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Gangwal A, Kumar N, Sangwan N, Dhasmana N, Dhawan U, Sajid A, Arora G, Singh Y. Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages. FEMS Microbiol Rev 2023; 47:fuad044. [PMID: 37533212 PMCID: PMC10465088 DOI: 10.1093/femsre/fuad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023] Open
Abstract
Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.
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Affiliation(s)
- Aakriti Gangwal
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nitika Sangwan
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Neha Dhasmana
- School of Medicine, New York University, 550 First Avenue New York-10016, New York, United States
| | - Uma Dhawan
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Andaleeb Sajid
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Gunjan Arora
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi-110007, India
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Marcion G, Seigneuric R, Chavanne E, Artur Y, Briand L, Hadi T, Gobbo J, Garrido C, Neiers F. C-terminal amino acids are essential for human heat shock protein 70 dimerization. Cell Stress Chaperones 2015; 20:61-72. [PMID: 25030382 PMCID: PMC4255253 DOI: 10.1007/s12192-014-0526-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/03/2014] [Accepted: 07/04/2014] [Indexed: 01/22/2023] Open
Abstract
The human inducible heat shock protein 70 (hHsp70), which is involved in several major pathologies, including neurodegenerative disorders and cancer, is a key molecular chaperone and contributes to the proper protein folding and maintenance of a large number of protein structures. Despite its role in disease, the current structural knowledge of hHsp70 is almost exclusively based on its Escherichia coli homolog, DnaK, even though these two proteins only share ~50 % amino acid identity. For the first time, we describe a complete heterologous production and purification strategy that allowed us to obtain a large amount of soluble, full-length, and non-tagged hHsp70. The protein displayed both an ATPase and a refolding activity when combined to the human Hsp40. Multi-angle light scattering and bio-layer interferometry analyses demonstrated the ability of hHsp70 to homodimerize. The role of the C-terminal part of hHsp70 was identified and confirmed by a study of a truncated version of hHsp70 that could neither dimerize nor present refolding activity.
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Affiliation(s)
- Guillaume Marcion
- INSERM, UMR 866, 7 blvd Jeanne d’Arc, 21000 Dijon, France
- Université de Bourgogne, Esplanade Erasme, Dijon, France
| | - Renaud Seigneuric
- INSERM, UMR 866, 7 blvd Jeanne d’Arc, 21000 Dijon, France
- Université de Bourgogne, Esplanade Erasme, Dijon, France
| | - Evelyne Chavanne
- Université de Bourgogne, Esplanade Erasme, Dijon, France
- Centre des Sciences du Goût et de l’Alimentation, INRA UMR 1324, CNRS UMR 6265, Université de Bourgogne, Dijon, France
| | - Yves Artur
- Université de Bourgogne, Esplanade Erasme, Dijon, France
- Centre des Sciences du Goût et de l’Alimentation, INRA UMR 1324, CNRS UMR 6265, Université de Bourgogne, Dijon, France
| | - Loïc Briand
- Centre des Sciences du Goût et de l’Alimentation, INRA UMR 1324, CNRS UMR 6265, Université de Bourgogne, Dijon, France
| | - Tarik Hadi
- INSERM, UMR 866, 7 blvd Jeanne d’Arc, 21000 Dijon, France
- Université de Bourgogne, Esplanade Erasme, Dijon, France
| | - Jessica Gobbo
- INSERM, UMR 866, 7 blvd Jeanne d’Arc, 21000 Dijon, France
- Université de Bourgogne, Esplanade Erasme, Dijon, France
- Anticancer Center Georges François Leclerc, Dijon, France
| | - Carmen Garrido
- INSERM, UMR 866, 7 blvd Jeanne d’Arc, 21000 Dijon, France
- Université de Bourgogne, Esplanade Erasme, Dijon, France
- Anticancer Center Georges François Leclerc, Dijon, France
| | - Fabrice Neiers
- Université de Bourgogne, Esplanade Erasme, Dijon, France
- Centre des Sciences du Goût et de l’Alimentation, INRA UMR 1324, CNRS UMR 6265, Université de Bourgogne, Dijon, France
- CSGA, 17 rue Sully, 21000 Dijon, France
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Purification and biochemical characterization of DnaK and its transcriptional activator RpoH from Neisseria gonorrhoeae. Mol Biol Rep 2014; 41:7945-53. [PMID: 25156536 DOI: 10.1007/s11033-014-3689-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 08/21/2014] [Indexed: 10/24/2022]
Abstract
DnaK plays a central role in stress response in the important human pathogen Neisseria gonorrhoeae. The genes encoding the DnaK chaperone machine (DnaK/DnaJ/GrpE) in N. gonorrhoeae are transcribed from RpoH (σ(32))-dependent promoters. In this study, we cloned, purified and biochemically characterised N. gonorrhoeae DnaK (NgDnaK) and RpoH. The NgDnaK and RpoH sequences are 73 and 50 % identical to the sequences of their respective E. coli counterparts. Similar to EcDnaK, nucleotide-free NgDnaK exists as a mix of monomers, dimers and higher oligomeric species in solution, and dissociates into monomers on addition of ATP. Like E. coli σ(32), RpoH of N. gonorrhoeae is monomeric in solution. Kinetic analysis of the basal ATPase activity of purified NgDnaK revealed a V max of 193 pmol phosphate released per minute per microgram DnaK (which is significantly higher than reported basal ATPase activity of EcDnaK), and the turnover number against ATP was 0.4 min(-1) under our assay conditions. Nucleotide-free NgDnaK bound a short model substrate, NR-peptide, with micromolar affinity close to that reported for EcDnaK. Our analysis showed that interaction between N. gonorrhoeae RpoH and DnaK appears to be ATP-dependent and non-specific, in stark contrast to the E. coli DnaK system where σ(32) and DnaK interact as monomers even in the absence of ATP. Sequence comparison showed that the DnaK-binding site of σ(32) is not conserved in RpoH. Our findings suggest that the mechanism of DnaK/RpoH recognition in N. gonorrhoeae is different from that in E. coli.
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Franco CF, Soares R, Pires E, Santos R, Coelho AV. Radial nerve cord protein phosphorylation dynamics during starfish arm tip wound healing events. Electrophoresis 2012; 33:3764-78. [DOI: 10.1002/elps.201200274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 07/05/2012] [Accepted: 07/14/2012] [Indexed: 01/14/2023]
Affiliation(s)
- Catarina F. Franco
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras; Portugal
| | - Renata Soares
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras; Portugal
| | - Elisabete Pires
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras; Portugal
| | | | - Ana V. Coelho
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras; Portugal
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Koponen J, Laakso K, Koskenniemi K, Kankainen M, Savijoki K, Nyman TA, de Vos WM, Tynkkynen S, Kalkkinen N, Varmanen P. Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG. J Proteomics 2012; 75:1357-74. [DOI: 10.1016/j.jprot.2011.11.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 10/19/2011] [Accepted: 11/07/2011] [Indexed: 10/15/2022]
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Schmidl SR, Gronau K, Pietack N, Hecker M, Becher D, Stülke J. The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: analysis of the complete known Ser/Thr kinome suggests the existence of novel kinases. Mol Cell Proteomics 2010; 9:1228-42. [PMID: 20097688 DOI: 10.1074/mcp.m900267-mcp200] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycoplasma pneumoniae belongs to the Mollicutes, the group of organisms with the smallest genomes that are capable of host-independent life. These bacteria show little regulation in gene expression, suggesting an important role for the control of protein activities. We have studied protein phosphorylation in M. pneumoniae to identify phosphorylated proteins. Two-dimensional gel electrophoresis and mass spectrometry allowed the detection of 63 phosphorylated proteins, many of them enzymes of central carbon metabolism and proteins related to host cell adhesion. We identified 16 phosphorylation sites, among them 8 serine and 8 threonine residues, respectively. A phosphoproteome analysis with mutants affected in the two annotated protein kinase genes or in the single known protein phosphatase gene suggested that only one protein (HPr) is phosphorylated by the HPr kinase, HPrK, whereas four adhesion-related or surface proteins were targets of the protein kinase C, PrkC. A comparison with the phosphoproteomes of other bacteria revealed that protein phosphorylation is evolutionarily only poorly conserved. Only one single protein with an identified phosphorylation site, a phosphosugar mutase (ManB in M. pneumoniae), is phosphorylated on a conserved serine residue in all studied organisms from archaea and bacteria to man. We demonstrate that this protein undergoes autophosphorylation. This explains the strong conservation of this phosphorylation event. For most other proteins, even if they are phosphorylated in different species, the actual phosphorylation sites are different. This suggests that protein phosphorylation is a form of adaptation of the bacteria to the specific needs of their particular ecological niche.
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Affiliation(s)
- Sebastian R Schmidl
- Department of General Microbiology, Georg-August-Universität Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Germany
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Eymann C, Becher D, Bernhardt J, Gronau K, Klutzny A, Hecker M. Dynamics of protein phosphorylation on Ser/Thr/Tyr inBacillus subtilis. Proteomics 2007; 7:3509-26. [PMID: 17726680 DOI: 10.1002/pmic.200700232] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The Ser/Thr/Tyr phosphoproteome of Bacillus subtilis was analyzed by a 2-D gel-based approach combining Pro-Q Diamond staining and [(33)P]-labeling. In exponentially growing B. subtilis cells 27 proteins could be identified after staining with Pro-Q Diamond and/or [(33)P]-labeling and one additional protein was labeled solely by [(33)P] resulting in a total of 28 potentially phosphorylated proteins. These proteins are mainly involved in enzymatic reactions of basic carbon metabolism and the regulation of the alternative sigma factor sigma(B). We also found significant changes of the phosphoproteome including increased phosphorylation and dephosphorylation rates of some proteins as well as the detection of four newly phosphorylated proteins in response to stress or starvation. For nine proteins, phosphorylation sites at serine or threonine residues were determined by MS. These include the known phosphorylation sites of Crh, PtsH, and RsbV. Additionally, we were able to identify novel phosphorylation sites of AroA, Pyk, and YbbT. Interestingly, the phosphorylation of RsbRA, B, C, and D, four proteins of a multicomponent protein complex involved in environmental stress signaling, was found during exponential growth. For RsbRA, B, and D, phosphorylation of one of the conserved threonine residues in their C-termini were verified by MS (T171, T186, T181, respectively).
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Affiliation(s)
- Christine Eymann
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
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Preneta R, Papavinasasundaram KG, Cozzone AJ, Duclos B. Autophosphorylation of the 16 kDa and 70 kDa antigens (Hsp 16.3 and Hsp 70) of Mycobacterium tuberculosis. MICROBIOLOGY-SGM 2004; 150:2135-2141. [PMID: 15256556 DOI: 10.1099/mic.0.26789-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Several antigens of Mycobacterium tuberculosis, identified by monoclonal antibodies, have been previously cloned and are being exploited in the development of improved vaccines and diagnostic reagents. In this study, the molecular characteristics of two of these antigens, the immunodominant proteins Hsp 16.3 and Hsp 70, were analysed in further detail by assessing their capacity to undergo protein phosphorylation, a chemical modification frequently used by organisms to adjust to environmental variations. Hsp 16.3 was overproduced in an Escherichia coli expression system and purified to homogeneity. Upon incubation in the presence of radioactive ATP, it was shown to possess autophosphorylation activity. Two-dimensional analysis of its phosphoamino acid content revealed that it was modified exclusively at serine residues. In addition, cross-linking experiments demonstrated that it could tightly bind to ATP. Purified Hsp 70 was also shown to autophosphorylate but phosphorylation occurred exclusively at threonine residues. This reaction was found to be strongly stimulated by calcium ions. These data indicate that both structural and functional similarities exist between Hsp 16.3 (Acr) and alpha-crystallin, a eukaryotic protein which plays an important role in maintaining the transparency of the vertebrate eye, and that the functional properties of Hsp 70 from M. tuberculosis are similar to those of other bacterial members of the Hsp 70 family, particularly the E. coli homologue DnaK.
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Affiliation(s)
- Rachel Preneta
- Institut de Biologie et Chimie des Protéines, Centre National de la Recherche Scientifique, Université de Lyon, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - K G Papavinasasundaram
- National Institute for Medical Research, Division of Mycobacterial Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Alain J Cozzone
- Institut de Biologie et Chimie des Protéines, Centre National de la Recherche Scientifique, Université de Lyon, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Bertrand Duclos
- Institut de Biologie et Chimie des Protéines, Centre National de la Recherche Scientifique, Université de Lyon, 7 passage du Vercors, 69367 Lyon Cedex 07, France
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Pavela-Vrancic M, Dieckmann R, von Döhren H. ATPase activity of non-ribosomal peptide synthetases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1696:83-91. [PMID: 14726208 DOI: 10.1016/j.bbapap.2003.09.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adenylation domains of non-ribosomal peptide synthetases (NRPS) catalyse the formation of aminoacyl adenylates, and in addition synthesize mono- and dinucleoside polyphosphates. Here, we show that NRPS systems furthermore contain an ATPase activity in the range of up to 2 P(i)/min. The hydrolysis rate by apo-tyrocidine synthetase 1 (apo-TY1) is enhanced in the presence of non-cognate amino acid substrates, correlating well with their structural features and the diminishing adenylation efficiency. A comparative analysis of the functional relevance of an analogous sequence motif in P-type ATPases and adenylate kinases (AK) allowed a putative assignment of the invariant aspartate residue from the TGDLA(V)R(K) core sequence in NRPS as the Mg(2+) binding site. Less pronounced variations in ATPase activity are observed in domains with relaxed amino acid specificity of gramicidin S synthetase 2 (GS2) and delta-(L-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS), known to produce a set of substitutional variants of the respective peptide product. These results disclose new perspectives about the mode of substrate selection by NRPS.
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Affiliation(s)
- Maja Pavela-Vrancic
- Department of Chemistry, Faculty of Natural Sciences, Mathematics and Education, University of Split, N Tesle 12, 21000 Split, Croatia
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Rosen R, Ron EZ. Proteome analysis in the study of the bacterial heat-shock response. MASS SPECTROMETRY REVIEWS 2002; 21:244-265. [PMID: 12533799 DOI: 10.1002/mas.10031] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In recent years, it has become clear that, in addition to the regulation of the expression of specific genes, there are global regulatory systems that control the simultaneous expression of a large number of genes in response to a variety of environmental stresses. The first of these global control systems, and of substantial importance, is the heat-shock response. The heat-shock response is characterized by the induction of a large set of proteins (heat-shock proteins-HSPs) upon shifts to higher temperature and upon exposure to conditions in which proteins are denatured (i.e., alcohols, heavy metals). The heat-shock response is universal and many of the heat-shock proteins are highly conserved among species. In bacteria, the heat-shock response has been studied extensively in several Gram-positive bacteria (Bacillus subtilis) and in the Gram-negative bacteria (i.e., Escherichia coli, Agrobacterium tumefaciens). The first recognition of the molecular abundance of the bacterial heat-shock proteins took place with the introduction of high-resolution two-dimensional polyacrylamide gels (2D gels) to analyze complex mixtures of cellular proteins. Two-dimensional gels, followed by mass spectrometry, were used to define the heat-shock stimulons in several bacteria, and to study the regulatory elements that control the heat-shock response. Here, we review the heat-shock response and its regulation in bacteria. The review will emphasize the use of proteome analysis in the study of this response, and will point out those open questions that can be investigated with proteomics, including mass spectrometry techniques.
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Affiliation(s)
- Ran Rosen
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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