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Dunstan RA, Hay ID, Lithgow T. Defining Membrane Protein Localization by Isopycnic Density Gradients. Methods Mol Biol 2024; 2715:91-98. [PMID: 37930523 DOI: 10.1007/978-1-0716-3445-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Bacterial membrane proteins account for around one-third of the proteome in many species and can represent much more than half of the mass of the membranes. Classic techniques in cell biology can be applied to characterize bacterial membranes and their membrane protein constituents, and here we describe a protocol for the purification of outer membranes and inner membranes from Escherichia coli. This allows for compositional analysis of the membranes as well as functional analyses. The procedure can be applied with minor modifications to other bacterial species including those carrying capsular polysaccharide attached to the outer membrane.
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Affiliation(s)
- Rhys A Dunstan
- Centre to Impact AMR, Monash University, Melbourne, VIC, Australia
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Iain D Hay
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Melbourne, VIC, Australia.
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia.
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2
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Rahman MA, Heme UH, Parvez MAK. In silico functional annotation of hypothetical proteins from the Bacillus paralicheniformis strain Bac84 reveals proteins with biotechnological potentials and adaptational functions to extreme environments. PLoS One 2022; 17:e0276085. [PMID: 36228026 PMCID: PMC9560612 DOI: 10.1371/journal.pone.0276085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/28/2022] [Indexed: 11/26/2022] Open
Abstract
Members of the Bacillus genus are industrial cell factories due to their capacity to secrete significant quantities of biomolecules with industrial applications. The Bacillus paralicheniformis strain Bac84 was isolated from the Red Sea and it shares a close evolutionary relationship with Bacillus licheniformis. However, a significant number of proteins in its genome are annotated as functionally uncharacterized hypothetical proteins. Investigating these proteins' functions may help us better understand how bacteria survive extreme environmental conditions and to find novel targets for biotechnological applications. Therefore, the purpose of our research was to functionally annotate the hypothetical proteins from the genome of B. paralicheniformis strain Bac84. We employed a structured in-silico approach incorporating numerous bioinformatics tools and databases for functional annotation, physicochemical characterization, subcellular localization, protein-protein interactions, and three-dimensional structure determination. Sequences of 414 hypothetical proteins were evaluated and we were able to successfully attribute a function to 37 hypothetical proteins. Moreover, we performed receiver operating characteristic analysis to assess the performance of various tools used in this present study. We identified 12 proteins having significant adaptational roles to unfavorable environments such as sporulation, formation of biofilm, motility, regulation of transcription, etc. Additionally, 8 proteins were predicted with biotechnological potentials such as coenzyme A biosynthesis, phenylalanine biosynthesis, rare-sugars biosynthesis, antibiotic biosynthesis, bioremediation, and others. Evaluation of the performance of the tools showed an accuracy of 98% which represented the rationality of the tools used. This work shows that this annotation strategy will make the functional characterization of unknown proteins easier and can find the target for further investigation. The knowledge of these hypothetical proteins' potential functions aids B. paralicheniformis strain Bac84 in effectively creating a new biotechnological target. In addition, the results may also facilitate a better understanding of the survival mechanisms in harsh environmental conditions.
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Affiliation(s)
- Md. Atikur Rahman
- Institute of Microbiology, Friedrich Schiller University Jena, Thuringia, Germany
| | - Uzma Habiba Heme
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Thuringia, Germany
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Ijaq J, Chandra D, Ray MK, Jagannadham MV. Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation. Front Genet 2022; 13:825269. [PMID: 35360867 PMCID: PMC8963723 DOI: 10.3389/fgene.2022.825269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/07/2022] [Indexed: 11/28/2022] Open
Abstract
Exploring the molecular mechanisms behind bacterial adaptation to extreme temperatures has potential biotechnological applications. In the present study, Pseudomonas sp. Lz4W, a Gram-negative psychrophilic bacterium adapted to survive in Antarctica, was selected to decipher the molecular mechanism underlying the cold adaptation. Proteome analysis of the isolates grown at 4°C was performed to identify the proteins and pathways that are responsible for the adaptation. However, many proteins from the expressed proteome were found to be hypothetical proteins (HPs), whose function is unknown. Investigating the functional roles of these proteins may provide additional information in the biological understanding of the bacterial cold adaptation. Thus, our study aimed to assign functions to these HPs and understand their role at the molecular level. We used a structured insilico workflow combining different bioinformatics tools and databases for functional annotation. Pseudomonas sp. Lz4W genome (CP017432, version 1) contains 4493 genes and 4412 coding sequences (CDS), of which 743 CDS were annotated as HPs. Of these, from the proteome analysis, 61 HPs were found to be expressed consistently at the protein level. The amino acid sequences of these 61 HPs were submitted to our workflow and we could successfully assign a function to 18 HPs. Most of these proteins were predicted to be involved in biological mechanisms of cold adaptations such as peptidoglycan metabolism, cell wall organization, ATP hydrolysis, outer membrane fluidity, catalysis, and others. This study provided a better understanding of the functional significance of HPs in cold adaptation of Pseudomonas sp. Lz4W. Our approach emphasizes the importance of addressing the “hypothetical protein problem” for a thorough understanding of mechanisms at the cellular level, as well as, provided the assessment of integrating proteomics methods with various annotation and curation approaches to characterize hypothetical or uncharacterized protein data. The MS proteomics data generated from this study has been deposited to the ProteomeXchange through PRIDE with the dataset identifier–PXD029741.
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Affiliation(s)
- Johny Ijaq
- Metabolomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Deepika Chandra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Malay Kumar Ray
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - M. V. Jagannadham
- Metabolomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India
- *Correspondence: M. V. Jagannadham,
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Pavankumar TL, Mittal P, Hallsworth JE. Molecular insights into the ecology of a psychrotolerant
Pseudomonas syringae. Environ Microbiol 2020; 23:3665-3681. [DOI: 10.1111/1462-2920.15304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Theetha L. Pavankumar
- Department of Microbiology and Molecular Genetics, Briggs Hall, One Shields Avenue University of California Davis CA USA
| | - Pragya Mittal
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine University of Edinburgh Crewe Road South, Edinburgh, EH42XU, Scotland UK
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological Sciences Queen's University Belfast 19 Chlorine Gardens, Belfast, BT9 5DL Northern Ireland UK
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Lee SK, Han JH, Park JH, Ha KS, Park WS, Hong SH, Na S, Cheng Y, Han ET. Evaluation of antibody responses to the early transcribed membrane protein family in Plasmodium vivax. Parasit Vectors 2019; 12:594. [PMID: 31856917 PMCID: PMC6921578 DOI: 10.1186/s13071-019-3846-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/09/2019] [Indexed: 11/25/2022] Open
Abstract
Background Malaria parasites form intracellular membranes that separate the parasite from the internal space of erythrocytes, and membrane proteins from the parasites are exported to the host via the membrane. In our previous study, Plasmodium vivax early transcribed membrane protein (PvETRAMP) 11.2, an intracellular membrane protein that is highly expressed in blood-stage parasites, was characterized as a highly immunogenic protein in P. vivax malaria patients. However, the other PvETRAMP family proteins have not yet been investigated. In this study, PvETRAMPs were expressed and evaluated to determine their immunological profiles. Methods The protein structure and amino acid alignment were carried out using bioinformatics analysis software. A total of six PvETRAMP family proteins were successfully expressed and purified using a wheat germ cell free protein expression system and the purified proteins were used for protein microarray and immunization of mice. The localization of the protein was determined with serum against PvETRAMP4. IgG subclasses were assessed from the immunized mice. Results In silico analysis showed that P. vivax exhibits nine genes encoding the ETRAMP family. The ETRAMP family proteins are relatively small molecules with conserved structural features. A total of 6 recombinant ETRAMP proteins were successfully expressed and purified. The serum positivity of P. vivax malaria patients and healthy individuals was evaluated using a protein microarray method. Among the PvETRAMPs, ETRAMP4 showed the highest positivity rate of 62%, comparable to that of PvETRAMP11.2, which served as the positive control, and a typical export pattern of PvETRAMP4 was observed in the P. vivax parasite. The assessment of IgG subclasses in mice immunized with PvETRAMP4 showed high levels of IgG1 and IgG2b. PvETRAMP family proteins were identified and characterized as serological markers. Conclusions The relatively high antibody responses to PvETRAMP4 as well as the specific IgG subclasses observed in immunized mice suggest that the ETRAMP family is immunogenic in pathogens and can be used as a protein marker and for vaccine development.![]()
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Affiliation(s)
- Seong-Kyun Lee
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Ji-Hoon Park
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Kwon-Soo Ha
- Department of Cellular and Molecular Biology, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Won Sun Park
- Department of Physiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Sunghun Na
- Department of Obstetrics and Gynecology, Kangwon National University Hospital, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Yang Cheng
- Department of Public Health and Preventive Medicine, Laboratory of Pathogen Infection and Immunity, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, People's Republic of China.
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea.
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Dunstan RA, Hay ID, Lithgow T. Defining Membrane Protein Localization by Isopycnic Density Gradients. Methods Mol Biol 2018; 1615:81-86. [PMID: 28667604 DOI: 10.1007/978-1-4939-7033-9_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
In many bacteria, membrane proteins account for around one-third of the proteome and can represent much more than half of the mass of a membrane. Classic techniques in cell biology can be applied to characterise bacterial membranes and their membrane protein constituents. Here we describe a protocol for the purification of outer and inner membranes from Escherichia coli. The procedure can be applied with minor modifications to other bacterial species, including those carrying capsular polysaccharide attached to the outer membrane.
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Affiliation(s)
- Rhys A Dunstan
- Department of Microbiology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, VIC, Melbourne, 3800, Australia
| | - Iain D Hay
- Department of Microbiology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, VIC, Melbourne, 3800, Australia
| | - Trevor Lithgow
- Department of Microbiology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, VIC, Melbourne, 3800, Australia.
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Saha B, Bhattacharya SG. Charting novel allergens from date palm pollen (Phoenix sylvestris) using homology driven proteomics. J Proteomics 2017; 165:1-10. [PMID: 28535932 DOI: 10.1016/j.jprot.2017.05.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/05/2017] [Accepted: 05/17/2017] [Indexed: 11/19/2022]
Abstract
Pollen grains from Phoenix sylvestris (date palm), a commonly cultivated tree in India has been found to cause severe allergic diseases in an increasing percentage of hypersensitive individuals. To unearth its allergenic components, pollen protein were profiled by two-dimensional gel electrophoresis followed by immunoblotting with date palm pollen sensitive patient sera. Allergens were identified by MALDI-TOF/TOF employing a layered proteomic approach combining conventional database dependent search and manual de novo sequencing followed by homology-based search as Phoenix sylvestris is unsequenced. Derivatization of tryptic peptides by acetylation has been demonstrated to differentiate the 'b' from the 'y' ions facilitating efficient de novo sequencing. Ten allergenic proteins were identified, out of which six showed homology with known allergens while others were reported for the first time. Amongst these, isoflavone reductase, beta-conglycinin, S-adenosyl methionine synthase, 1, 4 glucan synthase and beta-galactosidase were commonly reported as allergens from coconut pollen and presumably responsible for cross-reactivity. One of the allergens had IgE binding epitope recognized by its glycan moiety. The allergenic potency of date palm pollen has been demonstrated using in vitro tests. The identified allergens can be used to develop vaccines for immunotherapy against date palm pollen allergy. THE SIGNIFICANCE OF THE STUDY Identification of allergenic proteins from sources harboring them is essential in developing therapeutic interventions. This is the first comprehensive study on the identification of allergens from Phoenix sylvestris (date palm) pollen, one of the major aeroallergens in India using a proteomic approach. Proteomic methods are being increasingly used to identify allergens. However, since many of these proteins arise from species which are un-sequenced, it becomes difficult to interpret those using conventional proteomics. Date palm being an unsequenced species, the IgE-reactive proteins have been identified using a stratified proteomic workflow incorporating manual de novo sequencing and homology-based proteomics. This study also gives an insight into the presence of glycan nature of the IgE binding epitopes. Five proteins have been found to be common with coconut pollen allergens and presumably responsible for cross-reactivity. These can be used in diagnostics to differentiate patient cohorts allergic to both coconut and date palm pollen from true date palm pollen allergic subjects. This would also determine better specific immunotherapy regimes between the two cohorts. The allergens identified herein have potential towards vaccine development in date palm pollen allergy as well as in enriching the existing catalogue of allergenic proteins.
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Affiliation(s)
- Bodhisattwa Saha
- Division of Plant Biology, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Swati Gupta Bhattacharya
- Division of Plant Biology, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India.
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Saha B, Sircar G, Pandey N, Gupta Bhattacharya S. Mining Novel Allergens from Coconut Pollen Employing Manual De Novo Sequencing and Homology-Driven Proteomics. J Proteome Res 2015; 14:4823-33. [PMID: 26426307 DOI: 10.1021/acs.jproteome.5b00657] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coconut pollen, one of the major palm pollen grains is an important constituent among vectors of inhalant allergens in India and a major sensitizer for respiratory allergy in susceptible patients. To gain insight into its allergenic components, pollen proteins were analyzed by two-dimensional electrophoresis, immunoblotted with coconut pollen sensitive patient sera, followed by mass spectrometry of IgE reactive proteins. Coconut being largely unsequenced, a proteomic workflow has been devised that combines the conventional database-dependent analysis of tandem mass spectral data and manual de novo sequencing followed by a homology-based search for identifying the allergenic proteins. N-terminal acetylation helped to distinguish "b" ions from others, facilitating reliable sequencing. This led to the identification of 12 allergenic proteins. Cluster analysis with individual patient sera recognized vicilin-like protein as a major allergen, which was purified to assess its in vitro allergenicity and then partially sequenced. Other IgE-sensitive spots showed significant homology with well-known allergenic proteins such as 11S globulin, enolase, and isoflavone reductase along with a few which are reported as novel allergens. The allergens identified can be used as potential candidates to develop hypoallergenic vaccines, to design specific immunotherapy trials, and to enrich the repertoire of existing IgE reactive proteins.
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Affiliation(s)
- Bodhisattwa Saha
- Division of Plant Biology, Bose Institute , 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India
| | - Gaurab Sircar
- Division of Plant Biology, Bose Institute , 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India
| | - Naren Pandey
- Department of Allergy and Asthma, Belle View Clinic , 9, Dr U.N. Brahmachari Street, Kolkata 700017, West Bengal, India
| | - Swati Gupta Bhattacharya
- Division of Plant Biology, Bose Institute , 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India
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Sen S, Agrawal C, Mishra Y, Rai S, Chatterjee A, Yadav S, Singh S, Rai LC. Exploring the membrane proteome of the diazotropic cyanobacterium Anabaena PCC7120 through gel-based proteomics and in silico approaches. J Proteomics 2015. [PMID: 26210591 DOI: 10.1016/j.jprot.2015.07.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
UNLABELLED This paper focuses on the gel-based membrane proteomics from diazotrophic cyanobacterium Anabaena PCC7120 by modifying the protocol of Hall et al. [1]. The bioinformatic analysis revealed that 59 (29 integral, 30 peripheral) of the 67 proteins identified were membrane proteins. Of the 29 integral proteins, except Alr0834, the remaining 28 contained 1-12 transmembrane helices. Sixteen integral proteins harboring signal peptides (Sec/TAT/LipoP) suggest that protein targeting in Anabaena involves both sec-dependent and sec-independent pathways. While majority of photosynthesis and respiration proteins (21 of 24) were confined to broad pH gradient the hypothetical and unknown (12 of 13), and cell envelope proteins (3 of 3) preferred the narrow pH range. Of the 5 transporters and binding proteins, Na(+)/H(+)-exchanging protein and Alr2372 were present in broad, pstS1 and cmpD in narrow and cmpA was common to both pH ranges. The distribution of proteins across pH gradient, thus clearly indicates the functional and structural diversity in membrane proteome of Anabaena. It requires mention that protochlorophyllide oxido-reductase, Na(+)/H(+)-exchanging protein, All1355, Alr2055, Alr3514, Alr2903 and Alr2751 were new entries to the 2DE membrane protein profile of Anabaena. This study demonstrates suitability of the modified protocol for the study of membrane protein from filamentous cyanobacteria. SIGNIFICANCE Anabaena sp. PCC7120 is used as a model organism due to its agriculture significance as biofertilizer, close resemblance with higher plant chloroplast and availability of full genome sequence. Although cytosolic proteome has been explored a lot membrane proteins are still understudied as they are notoriously difficult to display using 2-D technology. Identification and characterization of these proteins is therefore required to elucidate and understand cellular mechanisms. The purpose of this study was to develop a protocol suitable for membrane protein extraction from Anabaena. Additionally, by homology comparison or domain assignment a possible function could be ascribed to novel uncharacterized proteins which will serve as a useful reference for further detailed studies of membrane system in filamentous cyanobacteria. Resolution of membrane proteins ranging from least (single transmembrane helix) to highly hydrophobic (several transmembrane helices) one on 2D gels recommends the gel based approach for identification of membrane proteomics from filamentous cyanobacteria. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Sonia Sen
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Chhavi Agrawal
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Yogesh Mishra
- Department of Botany, Punjab University, Sector 14, Chandigarh 160014, India
| | - Shweta Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Antra Chatterjee
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Shivam Yadav
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Shilpi Singh
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - L C Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India.
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The proteome of the outer membrane vesicles of an Antarctic bacterium Pseudomonas syringae Lz4W. Data Brief 2015; 4:406-9. [PMID: 26306312 PMCID: PMC4534585 DOI: 10.1016/j.dib.2015.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/02/2015] [Indexed: 11/22/2022] Open
Abstract
Outer membrane vesicles (OMVs) of gram-negative bacteria are released during all growth phases and play an important role in bacterial physiology. They consist of lipids, proteins, lipopolysaccharides and other molecules. The OMVs of the Antarctic bacterium Pseudomonas syringae Lz 4W were isolated and identified their proteins. The mass spectral data set deposited with PRIDE, accession number PXD 000221 is presented in this report. The proteins identified from the OMVs of P. syringae Lz4W, data of this study were published in the Journal of proteome research [1].
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Fulsundar S, Kulkarni HM, Jagannadham MV, Nair R, Keerthi S, Sant P, Pardesi K, Bellare J, Chopade BA. Molecular characterization of outer membrane vesicles released from Acinetobacter radioresistens and their potential roles in pathogenesis. Microb Pathog 2015; 83-84:12-22. [PMID: 25940676 DOI: 10.1016/j.micpath.2015.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 10/23/2022]
Abstract
Acinetobacter radioresistens is an important member of genus Acinetobacter from a clinical point of view. In the present study, we report that a clinical isolate of A. radioresistens releases outer membrane vesicles (OMVs) under in vitro growth conditions. OMVs were released in distinctive size ranges with diameters from 10 to 150 nm as measured by the dynamic light scattering (DLS) technique. Additionally, proteins associated with or present into OMVs were identified using LC-ESI-MS/MS. A total of 71 proteins derived from cytosolic, cell membrane, periplasmic space, outer membrane (OM), extracellular and undetermined locations were found in OMVs. The initial characterization of the OMV proteome revealed a correlation of some proteins to biofilm, quorum sensing, oxidative stress tolerance, and cytotoxicity functions. Thus, the OMVs of A. radioresistens are suggested to play a role in biofilm augmentation and virulence possibly by inducing apoptosis.
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Affiliation(s)
- Shweta Fulsundar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | | | | | - Rashmi Nair
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Sravani Keerthi
- Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Pooja Sant
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Karishma Pardesi
- Department of Microbiology, Savitribai Phule Pune University, Pune 411007, India
| | - Jayesh Bellare
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Balu Ananda Chopade
- Department of Microbiology, Savitribai Phule Pune University, Pune 411007, India; Dr. Babasaheb Ambedkar Marathwada University, Aurangabad 431 004, India.
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Moumène A, Marcelino I, Ventosa M, Gros O, Lefrançois T, Vachiéry N, Meyer DF, Coelho AV. Proteomic profiling of the outer membrane fraction of the obligate intracellular bacterial pathogen Ehrlichia ruminantium. PLoS One 2015; 10:e0116758. [PMID: 25710494 PMCID: PMC4339577 DOI: 10.1371/journal.pone.0116758] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 12/13/2014] [Indexed: 01/27/2023] Open
Abstract
The outer membrane proteins (OMPs) of Gram-negative bacteria play a crucial role in virulence and pathogenesis. Identification of these proteins represents an important goal for bacterial proteomics, because it aids in vaccine development. Here, we have developed such an approach for Ehrlichia ruminantium, the obligate intracellular bacterium that causes heartwater. A preliminary whole proteome analysis of elementary bodies, the extracellular infectious form of the bacterium, had been performed previously, but information is limited about OMPs in this organism and about their role in the protective immune response. Identification of OMPs is also essential for understanding Ehrlichia's OM architecture, and how the bacterium interacts with the host cell environment. First, we developed an OMP extraction method using the ionic detergent sarkosyl, which enriched the OM fraction. Second, proteins were separated via one-dimensional electrophoresis, and digested peptides were analyzed via nano-liquid chromatographic separation coupled with mass spectrometry (LC-MALDI-TOF/TOF). Of 46 unique proteins identified in the OM fraction, 18 (39%) were OMPs, including 8 proteins involved in cell structure and biogenesis, 4 in transport/virulence, 1 porin, and 5 proteins of unknown function. These experimental data were compared to the predicted subcellular localization of the entire E. ruminantium proteome, using three different algorithms. This work represents the most complete proteome characterization of the OM fraction in Ehrlichia spp. The study indicates that suitable subcellular fractionation experiments combined with straightforward computational analysis approaches are powerful for determining the predominant subcellular localization of the experimentally observed proteins. We identified proteins potentially involved in E. ruminantium pathogenesis, which are good novel targets for candidate vaccines. Thus, combining bioinformatics and proteomics, we discovered new OMPs for E. ruminantium that are valuable data for those investigating new vaccines against this organism. In summary, we provide both pioneering data and novel insights into the pathogenesis of this obligate intracellular bacterium.
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Affiliation(s)
- Amal Moumène
- CIRAD, UMR CMAEE, Site de Duclos, Prise d’eau, F-97170, Petit-Bourg, Guadeloupe, France
- INRA, UMR1309 CMAEE, F-34398, Montpellier, France
- Université des Antilles et de la Guyane, 97159, Pointe-à-Pitre cedex, Guadeloupe, France
| | - Isabel Marcelino
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Miguel Ventosa
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Olivier Gros
- Université des Antilles et de la Guyane, Institut de Biologie Paris Seine, UMR7138 UPMC-CNRS, Equipe Biologie de la Mangrove, UFR des Sciences Exactes et Naturelles, Département de Biologie, BP 592, 97159, Pointe-à-Pitre cedex, Guadeloupe, France
| | | | - Nathalie Vachiéry
- CIRAD, UMR CMAEE, Site de Duclos, Prise d’eau, F-97170, Petit-Bourg, Guadeloupe, France
- INRA, UMR1309 CMAEE, F-34398, Montpellier, France
| | - Damien F. Meyer
- CIRAD, UMR CMAEE, Site de Duclos, Prise d’eau, F-97170, Petit-Bourg, Guadeloupe, France
- INRA, UMR1309 CMAEE, F-34398, Montpellier, France
- * E-mail:
| | - Ana V. Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
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Mo J, Li J. In silico analysis for structure, function and T-cell epitopes of a hypothetical conserved (HP-C) protein coded by PVX_092425 in Plasmodium vivax. Pathog Glob Health 2015; 109:61-7. [PMID: 25706099 DOI: 10.1179/2047773215y.0000000005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
OBJECTIVE Plasmodium spp. merozoite glycosylphosphatidylinositol-anchored proteins (GPI-APs) considered as protective immunogen in novel vaccines against malaria. To analyze the structure and function of a hypothetical conserved (HP-C) GPI-AP coded by gene PVX_092425 from Plasmodium vivax, and find its potential T-cell epitopes for further vivax malaria vaccine study. METHODS The structure, function and T-cell epitopes of the HP-C protein named Pvx_092425 were analyzed and predicted by online and offline bioinformatics software. RESULTS The bioinformatics data showed that the Pvx_092425 is an 830 amino acid (AA) long polypeptide encoded by five exons gene PVX_092425.It contains a pectin lyase-like superfamily, an AA repeats region, a cys-rich region and a transmembrane domain (TM) in C-terminal region. The alignment analysis drew it has a unique AA repeats region among Plasmodium spp. It was located in the cytoplasm, secretory system or cellular nucleus of P. vivax merozoite. For the sequence, the fragment of I823-V829 inserts in the interior side of the membrane, and M1--A812 belongs to the cytoplasmic tail. It has seven protein-protein binding sites. The peptides with the best predicted binding affinities were human leucocyte antigen (HLA) HLA-A*0203, HLA-DRB1*0101 and HLA- DRB1*0701.Among these predicted peptides, 582FLWDKALFD590 epitope interacted with HLA-DRB1*0101 allele showed best binding affinity compared to others. Structural analysis explained that the epitope fits well into the epitope-binding groove of HLA-DRB1*0101. CONCLUSIONS It proposes that the Pvx_092425 plays a key role during erythrocyte stage and generates information that is useful for development of blood-stage vaccine to block the merozoites invasion.
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Kulkarni HM, Swamy CVB, Jagannadham MV. Molecular characterization and functional analysis of outer membrane vesicles from the antarctic bacterium Pseudomonas syringae suggest a possible response to environmental conditions. J Proteome Res 2014; 13:1345-58. [PMID: 24437924 DOI: 10.1021/pr4009223] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Outer membrane vesicles (OMVs) of Gram-negative bacteria form an important aspect of bacterial physiology as they are involved in various functions essential for their survival. The OMVs of the Antarctic bacterium Pseudomonas syringae Lz4W were isolated, and the proteins and lipids they contain were identified. The matrix-assisted laser desorption/ionization time of flight (MALDI-TOF/TOF) analysis revealed that phosphatidylethanolamines and phosphatidylglycerols are the main lipid components. The proteins of these vesicles were identified by separating them by one-dimensional gel electrophoresis and liquid chromatography coupled to electrospray ionization tandem mass spectrometry (ESI-MS/MS). They are composed of outer membrane and periplasmic proteins according to the subcellular localization predictions by Psortb v.3 and Cello V2.5. The functional annotation and gene ontology of these proteins provided hints for various functions attributed to OMVs and suggested a potential mechanism to respond to the extracellular environmental changes. The OMVs were found to protect the producer organism against the membrane active antibiotics colistin and melittin but not from streptomycin. The 1-N-phenylnapthylamine (NPN)-uptake assay revealed that the OMVs protect the bacterium from membrane active antibiotics by scavenging them and also showed that membrane and protein packing of the OMVs was similar to the parent bacterium. The sequestering depends on the composition and organization of lipids and proteins in the OMVs.
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Affiliation(s)
- Heramb M Kulkarni
- CSIR - Centre for Cellular and Molecular Biology , Tarnaka, Hyderabad - 500007, India
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Wang B, Lu F, Cheng Y, Li J, Ito D, Sattabongkot J, Tsuboi T, Han ET. Identification and characterization of the Plasmodium falciparum RhopH2 ortholog in Plasmodium vivax. Parasitol Res 2012; 112:585-93. [PMID: 23097184 DOI: 10.1007/s00436-012-3170-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/08/2012] [Indexed: 11/28/2022]
Abstract
Plasmodium vivax is one of the most important human malaria species that is geographically widely endemic and potentially affects a larger number of people than its more notorious cousin, Plasmodium falciparum. During invasion of red blood cells, the parasite requires the intervention of high molecular weight complex rhoptry proteins (RhopH) that are also essential for cytoadherence. PfRhopH2, a member of the RhopH multigene family, has been characterized as being crucial during P. falciparum infection. This study describes identifying and characterizing the pfrhoph2 orthologous gene in P. vivax (hereinafter named pvrhoph2). The PvRhopH2 is a 1,369-amino acid polypeptide encoded by PVX_099930 gene, for which orthologous genes have been identified in other Plasmodium species by bioinformatic approaches. Both P. falciparum and P. vivax genes contain nine introns, and there is a high degree of similarity between the deduced amino acid sequences of the two proteins. Moreover, PvRhopH2 contains a signal peptide at its N-terminus and 12 cysteines predominantly in its C-terminal half. PvRhopH2 is localized in one of the apical organelles of the merozoite, the rhoptry, and the localization pattern is similar to that of PfRhopH2 in P. falciparum. The recombinant PvRhopH2 protein is recognized by serum antibodies of patients naturally exposed to P. vivax, suggesting that PvRhopH2 is immunogenic in humans.
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Affiliation(s)
- Bo Wang
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Hyoja2-dong, Chuncheon, Gangwon-do 200-701, Republic of Korea
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Pv12, a 6-Cys antigen of Plasmodium vivax, is localized to the merozoite rhoptry. Parasitol Int 2012; 61:443-9. [DOI: 10.1016/j.parint.2012.02.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 02/09/2012] [Accepted: 02/21/2012] [Indexed: 11/21/2022]
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Jagannadham MV, Chowdhury C. Differential expression of membrane proteins helps Antarctic Pseudomonas syringae to acclimatize upon temperature variations. J Proteomics 2012; 75:2488-99. [PMID: 22418587 DOI: 10.1016/j.jprot.2012.02.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 02/15/2012] [Accepted: 02/25/2012] [Indexed: 01/16/2023]
Abstract
Antarctic bacteria are adapted to the extremely low temperature. The transcriptional and translational machineries of these bacteria are adapted to the sub-zero degrees of temperature. Studies directed towards identifying the changes in the protein profiles during changes in the growth temperatures of an Antarctic bacterium Pseudomonas syringae Lz4W may help in understanding the molecular basis of cold adaptation. In this study, subcellular fractionation methods of proteins were used for the enrichment and identification of proteins including low abundance proteins. The membrane proteins of the bacterium P. syringae Lz4W were prepared employing sucrose density gradient method. The proteins were separated through 2D gel-electrophoresis with the pH ranges 3-10, 4-7 and 5-8 using the detergent, amidosulfobetaine (ASB-14). The proteins separated on the 1D SDS PAGE and 2D gels were identified with the help of LC-ESI MS/MS and MALDI TOF TOF using bioinformatic programs MASCOT and SEQUEST. Since the genome sequence of P. syringae Lz4W is not available, the proteins are identified by using the genome database of the Pseudomonas sp. available at NCBI. The present studies focus on identifying temperature dependent expression of proteins by employing LC-MS/MS method and the functional significance of these proteins is discussed.
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Jagannadham M, Saranya S. Analysis of the Membrane proteins of an Antarctic Bacterium Pseudomonas Syringae. PROTEOMICS INSIGHTS 2011. [DOI: 10.4137/pri.s5383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The proteins of an Antarctic bacterium Pseudomonas syringae Lz4W, identified earlier by different membrane protein preparation methods, were combined together and the redundant identities removed. In total, 1479 proteins including 148 outer membrane proteins from this bacterium were predicted by the algorithm PSORTb3.0. A detailed analysis on their subcellular localization was undertaken which was determined using TMHMM, TMB-hunt and BOMP. A comparison of PSORTb predicted outer membrane proteins with BOMP, revealed that most of the proteins predicted by the former, contained β–barrels in the outer membranes. A comparative analysis of PSORTb, TMHMM and TMB-hunt reveals that most of the outer membranes proteins of this bacterium could be identified using this approach. Thus, by using a combination of biochemical and different bioinformatics algorithms, the membrane proteins of P. syringae are analyzed. In particular, PSORTb results are compared and supported by other algorithms, to improve the strength of OM proteins prediction. Several proteins, having an important role in cold adaptation of the organism, could also be identified.
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Affiliation(s)
- M.V. Jagannadham
- Scientist, Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Tarnaka, Hyderabad, India
| | - S. Saranya
- Depatment of Life Sciences, Bharathidasan University, Tiruchirapalli, Tamil Nadu, India
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