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Peregrino ES, Castañeda-Casimiro J, Vázquez-Flores L, Estrada-Parra S, Wong-Baeza C, Serafín-López J, Wong-Baeza I. The Role of Bacterial Extracellular Vesicles in the Immune Response to Pathogens, and Therapeutic Opportunities. Int J Mol Sci 2024; 25:6210. [PMID: 38892397 PMCID: PMC11172497 DOI: 10.3390/ijms25116210] [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: 05/01/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Pathogenic bacteria have several mechanisms to evade the host's immune response and achieve an efficient infection. Bacterial extracellular vesicles (EVs) are a relevant cellular communication mechanism, since they can interact with other bacterial cells and with host cells. In this review, we focus on the EVs produced by some World Health Organization (WHO) priority Gram-negative and Gram-positive pathogenic bacteria; by spore-producing bacteria; by Mycobacterium tuberculosis (a bacteria with a complex cell wall); and by Treponema pallidum (a bacteria without lipopolysaccharide). We describe the classification and the general properties of bacterial EVs, their role during bacterial infections and their effects on the host immune response. Bacterial EVs contain pathogen-associated molecular patterns that activate innate immune receptors, which leads to cytokine production and inflammation, but they also contain antigens that induce the activation of B and T cell responses. Understanding the many effects of bacterial EVs on the host's immune response can yield new insights on the pathogenesis of clinically important infections, but it can also lead to the development of EV-based diagnostic and therapeutic strategies. In addition, since EVs are efficient activators of both the innate and the adaptive immune responses, they constitute a promising platform for vaccine development.
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Affiliation(s)
- Eliud S. Peregrino
- Posgrado en Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (E.S.P.); (J.C.-C.)
| | - Jessica Castañeda-Casimiro
- Posgrado en Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (E.S.P.); (J.C.-C.)
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (S.E.-P.); (J.S.-L.)
| | - Luis Vázquez-Flores
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (L.V.-F.); (C.W.-B.)
| | - Sergio Estrada-Parra
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (S.E.-P.); (J.S.-L.)
| | - Carlos Wong-Baeza
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (L.V.-F.); (C.W.-B.)
| | - Jeanet Serafín-López
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (S.E.-P.); (J.S.-L.)
| | - Isabel Wong-Baeza
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (S.E.-P.); (J.S.-L.)
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2
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Singh RN, Sani RK. Genome-Wide Computational Prediction and Analysis of Noncoding RNAs in Oleidesulfovibrio alaskensis G20. Microorganisms 2024; 12:960. [PMID: 38792789 PMCID: PMC11124144 DOI: 10.3390/microorganisms12050960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Noncoding RNAs (ncRNAs) play key roles in the regulation of important pathways, including cellular growth, stress management, signaling, and biofilm formation. Sulfate-reducing bacteria (SRB) contribute to huge economic losses causing microbial-induced corrosion through biofilms on metal surfaces. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation. This study aimed to identify ncRNAs in the genome of a model SRB, Oleidesulfovibrio alaskensis G20 (OA G20). Three in silico approaches revealed genome-wide distribution of 37 ncRNAs excluding tRNAs in the OA G20. These ncRNAs belonged to 18 different Rfam families. This study identified riboswitches, sRNAs, RNP, and SRP. The analysis revealed that these ncRNAs could play key roles in the regulation of several pathways of biosynthesis and transport involved in biofilm formation by OA G20. Three sRNAs, Pseudomonas P10, Hammerhead type II, and sX4, which were found in OA G20, are rare and their roles have not been determined in SRB. These results suggest that applying various computational methods could enrich the results and lead to the discovery of additional novel ncRNAs, which could lead to understanding the "rules of life of OA G20" during biofilm formation.
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Affiliation(s)
- Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota Mines, Rapid City, SD 57701, USA
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3
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Swain MT, Radford EJ, Akanyeti AS, Hallwood JH, Whitworth DE. The RNA cargo of Myxococcus outer membrane vesicles. Mol Omics 2024; 20:138-145. [PMID: 38098456 DOI: 10.1039/d3mo00222e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The outer membrane vesicles (OMVs) secreted by some Gram-negative bacteria contain RNA cargo, which can be introduced into target cells, affecting their cellular processes. To test whether the antimicrobial OMVs secreted by predatory myxobacteria might contain cargo RNA with a role in prey killing, we purified OMVs and cells from four different strains of Myxococcus spp. for RNA-seq transcriptome sequencing. Myxobacterial OMVs contained distinct sets of RNA molecules. The abundance of major cellular transcripts correlated strongly with their abundance in OMVs, suggesting non-specific packaging into OMVs. However, many major cellular transcripts were absent entirely from OMVs and some transcripts were found exclusively in OMVs, suggesting OMV RNA cargo loading is not simply a consequence of sampling the cellular transcriptome. Despite considerable variation in OMV RNA cargo between biological replicates, a small number of transcripts were found consistently in replicate OMV preparations. These 'core' OMV transcripts were often found in the OMVs from multiple strains, and sometimes enriched relative to their abundance in cellular transcriptomes. In addition to providing the first transcriptomes for myxobacterial OMVs, and the first cellular transcriptomes for three strains of Myxococcus spp., we highlight five transcripts for further study. These transcripts are 'core' for at least two of the three strains of M. xanthus studied, and encode two alkyl hydroperoxidase proteins (AhpC and AhpD), two ribosome-associated inhibitors (RaiA-like) and a DO-family protease. It will be interesting to test whether the transcripts serve a biological function within OMVs, potentially being transported into prey cells for translation into toxic proteins.
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Affiliation(s)
- Martin T Swain
- Department of Life Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK.
| | - Emily J Radford
- Department of Life Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK.
| | - Allison S Akanyeti
- Department of Life Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK.
| | - James H Hallwood
- Department of Life Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK.
| | - David E Whitworth
- Department of Life Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK.
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4
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Roy Chowdhury M, Massé E. New Perspectives on Crosstalks Between Bacterial Regulatory RNAs from Outer Membrane Vesicles and Eukaryotic Cells. Methods Mol Biol 2024; 2741:183-194. [PMID: 38217654 DOI: 10.1007/978-1-0716-3565-0_10] [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
Regulatory small RNAs (sRNAs) help the bacteria to survive harsh environmental conditions by posttranscriptional regulation of genes involved in various biological pathways including stress responses, homeostasis, and virulence. These sRNAs can be found carried by different membrane-bound vesicles like extracellular vesicles (EVs), membrane vesicles (MVs), or outer membrane vesicles (OMVs). OMVs provide myriad functions in bacterial cells including carrying a cargo of proteins, lipids, and nucleic acids including sRNAs. A few interesting studies have shown that these sRNAs can be transported to the host cell by membrane vesicles and can regulate the host immune system. Although there is evidence that sRNAs can be exported to host cells and sometimes can even cross the blood-brain barrier, the exact mechanism is still unknown. In this review, we investigated the new techniques implemented in various studies, to elucidate the crosstalks between bacterial cells and human immune systems by membrane vesicles carrying bacterial regulatory sRNAs.
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Affiliation(s)
- Moumita Roy Chowdhury
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric Massé
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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5
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Gurunathan S, Ajmani A, Kim JH. Extracellular nanovesicles produced by Bacillus licheniformis: A potential anticancer agent for breast and lung cancer. Microb Pathog 2023; 185:106396. [PMID: 37863272 DOI: 10.1016/j.micpath.2023.106396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/26/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
Cancer is a major public burden and leading cause of death worldwide; furthermore, it is a significant barrier to increasing life expectancy in most countries of the world. Among various types of cancers, breast and lung cancers lead to significant mortality in both males and females annually. Bacteria-derived products have been explored for their use in cancer therapy. Although bacteria contain significant amounts of anticancer substances, attenuated bacteria may still pose a potential risk for infection owing to the variety of immunomodulatory molecules present in the parental bacteria; therefore, non-cellular bacterial extracellular vesicles (BEVs), which are naturally non-replicating, safer, and are considered to be potential anticancer agents, are preferred for cancer therapy. Gram-positive bacteria actively secrete cytoplasmic membrane vesicles that are spherical and vary between 10 and 400 nm in size. However, no studies have considered cytoplasmic membrane vesicles derived from Bacillus licheniformisin cancer treatment. In this study, we investigated the potential use of B. licheniformis extracellular nanovesicles (BENVs) as therapeutic agents to treat cancer. Purified BENVs from the culture supernatant of B. licheniformis using ultracentrifugation and ExoQuick were characterized using a series of analytical techniques. Human breast cancer cells (MDA-MB-231) and lung cancer cells (A549) were treated with different concentrations of purified BENVs, which inhibited the cell viability and proliferation, and increased cytotoxicity in a dose-dependent manner. To elucidate the mechanism underlying the anticancer activity of BENVs, the oxidative stress markers such as reactive oxygen species (ROS) and glutathione (GSH) levels were measured. The ROS levels were significantly higher in BENV-treated cells, whereas the GSH levels were markedly reduced. Cells treated with BENVs, doxorubicin (DOX), or a combination of BENVs and DOX showed significantly increased expression of p53, p21, caspase-9/3, and Bax, and concomitantly decreased expression of Bcl-2. The combination of BENVs and doxorubicin enhanced mitochondrial dysfunction, DNA damage, and apoptosis. To our knowledge, this is the first study to determine the anticancer properties of BENVs derived from industrially significant probacteria on breast and lung cancer cells.
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Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Biotechnology, Rathinam College of Arts and Science, RathinamTechzone Campus, Eachanari, Coimbatore, 641 021, Tamil Nadu, India.
| | - Abhishek Ajmani
- Institute of Advanced Virology, Thiruvananthapuram, 695014, Kerala, India
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, South Korea.
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6
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Sheikh A, Zechmann B, Sayes CM, Taube JH, Greathouse KL. A preparation of bacterial outer membrane with osmium tetroxide and uranyl acetate co-stain enables improved structural determination by transmission electron microscopy. Microscopy (Oxf) 2023; 72:515-519. [PMID: 37148329 PMCID: PMC10673695 DOI: 10.1093/jmicro/dfad027] [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: 01/20/2023] [Revised: 04/10/2023] [Accepted: 05/04/2023] [Indexed: 05/08/2023] Open
Abstract
Biological nanoparticles, such as bacterial outer membrane vesicles (OMVs), are routinely characterized through transmission electron microscopy (TEM). In this study, we report a novel method to prepare OMVs for TEM imaging. To preserve vesicular shape and structure, we developed a dual fixation protocol involving osmium tetroxide incubation prior to negative staining with uranyl acetate. Combining osmium tetroxide with uranyl acetate resulted in preservation of sub-50 nm vesicles and improved morphological stability, enhancing characterization of lipid-based nanoparticles by TEM.
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Affiliation(s)
- Aadil Sheikh
- Department of Biology, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - Bernd Zechmann
- Center for Microscopy and Imaging, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - Christie M Sayes
- Department of Environmental Science, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - Joseph H Taube
- Department of Biology, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - K Leigh Greathouse
- Department of Biology, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
- Nutrition Sciences, Baylor University, One Bear Place #97311, Waco, TX 76798, USA
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7
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Ayesha A, Chow FWN, Leung PHM. Role of Legionella pneumophila outer membrane vesicles in host-pathogen interaction. Front Microbiol 2023; 14:1270123. [PMID: 37817751 PMCID: PMC10561282 DOI: 10.3389/fmicb.2023.1270123] [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: 07/31/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023] Open
Abstract
Legionella pneumophila is an opportunistic intracellular pathogen that inhabits artificial water systems and can be transmitted to human hosts by contaminated aerosols. Upon inhalation, it colonizes and grows inside the alveolar macrophages and causes Legionnaires' disease. To effectively control and manage Legionnaires' disease, a deep understanding of the host-pathogen interaction is crucial. Bacterial extracellular vesicles, particularly outer membrane vesicles (OMVs) have emerged as mediators of intercellular communication between bacteria and host cells. These OMVs carry a diverse cargo, including proteins, toxins, virulence factors, and nucleic acids. OMVs play a pivotal role in disease pathogenesis by helping bacteria in colonization, delivering virulence factors into host cells, and modulating host immune responses. This review highlights the role of OMVs in the context of host-pathogen interaction shedding light on the pathogenesis of L. pneumophila. Understanding the functions of OMVs and their cargo provides valuable insights into potential therapeutic targets and interventions for combating Legionnaires' disease.
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Affiliation(s)
| | | | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
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8
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Luo R, Chang Y, Liang H, Zhang W, Song Y, Li G, Yang C. Interactions between extracellular vesicles and microbiome in human diseases: New therapeutic opportunities. IMETA 2023; 2:e86. [PMID: 38868436 PMCID: PMC10989913 DOI: 10.1002/imt2.86] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/21/2022] [Accepted: 01/14/2023] [Indexed: 06/14/2024]
Abstract
In recent decades, accumulating research on the interactions between microbiome homeostasis and host health has broadened new frontiers in delineating the molecular mechanisms of disease pathogenesis and developing novel therapeutic strategies. By transporting proteins, nucleic acids, lipids, and metabolites in their versatile bioactive molecules, extracellular vesicles (EVs), natural bioactive cell-secreted nanoparticles, may be key mediators of microbiota-host communications. In addition to their positive and negative roles in diverse physiological and pathological processes, there is considerable evidence to implicate EVs secreted by bacteria (bacterial EVs [BEVs]) in the onset and progression of various diseases, including gastrointestinal, respiratory, dermatological, neurological, and musculoskeletal diseases, as well as in cancer. Moreover, an increasing number of studies have explored BEV-based platforms to design novel biomedical diagnostic and therapeutic strategies. Hence, in this review, we highlight the recent advances in BEV biogenesis, composition, biofunctions, and their potential involvement in disease pathologies. Furthermore, we introduce the current and emerging clinical applications of BEVs in diagnostic analytics, vaccine design, and novel therapeutic development.
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Affiliation(s)
- Rongjin Luo
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Spine Surgery, Honghui HospitalXi'an Jiaotong UniversityXi'anChina
| | - Yanmin Chang
- Department of Neurology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Huaizhen Liang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Weifeng Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yu Song
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Gaocai Li
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Cao Yang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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9
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Composition and functions of bacterial membrane vesicles. Nat Rev Microbiol 2023:10.1038/s41579-023-00875-5. [PMID: 36932221 DOI: 10.1038/s41579-023-00875-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2023] [Indexed: 03/19/2023]
Abstract
Extracellular vesicles are produced by species across all domains of life, suggesting that vesiculation represents a fundamental principle of living matter. In Gram-negative bacteria, membrane vesicles (MVs) can originate either from blebs of the outer membrane or from endolysin-triggered explosive cell lysis, which is often induced by genotoxic stress. Although less is known about the mechanisms of vesiculation in Gram-positive and Gram-neutral bacteria, recent research has shown that both lysis and blebbing mechanisms also exist in these organisms. Evidence has accumulated over the past years that different biogenesis routes lead to distinct types of MV with varied structure and composition. In this Review, we discuss the different types of MV and their potential cargo packaging mechanisms. We summarize current knowledge regarding how MV composition determines their various functions including support of bacterial growth via the disposal of waste material, nutrient scavenging, export of bioactive molecules, DNA transfer, neutralization of phages, antibiotics and bactericidal functions, delivery of virulence factors and toxins to host cells and inflammatory and immunomodulatory effects. We also discuss the advantages of MV-mediated secretion compared with classic bacterial secretion systems and we introduce the concept of quantal secretion.
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10
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Rangel-Ramírez VV, González-Sánchez HM, Lucio-García C. Exosomes: from biology to immunotherapy in infectious diseases. Infect Dis (Lond) 2023; 55:79-107. [PMID: 36562253 DOI: 10.1080/23744235.2022.2149852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Exosomes are extracellular vesicles derived from the endosomal compartment, which are released by all kinds of eukaryotic and prokaryotic organisms. These vesicles contain a variety of biomolecules that differ both in quantity and type depending on the origin and cellular state. Exosomes are internalized by recipient cells, delivering their content and thus contributing to cell-cell communication in health and disease. During infections exosomes may exert a dual role, on one hand, they can transmit pathogen-related molecules mediating further infection and damage, and on the other hand, they can protect the host by activating the immune response and reducing pathogen spread. Selective packaging of pathogenic components may mediate these effects. Recently, quantitative analysis of samples by omics technologies has allowed a deep characterization of the proteins, lipids, RNA, and metabolite cargoes of exosomes. Knowledge about the content of these vesicles may facilitate their therapeutic application. Furthermore, as exosomes have been detected in almost all biological fluids, pathogenic or host-derived components can be identified in liquid biopsies, making them suitable for diagnosis and prognosis. This review attempts to organize the recent findings on exosome composition and function during viral, bacterial, fungal, and protozoan infections, and their contribution to host defense or to pathogen spread. Moreover, we summarize the current perspectives and future directions regarding the potential application of exosomes for prophylactic and therapeutic purposes.
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Affiliation(s)
| | | | - César Lucio-García
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
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11
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Liu L, Law COK, Nie Q, Pham HQ, Ma H, Zhang L, Ho PL, Lau TCK. Comparative analysis of outer membrane vesicles from uropathogenic Escherichia coli reveal the role of aromatic amino acids synthesis proteins in motility. Int J Med Microbiol 2023; 313:151573. [PMID: 36634604 DOI: 10.1016/j.ijmm.2023.151573] [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: 09/16/2022] [Revised: 12/15/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) are causative agent that causes urinary tract infections (UTIs) and the recent emergence of multidrug resistance (MDR) of UPEC increases the burden on the community. Recent studies of bacterial outer membrane vesicles (OMV) identified various factors including proteins, nucleic acids, and small molecules which provided inter-cellular communication within the bacterial population. However, the components of UPEC-specific OMVs and their functional role remain unclear. Here, we systematically determined the proteomes of UPEC-OMVs and identified the specific components that provide functions to the recipient bacteria. Based on the functional network of OMVs' proteomes, a group of signaling peptides was found in all OMVs which provide communication among bacteria. Moreover, we demonstrated that treatment with UPEC-OMVs affected the motility and biofilm formation of the recipient bacteria, and further identified aromatic amino acid (AAA) biosynthesis proteins as the key factors to provide their movement.
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Affiliation(s)
- LiangZhe Liu
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518000, China; Center for Clinical Precision Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China; School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Carmen Oi Kwan Law
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518000, China
| | - Qichang Nie
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518000, China
| | - Hoa Quynh Pham
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518000, China
| | - Haiying Ma
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Liang Zhang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Pak Leung Ho
- Department of Microbiology, Queen Mary Hospital, University of Hong Kong, Hong Kong Special Administrative Region
| | - Terrence Chi-Kong Lau
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518000, China.
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12
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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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13
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Imrat, Labala RK, Behara AK, Jeyaram K. Selective extracellular secretion of small double-stranded RNA by Tetragenococcus halophilus. Funct Integr Genomics 2022; 23:10. [PMID: 36542169 DOI: 10.1007/s10142-022-00934-9] [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: 09/05/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Small double-stranded RNAs (dsRNAs) abundantly produced by lactic acid bacteria demonstrate immunomodulatory activity and antiviral protective immunity. However, the extracellular secretion of dsRNA from lactic acid bacteria and their compositional and functional differences compared to the intracellular dsRNA is unknown. In this study, we compared the intracellular and secreted extracellular dsRNA of the lactic acid bacteria, Tetragenococcus halophilus, commonly present in fermented foods, by growing in RNA-free and RNase-free media. We used RNA deep sequencing and in-silico analysis to annotate potential regulatory functions for the comparison. A time series sampling of T. halophilus culture demonstrated growth phase-dependent dynamics in extracellular dsRNA secretion with no major change in the intracellular dsRNA profile. The RNA deep sequencing resulted in thousands of diverse dsRNA fragments with 14-21 nucleotides in size from T. halophilus culture. Over 70% of the secreted extracellular dsRNAs were unique in their sequences compared to the intracellular dsRNAs. Furthermore, the extracellular dsRNA abundantly contains sequences that are not T. halophilus genome encoded, not detected intracellularly and showed higher hits on human transcriptome during in-silico analysis, which suggests the presence of extrachromosomal mobile regulatory elements. Further analysis showed significant enrichment of dsRNA target genes of human transcriptome on cancer pathways and transcription process, indicating the extracellular dsRNA of T. halophilus is different not only at the sequence level but also in function. Studying the bacterial extracellular dsRNA is a promising area of future research, particularly for developing postbiotic fermented functional foods and understanding the impact of commensal gut bacteria on human health.
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Affiliation(s)
- Imrat
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India.,Department of Biotechnology, Gauhati University, Guwahati, 781014, Assam, India
| | - Rajendra Kumar Labala
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India
| | - Abhisek Kumar Behara
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India
| | - Kumaraswamy Jeyaram
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India.,IBSD Regional Centre, Tadong, Gangtok, 737102, Sikkim, India
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14
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Hosseini-Giv N, Basas A, Hicks C, El-Omar E, El-Assaad F, Hosseini-Beheshti E. Bacterial extracellular vesicles and their novel therapeutic applications in health and cancer. Front Cell Infect Microbiol 2022; 12:962216. [PMID: 36439225 PMCID: PMC9691856 DOI: 10.3389/fcimb.2022.962216] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/20/2022] [Indexed: 10/03/2023] Open
Abstract
Bacterial cells communicate with host cells and other bacteria through the release of membrane vesicles known as bacterial extracellular vesicles (BEV). BEV are established mediators of intracellular signaling, stress tolerance, horizontal gene transfer, immune stimulation and pathogenicity. Both Gram-positive and Gram-negative bacteria produce extracellular vesicles through different mechanisms based on cell structure. BEV contain and transfer different types of cargo such as nucleic acids, proteins and lipids, which are used to interact with and affect host cells such as cytotoxicity and immunomodulation. The role of these membranous microvesicles in host communication, intra- and inter-species cell interaction and signaling, and contribution to various diseases have been well demonstrated. Due to their structure, these vesicles can be easily engineered to be utilized for clinical application, as shown with its role in vaccine therapy, and could be used as a diagnostic and cancer drug delivery tool in the future. However, like other novel therapeutic approaches, further investigation and standardization is imperative for BEV to become a routine vector or a conventional treatment method.
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Affiliation(s)
- Niloufar Hosseini-Giv
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Alyza Basas
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Chloe Hicks
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Emad El-Omar
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Fatima El-Assaad
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Elham Hosseini-Beheshti
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
- The Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
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15
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Meng X, He M, Xia P, Wang J, Wang H, Zhu G. Functions of Small Non-Coding RNAs in Salmonella–Host Interactions. BIOLOGY 2022; 11:biology11091283. [PMID: 36138763 PMCID: PMC9495376 DOI: 10.3390/biology11091283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/18/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary In the process of infecting the host, Salmonella senses and adapts to the environment within the host, breaks through the host’s defense system, and survives and multiplies in the host cell. As a class of universal regulators encoded in intergenic space, an increasing number of small non-coding RNAs (sRNAs) have been found to be involved in a series of processes during Salmonella infection, and they play an important role in interactions with the host cell. In this review, we discuss how sRNAs help Salmonella resist acidic environmental stress by regulating acid resistance genes and modulate adhesion and invasion to non-phagocytic cells by regulating virulent genes such as fimbrial subunits and outer membrane proteins. In addition, sRNAs help Salmonella adapt to oxidative stress within host cells and promote survival within macrophages. Although the function of a variety of sRNAs has been studied during host–Salmonella interactions, many of sRNAs’ functions remain to be discovered. Abstract Salmonella species infect hosts by entering phagocytic and non-phagocytic cells, causing diverse disease symptoms, such as fever, gastroenteritis, and even death. Therefore, Salmonella has attracted much attention. Many factors are involved in pathogenesis, for example, the capsule, enterotoxins, Salmonella pathogenicity islands (SPIs), and corresponding regulators. These factors are all traditional proteins associated with virulence and regulation. Recently, small non-coding RNAs (sRNAs) have also been reported to function as critical regulators. Salmonella has become a model organism for studying sRNAs. sRNAs regulate gene expression by imperfect base-pairing with targets at the post-transcriptional level. sRNAs are involved in diverse biological processes, such as virulence, substance metabolism, and adaptation to stress environments. Although some studies have reported the crucial roles of sRNAs in regulating host–pathogen interactions, the function of sRNAs in host–Salmonella interactions has rarely been reviewed. Here, we review the functions of sRNAs during the infection of host cells by Salmonella, aiming to deepen our understanding of sRNA functions and the pathogenic mechanism of Salmonella.
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Affiliation(s)
- Xia Meng
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Prevention and Control of Important Animal infectious Diseases and Zoonotic Diseases of China, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou 225009, China
- Correspondence:
| | - Mengping He
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Prevention and Control of Important Animal infectious Diseases and Zoonotic Diseases of China, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou 225009, China
| | - Pengpeng Xia
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Prevention and Control of Important Animal infectious Diseases and Zoonotic Diseases of China, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou 225009, China
| | - Jinqiu Wang
- Department of Animal Husbandry and Veterinary Medicine, Beijing Agricultural Vocational College, Beijing 102442, China
| | - Heng Wang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Prevention and Control of Important Animal infectious Diseases and Zoonotic Diseases of China, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou 225009, China
| | - Guoqiang Zhu
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Prevention and Control of Important Animal infectious Diseases and Zoonotic Diseases of China, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou 225009, China
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16
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Yu S, Zhao Z, Hao P, Qiu Y, Zhao M, Zhou G, Zhang C, Kang J, Li P. Biological Functions and Cross-Kingdom Host Gene Regulation of Small RNAs in Lactobacillus plantarum-Derived Extracellular Vesicles. Front Microbiol 2022; 13:944361. [PMID: 36060780 PMCID: PMC9436029 DOI: 10.3389/fmicb.2022.944361] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Abstract
Extracellular vesicle-mediated transfer of microRNAs is a novel mode of cell-to-cell genetic transmission. Extracellular vesicles produced by microbes have been shown to contain significant quantities of physiologically active molecules such as proteins, lipids, and RNA, which could be transported to host cells and play a key role in both inter-kingdom signaling and physiological responses. In this study, we identified sRNAs by sequencing small RNAs (sRNAs) from Lactobacillus plantarum-derived extracellular vesicles (LDEVs) and detected the expression levels of vesicular sRNAs using quantitative reverse transcription-polymerase chain reaction (RT-PCR), which demonstrated the presence of microRNA-sized RNAs (msRNAs) within these vesicles. We chose sRNA71, a highly expressed msRNA, for further investigation, predicted its potential target genes for the human genome, and indicated that it could be translocated into mammalian cells. The biological functions of this sRNA71 were subsequently explored through cellular proteomics, western blot, and luciferase reporter assay. According to the findings, transfection with synthetic sRNA71 mimics substantially reduced Tp53 expression in HEK293T cells and suppressed the gene expression through binding to the 3′ UTR of Tp53 mRNA. In conclusion, it is hypothesized that microbial-derived extracellular vesicles serve as carriers of functional molecules such as sRNAs, which play an essential role in regulating microbial-host communication.
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Affiliation(s)
- Siran Yu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhehao Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yan Qiu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Meiyi Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Gang Zhou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chengqian Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Jiuhong Kang,
| | - Ping Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- *Correspondence: Ping Li,
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17
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Naskar A, Cho H, Lee S, Kim KS. Biomimetic Nanoparticles Coated with Bacterial Outer Membrane Vesicles as a New-Generation Platform for Biomedical Applications. Pharmaceutics 2021; 13:pharmaceutics13111887. [PMID: 34834302 PMCID: PMC8618801 DOI: 10.3390/pharmaceutics13111887] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
The biomedical field is currently reaping the benefits of research on biomimetic nanoparticles (NPs), which are synthetic nanoparticles fabricated with natural cellular materials for nature-inspired biomedical applications. These camouflage NPs are capable of retaining not only the physiochemical properties of synthetic nanoparticles but also the original biological functions of the cellular materials. Accordingly, NPs coated with cell-derived membrane components have achieved remarkable growth as prospective biomedical materials. Particularly, bacterial outer membrane vesicle (OMV), which is a cell membrane coating material for NPs, is regarded as an important molecule that can be employed in several biomedical applications, including immune response activation, cancer therapeutics, and treatment for bacterial infections with photothermal activity. The currently available cell membrane-coated NPs are summarized in this review. Furthermore, the general features of bacterial OMVs and several multifunctional NPs that could serve as inner core materials in the coating strategy are presented, and several methods that can be used to prepare OMV-coated NPs (OMV-NPs) and their characterization are highlighted. Finally, some perspectives of OMV-NPs in various biomedical applications for future potential breakthrough are discussed. This in-depth review, which includes potential challenges, will encourage researchers to fabricate innovative and improvised, new-generation biomimetic materials through future biomedical applications.
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18
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Amatya SB, Salmi S, Kainulainen V, Karihtala P, Reunanen J. Bacterial Extracellular Vesicles in Gastrointestinal Tract Cancer: An Unexplored Territory. Cancers (Basel) 2021; 13:5450. [PMID: 34771614 PMCID: PMC8582403 DOI: 10.3390/cancers13215450] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/19/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial extracellular vesicles are membrane-enclosed, lipid bi-layer nanostructures that carry different classes of biomolecules, such as nucleic acids, lipids, proteins, and diverse types of small molecular metabolites, as their cargo. Almost all of the bacteria in the gut secrete extracellular vesicles to assist them in competition, survival, material exchange, host immune modulation, infection, and invasion. The role of gut microbiota in the development, progression, and pathogenesis of gastrointestinal tract (GIT) cancer has been well documented. However, the possible involvement of bacterial extracellular vesicles (bEVs) in GIT cancer pathophysiology has not been given due attention. Studies have illustrated the ability of bEVs to cross physiological barriers, selectively accumulate near tumor cells, and possibly alter the tumor microenvironment (TME). A systematic search of original published works related to bacterial extracellular vesicles on gastrointestinal cancer was performed for this review. The current systemic review outlines the possible impact of gut microbiota derived bEVs in GIT cancer in light of present-day understanding. The necessity of using advanced sequencing technologies, such as genetic, proteomic, and metabolomic investigation methodologies, to facilitate an understanding of the interrelationship between cancer-associated bacterial vesicles and gastrointestinal cancer is also emphasized. We further discuss the clinical and pharmaceutical potential of bEVs, along with future efforts needed to understand the mechanism of interaction of bEVs in GIT cancer pathogenesis.
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Affiliation(s)
- Sajeen Bahadur Amatya
- Biocenter Oulu & Cancer and Translational Medicine Research Unit, University of Oulu, 90014 Oulu, Finland; (S.B.A.); (S.S.)
| | - Sonja Salmi
- Biocenter Oulu & Cancer and Translational Medicine Research Unit, University of Oulu, 90014 Oulu, Finland; (S.B.A.); (S.S.)
| | - Veera Kainulainen
- Human Microbiome Research Program Unit, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland;
| | - Peeter Karihtala
- Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, 00290 Helsinki, Finland;
| | - Justus Reunanen
- Biocenter Oulu & Cancer and Translational Medicine Research Unit, University of Oulu, 90014 Oulu, Finland; (S.B.A.); (S.S.)
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19
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Nakashima Y, Shiiyama N, Urabe T, Yamashita H, Yasuda S, Igoshi K, Kinoshita H. Functions of small RNAs in Lactobacillus casei-Pediococcus group of lactic acid bacteria using fragment analysis. FEMS Microbiol Lett 2021; 367:5928547. [PMID: 33068404 DOI: 10.1093/femsle/fnaa154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
Small RNAs (sRNA) are non-cording RNAs composed of 50∼400 nt responsible for coordinating the adaption of Escherichia coli and other bacteria to changing environmental conditions, including pH and temperature. However, the role of sRNAs in lactic acid bacteria (LAB) has not yet been clarified. In this study, we used the Lactobacillus casei-Pediococcus group to evaluate the function of sRNAs in LAB, using RNA sequencing in the exponential growth phase and stationary phase to map and analyze sRNA fragments, which were categorized as Pediococcus pentosaceus and Lactobacillus paracasei. We evaluated the role of sRNAs in nutrient synthesis for cell growth in exponential growth phase and in protein and biofilm biosynthesis for cell body durability. During exponential growth, the sRNA fragments were found to be involved in the stress response in Pediococcus pentosaceus and in environmental adaption in Lactobacillus paracasei. The results suggest that the function of sRNA can be characterized from sRNA fragments using RNA sequencing during the exponential growth and stationary phases in Lactobacillus casei-Pediococcus group.
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Affiliation(s)
- Yuki Nakashima
- Graduate School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Narumi Shiiyama
- Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Taihei Urabe
- Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Hideji Yamashita
- Graduate School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan.,Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Shin Yasuda
- Graduate School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan.,Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Keiji Igoshi
- Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
| | - Hideki Kinoshita
- Graduate School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan.,Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, Japan
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20
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Schorey JS, Cheng Y, McManus WR. Bacteria- and host-derived extracellular vesicles - two sides of the same coin? J Cell Sci 2021; 134:268991. [PMID: 34081134 DOI: 10.1242/jcs.256628] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Intracellular bacterial pathogens spend portions of their life cycle both inside and outside host cells. While in these two distinct environments, they release or shed bacterial components, including virulence factors that promote their survival and replication. Some of these components are released through extracellular vesicles, which are either derived from the bacteria themselves or from the host cells. Bacteria- and host-derived vesicles have been studied almost exclusively in isolation from each other, with little discussion of the other type of secreted vesicles, despite the fact that both are generated during an in vivo infection and both are likely play a role in bacterial pathogenesis and host immunity. In this Review, we aim to bridge this gap and discuss what we know of bacterial membrane vesicles in their generation and composition. We will compare and contrast this with the composition of host-derived vesicles with regard to bacterial components. We will also compare host cell responses to the different vesicles, with a focus on how these vesicles modulate the immune response, using Mycobacterium, Listeria and Salmonella as specific examples for these comparisons.
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Affiliation(s)
- Jeffrey S Schorey
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Yong Cheng
- Department of Biochemistry and Molecular Biology, Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - William R McManus
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA
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21
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White JR, Dauros-Singorenko P, Hong J, Vanholsbeeck F, Phillips A, Swift S. The complex, bidirectional role of extracellular vesicles in infection. Biochem Soc Trans 2021; 49:881-891. [PMID: 33860784 PMCID: PMC8106493 DOI: 10.1042/bst20200788] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022]
Abstract
Cells from all domains of life release extracellular vesicles (EVs), packages that carry a cargo of molecules that participate in communication, co-ordination of population behaviours, virulence and immune response mechanisms. Mammalian EVs play an increasingly recognised role to fight infection, yet may also be commandeered to disseminate pathogens and enhance infection. EVs released by bacterial pathogens may deliver toxins to host cells, signalling molecules and new DNA to other bacteria, and act as decoys, protecting infecting bacteria from immune killing. In this review, we explore the role of EVs in infection from the perspective of both the pathogen and host, and highlight their importance in the host/pathogen relationship. We highlight proposed strategies for EVs in therapeutics, and call attention to areas where existing knowledge and evidence is lacking.
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Affiliation(s)
- Joni Renee White
- Department of Molecular Medicine and Pathology, The University of Auckland, 85 Park Road, Auckland, New Zealand
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Department of Physics, Auckland 1010, University of Auckland, New Zealand
| | - Priscila Dauros-Singorenko
- Department of Molecular Medicine and Pathology, The University of Auckland, 85 Park Road, Auckland, New Zealand
- Surgical and Translational Research Centre, Department of Surgery, The University of Auckland, 22-30 Park Avenue, Auckland, New Zealand
| | - Jiwon Hong
- Surgical and Translational Research Centre, Department of Surgery, The University of Auckland, 22-30 Park Avenue, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland, New Zealand
| | - Frédérique Vanholsbeeck
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Department of Physics, Auckland 1010, University of Auckland, New Zealand
- Department of Physics, The University of Auckland, 38 Princes Street, Auckland, New Zealand
| | - Anthony Phillips
- Surgical and Translational Research Centre, Department of Surgery, The University of Auckland, 22-30 Park Avenue, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, The University of Auckland, 85 Park Road, Auckland, New Zealand
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22
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Torres AG, Martí E. Toward an Understanding of Extracellular tRNA Biology. Front Mol Biosci 2021; 8:662620. [PMID: 33937338 PMCID: PMC8082309 DOI: 10.3389/fmolb.2021.662620] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Extracellular RNAs (exRNAs) including abundant full length tRNAs and tRNA fragments (tRFs) have recently garnered attention as a promising source of biomarkers and a novel mediator in cell-to-cell communication in eukaryotes. Depending on the physiological state of cells, tRNAs/tRFs are released to the extracellular space either contained in extracellular vesicles (EVs) or free, through a mechanism that is largely unknown. In this perspective article, we propose that extracellular tRNAs (ex-tRNAs) and/or extracellular tRFs (ex-tRFs) are relevant paracrine signaling molecules whose activity depends on the mechanisms of release by source cells and capture by recipient cells. We speculate on how ex-tRNA/ex-tRFs orchestrate the effects in target cells, depending on the type of sequence and the mechanisms of uptake. We further propose that tRNA modifications may be playing important roles in ex-tRNA biology.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eulàlia Martí
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Epidemiología y Salud Pública, Madrid, Spain
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23
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Markelova N, Glazunova O, Alikina O, Panyukov V, Shavkunov K, Ozoline O. Suppression of Escherichia coli Growth Dynamics via RNAs Secreted by Competing Bacteria. Front Mol Biosci 2021; 8:609979. [PMID: 33937321 PMCID: PMC8082180 DOI: 10.3389/fmolb.2021.609979] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/11/2021] [Indexed: 11/13/2022] Open
Abstract
With the discovery of secreted RNAs, it has become apparent that the biological role of regulatory oligonucleotides likely goes beyond the borders of individual cells. However, the mechanisms of their action are still comprehended only in general terms and mainly for eukaryotic microRNAs, which can interfere with mRNAs even in distant recipient cells. It has recently become clear that bacterial cells lacking interference systems can also respond to eukaryotic microRNAs that have targets in their genomes. However, the question of whether bacteria can perceive information transmitted by oligonucleotides secreted by other prokaryotes remained open. Here we evaluated the fraction of short RNAs secreted by Escherichia coli during individual and mixed growth with Rhodospirillum rubrum or Prevotella copri, and found that in the presence of other bacteria E. coli tends to excrete oligonucleotides homologous to alien genomes. Based on this observation, we selected four RNAs secreted by either R. rubrum or P. copri, together with one E. coli-specific oligonucleotide. Both fragments of R. rubrum 23S-RNA suppressed the growth of E. coli. Of the two fragments secreted by P. copri, one abolished the stimulatory effect of E. coli RNA derived from the 3'-UTR of ProA mRNA, while the other inhibited bacterial growth only in the double-stranded state with complementary RNA. The ability of two RNAs secreted by cohabiting bacteria to enter E. coli cells was demonstrated using confocal microscopy. Since selected E. coli-specific RNA also affected the growth of this bacterium, we conclude that bacterial RNAs can participate in inter- and intraspecies signaling.
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Affiliation(s)
- Natalia Markelova
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Olga Glazunova
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Olga Alikina
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Valeriy Panyukov
- Department of Structural and Functional Genomics, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia.,Laboratory of Bioinformatics, Institute of Mathematical Problems of Biology, Pushchino, Russia
| | - Konstantin Shavkunov
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia.,Department of Structural and Functional Genomics, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Olga Ozoline
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia.,Department of Structural and Functional Genomics, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
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24
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Bitto NJ, Cheng L, Johnston EL, Pathirana R, Phan TK, Poon IKH, O'Brien-Simpson NM, Hill AF, Stinear TP, Kaparakis-Liaskos M. Staphylococcus aureus membrane vesicles contain immunostimulatory DNA, RNA and peptidoglycan that activate innate immune receptors and induce autophagy. J Extracell Vesicles 2021; 10:e12080. [PMID: 33815695 PMCID: PMC8015888 DOI: 10.1002/jev2.12080] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/12/2021] [Accepted: 03/04/2021] [Indexed: 12/14/2022] Open
Abstract
Gram‐positive bacteria ubiquitously produce membrane vesicles (MVs), and although they contribute to biological functions, our knowledge regarding their composition and immunogenicity remains limited. Here we examine the morphology, contents and immunostimulatory functions of MVs produced by three Staphylococcus aureus strains; a methicillin resistant clinical isolate, a methicillin sensitive clinical isolate and a laboratory‐adapted strain. We observed differences in the number and morphology of MVs produced by each strain and showed that they contain microbe‐associated molecular patterns (MAMPs) including protein, nucleic acids and peptidoglycan. Analysis of MV‐derived RNA indicated the presence of small RNA (sRNA). Furthermore, we detected variability in the amount and composition of protein, nucleic acid and peptidoglycan cargo carried by MVs from each S. aureus strain. S. aureus MVs activated Toll‐like receptor (TLR) 2, 7, 8, 9 and nucleotide‐binding oligomerization domain containing protein 2 (NOD2) signalling and promoted cytokine and chemokine release by epithelial cells, thus identifying that MV‐associated MAMPs including DNA, RNA and peptidoglycan are detected by pattern recognition receptors (PRRs). Moreover, S. aureus MVs induced the formation of and colocalized with autophagosomes in epithelial cells, while inhibition of lysosomal acidification using bafilomycin A1 resulted in accumulation of autophagosomal puncta that colocalized with MVs, revealing the ability of the host to degrade MVs via autophagy. This study reveals the ability of DNA, RNA and peptidoglycan associated with MVs to activate PRRs in host epithelial cells, and their intracellular degradation via autophagy. These findings advance our understanding of the immunostimulatory roles of Gram‐positive bacterial MVs in mediating pathogenesis, and their intracellular fate within the host.
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Affiliation(s)
- Natalie J Bitto
- Department of Physiology Anatomy and Microbiology La Trobe University Melbourne Victoria 3086 Australia.,Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia
| | - Lesley Cheng
- Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Melbourne Victoria 3086 Australia
| | - Ella L Johnston
- Department of Physiology Anatomy and Microbiology La Trobe University Melbourne Victoria 3086 Australia.,Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia
| | - Rishi Pathirana
- Department of Physiology Anatomy and Microbiology La Trobe University Melbourne Victoria 3086 Australia.,Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia
| | - Thanh Kha Phan
- Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Melbourne Victoria 3086 Australia
| | - Ivan K H Poon
- Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Melbourne Victoria 3086 Australia
| | - Neil M O'Brien-Simpson
- Centre for Oral Health Research Melbourne Dental School Bio21 Institute The University of Melbourne Parkville Victoria 3010 Australia
| | - Andrew F Hill
- Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Melbourne Victoria 3086 Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology Doherty Institute University of Melbourne Parkville Victoria 3010 Australia
| | - Maria Kaparakis-Liaskos
- Department of Physiology Anatomy and Microbiology La Trobe University Melbourne Victoria 3086 Australia.,Research Centre for Extracellular Vesicles School of Molecular Sciences La Trobe University Melbourne Victoria 3086 Australia
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25
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Luz BSRD, Nicolas A, Chabelskaya S, Rodovalho VDR, Le Loir Y, Azevedo VADC, Felden B, Guédon E. Environmental Plasticity of the RNA Content of Staphylococcus aureus Extracellular Vesicles. Front Microbiol 2021; 12:634226. [PMID: 33776967 PMCID: PMC7990786 DOI: 10.3389/fmicb.2021.634226] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/18/2021] [Indexed: 12/13/2022] Open
Abstract
The roles of bacterial extracellular vesicles (EVs) in cell-to-cell signaling are progressively being unraveled. These membranous spheres released by many living cells carry various macromolecules, some of which influence host-pathogen interactions. Bacterial EVs contain RNA, which may serve in communicating with their infected hosts. Staphylococcus aureus, an opportunistic human and animal pathogen, produces EVs whose RNA content is still poorly characterized. Here, we investigated in depth the RNA content of S. aureus EVs. A high-throughput RNA sequencing approach identified RNAs in EVs produced by the clinical S. aureus strain HG003 under different environmental conditions: early- and late-stationary growth phases, and presence or absence of a sublethal vancomycin concentration. On average, sequences corresponding to 78.0% of the annotated transcripts in HG003 genome were identified in HG003 EVs. However, only ~5% of them were highly covered by reads (≥90% coverage) indicating that a large fraction of EV RNAs, notably mRNAs and sRNAs, were fragmented in EVs. According to growth conditions, from 86 to 273 highly covered RNAs were identified into the EVs. They corresponded to 286 unique RNAs, including 220 mRNAs. They coded for numerous virulence-associated factors (hld encoded by the multifunctional sRNA RNAIII, agrBCD, psmβ1, sbi, spa, and isaB), ribosomal proteins, transcriptional regulators, and metabolic enzymes. Twenty-eight sRNAs were also detected, including bona fide RsaC. The presence of 22 RNAs within HG003 EVs was confirmed by reverse transcription quantitative PCR (RT-qPCR) experiments. Several of these 286 RNAs were shown to belong to the same transcriptional units in S. aureus. Both nature and abundance of the EV RNAs were dramatically affected depending on the growth phase and the presence of vancomycin, whereas much less variations were found in the pool of cellular RNAs of the parent cells. Moreover, the RNA abundance pattern differed between EVs and EV-producing cells according to the growth conditions. Altogether, our findings show that the environment shapes the RNA cargo of the S. aureus EVs. Although the composition of EVs is impacted by the physiological state of the producing cells, our findings suggest a selective packaging of RNAs into EVs, as proposed for EV protein cargo. Our study shedds light to the possible roles of potentially functional RNAs in S. aureus EVs, notably in host-pathogen interactions.
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Affiliation(s)
- Brenda Silva Rosa Da Luz
- INRAE, Institut Agro, STLO, Rennes, France.,Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Svetlana Chabelskaya
- BRM [Bacterial Regulatory RNAs and Medicine] UMR_S 1230, University of Rennes, Inserm, Rennes, France
| | - Vinícius de Rezende Rodovalho
- INRAE, Institut Agro, STLO, Rennes, France.,Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Vasco Ariston de Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Brice Felden
- BRM [Bacterial Regulatory RNAs and Medicine] UMR_S 1230, University of Rennes, Inserm, Rennes, France
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26
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Pérez-Cruz C, Briansó F, Sonnleitner E, Bläsi U, Mercadé E. RNA release via membrane vesicles in Pseudomonas aeruginosa PAO1 is associated with the growth phase. Environ Microbiol 2021; 23:5030-5041. [PMID: 33650279 DOI: 10.1111/1462-2920.15436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 02/12/2021] [Indexed: 12/20/2022]
Abstract
Pseudomonas aeruginosa PAO1 membrane vesicles (MVs) are known to play a role in cell-to-cell communication. Several studies have shown that the MV composition and physicochemical properties vary according to the bacterial growth stage, but the impact this might have on the externalization of RNA via MVs has not been addressed. Therefore, a study to characterize the RNA content from MVs retrieved at different growth phases was conducted. First, the transcriptome analyses revealed a higher abundance of around 300 RNA species in MVs when compared with the cells. The vesiculation rate along the growth curve was determined, showing that the release of MVs increased during the transition to the stationary phase, whereas it decreased in the late stationary phase. RNA-seq of MVs retrieved along the transition to the stationary phase demonstrated that the RNA cargo of vesicles did not vary. However, the amount of smaller RNAs (<200 nt) inside MVs retrieved in the late exponential phase was higher than in the stationary phase MVs. These results indicate that the externalization of RNA via MVs occurs during late exponential phase and implies the secretion of different types of MVs during growth.
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Affiliation(s)
- Carla Pérez-Cruz
- Marine Research Division, AZTI, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain.,Microbiology Unit, Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
| | - Ferran Briansó
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Elisabeth Sonnleitner
- Max Perutz Labs, Center of Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Udo Bläsi
- Max Perutz Labs, Center of Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Elena Mercadé
- Microbiology Unit, Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
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27
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Sokaribo AS, Perera SR, Sereggela Z, Krochak R, Balezantis LR, Xing X, Lam S, Deck W, Attah-Poku S, Abbott DW, Tamuly S, White AP. A GMMA-CPS-Based Vaccine for Non-Typhoidal Salmonella. Vaccines (Basel) 2021; 9:vaccines9020165. [PMID: 33671372 PMCID: PMC7922415 DOI: 10.3390/vaccines9020165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/16/2022] Open
Abstract
Non-typhoidal Salmonella are a major cause of gastroenteritis worldwide, as well as causing bloodstream infections in sub-Saharan Africa with a high fatality rate. No vaccine is currently available for human use. Current vaccine development strategies are focused on capsular polysaccharides (CPS) present on the surface of non-typhoidal Salmonella. This study aimed to boost the amount of CPS purified from S. Typhimurium for immunization trials. Random mutagenesis with Tn10 transposon increased the production of CPS colanic acid, by 10-fold compared to wildtype. Immunization with colanic acid or colanic acid conjugated to truncated glycoprotein D or inactivated diphtheria toxin did not induce a protective immune response in mice. However, immunization with Generalized Modules for Membrane Antigens (GMMAs) isolated from colanic acid overproducing isolates reduced Salmonella colonization in mice. Our results support the development of a GMMA-CPS-based vaccine against non-typhoidal Salmonella.
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Affiliation(s)
- Akosiererem S. Sokaribo
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Sumudu R. Perera
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Zoe Sereggela
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Ryan Krochak
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Lindsay R. Balezantis
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Xiaohui Xing
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J4B1, Canada; (X.X.); (D.W.A.)
| | - Shirley Lam
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
| | - William Deck
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
| | - Sam Attah-Poku
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
| | - Dennis Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J4B1, Canada; (X.X.); (D.W.A.)
| | - Shantanu Tamuly
- Department of Veterinary Biochemistry, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati 781022, Assam, India;
| | - Aaron P. White
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
- Correspondence: ; Tel.: +01-306-966-7485
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28
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Askenase PW. Ancient Evolutionary Origin and Properties of Universally Produced Natural Exosomes Contribute to Their Therapeutic Superiority Compared to Artificial Nanoparticles. Int J Mol Sci 2021; 22:1429. [PMID: 33572657 PMCID: PMC7866973 DOI: 10.3390/ijms22031429] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
Extracellular vesicles (EVs), such as exosomes, are newly recognized fundamental, universally produced natural nanoparticles of life that are seemingly involved in all biologic processes and clinical diseases. Due to their universal involvements, understanding the nature and also the potential therapeutic uses of these nanovesicles requires innovative experimental approaches in virtually every field. Of the EV group, exosome nanovesicles and larger companion micro vesicles can mediate completely new biologic and clinical processes dependent on the intercellular transfer of proteins and most importantly selected RNAs, particularly miRNAs between donor and targeted cells to elicit epigenetic alterations inducing functional cellular changes. These recipient acceptor cells are nearby (paracrine transfers) or far away after distribution via the circulation (endocrine transfers). The major properties of such vesicles seem to have been conserved over eons, suggesting that they may have ancient evolutionary origins arising perhaps even before cells in the primordial soup from which life evolved. Their potential ancient evolutionary attributes may be responsible for the ability of some modern-day exosomes to withstand unusually harsh conditions, perhaps due to unique membrane lipid compositions. This is exemplified by ability of the maternal milk exosomes to survive passing the neonatal acid/enzyme rich stomach. It is postulated that this resistance also applies to their durable presence in phagolysosomes, thus suggesting a unique intracellular release of their contained miRNAs. A major discussed issue is the generally poorly realized superiority of these naturally evolved nanovesicles for therapies when compared to human-engineered artificial nanoparticles, e.g., for the treatment of diseases like cancers.
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Affiliation(s)
- Phillip W Askenase
- Department of Internal Medicine, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
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29
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Joshi B, Singh B, Nadeem A, Askarian F, Wai SN, Johannessen M, Hegstad K. Transcriptome Profiling of Staphylococcus aureus Associated Extracellular Vesicles Reveals Presence of Small RNA-Cargo. Front Mol Biosci 2021; 7:566207. [PMID: 33521050 PMCID: PMC7838569 DOI: 10.3389/fmolb.2020.566207] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial extracellular vesicles (EVs) have a vital role in bacterial pathogenesis. However, to date, the small RNA-cargo of EVs released by the opportunistic pathogen Staphylococcus aureus has not been characterized. Here, we shed light on the association of small RNAs with EVs secreted by S. aureus MSSA476 cultured in iron-depleted bacteriologic media supplemented with a subinhibitory dosage of vancomycin to mimic infection condition. Confocal microscopy analysis on intact RNase-treated EVs indicated that RNA is associated with EV particles. Transcriptomic followed by bioinformatics analysis of EV-associated RNA revealed the presence of potential gene regulatory small RNAs and high levels of tRNAs. Among the EV-associated enriched small RNAs were SsrA, RsaC and RNAIII. Our finding invites new insights into the potential role of EV-associated RNA as a modulator of host-pathogen interaction.
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Affiliation(s)
- Bishnu Joshi
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Bhupender Singh
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Aftab Nadeem
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Fatemeh Askarian
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway.,Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Sun Nyunt Wai
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Mona Johannessen
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway.,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North-Norway, Tromsø, Norway
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30
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Kiselev S, Markelova N, Masulis I. Divergently Transcribed ncRNAs in Escherichia coli: Refinement of the Transcription Starts Assumes Functional Diversification. Front Mol Biosci 2021; 8:610453. [PMID: 33748186 PMCID: PMC7967276 DOI: 10.3389/fmolb.2021.610453] [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: 09/25/2020] [Accepted: 01/07/2021] [Indexed: 02/05/2023] Open
Abstract
Non-coding regulatory RNAs (ncRNAs) comprise specialized group of essential genetically encoded biological molecules involved in the wide variety of cellular metabolic processes. The progressive increase in the number of newly identified ncRNAs and the defining of their genome location indicate their predominant nesting in intergenic regions and expression under the control of their own regulatory elements. At the same time, the regulation of ncRNA's transcription cannot be considered in isolation from the processes occurring in the immediate genetic environment. A number of experimental data indicate the notable impact of positional regulation of gene expression mediated by dynamic temporal DNA rearrangements accompanying transcription events in the vicinity of neighboring genes. This issue can be perceived as particularly significant for divergently transcribed ncRNAs being actually subjected to double regulatory pressure. Based on available results of RNAseq experiments for Escherichia coli, we screened out divergent ncRNAs and the adjacent genes for the exact positions of transcription start sites (TSSs) and relative efficiency of RNA production. This analysis revealed extension or shortening of some previously annotated ncRNAs resulting in modified secondary structure, confirmed stable expression of four ncRNAs annotated earlier as putative, and approved the possibility of expression of divergently transcribed ncRNAs containing repetitive extragenic palindromic (REP) elements. The biogenesis of secreted ncRNAs from divergently transcribed ffs, chiX, ralA, and ryhB is discussed taking into account positions of TSSs. Refinement of TSSs for the neighboring genes renders some ncRNAs as true antisense overlapping with 5'UTR of divergently transcribed mRNAs.
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31
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Martin-Gallausiaux C, Malabirade A, Habier J, Wilmes P. Fusobacterium nucleatum Extracellular Vesicles Modulate Gut Epithelial Cell Innate Immunity via FomA and TLR2. Front Immunol 2020; 11:583644. [PMID: 33408714 PMCID: PMC7779620 DOI: 10.3389/fimmu.2020.583644] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Extracellular vesicles (EVs) derived from the gut microbiota are largely uncharacterized and their impacts on host intestinal physiology remain unresolved. Here, we isolated EVs from F. nucleatum for detailed characterization. Our analyses highlight the presence of the outer membrane protein porin FomA on EVs. Besides, we evaluated the impact of EVs on human intestinal epithelial cells (IECs) in a non-inflammatory context. Our results show no detrimental impact on the epithelial barrier. No internalization of EVs was observed. Moreover, we demonstrate that F. nucleatum EVs trigger innate immunity of IECs by promoting NF-κB activation via the dynamin-mediated endocytosis. The NF-κB activation was found to be TLR2-dependent yet, TLR4 was dispensable. Using competitive binding assays, we establish that FomA is involved in the NF-κB response. Taken together, our data indicate that EVs induce effects similar to those observed with whole F. nucleatum bacteria on IECs. In particular, our study highlights the role of TLR2 and FomA as major modulators of the gut epithelium immune responses to F. nucleatum.
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Affiliation(s)
| | - Antoine Malabirade
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Janine Habier
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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32
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Extracellular RNAs in Bacterial Infections: From Emerging Key Players on Host-Pathogen Interactions to Exploitable Biomarkers and Therapeutic Targets. Int J Mol Sci 2020; 21:ijms21249634. [PMID: 33348812 PMCID: PMC7766527 DOI: 10.3390/ijms21249634] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/04/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are key regulators of post-transcriptional gene expression in prokaryotic and eukaryotic organisms. These molecules can interact with mRNAs or proteins, affecting a variety of cellular functions. Emerging evidence shows that intra/inter-species and trans-kingdom regulation can also be achieved with exogenous RNAs, which are exported to the extracellular medium, mainly through vesicles. In bacteria, membrane vesicles (MVs) seem to be the more common way of extracellular communication. In several bacterial pathogens, MVs have been described as a delivery system of ncRNAs that upon entry into the host cell, regulate their immune response. The aim of the present work is to review this recently described mode of host-pathogen communication and to foster further research on this topic envisaging their exploitation in the design of novel therapeutic and diagnostic strategies to fight bacterial infections.
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33
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Mozaheb N, Mingeot-Leclercq MP. Membrane Vesicle Production as a Bacterial Defense Against Stress. Front Microbiol 2020; 11:600221. [PMID: 33362747 PMCID: PMC7755613 DOI: 10.3389/fmicb.2020.600221] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022] Open
Abstract
Membrane vesicles are the nano-sized vesicles originating from membranes. The production of membrane vesicles is a common feature among bacteria. Depending on the bacterial growth phase and environmental conditions, membrane vesicles show diverse characteristics. Various physiological and ecological roles have been attributed to membrane vesicles under both homeostatic and stressful conditions. Pathogens encounter several stressors during colonization in the hostile environment of host tissues. Nutrient deficiency, the presence of antibiotics as well as elements of the host’s immune system are examples of stressors threatening pathogens inside their host. To combat stressors and survive, pathogens have established various defensive mechanisms, one of them is production of membrane vesicles. Pathogens produce membrane vesicles to alleviate the destructive effects of antibiotics or other types of antibacterial treatments. Additionally, membrane vesicles can also provide benefits for the wider bacterial community during infections, through the transfer of resistance or virulence factors. Hence, given that membrane vesicle production may affect the activities of antibacterial agents, their production should be considered when administering antibacterial treatments. Besides, regarding that membrane vesicles play vital roles in bacteria, disrupting their production may suggest an alternative strategy for battling against pathogens. Here, we aim to review the stressors encountered by pathogens and shed light on the roles of membrane vesicles in increasing pathogen adaptabilities in the presence of stress-inducing factors.
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Affiliation(s)
- Negar Mozaheb
- Université catholique de Louvain (UCL), Louvain Drug Research Institute (LDRI), Cellular & Molecular Pharmacology Unit (FACM), Brussels, Belgium
| | - Marie-Paule Mingeot-Leclercq
- Université catholique de Louvain (UCL), Louvain Drug Research Institute (LDRI), Cellular & Molecular Pharmacology Unit (FACM), Brussels, Belgium
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34
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Abiotic stressors impact outer membrane vesicle composition in a beneficial rhizobacterium: Raman spectroscopy characterization. Sci Rep 2020; 10:21289. [PMID: 33277560 PMCID: PMC7719170 DOI: 10.1038/s41598-020-78357-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/13/2020] [Indexed: 11/08/2022] Open
Abstract
Outer membrane vesicles (OMVs) produced by Gram-negative bacteria have roles in cell-to-cell signaling, biofilm formation, and stress responses. Here, the effects of abiotic stressors on OMV contents and composition from biofilm cells of the plant health-promoting bacterium Pseudomonas chlororaphis O6 (PcO6) are examined. Two stressors relevant to this root-colonizing bacterium were examined: CuO nanoparticles (NPs)-a potential fertilizer and fungicide- and H2O2-released from roots during plant stress responses. Atomic force microscopy revealed 40–300 nm diameter OMVs from control and stressed biofilm cells. Raman spectroscopy with linear discriminant analysis (LDA) was used to identify changes in chemical profiles of PcO6 cells and resultant OMVs according to the cellular stressor with 84.7% and 83.3% accuracies, respectively. All OMVs had higher relative concentrations of proteins, lipids, and nucleic acids than PcO6 cells. The nucleic acid concentration in OMVs exhibited a cellular stressor-dependent increase: CuO NP-induced OMVs > H2O2-induced OMVs > control OMVs. Biochemical assays confirmed the presence of lipopolysaccharides, nucleic acids, and protein in OMVs; however, these assays did not discriminate OMV composition according to the cellular stressor. These results demonstrate the sensitivity of Raman spectroscopy using LDA to characterize and distinguish cellular stress effects on OMVs composition and contents.
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35
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Layton E, Fairhurst AM, Griffiths-Jones S, Grencis RK, Roberts IS. Regulatory RNAs: A Universal Language for Inter-Domain Communication. Int J Mol Sci 2020; 21:E8919. [PMID: 33255483 PMCID: PMC7727864 DOI: 10.3390/ijms21238919] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
In eukaryotes, microRNAs (miRNAs) have roles in development, homeostasis, disease and the immune response. Recent work has shown that plant and mammalian miRNAs also mediate cross-kingdom and cross-domain communications. However, these studies remain controversial and are lacking critical mechanistic explanations. Bacteria do not produce miRNAs themselves, and therefore it is unclear how these eukaryotic RNA molecules could function in the bacterial recipient. In this review, we compare and contrast the biogenesis and functions of regulatory RNAs in eukaryotes and bacteria. As a result, we discovered several conserved features and homologous components in these distinct pathways. These findings enabled us to propose novel mechanisms to explain how eukaryotic miRNAs could function in bacteria. Further understanding in this area is necessary to validate the findings of existing studies and could facilitate the use of miRNAs as novel tools for the directed remodelling of the human microbiota.
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Affiliation(s)
- Emma Layton
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
| | - Anna-Marie Fairhurst
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore;
| | - Sam Griffiths-Jones
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Richard K. Grencis
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
| | - Ian S. Roberts
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
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36
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Munhoz da Rocha IF, Amatuzzi RF, Lucena ACR, Faoro H, Alves LR. Cross-Kingdom Extracellular Vesicles EV-RNA Communication as a Mechanism for Host-Pathogen Interaction. Front Cell Infect Microbiol 2020; 10:593160. [PMID: 33312966 PMCID: PMC7708329 DOI: 10.3389/fcimb.2020.593160] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 10/13/2020] [Indexed: 01/04/2023] Open
Abstract
The extracellular vesicle (EVs) traffic has been highlighted as a very important pathway of cellular communication. EVs are produced by prokaryotes and eukaryotes organisms and can carry molecules to help maintain homeostasis, responding to general disbalance, infections, and allowing rapid modulation of the immune system. In the context of infection, EVs from both the host and the pathogen have been identified as playing roles in the recruitment of immunological molecules that can lead to the resolution of the infection or the host’s defeat. Bacterial vesicles RNA cargo play roles in the host cell by regulating gene expression and modulating immune response. In fungi the RNA molecules present in EVs are diverse and participate in communication between the host and pathogenic fungi. Little is known about how cross-kingdom sRNA trafficking occurs, although in recent years, there has been an increase in studies that relate EV participation in sRNA delivery. This review aims to elucidate and update the reader concerning the role of extracellular vesicles, with emphasis in the RNA content. We describe the EVs during infection from the host point-of-view, as well as the bacteria and fungi pathogens producing EVs that help the establishment of the disease.
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Affiliation(s)
| | - Rafaela Ferreira Amatuzzi
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Curitiba, Brazil
| | - Aline Castro Rodrigues Lucena
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Curitiba, Brazil
| | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Curitiba, Brazil
| | - Lysangela Ronalte Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Curitiba, Brazil
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The noncoding small RNA SsrA is released by Vibrio fischeri and modulates critical host responses. PLoS Biol 2020; 18:e3000934. [PMID: 33141816 PMCID: PMC7665748 DOI: 10.1371/journal.pbio.3000934] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/13/2020] [Accepted: 09/22/2020] [Indexed: 01/13/2023] Open
Abstract
The regulatory noncoding small RNAs (sRNAs) of bacteria are key elements influencing gene expression; however, there has been little evidence that beneficial bacteria use these molecules to communicate with their animal hosts. We report here that the bacterial sRNA SsrA plays an essential role in the light-organ symbiosis between Vibrio fischeri and the squid Euprymna scolopes. The symbionts load SsrA into outer membrane vesicles, which are transported specifically into the epithelial cells surrounding the symbiont population in the light organ. Although an SsrA-deletion mutant (ΔssrA) colonized the host to a normal level after 24 h, it produced only 2/10 the luminescence per bacterium, and its persistence began to decline by 48 h. The host's response to colonization by the ΔssrA strain was also abnormal: the epithelial cells underwent premature swelling, and host robustness was reduced. Most notably, when colonized by the ΔssrA strain, the light organ differentially up-regulated 10 genes, including several encoding heightened immune-function or antimicrobial activities. This study reveals the potential for a bacterial symbiont's sRNAs not only to control its own activities but also to trigger critical responses promoting homeostasis in its host. In the absence of this communication, there are dramatic fitness consequences for both partners.
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38
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Staphylococcus aureus secretes immunomodulatory RNA and DNA via membrane vesicles. Sci Rep 2020; 10:18293. [PMID: 33106559 PMCID: PMC7589478 DOI: 10.1038/s41598-020-75108-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/07/2020] [Indexed: 02/07/2023] Open
Abstract
Bacterial-derived RNA and DNA can function as ligands for intracellular receptor activation and induce downstream signaling to modulate the host response to bacterial infection. The mechanisms underlying the secretion of immunomodulatory RNA and DNA by pathogens such as Staphylococcus aureus and their delivery to intracellular host cell receptors are not well understood. Recently, extracellular membrane vesicle (MV) production has been proposed as a general secretion mechanism that could facilitate the delivery of functional bacterial nucleic acids into host cells. S. aureus produce membrane-bound, spherical, nano-sized, MVs packaged with a select array of bioactive macromolecules and they have been shown to play important roles in bacterial virulence and in immune modulation through the transmission of biologic signals to host cells. Here we show that S. aureus secretes RNA and DNA molecules that are mostly protected from degradation by their association with MVs. Importantly, we demonstrate that MVs can be delivered into cultured macrophage cells and subsequently stimulate a potent IFN-β response in recipient cells via activation of endosomal Toll-like receptors. These findings advance our understanding of the mechanisms by which bacterial nucleic acids traffic extracellularly to trigger the modulation of host immune responses.
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39
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Becker NS, Rollins RE, Nosenko K, Paulus A, Martin S, Krebs S, Takano A, Sato K, Kovalev SY, Kawabata H, Fingerle V, Margos G. High conservation combined with high plasticity: genomics and evolution of Borrelia bavariensis. BMC Genomics 2020; 21:702. [PMID: 33032522 PMCID: PMC7542741 DOI: 10.1186/s12864-020-07054-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/06/2020] [Indexed: 12/28/2022] Open
Abstract
Background Borrelia bavariensis is one of the agents of Lyme Borreliosis (or Lyme disease) in Eurasia. The genome of the Borrelia burgdorferi sensu lato species complex, that includes B. bavariensis, is known to be very complex and fragmented making the assembly of whole genomes with next-generation sequencing data a challenge. Results We present a genome reconstruction for 33 B. bavariensis isolates from Eurasia based on long-read (Pacific Bioscience, for three isolates) and short-read (Illumina) data. We show that the combination of both sequencing techniques allows proper genome reconstruction of all plasmids in most cases but use of a very close reference is necessary when only short-read sequencing data is available. B. bavariensis genomes combine a high degree of genetic conservation with high plasticity: all isolates share the main chromosome and five plasmids, but the repertoire of other plasmids is highly variable. In addition to plasmid losses and gains through horizontal transfer, we also observe several fusions between plasmids. Although European isolates of B. bavariensis have little diversity in genome content, there is some geographic structure to this variation. In contrast, each Asian isolate has a unique plasmid repertoire and we observe no geographically based differences between Japanese and Russian isolates. Comparing the genomes of Asian and European populations of B. bavariensis suggests that some genes which are markedly different between the two populations may be good candidates for adaptation to the tick vector, (Ixodes ricinus in Europe and I. persulcatus in Asia). Conclusions We present the characterization of genomes of a large sample of B. bavariensis isolates and show that their plasmid content is highly variable. This study opens the way for genomic studies seeking to understand host and vector adaptation as well as human pathogenicity in Eurasian Lyme Borreliosis agents.
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Affiliation(s)
- Noémie S Becker
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany.
| | - Robert E Rollins
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Kateryna Nosenko
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Alexander Paulus
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Samantha Martin
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany.,University of Helsinki, Biomedicum Helsinki, PO Box 63, Haartmaninkatu 8, FIN-00014, Helsinki, Finland
| | - Stefan Krebs
- Gene Center, Laboratory for Functional Genome Analysis, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Ai Takano
- Department of Veterinary Epidemiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Kozue Sato
- Department of Bacteriology-I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Sergey Y Kovalev
- Laboratory of Molecular Genetics, Institute of Natural Sciences and Mathematics, Ural Federal University, Lenin Avenue 51, Yekaterinburg, 620000, Russia
| | - Hiroki Kawabata
- Department of Bacteriology-I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Volker Fingerle
- National Reference Centre for Borrelia at the Bavarian Health and Food Safety Authority, Veterinärstr 2, 85764, Oberschleissheim, Germany
| | - Gabriele Margos
- National Reference Centre for Borrelia at the Bavarian Health and Food Safety Authority, Veterinärstr 2, 85764, Oberschleissheim, Germany
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40
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Dauros-Singorenko P, Hong J, Swift S, Phillips A, Blenkiron C. Effect of the Extracellular Vesicle RNA Cargo From Uropathogenic Escherichia coli on Bladder Cells. Front Mol Biosci 2020; 7:580913. [PMID: 33102527 PMCID: PMC7546368 DOI: 10.3389/fmolb.2020.580913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/03/2020] [Indexed: 12/14/2022] Open
Abstract
Iron restriction in mammals, part of innate antimicrobial defense, may be sensed as a signal by an infecting pathogen. Iron-dependent regulators not only activate the pathogen’s specific iron acquisition and storage mechanisms needed for survival but also influence a number of other processes. Bacterial extracellular vesicles (EVs) are a conserved communication mechanism, which can have roles in host colonization, transfer of antimicrobial resistance, modulation of the host’s immune response, and biofilm formation. Here we analyze the iron-responsive effect of RNA cargo from Escherichia coli EVs in bladder cells. No differences were found in total RNA quantified from EVs released from representative pathogenic and probiotic strains grown in different iron conditions; nevertheless, lipopolysaccharide (LPS) associated with purified RNA was 10 times greater from EVs derived from the pathogenic strain. The pathogen and probiotic EV-RNA have no substantial toxic effect on the viability of cultured bladder cells, regardless of the iron concentration during bacterial culture. Transcriptomic analysis of bladder cells treated with pathogen EV-RNA delivered in artificial liposomes revealed a gene expression profile with a strong similarity to that of cells treated with liposomes containing LPS alone, with the majority being immune response pathways. EV-RNA from the probiotic strain gave no significant perturbation of gene expression in bladder cells. Cytokine profiling showed that EV-LPS has a role modulating the immune response when internalized by bladder cells, highlighting a key factor that must be considered when evaluating functional studies of bacterial RNA.
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Affiliation(s)
- Priscila Dauros-Singorenko
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,Department of Surgery, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Jiwon Hong
- Department of Surgery, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,School of Biological Sciences, Faculty of Science, The University of Auckland, Auckland, New Zealand.,Surgical and Translational Research Centre, The University of Auckland, Auckland, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Anthony Phillips
- Department of Surgery, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,School of Biological Sciences, Faculty of Science, The University of Auckland, Auckland, New Zealand.,Surgical and Translational Research Centre, The University of Auckland, Auckland, New Zealand
| | - Cherie Blenkiron
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
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41
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Begić M, Josić D. Biofilm formation and extracellular microvesicles-The way of foodborne pathogens toward resistance. Electrophoresis 2020; 41:1718-1739. [PMID: 32901923 DOI: 10.1002/elps.202000106] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/08/2020] [Accepted: 07/15/2020] [Indexed: 12/21/2022]
Abstract
Almost all known foodborne pathogens are able to form biofilms as one of the strategies for survival under harsh living conditions, to ward off the inhibition and the disinfection during food production, transport and storage, as well as during cleaning and sanitation of corresponding facilities. Biofilms are communities where microbial cells live under constant intracellular interaction and communication. Members of the biofilm community are embedded into extracellular matrix that contains polysaccharides, DNA, lipids, proteins, and small molecules that protect microorganisms and enable their intercellular communication under stress conditions. Membrane vesicles (MVs) are produced by both Gram positive and Gram negative bacteria. These lipid membrane-enveloped nanoparticles play an important role in biofilm genesis and in communication between different biofilm members. Furthermore, MVs are involved in other important steps of bacterial life like cell wall modeling, cellular division, and intercellular communication. They also carry toxins and virulence factors, as well as nucleic acids and different metabolites, and play a key role in host infections. After entering host cells, MVs can start many pathologic processes and cause serious harm and cell death. Prevention and inhibition of both biofilm formation and shedding of MVs by foodborne pathogens has a very important role in food production, storage, and food safety in general. Better knowledge of biofilm formation and maintaining, as well as the role of microbial vesicles in this process and in the process of host cells' infection is essential for food safety and prevention of both food spoilage and host infection.
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Affiliation(s)
- Marija Begić
- Faculty of Medicine, Juraj Dobrila University, Pula, Croatia
| | - Djuro Josić
- Faculty of Medicine, Juraj Dobrila University, Pula, Croatia.,Warren Alpert Medical School, Brown University, Providence, RI, USA
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42
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Tosar JP, Cayota A. Extracellular tRNAs and tRNA-derived fragments. RNA Biol 2020; 17:1149-1167. [PMID: 32070197 PMCID: PMC7549618 DOI: 10.1080/15476286.2020.1729584] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 01/08/2023] Open
Abstract
Fragmentation of tRNAs generates a family of small RNAs collectively known as tRNA-derived fragments. These fragments vary in sequence and size but have been shown to regulate many processes involved in cell homoeostasis and adaptations to stress. Additionally, the field of extracellular RNAs (exRNAs) is rapidly growing because exRNAs are a promising source of biomarkers in liquid biopsies, and because exRNAs seem to play key roles in intercellular and interspecies communication. Herein, we review recent descriptions of tRNA-derived fragments in the extracellular space in all domains of life, both in biofluids and in cell culture. The purpose of this review is to find consensus on which tRNA-derived fragments are more prominent in each extracellular fraction (including extracellular vesicles, lipoproteins and ribonucleoprotein complexes). We highlight what is becoming clear and what is still controversial in this field, in order to stimulate future hypothesis-driven studies which could clarify the role of full-length tRNAs and tRNA-derived fragments in the extracellular space.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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43
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Ahmadi Badi S, Bruno SP, Moshiri A, Tarashi S, Siadat SD, Masotti A. Small RNAs in Outer Membrane Vesicles and Their Function in Host-Microbe Interactions. Front Microbiol 2020; 11:1209. [PMID: 32670219 PMCID: PMC7327240 DOI: 10.3389/fmicb.2020.01209] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/12/2020] [Indexed: 01/18/2023] Open
Affiliation(s)
- Sara Ahmadi Badi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Arfa Moshiri
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Tarashi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Andrea Masotti
- Research Laboratories, Children's Hospital Bambino Gesù-IRCCS, Rome, Italy
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44
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Diallo I, Provost P. RNA-Sequencing Analyses of Small Bacterial RNAs and their Emergence as Virulence Factors in Host-Pathogen Interactions. Int J Mol Sci 2020; 21:E1627. [PMID: 32120885 PMCID: PMC7084465 DOI: 10.3390/ijms21051627] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 12/14/2022] Open
Abstract
Proteins have long been considered to be the most prominent factors regulating so-called invasive genes involved in host-pathogen interactions. The possible role of small non-coding RNAs (sRNAs), either intracellular, secreted or packaged in outer membrane vesicles (OMVs), remained unclear until recently. The advent of high-throughput RNA-sequencing (RNA-seq) techniques has accelerated sRNA discovery. RNA-seq radically changed the paradigm on bacterial virulence and pathogenicity to the point that sRNAs are emerging as an important, distinct class of virulence factors in both gram-positive and gram-negative bacteria. The potential of OMVs, as protectors and carriers of these functional, gene regulatory sRNAs between cells, has also provided an additional layer of complexity to the dynamic host-pathogen relationship. Using a non-exhaustive approach and through examples, this review aims to discuss the involvement of sRNAs, either free or loaded in OMVs, in the mechanisms of virulence and pathogenicity during bacterial infection. We provide a brief overview of sRNA origin and importance, and describe the classical and more recent methods of identification that have enabled their discovery, with an emphasis on the theoretical lower limit of RNA sizes considered for RNA sequencing and bioinformatics analyses.
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Affiliation(s)
| | - Patrick Provost
- CHUQ Research Center/CHUL, Department of Microbiology-Infectious Disease and Immunity, Faculty of Medicine, Université Laval, Quebec, QC G1V 0A6, Canada;
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45
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Langlete P, Krabberød AK, Winther-Larsen HC. Vesicles From Vibrio cholerae Contain AT-Rich DNA and Shorter mRNAs That Do Not Correlate With Their Protein Products. Front Microbiol 2019; 10:2708. [PMID: 31824470 PMCID: PMC6883915 DOI: 10.3389/fmicb.2019.02708] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/08/2019] [Indexed: 12/29/2022] Open
Abstract
Extracellular vesicles secreted by Gram-negative bacteria have proven to be important in bacterial defense, communication and host–pathogen relationships. They resemble smaller versions of the bacterial mother cell, with similar contents of proteins, LPS, DNA, and RNA. Vesicles can elicit a protective immune response in a range of hosts, and as vaccine candidates, it is of interest to properly characterize their cargo. Genetic sequencing data is already available for vesicles from several bacterial strains, but it is not yet clear how the genetic makeup of vesicles differ from that of their parent cells, and which properties may characterize enriched genetic material. The present study provides evidence for DNA inside vesicles from Vibrio cholerae O395, and key characteristics of their genetic and proteomic content are compared to that of whole cells. DNA analysis reveals enrichment of fragments containing ToxR binding sites, as well as a positive correlation between AT-content and enrichment. Some mRNAs were highly enriched in the vesicle fraction, such as membrane protein genes ompV, ompK, and ompU, DNA-binding protein genes hupA, hupB, ihfB, fis, and ssb, and a negative correlation was found between mRNA enrichment and transcript length, suggesting mRNA inclusion in vesicles may be a size-dependent process. Certain non-coding and functional RNAs were found to be enriched, such as VrrA, GcvB, tmRNA, RNase P, CsrB2, and CsrB3. Mass spectrometry revealed enrichment of outer membrane proteins, known virulence factors, phage components, flagella and extracellular proteins in the vesicle fraction, and a low, negative correlation was found between transcript-, and protein enrichment. This result opposes the hypothesis that a significant degree of protein translation occurs in vesicles after budding. The abundance of viral-, and flagellar proteins in the vesicle fraction underlines the importance of purification during vesicle isolation.
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Affiliation(s)
- Petter Langlete
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway.,Centre for Integrative Microbial Evolution (CIME), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Anders Kristian Krabberød
- Centre for Integrative Microbial Evolution (CIME), Department of Biosciences, University of Oslo, Oslo, Norway.,Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Hanne Cecilie Winther-Larsen
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway.,Centre for Integrative Microbial Evolution (CIME), Department of Biosciences, University of Oslo, Oslo, Norway
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