-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/07/2022] [Indexed: 01/12/2023] Open
Abstract
The outer membrane vesicles (OMVs) produced by Porphyromonas gingivalis contain a variety of bioactive molecules that may be involved in the progression of periodontitis. However, the participation of P. gingivalis OMVs in the development of periodontitis has not been elucidated. Here, we isolated P. gingivalis OMVs and confirmed their participation in periodontitis both in vivo and in vitro. Microcomputed tomography (micro-CT) and histological analysis showed that under stimulation with P. gingivalis OMVs, the alveolar bone of rats was significantly resorbed in vivo. We found that P. gingivalis OMVs were taken up by human periodontal ligament cells ([hPDLCs]) in vitro, which subsequently resulted in apoptosis and inflammatory cytokine release, which was accomplished by the microRNA-size small RNA (msRNA) sRNA45033 in the P. gingivalis OMVs. Through bioinformatics analysis and screening of target genes, chromobox 5 (CBX5) was identified as the downstream target of screened-out sRNA45033. Using a dual-luciferase reporter assay, overexpression, and knockdown methods, sRNA45033 was confirmed to target CBX5 to regulate hPDLC apoptosis. In addition, CUT&Tag (cleavage under targets and tagmentation) analysis confirmed the mechanism that CBX5 regulates apoptosis through the methylation of p53 DNA. Collectively, these findings indicate that the role of P. gingivalis OMVs is immunologically relevant and related to bacterial virulence during the development of periodontitis. IMPORTANCE P. gingivalis is a bacterium often associated with periodontitis. This study demonstrates that (i) sRNA45033 in P. gingivalis OMVs targets CBX5, (ii) CBX5 regulates the methylation of p53 DNA and its expression, which is associated with apoptosis, and (iii) a novel mechanism of interaction between hosts and pathogens is mediated by OMVs in the occurrence of periodontitis.
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Affiliation(s)
- Ruyi Fan
- Department of Periodontics, the Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
| | - Yi Zhou
- Department of Periodontics, the Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
| | - Xu Chen
- Department of Periodontics, the Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
| | - Xianmei Zhong
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Periodontics, Taizhou Stomatological Hospital, Taizhou, China
| | - Fanzhen He
- Department of Periodontics, the Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Wenzao Peng
- Department of Periodontics, the Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Lu Li
- Department of Periodontics, the Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
| | - Xiaoqian Wang
- Department of Periodontics, the Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
| | - Yan Xu
- Department of Periodontics, the Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
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39
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Proteomics Profiling Reveals Regulation of Immune Response to Salmonella enterica Serovar Typhimurium Infection in Mice. Infect Immun 2023; 91:e0049922. [PMID: 36511704 PMCID: PMC9872662 DOI: 10.1128/iai.00499-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Regulation of the immune response to Salmonella enterica serovar Typhimurium (S. Typhimurium) infection is a complex process, influenced by the interaction between genetic and environmental factors. Different inbred strains of mice exhibit distinct levels of resistance to S. Typhimurium infection, ranging from susceptible (e.g., C57BL/6J) to resistant (e.g., DBA/2J) strains. However, the underlying molecular mechanisms contributing to the host response remain elusive. In this study, we present a comprehensive proteomics profiling of spleen tissue from C57BL/6J and DBA/2J strains with different doses of S. Typhimurium infection by tandem mass tag labeling coupled with two-dimensional liquid chromatography-tandem mass spectrometry (TMT-LC/LC-MS/MS). We identified and quantified 3,986 proteins, resulting in 475 differentially expressed proteins (DEPs) between C57BL/6J and DBA/2J strains. Functional enrichment analysis unveiled that the mechanisms of innate immune responses to S. Typhimurium infection could be associated with several signaling pathways, including the interferon (IFN) signaling pathway. We experimentally validated the roles of the IFN signaling pathway in the innate immune response to S. Typhimurium infection using an IFN-γ neutralization assay. We further illustrated the importance of macrophage and proinflammatory cytokines in the mechanisms underlying the resistance to S. Typhimurium using quantitative reverse transcription-PCR (qRT-PCR). Taken together, our results provided new insights into the genetic regulation of the immune response to S. Typhimurium infection in mice and might lead to the discovery of potential protein targets for controlling salmonellosis.
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40
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Fernandes JCR, Gonçalves ANA, Floeter-Winter LM, Nakaya HI, Muxel SM. Comparative transcriptomic analysis of long noncoding RNAs in Leishmania-infected human macrophages. Front Genet 2023; 13:1051568. [PMID: 36685903 PMCID: PMC9845402 DOI: 10.3389/fgene.2022.1051568] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/25/2022] [Indexed: 01/05/2023] Open
Abstract
It is well established that infection with Leishmania alters the host cell's transcriptome. Since mammalian cells have multiple mechanisms to control gene expression, different molecules, such as noncoding RNAs, can be involved in this process. MicroRNAs have been extensively studied upon Leishmania infection, but whether long noncoding RNAs (lncRNAs) are also altered in macrophages is still unexplored. We performed RNA-seq from THP-1-derived macrophages infected with Leishmania amazonensis (La), L. braziliensis (Lb), and L. infantum (Li), investigating a previously unappreciated fraction of macrophage transcriptome. We found that more than 24% of the total annotated transcripts and 30% of differentially expressed (DE) RNAs in Leishmania-infected macrophage correspond to lncRNAs. LncRNAs and protein coding RNAs with altered expression are similar among macrophages infected with the Leishmania species. Still, some species-specific alterations could occur due to distinct pathophysiology in which Li infection led to a more significant number of exclusively DE RNAs. The most represented classes among DE lncRNAs were intergenic and antisense lncRNAs. We also found enrichment for immune response-related pathways in the DE protein coding RNAs, as well as putative targets of the lncRNAs. We performed a coexpression analysis to explore potential cis regulation of coding and antisense noncoding transcripts. We identified that antisense lncRNAs are similarly regulated as its neighbor protein coding genes, such as the BAALC/BAALC-AS1, BAALC/BAALC-AS2, HIF1A/HIF1A-AS1, HIF1A/HIF1A-AS3 and IRF1/IRF1-AS1 pairs, which can occur as a species-specific modulation. These findings are a novelty in the field because, to date, no study has focused on analyzing lncRNAs in Leishmania-infected macrophage. Our results suggest that lncRNAs may account for a novel mechanism by which Leishmania can control macrophage function. Further research must validate putative lncRNA targets and provide additional prospects in lncRNA function during Leishmania infection.
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Affiliation(s)
- Juliane C. R. Fernandes
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil,Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Lucile M. Floeter-Winter
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Sandra M. Muxel
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil,*Correspondence: Sandra M. Muxel,
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41
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Däullary T, Imdahl F, Dietrich O, Hepp L, Krammer T, Fey C, Neuhaus W, Metzger M, Vogel J, Westermann AJ, Saliba AE, Zdzieblo D. A primary cell-based in vitro model of the human small intestine reveals host olfactomedin 4 induction in response to Salmonella Typhimurium infection. Gut Microbes 2023; 15:2186109. [PMID: 36939013 PMCID: PMC10038062 DOI: 10.1080/19490976.2023.2186109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Infection research largely relies on classical cell culture or mouse models. Despite having delivered invaluable insights into host-pathogen interactions, both have limitations in translating mechanistic principles to human pathologies. Alternatives can be derived from modern Tissue Engineering approaches, allowing the reconstruction of functional tissue models in vitro. Here, we combined a biological extracellular matrix with primary tissue-derived enteroids to establish an in vitro model of the human small intestinal epithelium exhibiting in vivo-like characteristics. Using the foodborne pathogen Salmonella enterica serovar Typhimurium, we demonstrated the applicability of our model to enteric infection research in the human context. Infection assays coupled to spatio-temporal readouts recapitulated the established key steps of epithelial infection by this pathogen in our model. Besides, we detected the upregulation of olfactomedin 4 in infected cells, a hitherto unrecognized aspect of the host response to Salmonella infection. Together, this primary human small intestinal tissue model fills the gap between simplistic cell culture and animal models of infection, and shall prove valuable in uncovering human-specific features of host-pathogen interplay.
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Affiliation(s)
- Thomas Däullary
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
- Faculty of Biology, Biocenter, Chair of Microbiology, Julius-Maximilians-Universität Würzburg (JMU), Würzburg, Germany
| | - Fabian Imdahl
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Oliver Dietrich
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Laura Hepp
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
| | - Tobias Krammer
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Christina Fey
- Fraunhofer Institute for Silicate Research (ISC),Translational Center Regenerative Therapies (TLC-RT), Würzburg, Germany
| | - Winfried Neuhaus
- Austrian Institute of Technology (AIT), Vienna, Austria
- Department of Medicine, Faculty of Medicine and Dentistry, Danube Private University (DPU), Krems, Austria
| | - Marco Metzger
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
- Fraunhofer Institute for Silicate Research (ISC),Translational Center Regenerative Therapies (TLC-RT), Würzburg, Germany
- Fraunhofer Institute for Silicate Research, Project Center for Stem Cell Process Engineering, Würzburg, Germany
| | - Jörg Vogel
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Alexander J Westermann
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz-Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Daniela Zdzieblo
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg (UKW), Würzburg, Germany
- Fraunhofer Institute for Silicate Research (ISC),Translational Center Regenerative Therapies (TLC-RT), Würzburg, Germany
- Fraunhofer Institute for Silicate Research, Project Center for Stem Cell Process Engineering, Würzburg, Germany
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42
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Abstract
Enteric bacterial infections contribute substantially to global disease burden and mortality, particularly in the developing world. In vitro 2D monolayer cultures have provided critical insights into the fundamental virulence mechanisms of a multitude of pathogens, including Salmonella enterica serovars Typhimurium and Typhi, Vibrio cholerae, Shigella spp., Escherichia coli and Campylobacter jejuni, which have led to the identification of novel targets for antimicrobial therapy and vaccines. In recent years, the arsenal of experimental systems to study intestinal infections has been expanded by a multitude of more complex models, which have allowed to evaluate the effects of additional physiological and biological parameters on infectivity. Organoids recapitulate the cellular complexity of the human intestinal epithelium while 3D bioengineered scaffolds and microphysiological devices allow to emulate oxygen gradients, flow and peristalsis, as well as the formation and maintenance of stable and physiologically relevant microbial diversity. Additionally, advancements in ex vivo cultures and intravital imaging have opened new possibilities to study the effects of enteric pathogens on fluid secretion, barrier integrity and immune cell surveillance in the intact intestine. This review aims to present a balanced and updated overview of current intestinal in vitro and ex vivo methods for modeling of enteric bacterial infections. We conclude that the different paradigms are complements rather than replacements and their combined use promises to further our understanding of host-microbe interactions and their impacts on intestinal health.
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Affiliation(s)
- Nayere Taebnia
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- CONTACT Ute Römling Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Volker M. Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- Volker M. Lauschke Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
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43
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Krohmaly KI, Freishtat RJ, Hahn AL. Bioinformatic and experimental methods to identify and validate bacterial RNA-human RNA interactions. J Investig Med 2023; 71:23-31. [PMID: 36162901 DOI: 10.1136/jim-2022-002509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 01/21/2023]
Abstract
Ample evidence supports the importance of the microbiota on human health and disease. Recent studies suggest that extracellular vesicles are an important means of bacterial-host communication, in part via the transport of small RNAs (sRNAs). Bacterial sRNAs have been shown to co-precipitate with human and mouse RNA-induced silencing complex, hinting that some may regulate gene expression as eukaryotic microRNAs do. Bioinformatic tools, including those that can incorporate an sRNA's secondary structure, can be used to predict interactions between bacterial sRNAs and human messenger RNAs (mRNAs). Validation of these potential interactions using reproducible experimental methods is essential to move the field forward. This review will cover the evidence of interspecies communication via sRNAs, bioinformatic tools currently available to identify potential bacterial sRNA-host (specifically, human) mRNA interactions, and experimental methods to identify and validate those interactions.
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Affiliation(s)
- Kylie I Krohmaly
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Institute for Biomedical Sciences, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Division of Emergency Medicine, Children's National Hospital, Washington, District of Columbia, USA.,Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Andrea L Hahn
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA.,Division of Infectious Diseases, Children's National Hospital, Washington, District of Columbia, USA
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44
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Hiramatsu Y, Nishida T, Nugraha DK, Osada-Oka M, Nakane D, Imada K, Horiguchi Y. Interference of flagellar rotation up-regulates the expression of small RNA contributing to Bordetella pertussis infection. SCIENCE ADVANCES 2022; 8:eade8971. [PMID: 36542710 PMCID: PMC9770993 DOI: 10.1126/sciadv.ade8971] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Bacterial small RNAs (sRNAs) posttranscriptionally regulate gene expressions involved in various biological processes, including pathogenicity. Our previous study identified sRNAs, the expression of which was up-regulated in Bordetella pertussis, the causative agent of whooping cough, upon tracheal colonization of the bacteria; however, their roles in bacterial infection remain unknown. Here, we found that one sRNA, Bpr4, contributes to B. pertussis infection by posttranscriptionally up-regulating filamentous hemagglutinin (FHA), a major adhesin of the bacteria. Bpr4 bound to the 5' untranslated region of fhaB mRNA encoding FHA and inhibited its degradation mediated by RNaseE. Our results demonstrated that Bpr4 up-regulation was triggered by the interference of flagellar rotation, which caused the disengagement of MotA, a flagellar stator. Subsequently, MotA activated a diguanylate cyclase to generate cyclic di-GMP, which plays a role in Bpr4 up-regulation through the RisK/RisA two-component system. Our findings indicate that a flagellum-triggered sensory system contributes to B. pertussis infection.
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Affiliation(s)
- Yukihiro Hiramatsu
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Takashi Nishida
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Dendi Krisna Nugraha
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Mayuko Osada-Oka
- Food Hygiene and Environmental Health, Division of Applied Life Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-8522, Japan
| | - Daisuke Nakane
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhiko Horiguchi
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, 2-8 Yamada-oka, Suita, Osaka 565-0871, Japan
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45
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Jim KK, Aprianto R, Koning R, Domenech A, Kurushima J, van de Beek D, Vandenbroucke-Grauls CMJE, Bitter W, Veening JW. Pneumolysin promotes host cell necroptosis and bacterial competence during pneumococcal meningitis as shown by whole-animal dual RNA-seq. Cell Rep 2022; 41:111851. [PMID: 36543127 PMCID: PMC9794515 DOI: 10.1016/j.celrep.2022.111851] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/16/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Pneumolysin is a major virulence factor of Streptococcus pneumoniae that plays a key role in interaction with the host during invasive disease. How pneumolysin influences these dynamics between host and pathogen interaction during early phase of central nervous system infection in pneumococcal meningitis remains unclear. Using a whole-animal in vivo dual RNA sequencing (RNA-seq) approach, we identify pneumolysin-specific transcriptional responses in both S. pneumoniae and zebrafish (Danio rerio) during early pneumococcal meningitis. By functional enrichment analysis, we identify host pathways known to be activated by pneumolysin and discover the importance of necroptosis for host survival. Inhibition of this pathway using the drug GSK'872 increases host mortality during pneumococcal meningitis. On the pathogen's side, we show that pneumolysin-dependent competence activation is crucial for intra-host replication and virulence. Altogether, this study provides new insights into pneumolysin-specific transcriptional responses and identifies key pathways involved in pneumococcal meningitis.
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Affiliation(s)
- Kin Ki Jim
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Microbiology and Infection Prevention, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Neurology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Rieza Aprianto
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Rutger Koning
- Amsterdam UMC Location University of Amsterdam, Department of Neurology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Arnau Domenech
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Jun Kurushima
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Diederik van de Beek
- Amsterdam UMC Location University of Amsterdam, Department of Neurology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Christina M J E Vandenbroucke-Grauls
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Microbiology and Infection Prevention, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Wilbert Bitter
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Microbiology and Infection Prevention, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, 1081 Amsterdam, the Netherlands
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland.
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Wang Z, Zhu S, Li C, Lyu L, Yu J, Wang D, Xu Z, Ni J, Gao B, Lu J, Yao YF. Gene essentiality profiling reveals a novel determinant of stresses preventing protein aggregation in Salmonella. Emerg Microbes Infect 2022; 11:1554-1571. [PMID: 35603550 PMCID: PMC9176671 DOI: 10.1080/22221751.2022.2081618] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Adaptation to various stresses during infection is important for Salmonella Typhimurium virulence, while the fitness determinants under infection-relevant stress conditions remain unknown. Here, we simulated conditions Salmonella encountered within the host or in the environment by 15 individual stresses as well as two model cell lines (epithelium and macrophage) to decipher the genes and pathways required for fitness. By high-resolution Tn-seq analysis, a total of 1242 genes were identified as essential for fitness under at least one stress condition. The comparative analysis of fitness determinants in 17 stress conditions indicated the essentiality of genes varied in different mimicking host niches. A total of 12 genes were identified as fitness determinants in all stress conditions, including recB, recC, and xseA (encode three exonuclease subunits necessary for DNA recombination repair) and a novel essential fitness gene yheM. YheM is a putative sulfurtransferase subunit that is responsible for tRNA modification, and our results showed that Salmonella lacking yheM accumulated more aggregates of endogenous protein than wild-type. Moreover, we established a scoring scheme for sRNA essentiality analysis and found STnc2080 of unknown function was essential for resistance to LL-37. In summary, we systematically dissected Salmonella gene essentiality profiling and demonstrated the general and specific adaptive requirements in infection-relevant niches. Our data not only provide valuable insights on how Salmonella responds to environmental stresses during infections but also highlight the potential clinical application of fitness determinants in vaccine development.
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Affiliation(s)
- Zuoqiang Wang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Siqi Zhu
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Congcong Li
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Lin Lyu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Jingchen Yu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Zhihong Xu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, People's Republic of China
| | - Jie Lu
- Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai, People's Republic of China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, People's Republic of China
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47
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Developing New Tools to Fight Human Pathogens: A Journey through the Advances in RNA Technologies. Microorganisms 2022; 10:microorganisms10112303. [DOI: 10.3390/microorganisms10112303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
A long scientific journey has led to prominent technological advances in the RNA field, and several new types of molecules have been discovered, from non-coding RNAs (ncRNAs) to riboswitches, small interfering RNAs (siRNAs) and CRISPR systems. Such findings, together with the recognition of the advantages of RNA in terms of its functional performance, have attracted the attention of synthetic biologists to create potent RNA-based tools for biotechnological and medical applications. In this review, we have gathered the knowledge on the connection between RNA metabolism and pathogenesis in Gram-positive and Gram-negative bacteria. We further discuss how RNA techniques have contributed to the building of this knowledge and the development of new tools in synthetic biology for the diagnosis and treatment of diseases caused by pathogenic microorganisms. Infectious diseases are still a world-leading cause of death and morbidity, and RNA-based therapeutics have arisen as an alternative way to achieve success. There are still obstacles to overcome in its application, but much progress has been made in a fast and effective manner, paving the way for the solid establishment of RNA-based therapies in the future.
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48
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Raad N, Tandon D, Hapfelmeier S, Polacek N. The stationary phase-specific sRNA FimR2 is a multifunctional regulator of bacterial motility, biofilm formation and virulence. Nucleic Acids Res 2022; 50:11858-11875. [PMID: 36354005 PMCID: PMC9723502 DOI: 10.1093/nar/gkac1025] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 10/06/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
Bacterial pathogens employ a plethora of virulence factors for host invasion, and their use is tightly regulated to maximize infection efficiency and manage resources in a nutrient-limited environment. Here we show that during Escherichia coli stationary phase the 3' UTR-derived small non-coding RNA FimR2 regulates fimbrial and flagellar biosynthesis at the post-transcriptional level, leading to biofilm formation as the dominant mode of survival under conditions of nutrient depletion. FimR2 interacts with the translational regulator CsrA, antagonizing its functions and firmly tightening control over motility and biofilm formation. Generated through RNase E cleavage, FimR2 regulates stationary phase biology by fine-tuning target mRNA levels independently of the chaperones Hfq and ProQ. The Salmonella enterica orthologue of FimR2 induces effector protein secretion by the type III secretion system and stimulates infection, thus linking the sRNA to virulence. This work reveals the importance of bacterial sRNAs in modulating various aspects of bacterial physiology including stationary phase and virulence.
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Affiliation(s)
- Nicole Raad
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, Bern, Switzerland,Graduate School for Cellular and Biomedical Sciences, Bern, Switzerland
| | - Disha Tandon
- Graduate School for Cellular and Biomedical Sciences, Bern, Switzerland,Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Norbert Polacek
- To whom correspondence should be addressed. Tel: +41 31 684 43 20;
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49
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Ji X, Han L, Zhang W, Sun L, Xu S, Qiu X, Fan S, Li Z. Molecular, cellular and neurological consequences of infection by the neglected human pathogen Nocardia. BMC Biol 2022; 20:251. [PMID: 36352407 PMCID: PMC9647956 DOI: 10.1186/s12915-022-01452-7] [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: 06/02/2022] [Accepted: 10/29/2022] [Indexed: 11/10/2022] Open
Abstract
Background Nocardia is a facultative intracellular pathogen that infects the lungs and brains of immunocompromised patients with consequences that can be fatal. The incidence of such infections is rising, immunocompetent individuals are also being infected, and there is a need to learn more about this neglected bacterial pathogen and the interaction with its human host. Results We have applied dual RNA-seq to assess the global transcriptome changes that occur simultaneously in Nocardia farcinica (N. farcinica) and infected human epithelial alveolar host cells, and have tested a series of mutants in this in vitro system to identify candidate determinants of virulence. Using a mouse model, we revealed the profiles of inflammation-related factors in the lung after intranasal infection and confirmed that nbtB and nbtS are key virulence genes for Nocardia infection in vivo. Regarding the host response to infection, we found that the expression of many histones was dysregulated during the infection of lung cells, indicating that epigenetic modification might play a crucial role in the host during Nocardia infection. In our mouse model, Nocardia infection led to neurological symptoms and we found that 15 of 22 Nocardia clinical strains tested could cause obvious PD-like symptoms. Further experiments indicated that Nocardia infection could activate microglia and drive M1 microglial polarization, promote iNOS and CXCL-10 production, and cause neuroinflammation in the substantia nigra, all of which may be involved in causing PD-like symptoms. Importantly, the deletion of nbtS in N. farcinica completely attenuated the neurological symptoms. Conclusions Our data contribute to an in-depth understanding of the characteristics of both the host and Nocardia during infection and provide valuable clues for future studies of this neglected human pathogen, especially those addressing the underlying causes of infection-related neurological symptoms. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01452-7.
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50
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Majumder R, Ghosh S, Das A, Singh MK, Samanta S, Saha A, Saha RP. Prokaryotic ncRNAs: Master regulators of gene expression. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100136. [PMID: 36568271 PMCID: PMC9780080 DOI: 10.1016/j.crphar.2022.100136] [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] [Received: 06/30/2022] [Revised: 09/11/2022] [Accepted: 10/14/2022] [Indexed: 12/14/2022] Open
Abstract
ncRNA plays a very pivotal role in various biological activities ranging from gene regulation to controlling important developmental networks. It is imperative to note that this small molecule is not only present in all three domains of cellular life, but is an important modulator of gene regulation too in all these domains. In this review, we discussed various aspects of ncRNA biology, especially their role in bacteria. The last two decades of scientific research have proved that this molecule plays an important role in the modulation of various regulatory pathways in bacteria including the adaptive immune system and gene regulation. It is also very surprising to note that this small molecule is also employed in various processes related to the pathogenicity of virulent microorganisms.
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Affiliation(s)
- Rajib Majumder
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Sanmitra Ghosh
- Department of Biological Sciences, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Arpita Das
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Manoj Kumar Singh
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Saikat Samanta
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Abinit Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India,Corresponding authors.
| | - Rudra P. Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India,Corresponding authors.
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