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Wongdontree P, Millan-Oropeza A, Upfold J, Lavergne JP, Halpern D, Lambert C, Page A, Kénanian G, Grangeasse C, Henry C, Fouet A, Gloux K, Anba-Mondoloni J, Gruss A. Oxidative stress is intrinsic to staphylococcal adaptation to fatty acid synthesis antibiotics. iScience 2024; 27:109505. [PMID: 38577105 PMCID: PMC10993138 DOI: 10.1016/j.isci.2024.109505] [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: 07/26/2023] [Revised: 12/08/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Antibiotics inhibiting the fatty acid synthesis pathway (FASII) of the major pathogen Staphylococcus aureus reach their enzyme targets, but bacteria continue growth by using environmental fatty acids (eFAs) to produce phospholipids. We assessed the consequences and effectors of FASII-antibiotic (anti-FASII) adaptation. Anti-FASII induced lasting expression changes without genomic rearrangements. Several identified regulators affected the timing of adaptation outgrowth. Adaptation resulted in decreased expression of major virulence factors. Conversely, stress responses were globally increased and adapted bacteria were more resistant to peroxide killing. Importantly, pre-exposure to peroxide led to faster anti-FASII-adaptation by stimulating eFA incorporation. This adaptation differs from reports of peroxide-stimulated antibiotic efflux, which leads to tolerance. In vivo, anti-FASII-adapted S. aureus killed the insect host more slowly but continued multiplying. We conclude that staphylococcal adaptation to FASII antibiotics involves reprogramming, which decreases virulence and increases stress resistance. Peroxide, produced by the host to combat infection, favors anti-FASII adaptation.
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Affiliation(s)
- Paprapach Wongdontree
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Aaron Millan-Oropeza
- PAPPSO Platform, Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Jennifer Upfold
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Jean-Pierre Lavergne
- Bacterial Pathogens and Protein Phosphorylation, Molecular Microbiology and Structural Biology, UMR 5086 - CNRS / Université de Lyon, Building IBCP, 7 Passage du Vercors, Lyon, France
| | - David Halpern
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Clara Lambert
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, Paris, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences, CNRS, UMS3444, INSERM US8, Université de Lyon, Lyon, France
| | - Gérald Kénanian
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Christophe Grangeasse
- Bacterial Pathogens and Protein Phosphorylation, Molecular Microbiology and Structural Biology, UMR 5086 - CNRS / Université de Lyon, Building IBCP, 7 Passage du Vercors, Lyon, France
| | - Céline Henry
- PAPPSO Platform, Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Agnès Fouet
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, Paris, France
| | - Karine Gloux
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Jamila Anba-Mondoloni
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Alexandra Gruss
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
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2
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Bhavana, Kohal R, Kumari P, Das Gupta G, Kumar Verma S. Druggable targets of protein tyrosine phosphatase Family, viz. PTP1B, SHP2, Cdc25, and LMW-PTP: Current scenario on medicinal Attributes, and SAR insights. Bioorg Chem 2024; 144:107121. [PMID: 38237392 DOI: 10.1016/j.bioorg.2024.107121] [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: 12/02/2023] [Revised: 01/02/2024] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Protein tyrosine phosphatases (PTPs) are the class of dephosphorylation enzymes that catalyze the removal of phosphate groups from tyrosine residues on proteins responsible for various cellular processes. Any disbalance in signal pathways mediated by PTPs leads to various disease conditions like diabetes, obesity, cancers, and autoimmune disorders. Amongst the PTP superfamily, PTP1B, SHP2, Cdc25, and LMW-PTP have been prioritized as druggable targets for developing medicinal agents. PTP1B is an intracellular PTP enzyme that downregulates insulin and leptin signaling pathways and is involved in insulin resistance and glucose homeostasis. SHP2 is involved in the RAS-MAPK pathway and T cell immunity. Cdk-cyclin complex activation occurs by Cdc25-PTPs involved in cell cycle regulation. LMW-PTPs are involved in PDGF/PDGFR, Eph/ephrin, and insulin signaling pathways, resulting in certain diseases like diabetes mellitus, obesity, and cancer. The signaling cascades of PTP1B, SHP2, Cdc25, and LMW-PTPs have been described to rationalize their medicinal importance in the pathophysiology of diabetes, obesity, and cancer. Their binding sites have been explored to overcome the hurdles in discovering target selective molecules with optimum potency. Recent developments in the synthetic molecules bearing heterocyclic moieties against these targets have been explored to gain insight into structural features. The elaborated SAR investigation revealed the effect of substituents on the potency and target selectivity, which can be implicated in the further discovery of newer medicinal agents targeting the druggable members of the PTP superfamily.
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Affiliation(s)
- Bhavana
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Rupali Kohal
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Preety Kumari
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Ghanshyam Das Gupta
- Department of Pharmaceutics, ISF College of Pharmacy, Moga 142 001, (Punjab), India
| | - Sant Kumar Verma
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142 001, (Punjab), India.
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Capuano N, Amato A, Dell’Annunziata F, Giordano F, Folliero V, Di Spirito F, More PR, De Filippis A, Martina S, Amato M, Galdiero M, Iandolo A, Franci G. Nanoparticles and Their Antibacterial Application in Endodontics. Antibiotics (Basel) 2023; 12:1690. [PMID: 38136724 PMCID: PMC10740835 DOI: 10.3390/antibiotics12121690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Root canal treatment represents a significant challenge as current cleaning and disinfection methodologies fail to remove persistent bacterial biofilms within the intricate anatomical structures. Recently, the field of nanotechnology has emerged as a promising frontier with numerous biomedical applications. Among the most notable contributions of nanotechnology are nanoparticles, which possess antimicrobial, antifungal, and antiviral properties. Nanoparticles cause the destructuring of bacterial walls, increasing the permeability of the cell membrane, stimulating the generation of reactive oxygen species, and interrupting the replication of deoxyribonucleic acid through the controlled release of ions. Thus, they could revolutionize endodontics, obtaining superior results and guaranteeing a promising short- and long-term prognosis. Therefore, chitosan, silver, graphene, poly(lactic) co-glycolic acid, bioactive glass, mesoporous calcium silicate, hydroxyapatite, zirconia, glucose oxidase magnetic, copper, and zinc oxide nanoparticles in endodontic therapy have been investigated in the present review. The diversified antimicrobial mechanisms of action, the numerous applications, and the high degree of clinical safety could encourage the scientific community to adopt nanoparticles as potential drugs for the treatment of endodontic diseases, overcoming the limitations related to antibiotic resistance and eradication of the biofilm.
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Affiliation(s)
- Nicoletta Capuano
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (N.C.); (F.D.); (F.G.); (V.F.); (F.D.S.); (S.M.); (M.A.)
| | - Alessandra Amato
- Department of Neuroscience, Reproductive Science and Dentistry, University of Naples Federico II, 80138 Naples, Italy;
| | - Federica Dell’Annunziata
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (N.C.); (F.D.); (F.G.); (V.F.); (F.D.S.); (S.M.); (M.A.)
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.R.M.); (A.D.F.); (M.G.)
| | - Francesco Giordano
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (N.C.); (F.D.); (F.G.); (V.F.); (F.D.S.); (S.M.); (M.A.)
| | - Veronica Folliero
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (N.C.); (F.D.); (F.G.); (V.F.); (F.D.S.); (S.M.); (M.A.)
| | - Federica Di Spirito
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (N.C.); (F.D.); (F.G.); (V.F.); (F.D.S.); (S.M.); (M.A.)
| | - Pragati Rajendra More
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.R.M.); (A.D.F.); (M.G.)
| | - Anna De Filippis
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.R.M.); (A.D.F.); (M.G.)
| | - Stefano Martina
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (N.C.); (F.D.); (F.G.); (V.F.); (F.D.S.); (S.M.); (M.A.)
| | - Massimo Amato
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (N.C.); (F.D.); (F.G.); (V.F.); (F.D.S.); (S.M.); (M.A.)
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.R.M.); (A.D.F.); (M.G.)
- Complex Operative Unity of Virology and Microbiology, University Hospital of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Alfredo Iandolo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (N.C.); (F.D.); (F.G.); (V.F.); (F.D.S.); (S.M.); (M.A.)
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (N.C.); (F.D.); (F.G.); (V.F.); (F.D.S.); (S.M.); (M.A.)
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Liu S, Cai C, Li L, Wen H, Liu J, Li L, Wang Q, Wang X. StSN2 interacts with the brassinosteroid signaling suppressor StBIN2 to maintain tuber dormancy. HORTICULTURE RESEARCH 2023; 10:uhad228. [PMID: 38156286 PMCID: PMC10753161 DOI: 10.1093/hr/uhad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/29/2023] [Indexed: 12/30/2023]
Abstract
After harvest, potato tubers undergo an important period of dormancy, which significantly impacts potato quality and seed vigor. StSN2 has been reported as a key gene for maintaining tuber dormancy; in this study, we explored the molecular mechanism by which StSN2 maintains dormancy. StBIN2 was first identified as a candidate protein that interacts with StSN2 by co-immunoprecipitation/mass spectrometry, and both qPCR and enzyme activity experiments showed that StSN2 can promote the StBIN2 expression and activity. In addition, the interaction between StSN2 and StBIN2 was verified by yeast two-hybrid, luciferase complementation experiments and co-immunoprecipitation. Bioinformatics analysis and site-directed mutagenesis confirmed the critical role of cysteine residues of StBIN2 in its binding to StSN2. Similar to that of StSN2, overexpression of StBIN2 extended the dormancy of potato tuber. Interaction between StSN2 and StBIN2 increased the activity of the StBIN2 enzyme, inhibited the expression of StBZR1, and suppressed BR signaling. On the contrary, this interaction promoted the expression of StSnRK2.2/2.3/2.4/2.6 and StABI5, key genes of ABA signaling, and the phosphorylation of StSnRK2.3, thereby promoting ABA signaling. Altogether, our results indicate that StSN2 interacts with StBIN2 through key cysteine residues and StBIN2 maintains tuber dormancy by affecting ABA and BR signaling. Findings of this research offer new insights into the molecular mechanism by which StSN2 maintains potato tuber dormancy through interaction with StSIN2 and provide guidance for potato improvement.
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Affiliation(s)
- Shifeng Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengcheng Cai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Luopin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - He Wen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Liqin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiyao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
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Amirian R, Azadi Badrbani M, Izadi Z, Samadian H, Bahrami G, Sarvari S, Abdolmaleki S, Nabavi SM, Derakhshankhah H, Jaymand M. Targeted protein modification as a paradigm shift in drug discovery. Eur J Med Chem 2023; 260:115765. [PMID: 37659194 DOI: 10.1016/j.ejmech.2023.115765] [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: 07/07/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Targeted Protein Modification (TPM) is an umbrella term encompassing numerous tools and approaches that use bifunctional agents to induce a desired modification over the POI. The most well-known TPM mechanism is PROTAC-directed protein ubiquitination. PROTAC-based targeted degradation offers several advantages over conventional small-molecule inhibitors, has shifted the drug discovery paradigm, and is acquiring increasing interest as over ten PROTACs have entered clinical trials in the past few years. Targeting the protein of interest for proteasomal degradation by PROTACS was the pioneer of various toolboxes for selective protein degradation. Nowadays, the ever-increasing number of tools and strategies for modulating and modifying the POI has expanded far beyond protein degradation, which phosphorylation and de-phosphorylation of the protein of interest, targeted acetylation, and selective modification of protein O-GlcNAcylation are among them. These novel strategies have opened new avenues for achieving more precise outcomes while remaining feasible and minimizing side effects. This field, however, is still in its infancy and has a long way to precede widespread use and translation into clinical practice. Herein, we investigate the pros and cons of these novel strategies by exploring the latest advancements in this field. Ultimately, we briefly discuss the emerging potential applications of these innovations in cancer therapy, neurodegeneration, viral infections, and autoimmune and inflammatory diseases.
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Affiliation(s)
- Roshanak Amirian
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mehdi Azadi Badrbani
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Zhila Izadi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Hadi Samadian
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Gholamreza Bahrami
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Sajad Sarvari
- Department of Pharmaceutical Science, School of Pharmacy, West Virginia University, Morgantown, WV, USA.
| | - Sara Abdolmaleki
- Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj, Iran.
| | - Seyed Mohammad Nabavi
- Department of Science and Technology, University of Sannio, 82100, Benevento, Italy.
| | - Hossein Derakhshankhah
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Liu S, Wang F, Chen H, Yang Z, Ning Y, Chang C, Yang D. New Insights into Radio-Resistance Mechanism Revealed by (Phospho)Proteome Analysis of Deinococcus Radiodurans after Heavy Ion Irradiation. Int J Mol Sci 2023; 24:14817. [PMID: 37834265 PMCID: PMC10572868 DOI: 10.3390/ijms241914817] [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: 08/29/2023] [Revised: 09/23/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Deinococcus radiodurans (D. radiodurans) can tolerate various extreme environments including radiation. Protein phosphorylation plays an important role in radiation resistance mechanisms; however, there is currently a lack of systematic research on this topic in D. radiodurans. Based on label-free (phospho)proteomics, we explored the dynamic changes of D. radiodurans under various doses of heavy ion irradiation and at different time points. In total, 2359 proteins and 1110 high-confidence phosphosites were identified, of which 66% and 23% showed significant changes, respectively, with the majority being upregulated. The upregulated proteins at different states (different doses or time points) were distinct, indicating that the radio-resistance mechanism is dose- and stage-dependent. The protein phosphorylation level has a much higher upregulation than protein abundance, suggesting phosphorylation is more sensitive to irradiation. There were four distinct dynamic changing patterns of phosphorylation, most of which were inconsistent with protein levels. Further analysis revealed that pathways related to RNA metabolism and antioxidation were activated after irradiation, indicating their importance in radiation response. We also screened some key hub phosphoproteins and radiation-responsive kinases for further study. Overall, this study provides a landscape of the radiation-induced dynamic change of protein expression and phosphorylation, which provides a basis for subsequent functional and applied studies.
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Affiliation(s)
- Shihao Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
| | - Fei Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
| | - Heye Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
| | - Zhixiang Yang
- College of Life Sciences, Hebei University, Baoding 071002, China;
| | - Yifan Ning
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
- College of Life Sciences, Hebei University, Baoding 071002, China;
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
| | - Dong Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
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7
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Zhao C, Wang H, Zhan W, Lv X, Ma X. Exploitation of Proximity-Mediated Effects in Drug Discovery: An Update of Recent Research Highlights in Perturbing Pathogenic Proteins and Correlated Issues. J Med Chem 2023; 66:10122-10149. [PMID: 37489834 DOI: 10.1021/acs.jmedchem.3c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The utilization of proximity-mediated effects to perturb pathogenic proteins of interest (POIs) has emerged as a powerful strategic alternative to conventional drug design approaches based on target occupancy. Over the past three years, the burgeoning field of targeted protein degradation (TPD) has witnessed the expansion of degradable POIs to membrane-associated, extracellular, proteasome-resistant, and even microbial proteins. Beyond TPD, researchers have achieved the proximity-mediated targeted protein stabilization, the recruitment of intracellular immunophilins to disturb undruggable targets, and the nonphysiological post-translational modifications of POIs. All of these strides provide new avenues for innovative drug discovery aimed at battling human malignancies and other major diseases. This perspective presents recent research highlights and discusses correlated issues in developing therapeutic modalities that exploit proximity-mediated effects to modulate pathogenic proteins, thereby guiding future academic and industrial efforts in this field.
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Affiliation(s)
- Can Zhao
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Henian Wang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Wenhu Zhan
- iCarbonX (Shenzhen) Co., Ltd., Shenzhen, 518000, China
| | - Xiaoqing Lv
- College of Medicine, Jiaxing University, Jiaxing 314001, China
| | - Xiaodong Ma
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
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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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9
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Wu X, Liu YK, Iliuk AB, Tao WA. Mass spectrometry-based phosphoproteomics in clinical applications. Trends Analyt Chem 2023; 163:117066. [PMID: 37215489 PMCID: PMC10195102 DOI: 10.1016/j.trac.2023.117066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is an essential post-translational modification that regulates many aspects of cellular physiology, and dysregulation of pivotal phosphorylation events is often responsible for disease onset and progression. Clinical analysis on disease-relevant phosphoproteins, while quite challenging, provides unique information for precision medicine and targeted therapy. Among various approaches, mass spectrometry (MS)-centered characterization features discovery-driven, high-throughput and in-depth identification of phosphorylation events. This review highlights advances in sample preparation and instrument in MS-based phosphoproteomics and recent clinical applications. We emphasize the preeminent data-independent acquisition method in MS as one of the most promising future directions and biofluid-derived extracellular vesicles as an intriguing source of the phosphoproteome for liquid biopsy.
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Affiliation(s)
- Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yi-Kai Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
| | - W. Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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10
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Ijaz S, Haq IU, Malik R, Nadeem G, Ali HM, Kaur S. In silico characterization of differentially expressed short-read nucleotide sequences identified in dieback stress-induced transcriptomic analysis reveals their role as antimicrobial peptides. FRONTIERS IN PLANT SCIENCE 2023; 14:1168221. [PMID: 37021314 PMCID: PMC10069654 DOI: 10.3389/fpls.2023.1168221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
We investigated the in silico characterization of short-length nucleotide sequences that were differentially expressed in dieback stress-induced transcriptomic analysis. They displayed homology with C-terminal flanking peptides and defensins-like proteins, revealing their antimicrobial activity. Their predicted fingerprints displayed protein signatures related to antimicrobial peptides. These short-length RGAs have been shown to possess structural motifs such as APLT P-type ATPase, casein kinase II (CK2), protein kinase 3, protein kinase C (PKC), and N-glycosylation site that are the attributes of disease resistance genes. The prediction of arginine and lysine residues in active binding sites in ligand docking analysis prophesied them as antimicrobial peptides due to their strong relation with antimicrobial activity. The in silico structural-functional characterization has predicted their role in resistance against microbial pathogens. Moreover, the predicted antimicrobial peptide regions showed their homology with the signature domain of PR-5-like protein and AMP family Thaumatin.
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Affiliation(s)
- Siddra Ijaz
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Imran Ul Haq
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Riffat Malik
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Ghalia Nadeem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Hayssam M. Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sukhwinder Kaur
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
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11
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Azemin WA, Alias N, Ali AM, Shamsir MS. In silico analysis prediction of HepTH1-5 as a potential therapeutic agent by targeting tumour suppressor protein networks. J Biomol Struct Dyn 2023; 41:1141-1167. [PMID: 34935583 DOI: 10.1080/07391102.2021.2017349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Many studies reported that the activation of tumour suppressor protein, p53 induced the human hepcidin expression. However, its expression decreased when p53 was silenced in human hepatoma cells. Contrary to Tilapia hepcidin TH1-5, HepTH1-5 was previously reported to trigger the p53 activation through the molecular docking approach. The INhibitor of Growth (ING) family members are also shown to directly interact with p53 and promote cell cycle arrest, senescence, apoptosis and participate in DNA replication and DNA damage responses to suppress the tumour initiation and progression. However, the interrelation between INGs and HepTH1-5 remains unknown. Therefore, this study aims to identify the mechanism and their protein interactions using in silico approaches. The finding revealed that HepTH1-5 and its ligands had interacted mostly on hotspot residues of ING proteins which involved in histone modifications via acetylation, phosphorylation, and methylation. This proves that HepTH1-5 might implicate in an apoptosis signalling pathway and preserve the protein structure and function of INGs by reducing the perturbation of histone binding upon oxidative stress response. This study would provide theoretical guidance for the design and experimental studies to decipher the role of HepTH1-5 as a potential therapeutic agent for cancer therapy. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wan-Atirah Azemin
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia.,Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia
| | - Nadiawati Alias
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Abdul Manaf Ali
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
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12
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Chen S, Ji X, Dedkova LM, Potuganti GR, Hecht SM. Site-Selective Tyrosine Phosphorylation in the Activation of the p50 Subunit of NF-κB for DNA Binding and Transcription. ACS Chem Biol 2023; 18:59-69. [PMID: 36534507 PMCID: PMC10026595 DOI: 10.1021/acschembio.2c00678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The family of NF-κB transcriptional activators controls the expression of many genes, including those involved in cell survival and development. The family consists of homo- and heterodimers constituted by combinations of five subunits. Subunit p50 includes 13 tyrosine residues, but the relationship between specific tyrosine phosphorylations and p50 function is not well understood. Subunits of p50 and p65 prepared in vitro formed a heterodimer, but this NF-κB would not bind to the interleukin-2 (IL-2) promoter DNA. Treatment of p50 with guanosine triphosphate (GTP) and a lysate from activated Jurkat cells, effected rapid p50 phosphorylation, and, in the presence of wild-type subunit p65, was accompanied on the same time scale by IL-2 promoter DNA binding. Modified p50s containing one of seven stoichiometrically phosphorylated tyrosines in NF-κB p50/p65 heterodimers, included three that facilitated binding to the IL-2 DNA promoter region to a greater extent than the wild type. One of these three stoichiometrically phosphorylated p50/p65 heterodimers of NF-κB, containing pTyr60 in the p50 subunit, was treated with a lysate from activated Jurkat cells + GTP and shown to be phosphorylated on the same time scale as wild-type p50. This modified NF-κB also developed IL-2 promoter DNA binding activity on the same time scale as the wild type but exhibited greater binding to the IL-2 DNA promoters than the wild type. The nature of this enhanced binding was studied in greater detail using a metabolically stable pTyr derivative at position 60 of p50 and cellular phosphatases. We suggest that enhanced DNA binding of modified NF-κB containing pTyr60 in the p50 subunit may reflect stoichiometric NF-κB phosphorylation at a site that is not normally fully phosphorylated, or not phosphorylated at all, and is relatively resistant to the effects of Jurkat cell tyrosine phosphatase activity. This conclusion was reinforced by demonstrating that modification of Tyr60 of p50 with a metabolically stable methylenephosphonate moiety further increased the stability of the formed NF-κB p50/p65 heterodimer against the action of activated Jurkat cell phosphatases.
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Affiliation(s)
- Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xun Ji
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Gal Reddy Potuganti
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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13
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Coates RJ, Young MT, Scofield S. Optimising expression and extraction of recombinant proteins in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1074531. [PMID: 36570881 PMCID: PMC9773421 DOI: 10.3389/fpls.2022.1074531] [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: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Recombinant proteins are of paramount importance for research, industrial and medical use. Numerous expression chassis are available for recombinant protein production, and while bacterial and mammalian cell cultures are the most widely used, recent developments have positioned transgenic plant chassis as viable and often preferential options. Plant chassis are easily maintained at low cost, are hugely scalable, and capable of producing large quantities of protein bearing complex post-translational modification. Several protein targets, including antibodies and vaccines against human disease, have been successfully produced in plants, highlighting the significant potential of plant chassis. The aim of this review is to act as a guide to producing recombinant protein in plants, discussing recent progress in the field and summarising the factors that must be considered when utilising plants as recombinant protein expression systems, with a focus on optimising recombinant protein expression at the genetic level, and the subsequent extraction and purification of target proteins, which can lead to substantial improvements in protein stability, yield and purity.
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14
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Lin H, Leman LJ, Krishnamurthy R. One-pot chemical pyro- and tri-phosphorylation of peptides by using diamidophosphate in water. Chem Sci 2022; 13:13741-13747. [PMID: 36544739 PMCID: PMC9713773 DOI: 10.1039/d2sc04160j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/30/2022] [Indexed: 12/24/2022] Open
Abstract
Protein (pyro)phosphorylation is emerging as a post-translational modification (PTM) in signalling pathways involved in many cellular processes. However, access to synthetic pyrophosphopeptides that can serve as tools for understanding protein pyrophosphorylation is quite limited. Herein, we report a chemical phosphorylation method that enables the synthesis of pyrophosphopeptides in aqueous medium without the need for protecting groups. The strategy employs diamidophosphate (DAP) in a one-pot sequential phosphorylation-hydrolysis of mono-phosphorylated peptide precursors. This operationally simple method exploits the intrinsic nucleophilicity of a phosphate moiety installed on serine, threonine or tyrosine residues in complex peptides with excellent chemoselectivity and good yields under mild conditions. We demonstrate the installation of the pyrophosphate group within a wide range of model peptides and showcase the potential of this methodology by selectively pyrophosphorylating the highly functionalized Nopp140 peptide fragment. The potential to produce higher (poly)phosphorylated peptides was demonstrated as a proof-of-principle experiment where we synthesized the triphosphorylated peptides using this one-pot strategy.
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Affiliation(s)
- Huacan Lin
- Department of Chemistry, The Scripps Research InstituteLa JollaCalifornia 92037USA
| | - Luke J. Leman
- Department of Chemistry, The Scripps Research InstituteLa JollaCalifornia 92037USA
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15
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Biswas D, Kumari N, Lachén-Montes M, Dutta S, Agrawal I, Samanta D, Shenoy SV, Halder A, Fernández-Irigoyen J, Padhye AR, Santamaría E, Srivastava S. Deep Phosphoproteome Landscape of Interhemispheric Functionality of Neuroanatomical Regions of the Human Brain. J Proteome Res 2022; 22:1043-1055. [PMID: 36317652 DOI: 10.1021/acs.jproteome.2c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Post-translational modifications (PTMs) are one of the compulsive and predominant biological processes that regulate the diverse molecular mechanism, modulate the onset of disease, and are the reason behind the functional diversity of proteins. Despite the widespread research findings in neuroproteomics, one of the key drawbacks has been the lack of proteome-level knowledge of hemispheric lateralization. We have investigated the proteome level expression in different neuroanatomical regions under the Human Brain Proteome Project (HBPP) and developed the global interhemispheric brain proteome map (Brainprot) earlier. Furthermore, this study has extended to decipher the phosphoproteome map of human brain interhemispheric regions through high-resolution mass spectrometry. The phosphoproteomics examination of 12 unique interhemispheric neurological brain regions using Orbitrap fusion liquid chromatography with tandem mass spectrometry provided comprehensive coverage of 996 phosphoproteins, 2010 phosphopeptides, and 3567 phosphosites. Moreover, interhemispheric phosphoproteome profiling has been categorized according to synaptic ontologies and interhemispheric expression to understand the functionality. Finally, we have integrated the phosphosites data under the PhosphoMap section in the Inter-Hemispheric Brain Proteome Map Portal (https://www.brainprot.org/) for the advancement and support of the ongoing neuroproteomics research worldwide. Data is available via ProteomeXchange with the identifier PXD031188.
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Affiliation(s)
- Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Neha Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sampurna Dutta
- School of Biological Sciences, Indian Association for the Cultivation of Science, 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Ishita Agrawal
- Department of Molecular and Human Genetics, Banaras Hindu University, Varanasi221005, India
| | - Debabrata Samanta
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal721302, India
| | - Sanjyot Vinayak Shenoy
- Department of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Advait Rahul Padhye
- Department of Computer Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
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16
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Phosphoproteome Dynamics of Streptomyces rimosus during Submerged Growth and Antibiotic Production. mSystems 2022; 7:e0019922. [PMID: 36094082 PMCID: PMC9600765 DOI: 10.1128/msystems.00199-22] [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] [Indexed: 12/24/2022] Open
Abstract
Streptomyces rimosus is an industrial streptomycete, best known as a producer of oxytetracycline, one of the most widely used antibiotics. Despite the significant contribution of Streptomyces species to the pharmaceutical industry, most omics analyses have only been conducted on the model organism Streptomyces coelicolor. In recent years, protein phosphorylation on serine, threonine, and tyrosine (Ser, Thr, and Tyr, respectively) has been shown to play a crucial role in the regulation of numerous cellular processes, including metabolic changes leading to antibiotic production and morphological changes. In this study, we performed a comprehensive quantitative (phospho)proteomic analysis during the growth of S. rimosus under conditions of oxytetracycline production and pellet fragmentation. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis combined with phosphopeptide enrichment detected a total of 3,725 proteins, corresponding to 45.6% of the proteome and 417 phosphorylation sites from 230 phosphoproteins. Significant changes in abundance during three distinct growth phases were determined for 494 proteins and 98 phosphorylation sites. Functional analysis revealed changes in phosphorylation events of proteins involved in important cellular processes, including regulatory mechanisms, primary and secondary metabolism, cell division, and stress response. About 80% of the phosphoproteins detected during submerged growth of S. rimosus have not yet been reported in streptomycetes, and 55 phosphoproteins were not reported in any prokaryote studied so far. This enabled the creation of a unique resource that provides novel insights into the dynamics of (phospho)proteins and reveals many potential regulatory events during antibiotic production in liquid culture of an industrially important bacterium. IMPORTANCE Streptomyces rimosus is best known as a primary source of oxytetracycline (OTC). The significant global market value of OTC highlights the need for a better understanding of the regulatory mechanisms that lead to production of this antibiotic. Our study provides, for the first time, a detailed insight into the dynamics of (phospho)proteomic profiles during growth and antibiotic production in liquid culture of S. rimosus. Significant changes in protein synthesis and phosphorylation have been revealed for a number of important cellular proteins during the growth stages that coincide with OTC production and morphological changes of this industrially important bacterium. Most of these proteins have not been detected in previous studies. Therefore, our results significantly expand the insight into phosphorylation events associated with important cellular processes and antibiotic production; they also greatly increase the phosphoproteome of streptomycetes and contribute with newly discovered phosphoproteins to the database of prokaryotic phosphoproteomes. This can consequently lead to the design of novel research directions in elucidation of the complex regulatory network in Streptomyces.
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17
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Garcia-Garcia T, Douché T, Giai Gianetto Q, Poncet S, El Omrani N, Smits WK, Cuenot E, Matondo M, Martin-Verstraete I. In-Depth Characterization of the Clostridioides difficile Phosphoproteome to Identify Ser/Thr Kinase Substrates. Mol Cell Proteomics 2022; 21:100428. [PMID: 36252736 PMCID: PMC9674922 DOI: 10.1016/j.mcpro.2022.100428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/13/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022] Open
Abstract
Clostridioides difficile is the leading cause of postantibiotic diarrhea in adults. During infection, the bacterium must rapidly adapt to the host environment by using survival strategies. Protein phosphorylation is a reversible post-translational modification employed ubiquitously for signal transduction and cellular regulation. Hanks-type serine/threonine kinases (STKs) and serine/threonine phosphatases have emerged as important players in bacterial cell signaling and pathogenicity. C. difficile encodes two STKs (PrkC and CD2148) and one phosphatase. We optimized a titanium dioxide phosphopeptide enrichment approach to determine the phosphoproteome of C. difficile. We identified and quantified 2500 proteins representing 63% of the theoretical proteome. To identify STK and serine/threonine phosphatase targets, we then performed comparative large-scale phosphoproteomics of the WT strain and isogenic ΔprkC, CD2148, Δstp, and prkC CD2148 mutants. We detected 635 proteins containing phosphorylated peptides. We showed that PrkC is phosphorylated on multiple sites in vivo and autophosphorylates in vitro. We were unable to detect a phosphorylation for CD2148 in vivo, whereas this kinase was phosphorylated in vitro only in the presence of PrkC. Forty-one phosphoproteins were identified as phosphorylated under the control of CD2148, whereas 114 proteins were phosphorylated under the control of PrkC including 27 phosphoproteins more phosphorylated in the ∆stp mutant. We also observed enrichment for phosphothreonine among the phosphopeptides more phosphorylated in the Δstp mutant. Both kinases targeted pathways required for metabolism, translation, and stress response, whereas cell division and peptidoglycan metabolism were more specifically controlled by PrkC-dependent phosphorylation in agreement with the phenotypes of the ΔprkC mutant. Using a combination of approaches, we confirmed that FtsK was phosphorylated in vivo under the control of PrkC and that Spo0A was a substrate of PrkC in vitro. This study provides a detailed mapping of kinase-substrate relationships in C. difficile, paving the way for the identification of new biomarkers and therapeutic targets.
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Affiliation(s)
- Transito Garcia-Garcia
- Laboratoire Pathogénese des Bactéries Anaérobies, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Thibaut Douché
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France
| | - Quentin Giai Gianetto
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France,Hub de bioinformatique et biostatistiques, Departement de Biologie computationelle, Institut Pasteur, Université Paris Cité, Paris, France
| | - Sandrine Poncet
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
| | - Nesrine El Omrani
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Elodie Cuenot
- Laboratoire Pathogénese des Bactéries Anaérobies, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Mariette Matondo
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France,For correspondence: Isabelle Martin-Verstraete; Mariette Matondo
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogénese des Bactéries Anaérobies, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France,Institut Universitaire de France, Paris, France,For correspondence: Isabelle Martin-Verstraete; Mariette Matondo
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18
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Role of serine/threonine protein phosphatase PrpN in the life cycle of Bacillus anthracis. PLoS Pathog 2022; 18:e1010729. [PMID: 35913993 PMCID: PMC9371265 DOI: 10.1371/journal.ppat.1010729] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 08/11/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022] Open
Abstract
Reversible protein phosphorylation at serine/threonine residues is one of the most common protein modifications, widely observed in all kingdoms of life. The catalysts controlling this modification are specific serine/threonine kinases and phosphatases that modulate various cellular pathways ranging from growth to cellular death. Genome sequencing and various omics studies have led to the identification of numerous serine/threonine kinases and cognate phosphatases, yet the physiological relevance of many of these proteins remain enigmatic. In Bacillus anthracis, only one ser/thr phosphatase, PrpC, has been functionally characterized; it was reported to be non-essential for bacterial growth and survival. In the present study, we characterized another ser/thr phosphatase (PrpN) of B. anthracis by various structural and functional approaches. To examine its physiological relevance in B. anthracis, a null mutant strain of prpN was generated and shown to have defects in sporulation and reduced synthesis of toxins (PA and LF) and the toxin activator protein AtxA. We also identified CodY, a global transcriptional regulator, as a target of PrpN and ser/thr kinase PrkC. CodY phosphorylation strongly controlled its binding to the promoter region of atxA, as shown using phosphomimetic and phosphoablative mutants. In nutshell, the present study reports phosphorylation-mediated regulation of CodY activity in the context of anthrax toxin synthesis in B. anthracis by a previously uncharacterized ser/thr protein phosphatase–PrpN. Reversible protein phosphorylation at specific ser/thr residues causes conformational changes in the protein structure, thereby modulating its cellular activity. In B. anthracis, though the role of ser/thr phosphorylation is implicated in various cellular pathways including pathogenesis, till date only one STP (PrpC) has been functionally characterized. This manuscript reports functional characterization of another STP (PrpN) in B. anthracis and with the aid of a null mutant strain (BAS ΔprpN) we provide important insight regarding the role of PrpN in the life cycle of B. anthracis. We have also identified the global transcriptional regulator, CodY as a target of PrpN and PrkC, and for the first time showed the physiological relevance of CodY phosphorylation status in the regulation of anthrax toxin synthesis.
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19
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Nipun VB, Amin KA. Recent Advances in Protein Kinase CK2, a Potential Therapeutic Target in Cancer. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:919-931. [DOI: 10.1134/s1068162022050144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- V. B. Nipun
- Cancer Research Center, Shantou University Medical Collage, Shantou, Guangdong, 515041, PR China
- Department of Chemistry, Faculty of Science, University of Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - K. A. Amin
- Department of Chemistry, Faculty of Science, University of Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
- Basic and Applied Scientific Research Center, Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
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20
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Role of Histone Deacetylases in T-Cell Development and Function. Int J Mol Sci 2022; 23:ijms23147828. [PMID: 35887172 PMCID: PMC9320103 DOI: 10.3390/ijms23147828] [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: 06/22/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 01/27/2023] Open
Abstract
Histone deacetylases (HDACs) are a group of enzymes called “epigenetic erasers”. They remove the acetyl group from histones changing the condensation state of chromatin, leading to epigenetic modification of gene expression and various downstream effects. Eighteen HDACs have been identified and grouped into four classes. The role of HDACs in T-cells has been extensively studied, and it has been proven that many of them are important players in T-cell development and function. In this review, we present the current state of knowledge on the role of HDACs in the early stages of T-cell development but also in the functioning of mature lymphocytes on the periphery, including activation, cytokine production, and metabolism regulation.
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21
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Hua L, Zhang Q, Zhu X, Wang R, You Q, Wang L. Beyond Proteolysis-Targeting Chimeric Molecules: Designing Heterobifunctional Molecules Based on Functional Effectors. J Med Chem 2022; 65:8091-8112. [PMID: 35686733 DOI: 10.1021/acs.jmedchem.2c00316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, with the successful development of proteolysis-targeting chimeric molecules (PROTACs), the potential of heterobifunctional molecules to contribute to reenvisioning drug design, especially small-molecule drugs, has been increasingly recognized. Inspired by PROTACs, diverse heterobifunctional molecules have been reported to simultaneously bind two or more molecules and bring them into proximity to interaction, such as ribonuclease-recruiting, autophagy-recruiting, lysosome-recruiting, kinase-recruiting, phosphatase-recruiting, glycosyltransferase-recruiting, and acetyltransferase-recruiting chimeras. On the basis of the heterobifunctional principle, more opportunities for advancing drug design by linking potential effectors to a protein of interest (POI) have emerged. Herein, we introduce heterobifunctional molecules other than PROTACs, summarize the limitations of existing molecules, list the main challenges, and propose perspectives for future research directions, providing insight into alternative design strategies based on substrate-proximity-based targeting.
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Affiliation(s)
- Liwen Hua
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Xinyue Zhu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Ruoning Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
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22
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Kim D, Jo YS, Jo HS, Bae S, Kwon YW, Oh YS, Yoon JH. Comparative Phosphoproteomics of Neuro-2a Cells under Insulin Resistance Reveals New Molecular Signatures of Alzheimer's Disease. Int J Mol Sci 2022; 23:ijms23021006. [PMID: 35055191 PMCID: PMC8781554 DOI: 10.3390/ijms23021006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 12/29/2022] Open
Abstract
Insulin in the brain is a well-known critical factor in neuro-development and regulation of adult neurogenesis in the hippocampus. The abnormality of brain insulin signaling is associated with the aging process and altered brain plasticity, and could promote neurodegeneration in the late stage of Alzheimer’s disease (AD). The precise molecular mechanism of the relationship between insulin resistance and AD remains unclear. The development of phosphoproteomics has advanced our knowledge of phosphorylation-mediated signaling networks and could elucidate the molecular mechanisms of certain pathological conditions. Here, we applied a reliable phosphoproteomic approach to Neuro2a (N2a) cells to identify their molecular features under two different insulin-resistant conditions with clinical relevance: inflammation and dyslipidemia. Despite significant difference in overall phosphoproteome profiles, we found molecular signatures and biological pathways in common between two insulin-resistant conditions. These include the integrin and adenosine monophosphate-activated protein kinase pathways, and we further verified these molecular targets by subsequent biochemical analysis. Among them, the phosphorylation levels of acetyl-CoA carboxylase and Src were reduced in the brain from rodent AD model 5xFAD mice. This study provides new molecular signatures for insulin resistance in N2a cells and possible links between the molecular features of insulin resistance and AD.
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Affiliation(s)
- Dayea Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI hub), Daegu 41061, Korea;
| | - Yeon Suk Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Korea; (Y.S.J.); (H.-S.J.); (S.B.); (Y.W.K.)
- Department of Brain-Cognitive Science, Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Han-Seul Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Korea; (Y.S.J.); (H.-S.J.); (S.B.); (Y.W.K.)
| | - Sungwon Bae
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Korea; (Y.S.J.); (H.-S.J.); (S.B.); (Y.W.K.)
| | - Yang Woo Kwon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Korea; (Y.S.J.); (H.-S.J.); (S.B.); (Y.W.K.)
| | - Yong-Seok Oh
- Department of Brain-Cognitive Science, Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
- Correspondence: (Y.-S.O.); (J.H.Y.); Tel.: +82-53-785-6114 (Y.-S.O.); +82-53-980-8341 (J.H.Y.)
| | - Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Korea; (Y.S.J.); (H.-S.J.); (S.B.); (Y.W.K.)
- Correspondence: (Y.-S.O.); (J.H.Y.); Tel.: +82-53-785-6114 (Y.-S.O.); +82-53-980-8341 (J.H.Y.)
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23
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Ulrych A, Fabrik I, Kupčík R, Vajrychová M, Doubravová L, Branny P. Cell Wall Stress Stimulates the Activity of the Protein Kinase StkP of Streptococcus pneumoniae, Leading to Multiple Phosphorylation. J Mol Biol 2021; 433:167319. [PMID: 34688688 DOI: 10.1016/j.jmb.2021.167319] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/06/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Streptococcus pneumoniae is an opportunistic human pathogen that encodes a single eukaryotic-type Ser/Thr protein kinase StkP and its functional counterpart, the protein phosphatase PhpP. These signaling enzymes play critical roles in coordinating cell division and growth in pneumococci. In this study, we determined the proteome and phosphoproteome profiles of relevant mutants. Comparison of those with the wild-type provided a representative dataset of novel phosphoacceptor sites and StkP-dependent substrates. StkP phosphorylates key proteins involved in cell division and cell wall biosynthesis in both the unencapsulated laboratory strain Rx1 and the encapsulated virulent strain D39. Furthermore, we show that StkP plays an important role in triggering an adaptive response induced by a cell wall-directed antibiotic. Phosphorylation of the sensor histidine kinase WalK and downregulation of proteins of the WalRK core regulon suggest crosstalk between StkP and the WalRK two-component system. Analysis of proteomic profiles led to the identification of gene clusters regulated by catabolite control mechanisms, indicating a tight coupling of carbon metabolism and cell wall homeostasis. The imbalance of steady-state protein phosphorylation in the mutants as well as after antibiotic treatment is accompanied by an accumulation of the global Spx regulator, indicating a Spx-mediated envelope stress response. In summary, StkP relays the perceived signal of cell wall status to key cell division and regulatory proteins, controlling the cell cycle and cell wall homeostasis.
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Affiliation(s)
- Aleš Ulrych
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Ivo Fabrik
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Rudolf Kupčík
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Marie Vajrychová
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Linda Doubravová
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Pavel Branny
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
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24
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Antibacterial Profile of a Microbicidal Agent Targeting Tyrosine Phosphatases and Redox Thiols, Novel Drug Targets. Antibiotics (Basel) 2021; 10:antibiotics10111310. [PMID: 34827248 PMCID: PMC8615086 DOI: 10.3390/antibiotics10111310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/23/2021] [Accepted: 10/24/2021] [Indexed: 11/16/2022] Open
Abstract
The activity profile of a protein tyrosine phosphatase (PTP) inhibitor and redox thiol oxidant, nitropropenyl benzodioxole (NPBD), was investigated across a broad range of bacterial species. In vitro assays assessed inhibitory and lethal activity patterns, the induction of drug variants on long term exposure, the inhibitory interactions of NPBD with antibiotics, and the effect of plasma proteins and redox thiols on activity. A literature review indicates the complexity of PTP and redox signaling and suggests likely metabolic targets. NPBD was broadly bactericidal to pathogens of the skin, respiratory, urogenital and intestinal tracts. It was effective against antibiotic resistant strains and slowly replicating and dormant cells. NPBD did not induce resistant or drug-tolerant phenotypes and showed low cross reactivity with antibiotics in synergy assays. Binding to plasma proteins indicated lowered in-vitro bioavailability and reduction of bactericidal activity in the presence of thiols confirmed the contribution of thiol oxidation and oxidative stress to lethality. This report presents a broad evaluation of the antibacterial effect of PTP inhibition and redox thiol oxidation, illustrates the functional diversity of bacterial PTPs and redox thiols, and supports their consideration as novel targets for antimicrobial drug development. NPBD is a dual mechanism agent with an activity profile which supports consideration of tyrosine phosphatases and bacterial antioxidant systems as promising targets for drug development.
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25
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Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence. Biochem Soc Trans 2021; 49:1905-1926. [PMID: 34374408 DOI: 10.1042/bst20191088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022]
Abstract
Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.
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26
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Fassler R, Zuily L, Lahrach N, Ilbert M, Reichmann D. The Central Role of Redox-Regulated Switch Proteins in Bacteria. Front Mol Biosci 2021; 8:706039. [PMID: 34277710 PMCID: PMC8282892 DOI: 10.3389/fmolb.2021.706039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/18/2021] [Indexed: 01/11/2023] Open
Abstract
Bacteria possess the ability to adapt to changing environments. To enable this, cells use reversible post-translational modifications on key proteins to modulate their behavior, metabolism, defense mechanisms and adaptation of bacteria to stress. In this review, we focus on bacterial protein switches that are activated during exposure to oxidative stress. Such protein switches are triggered by either exogenous reactive oxygen species (ROS) or endogenous ROS generated as by-products of the aerobic lifestyle. Both thiol switches and metal centers have been shown to be the primary targets of ROS. Cells take advantage of such reactivity to use these reactive sites as redox sensors to detect and combat oxidative stress conditions. This in turn may induce expression of genes involved in antioxidant strategies and thus protect the proteome against stress conditions. We further describe the well-characterized mechanism of selected proteins that are regulated by redox switches. We highlight the diversity of mechanisms and functions (as well as common features) across different switches, while also presenting integrative methodologies used in discovering new members of this family. Finally, we point to future challenges in this field, both in uncovering new types of switches, as well as defining novel additional functions.
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Affiliation(s)
- Rosi Fassler
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lisa Zuily
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Nora Lahrach
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Marianne Ilbert
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
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27
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The expanding world of protein kinase-like families in bacteria: forty families and counting. Biochem Soc Trans 2021; 48:1337-1352. [PMID: 32677675 DOI: 10.1042/bst20190712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022]
Abstract
The protein kinase-like clan/superfamily is a large group of regulatory, signaling and biosynthetic enzymes that were historically regarded as typically eukaryotic proteins, although bacterial members have also been known for a long time. In this review, we explore the diversity of bacterial protein kinase like families, and discuss functional versatility of these enzymes, both the ones acting within the bacterial cell, and those acting within eukaryotic cells as effectors during infection. We focus on novel bacterial kinase-like families discovered in the last five years. A bioinformatics perspective is held here, hence sequence and structure comparison overview is presented, and also a comparison of genomic neighbourhoods of the families. We perform a phylum-level census of the families. Also, we discuss apparent pseudokinases that turned out to perform alternative catalytic functions by repurposing their atypical kinase-like active sites. We also highlight some 'unpopular' kinase-like families that await characterisation.
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28
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McNeilly O, Mann R, Hamidian M, Gunawan C. Emerging Concern for Silver Nanoparticle Resistance in Acinetobacter baumannii and Other Bacteria. Front Microbiol 2021; 12:652863. [PMID: 33936010 PMCID: PMC8085274 DOI: 10.3389/fmicb.2021.652863] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
The misuse of antibiotics combined with a lack of newly developed ones is the main contributors to the current antibiotic resistance crisis. There is a dire need for new and alternative antibacterial options and nanotechnology could be a solution. Metal-based nanoparticles, particularly silver nanoparticles (NAg), have garnered widespread popularity due to their unique physicochemical properties and broad-spectrum antibacterial activity. Consequently, NAg has seen extensive incorporation in many types of products across the healthcare and consumer market. Despite clear evidence of the strong antibacterial efficacy of NAg, studies have raised concerns over the development of silver-resistant bacteria. Resistance to cationic silver (Ag+) has been recognised for many years, but it has recently been found that bacterial resistance to NAg is also possible. It is also understood that exposure of bacteria to toxic heavy metals like silver can induce the emergence of antibiotic resistance through the process of co-selection. Acinetobacter baumannii is a Gram-negative coccobacillus and opportunistic nosocomial bacterial pathogen. It was recently listed as the "number one" critical level priority pathogen because of the significant rise of antibiotic resistance in this species. NAg has proven bactericidal activity towards A. baumannii, even against strains that display multi-drug resistance. However, despite ample evidence of heavy metal (including silver; Ag+) resistance in this bacterium, combined with reports of heavy metal-driven co-selection of antibiotic resistance, little research has been dedicated to assessing the potential for NAg resistance development in A. baumannii. This is worrisome, as the increasingly indiscriminate use of NAg could promote the development of silver resistance in this species, like what has occurred with antibiotics.
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Affiliation(s)
- Oliver McNeilly
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Riti Mann
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Mohammad Hamidian
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Cindy Gunawan
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
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29
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Ahuja A, Kushwah J, Mathur C, Chauhan K, Dutta TK, Somvanshi VS. Identification of Galtox, a new protein toxin from Photorhabdus bacterial symbionts of Heterorhabditis nematodes. Toxicon 2021; 194:53-62. [PMID: 33610634 DOI: 10.1016/j.toxicon.2021.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/02/2021] [Accepted: 02/16/2021] [Indexed: 01/25/2023]
Abstract
The Gram-negative bacteria Photorhabdus lives in a symbiotic relationship with the insect-pathogenic Heterorhabditis nematodes and produces numerous hydrolytic enzymes, secondary metabolites and protein toxins. Seven Photorhabdus strains were previously isolated from the Heterorhabditis nematodes collected from different geographical regions of India. The strains IARI-SGMG3, IARI-SGHR2, IARI-SGHR4, IARI-SGMS1 and IARI-SGGJ2 were identified as P. akhurstii, whereas IARI-SGLDK1 and IARI-SGHP1 were identified as P. laumondii subsp. laumondii and P. laumondii subsp. clarkeii, respectively. A new and previously unreported 35 kDa molecular weight protein toxin 'Galtox' was identified from these Photorhabdus strains. The nucleotide sequences of the toxin gene from seven Photorhabdus strains were PCR amplified, sequenced, cloned into pET protein expression vector, and the protein toxin was expressed and purified. The Galtox sequence from various strains showed variations in sequence and toxicity against Galleria mellonella. The injection of purified Galtox protein into the 4th instar larvae showed median lethal dose (LD50) values of 2.39-26.08 ng toxin/g G. mellonella bodyweight after 48 h. The protein injection killed the insects quickly and exhibited a median lethal time (LT50) of 12-60 h when injected at the rate of 3.1-31.2 ng toxin/g G. mellonella bodyweight. Galtox protein sequence analysis indicated similarity to several bacterial toxin-related protein domains, such as 6rgnA domain of Bordetella membrane targeting toxin BteA, 6gy6 domain of Xenorhabdus α-Xenorhabdolysins, 4mu6A and 4xa9a domains similar to effector protein LegC3 from Legionella pneumophila and 1cv8.1 domain of staphylococcal cysteine proteinase staphopain B. The mode of action of Galtox needs to be understood to enable its use for the management of agricultural insect-pests.
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Affiliation(s)
- Amit Ahuja
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyoti Kushwah
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Chetna Mathur
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Khushbu Chauhan
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Tushar Kanti Dutta
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vishal Singh Somvanshi
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India.
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30
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Fontecilla-Camps JC. Primordial bioenergy sources: The two facets of adenosine triphosphate. J Inorg Biochem 2020; 216:111347. [PMID: 33450675 DOI: 10.1016/j.jinorgbio.2020.111347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023]
Abstract
Life requires energy to exist, to reproduce and to survive. Two major hypotheses have been put forward concerning the source of this energy at the very early stages of life evolution: (i) abiotic organics either brought to Earth by comets and/or meteorites, or produced at its atmosphere, and (ii) mineral surface-dependent bioinorganic catalytic reactions. Considering the latter possibility, I propose that, besides being a precursor of nucleic acids, adenosine triphosphate (ATP), which probably was used very early to improve the fidelity of nucleic acid polymerization, played an essential role in the transition between mineral-bound protocells and their free counterparts. Indeed, phosphorylation by ATP renders carboxylate groups electrophilic enough to react with nucleophiles such as amines, an effect that, thanks to their Lewis acid character, also have dehydrated metal ions on mineral surfaces. Early ATP synthesis for metabolic processes most likely depended on substrate level phosphorylation. However, the exaptation of a hexameric helicase-like ATPase and a transmembrane H+ pump (which evolved to counteract the acidity caused by fermentation reactions within the protocell) generated a much more efficient membrane-bound ATP synthase that uses chemiosmosis to make ATP.
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31
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Sharma DK, Bihani SC, Siddiqui MQ, Misra HS, Rajpurohit YS. WD40 domain of RqkA regulates its kinase activity and role in extraordinary radioresistance of D. radiodurans. J Biomol Struct Dyn 2020; 40:1246-1259. [PMID: 32990194 DOI: 10.1080/07391102.2020.1824810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
RqkA, a DNA damage responsive serine/threonine kinase, is characterized for its role in DNA repair and cell division in D. radiodurans. It has a unique combination of a kinase domain at N-terminus and a WD40 type domain at C-terminus joined through a linker. WD40 domain is comprised of eight β-propeller repeats held together via 'tryptophan-docking motifs' and forming a typical 'velcro' closure structure. RqkA mutants lacking the WD40 region (hereafter referred to as WD mutant) could not complement RqkA loss in γ radiation resistance in D. radiodurans and lacked γ radiation-mediated activation of kinase activity in vivo. WD mutants failed to phosphorylate its cognate substrate (e.g. DrRecA) in surrogate E. coli cells. Unlike wild-type enzyme, the kinase activity of its WD40 mutants was not stimulated by pyrroloquinoline quinine (PQQ) indicating the role of the WD motifs in PQQ interaction and stimulation of its kinase activity. Together, results highlighted the importance of the WD40 domain in the regulation of RqkA kinase signaling functions in vivo, and thus, the role of WD40 domain in the regulation of any STPK is first time demonstrated in bacteria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhirendra K Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Subhash C Bihani
- Radiation Biology and Health Science Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Mohammad Q Siddiqui
- Alberta RNA Research & Training Institute, Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
| | - Yogendra S Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
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32
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Thawornpan P, Jumpathong W, Thanapongpichat S, Tansila N, Win Tun A, de Jong L, Buncherd H. Magnetic Fraction of Fly Ash as a Low-Cost Magnetic Adsorbent for Selective Capture of Phosphoproteins. ANAL LETT 2020. [DOI: 10.1080/00032719.2020.1825467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Pongsakorn Thawornpan
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Watthanachai Jumpathong
- Program on Chemical Biology, Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Chulabhorn Graduate Institute, Bangkok, Thailand
| | | | - Natta Tansila
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand
| | - Aung Win Tun
- Faculty of Graduate Studies, Mahidol University, Salaya, Thailand
| | - Luitzen de Jong
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand
- Medical Science Research and Innovation Institute, Prince of Songkla University, Songkhla, Thailand
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33
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Siriwardena SU, Munkanatta Godage DNP, Shoba VM, Lai S, Shi M, Wu P, Chaudhary SK, Schreiber SL, Choudhary A. Phosphorylation-Inducing Chimeric Small Molecules. J Am Chem Soc 2020; 142:14052-14057. [DOI: 10.1021/jacs.0c05537] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sachini U. Siriwardena
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Dhanushka N. P. Munkanatta Godage
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Veronika M. Shoba
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sophia Lai
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Mengchao Shi
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Peng Wu
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Santosh K. Chaudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Stuart L. Schreiber
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
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34
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Shi Y, Zhang Y, Lin S, Wang C, Zhou J, Peng D, Xue Y. dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes. Sci Data 2020; 7:164. [PMID: 32472030 PMCID: PMC7260176 DOI: 10.1038/s41597-020-0506-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/30/2020] [Indexed: 12/20/2022] Open
Abstract
In prokaryotes, protein phosphorylation plays a critical role in regulating a broad spectrum of biological processes and occurs mainly on various amino acids, including serine (S), threonine (T), tyrosine (Y), arginine (R), aspartic acid (D), histidine (H) and cysteine (C) residues of protein substrates. Through literature curation and public database integration, here we reported an updated database of phosphorylation sites (p-sites) in prokaryotes (dbPSP 2.0) that contains 19,296 experimentally identified p-sites in 8,586 proteins from 200 prokaryotic organisms, which belong to 12 phyla of two kingdoms, bacteria and archaea. To carefully annotate these phosphoproteins and p-sites, we integrated the knowledge from 88 publicly available resources that covers 9 aspects, namely, taxonomy annotation, genome annotation, function annotation, transcriptional regulation, sequence and structure information, family and domain annotation, interaction, orthologous information and biological pathway. In contrast to version 1.0 (~30 MB), dbPSP 2.0 contains ~9 GB of data, with a 300-fold increased volume. We anticipate that dbPSP 2.0 can serve as a useful data resource for further investigating phosphorylation events in prokaryotes. dbPSP 2.0 is free for all users to access at: http://dbpsp.biocuckoo.cn.
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Affiliation(s)
- Ying Shi
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Shaofeng Lin
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Jiaqi Zhou
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Di Peng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
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Espinasse A, Wen X, Goodpaster JD, Carlson EE. Mechanistic Studies of Bioorthogonal ATP Analogues for Assessment of Histidine Kinase Autophosphorylation. ACS Chem Biol 2020; 15:1252-1260. [PMID: 32043868 DOI: 10.1021/acschembio.9b01024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Phosphorylation is an essential protein modification and is most commonly associated with hydroxyl-containing amino acids via an adenosine triphosphate (ATP) substrate. The last decades have brought greater appreciation to the roles that phosphorylation of myriad amino acids plays in biological signaling, metabolism, and gene transcription. Histidine phosphorylation occurs in both eukaryotes and prokaryotes but has been shown to dominate signaling networks in the latter due to its role in microbial two-component systems. Methods to investigate histidine phosphorylation have lagged behind those to study serine, threonine, and tyrosine modifications due to its inherent instability and the historical view that this protein modification was rare. An important strategy to overcome the reactivity of phosphohistidine is the development of substrate-based probes with altered chemical properties that improve modification longevity but that do not suffer from poor recognition or transfer by the protein. Here, we present combined experimental and computational studies to better understand the molecular requirements for efficient histidine phosphorylation by comparison of the native kinase substrate, ATP, and alkylated ATP derivatives. While recognition of the substrates by the histidine kinases is an important parameter for the formation of phosphohistidine derivatives, reaction sterics also affect the outcome. In addition, we found that stability of the resulting phosphohistidine moieties correlates with the stability of their hydrolysis products, specifically with their free energy in solution. Interestingly, alkylation dramatically affects the stability of the phosphohistidine derivatives at very acidic pH values. These results provide critical mechanistic insights into histidine phosphorylation and will facilitate the design of future probes to study enzymatic histidine phosphorylation.
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Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Xuelan Wen
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States
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Pióro M, Jakimowicz D. Chromosome Segregation Proteins as Coordinators of Cell Cycle in Response to Environmental Conditions. Front Microbiol 2020; 11:588. [PMID: 32351468 PMCID: PMC7174722 DOI: 10.3389/fmicb.2020.00588] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
Chromosome segregation is a crucial stage of the cell cycle. In general, proteins involved in this process are DNA-binding proteins, and in most bacteria, ParA and ParB are the main players; however, some bacteria manage this process by employing other proteins, such as condensins. The dynamic interaction between ParA and ParB drives movement and exerts positioning of the chromosomal origin of replication (oriC) within the cell. In addition, both ParA and ParB were shown to interact with the other proteins, including those involved in cell division or cell elongation. The significance of these interactions for the progression of the cell cycle is currently under investigation. Remarkably, DNA binding by ParA and ParB as well as their interactions with protein partners conceivably may be modulated by intra- and extracellular conditions. This notion provokes the question of whether chromosome segregation can be regarded as a regulatory stage of the cell cycle. To address this question, we discuss how environmental conditions affect chromosome segregation and how segregation proteins influence other cell cycle processes.
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Affiliation(s)
- Monika Pióro
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Dagmara Jakimowicz
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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Abstract
Over the past decade the number and variety of protein post-translational modifications that have been detected and characterized in bacteria have rapidly increased. Most post-translational protein modifications occur in a relatively low number of bacterial proteins in comparison with eukaryotic proteins, and most of the modified proteins carry low, substoichiometric levels of modification; therefore, their structural and functional analysis is particularly challenging. The number of modifying enzymes differs greatly among bacterial species, and the extent of the modified proteome strongly depends on environmental conditions. Nevertheless, evidence is rapidly accumulating that protein post-translational modifications have vital roles in various cellular processes such as protein synthesis and turnover, nitrogen metabolism, the cell cycle, dormancy, sporulation, spore germination, persistence and virulence. Further research of protein post-translational modifications will fill current gaps in the understanding of bacterial physiology and open new avenues for treatment of infectious diseases.
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38
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Kumar S, Creff G, Hennig C, Rossberg A, Steudtner R, Raff J, Vidaud C, Oberhaensli FR, Bottein MD, Auwer C. How Do Actinyls Interact with Hyperphosphorylated Yolk Protein Phosvitin? Chemistry 2019; 25:12332-12341. [DOI: 10.1002/chem.201902015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Sumit Kumar
- Institut de Chimie de NiceUniversité Côte d'Azur, CNRS 06108 Nice France
- Radioanalytical Chemistry DivisionBhabha Atomic Research Center Mumbai India
| | - Gaëlle Creff
- Institut de Chimie de NiceUniversité Côte d'Azur, CNRS 06108 Nice France
| | - Christoph Hennig
- Institute of Resource EcologyHelmholtz-Zentrum Dresden-Rossendorf Bautzner Landstrasse 400 01328 Dresden Germany
| | - André Rossberg
- Institute of Resource EcologyHelmholtz-Zentrum Dresden-Rossendorf Bautzner Landstrasse 400 01328 Dresden Germany
| | - Robin Steudtner
- Institute of Resource EcologyHelmholtz-Zentrum Dresden-Rossendorf Bautzner Landstrasse 400 01328 Dresden Germany
| | - Johannes Raff
- Institute of Resource EcologyHelmholtz-Zentrum Dresden-Rossendorf Bautzner Landstrasse 400 01328 Dresden Germany
| | | | | | | | - Christophe Auwer
- Institut de Chimie de NiceUniversité Côte d'Azur, CNRS 06108 Nice France
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Mycobacterial phosphatase PstP regulates global serine threonine phosphorylation and cell division. Sci Rep 2019; 9:8337. [PMID: 31171861 PMCID: PMC6554272 DOI: 10.1038/s41598-019-44841-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/24/2019] [Indexed: 12/28/2022] Open
Abstract
Protein phosphatase PstP is conserved throughout the Actinobacteria in a genetic locus related to cell wall synthesis and cell division. In many Actinobacteria it is the sole annotated serine threonine protein phosphatase to counter the activity of multiple serine threonine protein kinases. We used transcriptional knockdown, electron microscopy and comparative phosphoproteomics to investigate the putative dual functions of PstP as a specific regulator of cell division and as a global regulator of protein phosphorylation. Comparative phosphoproteomics in the early stages of PstP depletion showed hyperphosphorylation of protein kinases and their substrates, confirming PstP as a negative regulator of kinase activity and global serine and threonine phosphorylation. Analysis of the 838 phosphorylation sites that changed significantly, suggested that PstP may regulate diverse phosphoproteins, preferentially at phosphothreonine near acidic residues, near the protein termini, and within membrane associated proteins. Increased phosphorylation of the activation loop of protein kinase B (PknB) and of the essential PknB substrate CwlM offer possible explanations for the requirement for pstP for growth and for cell wall defects when PstP was depleted.
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40
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Nouri H, Monnier AF, Fossum-Raunehaug S, Maciag-Dorszynska M, Cabin-Flaman A, Képès F, Wegrzyn G, Szalewska-Palasz A, Norris V, Skarstad K, Janniere L. Multiple links connect central carbon metabolism to DNA replication initiation and elongation in Bacillus subtilis. DNA Res 2019; 25:641-653. [PMID: 30256918 PMCID: PMC6289782 DOI: 10.1093/dnares/dsy031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/17/2018] [Indexed: 12/27/2022] Open
Abstract
DNA replication is coupled to growth by an unknown mechanism. Here, we investigated this coupling by analyzing growth and replication in 15 mutants of central carbon metabolism (CCM) cultivated in three rich media. In about one-fourth of the condition tested, defects in replication resulting from changes in initiation or elongation were detected. This uncovered 11 CCM genes important for replication and showed that some of these genes have an effect in one, two or three media. Additional results presented here and elsewhere (Jannière, L., Canceill, D., Suski, C., et al. (2007), PLoS One, 2, e447.) showed that, in the LB medium, the CCM genes important for DNA elongation (gapA and ackA) are genetically linked to the lagging strand polymerase DnaE while those important for initiation (pgk and pykA) are genetically linked to the replication enzymes DnaC (helicase), DnaG (primase) and DnaE. Our work thus shows that the coupling between growth and replication involves multiple, medium-dependent links between CCM and replication. They also suggest that changes in CCM may affect initiation by altering the functional recruitment of DnaC, DnaG and DnaE at the chromosomal origin, and may affect elongation by altering the activity of DnaE at the replication fork. The underlying mechanism is discussed.
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Affiliation(s)
- Hamid Nouri
- iSSB, Génopole, CNRS, UEVE, Université Paris-Saclay, Evry France.,MICALIS, INRA, Jouy en Josas, France
| | | | | | | | | | - François Képès
- iSSB, Génopole, CNRS, UEVE, Université Paris-Saclay, Evry France
| | - Grzegorz Wegrzyn
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | | | - Vic Norris
- Laboratoire MERCI, AMMIS, Faculté des Sciences, Mont-Saint-Aignan, France
| | - Kirsten Skarstad
- Department of Cell Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Laurent Janniere
- iSSB, Génopole, CNRS, UEVE, Université Paris-Saclay, Evry France.,MICALIS, INRA, Jouy en Josas, France
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Humaidan D, Breinig F, Helms V. Adding phosphorylation events to the core oscillator driving the cell cycle of fission yeast. PLoS One 2018; 13:e0208515. [PMID: 30513113 PMCID: PMC6279014 DOI: 10.1371/journal.pone.0208515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/19/2018] [Indexed: 11/19/2022] Open
Abstract
Much is known about the regulatory elements controlling the cell cycle in fission yeast (Schizosaccharomyces pombe). This regulation is mainly done by the (cyclin-dependent kinase/cyclin) complex (Cdc2/Cdc13) that activates specific target genes and proteins via phosphorylation events during the cell cycle in a time-dependent manner. However, more work is still needed to complement the existing gaps in the current fission yeast gene regulatory network to be able to overcome abnormalities in its growth, repair and development, i.e. explain many phenomena including mitotic catastrophe. In this work we complement the previously presented core oscillator of the cell cycle of fission yeast by selected phosphorylation events and study their effects on the temporal evolution of the core oscillator based Boolean network. Thereby, we attempt to establish a regulatory link between the autonomous cell cycle oscillator and the remainder of the cell. We suggest the unclear yet regulatory effect of phosphorylation on the added components, and discuss many unreported points regarding the temporal evolution of the cell cycle and its components. To better visualize the results regardless of the programming background we developed an Android application that can be used to run the core and extended model of the fission yeast cell cycle step by step.
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Affiliation(s)
- Dania Humaidan
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany
- * E-mail:
| | - Frank Breinig
- Molecular and Cell Biology and Center of Human and Molecular Biology, Saarland University, Saarbruecken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany
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42
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García García T, Ventroux M, Derouiche A, Bidnenko V, Correia Santos S, Henry C, Mijakovic I, Noirot-Gros MF, Poncet S. Phosphorylation of the Bacillus subtilis Replication Controller YabA Plays a Role in Regulation of Sporulation and Biofilm Formation. Front Microbiol 2018; 9:486. [PMID: 29619013 PMCID: PMC5871692 DOI: 10.3389/fmicb.2018.00486] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/01/2018] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis cells can adopt different life-styles in response to various environmental cues, including planktonic cells during vegetative growth, sessile cells during biofilm formation and sporulation. While switching life-styles, bacteria must coordinate the progression of their cell cycle with their physiological status. Our current understanding of the regulatory pathways controlling the decision-making processes and triggering developmental switches highlights a key role of protein phosphorylation. The regulatory mechanisms that integrate the bacterial chromosome replication status with sporulation involve checkpoint proteins that target the replication initiator DnaA or the kinase phosphorelay controlling the master regulator Spo0A. B. subtilis YabA is known to interact with DnaA to prevent over-initiation of replication during vegetative growth. Here, we report that YabA is phosphorylated by YabT, a Ser/Thr kinase expressed during sporulation and biofilm formation. The phosphorylation of YabA has no effect on replication initiation control but hyper-phosphorylation of YabA leads to an increase in sporulation efficiency and a strong inhibition of biofilm formation. We also provide evidence that YabA phosphorylation affects the level of Spo0A-P in cells. These results indicate that YabA is a multifunctional protein with a dual role in regulating replication initiation and life-style switching, thereby providing a potential mechanism for cross-talk and coordination of cellular processes during adaptation to environmental change.
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Affiliation(s)
| | - Magali Ventroux
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Vladimir Bidnenko
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sara Correia Santos
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Céline Henry
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ivan Mijakovic
- Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden
| | | | - Sandrine Poncet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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43
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Shah R, Del Vecchio D. Signaling Architectures that Transmit Unidirectional Information Despite Retroactivity. Biophys J 2017; 113:728-742. [PMID: 28793226 PMCID: PMC5549655 DOI: 10.1016/j.bpj.2017.06.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/23/2017] [Accepted: 06/06/2017] [Indexed: 01/15/2023] Open
Abstract
A signaling pathway transmits information from an upstream system to downstream systems, ideally in a unidirectional fashion. A key obstacle to unidirectional transmission is retroactivity, the additional reaction flux that affects a system once its species interact with those of downstream systems. This raises the fundamental question of whether signaling pathways have developed specialized architectures that overcome retroactivity and transmit unidirectional signals. Here, we propose a general procedure based on mathematical analysis that provides an answer to this question. Using this procedure, we analyze the ability of a variety of signaling architectures to transmit one-way (from upstream to downstream) signals, as key biological parameters are tuned. We find that single stage phosphorylation and phosphotransfer systems that transmit signals from a kinase show a stringent design tradeoff that hampers their ability to overcome retroactivity. Interestingly, cascades of these architectures, which are highly represented in nature, can overcome this tradeoff and thus enable unidirectional transmission. By contrast, phosphotransfer systems, and single and double phosphorylation cycles that transmit signals from a substrate, are unable to mitigate retroactivity effects, even when cascaded, and hence are not well suited for unidirectional information transmission. These results are largely independent of the specific reaction-rate constant values, and depend on the topology of the architectures. Our results therefore identify signaling architectures that, allowing unidirectional transmission of signals, embody modular processes that conserve their input/output behavior across multiple contexts. These findings can be used to decompose natural signal transduction networks into modules, and at the same time, they establish a library of devices that can be used in synthetic biology to facilitate modular circuit design.
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Affiliation(s)
- Rushina Shah
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
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44
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Pompeo F, Foulquier E, Galinier A. Impact of Serine/Threonine Protein Kinases on the Regulation of Sporulation in Bacillus subtilis. Front Microbiol 2016; 7:568. [PMID: 27148245 PMCID: PMC4837961 DOI: 10.3389/fmicb.2016.00568] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/05/2016] [Indexed: 11/16/2022] Open
Abstract
Bacteria possess many kinases that catalyze phosphorylation of proteins on diverse amino acids including arginine, cysteine, histidine, aspartate, serine, threonine, and tyrosine. These protein kinases regulate different physiological processes in response to environmental modifications. For example, in response to nutritional stresses, the Gram-positive bacterium Bacillus subtilis can differentiate into an endospore; the initiation of sporulation is controlled by the master regulator Spo0A, which is activated by phosphorylation. Spo0A phosphorylation is carried out by a multi-component phosphorelay system. These phosphorylation events on histidine and aspartate residues are labile, highly dynamic and permit a temporal control of the sporulation initiation decision. More recently, another kind of phosphorylation, more stable yet still dynamic, on serine or threonine residues, was proposed to play a role in spore maintenance and spore revival. Kinases that perform these phosphorylation events mainly belong to the Hanks family and could regulate spore dormancy and spore germination. The aim of this mini review is to focus on the regulation of sporulation in B. subtilis by these serine and threonine phosphorylation events and the kinases catalyzing them.
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Affiliation(s)
- Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, CNRS, UMR 7283, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
| | - Elodie Foulquier
- Laboratoire de Chimie Bactérienne, CNRS, UMR 7283, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, CNRS, UMR 7283, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
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