1
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Luo G, Ming T, Yang L, He L, Tao T, Wang Y. Modulators targeting protein-protein interactions in Mycobacterium tuberculosis. Microbiol Res 2024; 284:127675. [PMID: 38636239 DOI: 10.1016/j.micres.2024.127675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/20/2024]
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis), mainly transmitted through droplets to infect the lungs, and seriously affecting patients' health and quality of life. Clinically, anti-TB drugs often entail side effects and lack efficacy against resistant strains. Thus, the exploration and development of novel targeted anti-TB medications are imperative. Currently, protein-protein interactions (PPIs) offer novel avenues for anti-TB drug development, and the study of targeted modulators of PPIs in M. tuberculosis has become a prominent research focus. Furthermore, a comprehensive PPI network has been constructed using computational methods and bioinformatics tools. This network allows for a more in-depth analysis of the structural biology of PPIs and furnishes essential insights for the development of targeted small-molecule modulators. Furthermore, this article provides a detailed overview of the research progress and regulatory mechanisms of PPI modulators in M. tuberculosis, the causative agent of TB. Additionally, it summarizes potential targets for anti-TB drugs and discusses the prospects of existing PPI modulators.
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Affiliation(s)
- Guofeng Luo
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianqi Ming
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Luchuan Yang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Lei He
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Tao Tao
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Yanmei Wang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China.
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2
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Henriksen C, Baek KT, Wacnik K, Gallay C, Veening JW, Foster SJ, Frees D. The ClpX chaperone and a hypermorphic FtsA variant with impaired self-interaction are mutually compensatory for coordinating Staphylococcus aureus cell division. Mol Microbiol 2024; 121:98-115. [PMID: 38041395 DOI: 10.1111/mmi.15200] [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: 08/28/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023]
Abstract
Bacterial cell division requires the coordinated assembly and disassembly of a large protein complex called the divisome; however, the exact role of molecular chaperones in this critical process remains unclear. We here provide genetic evidence that ClpX unfoldase activity is a determinant for proper coordination of bacterial cell division by showing the growth defect of a Staphylococcus aureus clpX mutant is rescued by a spontaneously acquired G325V substitution in the ATP-binding domain of the essential FtsA cell division protein. The polymerization state of FtsA is thought to control initiation of bacterial septum synthesis and, while restoring the aberrant FtsA dynamics in clpX cells, the FtsAG325V variant displayed reduced ability to interact with itself and other cell division proteins. In wild-type cells, the ftsAG325V allele shared phenotypes with Escherichia coli superfission ftsA mutants and accelerated the cell cycle, increased the risk of daughter cell lysis, and conferred sensitivity to heat and antibiotics inhibiting cell wall synthesis. Strikingly, lethality was mitigated by spontaneous mutations that inactivate ClpX. Taken together, our results suggest that ClpX promotes septum synthesis by antagonizing FtsA interactions and illuminates the critical role of a protein unfoldase in coordinating bacterial cell division.
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Affiliation(s)
- Camilla Henriksen
- Department of Veterinary and Animal Disease, University of Copenhagen, Frederiksberg, Denmark
| | - Kristoffer T Baek
- Department of Veterinary and Animal Disease, University of Copenhagen, Frederiksberg, Denmark
| | | | - Clement Gallay
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Simon J Foster
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Dorte Frees
- Department of Veterinary and Animal Disease, University of Copenhagen, Frederiksberg, Denmark
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3
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Schmitz KR, Handy EL, Compton CL, Gupta S, Bishai WR, Sauer RT, Sello JK. Acyldepsipeptide Antibiotics and a Bioactive Fragment Thereof Differentially Perturb Mycobacterium tuberculosis ClpXP1P2 Activity in Vitro. ACS Chem Biol 2023; 18:724-733. [PMID: 32083462 PMCID: PMC7842861 DOI: 10.1021/acschembio.9b00454] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proteolytic complexes in Mycobacterium tuberculosis (Mtb), the deadliest bacterial pathogen, are major foci in tuberculosis drug development programs. The Clp proteases, which are essential for Mtb viability, are high-priority targets. These proteases function through the collaboration of ClpP1P2, a barrel-shaped heteromeric peptidase, with associated ATP-dependent chaperones like ClpX and ClpC1 that recognize and unfold specific substrates in an ATP-dependent fashion. The critical interaction of the peptidase and its unfoldase partners is blocked by the competitive binding of acyldepsipeptide antibiotics (ADEPs) to the interfaces of the ClpP2 subunits. The resulting inhibition of Clp protease activity is lethal to Mtb. Here, we report the surprising discovery that a fragment of the ADEPs retains anti-Mtb activity yet stimulates rather than inhibits the ClpXP1P2-catalyzed degradation of proteins. Our data further suggest that the fragment stabilizes the ClpXP1P2 complex and binds ClpP1P2 in a fashion distinct from that of the intact ADEPs. A structure-activity relationship study of the bioactive fragment defines the pharmacophore and points the way toward the development of new drug leads for the treatment of tuberculosis.
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Affiliation(s)
- Karl R. Schmitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
- Department of Biological Sciences, University of Delaware, Newark, DE
| | - Emma L. Handy
- Department of Chemistry, Brown University, Providence, RI
| | | | - Shashank Gupta
- Department of Chemistry, Brown University, Providence, RI
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Jason K. Sello
- Department of Chemistry, Brown University, Providence, RI
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
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4
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Liu K, Gao Y, Li ZH, Liu M, Wang FQ, Wei DZ. CRISPR-Cas12a assisted precise genome editing of Mycolicibacterium neoaurum. N Biotechnol 2021; 66:61-69. [PMID: 34653700 DOI: 10.1016/j.nbt.2021.10.003] [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: 08/20/2020] [Revised: 10/09/2021] [Accepted: 10/10/2021] [Indexed: 12/27/2022]
Abstract
Efficient and convenient genetic manipulation of mycobacteria, important microorganisms in human healthcare and the pharmaceutical industry, is limited. In this study, using a model strain Mycolicibacterium neoaurum ATCC 25795, the classical bacterium for the production of valuable steroidal pharmaceuticals, a genome editing system employing CRISPR-Cas12a to achieve efficient and precise genetic manipulation has been developed. Targeted genome mutations could be easily achieved by the CRISPR-Cas12a system without exogenous donor templates, assisted by innate non-homologous end-joining (NHEJ). CRISPR-Cas12a enabled rapid one-step genomic DNA fragment deletions of 1 kb, 5 kb, 10 kb, 15 kb, 20 kb and 24 kb with efficiencies of 70 %, 30 %, 30 %, 20 %, 20 % and 10 %, respectively. Combined with the pNIL/pGOAL system, CRISPR-Cas12a successfully integrated the gene of interest into the targeted genomic site by single crossover and double crossovers with efficiencies of 100 % and 9 %, respectively, using a two-plasmid system. The robust CRISPR systems developed demonstrated strong potential for precise genome editing in M. neoaurum, including targeted deletion of DNA sequences of various lengths and integration of targeted genes into desired sites in the genome.
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Affiliation(s)
- Ke Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yang Gao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Zhen-Hai Li
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Min Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
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5
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Zou L, Evans CR, Do VD, Losefsky QP, Ngo DQ, McGillivray SM. Loss of the ClpXP Protease Leads to Decreased Resistance to Cell-Envelope Targeting Antimicrobials in Bacillus anthracis Sterne. Front Microbiol 2021; 12:719548. [PMID: 34497598 PMCID: PMC8419472 DOI: 10.3389/fmicb.2021.719548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
The ClpX ATPase is critical for resistance to cell envelope targeting antibiotics in Bacillus anthracis, however, it is unclear whether this is due to its function as an independent chaperone or as part of the ClpXP protease. In this study, we demonstrate that antibiotic resistance is due to formation of the ClpXP protease through construction of a ClpX complementation plasmid that is unable to interact with ClpP. Additionally, we genetically disrupted both clpP genes, clpP1 and clpP2, found in B. anthracis Sterne and find that the loss of either increases susceptibility to cell envelope targeting antimicrobials, although neither has as strong of a phenotype as loss of clpX and neither clpP gene is essential for virulence in a G. mellonella model of infection. Lastly, we looked at changes to cell envelope morphology that could contribute to increased antibiotic sensitivity. We find no difference in cell charge or cell lysis, although we do see increased hydrophobicity in the ΔclpX strain, decreased cellular density and slightly thinner cells walls. We also see significant cell division defects in ΔclpX, although only when cells are grown in the mammalian cell culture medium, RPMI. We conclude that the intrinsic resistance of B. anthracis to cell wall active antimicrobials is dependent on formation of the ClpXP protease and that this could be due, at least in part, to the role of ClpX in regulating cell envelope morphology.
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Affiliation(s)
- Lang Zou
- Department of Biology, Texas Christian University, Fort Worth, TX, United States
| | - Christopher R Evans
- Department of Biology, Texas Christian University, Fort Worth, TX, United States
| | - Vuong D Do
- Department of Biology, Texas Christian University, Fort Worth, TX, United States
| | - Quinn P Losefsky
- Department of Biology, Texas Christian University, Fort Worth, TX, United States
| | - Diem Q Ngo
- Department of Biology, Texas Christian University, Fort Worth, TX, United States
| | - Shauna M McGillivray
- Department of Biology, Texas Christian University, Fort Worth, TX, United States
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6
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Cazzaniga G, Mori M, Chiarelli LR, Gelain A, Meneghetti F, Villa S. Natural products against key Mycobacterium tuberculosis enzymatic targets: Emerging opportunities for drug discovery. Eur J Med Chem 2021; 224:113732. [PMID: 34399099 DOI: 10.1016/j.ejmech.2021.113732] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/15/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
For centuries, natural products (NPs) have served as powerful therapeutics against a variety of human ailments. Nowadays, they still represent invaluable resources for the treatment of many diseases, including bacterial infections. After nearly three decades since the World Health Organization's (WHO) declaration of tuberculosis (TB) as a global health emergency, Mycobacterium tuberculosis (Mtb) continues to claim millions of lives, remaining among the leading causes of death worldwide. In the last years, several efforts have been devoted to shortening and improving treatment outcomes, and to overcoming the increasing resistance phenomenon. Nature has always provided a virtually unlimited source of bioactive molecules, which have inspired the development of new drugs. NPs are characterized by an exceptional chemical and structural diversity, the result of millennia of evolutionary responses to various stimuli. Thanks to their favorable structural features and their enzymatic origin, they are naturally prone to bind proteins and exhibit bioactivities. Furthermore, their worldwide distribution and ease of accessibility has contributed to promote investigations on their activity. Overall, these characteristics make NPs excellent models for the design of novel therapeutics. This review offers a critical and comprehensive overview of the most promising NPs, isolated from plants, fungi, marine species, and bacteria, endowed with inhibitory properties against traditional and emerging mycobacterial enzymatic targets. A selection of 86 compounds is here discussed, with a special emphasis on their biological activity, structure-activity relationships, and mechanism of action. Our study corroborates the antimycobacterial potential of NPs, substantiating their relevance in future drug discovery and development efforts.
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Affiliation(s)
- Giulia Cazzaniga
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Laurent Roberto Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, via A. Ferrata 9, 27100, Pavia, Italy
| | - Arianna Gelain
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy.
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
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7
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Bordes P, Genevaux P. Control of Toxin-Antitoxin Systems by Proteases in Mycobacterium Tuberculosis. Front Mol Biosci 2021; 8:691399. [PMID: 34079824 PMCID: PMC8165232 DOI: 10.3389/fmolb.2021.691399] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/06/2021] [Indexed: 12/30/2022] Open
Abstract
Toxin-antitoxin (TA) systems are small genetic elements composed of a noxious toxin and a counteracting cognate antitoxin. Although they are widespread in bacterial chromosomes and in mobile genetic elements, their cellular functions and activation mechanisms remain largely unknown. It has been proposed that toxin activation or expression of the TA operon could rely on the degradation of generally less stable antitoxins by cellular proteases. The resulting active toxin would then target essential cellular processes and inhibit bacterial growth. Although interplay between proteases and TA systems has been observed, evidences for such activation cycle are very limited. Herein, we present an overview of the current knowledge on TA recognition by proteases with a main focus on the major human pathogen Mycobacterium tuberculosis, which harbours multiple TA systems (over 80), the essential AAA + stress proteases, ClpC1P1P2 and ClpXP1P2, and the Pup-proteasome system.
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Affiliation(s)
- Patricia Bordes
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
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8
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ClpX Is Essential and Activated by Single-Strand DNA Binding Protein in Mycobacteria. J Bacteriol 2021; 203:JB.00608-20. [PMID: 33229461 PMCID: PMC7847540 DOI: 10.1128/jb.00608-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/17/2020] [Indexed: 11/26/2022] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, imposes a major global health burden, surpassing HIV and malaria in annual deaths. The ClpP1P2 proteolytic complex and its cofactor ClpX are attractive drug targets, but their precise cellular functions are unclear. The ClpP1P2 proteolytic complex is essential in Mycobacterium tuberculosis. Proteolysis by ClpP1P2 requires an associated ATPase, either ClpX or ClpC1. Here, we sought to define the unique contributions of the ClpX ATPase to mycobacterial growth. We formally demonstrated that ClpX is essential for mycobacterial growth, and to understand its essential functions, we identified ClpX-His-interacting proteins by pulldown and tandem mass spectrometry. We found an unexpected association between ClpX and proteins involved in DNA replication, and we confirm a physical association between ClpX and the essential DNA maintenance protein single-stranded-DNA binding protein (SSB). Purified SSB is not degraded by ClpXP1P2; instead, SSB enhances ATP hydrolysis by ClpX and degradation of the model substrate GFP-SsrA by ClpXP1P2. This activation of ClpX is mediated by the C-terminal tail of SSB, which had been implicated in the activation of other ATPases associated with DNA replication. Consistent with the predicted interactions, depletion of clpX transcript perturbs DNA replication. These data reveal that ClpX participates in DNA replication and identify the first activator of ClpX in mycobacteria. IMPORTANCE Tuberculosis, caused by Mycobacterium tuberculosis, imposes a major global health burden, surpassing HIV and malaria in annual deaths. The ClpP1P2 proteolytic complex and its cofactor ClpX are attractive drug targets, but their precise cellular functions are unclear. This work confirms ClpX’s essentiality and describes a novel interaction between ClpX and SSB, a component of the DNA replication machinery. Further, we demonstrate that a loss of ClpX is sufficient to interrupt DNA replication, suggesting that the ClpX-SSB complex may play a role in DNA replication in mycobacteria.
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9
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Coulibaly S, Cimino M, Ouattara M, Lecoutey C, Buchieri MV, Alonso-Rodriguez N, Briffotaux J, Mornico D, Gicquel B, Rochais C, Dallemagne P. Phenanthrolinic analogs of quinolones show antibacterial activity against M. tuberculosis. Eur J Med Chem 2020; 207:112821. [PMID: 32950907 DOI: 10.1016/j.ejmech.2020.112821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 12/01/2022]
Abstract
Several phenanthrolinic analogs of quinolones have been synthesized and their antibacterial activity tested against Mycobacterium tuberculosis, other mycobacterial species and bacteria from other genera. Some of them show high activity (of the range observed for rifampicin) against M. tuberculosis replicating in vitro and in vivo (infected macrophages) conditions. These derivatives show the same activity with all or several M. tuberculosis complex bacterial mutants resistant to fluoroquinolones (FQ). This opens the way to the construction of new drugs for the treatment of FQ resistant bacterial infections, including tuberculosis. Several compounds showed also activity against Staphylococcus aureus and probably other species. These compounds do not show major toxicity. We conclude that the novel phenanthrolinic derivatives described here are potent hits for further developments of new antibiotics against bacterial infectious diseases including tuberculosis in particular those resistant to FQ.
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Affiliation(s)
- Songuigama Coulibaly
- Centre D'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Normandie. Univ, UNICAEN, F-14000, Caen, France; UFR Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët Boigny, Abidjan, Cote d'Ivoire
| | - Mena Cimino
- Unité de Génétique Mycobactérienne, Institut Pasteur, F-75724, Paris, France
| | - Mahama Ouattara
- UFR Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët Boigny, Abidjan, Cote d'Ivoire
| | - Cédric Lecoutey
- Centre D'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Normandie. Univ, UNICAEN, F-14000, Caen, France
| | - Maria V Buchieri
- Unité de Génétique Mycobactérienne, Institut Pasteur, F-75724, Paris, France
| | | | - Julien Briffotaux
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Damien Mornico
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Brigitte Gicquel
- Unité de Génétique Mycobactérienne, Institut Pasteur, F-75724, Paris, France; Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Christophe Rochais
- Centre D'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Normandie. Univ, UNICAEN, F-14000, Caen, France.
| | - Patrick Dallemagne
- Centre D'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Normandie. Univ, UNICAEN, F-14000, Caen, France.
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10
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Singhi D, Srivastava P. How similar or dissimilar cells are produced by bacterial cell division? Biochimie 2020; 176:71-84. [DOI: 10.1016/j.biochi.2020.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
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11
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Staphylococcus aureus ClpX localizes at the division septum and impacts transcription of genes involved in cell division, T7-secretion, and SaPI5-excision. Sci Rep 2019; 9:16456. [PMID: 31712583 PMCID: PMC6848492 DOI: 10.1038/s41598-019-52823-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/12/2019] [Indexed: 11/25/2022] Open
Abstract
In all living cells, molecular chaperones are essential for facilitating folding and unfolding of proteins. ClpX is a highly conserved ATP-dependent chaperone that besides functioning as a classical chaperone can associate with ClpP to form the ClpXP protease. To investigate the relative impact of the ClpXP protease and the ClpX chaperone in cell physiology of the important pathogenic bacterium Staphylococcus aureus, we assessed the transcriptional changes induced by inactivating only ClpXP, or by completely deleting ClpX. This analysis revealed that ClpX has a profound impact on S. aureus cell physiology that is mediated primarily via ClpXP-dependent pathways. As an example, ClpX impacts expression of virulence genes entirely via ClpXP-dependent mechanisms. Furthermore, ClpX controls a high number of genes and sRNAs via pathways involving both ClpXP protease and ClpX chaperone activities; an interesting example being genes promoting excision and replication of the pathogenicity island SaPI5. Independently of ClpP, ClpX, impacts transcription of only a restricted number of genes involved in peptidoglycan synthesis, cell division, and type seven secretion. Finally, we demonstrate that ClpX localizes in single foci in close proximity to the division septum lending support to the idea that ClpX plays a role in S. aureus cell division.
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12
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Veyron-Churlet R, Locht C. In Vivo Methods to Study Protein-Protein Interactions as Key Players in Mycobacterium Tuberculosis Virulence. Pathogens 2019; 8:pathogens8040173. [PMID: 31581602 PMCID: PMC6963305 DOI: 10.3390/pathogens8040173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
Studies on protein–protein interactions (PPI) can be helpful for the annotation of unknown protein functions and for the understanding of cellular processes, such as specific virulence mechanisms developed by bacterial pathogens. In that context, several methods have been extensively used in recent years for the characterization of Mycobacterium tuberculosis PPI to further decipher tuberculosis (TB) pathogenesis. This review aims at compiling the most striking results based on in vivo methods (yeast and bacterial two-hybrid systems, protein complementation assays) for the specific study of PPI in mycobacteria. Moreover, newly developed methods, such as in-cell native mass resonance and proximity-dependent biotinylation identification, will have a deep impact on future mycobacterial research, as they are able to perform dynamic (transient interactions) and integrative (multiprotein complexes) analyses.
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Affiliation(s)
- Romain Veyron-Churlet
- Institut Pasteur de Lille, CHU Lille, CNRS, Inserm, Université de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Camille Locht
- Institut Pasteur de Lille, CHU Lille, CNRS, Inserm, Université de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
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13
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Jensen C, Bæk KT, Gallay C, Thalsø-Madsen I, Xu L, Jousselin A, Ruiz Torrubia F, Paulander W, Pereira AR, Veening JW, Pinho MG, Frees D. The ClpX chaperone controls autolytic splitting of Staphylococcus aureus daughter cells, but is bypassed by β-lactam antibiotics or inhibitors of WTA biosynthesis. PLoS Pathog 2019; 15:e1008044. [PMID: 31518377 PMCID: PMC6760813 DOI: 10.1371/journal.ppat.1008044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/25/2019] [Accepted: 08/26/2019] [Indexed: 12/02/2022] Open
Abstract
β-lactam antibiotics interfere with cross-linking of the bacterial cell wall, but the killing mechanism of this important class of antibiotics is not fully understood. Serendipitously we found that sub-lethal doses of β-lactams rescue growth and prevent spontaneous lysis of Staphylococcus aureus mutants lacking the widely conserved chaperone ClpX, and we reasoned that a better understanding of the clpX phenotypes could provide novel insights into the downstream effects of β-lactam binding to the PBP targets. Super-resolution imaging revealed that clpX cells display aberrant septum synthesis, and initiate daughter cell separation prior to septum completion at 30°C, but not at 37°C, demonstrating that ClpX becomes critical for coordinating the S. aureus cell cycle as the temperature decreases. FtsZ localization and dynamics were not affected in the absence of ClpX, suggesting that ClpX affects septum formation and autolytic activation downstream of Z-ring formation. Interestingly, oxacillin antagonized the septum progression defects of clpX cells and prevented lysis of prematurely splitting clpX cells. Strikingly, inhibitors of wall teichoic acid (WTA) biosynthesis that work synergistically with β-lactams to kill MRSA synthesis also rescued growth of the clpX mutant, as did genetic inactivation of the gene encoding the septal autolysin, Sle1. Taken together, our data support a model in which Sle1 causes premature splitting and lysis of clpX daughter cells unless Sle1-dependent lysis is antagonized by β-lactams or by inhibiting an early step in WTA biosynthesis. The finding that β-lactams and inhibitors of WTA biosynthesis specifically prevent lysis of a mutant with dysregulated autolytic activity lends support to the idea that PBPs and WTA biosynthesis play an important role in coordinating cell division with autolytic splitting of daughter cells, and that β-lactams do not kill S. aureus simply by weakening the cell wall. The bacterium Staphylococcus aureus is a major cause of human disease, and the rapid spread of S. aureus strains that are resistant to almost all β-lactam antibiotics has made treatment increasingly difficult. β-lactams interfere with cross-linking of the bacterial cell wall but the killing mechanism of this important class of antibiotics is not fully understood. Here we provide novel insight into this topic by examining a defined S. aureus mutant that has the unusual property of growing markedly better in the presence of β-lactams. Without β-lactams this mutant dies spontaneously at a high frequency due to premature separation of daughter cells during cell division. Cell death of the mutant can, however, be prevented either by exposure to β-lactam antibiotics or by inhibiting synthesis of wall teichoic acid, a major component of the cell wall in Gram-positive bacteria with a conserved role in activation of autolytic splitting of daughter cells. The finding that β-lactam antibiotics can prevent lysis of a mutant with deregulated activity of autolytic enzymes involved in daughter cell splitting, emphasizes the idea that β-lactams interfere with the coordination between cell division and daughter cell splitting, and do not kill S. aureus simply by weakening the cell wall.
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Affiliation(s)
- Camilla Jensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer T. Bæk
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Clement Gallay
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Ida Thalsø-Madsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lijuan Xu
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ambre Jousselin
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Fernando Ruiz Torrubia
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wilhelm Paulander
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ana R. Pereira
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Mariana G. Pinho
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Dorte Frees
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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14
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Abstract
How do mycobacteria divide? Cell division has been studied extensively in the model rod-shaped bacteria Escherichia coli and Bacillus subtilis, but much less is understood about cell division in mycobacteria, a genus that includes the major human pathogens M. tuberculosis and M. leprae. In general, bacterial cell division requires the concerted effort of many proteins in both space and time to elongate the cell, replicate and segregate the chromosome, and construct and destruct the septum - processes which result in the creation of two new daughter cells. Here, we describe these distinct stages of cell division in B. subtilis and follow with the current knowledge in mycobacteria. As will become apparent, there are many differences between mycobacteria and B. subtilis in terms of both the broad outline of cell division and the molecular details. So, while the fundamental challenge of spatially and temporally organizing cell division is shared between these rod-shaped bacteria, they have solved these challenges in often vastly different ways.
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15
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Puffal J, García-Heredia A, Rahlwes KC, Siegrist MS, Morita YS. Spatial control of cell envelope biosynthesis in mycobacteria. Pathog Dis 2018; 76:4953754. [DOI: 10.1093/femspd/fty027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/25/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Julia Puffal
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Alam García-Heredia
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Kathryn C Rahlwes
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
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16
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Abstract
The last three decades have witnessed an explosion of discoveries about the mechanistic details of binary fission in model bacteria such as Escherichia coli, Bacillus subtilis, and Caulobacter crescentus. This was made possible not only by advances in microscopy that helped answer questions about cell biology but also by clever genetic manipulations that directly and easily tested specific hypotheses. More recently, research using understudied organisms, or nonmodel systems, has revealed several alternate mechanistic strategies that bacteria use to divide and propagate. In this review, we highlight new findings and compare these strategies to cell division mechanisms elucidated in model organisms.
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Affiliation(s)
- Prahathees J Eswara
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620;
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5132;
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17
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Abstract
Bacillus subtilis is the best described member of the Gram positive bacteria. It is a typical rod shaped bacterium and grows by elongation in its long axis, before dividing at mid cell to generate two similar daughter cells. B. subtilis is a particularly interesting model for cell cycle studies because it also carries out a modified, asymmetrical division during endospore formation, which can be simply induced by starvation. Cell growth occurs strictly by elongation of the rod, which maintains a constant diameter at all growth rates. This process involves expansion of the cell wall, requiring intercalation of new peptidoglycan and teichoic acid material, as well as controlled hydrolysis of existing wall material. Actin-like MreB proteins are the key spatial regulators that orchestrate the plethora of enzymes needed for cell elongation, many of which are thought to assemble into functional complexes called elongasomes. Cell division requires a switch in the orientation of cell wall synthesis and is organised by a tubulin-like protein FtsZ. FtsZ forms a ring-like structure at the site of impending division, which is specified by a range of mainly negative regulators. There it recruits a set of dedicated division proteins to form a structure called the divisome, which brings about the process of division. During sporulation, both the positioning and fine structure of the division septum are altered, and again, several dedicated proteins that contribute specifically to this process have been identified. This chapter summarises our current understanding of elongation and division in B. subtilis, with particular emphasis on the cytoskeletal proteins MreB and FtsZ, and highlights where the major gaps in our understanding remain.
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Sridevi D, Sudhakar KU, Ananthathatmula R, Nankar RP, Doble M. Mutation at G103 of MtbFtsZ Altered their Sensitivity to Coumarins. Front Microbiol 2017; 8:578. [PMID: 28428773 PMCID: PMC5382161 DOI: 10.3389/fmicb.2017.00578] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/21/2017] [Indexed: 02/02/2023] Open
Abstract
Coumarins are natural polyphenol lactones comprising of fused rings of benzene and α-pyrone. The current study demonstrates the inhibitory effect of coumarins with various substitutions on Mycobacterium smegmatis mc2 155. We also demonstrate the effect of pomegranate (Punica granatum) extract containing ellagic acid, on M. smegmatis as well as their affect on MtbFtsZ (FtsZ from Mycobacterium tuberculosis). The ellagic acid extracts from pomegranate peels inhibit mycobacteria with a MIC of 25 μM and 0.3 to 3.5 mg/mL, respectively, but failed to inhibit the polymerization of MtbFtsZ. However, the coumarins were shown to inhibit the polymerization and GTPase activity of the protein as well as have an inhibitory affect on M. smegmatis mc2 155. Docking of the most active coumarin (7-Dimethyl-4-methyl coumarin with MIC of 38.7 μM) to the GTP binding site suggests that it interacted with the G103 residue. Based on the docking results two mutants of varying activity (G103S and G103A) were constructed to elucidate the interaction of MtbFtsZ and coumarins. Mutation of G103 with Serine (a bulky group) results in an inactive mutant and substitution with alanine produces a variant that retains most of the activity of the wild type. There is a disruption of the protofilament formation of the MtbFtsZ upon interaction with coumarins as demonstrated by TEM. The coumarins increase the length of Mycobacteria five times and MtbFtsZ localization is disturbed. The mutant proteins altered the GTPase and polymerization activity of coumarins as compared to wild type protein. The results here support that coumarins inhibit proliferation of Mycobacteria by targeting the assembly of MtbFtsZ and provide the possible binding site of coumarins on MtbFtsZ. This study may aid in the design of natural products as anti-mycobacterial agents. The currently reported GTP analogs for FtsZ are toxic to the human cell lines; natural coumarins targeting the GTP binding site of MtbFtsZ may hold promise as an important drug lead for tuberculosis treatment.
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Affiliation(s)
- Duggirala Sridevi
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology MadrasChennai, India
| | - Karpagam U Sudhakar
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology MadrasChennai, India
| | - Ragamanvitha Ananthathatmula
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology MadrasChennai, India
| | - Rakesh P Nankar
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology MadrasChennai, India
| | - Mukesh Doble
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology MadrasChennai, India
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19
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Viola MG, LaBreck CJ, Conti J, Camberg JL. Proteolysis-Dependent Remodeling of the Tubulin Homolog FtsZ at the Division Septum in Escherichia coli. PLoS One 2017; 12:e0170505. [PMID: 28114338 PMCID: PMC5256927 DOI: 10.1371/journal.pone.0170505] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/05/2017] [Indexed: 11/18/2022] Open
Abstract
During bacterial cell division a dynamic protein structure called the Z-ring assembles at the septum. The major protein in the Z-ring in Escherichia coli is FtsZ, a tubulin homolog that polymerizes with GTP. FtsZ is degraded by the two-component ATP-dependent protease ClpXP. Two regions of FtsZ, located outside of the polymerization domain in the unstructured linker and at the C-terminus, are important for specific recognition and degradation by ClpXP. We engineered a synthetic substrate containing green fluorescent protein (Gfp) fused to an extended FtsZ C-terminal tail (residues 317–383), including the unstructured linker and the C-terminal conserved region, but not the polymerization domain, and showed that it is sufficient to target a non-native substrate for degradation in vitro. To determine if FtsZ degradation regulates Z-ring assembly during division, we expressed a full length Gfp-FtsZ fusion protein in wild type and clp deficient strains and monitored fluorescent Z-rings. In cells deleted for clpX or clpP, or cells expressing protease-defective mutant protein ClpP(S97A), Z-rings appear normal; however, after photobleaching a region of the Z-ring, fluorescence recovers ~70% more slowly in cells without functional ClpXP than in wild type cells. Gfp-FtsZ(R379E), which is defective for degradation by ClpXP, also assembles into Z-rings that recover fluorescence ~2-fold more slowly than Z-rings containing Gfp-FtsZ. In vitro, ClpXP cooperatively degrades and disassembles FtsZ polymers. These results demonstrate that ClpXP is a regulator of Z-ring dynamics and that the regulation is proteolysis-dependent. Our results further show that FtsZ-interacting proteins in E. coli fine-tune Z-ring dynamics.
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Affiliation(s)
- Marissa G. Viola
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, United States of America
| | - Christopher J. LaBreck
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, United States of America
| | - Joseph Conti
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, United States of America
| | - Jodi L. Camberg
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, United States of America
- * E-mail:
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20
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The Cell Wall Polymer Lipoteichoic Acid Becomes Nonessential in Staphylococcus aureus Cells Lacking the ClpX Chaperone. mBio 2016; 7:mBio.01228-16. [PMID: 27507828 PMCID: PMC4981727 DOI: 10.1128/mbio.01228-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Lipoteichoic acid (LTA) is an important cell wall component of Gram-positive bacteria and a promising target for the development of vaccines and antimicrobial compounds against Staphylococcus aureus Here we demonstrate that mutations in the conditionally essential ltaS (LTA synthase) gene arise spontaneously in an S. aureus mutant lacking the ClpX chaperone. A wide variety of ltaS mutations were selected, and among these, a substantial portion resulted in premature stop codons and other changes predicted to abolish LtaS synthesis. Consistent with this assumption, the clpX ltaS double mutants did not produce LTA, and genetic analyses confirmed that LTA becomes nonessential in the absence of the ClpX chaperone. In fact, inactivation of ltaS alleviated the severe growth defect conferred by the clpX deletion. Microscopic analyses showed that the absence of ClpX partly alleviates the septum placement defects of an LTA-depleted strain, while other phenotypes typical of LTA-negative S. aureus mutants, including increased cell size and decreased autolytic activity, are retained. In conclusion, our results indicate that LTA has an essential role in septum placement that can be bypassed by inactivating the ClpX chaperone. IMPORTANCE Lipoteichoic acid is an essential component of the Staphylococcus aureus cell envelope and an attractive target for the development of vaccines and antimicrobials directed against antibiotic-resistant Gram-positive bacteria such as methicillin-resistant S. aureus and vancomycin-resistant enterococci. In this study, we showed that the lipoteichoic acid polymer is essential for growth of S. aureus only as long as the ClpX chaperone is present in the cell. Our results indicate that lipoteichoic acid and ClpX play opposite roles in a pathway that controls two key cell division processes in S. aureus, namely, septum formation and autolytic activity. The discovery of a novel functional connection in the genetic network that controls cell division in S. aureus may expand the repertoire of possible strategies to identify compounds or compound combinations that kill antibiotic-resistant S. aureus.
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21
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Jurcic Smith KL, Lee S. Inhibition of apoptosis by Rv2456c through Nuclear factor-κB extends the survival of Mycobacterium tuberculosis. Int J Mycobacteriol 2016; 5:426-436. [PMID: 27931684 PMCID: PMC5975360 DOI: 10.1016/j.ijmyco.2016.06.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 02/03/2023] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, is an intracellular pathogen with several survival mechanisms aimed at subverting the host immune system. Apoptosis has been shown to be mycobactericidal, to activate CD8+ T cells, and to be modulated by mycobacterial proteins. Since few mycobacterial proteins have so far been directly implicated in the interactions between M. tuberculosis and host cell apoptosis, we screened M. tuberculosis H37Rv transposon mutants to identify mutants that fail to inhibit cell death (FID). One of these FID mutants, FID19, had a transposon insertion in Rv2456c and is important for survival in host cells. The lack of the protein resulted in enhanced caspase-3 mediated apoptosis, which is probably due to an inability to activate nuclear factor-κB. Additionally, FID19 infection enhanced polyfunctional CD8+ T cells and induced a higher frequency of interferon-γ secreting immune cells in a murine model. Taken together, our data suggest that Rv2456c is important for the survival of H37Rv by subduing the innate and ultimately adaptive immune responses of its host by preventing apoptosis of the infected cell. Better understanding of the host-mycobacterial interactions may be beneficial to develop novel drug targets and engineer more efficacious vaccine strains against tuberculosis.
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Affiliation(s)
- Kristen L Jurcic Smith
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Sunhee Lee
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA; Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
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22
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Tong J, Meng L, Wang X, Liu L, Lyu L, Wang C, Li Y, Gao Q, Yang C, Niu C. The FBPase Encoding Gene glpX Is Required for Gluconeogenesis, Bacterial Proliferation and Division In Vivo of Mycobacterium marinum. PLoS One 2016; 11:e0156663. [PMID: 27233038 PMCID: PMC4883791 DOI: 10.1371/journal.pone.0156663] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/17/2016] [Indexed: 01/12/2023] Open
Abstract
Lipids have been identified as important carbon sources for Mycobacterium tuberculosis (Mtb) to utilize in vivo. Thus gluconeogenesis bears a key role for Mtb to survive and replicate in host. A rate-limiting enzyme of gluconeogenesis, fructose 1, 6-bisphosphatase (FBPase) is encoded by the gene glpX. The functions of glpX were studied in M. marinum, a closely related species to Mtb. The glpX deletion strain (ΔglpX) displayed altered gluconeogenesis, attenuated virulence, and altered bacterial proliferation. Metabolic profiles indicate an accumulation of the FBPase substrate, fructose 1, 6-bisphosphate (FBP) and altered gluconeogenic flux when ΔglpX is cultivated in a gluconeogenic carbon substrate, acetate. In both macrophages and zebrafish, the proliferation of ΔglpX was halted, resulting in dramatically attenuated virulence. Intracellular ΔglpX exhibited an elongated morphology, which was also observed when ΔglpX was grown in a gluconeogenic carbon source. This elongated morphology is also supported by the observation of unseparated multi-nucleoid cell, indicating that a complete mycobacterial division in vivo is correlated with intact gluconeogenesis. Together, our results indicate that glpX has essential functions in gluconeogenesis, and plays an indispensable role in bacterial proliferation in vivo and virulence of M. marinum.
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Affiliation(s)
- Jingfeng Tong
- MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lu Meng
- MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Institutes of Biomedical Sciences and Institute of Medical Microbiology, Fudan University, Shanghai, China
| | - Xinwei Wang
- MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Lixia Liu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liangdong Lyu
- MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chuan Wang
- MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yang Li
- MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qian Gao
- MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Institutes of Biomedical Sciences and Institute of Medical Microbiology, Fudan University, Shanghai, China
| | - Chen Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (CY); (CN)
| | - Chen Niu
- MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- * E-mail: (CY); (CN)
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23
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Kirsebom LA, Dasgupta S, Fredrik Pettersson BM. Pleiomorphism in Mycobacterium. ADVANCES IN APPLIED MICROBIOLOGY 2016; 80:81-112. [PMID: 22794145 DOI: 10.1016/b978-0-12-394381-1.00004-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Morphological variants in mycobacterial cultures under different growth conditions, including aging of the culture, have been shown to include fibrous aggregates, biofilms, coccoids, and spores. Here we discuss the diversity in shape and size changes demonstrated by bacterial cells with special reference to pleiomorphism observed in Mycobacterium spp. in response to nutritional and other environmental stresses. Inherent asymmetry in cell division and compartmentalization of cell interior under different growth conditions might contribute toward the observed pleiomorphism in mycobacteria. The regulatory genes comprising the bacterial signaling pathway responsible for initiating morphogenesis are speculated upon from bioinformatic identifications of genes for known sensors, kinases, and phosphatases existing in mycobacterial genomes as well as on the basis of what is known in other bacteria.
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Buczek MS, Cardenas Arevalo AL, Janakiraman A. ClpXP and ClpAP control the Escherichia coli division protein ZapC by proteolysis. MICROBIOLOGY-SGM 2016; 162:909-920. [PMID: 26978224 DOI: 10.1099/mic.0.000278] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The bacterial FtsZ-ring is an essential cytokinetic structure under tight spatiotemporal regulation. In Escherichia coli, FtsZ polymerization and assembly into the Z-ring is controlled on multiple levels through interactions with positive and negative regulators. Among these regulatory factors are ZapC, a Z-ring stabilizer, and the conserved protease ClpXP, which has been shown to degrade FtsZ protofilaments in preference to FtsZ monomers. Here we report that ZapC and ClpX interact in a protein-protein interaction assay, and that ZapC is degraded in a ClpXP-dependent manner in vivo. The SspB adaptor protein is not required for targeting ZapC to the ClpXP proteolytic machinery. A mutation disrupting the zapC ssrA-like sequence (zapCDD) stabilizes ZapC consistent with a reduction in ClpXP-mediated ZapC degradation. ZapCDD retains the ability to interact with FtsZ and to promote bundling in vitro indicating that WT ZapC contains discrete FtsZ and ClpX recognition motifs. Additionally, ClpAP complexes are sufficient for degradation of ZapC in the absence of ClpX in vivo. Further, chromosomal expression of zapCDD suppresses filamentation of the temperature-sensitive ftsZ84 mutant, confirming the role of ZapC as a Z-ring stabilizer. Lastly, changes in ClpXP and ZapC levels lead to cell division effects, likely through their roles in modulating FtsZ assembly dynamics. Taken together, our results indicate that the Z-ring stabilizer ZapC is a substrate of both ClpXP and ClpAP in vivo. Our data also point to a more complex regulatory circuit that integrates FtsZ, ClpXP and ZapC in achieving Z-ring stability in E. coli and related species.
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Affiliation(s)
- Monika S Buczek
- Department of Biology, MR 526, The City College of CUNY, New York, NY 10031, USA.,The Graduate Center of CUNY, New York, NY 10016, USA
| | | | - Anuradha Janakiraman
- The Graduate Center of CUNY, New York, NY 10016, USA.,Department of Biology, MR 526, The City College of CUNY, New York, NY 10031, USA
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25
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Hurley KA, Santos TMA, Nepomuceno GM, Huynh V, Shaw JT, Weibel DB. Targeting the Bacterial Division Protein FtsZ. J Med Chem 2016; 59:6975-98. [DOI: 10.1021/acs.jmedchem.5b01098] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katherine A. Hurley
- Department of Pharmaceutical Sciences, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Thiago M. A. Santos
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Gabriella M. Nepomuceno
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Valerie Huynh
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Jared T. Shaw
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Douglas B. Weibel
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Biomedical Engineering, University of Wisconsin—Madison, 1550 Engineering Drive, Madison, Wisconsin 53706, United States
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26
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Abstract
It has recently been demonstrated that bacterial chromosomes are highly organized, with specific positioning of the replication initiation region. Moreover, the positioning of the replication machinery (replisome) has been shown to be variable and dependent on species-specific cell cycle features. Here, we analyzed replisome positions in Mycobacterium smegmatis, a slow-growing bacterium that exhibits characteristic asymmetric polar cell extension. Time-lapse fluorescence microscopy analyses revealed that the replisome is slightly off-center in mycobacterial cells, a feature that is likely correlated with the asymmetric growth of Mycobacterium cell poles. Estimates of the timing of chromosome replication in relation to the cell cycle, as well as cell division and chromosome segregation events, revealed that chromosomal origin-of-replication (oriC) regions segregate soon after the start of replication. Moreover, our data demonstrate that organization of the chromosome by ParB determines the replisome choreography. Despite significant progress in elucidating the basic processes of bacterial chromosome replication and segregation, understanding of chromosome dynamics during the mycobacterial cell cycle remains incomplete. Here, we provide in vivo experimental evidence that replisomes in Mycobacterium smegmatis are highly dynamic, frequently splitting into two distinct replication forks. However, unlike in Escherichia coli, the forks do not segregate toward opposite cell poles but remain in relatively close proximity. In addition, we show that replication cycles do not overlap. Finally, our data suggest that ParB participates in the positioning of newly born replisomes in M. smegmatis cells. The present results broaden our understanding of chromosome segregation in slow-growing bacteria. In view of the complexity of the mycobacterial cell cycle, especially for pathogenic representatives of the genus, understanding the mechanisms and factors that affect chromosome dynamics will facilitate the identification of novel antimicrobial factors.
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Plocinski P, Martinez L, Sarva K, Plocinska R, Madiraju M, Rajagopalan M. Mycobacterium tuberculosis CwsA overproduction modulates cell division and cell wall synthesis. Tuberculosis (Edinb) 2014; 93 Suppl:S21-7. [PMID: 24388644 DOI: 10.1016/s1472-9792(13)70006-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We recently showed that two small membrane proteins of Mycobacterium tuberculosis, CwsA and CrgA, interact with each other, and that loss of CwsA in M. smegmatis is associated with defects in the cell division and cell wall synthesis processes. Here we show that CwsA overproduction also affected growth, cell division and cell shape of M. smegmatis and M. tuberculosis. CwsA overproduction in M. tuberculosis led to increased sensitivity to cefsulodin, a penicillin-binding protein (PBP) 1A/1B targeting beta (β) -lactam, but was unaffected by other β-lactams and vancomycin. A M. smegmatis cwsA overexpressing strain showed bulgy cells, increased fluorescent vancomycin staining and altered localization of Wag31-mCherry fusion protein. However, the levels of phosphorylated Wag31, important for optimal peptidoglycan synthesis and growth in mycobacteria, were not affected. Interestingly, CwsA overproduction in E. coli led to the formation of large rounded cells that eventually lysed whereas the overproduction of FtsZ along with CwsA reversed this phenotype. Together, our results emphasize that optimal levels of CwsA are required for regulated cell wall synthesis, hence maintenance of cell shape, and that CwsA likely interacts with and modulates the activities of other cell wall synthetic components including PBPs.
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Affiliation(s)
- P Plocinski
- Biomedical Research, The University of Texas Health Science Center @ Tyler, Tyler, TX 75708, USA
| | - L Martinez
- Biomedical Research, The University of Texas Health Science Center @ Tyler, Tyler, TX 75708, USA
| | - K Sarva
- Biomedical Research, The University of Texas Health Science Center @ Tyler, Tyler, TX 75708, USA
| | - R Plocinska
- Biomedical Research, The University of Texas Health Science Center @ Tyler, Tyler, TX 75708, USA
| | - M Madiraju
- Biomedical Research, The University of Texas Health Science Center @ Tyler, Tyler, TX 75708, USA
| | - M Rajagopalan
- Biomedical Research, The University of Texas Health Science Center @ Tyler, Tyler, TX 75708, USA.
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Cui T, He ZG. Improved understanding of pathogenesis from protein interactions inMycobacteriumtuberculosis. Expert Rev Proteomics 2014; 11:745-55. [DOI: 10.1586/14789450.2014.971762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Chatterjee A, Chakrabarti G. Dimethyl sulphoxide and Ca2+ stimulate assembly of Vibrio cholerae FtsZ. Biochimie 2014; 105:64-75. [DOI: 10.1016/j.biochi.2014.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/13/2014] [Indexed: 10/25/2022]
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Mycobacterium tuberculosis MtrB sensor kinase interactions with FtsI and Wag31 proteins reveal a role for MtrB distinct from that regulating MtrA activities. J Bacteriol 2014; 196:4120-9. [PMID: 25225272 DOI: 10.1128/jb.01795-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The septal association of Mycobacterium tuberculosis MtrB, the kinase partner of the MtrAB two-component signal transduction system, is necessary for the optimal expression of the MtrA regulon targets, including ripA, fbpB, and ftsI, which are involved in cell division and cell wall synthesis. Here, we show that MtrB, irrespective of its phosphorylation status, interacts with Wag31, whereas only phosphorylation-competent MtrB interacts with FtsI. We provide evidence that FtsI depletion compromises the MtrB septal assembly and MtrA regulon expression; likewise, the absence of MtrB compromises FtsI localization and, possibly, FtsI activity. We conclude from these results that FtsI and MtrB are codependent for their activities and that FtsI functions as a positive modulator of MtrB activation and MtrA regulon expression. In contrast to FtsI, Wag31 depletion does not affect MtrB septal assembly and MtrA regulon expression, whereas the loss of MtrB increased Wag31 localization and the levels of PknA/PknB (PknA/B) serine-threonine protein kinase-mediated Wag31 phosphorylation. Interestingly, we found that FtsI decreased levels of phosphorylated Wag31 (Wag31∼P) and that MtrB interacted with PknA/B. Overall, our results indicate that MtrB interactions with FtsI, Wag31, and PknA/B are required for its optimal localization, MtrA regulon expression, and phosphorylation of Wag31. Our results emphasize a new role for MtrB in cell division and cell wall synthesis distinct from that regulating the MtrA phosphorylation activities.
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Williams B, Bhat N, Chien P, Shapiro L. ClpXP and ClpAP proteolytic activity on divisome substrates is differentially regulated following the Caulobacter asymmetric cell division. Mol Microbiol 2014; 93:853-66. [PMID: 24989075 PMCID: PMC4285227 DOI: 10.1111/mmi.12698] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2014] [Indexed: 12/01/2022]
Abstract
Proteolytic control of Caulobacter cell cycle proteins is primarily executed by ClpXP, a dynamically localized protease implicated in turnover of several factors critical for faithful cell cycle progression. Here, we show that the transient midcell localization of ClpXP that precedes cytokinesis requires the FtsZ component of the divisome. Although ClpAP does not exhibit subcellular localization, FtsZ is a substrate of both ClpXP and ClpAP in vivo and in vitro. A peptide containing the C-terminal portion of the FtsA divisome protein is a substrate of both ClpXP and ClpAP in vitro but is primarily degraded by ClpAP in vivo. Caulobacter carries out an asymmetric division in which FtsZ and FtsA are stable in stalked cells but degraded in the non-replicative swarmer cell where ClpAP alone degrades FtsA and both ClpAP and ClpXP degrade FtsZ. While asymmetric division in Caulobacter normally yields larger stalked and smaller swarmer daughters, we observe a loss of asymmetric size distribution among daughter cells when clpA is depleted from a strain in which FtsZ is constitutively produced. Taken together, these results suggest that the activity of both ClpXP and ClpAP on divisome substrates is differentially regulated in daughter cells.
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Affiliation(s)
- Brandon Williams
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
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Abstract
Mycobacterium tuberculosis, which is the aetiological agent of tuberculosis, owes much of its success as a pathogen to its unique cell wall and unusual mechanism of growth, which facilitate its adaptation to the human host and could have a role in clinical latency. Asymmetric growth and division increase population heterogeneity, which may promote antibiotic tolerance and the fitness of single cells. In this Review, we describe the unusual mechanisms of mycobacterial growth, cell wall biogenesis and division, and discuss how these processes might affect the survival of M. tuberculosis in vivo and contribute to the persistence of infection.
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Shi Z, Xuan C, Han H, Cheng X, Wang J, Feng Y, Srinivas S, Lu G, Gao GF. Gluconate 5-dehydrogenase (Ga5DH) participates in Streptococcus suis cell division. Protein Cell 2014; 5:761-9. [PMID: 24916441 PMCID: PMC4180457 DOI: 10.1007/s13238-014-0074-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/04/2014] [Indexed: 02/05/2023] Open
Abstract
Bacterial cell division is strictly regulated in the formation of equal daughter cells. This process is governed by a series of spatial and temporal regulators, and several new factors of interest to the field have recently been identified. Here, we report the requirement of gluconate 5-dehydrogenase (Ga5DH) in cell division of the zoonotic pathogen Streptococcus suis. Ga5DH catalyzes the reversible reduction of 5-ketogluconate to D-gluconate and was localized to the site of cell division. The deletion of Ga5DH in S. suis resulted in a plump morphology with aberrant septa joining the progeny. A significant increase was also observed in cell length. These defects were determined to be the consequence of Ga5DH deprivation in S. suis causing FtsZ delocalization. In addition, the interaction of FtsZ with Ga5DH in vitro was confirmed by protein interaction assays. These results indicate that Ga5DH may function to prevent the formation of ectopic Z rings during S. suis cell division.
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Affiliation(s)
- Zhongyu Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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Streptococcus pyogenes polymyxin B-resistant mutants display enhanced ExPortal integrity. J Bacteriol 2014; 196:2563-77. [PMID: 24794568 DOI: 10.1128/jb.01596-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The ExPortal protein secretion organelle in Streptococcus pyogenes is an anionic phospholipid-containing membrane microdomain enriched in Sec translocons and postsecretion protein biogenesis factors. Polymyxin B binds to and disrupts ExPortal integrity, resulting in defective secretion of several toxins. To gain insight into factors that influence ExPortal organization, a genetic screen was conducted to select for spontaneous polymyxin B-resistant mutants displaying enhanced ExPortal integrity. Whole-genome resequencing of 25 resistant mutants revealed from one to four mutations per mutant genome clustered primarily within a core set of 10 gene groups. Construction of mutants with individual deletions or insertions demonstrated that 7 core genes confer resistance and enhanced ExPortal integrity through loss of function, while 3 were likely due to gain of function and/or combinatorial effects. Core resistance genes include a transcriptional regulator of lipid biosynthesis, several genes involved in nutrient acquisition, and a variety of genes involved in stress responses. Two members of the latter class also function as novel regulators of the secreted SpeB cysteine protease. Analysis of the most frequently isolated mutation, a single nucleotide deletion in a track of 9 consecutive adenine residues in pstS, encoding a component of a high-affinity Pi transporter, suggests that this sequence functions as a molecular switch to facilitate stress adaptation. Together, these data suggest the existence of a membrane stress response that promotes enhanced ExPortal integrity and resistance to cationic antimicrobial peptides.
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Donovan C, Bramkamp M. Cell division in Corynebacterineae. Front Microbiol 2014; 5:132. [PMID: 24782835 PMCID: PMC3989709 DOI: 10.3389/fmicb.2014.00132] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 03/14/2014] [Indexed: 12/02/2022] Open
Abstract
Bacterial cells must coordinate a number of events during the cell cycle. Spatio-temporal regulation of bacterial cytokinesis is indispensable for the production of viable, genetically identical offspring. In many rod-shaped bacteria, precise midcell assembly of the division machinery relies on inhibitory systems such as Min and Noc. In rod-shaped Actinobacteria, for example Corynebacterium glutamicum and Mycobacterium tuberculosis, the divisome assembles in the proximity of the midcell region, however more spatial flexibility is observed compared to Escherichia coli and Bacillus subtilis. Actinobacteria represent a group of bacteria that spatially regulate cytokinesis in the absence of recognizable Min and Noc homologs. The key cell division steps in E. coli and B. subtilis have been subject to intensive study and are well-understood. In comparison, only a minimal set of positive and negative regulators of cytokinesis are known in Actinobacteria. Nonetheless, the timing of cytokinesis and the placement of the division septum is coordinated with growth as well as initiation of chromosome replication and segregation. We summarize here the current knowledge on cytokinesis and division site selection in the Actinobacteria suborder Corynebacterineae.
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Affiliation(s)
- Catriona Donovan
- Department of Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Marc Bramkamp
- Department of Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
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36
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Camberg JL, Viola MG, Rea L, Hoskins JR, Wickner S. Location of dual sites in E. coli FtsZ important for degradation by ClpXP; one at the C-terminus and one in the disordered linker. PLoS One 2014; 9:e94964. [PMID: 24722340 PMCID: PMC3983244 DOI: 10.1371/journal.pone.0094964] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/21/2014] [Indexed: 12/15/2022] Open
Abstract
ClpXP is a two-component ATP-dependent protease that unfolds and degrades proteins bearing specific recognition signals. One substrate degraded by Escherichia coli ClpXP is FtsZ, an essential cell division protein. FtsZ forms polymers that assemble into a large ring-like structure, termed the Z-ring, during cell division at the site of constriction. The FtsZ monomer is composed of an N-terminal polymerization domain, an unstructured linker region and a C-terminal conserved region. To better understand substrate selection by ClpXP, we engineered FtsZ mutant proteins containing amino acid substitutions or deletions near the FtsZ C-terminus. We identified two discrete regions of FtsZ important for degradation of both FtsZ monomers and polymers by ClpXP in vitro. One region is located 30 residues away from the C-terminus in the unstructured linker region that connects the polymerization domain to the C-terminal region. The other region is near the FtsZ C-terminus and partially overlaps the recognition sites for several other FtsZ-interacting proteins, including MinC, ZipA and FtsA. Mutation of either region caused the protein to be more stable and mutation of both caused an additive effect, suggesting that both regions are important. We also observed that in vitro MinC inhibits degradation of FtsZ by ClpXP, suggesting that some of the same residues in the C-terminal site that are important for degradation by ClpXP are important for binding MinC.
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Affiliation(s)
- Jodi L. Camberg
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Cell and Molecular Biology, College of Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, United States of America
- * E-mail: (JLC); (SW)
| | - Marissa G. Viola
- Department of Cell and Molecular Biology, College of Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, United States of America
| | - Leslie Rea
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joel R. Hoskins
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (JLC); (SW)
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Płociński P, Laubitz D, Cysewski D, Stoduś K, Kowalska K, Dziembowski A. Identification of protein partners in mycobacteria using a single-step affinity purification method. PLoS One 2014; 9:e91380. [PMID: 24664103 PMCID: PMC3963859 DOI: 10.1371/journal.pone.0091380] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 02/07/2014] [Indexed: 12/04/2022] Open
Abstract
Tuberculosis is a leading cause of death in developing countries. Efforts are being made to both prevent its spread and improve curability rates. Understanding the biology of the bacteria causing the disease, Mycobacterium tuberculosis (M. tuberculosis), is thus vital. We have implemented improved screening methods for protein–protein interactions based on affinity purification followed by high-resolution mass spectrometry. This method can be efficiently applied to both medium- and high-throughput studies aiming to characterize protein–protein interaction networks of tubercle bacilli. Of the 4 tested epitopes FLAG, enhanced green fluorescent protein (eGFP), protein A and haemagglutinin, the eGFP tag was found to be most useful on account of its easily monitored expression and its ability to function as a simultaneous tool for subcellular localization studies. It presents a relatively low background with cost-effective purification. RNA polymerase subunit A (RpoA) was used as a model for investigation of a large protein complex. When used as bait, it co-purified with all remaining RNA polymerase core subunits as well as many accessory proteins. The amount of RpoA strongly correlated with the amount of quantification peptide used as part of the tagging system in this study (SH), making it applicable for semi-quantification studies. Interactions between the components of the RpoA-eGFP protein complex were further confirmed using protein cross-linking. Dynamic changes in the composition of protein complexes under induction of UV damage were observed when UvrA-eGFP expressing cells treated with UV light were used to co-purify UvrA interaction partners.
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Affiliation(s)
- Przemysław Płociński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Daniel Laubitz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Krystian Stoduś
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Katarzyna Kowalska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail:
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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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Abstract
Proteases have been successfully targeted for the treatment of several diseases, including hypertension, type 2 diabetes, multiple myeloma, HIV and hepatitis C virus infections. Given the demonstrated pharmacological tractability of this enzyme family and the pressing need for novel drugs to combat antibiotic resistance, proteases have also attracted interest as antibacterial targets--particularly the widely conserved intracellular bacterial degradative proteases, which are often indispensable for normal bacterial growth or virulence. This Review summarizes the roles of the key prokaryotic degradative proteases, with a focus on the initial efforts and associated challenges in developing specific therapeutic modulators of these enzymes as novel classes of antibacterial drugs.
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40
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Velasco-García R, Vargas-Martínez R. The study of protein–protein interactions in bacteria. Can J Microbiol 2012; 58:1241-57. [DOI: 10.1139/w2012-104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Many of the functions fulfilled by proteins in the cell require specific protein–protein interactions (PPI). During the last decade, the use of high-throughput experimental technologies, primarily based on the yeast 2-hybrid system, generated extensive data currently located in public databases. This information has been used to build interaction networks for different species. Unfortunately, due to the nature of the yeast 2-hybrid system, these databases contain many false positives and negatives, thus they require purging. A method for confirming these PPI is to test them using a technique that operates in vivo and detects binary PPI. This article comprises an overview of the study of PPI and describes the main techniques that have been used to identify bacterial PPI, prioritizing those that can be used for their verification, and it also mentions a number of PPI that have been identified or confirmed using these methods.
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Affiliation(s)
- Roberto Velasco-García
- Laboratorio de Osmorregulación, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado de México, 54090
| | - Rocío Vargas-Martínez
- Laboratorio de Osmorregulación, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado de México, 54090
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Mycobacterium tuberculosis CwsA interacts with CrgA and Wag31, and the CrgA-CwsA complex is involved in peptidoglycan synthesis and cell shape determination. J Bacteriol 2012; 194:6398-409. [PMID: 23002219 DOI: 10.1128/jb.01005-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial cell division and cell wall synthesis are highly coordinated processes involving multiple proteins. Here, we show that Rv0008c, a novel small membrane protein from Mycobacterium tuberculosis, localizes to the poles and on membranes and shows an overall punctate localization throughout the cell. Furthermore, Rv0008c interacts with two proteins, CrgA and Wag31, implicated in peptidoglycan (PG) synthesis in mycobacteria. Deletion of the Rv0008c homolog in M. smegmatis, MSMEG_0023, caused bulged cell poles, formation of rounded cells, and defects in polar localization of Wag31 and cell wall synthesis, with cell wall synthesis measured by the incorporation of the [(14)C]N-acetylglucosamine cell wall precursor. The M. smegmatis MSMEG_0023 crgA double mutant strain showed severe defects in growth, viability, cell wall synthesis, cell shape, and the localization of the FtsZ, FtsI, and Wag31 proteins. The double mutant strain also exhibited increased autolytic activity in the presence of detergents. Because CrgA and Wag31 proteins interact with FtsI individually, we believe that regulated cell wall synthesis and cell shape maintenance require the concerted actions of the CrgA, Rv0008c, FtsI, and Wag31 proteins. We propose that, together, CrgA and Rv0008c, renamed CwsA for cell wall synthesis and cell shape protein A, play crucial roles in septal and polar PG synthesis and help coordinate these processes with the FtsZ-ring assembly in mycobacteria.
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Joyce G, Williams KJ, Robb M, Noens E, Tizzano B, Shahrezaei V, Robertson BD. Cell division site placement and asymmetric growth in mycobacteria. PLoS One 2012; 7:e44582. [PMID: 22970255 PMCID: PMC3438161 DOI: 10.1371/journal.pone.0044582] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 08/08/2012] [Indexed: 01/12/2023] Open
Abstract
Mycobacteria are members of the actinomycetes that grow by tip extension and lack apparent homologues of the known cell division regulators found in other rod-shaped bacteria. Previous work using static microscopy on dividing mycobacteria led to the hypothesis that these cells can grow and divide asymmetrically, and at a wide range of sizes, in contrast to the cell growth and division patterns observed in the model rod-shaped organisms. In this study, we test this hypothesis using live-cell time-lapse imaging of dividing Mycobacterium smegmatis labelled with fluorescent PBP1a, to probe peptidoglycan synthesis and label the cell septum. We demonstrate that the new septum is placed accurately at mid-cell, and that the asymmetric division observed is a result of differential growth from the cell tips, with a more than 2-fold difference in growth rate between fast and slow growing poles. We also show that the division site is not selected at a characteristic cell length, suggesting this is not an important cue during the mycobacterial cell cycle.
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Affiliation(s)
- Graham Joyce
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College, London, United Kingdom
| | - Kerstin J. Williams
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College, London, United Kingdom
| | - Matthew Robb
- Department of Mathematics, Imperial College, London, United Kingdom
| | - Elke Noens
- European Molecular Biology Laboratory, Hamburg, Germany
| | | | - Vahid Shahrezaei
- Department of Mathematics, Imperial College, London, United Kingdom
| | - Brian D. Robertson
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College, London, United Kingdom
- * E-mail:
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43
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Plocinska R, Purushotham G, Sarva K, Vadrevu IS, Pandeeti EVP, Arora N, Plocinski P, Madiraju MV, Rajagopalan M. Septal localization of the Mycobacterium tuberculosis MtrB sensor kinase promotes MtrA regulon expression. J Biol Chem 2012; 287:23887-99. [PMID: 22610443 DOI: 10.1074/jbc.m112.346544] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanisms responsible for activation of the MtrAB two-component regulatory signal transduction system, which includes sensor kinase MtrB and response regulator MtrA, are unknown. Here, we show that an MtrB-GFP fusion protein localized to the cell membrane, the septa, and the poles in Mycobacterium tuberculosis and Mycobacterium smegmatis. This localization was independent of MtrB phosphorylation status but dependent upon the assembly of FtsZ, the initiator of cell division. The M. smegmatis mtrB mutant was filamentous, defective for cell division, and contained lysozyme-sensitive cell walls. The mtrB phenotype was complemented by either production of MtrB protein competent for phosphorylation or overproduction of MtrA(Y102C) and MtrA(D13A) mutant proteins exhibiting altered phosphorylation potential, indicating that either MtrB phosphorylation or MtrB independent expression of MtrA regulon genes, including those involved in cell wall processing, are necessary for regulated cell division. In partial support of this observation, we found that the essential cell wall hydrolase ripA is an MtrA target and that the expression of bona fide MtrA targets ripA, fbpB, and dnaA were compromised in the mtrB mutant and partially rescued upon MtrA(Y102C) and MtrA(D13A) overproduction. MtrB septal assembly was compromised upon FtsZ depletion and exposure of cells to mitomycin C, a DNA damaging agent, which interferes with FtsZ ring assembly. Expression of MtrA targets was also compromised under the above conditions, indicating that MtrB septal localization and MtrA regulon expression are linked. We propose that MtrB septal association is a necessary feature of MtrB activation that promotes MtrA phosphorylation and MtrA regulon expression.
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Affiliation(s)
- Renata Plocinska
- Biomedical Research, The University of Texas Health Science Center, Tyler, Texas 75708-3154, USA
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Segregation of molecules at cell division reveals native protein localization. Nat Methods 2012; 9:480-2. [PMID: 22484850 PMCID: PMC3779060 DOI: 10.1038/nmeth.1955] [Citation(s) in RCA: 264] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 03/09/2012] [Indexed: 12/11/2022]
Abstract
We introduce a non-intrusive method exploiting post-division single-cell variability to validate protein localization. The results show that Clp proteases, widely reported to form biologically relevant foci, are in fact uniformly distributed inside Escherichia coli cells, and that many commonly used fluorescent proteins (FPs) cause severe mislocalization when fused to homo-oligomers. Re-tagging five other reportedly foci-forming proteins with the most monomeric FP tested suggests the foci were caused by the FPs.
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Cytoskeletal proteins of actinobacteria. Int J Cell Biol 2012; 2012:905832. [PMID: 22481946 PMCID: PMC3296230 DOI: 10.1155/2012/905832] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 10/06/2011] [Accepted: 10/23/2011] [Indexed: 11/19/2022] Open
Abstract
Although bacteria are considered the simplest life forms, we are now slowly unraveling their cellular complexity. Surprisingly, not only do bacterial cells have a cytoskeleton but also the building blocks are not very different from the cytoskeleton that our own cells use to grow and divide. Nonetheless, despite important advances in our understanding of the basic physiology of certain bacterial models, little is known about Actinobacteria, an ancient group of Eubacteria. Here we review current knowledge on the cytoskeletal elements required for bacterial cell growth and cell division, focusing on actinobacterial genera such as Mycobacterium, Corynebacterium, and Streptomyces. These include some of the deadliest pathogens on earth but also some of the most prolific producers of antibiotics and antitumorals.
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Maloney E, Madiraju SC, Rajagopalan M, Madiraju M. Localization of acidic phospholipid cardiolipin and DnaA in mycobacteria. Tuberculosis (Edinb) 2011; 91 Suppl 1:S150-5. [PMID: 22142462 DOI: 10.1016/j.tube.2011.10.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Acidic phospholipids such as cardiolipin (CL) have been shown to modulate Mycobacterium tuberculosis (Mtb) DnaA interactions with ATP. In the present study, using nonyl acridine orange fluorescent dye we localized CL-enriched regions to midcell septa and poles of actively dividing cells. We also found that CL-enriched regions were not visualized in cells defective for septa formation as a consequence of altered FtsZ levels. Using Mtb cultures synchronized for DNA replication we show that CL localization could be used as a marker for cell division and cell cycle progression. Finally, we show that the localization pattern of the DnaA-green fluorescent fusion protein is similar to CL. Our results suggest that DnaA colocalizes with CL during cell cycle progression.
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Affiliation(s)
- Erin Maloney
- Biomedical Research, The University of Texas Health Science Center, 11937 US Hwy @ 271, Tyler, TX 75708-3154, United States
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Vadrevu IS, Lofton H, Sarva K, Blasczyk E, Plocinska R, Chinnaswamy J, Madiraju M, Rajagopalan M. ChiZ levels modulate cell division process in mycobacteria. Tuberculosis (Edinb) 2011; 91 Suppl 1:S128-35. [PMID: 22094151 DOI: 10.1016/j.tube.2011.10.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have previously shown that expression of chiZ (Rv2719c), encoding a cell wall hydrolase, is upregulated in response to DNA damaging agents and exposure to cephalexin. Furthermore, increased levels of ChiZ lead to decreased viability, loss of membrane integrity and defects in FtsZ-GFP localization and cell division. We now show that ChiZ N'-terminal 110 amino acid region, containing the cell wall hydrolase activity, is sufficient to modulate FtsZ-GFP localization. Further, we found that FtsZ-GFP rings are stabilized in a chiZ deletion strain indicating that ChiZ activity regulates FtsZ assembly. Overexpression of ftsZ did not reverse the reduction in viability caused by overproduction of ChiZ indicating that ChiZ neither interacts with nor directly influences FtsZ assembly. Bacterial two-hybrid assays revealed that ChiZ interacts with FtsI and FtsQ, two other septasomal proteins, but not with FtsZ. Finally, we show that ChiZ is not required for virulence of Mycobacterium tuberculosis in murine macrophages and mice. Our data suggest that optimal levels and activity of the cell wall hydrolase ChiZ are required for regulated cell division in mycobacteria.
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Affiliation(s)
- Indumathi S Vadrevu
- Biomedical Research, The University of Texas Health Science Center, Tyler, TX, USA
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Characterization of CrgA, a new partner of the Mycobacterium tuberculosis peptidoglycan polymerization complexes. J Bacteriol 2011; 193:3246-56. [PMID: 21531798 DOI: 10.1128/jb.00188-11] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The role(s) in cell division of the Mycobacterium tuberculosis Rv0011c gene product, a homolog of the Streptomyces CrgA protein that is responsible for coordinating growth and cytokinesis in sporogenic aerial hyphae, is largely unknown. We show that an enhanced cyan fluorescent protein-M. tuberculosis CrgA (ECFP-CrgA(MT)) fusion protein is localized to the cell membrane, midcell, and cell pole regions in Mycobacterium smegmatis. Furthermore, the ECFP-CrgA(MT) fusion protein colocalized with FtsZ-enhanced yellow fluorescent protein (EYFP) in M. smegmatis. Bacterial two-hybrid assays indicated strong interactions of M. tuberculosis CrgA with FtsZ, FtsQ, and the class B penicillin-binding proteins, FtsI (PBPB) and PBPA. The midcell localization of CrgA(MT) was severely compromised under conditions of FtsZ depletion, which indicated that CrgA localizes to the midcell region after assembly of the FtsZ ring. M. tuberculosis cells with reduced CrgA levels were elongated and grew more slowly than wild-type cells, which indicated defects in cell division, whereas CrgA overproduction did not show growth defects. A M. smegmatis ΔcrgA strain exhibited a bulged cell morphology, elongated cells with a chain-like phenotype, cells with polar bulbous structures, and a modest growth defect. FtsZ and FtsI levels were not affected in cells producing altered levels of CrgA. Septal and membrane localization of GFP-FtsI was enhanced by CrgA overproduction and was diminished in a ΔcrgA strain, which indicates that one role of CrgA is to promote and/or stabilize FtsI localization. Overall, these data indicate that CrgA is a novel member of the cell division complex in mycobacteria and possibly facilitates septum formation.
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Vendeville A, Larivière D, Fourmentin E. An inventory of the bacterial macromolecular components and their spatial organization. FEMS Microbiol Rev 2011; 35:395-414. [DOI: 10.1111/j.1574-6976.2010.00254.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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Abstract
ClpXP is a two-component protease composed of ClpX, an ATP-dependent chaperone that recognizes and unfolds specific substrates, and ClpP, a serine protease. One ClpXP substrate in Escherichia coli is FtsZ, which is essential for cell division. FtsZ polymerizes and forms the FtsZ ring at midcell, where division occurs. To investigate the role of ClpXP in cell division, we examined the effects of clpX and clpP deletions in several strains that are defective for cell division. Together, our results suggested that ClpXP modulates cell division through degradation of FtsZ and possibly other cell division components that function downstream of FtsZ ring assembly. In the ftsZ84 strain, which is temperature sensitive for filamentation due to a mutation in ftsZ, we observed that deletion of clpX or clpP suppresses filamentation and reduces FtsZ84 degradation. These results are consistent with ClpXP playing a role in cell division by modulating the level of FtsZ through degradation. In another division-defective strain, ΔminC, the additional deletion of clpX or clpP delays cell division and exacerbates filamentation. Our results demonstrate that ClpXP modulates division in cells lacking MinC by a mechanism that requires ATP-dependent degradation. However, antibiotic chase experiments in vivo indicate that FtsZ degradation is slower in the ΔminC strain than in the wild type, suggesting there may be another cell division component degraded by ClpXP. Taken together these studies suggest that ClpXP may degrade multiple cell division proteins, thereby modulating the precise balance of the components required for division.
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