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Nie X, Li Q, Chen X, Onyango S, Xie J, Nie S. Bacterial extracellular vesicles: Vital contributors to physiology from bacteria to host. Microbiol Res 2024; 284:127733. [PMID: 38678680 DOI: 10.1016/j.micres.2024.127733] [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: 03/19/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
Bacterial extracellular vesicles (bEVs) represent spherical particles with diameters ranging from 20 to 400 nm filled with multiple parental bacteria-derived components, including proteins, nucleic acids, lipids, and other biomolecules. The production of bEVs facilitates bacteria interacting with their environment and exerting biological functions. It is increasingly evident that the bEVs play integral roles in both bacterial and host physiology, contributing to environmental adaptations to functioning as health promoters for their hosts. This review highlights the current state of knowledge on the composition, biogenesis, and diversity of bEVs and the mechanisms by which different bEVs elicit effects on bacterial physiology and host health. We posit that an in-depth exploration of the mechanistic aspects of bEVs activity is essential to elucidate their health-promoting effects on the host and may facilitate the translation of bEVs into applications as novel natural biological nanomaterials.
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Affiliation(s)
- Xinke Nie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Qiqiong Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Xinyang Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | | | - Junhua Xie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
| | - Shaoping Nie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
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2
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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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3
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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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4
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Çelik P, Derkuş B, Erdoğan K, Barut D, Manga EB, Yıldırım Y, Pecha S, Çabuk A. Bacterial membrane vesicle functions, laboratory methods, and applications. Biotechnol Adv 2021; 54:107869. [PMID: 34793882 DOI: 10.1016/j.biotechadv.2021.107869] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/19/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022]
Abstract
Bacterial membrane vesicles are cupped-shaped structures formed by bacteria in response to environmental stress, genetic alteration, antibiotic exposure, and others. Due to the structural similarities shared with the producer organism, they can retain certain characteristics like stimulating immune responses. They are also able to carry molecules for long distances, without changes in the concentration and integrity of the molecule. Bacteria originally secrete membrane vesicles for gene transfer, excretion, cell to cell interaction, pathogenesis, and protection against phages. These functions are unique and have several innovative applications in the pharmaceutical industry that have attracted both scientific and commercial interest.This led to the development of efficient methods to artificially stimulate vesicle production, purification, and manipulation in the lab at nanoscales. Also, for specific applications, engineering methods to impart pathogen antigens against specific diseases or customization as cargo vehicles to deliver payloads to specific cells have been reported. Many applications of bacteria membrane vesicles are in cancer drugs, vaccines, and adjuvant development with several candidates in clinical trials showing promising results. Despite this, applications in therapy and commercialization stay timid probably due to some challenges one of which is the poor understanding of biogenesis mechanisms. Nevertheless, so far, bacterial membrane vesicles seem to be a reliable and cost-efficient technology with several therapeutic applications. Research toward characterizing more membrane vesicles, genetic engineering, and nanotechnology will enable the scope of applications to widen. This might include solutions to other currently faced medical and healthcare-related challenges.
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Affiliation(s)
- PınarAytar Çelik
- Environmental Protection and Control Program, Eskişehir Osmangazi University, Eskişehir 26110, Turkey; 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
| | - Kübra Erdoğan
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey
| | - Dilan Barut
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey
| | - Enuh Blaise Manga
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey
| | - Yalın Yıldırım
- Department of Cardiovascular Surgery, University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Simon Pecha
- Department of Cardiovascular Surgery, University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Ahmet Çabuk
- Department of Biology, Faculty of Science and Letter, Eskişehir Osmangazi University, Eskişehir 26040, Turkey
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5
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Biller SJ, Lundeen RA, Hmelo LR, Becker KW, Arellano AA, Dooley K, Heal KR, Carlson LT, Van Mooy BAS, Ingalls AE, Chisholm SW. Prochlorococcus extracellular vesicles: molecular composition and adsorption to diverse microbes. Environ Microbiol 2021; 24:420-435. [PMID: 34766712 PMCID: PMC9298688 DOI: 10.1111/1462-2920.15834] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/29/2021] [Indexed: 12/19/2022]
Abstract
Extracellular vesicles are small (~50–200 nm diameter) membrane‐bound structures released by cells from all domains of life. While vesicles are abundant in the oceans, their functions, both for cells themselves and the emergent ecosystem, remain a mystery. To better characterize these particles – a prerequisite for determining function – we analysed the lipid, protein, and metabolite content of vesicles produced by the marine cyanobacterium Prochlorococcus. We show that Prochlorococcus exports a diverse array of cellular compounds into the surrounding seawater enclosed within discrete vesicles. Vesicles produced by two different strains contain some materials in common, but also display numerous strain‐specific differences, reflecting functional complexity within vesicle populations. The vesicles contain active enzymes, indicating that they can mediate extracellular biogeochemical reactions in the ocean. We further demonstrate that vesicles from Prochlorococcus and other bacteria associate with diverse microbes including the most abundant marine bacterium, Pelagibacter. Together, our data point toward hypotheses concerning the functional roles of vesicles in marine ecosystems including, but not limited to, possibly mediating energy and nutrient transfers, catalysing extracellular biochemical reactions, and mitigating toxicity of reactive oxygen species.
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Affiliation(s)
- Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Rachel A Lundeen
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Laura R Hmelo
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Kevin W Becker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Aldo A Arellano
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Keven Dooley
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katherine R Heal
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Laura T Carlson
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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6
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Maphosa S, Moleleki LN. Isolation and Characterization of Outer Membrane Vesicles of Pectobacterium brasiliense 1692. Microorganisms 2021; 9:1918. [PMID: 34576813 PMCID: PMC8469291 DOI: 10.3390/microorganisms9091918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/15/2022] Open
Abstract
Pectobacterium brasiliense (Pbr) 1692 is an aggressive phytopathogen affecting a broad host range of crops and ornamental plants, including potatoes. Previous research on animal pathogens, and a few plant pathogens, revealed that Outer Membrane Vesicles (OMVs) are part of Gram-negative bacteria's (GNB) adaptive toolkit. For this reason, OMV production and subsequent release from bacteria is a conserved process. Therefore, we hypothesized that OMVs might transport proteins that play a critical role in causing soft rot disease and in the survival and fitness of Pbr1692. Here, we show that the potato pathogen, Pbr1692, releases OMVs of various morphologies in Luria Bertani media at 31 °C. Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) confirmed the production of OMVs by Pbr1692 cells. Transmission Electron Microscopy showed that these exist as chain-, single-, and double-membrane morphologies. Mass spectrometry followed by Gene Ontology, Clusters of Orthologous Groups, Virulence Factor, CAZymes, Antibiotic Resistance Ontology, and Bastion6 T6SE annotations identified 129 OMV-associated proteins with diverse annotated roles, including antibiotic stress response, virulence, and competition. Pbr1692 OMVs contributed to virulence in potato tubers and elicited a hypersensitive response in Nicotiana benthamiana leaves. Furthermore, Pbr1692 OMVs demonstrated antibacterial activity against Dickeya dadantii.
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Affiliation(s)
- Silindile Maphosa
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lunnon Road, Pretoria 0028, South Africa;
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lunnon Road, Pretoria 0028, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lunnon Road, Pretoria 0028, South Africa;
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lunnon Road, Pretoria 0028, South Africa
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7
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Zlatkov N, Nadeem A, Uhlin BE, Wai SN. Eco-evolutionary feedbacks mediated by bacterial membrane vesicles. FEMS Microbiol Rev 2021; 45:fuaa047. [PMID: 32926132 PMCID: PMC7968517 DOI: 10.1093/femsre/fuaa047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial membrane vesicles (BMVs) are spherical extracellular organelles whose cargo is enclosed by a biological membrane. The cargo can be delivered to distant parts of a given habitat in a protected and concentrated manner. This review presents current knowledge about BMVs in the context of bacterial eco-evolutionary dynamics among different environments and hosts. BMVs may play an important role in establishing and stabilizing bacterial communities in such environments; for example, bacterial populations may benefit from BMVs to delay the negative effect of certain evolutionary trade-offs that can result in deleterious phenotypes. BMVs can also perform ecosystem engineering by serving as detergents, mediators in biochemical cycles, components of different biofilms, substrates for cross-feeding, defense systems against different dangers and enzyme-delivery mechanisms that can change substrate availability. BMVs further contribute to bacteria as mediators in different interactions, with either other bacterial species or their hosts. In short, BMVs extend and deliver phenotypic traits that can have ecological and evolutionary value to both their producers and the ecosystem as a whole.
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Affiliation(s)
- Nikola Zlatkov
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Aftab Nadeem
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Bernt Eric Uhlin
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Sun Nyunt Wai
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
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8
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Liang J, Xu J, Zhao W, Wang J, Chen K, Li Y, Tian Y. Benzo[a]pyrene might be transported by a TonB-dependent transporter in Novosphingobium pentaromativorans US6-1. JOURNAL OF HAZARDOUS MATERIALS 2021; 404:124037. [PMID: 33059256 DOI: 10.1016/j.jhazmat.2020.124037] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Sphingomonads are well known for their ability to efficiently degrade polycyclic aromatic hydrocarbons (PAHs), but little is known about the mechanism of PAH uptake and transport across the cell membrane. RNA sequencing analysis of a sphingomonad, Novosphingobium pentaromativorans US6-1 showed that 38 TonB-dependent transporter (TBDT) genes were significantly upregulated under 5-ring PAH-benzo[a]pyrene (BaP) stress. In order to reveal whether TBDTs are involved in uptake and transport BaP in US6-1, the key TBDT genes were deleted to generate mutants. The results showed that the growth status of these mutants was not different from that of the wild-type strains, but the PAH degradation ability decreased, especially for the mutant strain Δtbdt-11, which did not encode the tbdt-11 gene. Meanwhile, the cell surface hydrophobicity (CSH) of Δtbdt-11 was found to be significantly lower than that of the wild-type strain under BaP stress. Furthermore, the transcriptional activity of genes encoding PAH degradative enzymes was found to be greatly reduced in Δtbdt-11. Confocal microscopy observations showed that US6-1 could transport BaP across the outer membrane, but this transport capacity was significantly reduced in Δtbdt-11 and wild-type US6-1 treated with PMF uncoupler, further confirming that the tbdt-11 gene was associated with PAH active transport.
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Affiliation(s)
- Jiaqing Liang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiantao Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Weijun Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiaofeng Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Kai Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yuqian Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.
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9
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Lee SY, Yun SH, Lee H, Yi YS, Park EC, Kim W, Kim HY, Lee JC, Kim GH, Kim SI. Analysis of the Extracellular Proteome of Colistin-Resistant Korean Acinetobacter baumannii Strains. ACS OMEGA 2020; 5:5713-5720. [PMID: 32226849 PMCID: PMC7097930 DOI: 10.1021/acsomega.9b03723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/27/2020] [Indexed: 05/08/2023]
Abstract
We analyzed the extracellular proteome of colistin-resistant Korean Acinetobacter baumannii (KAB) strains to identify proteome profiles that can be used to characterize extensively drug-resistant KAB strains. Four colistin-resistant KAB strains with colistin resistance associated with point mutations in pmrB and pmrC genes were analyzed. Analysis of the extracellular proteome of these strains revealed the presence of 506 induced common proteins, which were hence considered as the core extracellular proteome. Class C ADC-30 and class D OXA-23 β-lactamases were abundantly induced in these strains. Porins (CarO and CarO-like porin), outer membrane proteins (OmpH and BamABDE), transport protein (AdeK), receptor (TonB), and several proteins of unknown function were among the specifically induced proteins. Based on the sequence homology analysis of proteins from the core proteome and those of other A. baumannii strains and pathogenic bacterial species as well as further in silico screening, we propose that CarO-like porin is an A. baumannii-specific protein and that two tryptic peptides that originate from CarO-like porin detected by tandem mass spectrometry are peptide makers of this protein.
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Affiliation(s)
- Sang-Yeop Lee
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Center
for Convegent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
| | - Sung Ho Yun
- Center
for Research Equipment, Korea Basic Science
Institute, Ochang 28119, Korea
| | - Hayoung Lee
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Department
of Bio-Analytical Science, University of
Science and Technology (UST), Daejeon 34113, Korea
| | - Yoon-Sun Yi
- Center
for Research Equipment, Korea Basic Science
Institute, Ochang 28119, Korea
| | - Edmond Changkyun Park
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Center
for Convegent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
- Department
of Bio-Analytical Science, University of
Science and Technology (UST), Daejeon 34113, Korea
| | - Wooyoung Kim
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Center
for Convegent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
- Department
of Toxicology, College of Pharmacy, Chungnam
National University, Daejeon 34134, Korea
| | - Hye-Yeon Kim
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Center
for Convegent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
| | - Je Chul Lee
- Department
of Microbiology, School of Medicine, Kyungpook
National University, Daegu 41944, Korea
| | - Gun-Hwa Kim
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Department
of Bio-Analytical Science, University of
Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Il Kim
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Center
for Convegent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
- Department
of Bio-Analytical Science, University of
Science and Technology (UST), Daejeon 34113, Korea
- E-mail: . Phone: +82-43-240-5422. Fax: +82-43-240-5416
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10
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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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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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12
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Gill S, Catchpole R, Forterre P. Extracellular membrane vesicles in the three domains of life and beyond. FEMS Microbiol Rev 2019; 43:273-303. [PMID: 30476045 PMCID: PMC6524685 DOI: 10.1093/femsre/fuy042] [Citation(s) in RCA: 259] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/20/2018] [Indexed: 02/06/2023] Open
Abstract
Cells from all three domains of life, Archaea, Bacteria and Eukarya, produce extracellular vesicles (EVs) which are sometimes associated with filamentous structures known as nanopods or nanotubes. The mechanisms of EV biogenesis in the three domains remain poorly understood, although studies in Bacteria and Eukarya indicate that the regulation of lipid composition plays a major role in initiating membrane curvature. EVs are increasingly recognized as important mediators of intercellular communication via transfer of a wide variety of molecular cargoes. They have been implicated in many aspects of cell physiology such as stress response, intercellular competition, lateral gene transfer (via RNA or DNA), pathogenicity and detoxification. Their role in various human pathologies and aging has aroused much interest in recent years. EVs can be used as decoys against viral attack but virus-infected cells also produce EVs that boost viral infection. Here, we review current knowledge on EVs in the three domains of life and their interactions with the viral world.
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Affiliation(s)
- Sukhvinder Gill
- Institute for Integrative Biology of the Cell (I2BC), Biologie Cellulaire des Archées (BCA), CEA, CNRS, Université Paris-Sud, 91405 Orsay cedex, France
| | - Ryan Catchpole
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, F75015 Paris, France
| | - Patrick Forterre
- Institute for Integrative Biology of the Cell (I2BC), Biologie Cellulaire des Archées (BCA), CEA, CNRS, Université Paris-Sud, 91405 Orsay cedex, France
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, F75015 Paris, France
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13
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Karthikeyan R, Gayathri P, Gunasekaran P, Jagannadham MV, Rajendhran J. Comprehensive proteomic analysis and pathogenic role of membrane vesicles of Listeria monocytogenes serotype 4b reveals proteins associated with virulence and their possible interaction with host. Int J Med Microbiol 2019; 309:199-212. [PMID: 30962079 DOI: 10.1016/j.ijmm.2019.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
Membrane vesicles (MVs) are produced by various Gram positive and Gram negative pathogenic bacteria and play an important role in virulence. In this study, the membrane vesicles (MVs) of L. monocytogenes were isolated from the culture supernatant. High-resolution electron microscopy and dynamic light scattering analysis revealed that L. monocytogenes MVs are spherical with a diameter of 200 to 300 nm in size. Further, comprehensive proteomic analyses of MVs and whole cells of L. monocytogenes were performed using LC/MS/MS. A total of 1355 and 312 proteins were identified in the L. monocytogenes cells and MVs, respectively. We identified that 296 proteins are found in both whole cells, and MV proteome and 16 proteins were identified only in the MVs. Also, we have identified the virulence factors such as listeriolysin O (LLO), internalin B (InlB), autolysin, p60, NLP/P60 family protein, UPF0356 protein, and PLC-A in MVs. Computational prediction of host-MV interactions revealed a total of 1841 possible interactions with the host involving 99 MV proteins and 1513 host proteins. We elucidated the possible pathway that mediates internalization of L. monocytogenes MV to host cells and the subsequent pathogenesis mechanisms. The in vitro infection assays showed that the purified MVs could induce cytotoxicity in Caco-2 cells. Using endocytosis inhibitors, we demonstrated that MVs are internalized via actin-mediated endocytosis. These results suggest that L. monocytogenes MVs can interact with host cell and contribute to the pathogenesis of L. monocytogenes during infection.
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Affiliation(s)
- Raman Karthikeyan
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India
| | - Pratapa Gayathri
- CSIR - Centre for Cellular and Molecular Biology, Tarnaka, Hyderabad, 500007, India
| | | | | | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India.
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14
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Jung DW, Ro HJ, Kim J, Kim SI, Yi GR, Lee G, Jun S. Biophysical restriction of growth area using a monodispersed gold sphere nanobarrier prolongs the mitotic phase in HeLa cells. RSC Adv 2019; 9:37497-37506. [PMID: 35542263 PMCID: PMC9075507 DOI: 10.1039/c9ra08410j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/08/2019] [Indexed: 11/21/2022] Open
Abstract
Homogeneous 83 nm gold nanospheres with a human fibronectin-coated substrate surrounding the cells induce biophysical cues which result in a delay in the mitotic phase of the cell cycle.
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Affiliation(s)
- Dae-Woong Jung
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
- Department of Chemical Engineering
- Sungkyunkwan University
| | - Hyun-Joo Ro
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
- Convergent Research Center for Emerging Virus Infection
- Korea Research Institute of Chemical Technology
| | - Junmin Kim
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
- Department of Chemical Engineering
- Sungkyunkwan University
| | - Seung Il Kim
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
- Convergent Research Center for Emerging Virus Infection
- Korea Research Institute of Chemical Technology
| | - Gi-Ra Yi
- Department of Chemical Engineering
- Sungkyunkwan University
- Suwon
- Republic of Korea
| | - Gaehang Lee
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
| | - Sangmi Jun
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
- Convergent Research Center for Emerging Virus Infection
- Korea Research Institute of Chemical Technology
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