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Zhao H, Peramuna T, Ajmal S, Wendt KL, Petrushenko ZM, Premachandra K, Cichewicz RH, Rybenkov VV. Inhibitor of Chromosome Segregation in Pseudomonas aeruginosa from Fungal Extracts. ACS Chem Biol 2024; 19:1387-1396. [PMID: 38843873 PMCID: PMC11197941 DOI: 10.1021/acschembio.4c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024]
Abstract
Chromosome segregation is an essential cellular process that has the potential to yield numerous targets for drug development. This pathway is presently underutilized partially due to the difficulties in the development of robust reporter assays suitable for high throughput screening. In bacteria, chromosome segregation is mediated by two partially redundant systems, condensins and ParABS. Based on the synthetic lethality of the two systems, we developed an assay suitable for screening and then screened a library of fungal extracts for potential inhibitors of the ParABS pathway, as judged by their enhanced activity on condensin-deficient cells. We found such activity in extracts of Humicola sp. Fractionation of the extract led to the discovery of four new analogues of sterigmatocystin, one of which, 4-hydroxy-sterigmatocystin (4HS), displayed antibacterial activity. 4HS induced the phenotype typical for parAB mutants including defects in chromosome segregation and cell division. Specifically, bacteria exposed to 4HS produced anucleate cells and were impaired in the assembly of the FtsZ ring. Moreover, 4HS binds to purified ParB in a ParS-modulated manner and inhibits its ParS-dependent CTPase activity. The data describe a small molecule inhibitor of ParB and expand the known spectrum of activities of sterigmatocystin to include bacterial chromosome segregation.
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Affiliation(s)
- Hang Zhao
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Thilini Peramuna
- Natural
Products Discovery Group, Institute for Natural Products Applications
and Research Technologies, Department of Chemistry & Biochemistry,
Stephenson Life Science Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Sidra Ajmal
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Karen L. Wendt
- Natural
Products Discovery Group, Institute for Natural Products Applications
and Research Technologies, Department of Chemistry & Biochemistry,
Stephenson Life Science Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zoya M. Petrushenko
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Kaushika Premachandra
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Robert H. Cichewicz
- Natural
Products Discovery Group, Institute for Natural Products Applications
and Research Technologies, Department of Chemistry & Biochemistry,
Stephenson Life Science Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Valentin V. Rybenkov
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
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2
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Liu C, Sun Y, Davis R, Cardona ST, Hu P. ABT-MPNN: an atom-bond transformer-based message-passing neural network for molecular property prediction. J Cheminform 2023; 15:29. [PMID: 36843022 PMCID: PMC9968697 DOI: 10.1186/s13321-023-00698-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/10/2023] [Indexed: 02/27/2023] Open
Abstract
Graph convolutional neural networks (GCNs) have been repeatedly shown to have robust capacities for modeling graph data such as small molecules. Message-passing neural networks (MPNNs), a group of GCN variants that can learn and aggregate local information of molecules through iterative message-passing iterations, have exhibited advancements in molecular modeling and property prediction. Moreover, given the merits of Transformers in multiple artificial intelligence domains, it is desirable to combine the self-attention mechanism with MPNNs for better molecular representation. We propose an atom-bond transformer-based message-passing neural network (ABT-MPNN), to improve the molecular representation embedding process for molecular property predictions. By designing corresponding attention mechanisms in the message-passing and readout phases of the MPNN, our method provides a novel architecture that integrates molecular representations at the bond, atom and molecule levels in an end-to-end way. The experimental results across nine datasets show that the proposed ABT-MPNN outperforms or is comparable to the state-of-the-art baseline models in quantitative structure-property relationship tasks. We provide case examples of Mycobacterium tuberculosis growth inhibitors and demonstrate that our model's visualization modality of attention at the atomic level could be an insightful way to investigate molecular atoms or functional groups associated with desired biological properties. The new model provides an innovative way to investigate the effect of self-attention on chemical substructures and functional groups in molecular representation learning, which increases the interpretability of the traditional MPNN and can serve as a valuable way to investigate the mechanism of action of drugs.
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Affiliation(s)
- Chengyou Liu
- grid.21613.370000 0004 1936 9609Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, MB Canada
| | - Yan Sun
- grid.21613.370000 0004 1936 9609Department of Computer Science, University of Manitoba, Winnipeg, MB Canada
| | - Rebecca Davis
- grid.21613.370000 0004 1936 9609Department of Chemistry, University of Manitoba, Winnipeg, MB Canada
| | - Silvia T. Cardona
- grid.21613.370000 0004 1936 9609Department of Microbiology, University of Manitoba, Winnipeg, MB Canada ,grid.21613.370000 0004 1936 9609Department of Medical Microbiology & Infectious Disease, University of Manitoba, Winnipeg, MB Canada
| | - Pingzhao Hu
- Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, MB, Canada. .,Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada. .,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada. .,Department of Biochemistry, Western University, Building Rm. 362, London, ON, N6A 5C1, Canada.
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3
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Liu C, Hogan AM, Sturm H, Khan MW, Islam MM, Rahman ASMZ, Davis R, Cardona ST, Hu P. Deep learning-driven prediction of drug mechanism of action from large-scale chemical-genetic interaction profiles. J Cheminform 2022; 14:12. [PMID: 35279211 PMCID: PMC8917716 DOI: 10.1186/s13321-022-00596-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 02/26/2022] [Indexed: 12/02/2022] Open
Abstract
Motivation Chemical–genetic interaction profiling is a genetic approach that quantifies the susceptibility of a set of mutants depleted in specific gene product(s) to a set of chemical compounds. With the recent advances in artificial intelligence, chemical–genetic interaction profiles (CGIPs) can be leveraged to predict mechanism of action of compounds. This can be achieved by using machine learning, where the data from a CGIP is fed into the machine learning platform along with the chemical descriptors to develop a chemogenetically trained model. As small molecules can be considered non-structural data, graph convolutional neural networks, which can learn from the chemical structures directly, can be used to successfully predict molecular properties. Clustering analysis, on the other hand, is a critical approach to get insights into the underlying biological relationships between the gene products in the high-dimensional chemical-genetic data. Methods and results In this study, we proposed a comprehensive framework based on the large-scale chemical-genetics dataset built in Mycobacterium tuberculosis for predicting CGIPs using graph-based deep learning models. Our approach is structured into three parts. First, by matching M. tuberculosis genes with homologous genes in Escherichia coli (E. coli) according to their gene products, we grouped the genes into clusters with distinct biological functions. Second, we employed a directed message passing neural network to predict growth inhibition against M. tuberculosis gene clusters using a collection of 50,000 chemicals with the profile. We compared the performance of different baseline models and implemented multi-label tasks in binary classification frameworks. Lastly, we applied the trained model to an externally curated drug set that had experimental results against M. tuberculosis genes to examine the effectiveness of our method. Overall, we demonstrate that our approach effectively created M. tuberculosis gene clusters, and the trained classifier is able to predict activity against essential M. tuberculosis targets with high accuracy. Conclusion This work provides an analytical framework for modeling large-scale chemical-genetic datasets for predicting CGIPs and generating hypothesis about mechanism of action of novel drugs. In addition, this work highlights the importance of graph-based deep neural networks in drug discovery. Supplementary Information The online version contains supplementary material available at 10.1186/s13321-022-00596-6.
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4
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Union is strength: target-based and whole-cell high throughput screens in antibacterial discovery. J Bacteriol 2021; 204:e0047721. [PMID: 34723646 DOI: 10.1128/jb.00477-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance is one of the greatest global health challenges today. For over three decades antibacterial discovery research and development has been focused on cell-based and target-based high throughput assays. Target-based screens use diagnostic enzymatic reactions to look for molecules that can bind directly and inhibit the target. Target-based screens are only applied to proteins that can be successfully expressed, purified and the activity of which can be effectively measured using a biochemical assay. Often times the molecules found in these in vitro screens are not active in cells due to poor permeability or efflux. On the other hand, cell-based screens use whole cells and look for growth inhibition. These screens give higher number of hits than target-based assays and can simultaneously test many targets of one process or pathway in their physiological context. Both strategies have pros and cons when used separately. In the past decade and a half our increasing knowledge of bacterial physiology has led to the development of innovative and sophisticated technologies to perform high throughput screening combining these two strategies and thus minimizing their disadvantages. In this review we discuss recent examples of high throughput approaches that used both target-based and whole-cell screening to find new antibacterials, the new insights they have provided and how this knowledge can be applied to other in vivo validated targets to develop new antimicrobials.
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5
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Sharma D, Sharma A, Singh B, Verma SK. Bioinformatic Exploration of Metal-Binding Proteome of Zoonotic Pathogen Orientia tsutsugamushi. Front Genet 2019; 10:797. [PMID: 31608099 PMCID: PMC6769048 DOI: 10.3389/fgene.2019.00797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/30/2019] [Indexed: 12/21/2022] Open
Abstract
Metal ions are involved in many essential biological processes and are crucial for the survival of all organisms. Identification of metal-binding proteins (MBPs) of human affecting pathogens may provide the blueprint for understanding biological metal usage and their putative roles in pathogenesis. This study is focused on the analysis of MBPs from Orientia tsutsugamushi (Ott), a causal agent of scrub typhus in humans. A total of 321 proteins were predicted as putative MBPs, based on sequence search and three-dimensional structure analysis. Majority of proteins could bind with magnesium, and the order of metal binding was Mg > Ca > Zn > Mn > Fe > Cd > Ni > Co > Cu, respectively. The predicted MBPs were functionally classified into nine broad classes. Among them, gene expression and regulation, metabolism, cell signaling, and transport classes were dominant. It was noted that the putative MBPs were localized in all subcellular compartments of Ott, but majorly found in the cytoplasm. Additionally, it was revealed that out of 321 predicted MBPs 245 proteins were putative bacterial toxins and among them, 98 proteins were nonhomologous to human proteome. Sixty putative MBPs showed the ability to interact with drug or drug-like molecules, which indicate that they may be used as broad-spectrum drug targets. These predicted MBPs from Ott could play vital role(s) in various cellular activities and virulence, hence may serve as plausible therapeutic targets to design metal-based drugs to curtail its infection.
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Affiliation(s)
- Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Ankita Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
| | - Shailender Kumar Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
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6
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Uhía I, Priestman M, Joyce G, Krishnan N, Shahrezaei V, Robertson BD. Analysis of ParAB dynamics in mycobacteria shows active movement of ParB and differential inheritance of ParA. PLoS One 2018; 13:e0199316. [PMID: 29920558 PMCID: PMC6007833 DOI: 10.1371/journal.pone.0199316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 06/05/2018] [Indexed: 01/16/2023] Open
Abstract
Correct chromosomal segregation, coordinated with cell division, is crucial for bacterial survival, but despite extensive studies, the mechanisms underlying this remain incompletely understood in mycobacteria. We report a detailed investigation of the dynamic interactions between ParA and ParB partitioning proteins in Mycobacterium smegmatis using microfluidics and time-lapse fluorescence microscopy to observe both proteins simultaneously. During growth and division, ParB presents as a focused fluorescent spot that subsequently splits in two. One focus moves towards a higher concentration of ParA at the new pole, while the other moves towards the old pole. We show ParB movement is in part an active process that does not rely on passive movement associated with cell growth. In some cells, another round of ParB segregation starts before cell division is complete, consistent with initiation of a second round of chromosome replication. ParA fluorescence distribution correlates with cell size, and in sister cells, the larger cell inherits a local peak of concentrated ParA, while the smaller sister inherits more homogeneously distributed protein. Cells which inherit more ParA grow faster than their sister cell, raising the question of whether inheritance of a local concentration of ParA provides a growth advantage. Alterations in levels of ParA and ParB were also found to disturb cell growth.
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Affiliation(s)
- Iria Uhía
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London, United Kingdom
| | - Miles Priestman
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London, United Kingdom
| | - Graham Joyce
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London, United Kingdom
| | - Nitya Krishnan
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London, United Kingdom
| | - Vahid Shahrezaei
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Brian D. Robertson
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London, United Kingdom
- * E-mail:
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7
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Misra HS, Maurya GK, Chaudhary R, Misra CS. Interdependence of bacterial cell division and genome segregation and its potential in drug development. Microbiol Res 2018; 208:12-24. [DOI: 10.1016/j.micres.2017.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 12/05/2017] [Accepted: 12/31/2017] [Indexed: 11/28/2022]
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Abstract
![]()
Current tuberculosis
(TB) drug development efforts are not sufficient
to end the global TB epidemic. Recent efforts have focused on the
development of whole-cell screening assays because biochemical, target-based
inhibitor screens during the last two decades have not delivered new
TB drugs. Mycobacterium tuberculosis (Mtb), the causative
agent of TB, encounters diverse microenvironments and can be found
in a variety of metabolic states in the human host. Due to the complexity
and heterogeneity of Mtb infection, no single model can fully recapitulate
the in vivo conditions in which Mtb is found in TB patients, and there
is no single “standard” screening condition to generate
hit compounds for TB drug development. However, current screening
assays have become more sophisticated as researchers attempt to mirror
the complexity of TB disease in the laboratory. In this review, we
describe efforts using surrogates and engineered strains of Mtb to
focus screens on specific targets. We explain model culture systems
ranging from carbon starvation to hypoxia, and combinations thereof,
designed to represent the microenvironment which Mtb encounters in
the human body. We outline ongoing efforts to model Mtb infection
in the lung granuloma. We assess these different models, their ability
to generate hit compounds, and needs for further TB drug development,
to provide direction for future TB drug discovery.
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Affiliation(s)
- Tianao Yuan
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Nicole S Sampson
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University , Stellenbosch 7600, South Africa
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9
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Kumar G, Hummel K, Welch TJ, Razzazi-Fazeli E, El-Matbouli M. Global proteomic profiling of Yersinia ruckeri strains. Vet Res 2017; 48:55. [PMID: 28931430 PMCID: PMC5607619 DOI: 10.1186/s13567-017-0460-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/06/2017] [Indexed: 11/10/2022] Open
Abstract
Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM) of salmonids. There is little information regarding the proteomics of Y. ruckeri. Herein, we perform whole protein identification and quantification of biotype 1 and biotype 2 strains of Y. ruckeri grown under standard culture conditions using a shotgun proteomic approach. Proteins were extracted, digested and peptides were separated by a nano liquid chromatography system and analyzed with a high-resolution hybrid triple quadrupole time of flight mass spectrometer coupled via a nano ESI interface. SWATH-MS technology and sophisticated statistical analyses were used to identify proteome differences among virulent and avirulent strains. GO annotation, subcellular localization, virulence proteins and antibiotic resistance ontology were predicted using bioinformatic tools. A total of 1395 proteins were identified in the whole cell of Y. ruckeri. These included proteases, chaperones, cell division proteins, outer membrane proteins, lipoproteins, receptors, ion binding proteins, transporters and catalytic proteins. In virulent strains, a total of 16 proteins were upregulated including anti-sigma regulatory factor, arginine deiminase, phosphate-binding protein PstS and superoxide dismutase Cu-Zu. Additionally, several virulence proteins were predicted such as Clp and Lon pro-teases, TolB, PPIases, PstS, PhoP and LuxR family transcriptional regulators. These putative virulence proteins might be used for development of novel targets for treatment of ERM in fish. Our study represents one of the first global proteomic reference profiles of Y. ruckeri and this data can be accessed via ProteomeXchange with identifier PXD005439. These proteomic profiles elucidate proteomic mechanisms, pathogenicity, host-interactions, antibiotic resistance ontology and localization of Y. ruckeri proteins.
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Affiliation(s)
- Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
| | - Karin Hummel
- VetCore Facility for Research/Proteomics Unit, University of Veterinary Medicine, Vienna, Austria
| | - Timothy J Welch
- National Center for Cool and Cold Water Aquaculture, Kearneysville, USA
| | - Ebrahim Razzazi-Fazeli
- VetCore Facility for Research/Proteomics Unit, University of Veterinary Medicine, Vienna, Austria
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
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10
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Identification of Mycobacterial Genes Involved in Antibiotic Sensitivity: Implications for the Treatment of Tuberculosis with β-Lactam-Containing Regimens. Antimicrob Agents Chemother 2017; 61:AAC.00425-17. [PMID: 28438925 DOI: 10.1128/aac.00425-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/09/2017] [Indexed: 12/25/2022] Open
Abstract
In a Mycobacterium smegmatis mutant library screen, transposon mutants with insertions in fhaA, dprE2, rpsT, and parA displayed hypersusceptibility to antibiotics, including the β-lactams meropenem, ampicillin, amoxicillin, and cefotaxime. Sub-MIC levels of octoclothepin, a psychotic drug inhibiting ParA, phenocopied the parA insertion and enhanced the bactericidal activity of meropenem against Mycobacterium tuberculosis in combination with clavulanate. Our study identifies novel factors associated with antibiotic resistance, with implications in repurposing β-lactams for tuberculosis treatment.
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11
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Majumder P, Moore PA, Richardson GP, Gale JE. Protecting Mammalian Hair Cells from Aminoglycoside-Toxicity: Assessing Phenoxybenzamine's Potential. Front Cell Neurosci 2017; 11:94. [PMID: 28503132 PMCID: PMC5408764 DOI: 10.3389/fncel.2017.00094] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/20/2017] [Indexed: 11/26/2022] Open
Abstract
Aminoglycosides (AGs) are widely used antibiotics because of their low cost and high efficacy against gram-negative bacterial infection. However, AGs are ototoxic, causing the death of sensory hair cells in the inner ear. Strategies aimed at developing or discovering agents that protect against aminoglycoside ototoxicity have focused on inhibiting apoptosis or more recently, on preventing antibiotic uptake by the hair cells. Recent screens for ototoprotective compounds using the larval zebrafish lateral line identified phenoxybenzamine as a potential protectant for aminoglycoside-induced hair cell death. Here we used live imaging of FM1-43 uptake as a proxy for aminoglycoside entry, combined with hair-cell death assays to evaluate whether phenoxybenzamine can protect mammalian cochlear hair cells from the deleterious effects of the aminoglycoside antibiotic neomycin. We show that phenoxybenzamine can block FM1-43 entry into mammalian hair cells in a reversible and dose-dependent manner, but pre-incubation is required for maximal inhibition of entry. We observed differential effects of phenoxybenzamine on FM1-43 uptake in the two different types of cochlear hair cell in mammals, the outer hair cells (OHCs) and inner hair cells (IHCs). The requirement for pre-incubation and reversibility suggests an intracellular rather than an extracellular site of action for phenoxybenzamine. We also tested the efficacy of phenoxybenzamine as an otoprotective agent. In mouse cochlear explants the hair cell death resulting from 24 h exposure to neomycin was steeply dose-dependent, with 50% cell death occurring at ~230 μM for both IHC and OHC. We used 250 μM neomycin in subsequent hair-cell death assays. At 100 μM with 1 h pre-incubation, phenoxybenzamine conferred significant protection to both IHCs and OHCs, however at higher concentrations phenoxybenzamine itself showed clear signs of ototoxicity and an additive toxic effect when combined with neomycin. These data do not support the use of phenoxybenzamine as a therapeutic agent in mammalian inner ear. Our findings do share parallels with the observations from the zebrafish lateral line model but they also highlight the necessity for validation in the mammalian system and the potential for differential effects on sensory hair cells from different species, in different systems and even between cells in the same organ.
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Affiliation(s)
| | | | - Guy P Richardson
- Sussex Neuroscience, School of Life Sciences, University of SussexFalmer, UK
| | - Jonathan E Gale
- UCL Ear Institute, University College LondonLondon, UK.,Department of Cell and Developmental Biology, University College LondonLondon, UK
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12
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Uhía I, Williams KJ, Shahrezaei V, Robertson BD. Mycobacterial Growth. Cold Spring Harb Perspect Med 2015; 5:cshperspect.a021097. [PMID: 25957314 DOI: 10.1101/cshperspect.a021097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In this work, we review progress made in understanding the molecular underpinnings of growth and division in mycobacteria, concentrating on work published since the last comprehensive review ( Hett and Rubin 2008). We have focused on exciting work making use of new time-lapse imaging technologies coupled with reporter-gene fusions and antimicrobial treatment to generate insights into how mycobacteria grow and divide in a heterogeneous manner. We try to reconcile the different observations reported, providing a model of how they might fit together. We also review the topic of mycobacterial spores, which has generated considerable discussion during the last few years. Resuscitation promoting factors, and regulation of growth and division, have also been actively researched, and we summarize progress in these areas.
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Affiliation(s)
- Iria Uhía
- Department of Medicine, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Kerstin J Williams
- Department of Medicine, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Vahid Shahrezaei
- Department of Mathematics, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Brian D Robertson
- Department of Medicine, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, United Kingdom
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13
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Target mechanism-based whole-cell screening identifies bortezomib as an inhibitor of caseinolytic protease in mycobacteria. mBio 2015; 6:e00253-15. [PMID: 25944857 PMCID: PMC4436076 DOI: 10.1128/mbio.00253-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A novel type of antibacterial screening method, a target mechanism-based whole-cell screening method, was developed to combine the advantages of target mechanism- and whole-cell-based approaches. A mycobacterial reporter strain with a synthetic phenotype for caseinolytic protease (ClpP1P2) activity was engineered, allowing the detection of inhibitors of this enzyme inside intact bacilli. A high-throughput screening method identified bortezomib, a human 26S proteasome drug, as a potent inhibitor of ClpP1P2 activity and bacterial growth. A battery of secondary assays was employed to demonstrate that bortezomib indeed exerts its antimicrobial activity via inhibition of ClpP1P2: Down- or upmodulation of the intracellular protease level resulted in hyper- or hyposensitivity of the bacteria, the drug showed specific potentiation of translation error-inducing aminoglycosides, ClpP1P2-specific substrate WhiB1 accumulated upon exposure, and growth inhibition potencies of bortezomib derivatives correlated with ClpP1P2 inhibition potencies. Furthermore, molecular modeling showed that the drug can bind to the catalytic sites of ClpP1P2. This work demonstrates the feasibility of target mechanism-based whole-cell screening, provides chemical validation of ClpP1P2 as a target, and identifies a drug in clinical use as a new lead compound for tuberculosis therapy. During the last decade, antibacterial drug discovery relied on biochemical assays, rather than whole-cell approaches, to identify molecules that interact with purified target proteins derived by genomics. This approach failed to deliver antibacterial compounds with whole-cell activity, either because of cell permeability issues that medicinal chemistry cannot easily fix or because genomic data of essentiality insufficiently predicted the vulnerability of the target identified. As a consequence, the field largely moved back to a whole-cell approach whose main limitation is its black-box nature, i.e., that it requires trial-and-error chemistry because the cellular target is unknown. We developed a novel type of antibacterial screening method, target mechanism-based whole-cell screening, to combine the advantages of both approaches. We engineered a mycobacterial reporter strain with a synthetic phenotype allowing us to identify inhibitors of the caseinolytic protease (ClpP1P2) inside the cell. This approach identified bortezomib, an anticancer drug, as a specific inhibitor of ClpP1P2. We further confirmed the specific “on-target” activity of bortezomib by independent approaches including, but not limited to, genetic manipulation of the target level (over- and underexpressing strains) and by establishing a dynamic structure-activity relationship between ClpP1P2 and growth inhibition. Identifying an “on-target” compound is critical to optimize the efficacy of the compound without compromising its specificity. This work demonstrates the feasibility of target mechanism-based whole-cell screening methods, validates ClpP1P2 as a druggable target, and delivers a lead compound for tuberculosis therapy.
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14
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Campen RL, Ackerley DF, Cook GM, O'Toole RF. Development of a Mycobacterium smegmatis transposon mutant array for characterising the mechanism of action of tuberculosis drugs: Findings with isoniazid and its structural analogues. Tuberculosis (Edinb) 2015; 95:432-9. [PMID: 25936537 DOI: 10.1016/j.tube.2015.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/23/2015] [Accepted: 03/29/2015] [Indexed: 01/31/2023]
Abstract
The development of new drugs is required to control human tuberculosis (TB). This study examined whether drug hypersensitive mutants could be used to reveal novel aspects of the mechanism of action of a TB drug. A transposon mutant collection with an estimated 1.1-fold genome coverage (7680 mutants) was constructed in Mycobacterium smegmatis and screened in high-throughput against isoniazid. Hypersensitive transposants with mutations in genes known to influence the mode of action of isoniazid were isolated. To further investigate the role of one of these genes, nudC, the corresponding mutant was tested for sensitivity towards isoniazid structural analogues. Overexpression of nudC, as well as inhA which encodes a known target of isoniazid, increased M. smegmatis resistance to isoniazid, but failed to increase resistance to three of the analogues, NSC27607, NSC33759, and NSC40350. In contrast, overexpression of katG resulted in increased sensitivity to each of the isoniazid analogues tested including NSC27607, NSC33759, and NSC40350. This provides evidence that the latter isoniazid analogues are activated by KatG in a NudC-independent manner and that InhA may not be their primary target. In summary, characterisation of drug hypersensitive mutants detected genes involved in the mode of action of isoniazid. Furthermore, it identified isoniazid analogues which are resilient to both InhA- and NudC-dependent mechanisms of resistance.
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Affiliation(s)
- Richard L Campen
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Ronan F O'Toole
- Breathe Well NHMRC Centre of Research Excellence, School of Medicine, University of Tasmania, Hobart, TAS, 7000, Australia.
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15
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Schnappinger D, Ehrt S. Regulated Expression Systems for Mycobacteria and Their Applications. Microbiol Spectr 2014; 2:03. [PMID: 25485177 PMCID: PMC4254785 DOI: 10.1128/microbiolspec.mgm2-0018-2013] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Indexed: 11/20/2022] Open
Abstract
For bacterial model organisms like Escherichia coli and Bacillus subtilis genetic tools to experimentally manipulate the activity of individual genes existed for decades. But for genetically less tractable yet medically important bacteria such as M. tuberculosis such tools have rarely been available. More recently several groups developed genetic switches that function efficiently in M. tuberculosis and other mycobacteria. Together these systems utilize six different transcription factors, eight different regulated promoters, and three different regulatory principles. Here we describe their design features, review their main applications, and discuss advantages and disadvantages of regulating transcription, translation, or protein stability for controlling gene activities in bacteria.
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Affiliation(s)
- Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Medical College, and Program in Molecular Biology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Medical College, and Program in Immunology and Microbial Pathogenesis, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065
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16
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Ilina EN, Shitikov EA, Ikryannikova LN, Alekseev DG, Kamashev DE, Malakhova MV, Parfenova TV, Afanas’ev MV, Ischenko DS, Bazaleev NA, Smirnova TG, Larionova EE, Chernousova LN, Beletsky AV, Mardanov AV, Ravin NV, Skryabin KG, Govorun VM. Comparative genomic analysis of Mycobacterium tuberculosis drug resistant strains from Russia. PLoS One 2013; 8:e56577. [PMID: 23437175 PMCID: PMC3577857 DOI: 10.1371/journal.pone.0056577] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 01/15/2013] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) strains is a growing problem in many countries. The availability of the complete nucleotide sequences of several MTB genomes allows to use the comparative genomics as a tool to study the relationships of strains and differences in their evolutionary history including acquisition of drug-resistance. In our work, we sequenced three genomes of Russian MTB strains of different phenotypes--drug susceptible, MDR and XDR. Of them, MDR and XDR strains were collected in Tomsk (Siberia, Russia) during the local TB outbreak in 1998-1999 and belonged to rare KQ and KY families in accordance with IS6110 typing, which are considered endemic for Russia. Based on phylogenetic analysis, our isolates belonged to different genetic families, Beijing, Ural and LAM, which made the direct comparison of their genomes impossible. For this reason we performed their comparison in the broader context of all M. tuberculosis genomes available in GenBank. The list of unique individual non-synonymous SNPs for each sequenced isolate was formed by comparison with all SNPs detected within the same phylogenetic group. For further functional analysis, all proteins with unique SNPs were ascribed to 20 different functional classes based on Clusters of Orthologous Groups (COG). We have confirmed drug resistant status of our isolates that harbored almost all known drug-resistance associated mutations. Unique SNPs of an XDR isolate CTRI-4(XDR), belonging to a Beijing family were compared in more detail with SNPs of additional 14 Russian XDR strains of the same family. Only type specific mutations in genes of repair, replication and recombination system (COG category L) were found common within this group. Probably the other unique SNPs discovered in CTRI-4(XDR) may have an important role in adaptation of this microorganism to its surrounding and in escape from antituberculosis drugs treatment.
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Affiliation(s)
- Elena N. Ilina
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Egor A. Shitikov
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | | | - Dmitry G. Alekseev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Dmitri E. Kamashev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Maja V. Malakhova
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | | | - Maxim V. Afanas’ev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Dmitry S. Ischenko
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Nikolai A. Bazaleev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | | | | | | | | | | | | | | | - Vadim M. Govorun
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
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17
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Ginda K, Bezulska M, Ziółkiewicz M, Dziadek J, Zakrzewska-Czerwińska J, Jakimowicz D. ParA ofMycobacterium smegmatisco-ordinates chromosome segregation with the cell cycle and interacts with the polar growth determinant DivIVA. Mol Microbiol 2013; 87:998-1012. [DOI: 10.1111/mmi.12146] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Katarzyna Ginda
- Faculty of Biotechnology; University of Wrocław; Wrocław; Poland
| | - Martyna Bezulska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy; Polish Academy of Sciences; Wrocław; Poland
| | | | - Jarosław Dziadek
- Medical Biology Institute; Polish Academy of Sciences; Lodowa 106; 93-232; Łódź; Poland
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18
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Ji Y, Lei T. Antisense RNA regulation and application in the development of novel antibiotics to combat multidrug resistant bacteria. Sci Prog 2013; 96:43-60. [PMID: 23738437 PMCID: PMC10365521 DOI: 10.3184/003685013x13617194309028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Despite the availability of antibiotics and vaccines, infectious diseases remain one of most dangerous threats to humans and animals. The overuse and misuse of antibacterial agents have led to the emergence of multidrug resistant bacterial pathogens. Bacterial cells are often resilient enough to survive in even the most extreme environments. To do so, the organisms have evolved different mechanisms, including a variety of two-component signal transduction systems, which allow the bacteria to sense the surrounding environment and regulate gene expression in order to adapt and respond to environmental stimuli. In addition, some bacteria evolve resistance to antibacterial agents while many bacterial cells are able to acquire resistance genes from other bacterial species to enable them to survive in the presence of toxic antimicrobial agents. The crisis of antimicrobial resistance is an unremitting menace to human health and a burden on public health. The rapid increase in antimicrobial resistant organisms and limited options for development of new classes of antibiotics heighten the urgent need to develop novel potent antibacterial therapeutics in order to combat multidrug resistant infections. In this review, we introduce the regulatory mechanisms of antisense RNA and significant applications of regulated antisense RNA interference technology in early drug discovery. This includes the identification and evaluation of drug targets in vitro and in vivo, the determination of mode of action for antibiotics and new antibacterial agents, as well as the development of peptide-nucleic acid conjugates as novel antibacterials.
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19
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Qian S, Dean R, Urban VS, Chaudhuri BN. The internal organization of mycobacterial partition assembly: does the DNA wrap a protein core? PLoS One 2012; 7:e52690. [PMID: 23285150 PMCID: PMC3527565 DOI: 10.1371/journal.pone.0052690] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/20/2012] [Indexed: 11/18/2022] Open
Abstract
Before cell division in many bacteria, the ParBs spread on a large segment of DNA encompassing the origin-proximal parS site(s) to form the partition assembly that participates in chromosome segregation. Little is known about the structural organization of chromosomal partition assembly. We report solution X-ray and neutron scattering data characterizing the size parameters and internal organization of a nucleoprotein assembly formed by the mycobacterial chromosomal ParB and a 120-meric DNA containing a parS-encompassing region from the mycobacterial genome. The cross-sectional radii of gyration and linear mass density describing the rod-like ParB-DNA assembly were determined from solution scattering. A "DNA outside, protein inside" mode of partition assembly organization consistent with the neutron scattering hydrogen/deuterium contrast variation data is discussed. In this organization, the high scattering DNA is positioned towards the outer region of the partition assembly. The new results presented here provide a basis for understanding how ParBs organize the parS-proximal chromosome, thus setting the stage for further interactions with the DNA condensins, the origin tethering factors and the ParA.
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Affiliation(s)
- Shuo Qian
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Rebecca Dean
- Hauptman Woodward Institute, Buffalo, New York, United States of America
| | - Volker S. Urban
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Barnali N. Chaudhuri
- Hauptman Woodward Institute, Buffalo, New York, United States of America
- Department of Structural Biology, State University of New York, Buffalo, New York, United States of America
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20
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Characterization of a conserved interaction between DNA glycosylase and ParA in Mycobacterium smegmatis and M. tuberculosis. PLoS One 2012; 7:e38276. [PMID: 22675536 PMCID: PMC3366916 DOI: 10.1371/journal.pone.0038276] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 05/02/2012] [Indexed: 11/19/2022] Open
Abstract
The chromosome partitioning proteins, ParAB, ensure accurate segregation of genetic materials into daughter cells and most bacterial species contain their homologs. However, little is known about the regulation of ParAB proteins. In this study, we found that 3-methyladenine DNA glycosylase I MsTAG(Ms5082) regulates bacterial growth and cell morphology by directly interacting with MsParA (Ms6939) and inhibiting its ATPase activity in Mycobacterium smegmatis. Using bacterial two-hybrid and pull-down techniques in combination with co-immunoprecipitation assays, we show that MsTAG physically interacts with MsParA both in vitro and in vivo. Expression of MsTAG under conditions of DNA damage induction exhibited similar inhibition of growth as the deletion of the parA gene in M. smegmatis. Further, the effect of MsTAG on mycobacterial growth was found to be independent of its DNA glycosylase activity, and to result instead from direct inhibition of the ATPase activity of MsParA. Co-expression of these two proteins could counteract the growth defect phenotypes observed in strains overexpressing MsTAG alone in response to DNA damage induction. Based on protein co-expression and fluorescent co-localization assays, MsParA and MsTAG were further found to co-localize in mycobacterial cells. In addition, the interaction between the DNA glycosylase and ParA, and the regulation of ParA by the glycosylase were conserved in M. tuberculosis and M. smegmatis. Our findings provide important new insights into the regulatory mechanism of cell growth and division in mycobacteria.
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21
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The evidence of large-scale DNA-induced compaction in the mycobacterial chromosomal ParB. J Mol Biol 2011; 413:901-7. [PMID: 21839743 DOI: 10.1016/j.jmb.2011.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/22/2011] [Accepted: 08/01/2011] [Indexed: 11/21/2022]
Abstract
The bacterial chromosome trafficking apparatus or the segrosome participates in the mitotic-like segregation of the chromosomes prior to cell division in several bacteria. ParB, which is the parS DNA-binding component of the segrosome, polymerizes on the parS-adjacent chromosome to form a nucleoprotein filament of unknown nature for the segregation function. We combined static light scattering, circular dichroism and small-angle X-ray scattering to present evidence that the apo form of the mycobacterial ParB forms an elongated dimer with intrinsically disordered regions as well as folded domains in solution. A comparison of the solution scattering of the apo and the parS-bound ParBs indicates a rather drastic compaction of the protein upon DNA binding. We propose that this binding-induced conformational transition is priming the ParB for polymerization on the DNA template.
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22
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Miller CH, O'Toole RF. Navigating tuberculosis drug discovery with target-based screening. Expert Opin Drug Discov 2011; 6:839-54. [DOI: 10.1517/17460441.2011.586999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Chaudhuri BN, Gupta S, Urban VS, Chance MR, D'Mello R, Smith L, Lyons K, Gee J. A combined global and local approach to elucidate spatial organization of the Mycobacterial ParB-parS partition assembly. Biochemistry 2011; 50:1799-807. [PMID: 21142182 PMCID: PMC3081668 DOI: 10.1021/bi1016759] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Combining diverse sets of data at global (size, shape) and local (residue) scales is an emerging trend for elucidating the organization and function of the cellular assemblies. We used such a strategy, combining data from X-ray and neutron scattering with H/D-contrast variation and X-ray footprinting with mass spectrometry, to elucidate the spatial organization of the ParB-parS assembly from Mycobacterium tuberculosis. The ParB-parS participates in plasmid and chromosome segregation and condensation in predivisional bacterial cells. ParB polymerizes around the parS centromere(s) to form a higher-order assembly that serves to recruit cyto-skeletal ParA ATPases and SMC proteins for chromosome segregation. A hybrid model of the ParB-parS was built by combining and correlating computational models with experiment-derived information about size, shape, position of the symmetry axis within the shape, internal topology, DNA-protein interface, exposed surface patches, and prior knowledge. This first view of the ParB-parS leads us to propose how ParB spread on the chromosome to form a larger assembly.
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24
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Ditkowski B, Troć P, Ginda K, Donczew M, Chater KF, Zakrzewska-Czerwińska J, Jakimowicz D. The actinobacterial signature protein ParJ (SCO1662) regulates ParA polymerization and affects chromosome segregation and cell division during Streptomyces sporulation. Mol Microbiol 2010; 78:1403-15. [PMID: 21143314 DOI: 10.1111/j.1365-2958.2010.07409.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial chromosome segregation usually involves cytoskeletal ParA proteins, ATPases which can form dynamic filaments. In aerial hyphae of the mycelial bacterium Streptomyces coelicolor, ParA filaments extend over tens of microns and are responsible for segregation of dozens of chromosomes. We have identified a novel interaction partner of S. coelicolor ParA, ParJ. ParJ negatively regulates ParA polymerization in vitro and is important for efficient chromosome segregation in sporulating aerial hyphae. ParJ-EGFP formed foci along aerial hyphae even in the absence of ParA. ParJ, which is encoded by sco1662, turned out to be one of the five actinobacterial signature proteins, and another of the five is a ParJ paralogue. We hypothesize that polar growth, which is characteristic not only of streptomycetes, but even of simple Actinobacteria, may be interlinked with ParA polymer assembly and its specific regulation by ParJ.
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Affiliation(s)
- Bartosz Ditkowski
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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