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Gulati P, Singh A, Patra S, Bhat S, Verma A. Restriction modification systems in archaea: A panoramic outlook. Heliyon 2024; 10:e27382. [PMID: 38644887 PMCID: PMC11033074 DOI: 10.1016/j.heliyon.2024.e27382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 04/23/2024] Open
Abstract
Restriction modification (RM) systems are one of the ubiquitous yet primitive defense responses employed by bacteria and archaea with the primary role of safeguarding themselves against invading bacteriophages. Protection of the host occurs by the cleavage of the invading foreign DNA via restriction endonucleases with concomitant methylation of host DNA with the aid of a methyltransferase counterpart. RM systems have been extensively studied in bacteria, however, in the case of archaea there are limited reports of RM enzymes that are investigated to date owing to their inhospitable growth demands. This review aims to broaden the knowledge about what is known about the diversity of RM systems in archaea and encapsulate the current knowledge on restriction and modification enzymes characterized in archaea so far and the role of RM systems in the milieu of archaeal biology.
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Affiliation(s)
- Pallavi Gulati
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Ashish Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi 110021, India
| | - Sandeep Patra
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Shreyas Bhat
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Anil Verma
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA-15213, USA
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2
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Vergine M, Vita F, Casati P, Passera A, Ricciardi L, Pavan S, Aprile A, Sabella E, De Bellis L, Luvisi A. Characterization of the olive endophytic community in genotypes displaying a contrasting response to Xylella fastidiosa. BMC PLANT BIOLOGY 2024; 24:337. [PMID: 38664617 PMCID: PMC11044560 DOI: 10.1186/s12870-024-04980-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 04/03/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Endophytes mediate the interactions between plants and other microorganisms, and the functional aspects of interactions between endophytes and their host that support plant-growth promotion and tolerance to stresses signify the ecological relevance of the endosphere microbiome. In this work, we studied the bacterial and fungal endophytic communities of olive tree (Olea europaea L.) asymptomatic or low symptomatic genotypes sampled in groves heavily compromised by Xylella fastidiosa subsp. pauca, aiming to characterize microbiota in genotypes displaying differential response to the pathogen. RESULTS The relationships between bacterial and fungal genera were analyzed both separately and together, in order to investigate the intricate correlations between the identified Operational Taxonomic Units (OTUs). Results suggested a dominant role of the fungal endophytic community compared to the bacterial one, and highlighted specific microbial taxa only associated with asymptomatic or low symptomatic genotypes. In addition, they indicated the occurrence of well-adapted genetic resources surviving after years of pathogen pressure in association with microorganisms such as Burkholderia, Quambalaria, Phaffia and Rhodotorula. CONCLUSIONS This is the first study to overview endophytic communities associated with several putatively resistant olive genotypes in areas under high X. fastidiosa inoculum pressure. Identifying these negatively correlated genera can offer valuable insights into the potential antagonistic microbial resources and their possible development as biocontrol agents.
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Affiliation(s)
- Marzia Vergine
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Federico Vita
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy.
| | - Paola Casati
- Department of Agricultural and Environmental Sciences, Production, Landscape, Agroenergy, University of Milan, Milano, Italy
| | - Alessandro Passera
- Department of Agricultural and Environmental Sciences, Production, Landscape, Agroenergy, University of Milan, Milano, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Bari, Italy
| | - Alessio Aprile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Erika Sabella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Andrea Luvisi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
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Bueno de Mesquita CP, Hartman WH, Ardón M, Tringe SG. Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland. ISME COMMUNICATIONS 2024; 4:ycae040. [PMID: 38628812 PMCID: PMC11020224 DOI: 10.1093/ismeco/ycae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
Seawater intrusion into freshwater wetlands causes changes in microbial communities and biogeochemistry, but the exact mechanisms driving these changes remain unclear. Here we use a manipulative laboratory microcosm experiment, combined with DNA sequencing and biogeochemical measurements, to tease apart the effects of sulfate from other seawater ions. We examined changes in microbial taxonomy and function as well as emissions of carbon dioxide, methane, and nitrous oxide in response to changes in ion concentrations. Greenhouse gas emissions and microbial richness and composition were altered by artificial seawater regardless of whether sulfate was present, whereas sulfate alone did not alter emissions or communities. Surprisingly, addition of sulfate alone did not lead to increases in the abundance of sulfate reducing bacteria or sulfur cycling genes. Similarly, genes involved in carbon, nitrogen, and phosphorus cycling responded more strongly to artificial seawater than to sulfate. These results suggest that other ions present in seawater, not sulfate, drive ecological and biogeochemical responses to seawater intrusion and may be drivers of increased methane emissions in soils that received artificial seawater addition. A better understanding of how the different components of salt water alter microbial community composition and function is necessary to forecast the consequences of coastal wetland salinization.
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Affiliation(s)
- Clifton P Bueno de Mesquita
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Wyatt H Hartman
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Marcelo Ardón
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Susannah G Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
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4
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Gwin CM, Gupta KR, Lu Y, Shao L, Rego EH. Spatial segregation and aging of metabolic processes underlie phenotypic heterogeneity in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569614. [PMID: 38076906 PMCID: PMC10705497 DOI: 10.1101/2023.12.01.569614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Individual cells within clonal populations of mycobacteria vary in size, growth rate, and antibiotic susceptibility. Heterogeneity is, in part, determined by LamA, a protein found exclusively in mycobacteria. LamA localizes to sites of new cell wall synthesis where it recruits proteins important for polar growth and establishing asymmetry. Here, we report that in addition to this function, LamA interacts with complexes involved in oxidative phosphorylation (OXPHOS) at a subcellular location distinct from cell wall synthesis. Importantly, heterogeneity depends on a unique extension of the mycobacterial ATP synthase, and LamA mediates the coupling between ATP production and cell growth in single cells. Strikingly, as single cells age, concentrations of proteins important for oxidative phosphorylation become less abundant, and older cells rely less on oxidative phosphorylation for growth. Together, our data reveal that central metabolism is spatially organized within a single mycobacterium and varies within a genetically identical population of mycobacteria. Designing therapeutic regimens to account for this heterogeneity may help to treat mycobacterial infections faster and more completely.
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Affiliation(s)
- Celena M. Gwin
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Kuldeepkumar R. Gupta
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Yao Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Lin Shao
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - E. Hesper Rego
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
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Malakar B, Chauhan K, Sanyal P, Naz S, Kalam H, Vivek-Ananth RP, Singh LV, Samal A, Kumar D, Nandicoori VK. Phosphorylation of CFP10 modulates Mycobacterium tuberculosis virulence. mBio 2023; 14:e0123223. [PMID: 37791794 PMCID: PMC10653824 DOI: 10.1128/mbio.01232-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/25/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Secreted virulence factors play a critical role in bacterial pathogenesis. Virulence effectors not only help bacteria to overcome the host immune system but also aid in establishing infection. Mtb, which causes tuberculosis in humans, encodes various virulence effectors. Triggers that modulate the secretion of virulence effectors in Mtb are yet to be fully understood. To gain mechanistic insight into the secretion of virulence effectors, we performed high-throughput proteomic studies. With the help of system-level protein-protein interaction network analysis and empirical validations, we unravelled a link between phosphorylation and secretion. Taking the example of the well-known virulence factor of CFP10, we show that the dynamics of CFP10 phosphorylation strongly influenced bacterial virulence and survival ex vivo and in vivo. This study presents the role of phosphorylation in modulating the secretion of virulence factors.
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Affiliation(s)
- Basanti Malakar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Komal Chauhan
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Priyadarshini Sanyal
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Centre for Cellular and Molecular Biology Campus, Hyderabad, India
| | - Saba Naz
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Haroon Kalam
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - R. P. Vivek-Ananth
- The Institute of Mathematical Sciences (IMSc), Homi Bhabha National Institute (HBNI), Chennai, India
| | - Lakshya Veer Singh
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Homi Bhabha National Institute (HBNI), Chennai, India
| | - Dhiraj Kumar
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Vinay Kumar Nandicoori
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Centre for Cellular and Molecular Biology Campus, Hyderabad, India
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6
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Russo CM, Howey KG, O'Reilly MC. Scalable and Chromatography-Free Synthesis of Efflux Pump Inhibitor Phenylalanine Arginine β-Naphthylamide for Its Validation in Wild-Type Bacterial Strains. ChemMedChem 2023; 18:e202300128. [PMID: 37126222 PMCID: PMC10524873 DOI: 10.1002/cmdc.202300128] [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: 03/03/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/02/2023]
Abstract
Phenylalanine arginine β-naphthylamine, or PAβN, is a C-terminus capped dipeptide discovered in 1999 as an RND-type efflux pump inhibitor (EPI). Since then, PAβN has become a standard tool compound in EPI research and development. Despite this, PAβN lacks a detailed or efficient synthesis, and standard parameters for its use in wild-type bacterial strains are inconsistent or non-existent. Therefore, a scalable and chromatography-free synthesis of PAβN was developed using streamlined traditional solution-phase peptide coupling chemistry. With this procedure, gram scale quantities of PAβN were synthesized alongside analogues and stereoisomers to build a focused library to evaluate simple structure activity relationships. While most analogues were less active than the broadly utilized L,L-PAβN itself, we identified that its enantiomer, D,D-PAβN, also provided 8- to 16-fold potentiation of the antibiotic levofloxacin at 40 to 50 μg/mL concentrations of EPI in various wild-type Pseudomonas aeruginosa strains. Additionally, D,D-PAβN was shown to be significantly more hydrolytically stable than L,L-PAβN, indicating that it may be a useful, and now readily synthesized, tool compound facilitating future EPI research.
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Affiliation(s)
| | - Kelsey G Howey
- Department of Chemistry, Villanova University, Villanova, PA 19085, USA
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Lim S. A Review of the Bacterial Phosphoproteomes of Beneficial Microbes. Microorganisms 2023; 11:microorganisms11040931. [PMID: 37110354 PMCID: PMC10145908 DOI: 10.3390/microorganisms11040931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
The number and variety of protein post-translational modifications (PTMs) found and characterized in bacteria over the past ten years have increased dramatically. Compared to eukaryotic proteins, most post-translational protein changes in bacteria affect relatively few proteins because the majority of modified proteins exhibit substoichiometric modification levels, which makes structural and functional analyses challenging. In addition, the number of modified enzymes in bacterial species differs widely, and degrees of proteome modification depend on environmental conditions. Nevertheless, evidence suggests that protein PTMs play essential roles in various cellular processes, including nitrogen metabolism, protein synthesis and turnover, the cell cycle, dormancy, spore germination, sporulation, persistence, and virulence. Additional investigations on protein post-translational changes will undoubtedly close knowledge gaps in bacterial physiology and create new means of treating infectious diseases. Here, we describe the role of the post-translation phosphorylation of major bacterial proteins and review the progress of research on phosphorylated proteins depending on bacterial species.
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Affiliation(s)
- Sooa Lim
- Department of Pharmaceutical Engineering, Hoseo University, Asan-si 31499, Republic of Korea
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8
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Mahreen N, Yasmin S, Asif M, Yahya M, Ejaz K, Mehboob-ur-Rahman, Yousaf S, Amin I, Zulfiqar S, Imran A, Khaliq S, Arif M. Mitigation of water scarcity with sustained growth of Rice by plant growth promoting bacteria. FRONTIERS IN PLANT SCIENCE 2023; 14:1081537. [PMID: 36755700 PMCID: PMC9900138 DOI: 10.3389/fpls.2023.1081537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/02/2023] [Indexed: 11/03/2023]
Abstract
Climate change augments the risk to food security by inducing drought stress and a drastic decline in global rice production. Plant growth-promoting bacteria (PGPB) have been known to improve plant growth under drought stress. Here in the present study, we isolated, identified, and well-characterized eight drought-tolerant bacteria from the rice rhizosphere that are tolerant to 20% PEG-8000. These strains exhibited multiple plant growth-promoting traits, i.e., 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, exopolysaccharide production, phosphate (P)-solubilizing activity (51-356 µg ml-1), indole-3 acetic acid (IAA) production (14.3-46.2 µg ml-1), and production of organic acids (72-178 µg ml-1). Inoculation of bacterial consortium (Bacillus subtilis NM-2, Brucella haematophilum NM-4, and Bacillus cereus NM-6) significantly improved seedling growth and vigor index (1009.2-1100) as compared to non-inoculated stressed plants (630-957). Through rhizoscanning, efficiency of the consortium was validated by improved root parameters such as root length (17%), diameter, and surface area (18%) of all tested genotypes as compared with respective non-inoculated stressed treatments. Furthermore, the response of consortium inoculation on three rice genotypes was positively correlated with improved plant growth and drought stress ameliorating traits by the accumulation of osmoprotectant, i.e., proline (85.8%-122%), relative water content (51%), membrane stability index (64%), and production of antioxidant enzymes to reduce oxidative damage by reactive oxygen species. A decrease in temperature and improved chlorophyll content of inoculated plants were found using infrared thermal imaging and soil plant analyzer development (SPAD), respectively. The key supporting role of inoculation toward stress responses was validated using robust techniques like infrared thermal imaging and an infrared gas analyzer. Furthermore, principal component analysis depicts the contribution of inoculation on stress responses and yield of tested rice genotypes under water stress. The integration of drought-tolerant rice genotype (NIBGE-DT02) and potential bacterial strains, i.e., NM-2, NM-4, and NM-6, can serve as an effective bioinoculant to cope with water scarcity under current alarming issues related to food security in fluctuating climate.
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Affiliation(s)
- Naima Mahreen
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Sumera Yasmin
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Mahreen Yahya
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Khansa Ejaz
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Mehboob-ur-Rahman
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Sumaira Yousaf
- Nuclear Institute for Agriculture and Biology (NIAB) College, Pakistan Institute for Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Sana Zulfiqar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Asma Imran
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Muhammad Arif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
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9
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Phosphoproteomics of Mycobacterium-host interaction and inspirations for novel measures against tuberculosis. Cell Signal 2022; 91:110238. [PMID: 34986388 DOI: 10.1016/j.cellsig.2021.110238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/19/2021] [Accepted: 12/29/2021] [Indexed: 11/23/2022]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (Mtb) remains a tremendous global public health concern. Deciphering the biology of the pathogen and its interaction with host can inspire new measures against tuberculosis. Phosphorylation plays versatile and important role in the pathogen and host physiology, such as virulence, signaling and immune response. Proteome-wide phosphorylation of Mtb and its infected host cells, namely phosphoproteome, can inform the post-translational modification of the interaction network between the pathogen and the host, key targets for novel antibiotics. We summarized the phosphoproteome of Mtb, as well as the host, focusing on potential application for new measures against tuberculosis.
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10
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Qi C, Sun F, Wei Q, Xu J, Li R, Zhang L, Lu F, Jiang X, Fu H, Zhang C, Li L. Quantitative phosphoproteomics reveals the effect of baeSR and acrB genes on protein phosphorylation in Salmonella enterica serovar Typhimurium. Res Microbiol 2021; 173:103886. [PMID: 34715324 DOI: 10.1016/j.resmic.2021.103886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/26/2021] [Accepted: 10/10/2021] [Indexed: 10/20/2022]
Abstract
The BaeSR two-component system and the AcrB efflux pump are closely associated with Salmonella resistance to antibiotics. However, the relationship between the two-component system, efflux pumps and protein phosphorylation of Salmonella is poorly understood. In this study, S. typhimurium ciprofloxacin-resistant strain CR, baeSR gene deletion strain CRΔbaeSR, acrB gene deletion strain CRΔacrB, and double gene deletion strain CRΔbaeSRΔacrB were used to explore phosphorylated proteins with significant difference, based on non-marker, quantitative phosphorylation modified proteomics technique. Consequently, 363 phosphosites of 213 phosphoproteins were identified in the four strains. More than 70% of the phosphosites were serine phosphorylation. In the CRΔbaeSR/CR, CRΔacrB/CR and CRΔbaeSRΔacrB/CR comparison groups, 36, 37 and 49 phosphosites were significantly altered, respectively. Bioinformatic analysis revealed that the main enrichment pathways of these differentially phosphorylated proteins were metabolic pathways, biosynthesis of antibiotics, phosphotransferase system (PTS), ABC transporters, and lipopolysaccharide biosynthesis. Furthermore, 21 differentially phosphorylated proteins were identified to be associated with antibiotic resistance. These results suggest that the BaeSR two-component system and the AcrB efflux pump affect the phosphorylation of proteins in S. typhimurium and may influence the drug resistance and virulence of S. typhimurium by affecting protein phosphorylation, providing a new idea to explore the mechanism of drug resistance in Salmonella.
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Affiliation(s)
- Caili Qi
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Feifei Sun
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China; Anhui Province Key Lab of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China
| | - Qiling Wei
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Jun Xu
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Rui Li
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Lin Zhang
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Fang Lu
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Xidi Jiang
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Hengfeng Fu
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Chunxiao Zhang
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Lin Li
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China; Anhui Province Key Lab of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.
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11
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Yahya M, Islam EU, Rasul M, Farooq I, Mahreen N, Tawab A, Irfan M, Rajput L, Amin I, Yasmin S. Differential Root Exudation and Architecture for Improved Growth of Wheat Mediated by Phosphate Solubilizing Bacteria. Front Microbiol 2021; 12:744094. [PMID: 34721342 PMCID: PMC8554232 DOI: 10.3389/fmicb.2021.744094] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/26/2021] [Indexed: 01/24/2023] Open
Abstract
Phosphorous (P) deficiency is a major challenge faced by global agriculture. Phosphate-solubilizing bacteria (PSB) provide a sustainable approach to supply available phosphates to plants with improved crop productivity through synergistic interaction with plant roots. The present study demonstrates an insight into this synergistic P-solubilizing mechanism of PSB isolated from rhizosphere soils of major wheat-growing agro-ecological zones of Pakistan. Seven isolates were the efficient P solubilizers based on in vitro P-solubilizing activity (233-365 μg ml-1) with a concomitant decrease in pH (up to 3.5) by the production of organic acids, predominantly acetic acid (∼182 μg ml-1) and gluconic acid (∼117 μg ml-1). Amplification and phylogenetic analysis of gcd, pqqE, and phy genes of Enterobacter sp. ZW32, Ochrobactrum sp. SSR, and Pantoea sp. S1 showed the potential of these PSB to release orthophosphate from recalcitrant forms of phosphorus. Principal component analysis indicates the inoculation response of PSB consortia on the differential composition of root exudation (amino acids, sugars, and organic acids) with subsequently modified root architecture of three wheat varieties grown hydroponically. Rhizoscanning showed a significant increase in root parameters, i.e., root tips, diameter, and surface area of PSB-inoculated plants as compared to uninoculated controls. Efficiency of PSB consortia was validated by significant increase in plant P and oxidative stress management under P-deficient conditions. Reactive oxygen species (ROS)-induced oxidative damages mainly indicated by elevated levels of malondialdehyde (MDA) and H2O2 contents were significantly reduced in inoculated plants by the production of antioxidant enzymes, i.e., superoxide dismutase, catalase, and peroxidase. Furthermore, the inoculation response of these PSB on respective wheat varieties grown in native soils under greenhouse conditions was positively correlated with improved plant growth and soil P contents. Additionally, grain yield (8%) and seed P (14%) were significantly increased in inoculated wheat plants with 20% reduced application of diammonium phosphate (DAP) fertilizer under net house conditions. Thus, PSB capable of such synergistic strategies can confer P biofortification in wheat by modulating root morphophysiology and root exudation and can alleviate oxidative stress under P deficit conditions.
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Affiliation(s)
- Mahreen Yahya
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Ejaz ul Islam
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Maria Rasul
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
- Department of Bioindustry and Bioresource Engineering, Sejong University, Seoul, South Korea
| | - Iqra Farooq
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Naima Mahreen
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Abdul Tawab
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Irfan
- Sustainable Agriculture and Food Programme (SAFP), World Wildlife Fund, Khanewal, Pakistan
| | - Lubna Rajput
- Plant Physiology and Biotechnology Agricultural Research Centre, Tandojam, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Sumera Yasmin
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
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12
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Nilkanth VV, Mande SC. Structure-sequence features based prediction of phosphosites of serine/threonine protein kinases of Mycobacterium tuberculosis. Proteins 2021; 90:131-141. [PMID: 34329517 DOI: 10.1002/prot.26195] [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: 03/03/2021] [Revised: 07/11/2021] [Accepted: 07/12/2021] [Indexed: 11/07/2022]
Abstract
Elucidation of signaling events in a pathogen is potentially important to tackle the infection caused by it. Such events mediated by protein phosphorylation play important roles in infection, and therefore, to predict the phosphosites and substrates of the serine/threonine protein kinases, we have developed a Machine learning-based approach for Mycobacterium tuberculosis serine/threonine protein kinases using kinase-peptide structure-sequence data. This approach utilizes features derived from kinase three-dimensional-structure environment and known phosphosite sequences to generate support vector machine (SVM)-based kinase-specific predictions of phosphosites of serine/threonine protein kinases (STPKs) with no or scarce data of their substrates. SVM outperformed the four machine learning algorithms we tried (random forest, logistic regression, SVM, and k-nearest neighbors) with an area under the curve receiver-operating characteristic value of 0.88 on the independent testing dataset and a 10-fold cross-validation accuracy of ~81.6% for the final model. Our predicted phosphosites of M. tuberculosis STPKs form a useful resource for experimental biologists enabling elucidation of STPK mediated posttranslational regulation of important cellular processes.
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Affiliation(s)
- Vipul V Nilkanth
- National Centre for Cell Science, S.P. Pune University Campus, Pune, India
| | - Shekhar C Mande
- Council of Scientific and Industrial Research, New Delhi, India
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13
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Forrest S, Welch M. Arming the troops: Post-translational modification of extracellular bacterial proteins. Sci Prog 2020; 103:36850420964317. [PMID: 33148128 PMCID: PMC10450907 DOI: 10.1177/0036850420964317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein secretion is almost universally employed by bacteria. Some proteins are retained on the cell surface, whereas others are released into the extracellular milieu, often playing a key role in virulence. In this review, we discuss the diverse types and potential functions of post-translational modifications (PTMs) occurring to extracellular bacterial proteins.
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Affiliation(s)
- Suzanne Forrest
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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14
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Bonne Køhler J, Jers C, Senissar M, Shi L, Derouiche A, Mijakovic I. Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis. FEBS Lett 2020; 594:2339-2369. [PMID: 32337704 DOI: 10.1002/1873-3468.13797] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation regulates a large variety of biological processes in all living cells. In pathogenic bacteria, the study of serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation has shed light on the course of infectious diseases, from adherence to host cells to pathogen virulence, replication, and persistence. Mass spectrometry (MS)-based phosphoproteomics has provided global maps of Ser/Thr/Tyr phosphosites in bacterial pathogens. Despite recent developments, a quantitative and dynamic view of phosphorylation events that occur during bacterial pathogenesis is currently lacking. Temporal, spatial, and subpopulation resolution of phosphorylation data is required to identify key regulatory nodes underlying bacterial pathogenesis. Herein, we discuss how technological improvements in sample handling, MS instrumentation, data processing, and machine learning should improve bacterial phosphoproteomic datasets and the information extracted from them. Such information is expected to significantly extend the current knowledge of Ser/Thr/Tyr phosphorylation in pathogenic bacteria and should ultimately contribute to the design of novel strategies to combat bacterial infections.
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Affiliation(s)
- Julie Bonne Køhler
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mériem Senissar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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15
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Le NH, Locard-Paulet M, Stella A, Tomas N, Molle V, Burlet-Schiltz O, Daffé M, Marrakchi H. The protein kinase PknB negatively regulates biosynthesis and trafficking of mycolic acids in mycobacteria. J Lipid Res 2020; 61:1180-1191. [PMID: 32487543 DOI: 10.1194/jlr.ra120000747] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis and remains one of the most widespread and deadliest bacterial pathogens in the world. A distinguishing feature of mycobacteria that sets them apart from other bacteria is the unique architecture of their cell wall, characterized by various species-specific lipids, most notably mycolic acids (MAs). Therefore, targeted inhibition of enzymes involved in MA biosynthesis, transport, and assembly has been extensively explored in drug discovery. Additionally, more recent evidence suggests that many enzymes in the MA biosynthesis pathway are regulated by kinase-mediated phosphorylation, thus opening additional drug-development opportunities. However, how phosphorylation regulates MA production remains unclear. Here, we used genetic strategies combined with lipidomics and phosphoproteomics approaches to investigate the role of protein phosphorylation in Mycobacterium The results of this analysis revealed that the Ser/Thr protein kinase PknB regulates the export of MAs and promotes the remodeling of the mycobacterial cell envelope. In particular, we identified the essential MmpL3 as a substrate negatively regulated by PknB. Taken together, our findings add to the understanding of how PknB activity affects the mycobacterial MA biosynthesis pathway and reveal the essential role of protein phosphorylation/dephosphorylation in governing lipid metabolism, paving the way for novel antimycobacterial strategies.
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Affiliation(s)
- Nguyen-Hung Le
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie Locard-Paulet
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Alexandre Stella
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nicolas Tomas
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Virginie Molle
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université de Montpellier, CNRS, UMR 5235, Montpellier, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Mamadou Daffé
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Hedia Marrakchi
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
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16
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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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17
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Baros SS, Blackburn JM, Soares NC. Phosphoproteomic Approaches to Discover Novel Substrates of Mycobacterial Ser/Thr Protein Kinases. Mol Cell Proteomics 2020; 19:233-244. [PMID: 31839597 PMCID: PMC7000118 DOI: 10.1074/mcp.r119.001668] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Mycobacterial Ser/Thr protein kinases (STPKs) play a critical role in signal transduction pathways that ultimately determine mycobacterial growth and metabolic adaptation. Identification of key physiological substrates of these protein kinases is, therefore, crucial to better understand how Ser/Thr phosphorylation contributes to mycobacterial environmental adaptation, including response to stress, cell division, and host-pathogen interactions. Various substrate detection methods have been employed with limited success, with direct targets of STPKs remaining elusive. Recently developed mass spectrometry (MS)-based phosphoproteomic approaches have expanded the list of potential STPK substrate identifications, yet further investigation is required to define the most functionally significant phosphosites and their physiological importance. Prior to the application of MS workflows, for instance, GarA was the only known and validated physiological substrate for protein kinase G (PknG) from pathogenic mycobacteria. A subsequent list of at least 28 candidate PknG substrates has since been reported with the use of MS-based analyses. Herein, we integrate and critically review MS-generated datasets available on novel STPK substrates and report new functional and subcellular localization enrichment analyses on novel candidate protein kinase A (PknA), protein kinase B (PknB) and PknG substrates to deduce the possible physiological roles of these kinases. In addition, we assess substrate specificity patterns across different mycobacterial STPKs by analyzing reported sets of phosphopeptides, in order to determine whether novel motifs or consensus regions exist for mycobacterial Ser/Thr phosphorylation sites. This review focuses on MS-based techniques employed for STPK substrate identification in mycobacteria, while highlighting the advantages and challenges of the various applications.
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Affiliation(s)
- Seanantha S Baros
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa; Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.
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18
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Li KK, Qu DH, Zhang HN, Chen FY, Xu L, Wang MY, Su HY, Tao SC, Wu FL. Global discovery the PstP interactions using Mtb proteome microarray and revealing novel connections with EthR. J Proteomics 2020; 215:103650. [PMID: 31958639 DOI: 10.1016/j.jprot.2020.103650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/08/2020] [Accepted: 01/16/2020] [Indexed: 10/25/2022]
Abstract
Mycobacterium tuberculosis (Mtb) serine/threonine protein phosphatase PstP plays an important role in regulating Mtb cell division and growth by reversible phosphorylation signaling. However, the substrates of Mtb with which the PstP interacts, and the underlying molecular mechanisms are still largely unknown. In this study, we performed an Mtb proteome microarray to globally identify the PstP bindings. In this way, we discovered 78 interactors between PstP and Mtb proteins, and found a novel connections with EthR. The interaction between PstP and EthR has been validated by Bio-Layer interferometry and Yeast-two-hybrid. And functional studies showed that PstP significantly enhances the binding between EthR and related DNA domain through its interaction with EthR. Phenotypically, overexpression of PstP promoted the resistance of Mycobacterium smegmatis with the antibiotic of ethionamide. Overall, we hopefully wish that the PstP interactors identified in this study will serve as a useful resource for further systematic studies of the roles that PstP plays in the regulation of Mtb dephosphorylation. SIGNIFICANCE: Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, which is responsible of ~1.5 million death per year. Understanding the knowledge about the basic biological regulation pathways in Mtb is an effective approach to discover the novel drug targets for cure TB. PstP is a serine/threonine protein phosphatase in Mtb, and plays important roles in regulating Mtb cell division and growth by reversible phosphorylation signaling. In this study, we identified 78 PstP interacting Mtb proteins using Mtb proteome microarray, which could preliminarily explain the roles of PstP played in Mtb. Moreover, functional analysis showed that a novel transcription factor EthR had been found regulated by PstP through binding, which could enhance the resistance to the antibiotic ETH. Overall, this network constructed with PstP-Mtb proteins could serve as a valuable resource for studying Mtb growth.
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Affiliation(s)
- Ke-Ke Li
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai 264025, China
| | - De-Hui Qu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Hai-Nan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Fei-Yan Chen
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai 264025, China
| | - Lei Xu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai 264025, China
| | - Meng-Yun Wang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai 264025, China
| | - Hong-Yan Su
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai 264025, China
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Fan-Lin Wu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai 264025, China.
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19
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Bellinzoni M, Wehenkel AM, Durán R, Alzari PM. Novel mechanistic insights into physiological signaling pathways mediated by mycobacterial Ser/Thr protein kinases. Microbes Infect 2019; 21:222-229. [PMID: 31254628 DOI: 10.1016/j.micinf.2019.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022]
Abstract
Protein phosphorylation is known to be one of the keystones of signal sensing and transduction in all living organisms. Once thought to be essentially confined to the eukaryotic kingdoms, reversible phosphorylation on serine, threonine and tyrosine residues, has now been shown to play a major role in many prokaryotes, where the number of Ser/Thr protein kinases (STPKs) equals or even exceeds that of two component systems. Mycobacterium tuberculosis, the etiological agent of tuberculosis, is one of the most studied organisms for the role of STPK-mediated signaling in bacteria. Driven by the interest and tractability of these enzymes as potential therapeutic targets, extensive studies revealed the remarkable conservation of protein kinases and their cognate phosphatases across evolution, and their involvement in bacterial physiology and virulence. Here, we present an overview of the current knowledge of mycobacterial STPKs structures and kinase activation mechanisms, and we then focus on PknB and PknG, two well-characterized STPKs that are essential for the intracellular survival of the bacillus. We summarize the mechanistic evidence that links PknB to the regulation of peptidoglycan synthesis in cell division and morphogenesis, and the major findings that establishes PknG as a master regulator of central carbon and nitrogen metabolism. Two decades after the discovery of STPKs in M. tuberculosis, the emerging landscape of O-phosphosignaling is starting to unveil how eukaryotic-like kinases can be engaged in unique, non-eukaryotic-like, signaling mechanisms in mycobacteria.
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Affiliation(s)
- Marco Bellinzoni
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Anne Marie Wehenkel
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Mataojo 2020, Montevideo 11400, Uruguay
| | - Pedro M Alzari
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France.
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20
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Bellinzoni M, Wehenkel AM, Durán R, Alzari PM. Novel mechanistic insights into physiological signaling pathways mediated by mycobacterial Ser/Thr protein kinases. Genes Immun 2019; 20:383-393. [DOI: 10.1038/s41435-019-0069-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
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21
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Kaur P, Rausch M, Malakar B, Watson U, Damle NP, Chawla Y, Srinivasan S, Sharma K, Schneider T, Jhingan GD, Saini D, Mohanty D, Grein F, Nandicoori VK. LipidII interaction with specific residues of Mycobacterium tuberculosis PknB extracytoplasmic domain governs its optimal activation. Nat Commun 2019; 10:1231. [PMID: 30874556 PMCID: PMC6428115 DOI: 10.1038/s41467-019-09223-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 02/28/2019] [Indexed: 02/08/2023] Open
Abstract
The Mycobacterium tuberculosis kinase PknB is essential for growth and survival of the pathogen in vitro and in vivo. Here we report the results of our efforts to elucidate the mechanism of regulation of PknB activity. The specific residues in the PknB extracytoplasmic domain that are essential for ligand interaction and survival of the bacterium are identified. The extracytoplasmic domain interacts with mDAP-containing LipidII, and this is abolished upon mutation of the ligand-interacting residues. Abrogation of ligand-binding or sequestration of the ligand leads to aberrant localization of PknB. Contrary to the prevailing hypothesis, abrogation of ligand-binding is linked to activation loop hyperphosphorylation, and indiscriminate hyperphosphorylation of PknB substrates as well as other proteins, ultimately causing loss of homeostasis and cell death. We propose that the ligand-kinase interaction directs the appropriate localization of the kinase, coupled to stringently controlled activation of PknB, and consequently the downstream processes thereof. The Mycobacterium tuberculosis kinase PknB regulates essential cell functions via interactions with muropeptides. Here the authors identify interaction sites in the extracytoplasmic PASTA domain and show that abrogation of ligand binding leads to a hyper-activated kinase, causing loss of homeostasis and cell death.
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Affiliation(s)
- Prabhjot Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Marvin Rausch
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, 53105, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, 53105, Germany
| | - Basanti Malakar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Uchenna Watson
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, 560012, India
| | - Nikhil P Damle
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,BIOSS, Center for Biological Signaling Studies, University of Freiburg, Freiburg, 79104, Germany
| | - Yogesh Chawla
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,Department of Microbiology and Immunology, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Sandhya Srinivasan
- Vproteomics, Valerian Chem Private Limited, Green Park Main, New Delhi, 110016, India
| | - Kanika Sharma
- Vproteomics, Valerian Chem Private Limited, Green Park Main, New Delhi, 110016, India
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, 53105, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, 53105, Germany
| | - Gagan Deep Jhingan
- Vproteomics, Valerian Chem Private Limited, Green Park Main, New Delhi, 110016, India
| | - Deepak Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, 560012, India
| | - Debasisa Mohanty
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Fabian Grein
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, 53105, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, 53105, Germany
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22
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New substrates and interactors of the mycobacterial Serine/Threonine protein kinase PknG identified by a tailored interactomic approach. J Proteomics 2019; 192:321-333. [DOI: 10.1016/j.jprot.2018.09.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/27/2018] [Accepted: 09/25/2018] [Indexed: 11/18/2022]
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23
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Singh A, Vijayan M, Nagaraju G. RecG wed : A probable novel regulator in the resolution of branched DNA structures in mycobacteria. IUBMB Life 2018; 70:786-794. [PMID: 30240108 DOI: 10.1002/iub.1881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 01/31/2023]
Abstract
Structure-specific helicases, such as RecG, play an important role in the resolution of recombination intermediates. A bioinformatic analysis of mycobacterial genomes led to the identification of a protein (RecGwed ) with a C-terminal "edge" domain, similar to the wedge domain of RecG. RecGwed is predominately found in the phylum Actinobacteria and in few human pathogens. Mycobacterium smegmatis RecGwed was able to bind branched DNA structures in vitro but failed to interact with single- or double-stranded DNA. The expression of recGwed in M. smegmatis cells was up-regulated during stationary phase/UV damage and down-regulated during MMS/H2 O2 treatment. These observations indicate the possible involvement of RecGwed in transactions during recombination events, that proceed though branched DNA intermediates. © 2018 IUBMB Life, 70(8):786-794, 2018.
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Affiliation(s)
- Amandeep Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
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24
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Khan MZ, Kaur P, Nandicoori VK. Targeting the messengers: Serine/threonine protein kinases as potential targets for antimycobacterial drug development. IUBMB Life 2018; 70:889-904. [DOI: 10.1002/iub.1871] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 04/22/2018] [Indexed: 02/03/2023]
Affiliation(s)
- Mehak Zahoor Khan
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi India
| | - Prabhjot Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi India
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25
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Jain P, Malakar B, Khan MZ, Lochab S, Singh A, Nandicoori VK. Delineating FtsQ-mediated regulation of cell division in Mycobacterium tuberculosis. J Biol Chem 2018; 293:12331-12349. [PMID: 29903917 DOI: 10.1074/jbc.ra118.003628] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/31/2018] [Indexed: 11/06/2022] Open
Abstract
Identifying and characterizing the individual contributors to bacterial cellular elongation and division will improve our understanding of their impact on cell growth and division. Here, we delineated the role of ftsQ, a terminal gene of the highly conserved division cell wall (dcw) operon, in growth, survival, and cell length maintenance in the human pathogen Mycobacterium tuberculosis (Mtb). We found that FtsQ overexpression significantly increases the cell length and number of multiseptate cells. FtsQ depletion in Mtb resulted in cells that were shorter than WT cells during the initial growth stages (4 days after FtsQ depletion) but were longer than WT cells at later stages (10 days after FtsQ depletion) and compromised the survival in vitro and in differentiated THP1 macrophages. Overexpression of N- and C-terminal FtsQ regions altered the cell length, and the C-terminal domain alone complemented the FtsQ depletion phenotype. MS analyses suggested robust FtsQ phosphorylation on Thr-24, and although phosphoablative and -mimetic mutants rescued the FtsQ depletion-associated cell viability defects, they failed to complement the cell length defects. MS and coimmunoprecipitation experiments identified 63 FtsQ-interacting partners, and we show that the interaction of FtsQ with the recently identified cell division protein SepIVA is independent of FtsQ phosphorylation and suggests a role of FtsQ in modulating cell division. FtsQ exhibited predominantly septal localization in both the presence and absence of SepIVA. Our results suggest a role for FtsQ in modulating the length, division, and survival of Mtb cells both in vitro and in the host.
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Affiliation(s)
- Preeti Jain
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Basanti Malakar
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Mehak Zahoor Khan
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Savita Lochab
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Archana Singh
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi 110025, India
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Biophysical Characterization of the Tandem FHA Domain Regulatory Module from the Mycobacterium tuberculosis ABC Transporter Rv1747. Structure 2018; 26:972-986.e6. [PMID: 29861345 DOI: 10.1016/j.str.2018.04.018] [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: 02/09/2018] [Revised: 04/13/2018] [Accepted: 04/27/2018] [Indexed: 11/23/2022]
Abstract
The Mycobacterium tuberculosis ATP-binding cassette transporter Rv1747 is a putative exporter of cell wall biosynthesis intermediates. Rv1747 has a cytoplasmic regulatory module consisting of two pThr-interacting Forkhead-associated (FHA) domains connected by a conformationally disordered linker with two phospho-acceptor threonines (pThr). The structures of FHA-1 and FHA-2 were determined by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, respectively. Relative to the canonical 11-strand β-sandwich FHA domain fold of FHA-1, FHA-2 is circularly permuted and lacking one β-strand. Nevertheless, the two share a conserved pThr-binding cleft. FHA-2 is less stable and more dynamic than FHA-1, yet binds model pThr peptides with moderately higher affinity (∼50 μM versus 500 μM equilibrium dissociation constants). Based on NMR relaxation and chemical shift perturbation measurements, when joined within a polypeptide chain, either FHA domain can bind either linker pThr to form intra- and intermolecular complexes. We hypothesize that this enables tunable phosphorylation-dependent multimerization to regulate Rv1747 transporter activity.
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27
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Global proteome and phosphoproteome dynamics indicate novel mechanisms of vitamin C induced dormancy in Mycobacterium smegmatis. J Proteomics 2018; 180:1-10. [DOI: 10.1016/j.jprot.2017.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/20/2017] [Accepted: 10/10/2017] [Indexed: 01/30/2023]
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28
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Santander RD, Figàs‐Segura À, Biosca EG. Erwinia amylovora catalases KatA and KatG are virulence factors and delay the starvation-induced viable but non-culturable (VBNC) response. MOLECULAR PLANT PATHOLOGY 2018; 19:922-934. [PMID: 28675630 PMCID: PMC6638134 DOI: 10.1111/mpp.12577] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/27/2017] [Accepted: 06/30/2017] [Indexed: 05/18/2023]
Abstract
The life cycle of the plant pathogen Erwinia amylovora comprises periods inside and outside the host in which it faces oxidative stress caused by hydrogen peroxide (H2 O2 ) and other compounds. The sources of this stress are plant defences, other microorganisms and/or exposure to starvation or other environmental challenges. However, the functional roles of H2 O2 -neutralizing enzymes, such as catalases, during plant-pathogen interactions and/or under starvation conditions in phytopathogens of the family Erwiniaceae or closely related families have not yet been investigated. In this work, the contribution of E. amylovora catalases KatA and KatG to virulence and survival in non-host environments was determined using catalase gene mutants and expression, as well as catalase activity analyses. The participation of E. amylovora exopolysaccharides (EPSs) in oxidative stress protection was also investigated. Our study revealed the following: (i) a different growth phase regulation of each catalase, with an induction by H2 O2 and host tissues; (ii) the significant role of E. amylovora catalases as virulence and survival factors during plant-pathogen interactions; (iii) the induction of EPSs by H2 O2 despite the fact that apparently they do not contribute to protection against this compound; and (iv) the participation of both catalases in the detoxification of the starvation-induced intracellular oxidative stress, favouring the maintenance of culturability, and hence delaying the development of the viable but non-culturable (VBNC) response.
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Affiliation(s)
- Ricardo D. Santander
- Departmento de Microbiología y EcologíaUniversitat de ValènciaBurjassotValència 46100Spain
| | - Àngela Figàs‐Segura
- Departmento de Microbiología y EcologíaUniversitat de ValènciaBurjassotValència 46100Spain
| | - Elena G. Biosca
- Departmento de Microbiología y EcologíaUniversitat de ValènciaBurjassotValència 46100Spain
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29
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Nakedi KC, Calder B, Banerjee M, Giddey A, Nel AJM, Garnett S, Blackburn JM, Soares NC. Identification of Novel Physiological Substrates of Mycobacterium bovis BCG Protein Kinase G (PknG) by Label-free Quantitative Phosphoproteomics. Mol Cell Proteomics 2018; 17:1365-1377. [PMID: 29549130 PMCID: PMC6030727 DOI: 10.1074/mcp.ra118.000705] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 01/09/2023] Open
Abstract
Mycobacterial Ser/Thr kinases play a critical role in bacterial physiology and pathogenesis. Linking kinases to the substrates they phosphorylate in vivo, thereby elucidating their exact functions, is still a challenge. The aim of this work was to associate protein phosphorylation in mycobacteria with important subsequent macro cellular events by identifying the physiological substrates of PknG in Mycobacterium bovis BCG. The study compared the phosphoproteome dynamics during the batch growth of M. bovis BCG versus the respective PknG knock-out mutant (ΔPknG-BCG) strains. We employed TiO2 phosphopeptide enrichment techniques combined with label-free quantitative phosphoproteomics workflow on LC-MS/MS. The comprehensive analysis of label-free data identified 603 phosphopeptides on 307 phosphoproteins with high confidence. Fifty-five phosphopeptides were differentially phosphorylated, of these, 23 phosphopeptides were phosphorylated in M. bovis BCG wild-type only and not in the mutant. These were further validated through targeted mass spectrometry assays (PRMs). Kinase-peptide docking studies based on a published crystal structure of PknG in complex with GarA revealed that the majority of identified phosphosites presented docking scores close to that seen in previously described PknG substrates, GarA, and ribosomal protein L13. Six out of the 22 phosphoproteins had higher docking scores than GarA, consistent with the proteins identified here being true PknG substrates. Based on protein functional analysis of the PknG substrates identified, this study confirms that PknG plays an important regulatory role in mycobacterial metabolism, through phosphorylation of ATP binding proteins and enzymes in the TCA cycle. This work also reinforces PknG's regulation of protein translation and folding machinery.
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Affiliation(s)
- Kehilwe C Nakedi
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Bridget Calder
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Mousumi Banerjee
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Alexander Giddey
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Andrew J M Nel
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Shaun Garnett
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Jonathan M Blackburn
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa.,§Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nelson C Soares
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa;
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30
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Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface. mBio 2018; 9:mBio.02333-17. [PMID: 29511081 PMCID: PMC5845002 DOI: 10.1128/mbio.02333-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis is the leading killer among infectious diseases worldwide. Increasing multidrug resistance has prompted new approaches for tuberculosis drug development, including targeted inhibition of virulence determinants and of signaling cascades that control many downstream pathways. We used a multisystem approach to determine the effects of a potent small-molecule inhibitor of the essential Mycobacterium tuberculosis Ser/Thr protein kinases PknA and PknB. We observed differential levels of phosphorylation of many proteins and extensive changes in levels of gene expression, protein abundance, cell wall lipids, and intracellular metabolites. The patterns of these changes indicate regulation by PknA and PknB of several pathways required for cell growth, including ATP synthesis, DNA synthesis, and translation. These data also highlight effects on pathways for remodeling of the mycobacterial cell envelope via control of peptidoglycan turnover, lipid content, a SigE-mediated envelope stress response, transmembrane transport systems, and protein secretion systems. Integrated analysis of phosphoproteins, transcripts, proteins, and lipids identified an unexpected pathway whereby threonine phosphorylation of the essential response regulator MtrA decreases its DNA binding activity. Inhibition of this phosphorylation is linked to decreased expression of genes for peptidoglycan turnover, and of genes for mycolyl transferases, with concomitant changes in mycolates and glycolipids in the cell envelope. These findings reveal novel roles for PknA and PknB in regulating multiple essential cell functions and confirm that these kinases are potentially valuable targets for new antituberculosis drugs. In addition, the data from these linked multisystems provide a valuable resource for future targeted investigations into the pathways regulated by these kinases in the M. tuberculosis cell. Tuberculosis is the leading killer among infectious diseases worldwide. Increasing drug resistance threatens efforts to control this epidemic; thus, new antitubercular drugs are urgently needed. We performed an integrated, multisystem analysis of Mycobacterium tuberculosis responses to inhibition of its two essential serine/threonine protein kinases. These kinases allow the bacterium to adapt to its environment by phosphorylating cellular proteins in response to extracellular signals. We identified differentially phosphorylated proteins, downstream changes in levels of specific mRNA and protein abundance, and alterations in the metabolite and lipid content of the cell. These results include changes previously linked to growth arrest and also reveal new roles for these kinases in regulating essential processes, including growth, stress responses, transport of proteins and other molecules, and the structure of the mycobacterial cell envelope. Our multisystem data identify PknA and PknB as promising targets for drug development and provide a valuable resource for future investigation of their functions.
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31
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Banaei-Esfahani A, Nicod C, Aebersold R, Collins BC. Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis. Curr Opin Microbiol 2017; 39:64-72. [PMID: 29032348 DOI: 10.1016/j.mib.2017.09.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/15/2017] [Accepted: 09/26/2017] [Indexed: 12/13/2022]
Abstract
Significant developments and improvements in basic and clinical research notwithstanding, infectious diseases still claim at least 13 million lives annually. Classical research approaches have deciphered many molecular mechanisms underlying infection. Today it is increasingly recognized that multiple molecular mechanisms cooperate to constitute a complex system that is used by a given pathogen to interfere with the biochemical processes of the host. Therefore, systems-level approaches now complement the standard molecular biology techniques to investigate pathogens and their interactions with the human host. Here we review omic studies in Mycobacterium tuberculosis, the causative agent of tuberculosis, with a particular focus on proteomic methods and their application to the bacilli. Likewise, the discussed methods are directly portable to other bacterial pathogens.
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Affiliation(s)
- Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Charlotte Nicod
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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32
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Birhanu AG, Yimer SA, Holm-Hansen C, Norheim G, Aseffa A, Abebe M, Tønjum T. N ε- and O-Acetylation in Mycobacterium tuberculosis Lineage 7 and Lineage 4 Strains: Proteins Involved in Bioenergetics, Virulence, and Antimicrobial Resistance Are Acetylated. J Proteome Res 2017; 16:4045-4059. [PMID: 28920697 DOI: 10.1021/acs.jproteome.7b00429] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Increasing evidence demonstrates that lysine acetylation is involved in Mycobacterium tuberculosis (Mtb) virulence and pathogenesis. However, previous investigations in Mtb have only monitored acetylation at lysine residues using selected reference strains. We analyzed the global Nε- and O-acetylation of three Mtb isolates: two lineage 7 clinical isolates and the lineage 4 H37Rv reference strain. Quantitative acetylome analysis resulted in identification of 2490 class-I acetylation sites, 2349 O-acetylation and 141 Nε-acetylation sites, derived from 953 unique proteins. Mtb O-acetylation was thereby significantly more abundant than Nε-acetylation. The acetylated proteins were found to be involved in central metabolism, translation, stress responses, and antimicrobial drug resistance. Notably, 261 acetylation sites on 165 proteins were differentially regulated between lineage 7 and lineage 4 strains. A total of 257 acetylation sites on 161 proteins were hypoacetylated in lineage 7 strains. These proteins are involved in Mtb growth, virulence, bioenergetics, host-pathogen interactions, and stress responses. This study provides the first global analysis of O-acetylated proteins in Mtb. This quantitative acetylome data expand the current understanding regarding the nature and diversity of acetylated proteins in Mtb and open a new avenue of research for exploring the role of protein acetylation in Mtb physiology.
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Affiliation(s)
- Alemayehu Godana Birhanu
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Addis Ababa University , Institute of Biotechnology, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Solomon Abebe Yimer
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
| | - Carol Holm-Hansen
- Infection Control and Environmental Health, Norwegian Institute of Public Health , P.O. Box 4404, Nydalen, NO-0403 Oslo, Norway
| | - Gunnstein Norheim
- Infection Control and Environmental Health, Norwegian Institute of Public Health , P.O. Box 4404, Nydalen, NO-0403 Oslo, Norway
| | - Abraham Aseffa
- Armauer Hansen Research Institute , Jimma Road, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Markos Abebe
- Armauer Hansen Research Institute , Jimma Road, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Tone Tønjum
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
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33
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Verma R, Pinto SM, Patil AH, Advani J, Subba P, Kumar M, Sharma J, Dey G, Ravikumar R, Buggi S, Satishchandra P, Sharma K, Suar M, Tripathy SP, Chauhan DS, Gowda H, Pandey A, Gandotra S, Prasad TSK. Quantitative Proteomic and Phosphoproteomic Analysis of H37Ra and H37Rv Strains of Mycobacterium tuberculosis. J Proteome Res 2017; 16:1632-1645. [DOI: 10.1021/acs.jproteome.6b00983] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- School
of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Sneha Maria Pinto
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
| | - Arun Hanumana Patil
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- School
of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Pratigya Subba
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | | | - Shashidhar Buggi
- Intermediate
Reference Laboratory, State Tuberculosis Training and Demonstration Centre, Someshwaranagar, SDSTRC and RGICD Campus, Bangalore 560029, India
- Department
of Cardio Thoracic Surgery, Super Specialty State Referral Hospital for Chest Diseases, Someshwaranagar First Main Road, Dharmaram College
Post, Bangalore 560029, India
| | | | - Kusum Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Mrutyunjay Suar
- School
of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Srikanth Prasad Tripathy
- National Institute
for Research in Tuberculosis (Indian Council of Medical Research), Chennai 600031, India
| | - Devendra Singh Chauhan
- Department of Microbiology, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (Indian Council of Medical Research), Agra 282004, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sheetal Gandotra
- CSIR-Institute of Genomics & Integrative Biology, SukhdevVihar, New Delhi 110020, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
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34
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Bastos PAD, da Costa JP, Vitorino R. A glimpse into the modulation of post-translational modifications of human-colonizing bacteria. J Proteomics 2016; 152:254-275. [PMID: 27888141 DOI: 10.1016/j.jprot.2016.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/22/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022]
Abstract
Protein post-translational modifications (PTMs) are a key bacterial feature that holds the capability to modulate protein function and responses to environmental cues. Until recently, their role in the regulation of prokaryotic systems has been largely neglected. However, the latest developments in mass spectrometry-based proteomics have allowed an unparalleled identification and quantification of proteins and peptides that undergo PTMs in bacteria, including in species which directly or indirectly affect human health. Herein, we address this issue by carrying out the largest and most comprehensive global pooling and comparison of PTM peptides and proteins from bacterial species performed to date. Data was collected from 91 studies relating to PTM bacterial peptides or proteins identified by mass spectrometry-based methods. The present analysis revealed that there was a considerable overlap between PTMs across species, especially between acetylation and other PTMs, particularly succinylation. Phylogenetically closer species may present more overlapping phosphoproteomes, but environmental triggers also contribute to this proximity. PTMs among bacteria were found to be extremely versatile and diverse, meaning that the same protein may undergo a wide variety of different modifications across several species, but it could also suffer different modifications within the same species.
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Affiliation(s)
- Paulo André Dias Bastos
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Chemistry, University of Aveiro, Portugal
| | | | - Rui Vitorino
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal.
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35
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Sharma AK, Arora D, Singh LK, Gangwal A, Sajid A, Molle V, Singh Y, Nandicoori VK. Serine/Threonine Protein Phosphatase PstP of Mycobacterium tuberculosis Is Necessary for Accurate Cell Division and Survival of Pathogen. J Biol Chem 2016; 291:24215-24230. [PMID: 27758870 DOI: 10.1074/jbc.m116.754531] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 02/06/2023] Open
Abstract
Protein phosphatases play vital roles in phosphorylation-mediated cellular signaling. Although there are 11 serine/threonine protein kinases in Mycobacterium tuberculosis, only one serine/threonine phosphatase, PstP, has been identified. Although PstP has been biochemically characterized and multiple in vitro substrates have been identified, its physiological role has not yet been elucidated. In this study, we have investigated the impact of PstP on cell growth and survival of the pathogen in the host. Overexpression of PstP led to elongated cells and partially compromised survival. We find that depletion of PstP is detrimental to cell survival, eventually leading to cell death. PstP depletion results in elongated multiseptate cells, suggesting a role for PstP in regulating cell division events. Complementation experiments performed with PstP deletion mutants revealed marginally compromised survival, suggesting that all of the domains, including the extracellular domain, are necessary for complete rescue. On the other hand, the catalytic activity of PstP is absolutely essential for the in vitro growth. Mice infection experiments establish a definitive role for PstP in pathogen survival within the host. Depletion of PstP from established infections causes pathogen clearance, indicating that the continued presence of PstP is necessary for pathogen survival. Taken together, our data suggest an important role for PstP in establishing and maintaining infection, possibly via the modulation of cell division events.
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Affiliation(s)
- Aditya K Sharma
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India.,the Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Delhi-110025, India
| | - Divya Arora
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Lalit K Singh
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Aakriti Gangwal
- the Department of Zoology, University of Delhi Delhi-110007, India
| | - Andaleeb Sajid
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Virginie Molle
- the Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université Montpellier 2, CNRS, UMR 5235, Montpellier, France, and
| | - Yogendra Singh
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India, .,the Department of Zoology, University of Delhi Delhi-110007, India
| | - Vinay Kumar Nandicoori
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India,
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36
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Le NH, Molle V, Eynard N, Miras M, Stella A, Bardou F, Galandrin S, Guillet V, André-Leroux G, Bellinzoni M, Alzari P, Mourey L, Burlet-Schiltz O, Daffé M, Marrakchi H. Ser/Thr Phosphorylation Regulates the Fatty Acyl-AMP Ligase Activity of FadD32, an Essential Enzyme in Mycolic Acid Biosynthesis. J Biol Chem 2016; 291:22793-22805. [PMID: 27590338 DOI: 10.1074/jbc.m116.748053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
Mycolic acids are essential components of the mycobacterial cell envelope, and their biosynthetic pathway is a well known source of antituberculous drug targets. Among the promising new targets in the pathway, FadD32 is an essential enzyme required for the activation of the long meromycolic chain of mycolic acids and is essential for mycobacterial growth. Following the in-depth biochemical, biophysical, and structural characterization of FadD32, we investigated its putative regulation via post-translational modifications. Comparison of the fatty acyl-AMP ligase activity between phosphorylated and dephosphorylated FadD32 isoforms showed that the native protein is phosphorylated by serine/threonine protein kinases and that this phosphorylation induced a significant loss of activity. Mass spectrometry analysis of the native protein confirmed the post-translational modifications and identified Thr-552 as the phosphosite. Phosphoablative and phosphomimetic FadD32 mutant proteins confirmed both the position and the importance of the modification and its correlation with the negative regulation of FadD32 activity. Investigation of the mycolic acid condensation reaction catalyzed by Pks13, involving FadD32 as a partner, showed that FadD32 phosphorylation also impacts the condensation activity. Altogether, our results bring to light FadD32 phosphorylation by serine/threonine protein kinases and its correlation with the enzyme-negative regulation, thus shedding a new horizon on the mycolic acid biosynthesis modulation and possible inhibition strategies for this promising drug target.
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Affiliation(s)
- Nguyen-Hung Le
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Virginie Molle
- the Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université de Montpellier, CNRS UMR 5235, Place Eugène Bataillon, 34095 Montpellier Cedex 05, and
| | - Nathalie Eynard
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Mathieu Miras
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Alexandre Stella
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Fabienne Bardou
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Ségolène Galandrin
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Valérie Guillet
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Gwenaëlle André-Leroux
- the Institut Pasteur, Unité de Microbiologie Structurale, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marco Bellinzoni
- the Institut Pasteur, Unité de Microbiologie Structurale, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Pedro Alzari
- the Institut Pasteur, Unité de Microbiologie Structurale, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Lionel Mourey
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Odile Burlet-Schiltz
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Mamadou Daffé
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS,
| | - Hedia Marrakchi
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS,
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37
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Soares NC, Blackburn JM. Mass Spectrometry Targeted Assays as a Tool to Improve Our Understanding of Post-translational Modifications in Pathogenic Bacteria. Front Microbiol 2016; 7:1216. [PMID: 27540373 PMCID: PMC4972818 DOI: 10.3389/fmicb.2016.01216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/21/2016] [Indexed: 01/03/2023] Open
Affiliation(s)
- Nelson C. Soares
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape TownCape Town, South Africa
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38
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Standish AJ, Teh MY, Tran ENH, Doyle MT, Baker PJ, Morona R. Unprecedented Abundance of Protein Tyrosine Phosphorylation Modulates Shigella flexneri Virulence. J Mol Biol 2016; 428:4197-4208. [PMID: 27380737 DOI: 10.1016/j.jmb.2016.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/06/2016] [Accepted: 06/23/2016] [Indexed: 01/09/2023]
Abstract
Evidence is accumulating that protein tyrosine phosphorylation plays a crucial role in the ability of important human bacterial pathogens to cause disease. While most works have concentrated on its role in the regulation of a major bacterial virulence factor, the polysaccharide capsule, recent studies have suggested a much broader role for this post-translational modification. This prompted us to investigate protein tyrosine phosphorylation in the human pathogen Shigella flexneri. We first completed a tyrosine phosphoproteome, identifying 905 unique tyrosine phosphorylation sites on at least 573 proteins (approximately 15% of all proteins). This is the most tyrosine-phosphorylated sites and proteins in a single bacterium identified to date, substantially more than the level seen in eukaryotic cells. Most had not previously been identified and included proteins encoded by the virulence plasmid, which is essential for S. flexneri to invade cells and cause disease. In order to investigate the function of these phosphorylation sites in important virulence factors, phosphomimetic and ablative mutations were constructed in the type 3 secretion system ATPase Spa47 and the master virulence regulator VirB. This revealed that tyrosine residues phosphorylated in our study are critical for Spa47 and VirB activity, and tyrosine phosphorylation likely regulates their functional activity and subsequently the virulence of this major human pathogen. This study suggests that tyrosine phosphorylation plays a critical role in regulating a wide variety of virulence factors in the human pathogen S. flexneri and serves as a base for future studies defining its complete role.
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Affiliation(s)
- Alistair James Standish
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Min Yan Teh
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Elizabeth Ngoc Hoa Tran
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew Thomas Doyle
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Paul J Baker
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Renato Morona
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
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39
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Guo J, Wang C, Han Y, Liu Z, Wu T, Liu Y, Liu Y, Tan Y, Cai X, Cao Y, Wang B, Zhang B, Liu C, Tan S, Zhang T. Identification of Lysine Acetylation in Mycobacterium abscessus Using LC-MS/MS after Immunoprecipitation. J Proteome Res 2016; 15:2567-78. [PMID: 27323652 DOI: 10.1021/acs.jproteome.6b00116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mycobacterium abscessus (MAB), which manifests in the pulmonary system, is one of the neglected causes of nontuberculous mycobacteria (NTM) infection. Treatment against MAB is difficult, characterized by its intrinsic antibiotic drug resistance. Lysine acetylation can alter the physiochemical property of proteins in living organisms. This study aimed to determine if this protein post-translational modification (PTM) exists in a clinical isolate M. abscessus GZ002. We used the antiacetyl-lysine immunoprecipitation to enrich the low-abundant PTM proteins, followed by the LC-MS/MS analysis. The lysine acetylome of M. abscessus GZ002 was determined. There were 459 lysine acetylation sites found in 289 acetylated proteins. Lysine acetylation occurred in 5.87% of the M. abscessus GZ002 proteome, and at least 25% of them were growth essential. Aerobic respiration and carbohydrate metabolic pathways of M. abscessus GZ002 were enriched with lysine acetylation. Through bioinformatics analysis, we identified four major acetyl motif logos (K(ac)Y, K(ac)F, K(ac)H, and DK(ac)). Further comparison of the reported M. tuberculosis (MTB) acetylomes and that of MAB GZ002 revealed several common features between these two species. The lysine residues of several antibiotic-resistance, virulence, and persistence-related proteins were acetylated in both MAB GZ002 and MTB. There were 51 identical acetylation sites in 37 proteins found in common between MAB GZ002 and MTB. Overall, we demonstrate a profile of lysine acetylation in MAB GZ002 proteome that shares similarities with MTB. Interventions that target at these conserved sections may be valuable as anti-NTM or anti-TB therapies.
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Affiliation(s)
- Jintao Guo
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Yi Han
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Tian Wu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Yan Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China.,School of Life Sciences, University of Anhui , Hefei, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Xinshan Cai
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Yuanyuan Cao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China.,School of Life Sciences, University of Anhui , Hefei, China
| | - Bangxing Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China.,School of Life Sciences, University of Anhui , Hefei, China
| | - Buchang Zhang
- School of Life Sciences, University of Anhui , Hefei, China
| | - Chunping Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
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40
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de Keijzer J, Mulder A, de Beer J, de Ru AH, van Veelen PA, van Soolingen D. Mechanisms of Phenotypic Rifampicin Tolerance in Mycobacterium tuberculosis Beijing Genotype Strain B0/W148 Revealed by Proteomics. J Proteome Res 2016; 15:1194-204. [PMID: 26930559 DOI: 10.1021/acs.jproteome.5b01073] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The "successful" Russian clone B0/W148 of Mycobacterium tuberculosis Beijing is well-known for its capacity to develop antibiotic resistance. During treatment, resistant mutants can occur that have inheritable resistance to specific antibiotics. Next to mutations, M. tuberculosis has several mechanisms that increase their tolerance to a variety of antibiotics. Insights in the phenotypic mechanisms that contribute to drug tolerance will increase our understanding of how antibiotic resistance develops in M. tuberculosis. In this study, we examined the (phospho)proteome dynamics in M. tuberculosis Beijing strain B0/W148 when exposed to a high dose of rifampicin; one of the most potent first-line antibiotics. A total of 2,534 proteins and 191 phosphorylation sites were identified, and revealed the differential regulation of DosR regulon proteins, which are necessary for the development of a dormant phenotype that is less susceptible to antibiotics. By examining independent phenotypic markers of dormancy, we show that persisters of in vitro rifampicin exposure entered a metabolically hypoactive state, which yields rifampicin and other antibiotics largely ineffective. These new insights in the role of protein regulation and post-translational modifications during the initial phase of rifampicin treatment reveal a shortcoming in the antituberculosis regimen that is administered to 8-9 million individuals annually.
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Affiliation(s)
- Jeroen de Keijzer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Arnout Mulder
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands
| | - Jessica de Beer
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands.,Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Medical Center , Nijmegen 6500 HB, The Netherlands
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41
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Calder B, Albeldas C, Blackburn JM, Soares NC. Mass Spectrometry Offers Insight into the Role of Ser/Thr/Tyr Phosphorylation in the Mycobacteria. Front Microbiol 2016; 7:141. [PMID: 26904014 PMCID: PMC4751927 DOI: 10.3389/fmicb.2016.00141] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 01/25/2016] [Indexed: 12/23/2022] Open
Abstract
Phosphorylation is a post translational modification which can rapidly regulate biochemical pathways by altering protein function, and has been associated with pathogenicity in bacteria. Once engulfed by host macrophages, pathogenic bacteria are exposed to harsh conditions and must respond rapidly in order to survive. The causative agent of TB, Mycobacterium tuberculosis, is unusual amongst the bacteria because it can survive within the host macrophage for decades in a latent state, demonstrating a remarkable capacity to successfully evade the host immune response. This ability may be mediated in part by regulatory mechanisms such as ser/thr/tyr phosphorylation. Mass spectrometry-based proteomics has afforded us the capacity to identify hundreds of phosphorylation sites in the bacterial proteome, allowing for comparative phosphoproteomic studies in the mycobacteria. There remains an urgent need to validate the reported phosphosites, and to elucidate their biological function in the context of pathogenicity. However, given the sheer number of putative phosphorylation events in the mycobacterial proteome, and the technical difficulty of assigning biological function to a phosphorylation event, it will not be trivial to do so. There are currently six published phosphoproteomic investigations of a member of mycobacteria. Here, we combine the datasets from these studies in order to identify commonly detected phosphopeptides and phosphosites in order to present high confidence candidates for further validation. By applying modern mass spectrometry-based techniques to improve our understanding of phosphorylation and other PTMs in pathogenic bacteria, we may identify candidates for therapeutic intervention.
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Affiliation(s)
- Bridget Calder
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Claudia Albeldas
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Jonathan M Blackburn
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Nelson C Soares
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
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42
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Manuse S, Fleurie A, Zucchini L, Lesterlin C, Grangeasse C. Role of eukaryotic-like serine/threonine kinases in bacterial cell division and morphogenesis. FEMS Microbiol Rev 2015; 40:41-56. [DOI: 10.1093/femsre/fuv041] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2015] [Indexed: 11/14/2022] Open
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43
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Touchette MH, Bommineni GR, Delle Bovi RJ, Gadbery JE, Nicora CD, Shukla AK, Kyle JE, Metz TO, Martin DW, Sampson NS, Miller WT, Tonge PJ, Seeliger JC. Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids. Biochemistry 2015; 54:5457-68. [PMID: 26271001 DOI: 10.1021/acs.biochem.5b00455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although they are classified as Gram-positive bacteria, Corynebacterineae possess an asymmetric outer membrane that imparts structural and thereby physiological similarity to more distantly related Gram-negative bacteria. Like lipopolysaccharide in Gram-negative bacteria, lipids in the outer membrane of Corynebacterineae have been associated with the virulence of pathogenic species such as Mycobacterium tuberculosis (Mtb). For example, Mtb strains that lack long, branched-chain alkyl esters known as dimycocerosates (DIMs) are significantly attenuated in model infections. The resultant interest in the biosynthetic pathway of these unusual virulence factors has led to the elucidation of many of the steps leading to the final esterification of the alkyl β-diol, phthiocerol, with branched-chain fatty acids known as mycocerosates. PapA5 is an acyltransferase implicated in these final reactions. Here, we show that PapA5 is indeed the terminal enzyme in DIM biosynthesis by demonstrating its dual esterification activity and chain-length preference using synthetic alkyl β-diol substrate analogues. By applying these analogues to a series of PapA5 mutants, we also revise a model for the substrate binding within PapA5. Finally, we demonstrate that the Mtb Ser/Thr kinases PknB and PknE modify PapA5 on three overlapping Thr residues and that a fourth Thr is unique to PknE phosphorylation. These results clarify the DIM biosynthetic pathway and indicate post-translational modifications that warrant further elucidation for their roles in the regulation of DIM biosynthesis.
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Affiliation(s)
| | | | | | | | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Anil K Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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44
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Zheng J, Liu L, Liu B, Jin Q. Phosphoproteomic analysis of bacillus Calmette-Guérin using gel-based and gel-free approaches. J Proteomics 2015; 126:189-99. [PMID: 26070398 DOI: 10.1016/j.jprot.2015.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 05/09/2015] [Accepted: 06/03/2015] [Indexed: 12/16/2022]
Abstract
Post-translational modifications regulate many aspects of protein behavior and provide options for expanding protein functionality in organisms. Protein phosphorylation is one of the major PTMs observed in bacteria, which are involved in regulating a myriad of physiological processes. Mycobacterium bovis bacillus Calmette-Guérin (BCG) has been recognized as an important weapon in the fight against tuberculosis (TB) worldwide for over 80 years. In this study, we conducted phosphoproteomic analysis in BCG bacteria using gel-based and gel-free complementary approaches and high-resolution Fourier transform mass spectrometry. In total, 501 phosphopeptides derived from 398 phosphoproteins were identified, representing the first phosphoproteomic analysis of BCG reported to date. Thirty-three novel protein products supported by 36 unique phosphorylated peptides were detected. Additionally, the translational start sites of 28 proteins were confirmed, and 31 proteins were validated through the extension of translational start sites based on N-terminus-derived peptides. The expression of three randomly selected phosphoproteins was validated through Western blotting. A number of proteins involved in metabolic pathways, including glycolysis, the tricarboxylic acid cycle, oxidative phosphorylation and two-component system, are discussed. We believe some of the proteins identified in this study may represent potential targets for the development of novel antibiotics for treating TB.
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Affiliation(s)
- Jianhua Zheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Liguo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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45
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Grangeasse C, Stülke J, Mijakovic I. Regulatory potential of post-translational modifications in bacteria. Front Microbiol 2015; 6:500. [PMID: 26074895 PMCID: PMC4446998 DOI: 10.3389/fmicb.2015.00500] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 05/06/2015] [Indexed: 11/30/2022] Open
Affiliation(s)
- Christophe Grangeasse
- Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086, Centre National de la Recherche Scientifique, University of Lyon Lyon, France
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Göttingen Göttingen, Germany
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology Göteborg, Sweden
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