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Chandra H, Gupta MK, Lam YW, Yadav JS. Predominantly Orphan Secretome in the Lung Pathogen Mycobacterium abscessus Revealed by a Multipronged Growth-Phase-Driven Strategy. Microorganisms 2024; 12:378. [PMID: 38399782 PMCID: PMC10892769 DOI: 10.3390/microorganisms12020378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The emerging lung pathogen Mycobacterium abscessus is understudied for its virulence determinants and molecular targets for diagnosis and therapeutics. Here, we report a comprehensive secretome (600 proteins) of this species, which was identified using a multipronged strategy based on genetic/genomic, proteomic, and bioinformatic approaches. In-solution digested bottom-up proteomics from various growth phases identified a total of 517 proteins, while 2D-GE proteomics identified 33 proteins. A reporter-gene-fusion-based genomic library that was custom-generated in this study enabled the detection of 23 secretory proteins. A genome-wide survey for N-terminal signal sequences using bioinformatic tools (Psortb 2.0 and SignalP 3.0) combined with a strategy of the subtraction of lipoproteins and proteins containing multiple transmembrane domains yielded 116 secretory proteins. A homology search against the M. tuberculosis database identified nine additional secretory protein homologs that lacked a secretory signal sequence. Considering the little overlap (80 proteins) among the different approaches used, this study emphasized the importance of using a multipronged strategy for a comprehensive understanding of the secretome. Notably, the majority of the secreted proteins identified (over 50%) turned out to be "orphans" (those with no known functional homologs). The revelation of these species-specific orphan proteins offers a hitherto unexplored repertoire of potential targets for diagnostic, therapeutic, and vaccine research in this emerging lung pathogen.
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Affiliation(s)
- Harish Chandra
- Pulmonary/Microbial Pathogenesis Laboratory, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (H.C.)
| | - Manish K. Gupta
- Pulmonary/Microbial Pathogenesis Laboratory, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (H.C.)
| | - Ying-Wai Lam
- Vermont Biomedical Research Network Proteomics Facility, University of Vermont, Burlington, VT 05405, USA
| | - Jagjit S. Yadav
- Pulmonary/Microbial Pathogenesis Laboratory, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (H.C.)
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Potential Plasticity of the Mannoprotein Repertoire Associated to Mycobacterium tuberculosis Virulence Unveiled by Mass Spectrometry-Based Glycoproteomics. Molecules 2020; 25:molecules25102348. [PMID: 32443484 PMCID: PMC7287972 DOI: 10.3390/molecules25102348] [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: 02/29/2020] [Revised: 05/04/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
To date, Mycobacterium tuberculosis (Mtb) remains the world’s greatest infectious killer. The rise of multidrug-resistant strains stresses the need to identify new therapeutic targets to fight the epidemic. We previously demonstrated that bacterial protein-O-mannosylation is crucial for Mtb infectiousness, renewing the interest of the bacterial-secreted mannoproteins as potential drug-targetable virulence factors. The difficulty of inventorying the mannoprotein repertoire expressed by Mtb led us to design a stringent multi-step workflow for the reliable identification of glycosylated peptides by large-scale mass spectrometry-based proteomics. Applied to the differential analyses of glycoproteins secreted by the wild-type Mtb strain—and by its derived mutant invalidated for the protein-O-mannosylating enzyme PMTub—this approach led to the identification of not only most already known mannoproteins, but also of yet-unknown mannosylated proteins. In addition, analysis of the glycoproteome expressed by the isogenic recombinant Mtb strain overexpressing the PMTub gene revealed an unexpected mannosylation of proteins, with predicted or demonstrated functions in Mtb growth and interaction with the host cell. Since in parallel, a transient increased expression of the PMTub gene has been observed in the wild-type bacilli when infecting macrophages, our results strongly suggest that the Mtb mannoproteome may undergo adaptive regulation during infection of the host cells. Overall, our results provide deeper insights into the complexity of the repertoire of mannosylated proteins expressed by Mtb, and open the way to novel opportunities to search for still-unexploited potential therapeutic targets.
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Cornejo-Granados F, Hurtado-Ramírez JM, Hernández-Pando R, Ochoa-Leyva A. Secret-AAR: a web server to assess the antigenic density of proteins and homology search against bacterial and parasite secretome proteins. Genomics 2018; 111:1514-1516. [PMID: 30316740 DOI: 10.1016/j.ygeno.2018.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 12/13/2022]
Abstract
The secretome refers to all the Excreted/Secreted (ES) proteins of a cell, and these are involved in critical biological processes, such as cell-cell communication, and host immune responses. Recently, we introduced the Abundance of Antigenic Aegions (AAR) value to assess the protein antigenic density and to evaluate the antigenic potential of secretomes. Here, to facilitate the AAR calculation, we implemented it as a user-friendly webserver. We extended the webserver capabilities implementing a sequence-based tool for searching homologous proteins across secretomes, including experimental and predicted secretomes of Mycobacterium tuberculosis and Taenia solium. Additionally, twelve secretomes of helminths, five of Mycobacterium and two of Gram-negative bacteria are also available. Our webserver is a useful tool for researchers working on immunoinformatics and reverse vaccinology, aiming at discovering candidate proteins for new vaccines or diagnostic tests, and it can be used to prioritize the experimental analysis of proteins for druggability assays. The Secret-AAR web server is available at http://microbiomics.ibt.unam.mx/tools/aar/.
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Affiliation(s)
- Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Juan Manuel Hurtado-Ramírez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Rogelio Hernández-Pando
- Experimental Pathology Section, National Institute of Medical Sciences and Nutrition "Salvador Zubirán", Mexico City 14000, Mexico
| | - Adrián Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico.
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Saha MS, Pal S, Sarkar I, Roy A, Das Mohapatra PK, Sen A. Comparative genomics of Mycobacterium reveals evolutionary trends of M. avium complex. Genomics 2018; 111:426-435. [PMID: 29501678 DOI: 10.1016/j.ygeno.2018.02.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/01/2017] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pathogenic species, Mycobacterium also contains opportunistic pathogens as well as free living non-pathogenic species. Disease related various analyses on Mycobacterium tuberculosis are very widespread. However, genomic study of overall Mycobacterium species for understanding the selection pressure on genes as well as evolution of the organism is still illusive. MLSA and 16s rDNA based analysis has been generated for 241 Mycobacterium strains and a detailed analysis of codon and amino acid usage bias of mycobacterial genes, their functional analysis have been done. Further the evolutionary features of M. avium complex also have been revealed. Mycobacterial genes are moderately GC rich showed higher expression level in PPs and significant negative correlation with biosynthetic cost of proteins. Translational selection pressure was observed in mycobacterial genes. MAC showed close relationship with NPs and higher evolutionary rate in MAC revealed their constant evolving nature.
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Affiliation(s)
- Mousumi Sarkar Saha
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India
| | - Shilpee Pal
- Department of Microbiology, Vidyasagar University, Midnapore 721102, India
| | - Indrani Sarkar
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India
| | - Ayan Roy
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India
| | | | - Arnab Sen
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India.
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Comprehensive profiling of functional attributes, virulence potential and evolutionary dynamics in mycobacterial secretomes. World J Microbiol Biotechnol 2017; 34:5. [DOI: 10.1007/s11274-017-2388-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 11/30/2017] [Indexed: 11/25/2022]
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Sarkar I, Tisa LS, Gtari M, Sen A. Biosynthetic energy cost of potentially highly expressed proteins vary with niche in selected actinobacteria. J Basic Microbiol 2017; 58:154-161. [PMID: 29144540 DOI: 10.1002/jobm.201700350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 10/27/2017] [Accepted: 11/05/2017] [Indexed: 11/08/2022]
Abstract
Amino acid and protein biosynthesis requires a number of high energy phosphate bonds and includes a dual energy cost for the synthesis of chemical intermediates during the fueling reactions and the conversion of precursor molecules to final products. One popular hypothesis is that the proteins encoded by putative highly expressed genes (hence called PHXPs) generally utilize low energy consuming amino acids to reduce the biosynthetic cost of the essential proteins. In our study, we found that this idea was not supported in the case of actinobacteria. With the actinobacteria, the energy costs of PHXPs varied in relation to their niche. Free-living, including aquatic, soil and extremophilic, and plant-associated actinobacteria were found to use energetically expensive amino acids in their PHXPs. An exception occurred with some animal-host-associated actinobacteria that used energy efficient amino acids. One explanation for these results may be due to the diverse metabolic patterns exhibited by actinobacteria under varied niches influenced by nutritional availability and physical environment.
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Affiliation(s)
- Indrani Sarkar
- NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri, India
| | - Louis S Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis Elmanar (FST), Université de Carthage (INSAT), Tunis, Tunisia
| | - Arnab Sen
- NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri, India
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Cornejo-Granados F, Zatarain-Barrón ZL, Cantu-Robles VA, Mendoza-Vargas A, Molina-Romero C, Sánchez F, Del Pozo-Yauner L, Hernández-Pando R, Ochoa-Leyva A. Secretome Prediction of Two M. tuberculosis Clinical Isolates Reveals Their High Antigenic Density and Potential Drug Targets. Front Microbiol 2017; 8:128. [PMID: 28223967 PMCID: PMC5293778 DOI: 10.3389/fmicb.2017.00128] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/18/2017] [Indexed: 12/15/2022] Open
Abstract
The Excreted/Secreted (ES) proteins play important roles during Mycobacterium tuberculosis invasion, virulence, and survival inside the host and they are a major source of immunogenic proteins. However, the molecular complexity of the bacillus cell wall has made difficult the experimental isolation of the total bacterial ES proteins. Here, we reported the genomes of two Beijing genotype M. tuberculosis clinical isolates obtained from patients from Vietnam (isolate 46) and South Africa (isolate 48). We developed a bioinformatics pipeline to predict their secretomes and observed that ~12% of the genome-encoded proteins are ES, being PE, PE-PGRS, and PPE the most abundant protein domains. Additionally, the Gene Ontology, KEGG pathways and Enzyme Classes annotations supported the expected functions for the secretomes. The ~70% of an experimental secretome compiled from literature was contained in our predicted secretomes, while only the 34–41% of the experimental secretome was contained in the two previously reported secretomes for H37Rv. These results suggest that our bioinformatics pipeline is better to predict a more complete set of ES proteins in M. tuberculosis genomes. The predicted ES proteins showed a significant higher antigenic density measured by Abundance of Antigenic Regions (AAR) value than the non-ES proteins and also compared to random constructed secretomes. Additionally, we predicted the secretomes for H37Rv, H37Ra, and two M. bovis BCG genomes. The antigenic density for BGG and for isolates 46 and 48 was higher than the observed for H37Rv and H37Ra secretomes. In addition, two sets of immunogenic proteins previously reported in patients with tuberculosis also showed a high antigenic density. Interestingly, mice infected with isolate 46 showed a significant lower survival rate than the ones infected with isolate 48 and both survival rates were lower than the one previously reported for the H37Rv in the same murine model. Finally, after a druggability analysis of the secretomes, we found potential drug targets such as cytochrome P450, thiol peroxidase, the Ag85C, and Ribonucleoside Reductase in the secreted proteins that could be used as drug targets for novel treatments against Tuberculosis.
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Affiliation(s)
- Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Zyanya L Zatarain-Barrón
- Experimental Pathology Laboratory, Department of Pathology, National Institute of Medical Science and Nutrition "Salvador Zubirán" Mexico City, Mexico
| | - Vito A Cantu-Robles
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | | | | | - Filiberto Sánchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Luis Del Pozo-Yauner
- Laboratorio de Estructura de Proteínas, National Institute of Genomic Medicine Mexico City, Mexico
| | - Rogelio Hernández-Pando
- Experimental Pathology Laboratory, Department of Pathology, National Institute of Medical Science and Nutrition "Salvador Zubirán" Mexico City, Mexico
| | - Adrián Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
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Cui T, He ZG. Improved understanding of pathogenesis from protein interactions inMycobacteriumtuberculosis. Expert Rev Proteomics 2014; 11:745-55. [DOI: 10.1586/14789450.2014.971762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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