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Park JH, Song S, Kim S, Kim M, Kim KS. Optimizing Conditions for the Production of Bacterial Extracellular Vesicles of Vibrio vulnificus and Analysis of the Inner Small RNA Compositions. J Microbiol Biotechnol 2024; 34:29-38. [PMID: 38044684 PMCID: PMC10840491 DOI: 10.4014/jmb.2310.10002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Chemical and physical elements affecting the production of bacterial extracellular vesicles (BEVs) of the human pathogen Vibrio vulnificus were quantitatively assessed to optimize the conditions for the BEV production by using the western blot quantification for an outer membrane porin OmpU and by fluorescent dye FM4-64. When cells were cultured at 37°C in an enriched medium (2 × Luria Bertani; 2 × LB) in the presence of EDTA, they produced about 70% more BEVs. BEVs were purified from the cells cultured in the established optimal conditions by the density gradient ultracentrifugation. The dynamic light scattering measurement of the purified BEVs showed that the diameter of them ranged from approximately 25 nm to 161 nm. We hypothesized that there may be some features in nucleotide sequences specific to RNAs packaged in BEVs compared to those in cellular RNA molecules. We compared the nucleotide sequences and abundance of sRNAs between in the cellular fraction and in BEVs through next-generation sequencing (NGS). While no distinct feature was observed in the nucleotide sequences of sRNAs between two groups, the length of sRNA fragments from BEVs were significantly shorter than those in cytoplasm.
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Affiliation(s)
- Jeong Heon Park
- Department of Life Sciences, Sogang University, Seoul 04107, Republic of Korea
| | - Suji Song
- Department of Life Sciences, Sogang University, Seoul 04107, Republic of Korea
| | - Soyee Kim
- Department of Life Sciences, Sogang University, Seoul 04107, Republic of Korea
| | - Minjeong Kim
- Department of Life Sciences, Sogang University, Seoul 04107, Republic of Korea
| | - Kun-Soo Kim
- Department of Life Sciences, Sogang University, Seoul 04107, Republic of Korea
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2
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Warsi OM, Gedda L, Edwards K, Andersson DI. Vesicle-enriched secretomes alter bacterial competitive abilities and are drivers of evolution in microbial communities. FEMS Microbiol Ecol 2023; 99:fiad141. [PMID: 37884450 PMCID: PMC10653989 DOI: 10.1093/femsec/fiad141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023] Open
Abstract
Microbial membrane vesicles can carry compounds that inhibit bacterial growth, but how they impact the fitness of the vesicle-producing bacterial species and influence community dynamics remain unexplored questions. To address these questions, we examined the effect of vesicle-enriched secretomes (VESs) in different single-species and multi-species systems. Effects of VESs on single-species growth dynamics were determined for nine bacterial species belonging to four genera (Escherichia, Salmonella, Pseudomonas and Bacillus) in nutrient-rich and poor growth media. Results showed both species-specific and nutrient-dependent effects of the VESs on bacterial growth. The strongest antagonistic effects were observed for VES isolated from the natural isolates of E. coli, while those isolated from P. aeruginosa PA14 affected the highest number of species. We further demonstrated that these VESs altered the competitive abilities of the species involved in two-species (S. Typhimurium LT2 and S. arizonae) and three-species systems (E. coli, S. Typhimurium LT2 and B. subtilis). Finally, using experimental evolution we showed that different bacterial species could rapidly acquire mutations that abrogated the antagonistic effects of VESs. This study demonstrates how VESs can contribute in shaping microbial communities, both by increasing the competitive ability of a given bacterial species and as a driver of genetic adaptation.
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Affiliation(s)
- Omar M Warsi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
| | - Lars Gedda
- Department of Chemistry-Ångström, Uppsala University, Uppsala 75237, Sweden
| | - Katarina Edwards
- Department of Chemistry-Ångström, Uppsala University, Uppsala 75237, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
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3
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Rogers NMK, McCumber AW, McMillan HM, McNamara RP, Dittmer DP, Kuehn MJ, Hendren CO, Wiesner MR. Comparative electrokinetic properties of extracellular vesicles produced by yeast and bacteria. Colloids Surf B Biointerfaces 2023; 225:113249. [PMID: 36905832 PMCID: PMC10085849 DOI: 10.1016/j.colsurfb.2023.113249] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/13/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
Extracellular vesicles (EVs) are nano-sized, biocolloidal proteoliposomes that have been shown to be produced by all cell types studied to date and are ubiquitous in the environment. Extensive literature on colloidal particles has demonstrated the implications of surface chemistry on transport behavior. Hence, one may anticipate that physicochemical properties of EVs, particularly surface charge-associated properties, may influence EV transport and specificity of interactions with surfaces. Here we compare the surface chemistry of EVs as expressed by zeta potential (calculated from electrophoretic mobility measurements). The zeta potentials of EVs produced by Pseudomonas fluorescens, Staphylococcus aureus, and Saccharomyces cerevisiae were largely unaffected by changes in ionic strength and electrolyte type, but were affected by changes in pH. The addition of humic acid altered the calculated zeta potential of the EVs, especially for those from S. cerevisiae. Differences in zeta potential were compared between EVs and their respective parent cell with no consistent trend emerging; however, significant differences were discovered between the different cell types and their EVs. These findings imply that, while EV surface charge (as estimated from zeta potential) is relatively insensitive to the evaluated environmental conditions, EVs from different organisms can differ regarding which conditions will cause colloidal instability.
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Affiliation(s)
- Nicholas M K Rogers
- Department of Mechanical Engineering, Tel Aviv University, Tel Aviv 69978, Israel; Porter School of Earth and Environmental Studies, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Alexander W McCumber
- Department of Environmental Sciences and Engineering, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Hannah M McMillan
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Ryan P McNamara
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Dirk P Dittmer
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Meta J Kuehn
- Department of Biochemistry, Duke University, Durham, NC, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Christine Ogilvie Hendren
- Center for the Environmental Implications of Nanotechnology, Duke University, Durham, NC, USA; Department of Geological and Environmental Sciences, Appalachian State University, Boone, NC, USA; Research Institute for Environment, Energy and Economics, Appalachian State University, Boone, NC, USA
| | - Mark R Wiesner
- Department of Civil & Environmental Engineering, Duke University, Durham, NC, USA; Center for the Environmental Implications of Nanotechnology, Duke University, Durham, NC, USA
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4
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Ayilam Ramachandran R, Lemoff A, Robertson DM. Pseudomonas aeruginosa-Derived Extracellular Vesicles Modulate Corneal Inflammation: Role in Microbial Keratitis? Infect Immun 2023; 91:e0003623. [PMID: 36995231 PMCID: PMC10112165 DOI: 10.1128/iai.00036-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/16/2023] [Indexed: 03/31/2023] Open
Abstract
Pseudomonas aeruginosa keratitis occurs following trauma, in immunocompromised patients, and in otherwise healthy contact lens wearers. Characterized by a light-blocking infiltrate, P. aeruginosa keratitis is the most serious complication associated with contact lens wear and, in severe cases, can lead to vision loss. Bacterial extracellular vesicles (B EVs) are membrane-enclosed nanometer-scale particles secreted from bacteria and are packed with bioactive molecules. B EVs have been shown to mediate biological functions that regulate host pathogenic responses. In the present study, we isolated P. aeruginosa-derived EVs using size exclusion chromatography and compared the proteomic compositions and functional activities of P. aeruginosa-derived EVs and P. aeruginosa-derived free protein (FP) on corneal epithelial cells and neutrophils. Importantly, P. aeruginosa-derived EVs and FP exhibited unique protein profiles, with EVs being enriched in P. aeruginosa virulence proteins. P. aeruginosa-derived EVs promoted corneal epithelial cell secretion of interleukin-6 (IL-6) and IL-8, whereas these cytokines were not upregulated following treatment with FP. In contrast, FP had a negative effect on the host inflammatory response and impaired neutrophil killing. Both P. aeruginosa-derived EVs and FP promoted intracellular bacterial survival in corneal epithelial cells. Collectively, these data suggest that P. aeruginosa-derived EVs and FP may play a critical role in the pathogenesis of corneal infection by interfering with host innate immune defense mechanisms.
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Affiliation(s)
| | - Andrew Lemoff
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, Texas, USA
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5
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Belmok A, de Almeida FM, Rocha RT, Vizzotto CS, Tótola MR, Ramada MHS, Krüger RH, Kyaw CM, Pappas GJ. Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid. Braz J Microbiol 2023; 54:239-258. [PMID: 36701110 PMCID: PMC9944591 DOI: 10.1007/s42770-022-00900-4] [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: 01/29/2022] [Accepted: 10/02/2022] [Indexed: 01/27/2023] Open
Abstract
A novel bacterial strain, designated GeG2T, was isolated from soils of the native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene analysis of GeG2T revealed high sequence identity (100%) to the alphaproteobacterium Novosphingobium rosa; however, comparisons with N. rosa DSM 7285T showed several distinctive features, prompting a full characterization of the new strain in terms of physiology, morphology, and, ultimately, its genome. GeG2T cells were Gram-stain-negative bacilli, facultatively anaerobic, motile, positive for catalase and oxidase activities, and starch hydrolysis. Strain GeG2T presented planktonic-sessile dimorphism and cell aggregates surrounded by extracellular matrix and nanometric spherical structures were observed, suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles (OMVs). Despite high 16S rDNA identity, strain GeG2T showed 90.38% average nucleotide identity and 42.60% digital DNA-DNA hybridization identity with N. rosa, below species threshold. Whole-genome assembly revealed four circular replicons: a 4.1 Mb chromosome, a 2.7 Mb extrachromosomal megareplicon, and two plasmids (212.7 and 68.6 kb). The megareplicon contains a few core genes and plasmid-type replication/maintenance systems, consistent with its classification as a chromid. Genome annotation shows a vast repertoire of carbohydrate-active enzymes and genes involved in the degradation of aromatic compounds, highlighting the biotechnological potential of the new isolate. Chemotaxonomic features, including polar lipid and fatty acid profiles, as well as physiological, molecular, and whole-genome comparisons showed significant differences between strain GeG2T and N. rosa, indicating that it represents a novel species, for which the name Novosphingobium terrae is proposed. The type strain is GeG2T (= CBMAI 2313T = CBAS 753 T).
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Affiliation(s)
- Aline Belmok
- Laboratório de Microbiologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
| | - Felipe Marques de Almeida
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Rodrigo Theodoro Rocha
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Carla Simone Vizzotto
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Faculdade de Tecnologia, Universidade de Brasília, Brasilia, DF, Brazil
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcelo Henrique Soller Ramada
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasilia, DF, Brazil
- Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasilia, DF, Brazil
| | - Ricardo Henrique Krüger
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Cynthia Maria Kyaw
- Laboratório de Microbiologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
| | - Georgios J Pappas
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
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6
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Barut D, Enuh BM, Derkuş B, Güler Ü, Salih B, Aytar Çelik P. The relationship between bacterial outer membrane vesicles and halophilic adaptation. Mol Omics 2023; 19:174-181. [PMID: 36597842 DOI: 10.1039/d2mo00259k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many cells are known to actively release nano-sized outer membrane vesicles (OMVs) that contain bioactive proteins, lipids, and nucleic acids into the extracellular environment. These vesicles have been associated with adaptation to environmental stress in other species, but their role in halophilic salt stress adaptation is not known. This study aimed to isolate and characterize the OMVs of Halomonas caseinilytica KB2 at various salt concentrations [6% (KB2-6), 12% (KB2-12), and 18% (KB2-18)] and to identify the patterns of adaptations to increasing salinity in its structure, protein composition, and expression. Also, a comparison with the composition of OMVs of E. coli, a mesophilic bacterium, was performed. Bioinformatics and statistical analysis were carried out to elucidate the underlying proteome differences that may exist as a result of increasing salinity. The results show that OMV production in H. caseinilytica KB2 is promoted by a decrease in salinity. OMVs also revealed possible structural and metabolic changes happening in the cells which led to the deduction that cells become more stable with increasing salt concentrations. Cell wall integrity, protein expression and folding are important. Although H. caseinilytica KB2 OMVs show cellular changes with changing salt concentration, they may not play a direct role in adaptation to changing salinity.
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Affiliation(s)
- Dilan Barut
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey.
| | - Blaise M Enuh
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey.
| | - Burak Derkuş
- Department of Chemistry, Faculty of Science, Ankara University, 06560, Ankara, Turkey
| | - Ülkü Güler
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Bekir Salih
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Pınar Aytar Çelik
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey. .,Environmental Protection and Control Program, Eskişehir Osmangazi University, Eskişehir 26110, Turkey
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7
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Proteomic Profiling Reveals Distinct Bacterial Extracellular Vesicle Subpopulations with Possibly Unique Functionality. Appl Environ Microbiol 2023; 89:e0168622. [PMID: 36533919 PMCID: PMC9888257 DOI: 10.1128/aem.01686-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial outer membrane vesicles (OMVs) are 20- to 200-nm secreted packages of lipids, small molecules, and proteins that contribute to diverse bacterial processes. In plant systems, OMVs from pathogenic and beneficial strains elicit plant immune responses that inhibit seedling growth and protect against future pathogen challenge. Previous studies of OMV-plant interactions suggest functionally important differences in the protein composition of Pseudomonas syringae and Pseudomonas fluorescens OMVs, and that their composition and activity differ as a result of medium culture conditions. Here, we show that plant apoplast-mimicking minimal medium conditions impact OMV protein content dramatically in P. syringae but not in P. fluorescens relative to complete medium conditions. Comparative, 2-way analysis of the four conditions reveals subsets of proteins that may contribute to OMV-mediated bacterial virulence and plant immune activation as well as those involved in bacterial stress tolerance or adaptation to a beneficial relationship with plants. Additional localization enrichment analysis of these subsets suggests the presence of outer-inner membrane vesicles (OIMVs). Collectively, these results reveal distinct differences in bacterial extracellular vesicle cargo and biogenesis routes from pathogenic and beneficial plant bacteria in different medium conditions and point to distinct populations of vesicles with diverse functional roles. IMPORTANCE Recent publications have shown that bacterial vesicles play important roles in interkingdom communication between bacteria and plants. Indeed, our recently published data reveal that bacterial vesicles from pathogenic and beneficial strains elicit immune responses in plants that protect against future pathogen challenge. However, the molecules underlying these striking phenomena remain unknown. Our recent work indicated that proteins packaged in vesicles are critically important for vesicle-mediated seedling growth inhibition, often considered an indirect measure of plant immune activation. In this study, we characterize the protein cargo of vesicles from Pseudomonas syringae pathovar tomato DC3000 and Pseudomonas fluorescens from two different medium conditions and show that distinct subpopulations of vesicles contribute to bacterial virulence and stress tolerance. Furthermore, we reveal differences in how beneficial and pathogenic bacterial species respond to harsh environmental conditions through vesicle packaging. Importantly, we find that protein cargo implicates outer-inner membrane vesicles in bacterial stress responses, while outer membrane vesicles are packaged for virulence.
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8
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Lahiri P, Gogoi P, Ghosh D. Single-Step Capture and Targeted Metabolomics of Alkyl-Quinolones in Outer Membrane Vesicles (OMVs) of Pseudomonas Aeruginosa. Methods Mol Biol 2023; 2625:201-216. [PMID: 36653645 DOI: 10.1007/978-1-0716-2966-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Outer membrane vesicles (OMVs), also called as bacterial membrane vesicles (BMVs), are secreted by many Gram-negative bacterial pathogens. These nanoscale vesicles traffic discrete arrays of virulence factors that can often induce complex pathologies far from the infection sites. The OMVs of P. aeruginosa, often regarded as the gold standard of BMVs are known to traffic a battery of specific small MW alkyl-quinolones (AQs). These AQs function like primordial hormones by modulating intra-species and inter-species bacterial interactions. They can also perform cross-kingdom signaling with the human host and directly exacerbate pathogenesis. The discrete isotopic signatures of AQs enjoy potential in the mass spectrometry-based diagnosis P. aeruginosa infections. Matrix-free laser desorption/ionization mass spectrometry (LDI-MS) presents a robust, cost-effective platform to fit this demand. We describe a LDI-MS system using inert ceramic filters that performs dual role of single-step enrichment of OMVs and matrix-free ionization/identification of AQs in situ.
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Affiliation(s)
- Pallavi Lahiri
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Priyakshi Gogoi
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Dipankar Ghosh
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.
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9
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Suri K, D'Souza A, Huang D, Bhavsar A, Amiji M. Bacterial extracellular vesicle applications in cancer immunotherapy. Bioact Mater 2022; 22:551-566. [PMID: 36382022 PMCID: PMC9637733 DOI: 10.1016/j.bioactmat.2022.10.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/10/2022] [Accepted: 10/22/2022] [Indexed: 12/03/2022] Open
Abstract
Cancer therapy is undergoing a paradigm shift toward immunotherapy focusing on various approaches to activate the host immune system. As research to identify appropriate immune cells and activate anti-tumor immunity continues to expand, scientists are looking at microbial sources given their inherent ability to elicit an immune response. Bacterial extracellular vesicles (BEVs) are actively studied to control systemic humoral and cellular immune responses instead of using whole microorganisms or other types of extracellular vesicles (EVs). BEVs also provide the opportunity as versatile drug delivery carriers. Unlike mammalian EVs, BEVs have already made it to the clinic with the meningococcal vaccine (Bexsero®). However, there are still many unanswered questions in the use of BEVs, especially for chronic systemically administered immunotherapies. In this review, we address the opportunities and challenges in the use of BEVs for cancer immunotherapy and provide an outlook towards development of BEV products that can ultimately translate to the clinic.
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Affiliation(s)
- Kanika Suri
- Department of Bioengineering, College of Engineering, Northeastern University, Boston, MA, 02115, USA
| | - Anisha D'Souza
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA, 02115, USA,Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 20115, USA
| | - Di Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA, 02115, USA,Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 20115, USA
| | - Aashray Bhavsar
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA, 02115, USA
| | - Mansoor Amiji
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA, 02115, USA,Department of Chemical Engineering, College of Engineering, Northeastern University, Boston, MA, 02115, USA,Corresponding author. Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA, 02115, USA.
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10
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Jiang M, Wang Z, Xia F, Wen Z, Chen R, Zhu D, Wang M, Zhuge X, Dai J. Reductions in bacterial viability stimulate the production of Extra-intestinal Pathogenic Escherichia coli (ExPEC) cytoplasm-carrying Extracellular Vesicles (EVs). PLoS Pathog 2022; 18:e1010908. [PMID: 36260637 PMCID: PMC9621596 DOI: 10.1371/journal.ppat.1010908] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/31/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
Extra-intestinal Pathogenic Escherichia coli (ExPEC) is defined as an extra-intestinal foodborne pathogen, and several dominant sequence types (STs) ExPEC isolates are highly virulent, with zoonotic potential. Bacteria extracellular vesicles (EVs) carry specific subsets of molecular cargo, which affect various biological processes in bacteria and host. The mechanisms of EVs formation in ExPEC remains to be elucidated. Here, the purified EVs of ExPEC strains of different STs were isolated with ultracentrifugation processes. A comparative analysis of the strain proteomes showed that cytoplasmic proteins accounted for a relatively high proportion of the proteins among ExPEC EVs. The proportion of cytoplasm-carrying vesicles in ExPEC EVs was calculated with a simple green fluorescent protein (GFP) expression method. The RecA/LexA-dependent SOS response is a critical mediator of generation of cytoplasm-carrying EVs. The SOS response activates the expression of prophage-associated endolysins, Epel1, Epel2.1, and Epel2.2, which triggered cell lysis, increasing the production of ExPEC cytoplasm-carrying EVs. The repressor LexA controlled directly the expression of these endolysins by binding to the SOS boxes in the endolysin promoter regions. Reducing bacterial viability stimulated the production of ExPEC EVs, especially cytoplasm-carrying EVs. The imbalance in cell division caused by exposure to H2O2, the deletion of ftsK genes, or t6A synthesis defects activated the RecA/LexA-dependent SOS response, inducing the expression of endolysins, and thus increasing the proportion of cytoplasm-carrying EVs in the total ExPEC EVs. Antibiotics, which decreased bacterial viability, also increase the production of ExPEC cytoplasm-carrying EVs through the SOS response. Changes in the proportion of cytoplasm-carrying EVs affected the total DNA content of ExPEC EVs. When macrophages are exposed to a higher proportion of cytoplasm-carrying vesicles, ExPEC EVs were more cytotoxic to macrophages, accompanied with more-severe mitochondrial disruption and a higher level of induced intrinsic apoptosis. In summary, we offered comprehensive insight into the proteome analysis of ExPEC EVs. This study demonstrated the novel formation mechanisms of E. coli cytoplasm-carrying EVs. Bacteria can release extracellular vesicles (EVs) into the extracellular environment. Bacterial EVs are primarily composed of protein, DNA, RNA, lipopolysaccharide (LPS), and diverse metabolite molecules. The molecular cargoes of EVs are critical for the interaction between microbes and their hosts, and affected various host biological processes. However, the mechanisms underlying the biogenesis of bacterial EVs had not been fully clarified in extra-intestinal pathogenic Escherichia coli (ExPEC). In this study, we demonstrated ExPEC EVs contained at least three types of vesicles, including outer membrane vesicles (OMVs), outer-inner membrane vesicles (OIMVs), and explosive outer membrane vesicles (EOMVs). Our results systematically identified important factors affecting the production of ExPEC cytoplasm-carrying EVs, especially EOMVs. A reduction in bacterial viability activated the RecA/LexA-dependent SOS response, inducing the expression of endolysins, which increased the production of ExPEC cytoplasm-carrying EVs. This increase in the proportion of cytoplasm-carrying EVs increased the cytotoxicity of EVs. It was noteworthy that antibiotics increased the production of ExPEC EVs, especially the numbers of cytoplasm-carrying EVs, which in turn increased EV cytotoxicity, suggesting that the treatment of infections of multidrug-resistant strains infection with antibiotics might cause greater host damage. Our study should improve the prevention and treatment of ExPEC infections.
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Affiliation(s)
- Min Jiang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China,Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, China
| | - Zhongxing Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China,Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, China
| | - Fufang Xia
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China,Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, China
| | - Zhe Wen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China,Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, China
| | - Rui Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China,Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, China
| | - Dongyu Zhu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China,Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, China
| | - Min Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, China
| | - Xiangkai Zhuge
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, China,* E-mail: (XZ); (JD)
| | - Jianjun Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China,College of Pharmacy, China Pharmaceutical University, Nanjing, China,* E-mail: (XZ); (JD)
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11
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Zhang Y, Li X, Tian H, An B, Yan B, Cai J. Vegetative Insecticidal Protein Vip3Aa Is Transported via Membrane Vesicles in Bacillus thuringiensis BMB171. Toxins (Basel) 2022; 14:toxins14070480. [PMID: 35878218 PMCID: PMC9319297 DOI: 10.3390/toxins14070480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Vegetative insecticidal protein Vip3Aa, secreted by many Bacillus thuringiensis (Bt) strains during the vegetative growth stage, represents the second-generation insecticidal toxin. In recent years, significant progress has been made on its structure and action mechanism. However, how it is translocated across the cytoplasmic membrane into the environment remains a mystery. This work demonstrates that Vip3Aa is not secreted by the General Secretion (Sec) System. To reveal the secretory pathway of Vip3A, we purified the membrane vesicles (MVs) of B. thuringiensis BMB171 and observed by TEM. The size of MVs was determined by the dynamic light scattering method, and their diameter was approximately 40–200 nm, which is consistent with the vesicles in Gram-negative bacteria. Moreover, Vip3A could be detected in the purified MVs by Western blot, and immunoelectron microscopy reveals Vip3A antibody-coated gold particles located in the MVs. After deleting its signal peptide, chitinase B (ChiB) failed to be secreted. However, the recombinant ChiB, whose signal peptide was substituted with the N-terminal 39 amino acids from Vip3A, was secreted successfully through MVs. Thus, this sequence is proposed as the signal region responsible for vesicle transport. Together, our results revealed for the first time that Vip3Aa is transported to the medium via MVs.
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Affiliation(s)
- Yizhuo Zhang
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (Y.Z.); (X.L.); (H.T.); (B.A.); (B.Y.)
| | - Xuelian Li
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (Y.Z.); (X.L.); (H.T.); (B.A.); (B.Y.)
| | - Hongwei Tian
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (Y.Z.); (X.L.); (H.T.); (B.A.); (B.Y.)
| | - Baoju An
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (Y.Z.); (X.L.); (H.T.); (B.A.); (B.Y.)
| | - Bing Yan
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (Y.Z.); (X.L.); (H.T.); (B.A.); (B.Y.)
| | - Jun Cai
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (Y.Z.); (X.L.); (H.T.); (B.A.); (B.Y.)
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300071, China
- Correspondence:
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12
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Extracellular degradation of a polyurethane oligomer involving outer membrane vesicles and further insights on the degradation of 2,4-diaminotoluene in Pseudomonas capeferrum TDA1. Sci Rep 2022; 12:2666. [PMID: 35177693 PMCID: PMC8854710 DOI: 10.1038/s41598-022-06558-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/02/2022] [Indexed: 11/16/2022] Open
Abstract
The continuing reports of plastic pollution in various ecosystems highlight the threat posed by the ever-increasing consumption of synthetic polymers. Therefore, Pseudomonas capeferrum TDA1, a strain recently isolated from a plastic dump site, was examined further regarding its ability to degrade polyurethane (PU) compounds. The previously reported degradation pathway for 2,4-toluene diamine, a precursor and degradation intermediate of PU, could be confirmed by RNA-seq in this organism. In addition, different cell fractions of cells grown on a PU oligomer were tested for extracellular hydrolytic activity using a standard assay. Strikingly, purified outer membrane vesicles (OMV) of P. capeferrum TDA1 grown on a PU oligomer showed higher esterase activity than cell pellets. Hydrolases in the OMV fraction possibly involved in extracellular PU degradation were identified by mass spectrometry. On this basis, we propose a model for extracellular degradation of polyester-based PUs by P. capeferrum TDA1 involving the role of OMVs in synthetic polymer degradation.
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13
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Qiao L, Rao Y, Zhu K, Rao X, Zhou R. Engineered Remolding and Application of Bacterial Membrane Vesicles. Front Microbiol 2021; 12:729369. [PMID: 34690971 PMCID: PMC8532528 DOI: 10.3389/fmicb.2021.729369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/31/2021] [Indexed: 11/14/2022] Open
Abstract
Bacterial membrane vesicles (MVs) are produced by both Gram-positive and Gram-negative bacteria during growth in vitro and in vivo. MVs are nanoscale vesicular structures with diameters ranging from 20 to 400 nm. MVs incorporate bacterial lipids, proteins, and often nucleic acids, and can effectively stimulate host immune response against bacterial infections. As vaccine candidates and drug delivery systems, MVs possess high biosafety owing to the lack of self-replication ability. However, wild-type bacterial strains have poor MV yield, and MVs from the wild-type strains may be harmful due to the carriage of toxic components, such as lipopolysaccharides, hemolysins, enzymes, etc. In this review, we summarize the genetic modification of vesicle-producing bacteria to reduce MV toxicity, enhance vesicle immunogenicity, and increase vesicle production. The engineered MVs exhibit broad applications in vaccine designs, vaccine delivery vesicles, and drug delivery systems.
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Affiliation(s)
- Li Qiao
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yifan Rao
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Keting Zhu
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, China
| | - Renjie Zhou
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
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14
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Dataset of single nucleotide polymorphisms and comprehensive proteomic analysis of Streptococcus equi subsp. equi ATCC 39506. Data Brief 2021; 38:107402. [PMID: 34621931 PMCID: PMC8479396 DOI: 10.1016/j.dib.2021.107402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/02/2022] Open
Abstract
Streptococcus equi subspecies equi (S. equi) is an opportunistic pathogen and a major causative agent of equine strangles, a contagious respiratory infection in horses and other equines. In this study, we provide the dataset associated with our research publication “Streptococcus equi-derived extracellular vesicles as a vaccine candidate against Streptococcus equi infections” [1]. We describe the genomic differences between S. equi 4047 and S. equi ATCC 39506 and outline the comprehensive proteome information of various fractions, including the whole cell lysate, membrane proteome, secretory proteome, and extracellular vesicle proteome. In addition, we included a dataset of highly immunoreactive proteins identified through immunoprecipitation. The specifications table provides a detailed summary of the gene annotation and quantitative information obtained for each proteome. The proteomics data were analyzed using shotgun proteomics with LTQ Velos and Q Exactive mass spectrometry in the data-dependent acquisition mode. We have deposited the acquired data, including the mass spectrometry raw files and exported MASCOT search results, in the PRIDE public repository under the accession numbers PXD025152 and PXD025527.
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15
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Streptococcus equi-derived extracellular vesicles as a vaccine candidate against Streptococcus equi infection. Vet Microbiol 2021; 259:109165. [PMID: 34225054 DOI: 10.1016/j.vetmic.2021.109165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/22/2021] [Indexed: 02/08/2023]
Abstract
Streptococcus equi subspecies equi is a pathogenic bacterium that causes strangles, a highly contagious respiratory infection in horses and other equines. The limitations of current vaccines against S. equi infection warrants the development of an affordable, safe, and effective vaccine. Because gram-positive extracellular vesicles (EVs) transport various immunogenic antigens, they are attractive vaccine candidates. Here, we purified the EVs of S. equi ATCC 39506 and evaluated them as a vaccine candidate against S. equi infection in mice. As an initial step, comparative proteomic analysis was performed to characterize the functional features of the EVs. Reverse vaccinology and knowledge-based annotations were then used to screen potential vaccine candidates (PVCs) for S. equi ATCC 39506. Finally, 32 PVCs were found to be enriched in the EV fraction, suggesting the usefulness of this fraction as a vaccine. Importantly, a significantly higher survival rate after S. equi infection was detected in mice immunized with S. equi-derived EVs via the intraperitoneal route than in mice immunized with heat-killed bacteria. Of note, immunoprecipitation-mass spectrometry results validated various immunogenic antigens within the EV proteome. In conclusion, our results suggest that S. equi-derived EVs can serve as a vaccine candidate against S. equi infection.
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16
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McMillan HM, Rogers N, Wadle A, Hsu-Kim H, Wiesner MR, Kuehn MJ, Hendren CO. Microbial vesicle-mediated communication: convergence to understand interactions within and between domains of life. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:664-677. [PMID: 33899070 DOI: 10.1039/d1em00022e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
All cells produce extracellular vesicles (EVs). These biological packages contain complex mixtures of molecular cargo and have a variety of functions, including interkingdom communication. Recent discoveries highlight the roles microbial EVs may play in the environment with respect to interactions with plants as well as nutrient cycling. These studies have also identified molecules present within EVs and associated with EV surfaces that contribute to these functions. In parallel, studies of engineered nanomaterials have developed methods to track and model small particle behavior in complex systems and measure the relative importance of various surface features on transport and function. While studies of EV behavior in complex environmental conditions have not yet employed transdisciplinary approaches, it is increasingly clear that expertise from disparate fields will be critical to understand the role of EVs in these systems. Here, we outline how the convergence of biology, soil geochemistry, and colloid science can both develop and address questions surrounding the basic principles governing EV-mediated interkingdom interactions.
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Affiliation(s)
- Hannah M McMillan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas Rogers
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Austin Wadle
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Heileen Hsu-Kim
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Mark R Wiesner
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Meta J Kuehn
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA and Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Christine Ogilvie Hendren
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA and Department of Geological and Environmental Sciences, Appalachian State University, Boone, NC 28608, USA.
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17
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Lee SH, Lira-Albarrán S, Saadeldin IM. Comprehensive Proteomics Analysis of In Vitro Canine Oviductal Cell-Derived Extracellular Vesicles. Animals (Basel) 2021; 11:ani11020573. [PMID: 33672125 PMCID: PMC7926305 DOI: 10.3390/ani11020573] [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: 11/30/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary As the dog shows unique and peculiar reproductive characteristics, assisted reproductive techniques such as in vitro maturation and in vitro fertilization have not been well-established compared with those of other mammals. Our recent work demonstrated the interplay between in vitro oviductal cell-derived extracellular vesicles (OC-EVs) and cumulus-oocyte complexes in dogs. Here, we provided for the first time a comprehensive proteomic analysis of OC-EVs. A total of 398 proteins were identified in all OC-EVs samples. A functional enrichment analysis indicated that these core proteins were involved in the key cellular metabolic process related to oocyte maturation and embryonic development. The current comprehensive description of the canine OC-EVs proteome would provide a fundamental resource for further understanding canine reproductive physiology, the interaction of sperms with female counterparts during fertilization, early pregnancy, and establishing an efficient system of in vitro embryo production. Abstract Dogs (Canis lupus familiaris) have unique and peculiar reproductive characteristics. While the interplay between in vitro oviductal cell-derived extracellular vesicles (OC-EVs) and cumulus-oocyte complexes in dogs has begun to be elucidated, no study has yet provided extensive information on the biological content and physiological function of OC-EVs and their role in canine oocyte development. Here, we aimed to provide the first comprehensive proteomic analysis of OC-EVs. We identified 398 proteins as present in all OC-EVs samples. The functional enrichment analysis using Gene Ontology terms and an Ingenuity Pathway Analysis revealed that the identified proteins were involved in several cellular metabolic processes, including translation, synthesis, expression, and protein metabolism. Notably, the proteins were also involved in critical canonical pathways with essential functions in oocyte and embryo development, such as ERK/MAPK, EIF2, PI3K/AKT, and mTOR signaling. These data would be an important resource for studying canine reproductive physiology and establishing a successful in vitro embryo production system in dogs.
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Affiliation(s)
- Seok Hee Lee
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA;
- Correspondence: (S.H.L.); (I.M.S.); Tel.: +1-4154760932 (S.H.L.); +966-530910740 (I.M.S.)
| | - Saúl Lira-Albarrán
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA;
| | - Islam M Saadeldin
- Department of Physiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
- King Faisal Specialist Hospital & Research Centre, Department of Comparative Medicine, Riyadh 11211, Saudi Arabia
- Correspondence: (S.H.L.); (I.M.S.); Tel.: +1-4154760932 (S.H.L.); +966-530910740 (I.M.S.)
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18
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Environmental conditions modulate the protein content and immunomodulatory activity of extracellular vesicles produced by the probiotic Propionibacterium freudenreichii. Appl Environ Microbiol 2021; 87:AEM.02263-20. [PMID: 33310709 PMCID: PMC7851693 DOI: 10.1128/aem.02263-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Propionibacterium freudenreichii is a probiotic Gram-positive bacterium with promising immunomodulatory properties. It modulates regulatory cytokines, mitigates the inflammatory response in vitro and in vivo These properties were initially attributed to specific bacterial surface proteins. Recently, we showed that extracellular vesicles (EVs) produced by P. freudenreichii CIRM-BIA129 mimic the immunomodulatory features of parent cells in vitro (i.e. modulating NF-κB transcription factor activity and IL-8 release) which underlies the role of EVs as mediators of the probiotic effects of the bacterium. The modulation of EV properties, and particularly of those with potential therapeutic applications such as the EVs produced by the probiotic P. freudenreichii, is one of the challenges in the field to achieve efficient yields with the desired optimal functionality. Here we evaluated whether the culture medium in which the bacteria are grown could be used as a lever to modulate the protein content and hence the properties of P. freudenreichii CIRM-BIA129 EVs. The physical, biochemical and functional properties of EVs produced from cells cultivated on laboratory Yeast Extract Lactate (YEL) medium and cow milk ultrafiltrate (UF) medium were compared. UF-derived EVs were more abundant, smaller in diameter and displayed more intense anti-inflammatory activity than YEL-derived EVs. Furthermore, the growth media modulated EV content in terms of both the identities and abundances of their protein cargos, suggesting different patterns of interaction with the host. Proteins involved in amino acid metabolism and central carbon metabolism were modulated, as were the key surface proteins mediating host-propionibacteria interactions.Importance Extracellular vesicles (EVs) are cellular membrane-derived nanosized particles that are produced by most cells in all three kingdoms of life. They play a pivotal role in cell-cell communication through their ability to transport bioactive molecules from donor to recipient cells. Bacterial EVs are important factors in host-microbe interactions. Recently we have shown that EVs produced by the probiotic P. freudenreichii exhibited immunomodulatory properties. We evaluate here the impact of environmental conditions, notably culture media, on P. freudenreichii EV production and function. We show that EVs display considerable differences in protein cargo and immunomodulation depending on the culture medium used. This work offers new perspectives for the development of probiotic EV-based molecular delivery systems, and reinforces the optimization of growth conditions as a tool to modulate the potential therapeutic applications of EVs.
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19
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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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20
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Mutyala S, Kim C, Song YE, Khandelwal H, Baek J, Seol E, Oh YK, Kim JR. Enabling anoxic acetate assimilation by electrode-driven respiration in the obligate aerobe, Pseudomonas putida. Bioelectrochemistry 2020; 138:107690. [PMID: 33190096 DOI: 10.1016/j.bioelechem.2020.107690] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 10/17/2020] [Accepted: 10/20/2020] [Indexed: 10/23/2022]
Abstract
This study examined the obligate aerobe, Pseudomonas putida, using acetate as the sole carbon and energy source, and respiration via an anode as the terminal electron acceptor under anoxic conditions. P. putida showed significantly different acetate assimilation in a closed-circuit microbial fuel cell (CC-MFC) compared to an open circuit MFC (OC-MFC). More than 72% (2.6 mmol) of acetate was consumed during 84 hrs in the CC-MFC in contrast to the no acetate consumption observed in the OC-MFC. The CC-MFC produced 150 μA (87 C) from acetate metabolization. Electrode-based respiration reduced the NADH/NAD+ ratio anaerobically, which is similar to the aerobic condition. The CC-MFC showed significantly higher acetyl-CoA synthetase activity than the OC-MFC (0.028 vs. 0.001 μmol/min/mg), which was comparable to the aerobic condition (circa 60%). Overall, electrode-based respiration enables P. putida to metabolize acetate under anoxic conditions and provide a platform to regulate the bacterial redox balance without oxygen.
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Affiliation(s)
- Sakuntala Mutyala
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
| | - Changman Kim
- Advanced Biofuel and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
| | - Young Eun Song
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
| | - Himanshu Khandelwal
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
| | - Jiyun Baek
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
| | - Eunhee Seol
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
| | - You-Kwan Oh
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
| | - Jung Rae Kim
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea.
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21
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Zhao ZM, Liu ZH, Pu Y, Meng X, Xu J, Yuan JS, Ragauskas AJ. Emerging Strategies for Modifying Lignin Chemistry to Enhance Biological Lignin Valorization. CHEMSUSCHEM 2020; 13:5423-5432. [PMID: 32750220 DOI: 10.1002/cssc.202001401] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/19/2020] [Indexed: 06/11/2023]
Abstract
Biological lignin valorization represents a promising approach contributing to sustainable and economic biorefineries. The low level of valuable lignin-derived products remains a major challenge hindering the implementation of microbial lignin conversion. Lignin's properties play a significant role in determining the efficiency of lignin bioconversion. To date, despite significant progress in the development of biomass pretreatment, lignin fractionation, and fermentation over the last few decades, little efforts have gone into identifying the ideal lignin substrates for an efficient microbial metabolism. In this Minireview, emerging and state-of-the-art strategies for biomass pretreatment and lignin fractionation are summarized to elaborate their roles in modifying lignin structure for bioconversion. Fermentation strategies aimed at enhancing lignin depolymerization for microbial utilization are systematically reviewed as well. With an improved understanding of the ideal lignin structure elucidated by comprehensive metabolic pathways and/or big data analysis, modifying lignin chemistry could be more directional and effective. Ultimately, together with the progress of fermentation process optimization, biological lignin valorization will become more competitive in biorefineries.
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Affiliation(s)
- Zhi-Min Zhao
- School of Ecology and Environment, Inner Mongolia Key Laboratory of Environmental Pollution Controlling and Wastes Recycling, Inner Mongolia University, Hohhot, 010021, P. R. China
- Department of Chemical & Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Zhi-Hua Liu
- Synthetic and Systems Biology Innovation Hub (SSBiH), Texas A&M University, College Station, TX 77843, USA
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Yunqiao Pu
- Center for Bioenergy Innovation, Joint Institute of Biological Science, Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831, USA
| | - Xianzhi Meng
- Department of Chemical & Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Jifei Xu
- School of Ecology and Environment, Inner Mongolia Key Laboratory of Environmental Pollution Controlling and Wastes Recycling, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Joshua S Yuan
- Synthetic and Systems Biology Innovation Hub (SSBiH), Texas A&M University, College Station, TX 77843, USA
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Arthur J Ragauskas
- Department of Chemical & Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, USA
- Center for Bioenergy Innovation, Joint Institute of Biological Science, Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831, USA
- Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN 37996, USA
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22
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Avila-Calderón ED, Medina-Chávez O, Flores-Romo L, Hernández-Hernández JM, Donis-Maturano L, López-Merino A, Arellano-Reynoso B, Aguilera-Arreola MG, Ruiz EA, Gomez-Lunar Z, Witonsky S, Contreras-Rodríguez A. Outer Membrane Vesicles From Brucella melitensis Modulate Immune Response and Induce Cytoskeleton Rearrangement in Peripheral Blood Mononuclear Cells. Front Microbiol 2020; 11:556795. [PMID: 33193138 PMCID: PMC7604303 DOI: 10.3389/fmicb.2020.556795] [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: 04/28/2020] [Accepted: 09/17/2020] [Indexed: 02/01/2023] Open
Abstract
Similar to what has been described in other Gram-negative bacteria, Brucella melitensis releases outer membrane vesicles (OMVs). OMVs from B. melitensis 16M and the rough-mutant B. melitensis VTRM1 were able to induce a protective immune response against virulent B. melitensis in mice models. The presence of some proteins which had previously been reported to induce protection against Brucella were found in the proteome of OMVs from B. melitensis 16M. However, the proteome of OMVs from B. melitensis VTRM1 had not previously been determined. In order to be better understand the role of OMVs in host-cell interactions, the aim of this work was to compare the proteomes of OMVs from B. melitensis 16M and the derived rough-mutant B. melitensis VTRM1, as well as to characterize the immune response induced by vesicles on host cells. Additionally, the effect of SDS and proteinase K on the stability of OMVs was analyzed. OMVs from B. melitensis 16M (smooth strain) and the B. melitensis VTRM1 rough mutant (lacking the O-polysaccharide side chain) were analyzed through liquid chromatography-mass spectrometry (LC-MS/MS). OMVs were treated with proteinase K, sodium deoxycholate, and SDS, and then their protein profile was determined using SDS-PAGE. Furthermore, PBMCs were treated with OMVs in order to measure their effect on cytoskeleton, surface molecules, apoptosis, DNA damage, proliferation, and cytokine-induction. A total of 131 proteins were identified in OMVs from B. melitensis16M, and 43 in OMVs from B. melitensis VTRM1. Proteome comparison showed that 22 orthologous proteins were common in vesicles from both strains, and their core proteome contained Omp31, Omp25, GroL, and Omp16. After a subsequent detergent and enzyme treatment, OMVs from B. melitensis VTRM1 exhibited higher sensitive compared to OMVs from the B. melitensis 16M strain. Neither OMVs induced IL-17, proliferation, apoptosis or DNA damage. Nonetheless, OMVs from the smooth and rough strains induced overproduction of TNFα and IL-6, as well as actin and tubulin rearrangements in the cytoskeleton. Moreover, OMVs from both strains inhibited PD-L1 expression in T-cells. These data revealed significant differences in OMVs derived from the rough and smooth Brucella strains, among which, the presence or absence of complete LPS appeared to be crucial to protect proteins contained within vesicles and to drive the immune response.
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Affiliation(s)
- Eric Daniel Avila-Calderón
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.,Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Olín Medina-Chávez
- Centro de Biotecnología FEMSA, Escuela de Ingeniería y Ciencias, Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
| | - Leopoldo Flores-Romo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Mexico City, Mexico
| | - José Manuel Hernández-Hernández
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Luis Donis-Maturano
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ahidé López-Merino
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Beatriz Arellano-Reynoso
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ma Guadalupe Aguilera-Arreola
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Enrico A Ruiz
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Zulema Gomez-Lunar
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sharon Witonsky
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States.,Large Animal Clinical Sciences, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Araceli Contreras-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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Dineshkumar K, Aparna V, Wu L, Wan J, Abdelaziz MH, Su Z, Wang S, Xu H. Bacterial bug-out bags: outer membrane vesicles and their proteins and functions. J Microbiol 2020; 58:531-542. [DOI: 10.1007/s12275-020-0026-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 01/08/2023]
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24
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Yu Q, Mishra B, Fein JB. Role of bacterial cell surface sulfhydryl sites in cadmium detoxification by Pseudomonas putida. JOURNAL OF HAZARDOUS MATERIALS 2020; 391:122209. [PMID: 32036314 DOI: 10.1016/j.jhazmat.2020.122209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
Understanding bacterial metal detoxification systems is crucial for determining the environmental impacts of metal pollution and for developing advanced bioremediation and water disinfection strategies. Here, we explore the role of cell surface sulfhydryl sites in bacterial detoxification of Cd, using Pseudomonas putida with surface sulfhydryl sites mostly on its EPS molecules as a model organism. Our results show that 5 and 20 ppm Cd in LB growth medium affects the lag phase of P. putida, but not the overall extent of cell growth at stationary phase, indicating that P. putida can detoxify Cd at these concentrations. EXAFS analysis of Cd bound to biomass from the different growth stages indicates that Cd binds to both sulfhydryl and non-sulfhydryl sites, but that the importance of Cd-sulfhydryl binding increases from early exponential to stationary phase. Cell growth is positively correlated to the measured sulfhydryl concentration on different biomass samples, but is independent of the measured non-sulfhydryl binding site concentration on the cell surfaces. Taken together, our results demonstrate that the sulfhydryl binding sites on EPS molecules can play an important role in binding and detoxifying toxic metals, significantly decreasing the bioavailability of the metal by sequestering it away from the bacterial cells.
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Affiliation(s)
- Qiang Yu
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, United States.
| | - Bhoopesh Mishra
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS29JT, United Kingdom
| | - Jeremy B Fein
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, United States
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25
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Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440. Proc Natl Acad Sci U S A 2020; 117:9302-9310. [PMID: 32245809 DOI: 10.1073/pnas.1921073117] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lignin is an abundant and recalcitrant component of plant cell walls. While lignin degradation in nature is typically attributed to fungi, growing evidence suggests that bacteria also catabolize this complex biopolymer. However, the spatiotemporal mechanisms for lignin catabolism remain unclear. Improved understanding of this biological process would aid in our collective knowledge of both carbon cycling and microbial strategies to valorize lignin to value-added compounds. Here, we examine lignin modifications and the exoproteome of three aromatic-catabolic bacteria: Pseudomonas putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116. P. putida cultivation in lignin-rich media is characterized by an abundant exoproteome that is dynamically and selectively packaged into outer membrane vesicles (OMVs). Interestingly, many enzymes known to exhibit activity toward lignin-derived aromatic compounds are enriched in OMVs from early to late stationary phase, corresponding to the shift from bioavailable carbon to oligomeric lignin as a carbon source. In vivo and in vitro experiments demonstrate that enzymes contained in the OMVs are active and catabolize aromatic compounds. Taken together, this work supports OMV-mediated catabolism of lignin-derived aromatic compounds as an extracellular strategy for nutrient acquisition by soil bacteria and suggests that OMVs could potentially be useful tools for synthetic biology and biotechnological applications.
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26
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Lécrivain AL, Beckmann BM. Bacterial RNA in extracellular vesicles: A new regulator of host-pathogen interactions? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194519. [PMID: 32142907 DOI: 10.1016/j.bbagrm.2020.194519] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/17/2020] [Accepted: 02/25/2020] [Indexed: 01/26/2023]
Abstract
Extracellular vesicles (EVs) are released by cells from all kingdoms and represent one form of cell-cell interaction. This universal system of communication blurs cells type boundaries, offering an new avenue for pathogens to infect their hosts. EVs carry with them an arsenal of virulence factors that have been the focus of numerous studies. During the last years, the RNA content of EVs has also gained increasing attention, particularly in the context of infection. Secreted RNA in EVs (evRNA) from several bacterial pathogens have been characterised but the exact mechanisms promoting pathogenicity remain elusive. In this review, we evaluate the potential of such transcripts to directly interact with targets in infected cells and, by this, represent a novel angle of host cell manipulation during bacterial infection. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.
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27
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Kim OH, Hong HE, Seo H, Kwak BJ, Choi HJ, Kim KH, Ahn J, Lee SC, Kim SJ. Generation of induced secretome from adipose-derived stem cells specialized for disease-specific treatment: An experimental mouse model. World J Stem Cells 2020; 12:70-86. [PMID: 32110276 PMCID: PMC7031761 DOI: 10.4252/wjsc.v12.i1.70] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/16/2019] [Accepted: 09/26/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Recently, the exclusive use of mesenchymal stem cell (MSC)-secreted molecules, named as the secretome, have been evaluated for overcoming the limitations of cell-based therapy while maintaining its advantages.
AIM To improve cell-free therapy by adding disease-specificity through stimulation of MSCs using disease-causing materials.
METHODS We collected the secretory materials (named as inducers) released from AML12 hepatocytes that had been pretreated with thioacetamide (TAA) and generated the TAA-induced secretome (TAA-isecretome) after stimulating adipose-derived stem cells with the inducers. The TAA-isecretome was intravenously administered to mice with TAA-induced hepatic failure and those with partial hepatectomy.
RESULTS TAA-isecretome infusion showed higher therapeutic potential in terms of (1) restoring disorganized hepatic tissue to normal tissue; (2) inhibiting proinflammatory cytokines (interleukin-6 and tumor necrosis factor-α); and (3) reducing abnormally elevated liver enzymes (aspartate aminotransferase and alanine aminotransferase) compared to the naïve secretome infusion in mice with TAA-induced hepatic failure. However, the TAA-isecretome showed inferior therapeutic potential for restoring hepatic function in partially hepatectomized mice. Proteomic analysis of TAA-isecretome identified that antioxidant processes were the most predominant enriched biological networks of the proteins exclusively identified in the TAA-isecretome. In addition, peroxiredoxin-1, a potent antioxidant protein, was found to be one of representative components of TAA-isecretome and played a central role in the protection of TAA-induced hepatic injury.
CONCLUSION Appropriate stimulation of adipose-derived stem cells with TAA led to the production of a secretome enriched with proteins, especially peroxiredoxin-1, with higher antioxidant activity. Our results suggest that appropriate stimulation of MSCs with pathogenic agents can lead to the production of a secretome specialized for protecting against the pathogen. This approach is expected to open a new way of developing various specific therapeutics based on the high plasticity and responsiveness of MSCs.
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Affiliation(s)
- Ok-Hee Kim
- Catholic Central Laboratory of Surgery, Institute of Biomedical Industry, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
- Department of Surgery, Division of Hepato-biliary Pancreatic Surgery, Seoul St. Mary’s Hospital, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
| | - Ha-Eun Hong
- Catholic Central Laboratory of Surgery, Institute of Biomedical Industry, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
- Department of Surgery, Division of Hepato-biliary Pancreatic Surgery, Seoul St. Mary’s Hospital, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
| | - Haeyeon Seo
- Catholic Central Laboratory of Surgery, Institute of Biomedical Industry, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
- Department of Surgery, Division of Hepato-biliary Pancreatic Surgery, Seoul St. Mary’s Hospital, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
| | - Bong Jun Kwak
- Department of Surgery, Division of Hepato-biliary Pancreatic Surgery, Seoul St. Mary’s Hospital, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
| | - Ho Joong Choi
- Department of Surgery, Division of Hepato-biliary Pancreatic Surgery, Seoul St. Mary’s Hospital, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
| | - Kee-Hwan Kim
- Catholic Central Laboratory of Surgery, Institute of Biomedical Industry, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
- Department of Surgery, Uijeongbu St. Mary's Hospital, College of Medicine, the Catholic University of Korea, Seoul 11765, South Korea
| | - Joseph Ahn
- Department of Surgery, Division of Hepato-biliary Pancreatic Surgery, Seoul St. Mary’s Hospital, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
| | - Sang Chul Lee
- Catholic Central Laboratory of Surgery, Institute of Biomedical Industry, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
- Department of Surgery, Daejeon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 34943, South Korea
| | - Say-June Kim
- Catholic Central Laboratory of Surgery, Institute of Biomedical Industry, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
- Department of Surgery, Division of Hepato-biliary Pancreatic Surgery, Seoul St. Mary’s Hospital, College of Medicine, the Catholic University of Korea, Seoul 06591, South Korea
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28
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Nagakubo T, Nomura N, Toyofuku M. Cracking Open Bacterial Membrane Vesicles. Front Microbiol 2020; 10:3026. [PMID: 32038523 PMCID: PMC6988826 DOI: 10.3389/fmicb.2019.03026] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/17/2019] [Indexed: 12/24/2022] Open
Abstract
Membrane vesicles (MVs) are nanoparticles composed of lipid membranes that are produced by both Gram-negative and Gram-positive bacteria. MVs have been assigned diverse biological functions, and they show great potential for applications in various fields. However, the mechanisms underlying their functions and biogenesis are not completely understood. Accumulating evidence shows that MVs are heterogenous, and different types of MVs with different compositions are released from the same species. To understand the origin and function of these MVs, determining the biochemical properties of MVs is important. In this review, we will discuss recent progress in understanding the biochemical composition and properties of MVs.
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Affiliation(s)
- Toshiki Nagakubo
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Nobuhiko Nomura
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Masanori Toyofuku
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
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29
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Hong HE, Kim OH, Kwak BJ, Choi HJ, Im KH, Ahn J, Kim SJ. Antioxidant action of hypoxic conditioned media from adipose-derived stem cells in the hepatic injury of expressing higher reactive oxygen species. Ann Surg Treat Res 2019; 97:159-167. [PMID: 31620389 PMCID: PMC6779955 DOI: 10.4174/astr.2019.97.4.159] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/19/2019] [Accepted: 07/10/2019] [Indexed: 12/30/2022] Open
Abstract
Purpose Almost all liver diseases are known to be accompanied by increased levels of reactive oxygen species (ROS), regardless of the cause of the liver disorder. However, little is known about the role of hypoxic conditioned media (HCM) in the view of pro-oxidative/antioxidative balance. Methods Normoxic conditioned media (NCM) and HCM were obtained after culturing adipose-derived stem cells in 20% O2 or 1% O2 for 24 hours, respectively. Their effects on the expression of various markers reflecting pro-oxidative/antioxidative balance were investigated in both in vitro (thioacetamide-treated AML12 cells) and in vivo (partially hepatectomized mice) models of liver injury, respectively. Results HCM treatment induced the higher expression of antioxidant enzymes, such as superoxide dismutase, glutathione peroxidase, and catalase than did NCM in the in vitro model of liver injury. We also found that HCM increased the expression of nuclear factor erythroid 2-related factor (NRF2). The in vivo models of liver injury consistently validated the phenomenon of upregulated expression of antioxidant enzymes by HCM. Conclusion We thus could conclude that HCM provides protection against ROS-related toxicity by increasing the expression of antioxidant enzymes, in part by releasing NRF2 in the injured liver.
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Affiliation(s)
- Ha-Eun Hong
- Catholic Central Laboratory of Surgery, Institute of Biomedical Industry, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ok-Hee Kim
- Catholic Central Laboratory of Surgery, Institute of Biomedical Industry, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Bong Jun Kwak
- Department of Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ho Joong Choi
- Department of Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kee-Hwan Im
- Catholic Central Laboratory of Surgery, Institute of Biomedical Industry, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Surgery, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joseph Ahn
- Department of Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Say-June Kim
- Catholic Central Laboratory of Surgery, Institute of Biomedical Industry, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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30
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Kim MH, Kim SY, Son JH, Kim SI, Lee H, Kim S, Shin M, Lee JC. Production of Membrane Vesicles by Enterococcus faecium Cultured With or Without Subinhibitory Concentrations of Antibiotics and Their Pathological Effects on Epithelial Cells. Front Cell Infect Microbiol 2019; 9:295. [PMID: 31475120 PMCID: PMC6702262 DOI: 10.3389/fcimb.2019.00295] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/30/2019] [Indexed: 12/25/2022] Open
Abstract
Enterococcus faecium is a clinically important pathogen associated with opportunistic infection and multi-drug resistance. E. faecium has been shown to produce membrane vesicles (MVs), but MV production by E. faecium under antibiotic stress conditions and the pathogenic traits thereof have yet to be determined. This study investigated the production of MVs in E. faecium ATCC 700221 cultured with sub-minimum inhibitory concentrations (MICs) of vancomycin or linezolid and determined their pathologic effects on colon epithelial Caco-2 cells. E. faecium ATCC 700221 cultured with 1/2 MIC of vancomycin or linezolid produced 3.0 and 1.5 times more MV proteins than bacteria cultured without antibiotics, respectively. Totals of 438, 461, and 513 proteins were identified in MVs from E. faecium cultured in brain heart infusion broth (MVs/BHI), BHI broth with 1/2 MIC of vancomycin (MVs/VAN), or BHI broth with 1/2 MIC of linezolid (MVs/LIN), respectively. Intact MVs/BHI induced cytotoxicity and the expression of pro-inflammatory cytokine and chemokine genes in Caco-2 cells in a dose-dependent manner, but proteinase K-treated MVs significantly suppressed these pro-inflammatory responses. MVs/LIN were more cytotoxic toward Caco-2 cells than MVs/BHI and MVs/VAN, whereas MVs/VAN stimulated more pro-inflammatory cytokine gene expression in Caco-2 cells than MVs/BHI and MVs/LIN. Overall results indicated that antibiotics modulate the biogenesis and proteomes of MVs in E. faecium at subinhibitory concentrations. MVs produced by E. faecium cultured under antibiotic stress conditions induce strong host cell responses that may contribute to the pathogenesis E. faecium.
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Affiliation(s)
- Mi Hyun Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Se Yeon Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Joo Hee Son
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Seung Il Kim
- Drug and Disease Target Team, Korea Basic Science Institute, Ochang, South Korea.,Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, South Korea
| | - Hayoung Lee
- Drug and Disease Target Team, Korea Basic Science Institute, Ochang, South Korea.,Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, South Korea
| | - Shukho Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Minsang Shin
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Je Chul Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, South Korea
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31
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Feitosa-Junior OR, Stefanello E, Zaini PA, Nascimento R, Pierry PM, Dandekar AM, Lindow SE, da Silva AM. Proteomic and Metabolomic Analyses of Xylella fastidiosa OMV-Enriched Fractions Reveal Association with Virulence Factors and Signaling Molecules of the DSF Family. PHYTOPATHOLOGY 2019; 109:1344-1353. [PMID: 30973310 DOI: 10.1094/phyto-03-19-0083-r] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Xylella fastidiosa releases outer membrane vesicles (OMVs) known to play a role in the systemic dissemination of this pathogen. OMVs inhibit bacterial attachment to xylem wall and traffic lipases/esterases that act on the degradation of plant cell wall. Here, we extended the characterization of X. fastidiosa OMVs by identifying proteins and metabolites potentially associated with OMVs produced by Temecula1, a Pierce's disease strain, and by 9a5c and Fb7, two citrus variegated chlorosis strains. These results strengthen that one of the OMVs multiple functions is to carry determinants of virulence, such as lipases/esterases, adhesins, proteases, porins, and a pectin lyase-like protein. For the first time, we show that the two citrus variegated chlorosis strains produce X. fastidiosa diffusible signaling factor 2 (DSF2) and citrus variegated chlorosis-DSF (likewise, Temecula1) and most importantly, that these compounds of the DSF (X. fastidiosa DSF) family are associated with OMV-enriched fractions. Altogether, our findings widen the potential functions of X. fastidiosa OMVs in intercellular signaling and host-pathogen interactions.
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Affiliation(s)
- Oséias R Feitosa-Junior
- 1Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | - Eliezer Stefanello
- 1Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | - Paulo A Zaini
- 1Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
- 2Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - Rafael Nascimento
- 1Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
- 3Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Uberlândia, MG 38400-902, Brazil
| | - Paulo M Pierry
- 1Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | - Abhaya M Dandekar
- 2Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - Steven E Lindow
- 4Department Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A
| | - Aline M da Silva
- 1Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
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32
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Novosphingobium sp. PP1Y as a novel source of outer membrane vesicles. J Microbiol 2019; 57:498-508. [PMID: 31054137 DOI: 10.1007/s12275-019-8483-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/12/2018] [Accepted: 12/24/2018] [Indexed: 02/06/2023]
Abstract
Outer membrane vesicles (OMVs) are nanostructures of 20-200 nm diameter deriving from the surface of several Gram-negative bacteria. OMVs are emerging as shuttles involved in several mechanisms of communication and environmental adaptation. In this work, OMVs were isolated and characterized from Novosphingobium sp. PP1Y, a Gram-negative non-pathogenic microorganism lacking LPS on the outer membrane surface and whose genome was sequenced and annotated. Scanning electron microscopy performed on samples obtained from a culture in minimal medium highlighted the presence of PP1Y cells embedded in an extracellular matrix rich in vesicular structures. OMVs were collected from the exhausted growth medium during the mid-exponential phase, and purified by ultracentrifugation on a sucrose gradient. Atomic force microscopy, dynamic light scattering and nanoparticle tracking analysis showed that purified PP1Y OMVs had a spherical morphology with a diameter of ca. 150 nm and were homogenous in size and shape. Moreover, proteomic and fatty acid analysis of purified OMVs revealed a specific biochemical "fingerprint", suggesting interesting details concerning their biogenesis and physiological role. Moreover, these extracellular nanostructures do not appear to be cytotoxic on HaCaT cell line, thus paving the way to their future use as novel drug delivery systems.
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33
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Shin MS, Kim YG, Shin YJ, Ko BJ, Kim S, Kim HD. Deep sequencing salivary proteins for periodontitis using proteomics. Clin Oral Investig 2018; 23:3571-3580. [PMID: 30554327 DOI: 10.1007/s00784-018-2779-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Saliva is a bodily fluid transuded from gingival crevice fluid and blood and contains many proteins. Proteins in saliva have been studied as markers for periodontal diseases. Mass spectrometric analysis is applied to investigate biomarker proteins that are related to periodontitis. MATERIAL AND METHODS Saliva samples were collected from 207 participants including 36 pairs matched for age, sex, and smoking who joined Yangpyeong health cohort. Periodontitis was defined by 2005 5th European guideline. Shotgun proteomics was applied to detect proteins from saliva samples. Principal component analysis and Ingenuity Pathway Analysis for canonical pathway and protein pathway were applied. Protein-protein interaction was also applied. Enzyme-linked immunosorbent assay (ELISA) was used to verify the candidate protein markers among another matched participants (n = 80). RESULTS Shotgun proteomics indicated that salivary S100A8 and S100A9 were candidate biomarkers for periodontitis. ELISA confirmed that both salivary S100A8 and S100A9 were higher in those with periodontitis compared to those without periodontitis (paired-t test, p < 0.05). CONCLUSION Our proteomics data showed that S100A8 and S100A9 in saliva could be candidate biomarkers for periodontitis. The rapid-test-kit using salivary S100A8 and S100A9 will be a practical tool for reducing the risk of periodontitis and promotion of periodontal health. CLINICAL RELEVANCE A rapid-test-kit using salivary biomarkers, S100A8 and S100A9, could be utilized by clinicians and individuals for screening periodontitis, which might reduce the morbidity of periodontitis and promote periodontal health.
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Affiliation(s)
- Myung-Seop Shin
- Department of Preventive and Social Dentistry, School of Dentistry, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Yoo Jin Shin
- Department of Preventive and Social Dentistry, School of Dentistry, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Byoung Joon Ko
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, South Korea
| | - Sungtae Kim
- Department of Periodontology, Seoul National University Dental Hospital, Seoul, South Korea.,Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Hyun-Duck Kim
- Department of Preventive and Social Dentistry, School of Dentistry, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea. .,Dental Research Institute, Seoul National University, Seoul, South Korea.
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34
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Comparative exoproteome profiling of an invasive and a commensal Staphylococcus haemolyticus isolate. J Proteomics 2018; 197:106-114. [PMID: 30472255 DOI: 10.1016/j.jprot.2018.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/01/2018] [Accepted: 11/17/2018] [Indexed: 01/06/2023]
Abstract
Staphylococcus haemolyticus is a skin commensal emerging as an opportunistic pathogen. Nosocomial isolates of S. haemolyticus are the most antibiotic resistant members of the coagulase negative staphylococci (CoNS), but information about other S. haemolyticus virulence factors is scarce. Bacterial membrane vesicles (MVs) are one mediator of virulence by enabling secretion and long distance delivery of bacterial effector molecules while protecting the cargo from proteolytic degradation from the environment. We wanted to determine if the MV protein cargo of S. haemolyticus is strain specific and enriched in certain MV associated proteins compared to the totalsecretome. The present study shows that both clinical and commensal S. haemolyticus isolates produce membrane vesicles. The MV cargo of both strains was enriched in proteins involved in adhesion and acquisition of iron. The MV cargo of the clinical strain was further enriched in antimicrobial resistance proteins. Data are available via ProteomeXchange with identifier PXD010389. BIOLOGICAL SIGNIFICANCE: Clinical isolates of Staphylococcus haemolyticus are usually multidrug resistant, their main virulence factor is formation of biofilms, both factors leading to infections that are difficult to treat. We show that both clinical and commensal S. haemolyticus isolates produce membrane vesicles. Identification of staphylococcal membrane vesicles can potentially be used in novel approaches to combat staphylococcal infections, such as development of vaccines.
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Taboada H, Meneses N, Dunn MF, Vargas-Lagunas C, Buchs N, Castro-Mondragón JA, Heller M, Encarnación S. Proteins in the periplasmic space and outer membrane vesicles of Rhizobium etli CE3 grown in minimal medium are largely distinct and change with growth phase. MICROBIOLOGY-SGM 2018; 165:638-650. [PMID: 30358529 DOI: 10.1099/mic.0.000720] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Rhizobium etli CE3 grown in succinate-ammonium minimal medium (MM) excreted outer membrane vesicles (OMVs) with diameters of 40 to 100 nm. Proteins from the OMVs and the periplasmic space were isolated from 6 and 24 h cultures and identified by proteome analysis. A total of 770 proteins were identified: 73.8 and 21.3 % of these occurred only in the periplasm and OMVs, respectively, and only 4.9 % were found in both locations. The majority of proteins found in either location were present only at 6 or 24 h: in the periplasm and OMVs, only 24 and 9 % of proteins, respectively, were present at both sampling times, indicating a time-dependent differential sorting of proteins into the two compartments. The OMVs contained proteins with physiologically varied roles, including Rhizobium adhering proteins (Rap), polysaccharidases, polysaccharide export proteins, auto-aggregation and adherence proteins, glycosyl transferases, peptidoglycan binding and cross-linking enzymes, potential cell wall-modifying enzymes, porins, multidrug efflux RND family proteins, ABC transporter proteins and heat shock proteins. As expected, proteins with known periplasmic localizations (phosphatases, phosphodiesterases, pyrophosphatases) were found only in the periplasm, along with numerous proteins involved in amino acid and carbohydrate metabolism and transport. Nearly one-quarter of the proteins present in the OMVs were also found in our previous analysis of the R. etli total exproteome of MM-grown cells, indicating that these nanoparticles are an important mechanism for protein excretion in this species.
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Affiliation(s)
- Hermenegildo Taboada
- 1Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C. P. 62210, México
| | - Niurka Meneses
- 1Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C. P. 62210, México.,3Faculty of Science, Department of Chemistry and Biochemistry, University of Bern, 3010 Bern, Switzerland.,2Mass Spectrometry and Proteomics Laboratory, Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Michael F Dunn
- 1Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C. P. 62210, México
| | - Carmen Vargas-Lagunas
- 1Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C. P. 62210, México
| | - Natasha Buchs
- 2Mass Spectrometry and Proteomics Laboratory, Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Jaime A Castro-Mondragón
- 4Aix Marseille University, INSERM, TAGC, Theory and Approaches of Genomic Complexity, UMR_S 1090, Marseille, France
| | - Manfred Heller
- 2Mass Spectrometry and Proteomics Laboratory, Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Sergio Encarnación
- 1Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos C. P. 62210, México
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Enterococcus faecium produces membrane vesicles containing virulence factors and antimicrobial resistance related proteins. J Proteomics 2018; 187:28-38. [DOI: 10.1016/j.jprot.2018.05.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/25/2018] [Accepted: 05/29/2018] [Indexed: 11/19/2022]
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Antibiotic treatment modulates protein components of cytotoxic outer membrane vesicles of multidrug-resistant clinical strain, Acinetobacter baumannii DU202. Clin Proteomics 2018; 15:28. [PMID: 30186054 PMCID: PMC6118003 DOI: 10.1186/s12014-018-9204-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/16/2018] [Indexed: 12/31/2022] Open
Abstract
Background Outer membrane vesicles (OMVs) of Acinetobacter baumannii are cytotoxic and elicit a potent innate immune response. OMVs were first identified in A. baumannii DU202, an extensively drug-resistant clinical strain. Herein, we investigated protein components of A. baumannii DU202 OMVs following antibiotic treatment by proteogenomic analysis. Methods Purified OMVs from A. baumannii DU202 grown in different antibiotic culture conditions were screened for pathogenic and immunogenic effects, and subjected to quantitative proteomic analysis by one-dimensional electrophoresis and liquid chromatography combined with tandem mass spectrometry (1DE-LC-MS/MS). Protein components modulated by imipenem were identified and discussed. Results OMV secretion was increased > twofold following imipenem treatment, and cytotoxicity toward A549 human lung carcinoma cells was elevated. A total of 277 proteins were identified as components of OMVs by imipenem treatment, among which β-lactamase OXA-23, various proteases, outer membrane proteins, β-barrel assembly machine proteins, peptidyl-prolyl cis–trans isomerases and inherent prophage head subunit proteins were significantly upregulated. Conclusion In vitro stress such as antibiotic treatment can modulate proteome components in A. baumannii OMVs and thereby influence pathogenicity. Electronic supplementary material The online version of this article (10.1186/s12014-018-9204-2) contains supplementary material, which is available to authorized users.
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Löwe H, Sinner P, Kremling A, Pflüger-Grau K. Engineering sucrose metabolism in Pseudomonas putida highlights the importance of porins. Microb Biotechnol 2018; 13:97-106. [PMID: 29808622 PMCID: PMC6922520 DOI: 10.1111/1751-7915.13283] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 12/19/2022] Open
Abstract
Using agricultural wastes as a substrate for biotechnological processes is of great interest in industrial biotechnology. A prerequisite for using these wastes is the ability of the industrially relevant microorganisms to metabolize the sugars present therein. Therefore, many metabolic engineering approaches are directed towards widening the substrate spectrum of the workhorses of industrial biotechnology like Escherichia coli, yeast or Pseudomonas putida. For instance, neither xylose or arabinose from cellulosic residues, nor sucrose, the main sugar in waste molasses, can be metabolized by most E. coli and P. putida wild types. We evaluated a new, so far uncharacterized gene cluster for sucrose metabolism from Pseudomonas protegens Pf‐5 and showed that it enables P. putida to grow on sucrose as the sole carbon and energy source. Even when integrated into the genome of P. putida, the resulting strain grew on sucrose at rates similar to the rate of the wild type on glucose – making it the fastest growing, plasmid‐free P. putida strain known so far using sucrose as substrate. Next, we elucidated the role of the porin, an orthologue of the sucrose porin ScrY, in the gene cluster and found that in P. putida, a porin is needed for sucrose transport across the outer membrane. Consequently, native porins were not sufficient to allow unlimited growth on sucrose. Therefore, we concluded that the outer membrane can be a considerable barrier for substrate transport, depending on strain, genotype and culture conditions, all of which should be taken into account in metabolic engineering approaches. We additionally showed the potential of the engineered P. putida strains by growing them on molasses with efficiencies twice as high as obtained with the wild‐type P. putida. This can be seen as a further step towards the production of low‐value chemicals and biofuels with P. putida from alternative and more affordable substrates in the future.
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Affiliation(s)
- Hannes Löwe
- Systems Biotechnology, Technical University of Munich, 85748, Garching, Germany
| | - Peter Sinner
- Systems Biotechnology, Technical University of Munich, 85748, Garching, Germany
| | - Andreas Kremling
- Systems Biotechnology, Technical University of Munich, 85748, Garching, Germany
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Ma Y, Kim SS, Kwag DG, Kim SH, Kim MS, Ryu SH, Lee DH, So JH, Nam BH, Kim YO, An CM, Park JS. High-Level Expression and Purification of Tag-free Peptides Containing Multiple Disulfide Bond in Pichia pastoris. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yunqi Ma
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - So-Sun Kim
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Dong-Geon Kwag
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Seo-Hyun Kim
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Min-Seob Kim
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Seung-Ho Ryu
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Dong-Hoon Lee
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Jae-Hyeong So
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, Aquaculture Industry Department; National Fisheries Research and Development Institute; Busan 619-902 Republic of Korea
| | - Yong-Ok Kim
- Biotechnology Research Division, Aquaculture Industry Department; National Fisheries Research and Development Institute; Busan 619-902 Republic of Korea
| | - Cheul-Min An
- Biotechnology Research Division, Aquaculture Industry Department; National Fisheries Research and Development Institute; Busan 619-902 Republic of Korea
| | - Jang-Su Park
- Department of Chemistry and Chemistry Institute of Functional Materials; Pusan National University; Busan 609-735 Republic of Korea
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Choudhary A, Purohit H, Phale PS. Benzoate transport in Pseudomonas putida CSV86. FEMS Microbiol Lett 2018; 364:3861963. [PMID: 28591829 DOI: 10.1093/femsle/fnx118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 06/06/2017] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas putida strain CSV86 metabolizes variety of aromatic compounds as the sole carbon source. Genome analysis revealed the presence of genes encoding putative transporters for benzoate, p-hydroxybenzoate, phenylacetate, p-hydroxyphenylacetate and vanillate. Bioinformatic analysis revealed that benzoate transport and metabolism genes are clustered at the ben locus as benK-catA-benE-benF. Protein topology prediction suggests that BenK (aromatic acid-H+ symporter of major facilitator superfamily) has 12 transmembrane α-helices with the conserved motif LADRXGRKX in loop 2, while BenE (benzoate-H+ symporter protein) has 11 predicted transmembrane α-helices. benF and catA encode benzoate specific porin, OprD and catechol 1,2-dioxygenase, respectively. Biochemical studies suggest that benzoate was transported by an inducible and active process. Inhibition (90%-100%) in the presence of dinitrophenol suggests that the energy for the transport process is derived from the proton motive force. The maximum rate of benzoate transport was 484 pmole min-1 mg-1 cells with an affinity constant, Kmof 4.5 μM. Transcriptional analysis of the benzoate and glucose-grown cells showed inducible expression of benF, benK and benE, suggesting that besides outer membrane porin, both inner membrane transporters probably contribute for the benzoate transport in P. putida strain CSV86.
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Affiliation(s)
- Alpa Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400076, India
| | - Hemant Purohit
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur 440020; India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400076, India
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Elmi A, Dorey A, Watson E, Jagatia H, Inglis NF, Gundogdu O, Bajaj-Elliott M, Wren BW, Smith DGE, Dorrell N. The bile salt sodium taurocholate induces Campylobacter jejuni outer membrane vesicle production and increases OMV-associated proteolytic activity. Cell Microbiol 2017; 20. [PMID: 29205766 DOI: 10.1111/cmi.12814] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 02/06/2023]
Abstract
Campylobacter jejuni, the leading cause of bacterial acute gastroenteritis worldwide, secretes an arsenal of virulence-associated proteins within outer membrane vesicles (OMVs). C. jejuni OMVs contain three serine proteases (HtrA, Cj0511, and Cj1365c) that cleave the intestinal epithelial cell (IEC) tight and adherens junction proteins occludin and E-cadherin, promoting enhanced C. jejuni adhesion to and invasion of IECs. C. jejuni OMVs also induce IECs innate immune responses. The bile salt sodium taurocholate (ST) is sensed as a host signal to coordinate the activation of virulence-associated genes in the enteric pathogen Vibrio cholerae. In this study, the effect of ST on C. jejuni OMVs was investigated. Physiological concentrations of ST do not have an inhibitory effect on C. jejuni growth until the early stationary phase. Coculture of C. jejuni with 0.1% or 0.2% (w/v) ST stimulates OMV production, increasing both lipid and protein concentrations. C. jejuni ST-OMVs possess increased proteolytic activity and exhibit a different protein profile compared to OMVs isolated in the absence of ST. ST-OMVs exhibit enhanced cytotoxicity and immunogenicity to T84 IECs and enhanced killing of Galleria mellonella larvae. ST increases the level of mRNA transcripts of the OMVs-associated serine protease genes and the cdtABC operon that encodes the cytolethal distending toxin. Coculture with ST significantly enhances the OMVs-induced cleavage of E-cadherin and occludin. C. jejuni OMVs also cleave the major endoplasmic reticulum chaperone protein BiP/GRP78 and this activity is associated with the Cj1365c protease. These data suggest that C. jejuni responds to the presence of physiological concentrations of the bile salt ST that increases OMV production and the synthesis of virulence-associated factors that are secreted within the OMVs. We propose that these events contribute to pathogenesis.
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Affiliation(s)
- Abdi Elmi
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Amber Dorey
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Heena Jagatia
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Ozan Gundogdu
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Mona Bajaj-Elliott
- Infection, Immunity, Inflammation and Physiological Medicine, UCL Institute of Child Health, London, UK
| | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - David G E Smith
- School of Engineering & Physical Sciences, Heriot-Watt University, Edinburgh, UK
| | - Nick Dorrell
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation - A chance for metabolic engineering. Metab Eng 2017; 45:109-120. [PMID: 29229581 DOI: 10.1016/j.ymben.2017.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 09/15/2017] [Accepted: 12/06/2017] [Indexed: 01/05/2023]
Abstract
More and more microbes are discovered that are capable of extracellular electron transfer, a process in which they use external electrodes as electron donors or acceptors for metabolic reactions. This feature can be used to overcome cellular redox limitations and thus optimizing microbial production. The technologies, termed microbial electrosynthesis and electro-fermentation, have the potential to open novel bio-electro production platforms from sustainable energy and carbon sources. However, the performance of reported systems is currently limited by low electron transport rates between microbes and electrodes and our limited ability for targeted engineering of these systems due to remaining knowledge gaps about the underlying fundamental processes. Metabolic engineering offers many opportunities to optimize these processes, for instance by genetic engineering of pathways for electron transfer on the one hand and target product synthesis on the other hand. With this review, we summarize the status quo of knowledge and engineering attempts around chemical production in bio-electrochemical systems from a microbe perspective. Challenges associated with the introduction or enhancement of extracellular electron transfer capabilities into production hosts versus the engineering of target compound synthesis pathways in natural exoelectrogens are discussed. Recent advances of the research community in both directions are examined critically. Further, systems biology approaches, for instance using metabolic modelling, are examined for their potential to provide insight into fundamental processes and to identify targets for metabolic engineering.
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Sakuda A, Suzuki-Minakuchi C, Matsui K, Takahashi Y, Okada K, Yamane H, Shintani M, Nojiri H. Divalent cations increase the conjugation efficiency of the incompatibility P-7 group plasmid pCAR1 among different Pseudomonas hosts. MICROBIOLOGY-SGM 2017; 164:20-27. [PMID: 29185954 DOI: 10.1099/mic.0.000583] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The incompatibility (Inc) P-7 group plasmid pCAR1 can be efficiently transferred among bacteria in artificial microcosms in the presence of divalent cations Ca2+ and Mg2+. One-on-one mating assays between Pseudomonas strains with different plasmids showed that the promotion of conjugation efficiency by divalent cations was exhibited in other plasmids, including pB10 and NAH7; however, this effect was larger in IncP-7 plasmids. The impact on pCAR1 conjugation differed according to donor-recipient pairs, and conjugation efficiency promotion was clearly detected between the donors P. resinovorans CA10dm4 and P. fluorescens Pf0-1 and the recipients P. putida KT2440 and CA10dm4. Transcriptome analyses showed that pCAR1 gene expression did not respond to cation changes, including the tra/trh genes involved in its transfer. However, the transcription of oprH genes, encoding putative outer-membrane proteins in both the donor and the recipient, were commonly upregulated under cation-limited conditions. The conjugation frequency of pCAR1 in the KT2440 oprH mutant was found not to respond to cations. This effect was partially recovered by complementation with the oprH gene, suggesting that OprH is involved in the increase of pCAR1 conjugation efficiency by divalent cations.
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Affiliation(s)
- Ayako Sakuda
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
| | | | - Kazuhiro Matsui
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
| | - Yurika Takahashi
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan.,Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hisakazu Yamane
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan.,Present address: Department of Biosciences, Teikyo University, Tochigi 320-8551, Japan
| | - Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 432-8561, Japan.,Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka 432-8561, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
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Oliver C, Hernández MA, Tandberg JI, Valenzuela KN, Lagos LX, Haro RE, Sánchez P, Ruiz PA, Sanhueza-Oyarzún C, Cortés MA, Villar MT, Artigues A, Winther-Larsen HC, Avendaño-Herrera R, Yáñez AJ. The Proteome of Biologically Active Membrane Vesicles from Piscirickettsia salmonis LF-89 Type Strain Identifies Plasmid-Encoded Putative Toxins. Front Cell Infect Microbiol 2017; 7:420. [PMID: 29034215 PMCID: PMC5625009 DOI: 10.3389/fcimb.2017.00420] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/12/2017] [Indexed: 01/16/2023] Open
Abstract
Piscirickettsia salmonis is the predominant bacterial pathogen affecting the Chilean salmonid industry. This bacterium is the etiological agent of piscirickettsiosis, a significant fish disease. Membrane vesicles (MVs) released by P. salmonis deliver several virulence factors to host cells. To improve on existing knowledge for the pathogenicity-associated functions of P. salmonis MVs, we studied the proteome of purified MVs from the P. salmonis LF-89 type strain using multidimensional protein identification technology. Initially, the cytotoxicity of different MV concentration purified from P. salmonis LF-89 was confirmed in an in vivo adult zebrafish infection model. The cumulative mortality of zebrafish injected with MVs showed a dose-dependent pattern. Analyses identified 452 proteins of different subcellular origins; most of them were associated with the cytoplasmic compartment and were mainly related to key functions for pathogen survival. Interestingly, previously unidentified putative virulence-related proteins were identified in P. salmonis MVs, such as outer membrane porin F and hemolysin. Additionally, five amino acid sequences corresponding to the Bordetella pertussis toxin subunit 1 and two amino acid sequences corresponding to the heat-labile enterotoxin alpha chain of Escherichia coli were located in the P. salmonis MV proteome. Curiously, these putative toxins were located in a plasmid region of P. salmonis LF-89. Based on the identified proteins, we propose that the protein composition of P. salmonis LF-89 MVs could reflect total protein characteristics of this P. salmonis type strain.
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Affiliation(s)
- Cristian Oliver
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Universidad Andrés Bello, Viña del Mar, Chile.,Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Mauricio A Hernández
- Austral-OMICS, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Julia I Tandberg
- Center of Integrative Microbiology and Evolution, University of Oslo, Oslo, Norway.,Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Karla N Valenzuela
- Microbiology and Immunology Department, Dalhousie University, Halifax, NS, Canada
| | - Leidy X Lagos
- Center of Integrative Microbiology and Evolution, University of Oslo, Oslo, Norway.,Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Ronie E Haro
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
| | - Patricio Sánchez
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Pamela A Ruiz
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Constanza Sanhueza-Oyarzún
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Marcos A Cortés
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - María T Villar
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Antonio Artigues
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Hanne C Winther-Larsen
- Center of Integrative Microbiology and Evolution, University of Oslo, Oslo, Norway.,Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Universidad Andrés Bello, Viña del Mar, Chile.,Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Alejandro J Yáñez
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Interdisciplinary Center for Aquaculture Research, Concepción, Chile.,Austral-OMICS, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Abstract
Bacterial membrane vesicles (BMVs) are closed spherical nanostructures that are shed naturally and ubiquitously by most bacterial species both in vivo and in vitro. Researchers have elucidated their roles in long-distance transport of a wide array of cargoes, such as proteins, toxins, antigens, virulence factors, microbicidal agents and antibiotics. Given that these natural carriers are important players in intercellular communication, it has been hypothesized that they are equally well attuned for transport and delivery of exogenous therapeutic cargoes. Additionally, BMVs appear to possess specific properties that enable their utilization as drug delivery vehicles. These include their ability to evade the host immune system, protection of the therapeutic payload and natural stability. Using bioengineering approaches, BMVs have been applied as carriers of therapeutic moieties in vaccines and for targeted delivery in cancer. In this article, we explore BMVs from the perspective of understanding their applicability to drug delivery. BMV biology, including biogenesis, physiology and pathology, is briefly reviewed. Practical issues related to bioprocessing, loading of therapeutic moieties and characterization for enabling scalability and commercial viability are evaluated. Finally, challenges to clinical translation and rational design approaches for novel BMV formulations are presented. Although the realization of the full potential of BMVs in drug delivery hinges on the development of scalable approaches for their production as well as the refinement of targeting and loading methods, they are promising candidates for development of a novel generation of drug delivery vehicles in future.
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Affiliation(s)
- Sapna Jain
- Implants, Devices and Drug Delivery Systems Laboratory, Centre for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Jonathan Pillai
- Implants, Devices and Drug Delivery Systems Laboratory, Centre for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, Haryana, India
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Orench-Rivera N, Kuehn MJ. Environmentally controlled bacterial vesicle-mediated export. Cell Microbiol 2017; 18:1525-1536. [PMID: 27673272 DOI: 10.1111/cmi.12676] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/15/2016] [Accepted: 09/21/2016] [Indexed: 01/01/2023]
Abstract
Over the past two decades, researchers studying both microbial and host cell communities have gained an appreciation for the ability of bacteria to produce, regulate, and functionally utilize outer membrane vesicles (OMVs) as a means to survive and interact with their cellular and acellular environments. Common ground has emerged, as it appears that vesicle production is an environmentally controlled and specific secretion process; however, it has been challenging to discover the principles that govern fundamentals of vesicle-mediated transport. Namely, there does not appear to be a single mechanism modulating OMV export, nor universal "markers" for OMV cargo incorporation, nor particular host cell responses common to treatment with all OMVs. Given the diversity of species studied, their differences in envelope architecture and composition, the diversity of environmentally regulated bacterial processes, and the variety of interactions between bacteria and their abiotic and biotic environments, this is hardly surprising. Nevertheless, the ability of bacteria to control exported material in the context of a packaged insoluble particle, a vesicle, is emerging as a significant contribution to bacterial viability, biofilm communities, and bacterial-host interactions. In this review, we focus on detailing important, recent findings regarding the content and functional differences in bacterially secreted vesicles that are influenced by growth conditions.
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Affiliation(s)
- Nichole Orench-Rivera
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Meta J Kuehn
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA.
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Potential Usefulness of Streptococcus pneumoniae Extracellular Membrane Vesicles as Antibacterial Vaccines. J Immunol Res 2017; 2017:7931982. [PMID: 28210633 PMCID: PMC5292160 DOI: 10.1155/2017/7931982] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/24/2016] [Accepted: 12/21/2016] [Indexed: 11/17/2022] Open
Abstract
The secretion of extracellular membrane vesicles (EMVs) is a common phenomenon that occurs in archaea, bacteria, and mammalian cells. The EMVs of bacteria play important roles in their virulence, biogenesis mechanisms, and host cell interactions. Bacterial EMVs have recently become the focus of attention because of their potential as highly effective vaccines that cause few side effects. Here, we isolated the EMVs of Streptococcus pneumoniae and examined their potential as new vaccine candidates. Although the S. pneumoniae bacteria were highly pathogenic in a mouse model, the EMVs purified from these bacteria showed low pathological activity both in cell culture and in mice. When mice were injected intraperitoneally with S. pneumoniae EMVs and then challenged, they were protected from both the homologous strain and another pathogenic serotype of S. pneumoniae. We also identified a number of proteins that may have immunogenic activity and may be responsible for the immune responses by the hosts. These results suggest that S. pneumoniae EMVs or their individual immunogenic antigens may be useful as new vaccine agents.
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Lahiri P, Ghosh D. Single-Step Capture and Targeted Metabolomics of Alkyl-Quinolones in Outer Membrane Vesicles of Pseudomonas aeruginosa. Methods Mol Biol 2017; 1609:171-184. [PMID: 28660582 DOI: 10.1007/978-1-4939-6996-8_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Outer membrane vesicles (OMVs) are secreted by all Gram-ve pathogens. These nano-scale delivery vehicles contain discrete arrays of prokaryotic pathogenic determinants, including a family of low molecular weight (MW) lipidic quorum signaling alkyl-quinolones (AQs). These are synthesized from β-keto-fatty acids and function like primordial lipidic hormones, which regulate numerous pathogenic factors both inter-species and intra-species. Significantly, AQs can also directly exacerbate pathogenesis by cross-kingdom signaling with the host immune, metabolic, and other systems. In Pseudomonas aeruginosa more than 50 AQs are reported; many with pathogenic mechanisms that are largely unknown. Some of these AQs are exclusively associated with OMVs. Accurate characterization of these OMV-AQs may reveal novel mechanism of diseases and Pseudomonas aeruginosa presents an ideal model. Matrix-free laser desorption/ionization mass spectrometry (LDI-MS) technologies enjoy unique advantages in mass spectrometry (MS)-based imaging and low MW analysis. We report single-step isolation of Pseudomonas aeruginosa OMV on inert ceramic filters and high-resolution mass spectrometry (HRMS) analysis of AQs vesicle in situ.
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Affiliation(s)
- Pallavi Lahiri
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Dipankar Ghosh
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
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Yun SH, Lee SY, Choi CW, Lee H, Ro HJ, Jun S, Kwon YM, Kwon KK, Kim SJ, Kim GH, Kim SI. Proteomic characterization of the outer membrane vesicle of the halophilic marine bacterium Novosphingobium pentaromativorans US6-1. J Microbiol 2016; 55:56-62. [PMID: 28035602 DOI: 10.1007/s12275-017-6581-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/06/2016] [Accepted: 12/08/2016] [Indexed: 12/12/2022]
Abstract
Novosphingobium pentaromativorans US6-1 is a Gram-negative halophilic marine bacterium able to utilize several polycyclic aromatic hydrocarbons such as phenanthrene, pyrene, and benzo[a]pyrene. In this study, using transmission electron microscopy, we confirmed that N. pentaromativorans US6-1 produces outer membrane vesicles (OMVs). N. pentaromativorans OMVs (hereafter OMVNovo) are spherical in shape, and the average diameter of OMVNovo is 25-70 nm. Proteomic analysis revealed that outer membrane proteins and periplasmic proteins of N. pentaromativorans are the major protein components of OMVNovo. Comparative proteomic analysis with the membrane-associated protein fraction and correlation analysis demonstrated that the outer membrane proteins of OMVNovo originated from the membrane- associated protein fraction. To the best of our knowledge, this study is the first to characterize OMV purified from halophilic marine bacteria.
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Affiliation(s)
- Sung Ho Yun
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea
| | - Sang-Yeop Lee
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea
| | - Chi-Won Choi
- Tunneling Nanotube Research Center, Division of Life Science, Korea University, Seoul, 02841, Republic of Korea
| | - Hayoung Lee
- Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Hyun-Joo Ro
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea
| | - Sangmi Jun
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea
| | - Yong Min Kwon
- National Marine Biodiversity Institute of Korea, Seocheon, 33662, Republic of Korea
| | - Kae Kyoung Kwon
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Sang-Jin Kim
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea.,National Marine Biodiversity Institute of Korea, Seocheon, 33662, Republic of Korea
| | - Gun-Hwa Kim
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea
| | - Seung Il Kim
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea. .,Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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50
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Santiago ADS, Mendes JS, Dos Santos CA, de Toledo MAS, Beloti LL, Crucello A, Horta MAC, Favaro MTDP, Munar DMM, de Souza AA, Cotta MA, de Souza AP. The Antitoxin Protein of a Toxin-Antitoxin System from Xylella fastidiosa Is Secreted via Outer Membrane Vesicles. Front Microbiol 2016; 7:2030. [PMID: 28066356 PMCID: PMC5167779 DOI: 10.3389/fmicb.2016.02030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 12/02/2016] [Indexed: 11/22/2022] Open
Abstract
The Xylella fastidiosa subsp pauca strain 9a5c is a Gram-negative, xylem-limited bacterium that is able to form a biofilm and affects citrus crops in Brazil. Some genes are considered to be involved in biofilm formation, but the specific mechanisms involved in this process remain unknown. This limited understanding of how some bacteria form biofilms is a major barrier to our comprehension of the progression of diseases caused by biofilm-producing bacteria. Several investigations have shown that the toxin-antitoxin (TA) operon is related to biofilm formation. This operon is composed of a toxin with RNAse activity and its cognate antitoxin. Previous reports have indicated that the antitoxin is able to inhibit toxin activity and modulate the expression of the operon as well as other target genes involved in oxidative stress and mobility. In this study, we characterize a toxin-antitoxin system consisting of XfMqsR and XfYgiT, respectively, from X. fastidiosa subsp. pauca strain 9a5c. These proteins display a high similarity to their homologs in X. fastidiosa strain Temecula and a predicted tridimensional structure that is similar to MqsR-YgiT from Escherichia coli. The characterization was performed using in vitro assays such as analytical ultracentrifugation (AUC), size exclusion chromatography, isothermal titration calorimetry, and Western blotting. Using a fluorometric assay to detect RNAses, we demonstrated that XfMqsR is thermostable and can degrade RNA. XfMqsR is inhibited by XfYgiT, which interacts with its own promoter. XfYgiT is known to be localized in the intracellular compartment; however, we provide strong evidence that X. fastidiosa secretes wild-type XfYgiT into the extracellular environment via outer membrane vesicles, as confirmed by Western blotting and specific immunofluorescence labeling visualized by fluorescence microscopy. Taken together, our results characterize the TA system from X. fastidiosa strain 9a5c, and we also discuss the possible influence of wild-type XfYgiT in the cell.
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Affiliation(s)
- André da Silva Santiago
- Centro de Biologia Molecular e Engenharia Genética, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Brazil
| | - Juliano S Mendes
- Centro de Biologia Molecular e Engenharia Genética, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Brazil
| | - Clelton A Dos Santos
- Centro de Biologia Molecular e Engenharia Genética, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Brazil
| | - Marcelo A S de Toledo
- Centro de Biologia Molecular e Engenharia Genética, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Brazil
| | - Lilian L Beloti
- Centro de Biologia Molecular e Engenharia Genética, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Brazil
| | - Aline Crucello
- Centro de Biologia Molecular e Engenharia Genética, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Brazil
| | - Maria A C Horta
- Centro de Biologia Molecular e Engenharia Genética, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Brazil
| | - Marianna T de Pinho Favaro
- Centro de Biologia Molecular e Engenharia Genética, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Brazil
| | - Duber M M Munar
- Departamento de Física Aplicada, Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas Campinas, Brazil
| | | | - Mônica A Cotta
- Departamento de Física Aplicada, Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas Campinas, Brazil
| | - Anete P de Souza
- Centro de Biologia Molecular e Engenharia Genética, Instituto de Biologia, Universidade Estadual de CampinasCampinas, Brazil; Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de CampinasCampinas, Brazil
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