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Block AM, Wiegert PC, Namugenyi SB, Tischler AD. Transposon sequencing reveals metabolic pathways essential for Mycobacterium tuberculosis infection. PLoS Pathog 2024; 20:e1011663. [PMID: 38498580 PMCID: PMC10977890 DOI: 10.1371/journal.ppat.1011663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 03/28/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
New drugs are needed to shorten and simplify treatment of tuberculosis caused by Mycobacterium tuberculosis. Metabolic pathways that M. tuberculosis requires for growth or survival during infection represent potential targets for anti-tubercular drug development. Genes and metabolic pathways essential for M. tuberculosis growth in standard laboratory culture conditions have been defined by genome-wide genetic screens. However, whether M. tuberculosis requires these essential genes during infection has not been comprehensively explored because mutant strains cannot be generated using standard methods. Here we show that M. tuberculosis requires the phenylalanine (Phe) and de novo purine and thiamine biosynthetic pathways for mammalian infection. We used a defined collection of M. tuberculosis transposon (Tn) mutants in essential genes, which we generated using a custom nutrient-rich medium, and transposon sequencing (Tn-seq) to identify multiple central metabolic pathways required for fitness in a mouse infection model. We confirmed by individual retesting and complementation that mutations in pheA (Phe biosynthesis) or purF (purine and thiamine biosynthesis) cause death of M. tuberculosis in the absence of nutrient supplementation in vitro and strong attenuation in infected mice. Our findings show that Tn-seq with defined Tn mutant pools can be used to identify M. tuberculosis genes required during mouse lung infection. Our results also demonstrate that M. tuberculosis requires Phe and purine/thiamine biosynthesis for survival in the host, implicating these metabolic pathways as prime targets for the development of new antibiotics to combat tuberculosis.
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Affiliation(s)
- Alisha M. Block
- Department of Microbiology and Immunology, University of Minnesota, Twin Cities Campus, Minneapolis, Minnesota, United States of America
| | - Parker C. Wiegert
- Department of Microbiology and Immunology, University of Minnesota, Twin Cities Campus, Minneapolis, Minnesota, United States of America
| | - Sarah B. Namugenyi
- Department of Microbiology and Immunology, University of Minnesota, Twin Cities Campus, Minneapolis, Minnesota, United States of America
| | - Anna D. Tischler
- Department of Microbiology and Immunology, University of Minnesota, Twin Cities Campus, Minneapolis, Minnesota, United States of America
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Kanaparthi KJ, Afroz S, Minhas G, Moitra A, Khan RA, Medikonda J, Naz S, Cholleti SN, Banerjee S, Khan N. Immunogenic profiling of Mycobacterium tuberculosis DosR protein Rv0569 reveals its ability to switch on Th1 based immunity. Immunol Lett 2022; 242:27-36. [PMID: 35007662 DOI: 10.1016/j.imlet.2022.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 12/15/2021] [Accepted: 01/05/2022] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis (M.tb) is a multifaceted bacterial pathogen known to infect more than 2 billion people globally. However, a majority of the individuals (>90%) show no overt clinical symptoms of active Tuberculosis (TB) and, it is reported that M.tb in these individuals resides in the latent form. Therefore, huge burden of latently infected population poses serious threat to human health. Inconsistent efficacy of BCG vaccine and poor understanding of latency-associated determinants contribute to the failure of combating M.tb. The discovery of DosR as the master regulator of dormancy, opened new avenues to understand the pathophysiology of the bacterium. Though the specific functions of various DosR genes are yet to be discovered, they have been reported as potent T-cell activators and could elicit strong protective immune responses. Rv0569 is a DosR-encoded conserved hypothetical protein overexpressed during dormancy. However, it is not clearly understood how this protein modulates the host immune response. In the present study, we have demonstrated that Rv0569 has a high antigenic index and induces enhanced secretion of Th1 cytokines IL-12p40 and TNF-α as compared to Th2 cytokine IL-10 in macrophages. Mechanistically, Rv0569 induced the transcription of these pro-inflammatory signatures through the activation of NF-κB pathway. Further, immunization of mice with DosR protein Rv0569 switched the immune response towards Th1-biased cytokine pattern, characterized by the enhanced production of IFN-γ, IL-12p40, and TNF-α. Rv0569 augmented the expansion of antigen-specific IFN-γ and IL-2 producing effector CD4+ and CD8+ T-cells which are hallmarks of Th1 biased protective immunity. Additionally, IgG2a/IgG1 and IgG2b/IgG1 ratio in the serum of immunized mice further confirmed the ability of Rv0569 to skew Th1 biased immune response. In conclusion, we emphasize that Rv0569 has the ability to generate signals to switch on Th1-dominated responses and further suggest that it could be a potential vaccine candidate against latent M.tb infection.
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Affiliation(s)
- Kala Jyothi Kanaparthi
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Sumbul Afroz
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Gillipsie Minhas
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Anurupa Moitra
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Rafiq Ahmad Khan
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Jayashankar Medikonda
- Department of Biochemistry, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Saima Naz
- Department of Biochemistry, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Sai Nikhith Cholleti
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Nooruddin Khan
- Department of Biotechnology and Bioinformatics, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India.; Department of Animal Biology, School of Life-Sciences, University of Hyderabad, Hyderabad-500046, Telangana, India..
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3
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Reddy GS, Shukla S, Bhuktar H, Hossain KA, Edwin RK, Giliyaru VB, Misra P, Pal M. Pd/Cu-catalyzed access to novel 3-(benzofuran-2-ylmethyl) substituted (pyrazolo/benzo)triazinone derivatives: their in silico/ in vitro evaluation as inhibitors of chorismate mutase (CM). RSC Adv 2022; 12:26686-26695. [PMID: 36275143 PMCID: PMC9490447 DOI: 10.1039/d2ra05255e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/12/2022] [Indexed: 11/21/2022] Open
Abstract
In view of the reported chorismate mutase (CM or MtbCM) inhibitory activities of 3-indolylmethyl substituted (pyrazolo/benzo)triazinone derivatives the structurally similar 3-(benzofuran-2-ylmethyl) substituted (pyrazolo/benzo)triazinones were designed and evaluated in silico against CM. The docking of target molecules was performed at the interface site of MtbCM (PDB: 2FP2). All the best ranked molecules participated in a strong H-bonding with the ILE67 of the B chain at the backbone position in addition to several hydrophobic/van der Waals interactions with the hydrophobic residues. Based on encouraging docking results, the one-pot synthesis of newly designed benzofuran derivatives was carried out using tandem Pd/Cu-catalyzed Sonogashira cross-coupling followed by intramolecular cyclization of 2-iodophenols with appropriate terminal alkynes. A range of novel 3-(benzofuran-2-ylmethyl) substituted (pyrazolo/benzo)triazinone derivatives were prepared in high (>80%) yields. Three molecules i.e.3h, 3i and 3m that participated in good interaction with CM in silico showed encouraging (64–65%) inhibition at 30 μM in vitro. An SAR within this class of molecules suggested that the benzotriazinone series in general was better than the pyrazolotriazinone series. Based on molecular docking in silico, CM inhibition in vitro and computational ADME prediction the benzofuran derivatives 3i and 3m seemed to be of further medicinal interest in the context of discovery and development of new anti-tubercular agents. We report the Pd/Cu-catalyzed synthesis, in silico molecular docking, in vitro CM inhibition and computational ADME prediction of novel 3-(benzofuran-2-ylmethyl) substituted (pyrazolo/benzo)triazinone derivatives.![]()
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Affiliation(s)
- Gangireddy Sujeevan Reddy
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Sharda Shukla
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Harshavardhan Bhuktar
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Kazi Amirul Hossain
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Rebecca Kristina Edwin
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Varadaraj Bhat Giliyaru
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Parimal Misra
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Manojit Pal
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
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Lee HA, Chu KB, Kim MJ, Quan FS, Kong HH, Moon EK. Chorismate mutase peptide antibody enables specific detection of Acanthamoeba. PLoS One 2021; 16:e0250342. [PMID: 33891646 PMCID: PMC8064552 DOI: 10.1371/journal.pone.0250342] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/05/2021] [Indexed: 11/19/2022] Open
Abstract
Accurate and rapid diagnosis of Acanthamoeba keratitis (AK) is difficult. Although the diagnostic procedure for AK has improved, further development and effective diagnostic tool utilization for AK need to continue. Chorismate mutase is a key regulatory enzyme involved in the shikimate pathway, a metabolic pathway absent in mammals but central for amino acid biosynthesis in bacteria, fungi, algae, and plants. In this study, we describe the identification and production of a polyclonal peptide antibody targeting chorismate mutase secreted by A. castellanii, which could be used for AK diagnosis. Western blot was performed using the protein lysates and conditioned media of the human corneal epithelial (HCE) cells, non-pathogenic Acanthamoeba, pathogenic Acanthamoeba, clinical isolate of Acanthamoeba spp., and other causes of keratitis such as Fusarium solani, Pseudomonas aeruginosa, and Staphylococcus aureus. Polyclonal antibodies raised against A. castellanii chorismate mutase specifically interacted with lysates of Acanthamoeba origin and their culture media, while such interactions were not observed from other samples. Acanthamoeba-specificity of chorismate mutase was also confirmed using immunocytochemistry after co-culturing Acanthamoeba with HCE cells. Specific binding of the chorismate mutase antibody to Acanthamoeba was observed, which were absent in the case of HCE cells. These results indicate that the chorismate mutase antibody of Acanthamoeba may serve as a method for rapid and differential Acanthamoeba identification.
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Affiliation(s)
- Hae-Ahm Lee
- Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science Institute, School of Medicine, Graduate School, Kyung Hee University, Seoul, Korea
| | - Ki-Back Chu
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Min-Jeong Kim
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Fu-Shi Quan
- Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science Institute, School of Medicine, Graduate School, Kyung Hee University, Seoul, Korea
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul, Korea
| | - Hyun-Hee Kong
- Department of Parasitology, Dong-A University College of Medicine, Busan, Korea
| | - Eun-Kyung Moon
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul, Korea
- * E-mail:
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Dhananjaya G, Rao AD, Hossain KA, Anna VR, Pal M. In silico studies and β-cyclodextrin mediated neutral synthesis of 4-oxo-4,5,6,7-tetrahydroindoles of potential biological interest. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Reddy GS, Hossain KA, Kumar JS, Thirupataiah B, Edwin RK, Giliyaru VB, Chandrashekhar Hariharapura R, Shenoy GG, Misra P, Pal M. Novel isatin–indole derivatives as potential inhibitors of chorismate mutase (CM): their synthesis along with unexpected formation of 2-indolylmethylamino benzoate ester under Pd–Cu catalysis. RSC Adv 2020; 10:289-297. [PMID: 35492515 PMCID: PMC9047634 DOI: 10.1039/c9ra09236f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/18/2019] [Indexed: 11/29/2022] Open
Abstract
A series of novel isatin–indole derivatives has been designed as potential inhibitors of chorismate mutase (CM) that is known to be present in bacteria, fungi and higher plants but not in human. The design was supported by in silico docking studies that predicted strong interactions of these molecules with CM. The target compounds were synthesized via the one-pot coupling/cyclization method involving the reaction of an isatin based terminal alkyne with 2-iodosulfanilides under Pd–Cu catalysis. A number of isatin–indole derivatives were prepared using this method. A side product e.g. 2-indolylmethylamino benzoate ester derivative was obtained as a result of isatin ring opening (ethanolysis) of products in certain cases. Additionally, regioselective reduction of selected compounds afforded the corresponding C-3 hydroxy derivatives. All isatin–indole derivatives showed good to high inhibition of CM in vitro among which two compounds (3e and 3f) showed inhibition at nanomolar concentration. Design, synthesis and evaluation of isatin–indole derivatives were undertaken to identify potent inhibitors of chorismate mutase.![]()
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Affiliation(s)
- Gangireddy Sujeevan Reddy
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
- Manipal College of Pharmaceutical Sciences
| | - Kazi Amirul Hossain
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
| | - Jetta Sandeep Kumar
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
- Manipal College of Pharmaceutical Sciences
| | - B. Thirupataiah
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
- Manipal College of Pharmaceutical Sciences
| | - Rebecca Kristina Edwin
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
| | | | | | - G. Gautham Shenoy
- Manipal College of Pharmaceutical Sciences
- Manipal Academy of Higher Education
- Manipal
- India
| | - Parimal Misra
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
| | - Manojit Pal
- Dr Reddy's Institute of Life Sciences
- University of Hyderabad Campus
- Hyderabad 500 046
- India
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7
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Reddy GS, Snehalatha AV, Edwin RK, Hossain KA, Giliyaru VB, Hariharapura RC, Gautham Shenoy G, Misra P, Pal M. Synthesis of 3-indolylmethyl substituted (pyrazolo/benzo)triazinone derivatives under Pd/Cu-catalysis: Identification of potent inhibitors of chorismate mutase (CM). Bioorg Chem 2019; 91:103155. [PMID: 31400552 DOI: 10.1016/j.bioorg.2019.103155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/04/2019] [Accepted: 07/24/2019] [Indexed: 11/17/2022]
Abstract
The chorismate mutase (CM) is considered as an attractive target for the identification of potential antitubercular agents due to its absence in animals but not in bacteria. A series of 3-indolylmethyl substituted pyrazolotriazinone derivatives were designed and docked into CM in silico as potential inhibitors. These compounds were efficiently synthesized using the Pd/Cu-catalyzed coupling-cyclization in a single pot involving the construction of indole ring. The methodology was later extended to the preparation of corresponding benzo analogs of pyrazolotriazinones i.e. 3-indolylmethyl substituted benzotriazinone derivatives. Several of these novel compounds showed significant inhibition of CM when tested in vitro at 30 µM. The SAR (Structure-Activity-Relationship) studies suggested that benzotriazinone moiety was more favorable over the pyrazolotriazinone ring. The two best active compounds showed IC50 ∼ 0.4-0.9 µM (better than the reference/known compounds used) and no toxicity till 30 µM in vitro.
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Affiliation(s)
- Gangireddy Sujeevan Reddy
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Ampalam Venkata Snehalatha
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Rebecca Kristina Edwin
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Kazi Amirul Hossain
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Varadaraj Bhat Giliyaru
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | | | - G Gautham Shenoy
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Parimal Misra
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Manojit Pal
- Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India.
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8
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Synthesis and evaluation of antimicrobial, antitubercular and anticancer activities of benzimidazole derivatives. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.ejbas.2017.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Mycobacterium tuberculosis chorismate mutase: A potential target for TB. Bioorg Med Chem 2017; 25:1725-1736. [PMID: 28202315 DOI: 10.1016/j.bmc.2017.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/01/2017] [Indexed: 12/27/2022]
Abstract
Mycobacterium tuberculosis chorismate mutase (MtbCM) catalyzes the rearrangement of chorismate to prephenate in the shikimate biosynthetic pathway to form the essential amino acids, phenylalanine and tyrosine. Two genes encoding chorismate mutase have been identified in Mtb. The secretory form,∗MtbCM (encoded by Rv1885c) is assumed to play a key role in pathogenesis of tuberculosis. Also, the inhibition of MtbCM may hinder the supply of nutrients to the organism. Indeed, the existence of chorismate mutase (CM) in bacteria, fungi and higher plants but not in human and low sequence homology among known CM makes it an interesting target for the discovery of anti-tubercular agents. The present article mainly focuses on the recent developments in the structure, function and inhibition of MtbCM. The understanding of various aspects of MtbCM as presented in the current article may facilitate the design and subsequent chemical synthesis of new inhibitors against ∗MtbCM, that could lead to the discovery and development of novel and potent anti-tubercular agents in future.
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Mitchell NJ, Malins LR, Liu X, Thompson RE, Chan B, Radom L, Payne RJ. Rapid Additive-Free Selenocystine–Selenoester Peptide Ligation. J Am Chem Soc 2015; 137:14011-4. [DOI: 10.1021/jacs.5b07237] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Lara R. Malins
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Xuyu Liu
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Robert E. Thompson
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bun Chan
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Leo Radom
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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Arora A, Chandra NR, Das A, Gopal B, Mande SC, Prakash B, Ramachandran R, Sankaranarayanan R, Sekar K, Suguna K, Tyagi AK, Vijayan M. Structural biology of Mycobacterium tuberculosis proteins: The Indian efforts. Tuberculosis (Edinb) 2011; 91:456-68. [DOI: 10.1016/j.tube.2011.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 03/15/2011] [Accepted: 03/16/2011] [Indexed: 01/23/2023]
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12
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Banerjee S, Farhana A, Ehtesham NZ, Hasnain SE. Iron acquisition, assimilation and regulation in mycobacteria. INFECTION GENETICS AND EVOLUTION 2011; 11:825-38. [PMID: 21414421 DOI: 10.1016/j.meegid.2011.02.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 02/25/2011] [Accepted: 02/28/2011] [Indexed: 11/28/2022]
Abstract
Iron is as crucial to the pathogen as it is to the host. The tuberculosis causing bacillus, Mycobacterium tuberculosis (M.tb), is an exceptionally efficient pathogen that has evolved proficient mechanisms to sequester iron from the host despite its thick mycolate-rich outer covering and a highly impermeable membrane of phagolysosome within which it persists inside an infected host macrophage. Further, both overindulgence and moderation of iron inside a host are a threat to mycobacterial persistence. While for removing iron from the host reservoirs, mycobacteria synthesize molecules that have several times higher affinity for iron than their host counterparts, they also synthesize molecules for efficient storage of excess iron. This is supported by tightly regulated iron dependent global gene expressions. In this review we discuss the various molecules and pathways evolved by mycobacteria for an efficient iron metabolism. We also discuss the less investigated players, like iron responsive proteins and iron responsive elements in mycobacteria, and highlight the lacunae in our current understanding of iron acquisition and utilization in mycobacteria with an ultimate aim to make iron metabolism as a possible anti-mycobacterial target.
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Affiliation(s)
- Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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Kumar S, Sardesai AA, Basu D, Muniyappa K, Hasnain SE. DNA clasping by mycobacterial HU: the C-terminal region of HupB mediates increased specificity of DNA binding. PLoS One 2010; 5:e12551. [PMID: 20824060 PMCID: PMC2932737 DOI: 10.1371/journal.pone.0012551] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 08/04/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND HU a small, basic, histone like protein is a major component of the bacterial nucleoid. E. coli has two subunits of HU coded by hupA and hupB genes whereas Mycobacterium tuberculosis (Mtb) has only one subunit of HU coded by ORF Rv2986c (hupB gene). One noticeable feature regarding Mtb HupB, based on sequence alignment of HU orthologs from different bacteria, was that HupB(Mtb) bears at its C-terminal end, a highly basic extension and this prompted an examination of its role in Mtb HupB function. METHODOLOGY/PRINCIPAL FINDINGS With this objective two clones of Mtb HupB were generated; one expressing full length HupB protein (HupB(Mtb)) and another which expresses only the N terminal region (first 95 amino acid) of hupB (HupB(MtbN)). Gel retardation assays revealed that HupB(MtbN) is almost like E. coli HU (heat stable nucleoid protein) in terms of its DNA binding, with a binding constant (K(d)) for linear dsDNA greater than 1000 nM, a value comparable to that obtained for the HUalphaalpha and HUalphabeta forms. However CTR (C-terminal Region) of HupB(Mtb) imparts greater specificity in DNA binding. HupB(Mtb) protein binds more strongly to supercoiled plasmid DNA than to linear DNA, also this binding is very stable as it provides DNase I protection even up to 5 minutes. Similar results were obtained when the abilities of both proteins to mediate protection against DNA strand cleavage by hydroxyl radicals generated by the Fenton's reaction, were compared. It was also observed that both the proteins have DNA binding preference for A:T rich DNA which may occur at the regulatory regions of ORFs and the oriC region of Mtb. CONCLUSIONS/SIGNIFICANCE These data thus point that HupB(Mtb) may participate in chromosome organization in-vivo, it may also play a passive, possibly an architectural role.
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Affiliation(s)
- Sandeep Kumar
- Laboratory of Molecular and Cellular Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Abhijit A. Sardesai
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Debashree Basu
- Laboratory of Structural Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Seyed E. Hasnain
- Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India
- Department of Biochemistry, University of Hyderabad, Hyderabad, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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14
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Degrassi G, Devescovi G, Bigirimana J, Venturi V. Xanthomonas oryzae pv. oryzae XKK.12 contains an AroQgamma chorismate mutase that is involved in rice virulence. PHYTOPATHOLOGY 2010; 100:262-270. [PMID: 20128700 DOI: 10.1094/phyto-100-3-0262] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Chorismate mutase (CM) is a key enzyme in the shikimate pathway which is responsible for the synthesis of aromatic amino acids. There are two classes of CMs, AroQ and AroH, and several pathogenic bacteria have been reported to possess a subgroup of CMs designated AroQ(gamma). These CMs are usually exported to the periplasm or outside the cell; in a few cases, they have been reported to be involved in virulence and their precise role is currently unknown. Here, we report that the important rice pathogen Xanthomonas oryzae pv. oryzae XKK.12 produces an AroQ(gamma) CM which we have purified and characterized from spent supernatants. This enzyme is synthesized in planta and X. oryzae pv. oryzae knock-out mutants are hypervirulent to rice. The role of this enzyme in X. oryzae pv. oryzae rice virulence is discussed.
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Affiliation(s)
- Giuliano Degrassi
- Bacteriology Group, International Centre for Genetic Engineering & Biotechnology, Trieste, Italy.
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15
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Bashir N, Kounsar F, Mukhopadhyay S, Hasnain SE. Mycobacterium tuberculosis conserved hypothetical protein rRv2626c modulates macrophage effector functions. Immunology 2010; 130:34-45. [PMID: 20201990 DOI: 10.1111/j.1365-2567.2009.03196.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Secretory proteins of Mycobacterium tuberculosis are the major immunomodulators of the host immune response. Open reading frame (ORF) Rv2626c, encoding a conserved hypothetical protein eliciting a strong humoral immune response in patients with tuberculosis (TB), was shown to be up-regulated upon infection in mice under hypoxic conditions. We now show that recombinant Rv2626c protein (rRv2626c) can bind to the surface of murine macrophages and elicit the type-1 immune response, as manifested by nitric oxide (NO) secretion and expression of inducible nitric oxide synthase (iNOS). Significant induction of pro-inflammatory cytokines [interleukin (IL)-12 and tumour necrosis factor (TNF)-alpha] was evident upon stimulation of murine macrophages, as well as peripheral blood mononuclear cells (PBMCs) isolated from patients with active TB disease, with rRv2626c. Stimulation with rRv2626c also enhanced the expression of costimulatory molecules such as B7-1, B7-2 and CD40 on murine macrophages. We further show that the production of NO and pro-inflammatory cytokines in response to rRv2626c is mediated by the transcription factor nuclear factor (NF)-kappaB, and this was further confirmed using pyrrolidine dithiocarbamate (PDTC), a specific pharmacological inhibitor of NF-kappaB. Rv2626c therefore appears to modulate macrophage effector functions by eliciting both innate and adaptive immune responses, suggesting its possible use as a vaccine candidate.
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Affiliation(s)
- Nasreena Bashir
- Department of Biochemistry, University of Hyderabad, Hyderabad, India.
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Sharadamma N, Harshavardhana Y, Singh P, Muniyappa K. Mycobacterium tuberculosis nucleoid-associated DNA-binding protein H-NS binds with high-affinity to the Holliday junction and inhibits strand exchange promoted by RecA protein. Nucleic Acids Res 2010; 38:3555-69. [PMID: 20176569 PMCID: PMC2887947 DOI: 10.1093/nar/gkq064] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A number of studies have shown that the structure and composition of bacterial nucleoid influences many a processes related to DNA metabolism. The nucleoid-associated proteins modulate not only the DNA conformation but also regulate the DNA metabolic processes such as replication, recombination, repair and transcription. Understanding of how these processes occur in the context of Mycobacterium tuberculosis nucleoid is of considerable medical importance because the nucleoid structure may be constantly remodeled in response to environmental signals and/or growth conditions. Many studies have concluded that Escherichia coli H-NS binds to DNA in a sequence-independent manner, with a preference for A-/T-rich tracts in curved DNA; however, recent studies have identified the existence of medium- and low-affinity binding sites in the vicinity of the curved DNA. Here, we show that the M. tuberculosis H-NS protein binds in a more structure-specific manner to DNA replication and repair intermediates, but displays lower affinity for double-stranded DNA with relatively higher GC content. Notably, M. tuberculosis H-NS was able to bind Holliday junction (HJ), the central recombination intermediate, with substantially higher affinity and inhibited the three-strand exchange promoted by its cognate RecA. Likewise, E. coli H-NS was able to bind the HJ and suppress DNA strand exchange promoted by E. coli RecA, although much less efficiently compared to M. tuberculosis H-NS. Our results provide new insights into a previously unrecognized function of H-NS protein, with implications for blocking the genome integration of horizontally transferred genes by homologous and/or homeologous recombination.
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Affiliation(s)
- N Sharadamma
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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17
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Li PP, Liu YJ, Liu SJ. Genetic and biochemical identification of the chorismate mutase from Corynebacterium glutamicum. Microbiology (Reading) 2009; 155:3382-3391. [DOI: 10.1099/mic.0.029819-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chorismate mutase (CM) catalyses the rearrangement of chorismate to prephenate and is also the first and the key enzyme that diverges the shikimate pathway to either tryptophan (Trp) or phenylalanine (Phe) and tyrosine (Tyr). Corynebacterium glutamicum is one of the most important amino acid producers for the fermentation industry and has been widely investigated. However, the gene(s) encoding CM has not been experimentally identified in C. glutamicum. In this study, the ncgl0819 gene, which was annotated as ‘conserved hypothetical protein’ in the C. glutamicum genome, was genetically characterized to be essential for growth in minimal medium, and a mutant deleted of ncgl0819 was a Phe and Tyr auxotroph. Genetic cloning and expression of ncgl0819 in Escherichia coli resulted in the formation of a new protein (NCgl0819) having CM activity. It was concluded that ncgl0819 encoded the CM of C. glutamicum (CM0819). CM0819 was demonstrated to be a homodimer and is a new member of the monofunctional CMs of the AroQ structural class. The CM0819 activity was not affected by Phe, Tyr or Trp. Two 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthases (DS0950 and DS2098, formerly NCgl0950 and NCgl2098) had been previously identified from C. glutamicum. CM0819 significantly stimulated DAHP synthase (DS2098) activity. Physical interaction between CM0819 and DS2098 was observed. When CM0819 was present, DS2098 activity was subject to allosteric inhibition by chorismate and prephenate. Conserved hypothetical proteins homologous to CM0819 were identified in all known Corynebacterium genomes, suggesting a universal occurrence of CM0819-like CMs in the genus Corynebacterium.
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Affiliation(s)
- Pan-Pan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ya-Jun Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuang-Jiang Liu
- Environmental Microbiology and Biotechnology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Sasso S, Okvist M, Roderer K, Gamper M, Codoni G, Krengel U, Kast P. Structure and function of a complex between chorismate mutase and DAHP synthase: efficiency boost for the junior partner. EMBO J 2009; 28:2128-42. [PMID: 19556970 DOI: 10.1038/emboj.2009.165] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 05/26/2009] [Indexed: 11/09/2022] Open
Abstract
Chorismate mutase catalyzes a key step in the shikimate biosynthetic pathway towards phenylalanine and tyrosine. Curiously, the intracellular chorismate mutase of Mycobacterium tuberculosis (MtCM; Rv0948c) has poor activity and lacks prominent active-site residues. However, its catalytic efficiency increases >100-fold on addition of DAHP synthase (MtDS; Rv2178c), another shikimate-pathway enzyme. The 2.35 A crystal structure of the MtCM-MtDS complex bound to a transition-state analogue shows a central core formed by four MtDS subunits sandwiched between two MtCM dimers. Structural comparisons imply catalytic activation to be a consequence of the repositioning of MtCM active-site residues on binding to MtDS. The mutagenesis of the C-terminal extrusion of MtCM establishes conserved residues as part of the activation machinery. The chorismate-mutase activity of the complex, but not of MtCM alone, is inhibited synergistically by phenylalanine and tyrosine. The complex formation thus endows the shikimate pathway of M. tuberculosis with an important regulatory feature. Experimental evidence suggests that such non-covalent enzyme complexes comprising an AroQ(delta) subclass chorismate mutase like MtCM are abundant in the bacterial order Actinomycetales.
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Affiliation(s)
- Severin Sasso
- Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
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Kumar S, Farhana A, Hasnain SE. In-vitro helix opening of M. tuberculosis oriC by DnaA occurs at precise location and is inhibited by IciA like protein. PLoS One 2009; 4:e4139. [PMID: 19127296 PMCID: PMC2607554 DOI: 10.1371/journal.pone.0004139] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Accepted: 12/01/2008] [Indexed: 11/19/2022] Open
Abstract
Background Mycobacterium tuberculosis (M.tb), the pathogen that causes tuberculosis, is capable of staying asymptomatically in a latent form, persisting for years in very low replicating state, before getting reactivated to cause active infection. It is therefore important to study M.tb chromosome replication, specifically its initiation and regulation. While the region between dnaA and dnaN gene is capable of autonomous replication, little is known about the interaction between DnaA initiator protein, oriC origin of replication sequences and their negative effectors of replication. Methodology/Principal Findings By KMnO4 mapping assays the sequences involved in open complex formation within oriC, mediated by M.tb DnaA protein, were mapped to position −500 to −518 with respect to the dnaN gene. Contrary to E. coli, the M.tb DnaA in the presence of non-hydrolysable analogue of ATP (ATPγS) was unable to participate in helix opening thereby pointing to the importance of ATP hydrolysis. Interestingly, ATPase activity in the presence of supercoiled template was higher than that observed for DnaA box alone. M.tb rRv1985c, a homologue of E.coli IciA (Inhibitor of chromosomal initiation) protein, could inhibit DnaA-mediated in-vitro helix opening by specifically binding to A+T rich region of oriC, provided the open complex formation had not initiated. rIciA could also inhibit in-vitro replication of plasmid carrying the M.tb origin of replication. Conclusions/Significance These results have a bearing on the functional role of the important regulator of M.tb chromosomal replication belonging to the LysR family of bacterial regulatory proteins in the context of latency.
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Affiliation(s)
- Sandeep Kumar
- Laboratory of Molecular and Cellular Biology, CDFD, Hyderabad, India
| | - Aisha Farhana
- Laboratory of Molecular and Cellular Biology, CDFD, Hyderabad, India
| | - Seyed E. Hasnain
- Institute of Life Sciences, University of Hyderabad, Hyderabad, India
- Department of Biochemistry, University of Hyderabad, Hyderabad, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
- * E-mail:
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Luthra A, Malik SS, Ramachandran R. Cloning, purification and comparative structural analysis of two hypothetical proteins from Mycobacterium tuberculosis found in the human granuloma during persistence and highly up-regulated under carbon-starvation conditions. Protein Expr Purif 2008; 62:64-74. [DOI: 10.1016/j.pep.2008.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 06/23/2008] [Accepted: 06/24/2008] [Indexed: 10/21/2022]
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Kim SK, Reddy SK, Nelson BC, Robinson H, Reddy PT, Ladner JE. A comparative biochemical and structural analysis of the intracellular chorismate mutase (Rv0948c) from Mycobacterium tuberculosis H37Rv and the secreted chorismate mutase (y2828) from Yersinia pestis. FEBS J 2008; 275:4824-35. [DOI: 10.1111/j.1742-4658.2008.06621.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Mechanistic insights into a novel exporter-importer system of Mycobacterium tuberculosis unravel its role in trafficking of iron. PLoS One 2008; 3:e2087. [PMID: 18461140 PMCID: PMC2330087 DOI: 10.1371/journal.pone.0002087] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Accepted: 03/23/2008] [Indexed: 12/04/2022] Open
Abstract
Background Elucidation of the basic mechanistic and biochemical principles underlying siderophore mediated iron uptake in mycobacteria is crucial for targeting this principal survival strategy vis-à-vis virulence determinants of the pathogen. Although, an understanding of siderophore biosynthesis is known, the mechanism of their secretion and uptake still remains elusive. Methodology/Principal Findings Here, we demonstrate an interplay among three iron regulated Mycobacterium tuberculosis (M.tb) proteins, namely, Rv1348 (IrtA), Rv1349 (IrtB) and Rv2895c in export and import of M.tb siderophores across the membrane and the consequent iron uptake. IrtA, interestingly, has a fused N-terminal substrate binding domain (SBD), representing an atypical subset of ABC transporters, unlike IrtB that harbors only the permease and ATPase domain. SBD selectively binds to non-ferrated siderophores whereas Rv2895c exhibits relatively higher affinity towards ferrated siderophores. An interaction between the permease domain of IrtB and Rv2895c is evident from GST pull-down assay. In vitro liposome reconstitution experiments further demonstrate that IrtA is indeed a siderophore exporter and the two-component IrtB-Rv2895c system is an importer of ferrated siderophores. Knockout of msmeg_6554, the irtA homologue in Mycobacterium smegmatis, resulted in an impaired M.tb siderophore export that is restored upon complementation with M.tb irtA. Conclusion Our data suggest the interplay of three proteins, namely IrtA, IrtB and Rv2895c in synergizing the balance of siderophores and thus iron inside the mycobacterial cell.
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The two chorismate mutases from both Mycobacterium tuberculosis and Mycobacterium smegmatis: biochemical analysis and limited regulation of promoter activity by aromatic amino acids. J Bacteriol 2007; 190:122-34. [PMID: 17965159 DOI: 10.1128/jb.01332-07] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chorismate mutase (CM) catalyzes the rearrangement of chorismate to prephenate in the biosynthetic pathway that forms phenylalanine and tyrosine in bacteria, fungi, plants, and apicomplexan parasites. Since this enzyme is absent from mammals, it represents a promising target for the development of new antimycobacterial drugs, which are needed to combat Mycobacterium tuberculosis, the causative agent of tuberculosis. Until recently, two putative open reading frames (ORFs), Rv0948c and Rv1885c, showing low sequence similarity to CMs have been described as "conserved hypothetical proteins" in the M. tuberculosis genome. However, we and others demonstrated that these ORFs are in fact monofunctional CMs of the AroQ structural class and that they are differentially localized in the mycobacterial cell. Since homologues to the M. tuberculosis enzymes are also present in Mycobacterium smegmatis, we cloned the coding sequences corresponding to ORFs MSMEG5513 and MSMEG2114 from the latter. The CM activities of both ORFs was determined, as well as their translational start sites. In addition, we analyzed the promoter activities of three M. tuberculosis loci related to phenylalanine and tyrosine biosynthesis under a variety of conditions using M. smegmatis as a surrogate host. Our results indicate that the aroQ (Rv0948c), *aroQ (Rv1885c), and fbpB (Rv1886c) genes from M. tuberculosis are constitutively expressed or subjected to minor regulation by aromatic amino acids levels, especially tryptophan.
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Agrawal H, Kumar A, Bal NC, Siddiqi MI, Arora A. Ligand based virtual screening and biological evaluation of inhibitors of chorismate mutase (Rv1885c) from Mycobacterium tuberculosis H37Rv. Bioorg Med Chem Lett 2007; 17:3053-8. [PMID: 17418569 DOI: 10.1016/j.bmcl.2007.03.053] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Revised: 02/28/2007] [Accepted: 03/16/2007] [Indexed: 11/25/2022]
Abstract
We have identified new lead candidates that possess inhibitory activity against Mycobacterium tuberculosis H37Rv chorismate mutase by a ligand-based virtual screening optimized for lead evaluation in combination with in vitro enzymatic assay. The initial virtual screening using a ligand-based pharmacophore model identified 95 compounds from an in-house small molecule database of 15,452 compounds. The obtained hits were further evaluated by molecular docking and 15 compounds were short listed based on docking scores and the other scoring functions and subjected to biological assay. Chorismate mutase activity assays identified four compounds as inhibitors of M. tuberculosis chorismate mutase (MtCM) with low K(i) values. The structural models for these ligands in the chorismate mutase binding site will facilitate medicinal chemistry efforts for lead optimization against this protein.
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Affiliation(s)
- Himanshu Agrawal
- Molecular and Structural Biology, Central Drug Research Institute, Lucknow 226 001, India
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Kim SK, Reddy SK, Nelson BC, Vasquez GB, Davis A, Howard AJ, Patterson S, Gilliland GL, Ladner JE, Reddy PT. Biochemical and structural characterization of the secreted chorismate mutase (Rv1885c) from Mycobacterium tuberculosis H37Rv: an *AroQ enzyme not regulated by the aromatic amino acids. J Bacteriol 2007; 188:8638-48. [PMID: 17146044 PMCID: PMC1698256 DOI: 10.1128/jb.00441-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene Rv1885c from the genome of Mycobacterium tuberculosis H37Rv encodes a monofunctional and secreted chorismate mutase (*MtCM) with a 33-amino-acid cleavable signal sequence; hence, it belongs to the *AroQ class of chorismate mutases. Consistent with the heterologously expressed *MtCM having periplasmic destination in Escherichia coli and the absence of a discrete periplasmic compartment in M. tuberculosis, we show here that *MtCM secretes into the culture filtrate of M. tuberculosis. *MtCM functions as a homodimer and exhibits a dimeric state of the protein at a concentration as low as 5 nM. *MtCM exhibits simple Michaelis-Menten kinetics with a Km of 0.5 +/- 0.05 mM and a k(cat) of 60 s(-1) per active site (at 37 degrees C and pH 7.5). The crystal structure of *MtCM has been determined at 1.7 A resolution (Protein Data Bank identifier 2F6L). The protein has an all alpha-helical structure, and the active site is formed within a single chain without any contribution from the second chain in the dimer. Analysis of the structure shows a novel fold topology for the protein with a topologically rearranged helix containing Arg134. We provide evidence by site-directed mutagenesis that the residues Arg49, Lys60, Arg72, Thr105, Glu109, and Arg134 constitute the catalytic site; the numbering of the residues includes the signal sequence. Our investigation on the effect of phenylalanine, tyrosine, and tryptophan on *MtCM shows that *MtCM is not regulated by the aromatic amino acids. Consistent with this observation, the X-ray structure of *MtCM does not have an allosteric regulatory site.
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Affiliation(s)
- Sook-Kyung Kim
- Biochemical Science Division, National Institute of Standards and Technology, Mail stop 831.2, Bldg. 227, Room B244, Gaithersburg, MD 20899, USA
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Krengel U, Dey R, Sasso S, Okvist M, Ramakrishnan C, Kast P. Preliminary X-ray crystallographic analysis of the secreted chorismate mutase from Mycobacterium tuberculosis: a tricky crystallization problem solved. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:441-5. [PMID: 16682771 PMCID: PMC2219981 DOI: 10.1107/s1744309106012036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Accepted: 04/03/2006] [Indexed: 11/10/2022]
Abstract
Chorismate mutase catalyzes the conversion of chorismate to prephenate in the biosynthesis of the aromatic amino acids tyrosine and phenylalanine in bacteria, fungi and plants. Here, the crystallization of the unusual secreted chorismate mutase from Mycobacterium tuberculosis (encoded by Rv1885c), a 37.2 kDa dimeric protein belonging to the AroQ(gamma) subclass of mutases, is reported. Crystal optimization was non-trivial and is discussed in detail. To obtain crystals of sufficient quality, it was critical to initiate crystallization at higher precipitant concentration and then transfer the drops to lower precipitant concentrations within 5-15 min, in an adaptation of a previously described technique [Saridakis & Chayen (2000), Protein Sci. 9, 755-757]. As a result of the optimization, diffraction improved from 3.5 to 1.3 A resolution. The crystals belong to space group P2(1), with unit-cell parameters a = 42.6, b = 72.6, c = 62.0 angstroms, beta = 104.5 degrees. The asymmetric unit contains one biological dimer, with 167 amino acids per protomer. A soak with a transition-state analogue is also described.
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Affiliation(s)
- Ute Krengel
- Department of Chemistry and Bioscience, Chalmers University of Technology, PO Box 462, SE-40530 Göteborg, Sweden.
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Okvist M, Dey R, Sasso S, Grahn E, Kast P, Krengel U. 1.6 A crystal structure of the secreted chorismate mutase from Mycobacterium tuberculosis: novel fold topology revealed. J Mol Biol 2006; 357:1483-99. [PMID: 16499927 DOI: 10.1016/j.jmb.2006.01.069] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 01/17/2006] [Accepted: 01/18/2006] [Indexed: 10/25/2022]
Abstract
The presence of exported chorismate mutases produced by certain organisms such as Mycobacterium tuberculosis has been shown to correlate with their pathogenicity. As such, these proteins comprise a new group of promising selective drug targets. Here, we report the high-resolution crystal structure of the secreted dimeric chorismate mutase from M. tuberculosis (*MtCM; encoded by Rv1885c), which represents the first 3D-structure of a member of this chorismate mutase family, termed the AroQ(gamma) subclass. Structures are presented both for the unliganded enzyme and for a complex with a transition state analog. The protomer fold resembles the structurally characterized (dimeric) Escherichia coli chorismate mutase domain, but exhibits a new topology, with helix H4 of *MtCM carrying the catalytic site residue missing in the shortened helix H1. Furthermore, the structure of each *MtCM protomer is significantly more compact and only harbors one active site pocket, which is formed entirely by one polypeptide chain. Apart from the structural model, we present evidence as to how the substrate may enter the active site.
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Affiliation(s)
- Mats Okvist
- Department of Chemistry and Bioscience, Chalmers University of Technology, P.O. Box 462, SE-40530 Göteborg, Sweden
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