1
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Simonsen S, Søgaard CK, Olsen JG, Otterlei M, Kragelund BB. The bacterial DNA sliding clamp, β-clamp: structure, interactions, dynamics and drug discovery. Cell Mol Life Sci 2024; 81:245. [PMID: 38814467 PMCID: PMC11139829 DOI: 10.1007/s00018-024-05252-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
Abstract
DNA replication is a tightly coordinated event carried out by a multiprotein replication complex. An essential factor in the bacterial replication complex is the ring-shaped DNA sliding clamp, β-clamp, ensuring processive DNA replication and DNA repair through tethering of polymerases and DNA repair proteins to DNA. β -clamp is a hub protein with multiple interaction partners all binding through a conserved clamp binding sequence motif. Due to its central role as a DNA scaffold protein, β-clamp is an interesting target for antimicrobial drugs, yet little effort has been put into understanding the functional interactions of β-clamp. In this review, we scrutinize the β-clamp structure and dynamics, examine how its interactions with a plethora of binding partners are regulated through short linear binding motifs and discuss how contexts play into selection. We describe the dynamic process of clamp loading onto DNA and cover the recent advances in drug development targeting β-clamp. Despite decades of research in β-clamps and recent landmark structural insight, much remains undisclosed fostering an increased focus on this very central protein.
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Affiliation(s)
- Signe Simonsen
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Caroline K Søgaard
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Johan G Olsen
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Department of Biology, REPIN, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| | - Birthe B Kragelund
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
- Department of Biology, REPIN, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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2
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Zein U, Turgimbayeva A, Abeldenov S. Biochemical Assessment of the Mutant Sliding β-Clamp on Stimulation of Endonuclease IV from Staphylococcus aureus. Indian J Microbiol 2024; 64:165-174. [PMID: 38468727 PMCID: PMC10924856 DOI: 10.1007/s12088-023-01148-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/13/2023] [Indexed: 03/13/2024] Open
Abstract
Staphylococcus aureus is a pathogenic bacterium that causes various infections in humans. The emergence of methicillin-resistant Staphylococcus aureus makes treatment more challenging. Recent research has shown that bacterial β-clamp is not only a processivity factor but can also stimulate the activity of other enzymes of DNA metabolism. This article examines the interaction between apurinic/apyrimidinic (AP) endonuclease IV (Nfo) and β-clamp from Staphylococcus aureus, which has not been previously researched. Recombinant DNA repair enzymes, beta-clamp, were cloned, expressed, and purified. Biochemical methods were employed to assess the stimulation of beta-clamp-activated AP endonuclease activity of Nfo. We demonstrated that mutations in the C-terminal conserved region led to disruption of stimulation of Nfo AP endonuclease activity. The study provides evidence of a specific interaction between Nfo and β-clamp, which suggests that β-clamp may play a more direct role in DNA repair processes than previously thought. These findings have important implications for understanding the mechanism of DNA repair, particularly in relation to the role of β-clamp. Understanding the underlying mechanisms of interaction between DNA metabolism enzymes can aid in predicting new drug targets for antibiotic resistance battle. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01148-8.
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Affiliation(s)
- Ulan Zein
- National Center for Biotechnology, Astana, 010000 Kazakhstan
- L. N. Gumilyov Eurasian National University, Astana, 010000 Kazakhstan
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3
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Compain G, Monsarrat C, Blagojevic J, Brillet K, Dumas P, Hammann P, Kuhn L, Martiel I, Engilberge S, Oliéric V, Wolff P, Burnouf DY, Wagner J, Guichard G. Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp. JACS AU 2024; 4:432-440. [PMID: 38425897 PMCID: PMC10900491 DOI: 10.1021/jacsau.3c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 03/02/2024]
Abstract
Peptide-based covalent inhibitors targeted to nucleophilic protein residues have recently emerged as new modalities to target protein-protein interactions (PPIs) as they may provide some benefits over more classic competitive inhibitors. Covalent inhibitors are generally targeted to cysteine, the most intrinsically reactive amino acid residue, and to lysine, which is more abundant at the surface of proteins but much less frequently to histidine. Herein, we report the structure-guided design of targeted covalent inhibitors (TCIs) able to bind covalently and selectively to the bacterial sliding clamp (SC), by reacting with a well-conserved histidine residue located on the edge of the peptide-binding pocket. SC is an essential component of the bacterial DNA replication machinery, identified as a promising target for the development of new antibacterial compounds. Thermodynamic and kinetic analyses of ligands bearing different mild electrophilic warheads confirmed the higher efficiency of the chloroacetamide compared to Michael acceptors. Two high-resolution X-ray structures of covalent inhibitor-SC adducts were obtained, revealing the canonical orientation of the ligand and details of covalent bond formation with histidine. Proteomic studies were consistent with a selective SC engagement by the chloroacetamide-based TCI. Finally, the TCI of SC was substantially more active than the parent noncovalent inhibitor in an in vitro SC-dependent DNA synthesis assay, validating the potential of the approach to design covalent inhibitors of protein-protein interactions targeted to histidine.
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Affiliation(s)
- Guillaume Compain
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 Rue Robert Escarpit, F-33607 Pessac, France
| | - Clément Monsarrat
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 Rue Robert Escarpit, F-33607 Pessac, France
| | - Julie Blagojevic
- Université
de Strasbourg, CNRS, FR1589, Plateforme Protéomique Strasbourg
Esplanade, 2 Allée K. Roentgen, 67084 Strasbourg, France
| | - Karl Brillet
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Philippe Dumas
- Department
of Integrative Structural Biology, IGBMC, Strasbourg University, ESBS, 1 Rue Laurent Fries, 67404 Illkirch, Cedex, France
| | - Philippe Hammann
- Université
de Strasbourg, CNRS, FR1589, Plateforme Protéomique Strasbourg
Esplanade, 2 Allée K. Roentgen, 67084 Strasbourg, France
| | - Lauriane Kuhn
- Université
de Strasbourg, CNRS, FR1589, Plateforme Protéomique Strasbourg
Esplanade, 2 Allée K. Roentgen, 67084 Strasbourg, France
| | - Isabelle Martiel
- Swiss
Light Source (SLS), Paul Scherrer Institute
(PSI), 5232 Villigen-PSI, Switzerland
| | - Sylvain Engilberge
- Swiss
Light Source (SLS), Paul Scherrer Institute
(PSI), 5232 Villigen-PSI, Switzerland
| | - Vincent Oliéric
- Swiss
Light Source (SLS), Paul Scherrer Institute
(PSI), 5232 Villigen-PSI, Switzerland
| | - Philippe Wolff
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Dominique Y. Burnouf
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Jérôme Wagner
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Gilles Guichard
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 Rue Robert Escarpit, F-33607 Pessac, France
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4
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Hishiki A, Okazaki S, Hara K, Hashimoto H. Crystal structure of the sliding DNA clamp from the Gram-positive anaerobic bacterium Clostridioides difficile. J Biochem 2022; 173:13-20. [PMID: 36166824 DOI: 10.1093/jb/mvac079] [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: 07/05/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 01/07/2023] Open
Abstract
The sliding DNA clamp is a ring-shaped protein that encircles DNA within its central channel. It binds to multiple proteins, such as DNA polymerases and DNA repair enzymes, and stimulates their enzymatic activities, thereby playing a crucial role in cell survival and proliferation. Accordingly, the bacterial clamp DnaN is considered to be a promising target for bacterial infection therapy. In this regard, 3D structures of DnaN from pathogenic bacteria are essential for the development of chemical compounds with antimicrobial activity. Here, the crystal structure of DnaN from a Gram-positive bacterium Clostridioides difficile, a human pathogen causing infectious diarrhoea, has been determined at 2.13 Å resolution. A comparison of the structures of DnaN from other bacteria indicates that the structural features of DnaN in terms of overall organization are essentially conserved within Gram-positive and Gram-negative bacteria. However, DnaN from C. difficile has structural differences in the potential binding pocket for partner proteins, implying a non-conventional interaction with its binding partners. Our findings will provide insight into the development of new therapies for C. difficile infection.
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Affiliation(s)
- Asami Hishiki
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Sumire Okazaki
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Kodai Hara
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Hiroshi Hashimoto
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
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5
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Mulye M, Singh MI, Jain V. From Processivity to Genome Maintenance: The Many Roles of Sliding Clamps. Genes (Basel) 2022; 13:2058. [PMID: 36360296 PMCID: PMC9690074 DOI: 10.3390/genes13112058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 07/30/2023] Open
Abstract
Sliding clamps play a pivotal role in the process of replication by increasing the processivity of the replicative polymerase. They also serve as an interacting platform for a plethora of other proteins, which have an important role in other DNA metabolic processes, including DNA repair. In other words, clamps have evolved, as has been correctly referred to, into a mobile "tool-belt" on the DNA, and provide a platform for several proteins that are involved in maintaining genome integrity. Because of the central role played by the sliding clamp in various processes, its study becomes essential and relevant in understanding these processes and exploring the protein as an important drug target. In this review, we provide an updated report on the functioning, interactions, and moonlighting roles of the sliding clamps in various organisms and its utilization as a drug target.
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Affiliation(s)
- Meenakshi Mulye
- Correspondence: (M.M.); (V.J.); Tel.: +91-755-269-1425 (V.J.); Fax: +91-755-269-2392 (V.J.)
| | | | - Vikas Jain
- Correspondence: (M.M.); (V.J.); Tel.: +91-755-269-1425 (V.J.); Fax: +91-755-269-2392 (V.J.)
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6
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Hu Y, Xu F, Huang B, Chen X, Lin S. A Python script to design primers for overlap extension PCR to ligate two DNA fragments. PeerJ 2022; 10:e14283. [PMID: 36340189 PMCID: PMC9632469 DOI: 10.7717/peerj.14283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/30/2022] [Indexed: 12/02/2022] Open
Abstract
Ligating two or more DNA fragments is a regular operation for the subcloning and the engineering of vectors. The overlap extension PCR serves as a straightforward method to solve this issue. However, it takes a relatively long time to design the appropriate overlapping primers and the primers for the full-length sequence, and there has not been a professional offline software for such kind of primer design. Here, we propose a Python script to search, calculate and sort thousands of combinations of primers for users according to the predefined parameters. The results of script running and experimental validation show that this script is capable of generating the optimal pairs of primers based on the proper melting temperatures and lengths of the primers, which facilitates gene modification in research.
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Affiliation(s)
- Yunzhuo Hu
- Fujian Agriculture and Forestry University, Key Laboratory of Crop Biotechnology, Fuzhou, Fujian, China,Fujian Agriculture and Forestry University, College of Agronomy, Fuzhou, Fujian, China
| | - Fei Xu
- Fujian Agriculture and Forestry University, College of Life Science, Fuzhou, Fujian, China
| | - Bifang Huang
- Fujian Agriculture and Forestry University, College of Life Science, Fuzhou, Fujian, China
| | - Xuanyang Chen
- Fujian Agriculture and Forestry University, Key Laboratory of Crop Biotechnology, Fuzhou, Fujian, China,Fujian Agriculture and Forestry University, College of Agronomy, Fuzhou, Fujian, China
| | - Shiqiang Lin
- Fujian Agriculture and Forestry University, Key Laboratory of Crop Biotechnology, Fuzhou, Fujian, China,Fujian Agriculture and Forestry University, College of Life Science, Fuzhou, Fujian, China
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7
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Monsarrat C, Compain G, André C, Engilberge S, Martiel I, Oliéric V, Wolff P, Brillet K, Landolfo M, Silva da Veiga C, Wagner J, Guichard G, Burnouf DY. Iterative Structure-Based Optimization of Short Peptides Targeting the Bacterial Sliding Clamp. J Med Chem 2021; 64:17063-17078. [PMID: 34806883 DOI: 10.1021/acs.jmedchem.1c00918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The bacterial DNA sliding clamp (SC), or replication processivity factor, is a promising target for the development of novel antibiotics. We report a structure-activity relationship study of a new series of peptides interacting within the Escherichia coli SC (EcSC) binding pocket. Various modifications were explored including N-alkylation of the peptide bonds, extension of the N-terminal moiety, and introduction of hydrophobic and constrained residues at the C-terminus. In each category, single modifications were identified that increased affinity to EcSC. A combination of such modifications yielded in several cases to a substantially increased affinity compared to the parent peptides with Kd in the range of 30-80 nM. X-ray structure analysis of 11 peptide/EcSC co-crystals revealed new interactions at the peptide-protein interface (i.e., stacking interactions, hydrogen bonds, and hydrophobic contacts) that can account for the improved binding. Several compounds among the best binders were also found to be more effective in inhibiting SC-dependent DNA synthesis.
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Affiliation(s)
- Clément Monsarrat
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Guillaume Compain
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Christophe André
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Sylvain Engilberge
- Swiss Light Source (SLS), Paul Scherrer Institute (PSI), Forschungstrasse 111, 5232 Villigen-PSI, Switzerland
| | - Isabelle Martiel
- Swiss Light Source (SLS), Paul Scherrer Institute (PSI), Forschungstrasse 111, 5232 Villigen-PSI, Switzerland
| | - Vincent Oliéric
- Swiss Light Source (SLS), Paul Scherrer Institute (PSI), Forschungstrasse 111, 5232 Villigen-PSI, Switzerland
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 rue Conrad Roentgen, F-67000 Strasbourg, France
| | - Karl Brillet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 rue Conrad Roentgen, F-67000 Strasbourg, France
| | - Marie Landolfo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 rue Conrad Roentgen, F-67000 Strasbourg, France
| | - Cyrielle Silva da Veiga
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 rue Conrad Roentgen, F-67000 Strasbourg, France
| | - Jérôme Wagner
- Biotechnologie et Signalisation Cellulaire, UMR 7242 CNRS/Université de Strasbourg, ESBS, 300 Boulevard Sébastien Brant, 67412 Illkirch, France
| | - Gilles Guichard
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Dominique Y Burnouf
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 rue Conrad Roentgen, F-67000 Strasbourg, France
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8
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Lata K, Vishwakarma J, Kumar S, Khanam T, Ramachandran R. Mycobacterium tuberculosis Endonuclease VIII 2 (Nei2) forms a prereplicative BER complex with DnaN: Identification, characterization, and disruption of complex formation. Mol Microbiol 2021; 117:320-333. [PMID: 34820919 DOI: 10.1111/mmi.14848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022]
Abstract
Mycobacterium tuberculosis Nei2 (Rv3297) is a BER glycosylase that removes oxidized base lesions from ssDNA and replication fork-mimicking substrates. We show that Endonuclease VIII 2 (Nei2) forms a BER complex with the β-clamp (DnaN, Rv0002) with a KD of 170 nM. The Nei2-β-clamp interactions enhance Nei2's activities up to several folds. SEC analysis shows that one molecule of Nei2 binds to a single β-clamp dimer. Nei2 interacts with subsites I and II of the β-clamp via a noncanonical 223 QGCRRCGTLIAY239 Clamp Interacting Protein (CIP) motif in the C-terminal zinc-finger domain, which was previously shown by us to be dispensable for intrinsic Nei2 activity. The 12-mer peptide alone exhibited a KD of 10.28 nM, suggesting that the motif is a key mediator of Nei2-β-clamp interactions. Finally, we identified inhibitors of Nei2-β-clamp interactions using rational methods, in vitro disruption, and SPR assays after querying a database of natural products. We found that Tubulosine, Fumitremorgin C, Toyocamycin, and Aleuritic acid exhibit IC50 values of 94.47, 83.49, 109.7, and 71.49 µM, respectively. They act by disrupting Nei2-β-clamp interactions and do not affect intrinsic Nei2 activity. Among other things, the present study gives insights into the role of Nei2 in bacterial prereplicative BER.
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Affiliation(s)
- Kiran Lata
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Jyoti Vishwakarma
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanjay Kumar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Taran Khanam
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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9
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Waneka G, Vasquez YM, Bennett GM, Sloan DB. Mutational Pressure Drives Differential Genome Conservation in Two Bacterial Endosymbionts of Sap-Feeding Insects. Genome Biol Evol 2020; 13:6020258. [PMID: 33275136 PMCID: PMC7952229 DOI: 10.1093/gbe/evaa254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2020] [Indexed: 11/16/2022] Open
Abstract
Compared with free-living bacteria, endosymbionts of sap-feeding insects have tiny and rapidly evolving genomes. Increased genetic drift, high mutation rates, and relaxed selection associated with host control of key cellular functions all likely contribute to genome decay. Phylogenetic comparisons have revealed massive variation in endosymbiont evolutionary rate, but such methods make it difficult to partition the effects of mutation versus selection. For example, the ancestor of Auchenorrhynchan insects contained two obligate endosymbionts, Sulcia and a betaproteobacterium (BetaSymb; called Nasuia in leafhoppers) that exhibit divergent rates of sequence evolution and different propensities for loss and replacement in the ensuing ∼300 Ma. Here, we use the auchenorrhynchan leafhopper Macrosteles sp. nr. severini, which retains both of the ancestral endosymbionts, to test the hypothesis that differences in evolutionary rate are driven by differential mutagenesis. We used a high-fidelity technique known as duplex sequencing to measure and compare low-frequency variants in each endosymbiont. Our direct detection of de novode novo mutations reveals that the rapidly evolving endosymbiont (Nasuia) has a much higher frequency of single-nucleotide variants than the more stable endosymbiont (Sulcia) and a mutation spectrum that is potentially even more AT-biased than implied by the 83.1% AT content of its genome. We show that indels are common in both endosymbionts but differ substantially in length and distribution around repetitive regions. Our results suggest that differences in long-term rates of sequence evolution in Sulcia versus BetaSymb, and perhaps the contrasting degrees of stability of their relationships with the host, are driven by differences in mutagenesis.
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Affiliation(s)
- Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Yumary M Vasquez
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
| | - Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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10
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Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R. M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair. Nucleic Acids Res 2020; 48:4325-4343. [PMID: 32232338 PMCID: PMC7530888 DOI: 10.1093/nar/gkaa188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/24/2020] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
Class-II AP-endonuclease (XthA) and NAD+-dependent DNA ligase (LigA) are involved in initial and terminal stages of bacterial DNA base excision repair (BER), respectively. XthA acts on abasic sites of damaged DNA to create nicks with 3′OH and 5′-deoxyribose phosphate (5′-dRP) moieties. Co-immunoprecipitation using mycobacterial cell-lysate, identified MtbLigA-MtbXthA complex formation. Pull-down experiments using purified wild-type, and domain-deleted MtbLigA mutants show that LigA-XthA interactions are mediated by the BRCT-domain of LigA. Small-Angle-X-ray scattering, 15N/1H-HSQC chemical shift perturbation experiments and mutational analysis identified the BRCT-domain region that interacts with a novel 104DGQPSWSGKP113 motif on XthA for complex-formation. Isothermal-titration calorimetry experiments show that a synthetic peptide with this sequence interacts with MtbLigA and disrupts XthA–LigA interactions. In vitro assays involving DNA substrate and product analogs show that LigA can efficiently reseal 3′OH and 5′dRP DNA termini created by XthA at abasic sites. Assays and SAXS experiments performed in the presence and absence of DNA, show that XthA inhibits LigA by specifically engaging with the latter's BRCT-domain to prevent it from encircling substrate DNA. Overall, the study suggests a coordinating function for XthA whereby it engages initially with LigA to prevent the undesirable consequences of futile cleavage and ligation cycles that might derail bacterial BER.
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Affiliation(s)
- Taran Khanam
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Mohammad Afsar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Ankita Shukla
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Faiyaz Alam
- Sophisticated Analytical Instruments Based Facility and Research Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Sanjay Kumar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Horam Soyar
- Microbiology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Kunzes Dolma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Mukesh Pasupuleti
- Microbiology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Kishore Kumar Srivastava
- Microbiology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Ravi Sankar Ampapathi
- Sophisticated Analytical Instruments Based Facility and Research Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
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11
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El-Safty S, Shenashen M. Nanoscale dynamic chemical, biological sensor material designs for control monitoring and early detection of advanced diseases. Mater Today Bio 2020; 5:100044. [PMID: 32181446 PMCID: PMC7066237 DOI: 10.1016/j.mtbio.2020.100044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 12/25/2022] Open
Abstract
Early detection and easy continuous monitoring of emerging or re-emerging infectious, contagious or other diseases are of particular interest for controlling healthcare advances and developing effective medical treatments to reduce the high global cost burden of diseases in the backdrop of lack of awareness regarding advancing diseases. Under an ever-increasing demand for biosensor design reliability for early stage recognition of infectious agents or contagious diseases and potential proteins, nanoscale manufacturing designs had developed effective nanodynamic sensing assays and compact wearable devices. Dynamic developments of biosensor technology are also vital to detect and monitor advanced diseases, such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), diabetes, cancers, liver diseases, cardiovascular diseases (CVDs), tuberculosis, and central nervous system (CNS) disorders. In particular, nanoscale biosensor designs have indispensable contribution to improvement of health concerns by early detection of disease, monitoring ecological and therapeutic agents, and maintaining high safety level in food and cosmetics. This review reports an overview of biosensor designs and their feasibility for early investigation, detection, and quantitative determination of many advanced diseases. Biosensor strategies are highlighted to demonstrate the influence of nanocompact and lightweight designs on accurate analyses and inexpensive sensing assays. To date, the effective and foremost developments in various nanodynamic designs associated with simple analytical facilities and procedures remain challenging. Given the wide evolution of biosensor market requirements and the growing demand in the creation of early stage and real-time monitoring assays, precise output signals, and easy-to-wear and self-regulating analyses of diseases, innovations in biosensor designs based on novel fabrication of nanostructured platforms with active surface functionalities would produce remarkable biosensor devices. This review offers evidence for researchers and inventors to focus on biosensor challenge and improve fabrication of nanobiosensors to revolutionize consumer and healthcare markets.
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Affiliation(s)
- S.A. El-Safty
- National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukubashi, Ibaraki-ken, 305-0047, Japan
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12
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Jiang X, Zhang L, An J, Wang M, Teng M, Guo Q, Li X. Caulobacter crescentus β sliding clamp employs a noncanonical regulatory model of DNA replication. FEBS J 2019; 287:2292-2311. [PMID: 31725950 DOI: 10.1111/febs.15138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/23/2019] [Accepted: 11/12/2019] [Indexed: 01/19/2023]
Abstract
The eubacterial β sliding clamp (DnaN) plays a crucial role in DNA metabolism through direct interactions with DNA, polymerases, and a variety of protein factors. A canonical protein-DnaN interaction has been identified in Escherichia coli and some other species, during which protein partners are tethered into the conserved canonical hydrophobic crevice of DnaN via the consensus β-binding motif. Caulobacter crescentus is an excellent research model for use in the investigation of DNA replication and cell-cycle regulation due to its unique asymmetric cell division pattern with restricted replication initiation; however, little is known about the specific features of C. crescentus DnaN (CcDnaN). Here, we report a significant divergence in the association of CcDnaN with proteins based on docking analysis and crystal structures that show that the β-binding motifs of its protein partners bind a novel pocket instead of the canonical site. Pull-down and isothermal titration calorimetry results revealed that mutations within the novel pocket disrupt protein-CcDnaN interactions. It was also shown by replication and regulatory inactivation of DnaA assays that mediation of protein interaction by the novel pocket is closely related to the performance of CcDnaN during replication and the DnaN-mediated regulation process. Moreover, assessments of clamp competition showed that DNA does not compete with protein partners when binding to the novel pocket. Overall, our structural and biochemical analyses provide strong evidence that CcDnaN employs a noncanonical protein association pattern.
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Affiliation(s)
- Xuguang Jiang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Linjuan Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Jiancheng An
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Mingxing Wang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Qiong Guo
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
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13
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McGrath AE, Martyn AP, Whittell LR, Dawes FE, Beck JL, Dixon NE, Kelso MJ, Oakley AJ. Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens. J Struct Biol 2018; 204:396-405. [DOI: 10.1016/j.jsb.2018.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022]
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14
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Golichenari B, Velonia K, Nosrati R, Nezami A, Farokhi-Fard A, Abnous K, Behravan J, Tsatsakis AM. Label-free nano-biosensing on the road to tuberculosis detection. Biosens Bioelectron 2018; 113:124-135. [DOI: 10.1016/j.bios.2018.04.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/14/2018] [Accepted: 04/28/2018] [Indexed: 12/16/2022]
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15
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Rv0004 is a new essential member of the mycobacterial DNA replication machinery. PLoS Genet 2017; 13:e1007115. [PMID: 29176877 PMCID: PMC5720831 DOI: 10.1371/journal.pgen.1007115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 12/07/2017] [Accepted: 11/14/2017] [Indexed: 11/30/2022] Open
Abstract
DNA replication is fundamental for life, yet a detailed understanding of bacterial DNA replication is limited outside the organisms Escherichia coli and Bacillus subtilis. Many bacteria, including mycobacteria, encode no identified homologs of helicase loaders or regulators of the initiator protein DnaA, despite these factors being essential for DNA replication in E. coli and B. subtilis. In this study we discover that a previously uncharacterized protein, Rv0004, from the human pathogen Mycobacterium tuberculosis is essential for bacterial viability and that depletion of Rv0004 leads to a block in cell cycle progression. Using a combination of genetic and biochemical approaches, we found that Rv0004 has a role in DNA replication, interacts with DNA and the replicative helicase DnaB, and affects DnaB-DnaA complex formation. We also identify a conserved domain in Rv0004 that is predicted to structurally resemble the N-terminal protein-protein interaction domain of DnaA. Mutation of a single conserved tryptophan within Rv0004’s DnaA N-terminal-like domain leads to phenotypes similar to those observed upon Rv0004 depletion and can affect the association of Rv0004 with DnaB. In addition, using live cell imaging during depletion of Rv0004, we have uncovered a previously unappreciated role for DNA replication in coordinating mycobacterial cell division and cell size. Together, our data support that Rv0004 encodes a homolog of the recently identified DciA family of proteins found in most bacteria that lack the DnaC-DnaI helicase loaders in E. coli and B. subtilis. Therefore, the mechanisms of Rv0004 elucidated here likely apply to other DciA homologs and reveal insight into the diversity of bacterial strategies in even the most conserved biological processes. DNA is the molecule that encodes all of the genetic information of an organism. In order to pass genes onto the next generation, DNA has to first be copied through a process called DNA replication. Most of the initial studies on bacterial DNA replication were performed in Escherichia coli and Bacillus subtilis. While these studies were very informative, there is an increasing appreciation that more distantly related bacteria have diverged from these organisms in even the most fundamental processes. Mycobacteria, a group of bacteria that includes the human pathogen Mycobacterium tuberculosis, are distantly related to E. coli and B. subtilis and lack some of the proteins used for DNA replication in those model organisms. In this study, we discover that a previously uncharacterized protein in Mycobacteria, named Rv0004, is essential for bacterial viability and involved in DNA replication. Rv0004 is conserved in most bacteria but is absent from E. coli and B. subtilis. Since Rv0004 is essential for mycobacterial viability, this study both identifies a future target for antibiotic therapy and expands our knowledge on the diversity of bacterial DNA replication strategies, which may be applicable to other organisms.
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16
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High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center. Nat Commun 2017; 8:855. [PMID: 29021523 PMCID: PMC5636811 DOI: 10.1038/s41467-017-00886-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/02/2017] [Indexed: 01/07/2023] Open
Abstract
High-fidelity DNA replication depends on a proofreading 3′–5′ exonuclease that is associated with the replicative DNA polymerase. The replicative DNA polymerase DnaE1 from the major pathogen Mycobacterium tuberculosis (Mtb) uses its intrinsic PHP-exonuclease that is distinct from the canonical DEDD exonucleases found in the Escherichia coli and eukaryotic replisomes. The mechanism of the PHP-exonuclease is not known. Here, we present the crystal structure of the Mtb DnaE1 polymerase. The PHP-exonuclease has a trinuclear zinc center, coordinated by nine conserved residues. Cryo-EM analysis reveals the entry path of the primer strand in the PHP-exonuclease active site. Furthermore, the PHP-exonuclease shows a striking similarity to E. coli endonuclease IV, which provides clues regarding the mechanism of action. Altogether, this work provides important insights into the PHP-exonuclease and reveals unique properties that make it an attractive target for novel anti-mycobacterial drugs. The polymerase and histidinol phosphatase (PHP) domain in the DNA polymerase DnaE1 is essential for mycobacterial high-fidelity DNA replication. Here, the authors determine the DnaE1 crystal structure, which reveals the PHP-exonuclease mechanism that can be exploited for antibiotic development.
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17
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Machaba KE, Cele FN, Mhlongo NN, Soliman MES. Sliding Clamp of DNA Polymerase III as a Drug Target for TB Therapy: Comprehensive Conformational and Binding Analysis from Molecular Dynamic Simulations. Cell Biochem Biophys 2017; 74:473-481. [PMID: 27651172 DOI: 10.1007/s12013-016-0764-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, is one of the most common causes of death in the world. Mycobacterium tuberculosis -sliding clamp is a protein essential for many important DNA transactions including replication and DNA repair proteins, thus, a potential drug target for tuberculosis. Further investigation is needed in understanding DNA polymerase sliding clamp structure, especially from a computational perspective. In this study, we employ a wide-range of comparative molecular dynamic analyses on two systems: Mycobacterium tuberculosis - sliding clamp enzyme in its apo and bound form. The results reported in this study shows apo conformation to be less stable, as compared to bound conformation with an average radius of gyration of 25.812 and 25.459 Å, respectively. This was further supported by root mean square fluctuation, where an apo enzyme showed a higher degree of flexibility. However, the presence of the ligand lowers radius of gyration and root mean square fluctuation and also leads to an existence of negative correlated motions. Principal component analysis further justifies the same findings, whereby the apo enzyme exhibits a higher fluctuation compared to the bound complex. In addition, a stable 310 helix located at the binding site appears to be unstable in the presence of the ligand. Hence, it is possible that the binding of the ligand may have caused a rearrangement of the structure, leading to a change in the unwinding of 310 helix. Findings reported in this study further enhance the understanding of Mycobacterium tuberculosis -DnaN and also give a lead to the development of potent tuberculosis drugs.
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Affiliation(s)
- Kgothatso E Machaba
- Molecular Modeling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Favorite N Cele
- Molecular Modeling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Ndumiso N Mhlongo
- Molecular Modeling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Modeling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa.
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18
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Recent advancements in the development of anti-tuberculosis drugs. Bioorg Med Chem Lett 2016; 27:370-386. [PMID: 28017531 DOI: 10.1016/j.bmcl.2016.11.084] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/16/2016] [Accepted: 11/27/2016] [Indexed: 01/09/2023]
Abstract
Modern chemotherapy has significantly improved patient outcomes against drug-sensitive tuberculosis. However, the rapid emergence of drug-resistant tuberculosis, together with the bacterium's ability to persist and remain latent present a major public health challenge. To overcome this problem, research into novel anti-tuberculosis targets and drug candidates is thus of paramount importance. This review article provides an overview of tuberculosis highlighting the recent advances and tools that are employed in the field of anti-tuberculosis drug discovery. The predominant focus is on anti-tuberculosis agents that are currently in the pipeline, i.e. clinical trials.
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19
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Wegrzyn KE, Gross M, Uciechowska U, Konieczny I. Replisome Assembly at Bacterial Chromosomes and Iteron Plasmids. Front Mol Biosci 2016; 3:39. [PMID: 27563644 PMCID: PMC4980987 DOI: 10.3389/fmolb.2016.00039] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/25/2016] [Indexed: 11/13/2022] Open
Abstract
The proper initiation and occurrence of DNA synthesis depends on the formation and rearrangements of nucleoprotein complexes within the origin of DNA replication. In this review article, we present the current knowledge on the molecular mechanism of replication complex assembly at the origin of bacterial chromosome and plasmid replicon containing direct repeats (iterons) within the origin sequence. We describe recent findings on chromosomal and plasmid replication initiators, DnaA and Rep proteins, respectively, and their sequence-specific interactions with double- and single-stranded DNA. Also, we discuss the current understanding of the activities of DnaA and Rep proteins required for replisome assembly that is fundamental to the duplication and stability of genetic information in bacterial cells.
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Affiliation(s)
- Katarzyna E Wegrzyn
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Marta Gross
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Urszula Uciechowska
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Igor Konieczny
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
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20
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Maitra A, Bates S, Shaik M, Evangelopoulos D, Abubakar I, McHugh TD, Lipman M, Bhakta S. Repurposing drugs for treatment of tuberculosis: a role for non-steroidal anti-inflammatory drugs. Br Med Bull 2016; 118:138-48. [PMID: 27151954 PMCID: PMC5127427 DOI: 10.1093/bmb/ldw019] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/31/2016] [Indexed: 12/20/2022]
Abstract
INTRODUCTION The number of cases of drug-resistant Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), has risen rapidly in recent years. This has led to the resurgence in repurposing existing drugs, such as non-steroidal anti-inflammatory drugs (NSAIDs), for anti-TB treatment. SOURCES OF DATA Evidence from novel drug screening in vitro, in vivo, pharmacokinetic/pharmacodynamics analyses and clinical trials has been used for the preparation of this systematic review of the potential of NSAIDs for use as an adjunct in new TB chemotherapies. AREAS OF AGREEMENT Certain NSAIDs have demonstrated inhibitory properties towards actively replicating, dormant and drug-resistant clinical isolates of M. tuberculosis cells. AREAS OF CONTROVERSY NSAIDs are a diverse class of drugs, which have reported off-target activities, and their endogenous antimicrobial mechanism(s) of action is still unclear. GROWING POINTS It is essential that clinical trials of NSAIDs continue, in order to assess their suitability for addition to the current TB treatment regimen. Repurposing molecules such as NSAIDs is a vital, low-risk strategy to combat the trend of rapidly increasing antibiotic resistance.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sadé Bates
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Monisha Shaik
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | | | - Ibrahim Abubakar
- Medical Research Council Clinical Trials Unit at University College London, London, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, University College London, London NW3 2PF, UK
| | - Marc Lipman
- Royal Free London NHS Foundation Trust, and University College London, London, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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21
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Abstract
DNA replication in Escherichia coli initiates at oriC, the origin of replication and proceeds bidirectionally, resulting in two replication forks that travel in opposite directions from the origin. Here, we focus on events at the replication fork. The replication machinery (or replisome), first assembled on both forks at oriC, contains the DnaB helicase for strand separation, and the DNA polymerase III holoenzyme (Pol III HE) for DNA synthesis. DnaB interacts transiently with the DnaG primase for RNA priming on both strands. The Pol III HE is made up of three subassemblies: (i) the αɛθ core polymerase complex that is present in two (or three) copies to simultaneously copy both DNA strands, (ii) the β2 sliding clamp that interacts with the core polymerase to ensure its processivity, and (iii) the seven-subunit clamp loader complex that loads β2 onto primer-template junctions and interacts with the α polymerase subunit of the core and the DnaB helicase to organize the two (or three) core polymerases. Here, we review the structures of the enzymatic components of replisomes, and the protein-protein and protein-DNA interactions that ensure they remain intact while undergoing substantial dynamic changes as they function to copy both the leading and lagging strands simultaneously during coordinated replication.
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Affiliation(s)
- J S Lewis
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - S Jergic
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - N E Dixon
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
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22
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Abstract
The development and application of a highly versatile suite of tools for mycobacterial genetics, coupled with widespread use of "omics" approaches to elucidate the structure, function, and regulation of mycobacterial proteins, has led to spectacular advances in our understanding of the metabolism and physiology of mycobacteria. In this article, we provide an update on nucleotide metabolism and DNA replication in mycobacteria, highlighting key findings from the past 10 to 15 years. In the first section, we focus on nucleotide metabolism, ranging from the biosynthesis, salvage, and interconversion of purine and pyrimidine ribonucleotides to the formation of deoxyribonucleotides. The second part of the article is devoted to DNA replication, with a focus on replication initiation and elongation, as well as DNA unwinding. We provide an overview of replication fidelity and mutation rates in mycobacteria and summarize evidence suggesting that DNA replication occurs during states of low metabolic activity, and conclude by suggesting directions for future research to address key outstanding questions. Although this article focuses primarily on observations from Mycobacterium tuberculosis, it is interspersed, where appropriate, with insights from, and comparisons with, other mycobacterial species as well as better characterized bacterial models such as Escherichia coli. Finally, a common theme underlying almost all studies of mycobacterial metabolism is the potential to identify and validate functions or pathways that can be exploited for tuberculosis drug discovery. In this context, we have specifically highlighted those processes in mycobacterial DNA replication that might satisfy this critical requirement.
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23
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Gu S, Li W, Zhang H, Fleming J, Yang W, Wang S, Wei W, Zhou J, Zhu G, Deng J, Hou J, Zhou Y, Lin S, Zhang XE, Bi L. The β2 clamp in the Mycobacterium tuberculosis DNA polymerase III αβ2ε replicase promotes polymerization and reduces exonuclease activity. Sci Rep 2016; 6:18418. [PMID: 26822057 PMCID: PMC4731781 DOI: 10.1038/srep18418] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/17/2015] [Indexed: 12/20/2022] Open
Abstract
DNA polymerase III (DNA pol III) is a multi-subunit replication machine responsible for the accurate and rapid replication of bacterial genomes, however, how it functions in Mycobacterium tuberculosis (Mtb) requires further investigation. We have reconstituted the leading-strand replication process of the Mtb DNA pol III holoenzyme in vitro, and investigated the physical and functional relationships between its key components. We verify the presence of an αβ2ε polymerase-clamp-exonuclease replicase complex by biochemical methods and protein-protein interaction assays in vitro and in vivo and confirm that, in addition to the polymerase activity of its α subunit, Mtb DNA pol III has two potential proofreading subunits; the α and ε subunits. During DNA replication, the presence of the β2 clamp strongly promotes the polymerization of the αβ2ε replicase and reduces its exonuclease activity. Our work provides a foundation for further research on the mechanism by which the replication machinery switches between replication and proofreading and provides an experimental platform for the selection of antimicrobials targeting DNA replication in Mtb.
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Affiliation(s)
- Shoujin Gu
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjuan Li
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongtai Zhang
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Joy Fleming
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiqiang Yang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shihua Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenjing Wei
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Zhou
- The Fourth People's Hospital, Foshan 528000, China
| | - Guofeng Zhu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Jiaoyu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jian Hou
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Zhou
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shiqiang Lin
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xian-En Zhang
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lijun Bi
- Key Laboratory of RNA Biology &National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Singh MI, Jain V. Molecular Dissection of the Homotrimeric Sliding Clamp of T4 Phage: Two Domains of a Subunit Display Asymmetric Characteristics. Biochemistry 2016; 55:588-96. [DOI: 10.1021/acs.biochem.5b01204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manika Indrajit Singh
- Microbiology
and Molecular
Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India
| | - Vikas Jain
- Microbiology
and Molecular
Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India
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25
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Singh S, Singh DB, Singh A, Gautam B, Ram G, Dwivedi S, Ramteke PW. An Approach for Identification of Novel Drug Targets in Streptococcus pyogenes SF370 Through Pathway Analysis. Interdiscip Sci 2016; 8:388-394. [PMID: 26750924 DOI: 10.1007/s12539-015-0139-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 06/29/2015] [Accepted: 08/25/2015] [Indexed: 11/25/2022]
Abstract
Streptococcus pyogenes is one of the most important pathogens as it is involved in various infections affecting upper respiratory tract and skin. Due to the emergence of multidrug resistance and cross-resistance, S. Pyogenes is becoming more pathogenic and dangerous. In the present study, an in silico comparative analysis of total 65 metabolic pathways of the host (Homo sapiens) and the pathogen was performed. Initially, 486 paralogous enzymes were identified so that they can be removed from possible drug target list. The 105 enzymes of the biochemical pathways of S. pyogenes from the KEGG metabolic pathway database were compared with the proteins from the Homo sapiens by performing a BLASTP search against the non-redundant database restricted to the Homo sapiens subset. Out of these, 83 enzymes were identified as non-human homologous while 30 enzymes of inadequate amino acid length were removed for further processing. Essential enzymes were finally mined from remaining 53 enzymes. Finally, 28 essential enzymes were identified in S. pyogenes SF370 (serotype M1). In subcellular localization study, 18 enzymes were predicted with cytoplasmic localization and ten enzymes with the membrane localization. These ten enzymes with putative membrane localization should be of particular interest. Acyl-carrier-protein S-malonyltransferase, DNA polymerase III subunit beta and dihydropteroate synthase are novel drug targets and thus can be used to design potential inhibitors against S. pyogenes infection. 3D structure of dihydropteroate synthase was modeled and validated that can be used for virtual screening and interaction study of potential inhibitors with the target enzyme.
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Affiliation(s)
- Satendra Singh
- Department of Computational Biology and Bioinformatics, SHIATS, Allahabad, 211007, India
| | - Dev Bukhsh Singh
- Department of Biotechnology, Institute of Biosciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, 208024, India.
| | | | - Budhayash Gautam
- Department of Computational Biology and Bioinformatics, SHIATS, Allahabad, 211007, India
| | - Gurudayal Ram
- Department of Molecular and Cellular Engineering, SHIATS, Allahabad, 211007, India
| | - Seema Dwivedi
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201308, Uttar Pradesh, India
| | - Pramod W Ramteke
- Department of Biological Sciences, SHIATS, Allahabad, 211007, India
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Klahn P, Brönstrup M. New Structural Templates for Clinically Validated and Novel Targets in Antimicrobial Drug Research and Development. Curr Top Microbiol Immunol 2016; 398:365-417. [PMID: 27704270 DOI: 10.1007/82_2016_501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The development of bacterial resistance against current antibiotic drugs necessitates a continuous renewal of the arsenal of efficacious drugs. This imperative has not been met by the output of antibiotic research and development of the past decades for various reasons, including the declining efforts of large pharma companies in this area. Moreover, the majority of novel antibiotics are chemical derivatives of existing structures that represent mostly step innovations, implying that the available chemical space may be exhausted. This review negates this impression by showcasing recent achievements in lead finding and optimization of antibiotics that have novel or unexplored chemical structures. Not surprisingly, many of the novel structural templates like teixobactins, lysocin, griselimycin, or the albicidin/cystobactamid pair were discovered from natural sources. Additional compounds were obtained from the screening of synthetic libraries and chemical synthesis, including the gyrase-inhibiting NTBI's and spiropyrimidinetrione, the tarocin and targocil inhibitors of wall teichoic acid synthesis, or the boronates and diazabicyclo[3.2.1]octane as novel β-lactamase inhibitors. A motif that is common to most clinically validated antibiotics is that they address hotspots in complex biosynthetic machineries, whose functioning is essential for the bacterial cell. Therefore, an introduction to the biological targets-cell wall synthesis, topoisomerases, the DNA sliding clamp, and membrane-bound electron transport-is given for each of the leads presented here.
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Affiliation(s)
- Philipp Klahn
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
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Kling A, Lukat P, Almeida DV, Bauer A, Fontaine E, Sordello S, Zaburannyi N, Herrmann J, Wenzel SC, König C, Ammerman NC, Barrio MB, Borchers K, Bordon-Pallier F, Brönstrup M, Courtemanche G, Gerlitz M, Geslin M, Hammann P, Heinz DW, Hoffmann H, Klieber S, Kohlmann M, Kurz M, Lair C, Matter H, Nuermberger E, Tyagi S, Fraisse L, Grosset JH, Lagrange S, Müller R. Antibiotics. Targeting DnaN for tuberculosis therapy using novel griselimycins. Science 2015; 348:1106-12. [PMID: 26045430 DOI: 10.1126/science.aaa4690] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The discovery of Streptomyces-produced streptomycin founded the age of tuberculosis therapy. Despite the subsequent development of a curative regimen for this disease, tuberculosis remains a worldwide problem, and the emergence of multidrug-resistant Mycobacterium tuberculosis has prioritized the need for new drugs. Here we show that new optimized derivatives from Streptomyces-derived griselimycin are highly active against M. tuberculosis, both in vitro and in vivo, by inhibiting the DNA polymerase sliding clamp DnaN. We discovered that resistance to griselimycins, occurring at very low frequency, is associated with amplification of a chromosomal segment containing dnaN, as well as the ori site. Our results demonstrate that griselimycins have high translational potential for tuberculosis treatment, validate DnaN as an antimicrobial target, and capture the process of antibiotic pressure-induced gene amplification.
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Affiliation(s)
- Angela Kling
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Peer Lukat
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany. Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Deepak V Almeida
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA. KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban 4001, South Africa
| | - Armin Bauer
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Evelyne Fontaine
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Sylvie Sordello
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Nestor Zaburannyi
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Silke C Wenzel
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Claudia König
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Nicole C Ammerman
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA. KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban 4001, South Africa
| | - María Belén Barrio
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Kai Borchers
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Florence Bordon-Pallier
- Sanofi-Aventis R&D, Strategy, Science Policy & External Innovation (S&I), 75008 Paris, France
| | - Mark Brönstrup
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany. Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Gilles Courtemanche
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Martin Gerlitz
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Michel Geslin
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Peter Hammann
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 65926 Frankfurt, Germany
| | - Dirk W Heinz
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany. Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Holger Hoffmann
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Sylvie Klieber
- Sanofi-Aventis R&D, Disposition Safety and Animal Research, 34184 Montpellier, France
| | - Markus Kohlmann
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Michael Kurz
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Christine Lair
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Hans Matter
- Sanofi-Aventis R&D, LGCR/Chemistry, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Eric Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Sandeep Tyagi
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Laurent Fraisse
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Jacques H Grosset
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA. KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Durban 4001, South Africa
| | - Sophie Lagrange
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Strategic Unit, 31036 Toulouse, France
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany.
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28
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Khanam T, Rai N, Ramachandran R. Mycobacterium tuberculosis class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III exhibits DNA regulated modes of interaction with the sliding DNA β-clamp. Mol Microbiol 2015; 98:46-68. [PMID: 26103519 DOI: 10.1111/mmi.13102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2015] [Indexed: 11/30/2022]
Abstract
The class-II AP-endonuclease (XthA) acts on abasic sites of damaged DNA in bacterial base excision repair. We identified that the sliding DNA β-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239 QLRFPKK245 motif in the DNA-binding domain of XthA was found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of β-clamp located on different domains interact with XthA. The β-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. We also identified that β-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the β-clamp onto DNA is required for activity stimulation. A reduction in XthA activity stimulation was observed in the presence of β-clamp binding peptides supporting that direct interactions between the proteins are necessary to cause stimulation. Finally, we found that in the absence of DNA, the PBG located on the second domain of the β-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence.
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Affiliation(s)
- Taran Khanam
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
| | - Niyati Rai
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
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29
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Melak T, Gakkhar S. Maximum flow approach to prioritize potential drug targets of Mycobacterium tuberculosis H37Rv from protein-protein interaction network. Clin Transl Med 2015; 4:61. [PMID: 26061871 PMCID: PMC4467812 DOI: 10.1186/s40169-015-0061-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 06/02/2015] [Indexed: 01/26/2023] Open
Abstract
Background In spite of the implementations of several strategies, tuberculosis (TB) is overwhelmingly a serious global public health problem causing millions of infections and deaths every year. This is mainly due to the emergence of drug-resistance varieties of TB. The current treatment strategies for the drug-resistance TB are of longer duration, more expensive and have side effects. This highlights the importance of identification and prioritization of targets for new drugs. This study has been carried out to prioritize potential drug targets of Mycobacteriumtuberculosis H37Rv based on their flow to resistance genes. Methods The weighted proteome interaction network of the pathogen was constructed using a dataset from STRING database. Only a subset of the dataset with interactions that have a combined score value ≥770 was considered. Maximum flow approach has been used to prioritize potential drug targets. The potential drug targets were obtained through comparative genome and network centrality analysis. The curated set of resistance genes was retrieved from literatures. Detail literature review and additional assessment of the method were also carried out for validation. Results A list of 537 proteins which are essential to the pathogen and non-homologous with human was obtained from the comparative genome analysis. Through network centrality measures, 131 of them were found within the close neighborhood of the centre of gravity of the proteome network. These proteins were further prioritized based on their maximum flow value to resistance genes and they are proposed as reliable drug targets of the pathogen. Proteins which interact with the host were also identified in order to understand the infection mechanism. Conclusion Potential drug targets of Mycobacteriumtuberculosis H37Rv were successfully prioritized based on their flow to resistance genes of existing drugs which is believed to increase the druggability of the targets since inhibition of a protein that has a maximum flow to resistance genes is more likely to disrupt the communication to these genes. Purposely selected literature review of the top 14 proteins showed that many of them in this list were proposed as drug targets of the pathogen. Electronic supplementary material The online version of this article (doi:10.1186/s40169-015-0061-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tilahun Melak
- Department of Computer Science, Dilla University, Gedeo, Ethiopia,
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30
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Yin Z, Whittell LR, Wang Y, Jergic S, Ma C, Lewis PJ, Dixon NE, Beck JL, Kelso MJ, Oakley AJ. Bacterial Sliding Clamp Inhibitors that Mimic the Sequential Binding Mechanism of Endogenous Linear Motifs. J Med Chem 2015; 58:4693-702. [PMID: 25970224 DOI: 10.1021/acs.jmedchem.5b00232] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The bacterial DNA replication machinery presents new targets for the development of antibiotics acting via novel mechanisms. One such target is the protein-protein interaction between the DNA sliding clamp and the conserved peptide linear motifs in DNA polymerases. We previously established that binding of linear motifs to the Escherichia coli sliding clamp occurs via a sequential mechanism that involves two subsites (I and II). Here, we report the development of small-molecule inhibitors that mimic this mechanism. The compounds contain tetrahydrocarbazole moieties as "anchors" to occupy subsite I. Functional groups appended at the tetrahydrocarbazole nitrogen bind to a channel gated by the side chain of M362 and lie at the edge of subsite II. One derivative induced the formation of a new binding pocket, termed subsite III, by rearrangement of a loop adjacent to subsite I. Discovery of the extended binding area will guide further inhibitor development.
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Affiliation(s)
- Zhou Yin
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Louise R Whittell
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Yao Wang
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Slobodan Jergic
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Cong Ma
- ‡School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Peter J Lewis
- ‡School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Nicholas E Dixon
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Jennifer L Beck
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Michael J Kelso
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Aaron J Oakley
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
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31
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Niiranen L, Lian K, Johnson KA, Moe E. Crystal structure of the DNA polymerase III β subunit (β-clamp) from the extremophile Deinococcus radiodurans. BMC STRUCTURAL BIOLOGY 2015; 15:5. [PMID: 25886944 PMCID: PMC4350885 DOI: 10.1186/s12900-015-0032-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/13/2015] [Indexed: 02/08/2023]
Abstract
BACKGROUND Deinococcus radiodurans is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III β subunit (β-clamp) acts as a sliding clamp on DNA, promoting the binding and processivity of many DNA-acting proteins, and here we report the crystal structure of D. radiodurans β-clamp (Drβ-clamp) at 2.0 Å resolution. RESULTS The sequence verification process revealed that at the time of the study the gene encoding Drβ-clamp was wrongly annotated in the genome database, encoding a protein of 393 instead of 362 amino acids. The short protein was successfully expressed, purified and used for crystallisation purposes in complex with Cy5-labeled DNA. The structure, which was obtained from blue crystals, shows a typical ring-shaped bacterial β-clamp formed of two monomers, each with three domains of identical topology, but with no visible DNA in electron density. A visualisation of the electrostatic surface potential reveals a highly negatively charged outer surface while the inner surface and the dimer forming interface have a more even charge distribution. CONCLUSIONS The structure of Drβ-clamp was determined to 2.0 Å resolution and shows an evenly distributed electrostatic surface charge on the DNA interacting side. We hypothesise that this charge distribution may facilitate efficient movement on encircled DNA and help ensure efficient DNA metabolism in D. radiodurans upon exposure to high doses of ionizing irradiation or desiccation.
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Affiliation(s)
- Laila Niiranen
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UIT - the Arctic University of Norway, N-9037, Tromsø, Norway.
| | - Kjersti Lian
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UIT - the Arctic University of Norway, N-9037, Tromsø, Norway.
| | - Kenneth A Johnson
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UIT - the Arctic University of Norway, N-9037, Tromsø, Norway.
| | - Elin Moe
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UIT - the Arctic University of Norway, N-9037, Tromsø, Norway. .,The Macromolecular Crystallography Unit, Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal.
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Yadav N, Khanam T, Shukla A, Rai N, Hajela K, Ramachandran R. Tricyclic dihydrobenzoxazepine and tetracyclic indole derivatives can specifically target bacterial DNA ligases and can distinguish them from human DNA ligase I. Org Biomol Chem 2015; 13:5475-87. [DOI: 10.1039/c5ob00439j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA ligases are critical components for DNA metabolism in all organisms.
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Affiliation(s)
- Nisha Yadav
- From Medicinal and Process Chemistry
- CSIR-Central Drug Research Institute
- India
| | - Taran Khanam
- From the Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- India
| | - Ankita Shukla
- From the Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- India
| | - Niyati Rai
- From the Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- India
| | - Kanchan Hajela
- From Medicinal and Process Chemistry
- CSIR-Central Drug Research Institute
- India
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Wolff P, Amal I, Oliéric V, Chaloin O, Gygli G, Ennifar E, Lorber B, Guichard G, Wagner J, Dejaegere A, Burnouf DY. Differential modes of peptide binding onto replicative sliding clamps from various bacterial origins. J Med Chem 2014; 57:7565-76. [PMID: 25170813 DOI: 10.1021/jm500467a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial sliding clamps are molecular hubs that interact with many proteins involved in DNA metabolism through their binding, via a conserved peptidic sequence, into a universally conserved pocket. This interacting pocket is acknowledged as a potential molecular target for the development of new antibiotics. We previously designed short peptides with an improved affinity for the Escherichia coli binding pocket. Here we show that these peptides differentially interact with other bacterial clamps, despite the fact that all pockets are structurally similar. Thermodynamic and modeling analyses of the interactions differentiate between two categories of clamps: group I clamps interact efficiently with our designed peptides and assemble the Escherichia coli and related orthologs clamps, whereas group II clamps poorly interact with the same peptides and include Bacillus subtilis and other Gram-positive clamps. These studies also suggest that the peptide binding process could occur via different mechanisms, which depend on the type of clamp.
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Affiliation(s)
- Philippe Wolff
- Université de Strasbourg , UPR9002, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15, rue René Descartes, 67084 Strasbourg, France
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Yin Z, Wang Y, Whittell L, Jergic S, Liu M, Harry E, Dixon N, Kelso M, Beck J, Oakley A. DNA Replication Is the Target for the Antibacterial Effects of Nonsteroidal Anti-Inflammatory Drugs. ACTA ACUST UNITED AC 2014; 21:481-487. [DOI: 10.1016/j.chembiol.2014.02.009] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/03/2014] [Accepted: 02/13/2014] [Indexed: 12/11/2022]
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35
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Yin Z, Whittell LR, Wang Y, Jergic S, Liu M, Harry EJ, Dixon NE, Beck JL, Kelso MJ, Oakley AJ. Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach. J Med Chem 2014; 57:2799-806. [PMID: 24592885 DOI: 10.1021/jm500122r] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bacterial sliding clamp (SC), also known as the DNA polymerase III β subunit, is an emerging antibacterial target that plays a central role in DNA replication, serving as a protein-protein interaction hub with a common binding pocket to recognize linear motifs in the partner proteins. Here, fragment-based screening using X-ray crystallography produced four hits bound in the linear-motif-binding pocket of the Escherichia coli SC. Compounds structurally related to the hits were identified that inhibited the E. coli SC and SC-mediated DNA replication in vitro. A tetrahydrocarbazole derivative emerged as a promising lead whose methyl and ethyl ester prodrug forms showed minimum inhibitory concentrations in the range of 21-43 μg/mL against representative Gram-negative and Gram-positive bacteria species. The work demonstrates the utility of a fragment-based approach for identifying bacterial sliding clamp inhibitors as lead compounds with broad-spectrum antibacterial activity.
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Affiliation(s)
- Zhou Yin
- School of Chemistry and Centre for Medical and Molecular Bioscience, University of Wollongong , Wollongong, New South Wales 2522, Australia
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Kukshal V, Khanam T, Chopra D, Singh N, Sanyal S, Ramachandran R. M. tuberculosis sliding β-clamp does not interact directly with the NAD+-dependent DNA ligase. PLoS One 2012; 7:e35702. [PMID: 22545130 PMCID: PMC3335792 DOI: 10.1371/journal.pone.0035702] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 03/20/2012] [Indexed: 11/26/2022] Open
Abstract
The sliding β-clamp, an important component of the DNA replication and repair machinery, is drawing increasing attention as a therapeutic target. We report the crystal structure of the M. tuberculosis β-clamp (Mtbβ-clamp) to 3.0 Å resolution. The protein crystallized in the space group C222(1) with cell-dimensions a = 72.7, b = 234.9 & c = 125.1 Å respectively. Mtbβ-clamp is a dimer, and exhibits head-to-tail association similar to other bacterial clamps. Each monomer folds into three domains with similar structures respectively and associates with its dimeric partner through 6 salt-bridges and about 21 polar interactions. Affinity experiments involving a blunt DNA duplex, primed-DNA and nicked DNA respectively show that Mtbβ-clamp binds specifically to primed DNA about 1.8 times stronger compared to the other two substrates and with an apparent K(d) of 300 nM. In bacteria like E. coli, the β-clamp is known to interact with subunits of the clamp loader, NAD(+)-dependent DNA ligase (LigA) and other partners. We tested the interactions of the Mtbβ-clamp with MtbLigA and the γ-clamp loader subunit through radioactive gel shift assays, size exclusion chromatography, yeast-two hybrid experiments and also functionally. Intriguingly while Mtbβ-clamp interacts in vitro with the γ-clamp loader, it does not interact with MtbLigA unlike in bacteria like E. coli where it does. Modeling studies involving earlier peptide complexes reveal that the peptide-binding site is largely conserved despite lower sequence identity between bacterial clamps. Overall the results suggest that other as-yet-unidentified factors may mediate interactions between the clamp, LigA and DNA in mycobacteria.
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Affiliation(s)
- Vandna Kukshal
- Molecular and Structural Biology Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Taran Khanam
- Molecular and Structural Biology Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Deepti Chopra
- Molecular and Structural Biology Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Nidhi Singh
- Drug Target Discovery and Development Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Sabyasachi Sanyal
- Drug Target Discovery and Development Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
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