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Tomasi FG, Hall AMJ, Schweber JTP, Dulberger CL, McGowen K, Liu Q, Fortune SM, Helaine S, Rubin EJ. A tRNA-Acetylating Toxin and Detoxifying Enzyme in Mycobacterium tuberculosis. Microbiol Spectr 2022; 10:e0058022. [PMID: 35638832 PMCID: PMC9241777 DOI: 10.1128/spectrum.00580-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 11/20/2022] Open
Abstract
Toxin-antitoxin (TA) systems allow bacteria to adapt to changing environments without altering gene expression. Despite being overrepresented in Mycobacterium tuberculosis, their physiological roles remain elusive. We describe a TA system in M. tuberculosis which we named TacAT due to its homology to previously discovered systems in Salmonella. The toxin, TacT, blocks growth by acetylating glycyl-tRNAs and inhibiting translation. Its effects are reversed by the enzyme peptidyl tRNA hydrolase (Pth), which also cleaves peptidyl tRNAs that are prematurely released from stalled ribosomes. Pth is essential in most bacteria and thereby has been proposed as a promising drug target for complex pathogens like M. tuberculosis. Transposon sequencing data suggest that the tacAT operon is nonessential for M. tuberculosis growth in vitro, and premature stop mutations in this TA system present in some clinical isolates suggest that it is also dispensable in vivo. We assessed whether TacT modulates pth essentiality in M. tuberculosis because drugs targeting Pth might prompt resistance if TacAT is disrupted. We show that pth essentiality is unaffected by the absence of tacAT. These results highlight a fundamental aspect of mycobacterial biology and indicate that Pth's essential role hinges on its peptidyl-tRNA hydrolase activity. Our work underscores Pth's potential as a viable target for new antibiotics. IMPORTANCE The global rise in antibiotic-resistant tuberculosis has prompted an urgent search for new drugs. Toxin-antitoxin (TA) systems allow bacteria to adapt rapidly to environmental changes, and Mycobacterium tuberculosis encodes more TA systems than any known pathogen. We have characterized a new TA system in M. tuberculosis: the toxin, TacT, acetylates charged tRNA to block protein synthesis. TacT's effects are reversed by the essential bacterial enzyme peptidyl tRNA hydrolase (Pth), which is currently being explored as an antibiotic target. Pth also cleaves peptidyl tRNAs that are prematurely released from stalled ribosomes. We assessed whether TacT modulates pth essentiality in M. tuberculosis because drugs targeting Pth might prompt resistance if TacT is disrupted. We show that pth essentiality is unaffected by the absence of this TA system, indicating that Pth's essential role hinges on its peptidyl-tRNA hydrolase activity. Our work underscores Pth's potential as a viable target for new antibiotics.
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Affiliation(s)
- Francesca G. Tomasi
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Jessica T. P. Schweber
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Charles L. Dulberger
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kerry McGowen
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sophie Helaine
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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Strange DS, Gaffin SS, Holloway WB, Kinsella MD, Wisotsky JN, McFeeters H, McFeeters RL. Natural Product Inhibition and Enzyme Kinetics Related to Phylogenetic Characterization for Bacterial Peptidyl-tRNA Hydrolase 1. Molecules 2021; 26:molecules26082281. [PMID: 33920799 PMCID: PMC8071115 DOI: 10.3390/molecules26082281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 12/03/2022] Open
Abstract
With the relentless development of drug resistance and re-emergence of many pathogenic bacteria, the need for new antibiotics and new antibiotic targets is urgent and growing. Bacterial peptidyl-tRNA hydrolase, Pth1, is emerging as a promising new target for antibiotic development. From the conserved core and high degree of structural similarity, broad-spectrum inhibition is postulated. However, Pth1 small-molecule inhibition is still in the earliest stages. Focusing on pathogenic bacteria, herein we report the phylogenetic classification of Pth1 and natural product inhibition spanning phylogenetic space. While broad-spectrum inhibition is found, narrow-spectrum and even potentially clade-specific inhibition is more frequently observed. Additionally reported are enzyme kinetics and general in vitro Pth1 solubility that follow phylogenetic boundaries along with identification of key residues in the gate loop region that appear to govern both. The studies presented here demonstrate the sizeable potential for small-molecule inhibition of Pth1, improve understanding of Pth enzymes, and advance Pth1 as a much-needed novel antibiotic target.
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Affiliation(s)
- D. Scott Strange
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA; (D.S.S.); (W.B.H.); (H.M.)
| | - Steven S. Gaffin
- Department of Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA; (S.S.G.); (M.D.K.); (J.N.W.)
| | - W. Blake Holloway
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA; (D.S.S.); (W.B.H.); (H.M.)
| | - Meredyth D. Kinsella
- Department of Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA; (S.S.G.); (M.D.K.); (J.N.W.)
| | - Jacob N. Wisotsky
- Department of Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA; (S.S.G.); (M.D.K.); (J.N.W.)
| | - Hana McFeeters
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA; (D.S.S.); (W.B.H.); (H.M.)
| | - Robert L. McFeeters
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA; (D.S.S.); (W.B.H.); (H.M.)
- Correspondence: ; Tel.: +1-256-824-6023
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Mundra S, Pal RK, Tripathi S, Jain A, Arora A. Structural and functional characterization of peptidyl-tRNA hydrolase from Klebsiella pneumoniae. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140554. [PMID: 33068756 DOI: 10.1016/j.bbapap.2020.140554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
Abstract
Klebsiella pneumoniae is a member of the ESKAPE panel of pathogens that are top priority to tackle AMR. Bacterial peptidyl tRNA hydrolase (Pth), an essential, ubiquitous enzyme, hydrolyzes the peptidyl-tRNAs that accumulate in the cytoplasm because of premature termination of translation. Pth cleaves the ester bond between 2' or 3' hydroxyl of the ribose in the tRNA and C-terminal carboxylate of the peptide, thereby making free tRNA available for repeated cycles of protein synthesis and preventing cell death by alleviating tRNA starvation. Pth structures have been determined in peptide-bound or peptide-free states. In peptide-bound state, highly conserved residues F67, N69 and N115 adopt a conformation that is conducive to their interaction with peptide moiety of the substrate. While, in peptide-free state, these residues move away from the catalytic center, perhaps, in order to facilitate release of hydrolysed peptide. Here, we present a novel X-ray crystal structure of Pth from Klebsiella pneumoniae (KpPth), at 1.89 Å resolution, in which out of the two molecules in the asymmetric unit, one reflects the peptide-bound while the other reflects peptide-free conformation of the conserved catalytic site residues. Each molecule of the protein has canonical structure with seven stranded β-sheet structure surrounded by six α-helices. MD simulations indicate that both the forms converge over 500 ns simulation to structures with wider opening of the crevice at peptide-binding end. In solution, KpPth is monomeric and its 2D-HSQC spectrum displays a single set of well dispersed peaks. Further, KpPth was demonstrated to be enzymatically active on BODIPY-Lys-tRNALys3.
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Affiliation(s)
- Surbhi Mundra
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Department of Science and Technology, New Delhi 110016, India
| | - Ravi Kant Pal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India
| | - Sarita Tripathi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Anupam Jain
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Ashish Arora
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Characterization of active/binding site residues of peptidyl-tRNA hydrolase using biophysical and computational studies. Int J Biol Macromol 2020; 159:877-885. [PMID: 32445815 DOI: 10.1016/j.ijbiomac.2020.05.133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/09/2020] [Accepted: 05/17/2020] [Indexed: 11/21/2022]
Abstract
All mRNAs cannot be translated into full-length proteins due to ribosome-stalling that leads to release of peptidyl-tRNA which can be lethal for bacterial survival. The enzyme peptidyl-tRNA hydrolase (PtH) hydrolyses the ester bond between nascent peptide and tRNA of peptidyl-tRNA and rescues the cells from toxicity. PtH is an essential enzyme in bacteria and inhibiting this crucial enzyme can serve to combat bacterial diseases. But due to lack of understanding about the catalytic mechanism of PtH, its inhibitors have not been developed. In this work, we have carried out the binding studies of M. tuberculosis and E. coli PtH with the peptidyl-tRNA analogue (puromycin) using ITC, FTIR, CD experiments followed by docking and MD simulations to identify the potential active site residues that would help to design PtH inhibitors. Binding studies of puromycin with both PtH by ITC experiments demonstrate similar thermodynamic parameters and three fold difference in their KD. CD and FTIR studies detected changes in secondary structure composition of PtH in the presence of puromycin with different degree of perturbation. Though interactions with puromycin are conserved in both proteins, modelling studies revealed that water mediated interactions in M. tb-PtH resulting in higher affinity to puromycin.
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Matsumoto A, Uehara Y, Shimizu Y, Ueda T, Uchiumi T, Ito K. High-resolution crystal structure of peptidyl-tRNA hydrolase fromThermus thermophilus. Proteins 2018; 87:226-235. [DOI: 10.1002/prot.25643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/11/2018] [Accepted: 11/29/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Ami Matsumoto
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
| | - Yuji Uehara
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
| | - Yoshihiro Shimizu
- Department of Medical Genome Sciences; Graduate School of Frontier Sciences, The University of Tokyo; Chiba Japan
- Laboratory for Cell-Free Protein Synthesis; RIKEN Center for Biosystems Dynamics Research; Osaka Japan
| | - Takuya Ueda
- Department of Medical Genome Sciences; Graduate School of Frontier Sciences, The University of Tokyo; Chiba Japan
| | - Toshio Uchiumi
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
| | - Kosuke Ito
- Faculty of Science, Department of Biology; Niigata University; Niigata Japan
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Shahid S, Kabra A, Mundra S, Pal RK, Tripathi S, Jain A, Arora A. Role of methionine 71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:865-874. [DOI: 10.1016/j.bbapap.2018.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/19/2018] [Accepted: 05/03/2018] [Indexed: 01/25/2023]
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Solution NMR Studies of Mycobacterium tuberculosis Proteins for Antibiotic Target Discovery. Molecules 2017; 22:molecules22091447. [PMID: 28858250 PMCID: PMC6151718 DOI: 10.3390/molecules22091447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/27/2017] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis is an infectious disease caused by Mycobacteriumtuberculosis, which triggers severe pulmonary diseases. Recently, multidrug/extensively drug-resistant tuberculosis strains have emerged and continue to threaten global health. Because of the development of drug-resistant tuberculosis, there is an urgent need for novel antibiotics to treat these drug-resistant bacteria. In light of the clinical importance of M. tuberculosis, 2067 structures of M. tuberculsosis proteins have been determined. Among them, 52 structures have been solved and studied using solution nuclear magnetic resonance (NMR). The functional details based on structural analysis of M. tuberculosis using NMR can provide essential biochemical data for the development of novel antibiotic drugs. In this review, we introduce diverse structural and biochemical studies on M. tuberculosis proteins determined using NMR spectroscopy.
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Kabra A, Shahid S, Pal RK, Yadav R, Pulavarti SVSRK, Jain A, Tripathi S, Arora A. Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase. RNA (NEW YORK, N.Y.) 2017; 23:202-216. [PMID: 28096445 PMCID: PMC5238795 DOI: 10.1261/rna.057620.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
Bacterial peptidyl-tRNA hydrolase (Pth; EC 3.1.1.29) hydrolyzes the peptidyl-tRNAs accumulated in the cytoplasm and thereby prevents cell death by alleviating tRNA starvation. X-ray and NMR studies of Vibrio cholerae Pth (VcPth) and mutants of its key residues involved in catalysis show that the activity and selectivity of the protein depends on the stereochemistry and dynamics of residues H24, D97, N118, and N14. D97-H24 interaction is critical for activity because it increases the nucleophilicity of H24. The N118 and N14 have orthogonally competing interactions with H24, both of which reduce the nucleophilicity of H24 and are likely to be offset by positioning of a peptidyl-tRNA substrate. The region proximal to H24 and the lid region exhibit slow motions that may assist in accommodating the substrate. Helix α3 exhibits a slow wobble with intermediate time scale motions of its N-cap residue N118, which may work as a flypaper to position the scissile ester bond of the substrate. Overall, the dynamics of interactions between the side chains of N14, H24, D97, and N118, control the catalysis of substrate by this enzyme.
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Affiliation(s)
- Ashish Kabra
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Salman Shahid
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research, New Delhi 110025, India
| | - Ravi Kant Pal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India
| | - Rahul Yadav
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | | | - Anupam Jain
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Sarita Tripathi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Ashish Arora
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research, New Delhi 110025, India
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9
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Bal NC, Jena N, Chakravarty H, Kumar A, Chi M, Balaraju T, Rawale SV, Rawale JS, Sharon A, Periasamy M. The C-terminal calcium-sensitive disordered motifs regulate isoform-specific polymerization characteristics of calsequestrin. Biopolymers 2016; 103:15-22. [PMID: 25091206 DOI: 10.1002/bip.22534] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 07/31/2014] [Accepted: 08/01/2014] [Indexed: 12/14/2022]
Abstract
Calsequestrin (CASQ) exists as two distinct isoforms CASQ1 and CASQ2 in all vertebrates. Although the isoforms exhibit unique functional characteristic, the structural basis for the same is yet to be fully defined. Interestingly, the C-terminal region of the two isoforms exhibit significant differences both in length and amino acid composition; forming Dn-motif and DEXn-motif in CASQ1 and CASQ2, respectively. Here, we investigated if the unique C-terminal motifs possess Ca(2+)-sensitivity and affect protein function. Sequence analysis shows that both the Dn- and DEXn-motifs are intrinsically disordered regions (IDRs) of the protein, a feature that is conserved from fish to man. Using purified synthetic peptides, we show that these motifs undergo distinctive Ca(2+)-mediated folding suggesting that these disordered motifs are Ca(2+)-sensitivity. We generated chimeric proteins by swapping the C-terminal portions between CASQ1 and CASQ2. Our studies show that the C-terminal portions do not play significant role in protein folding. An interesting finding of the current study is that the switching of the C-terminal portion completely reverses the polymerization kinetics. Collectively, these data suggest that these Ca(2+)-sensitivity IDRs located at the back-to-back dimer interface influence isoform-specific Ca(2+)-dependent polymerization properties of CASQ.
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Affiliation(s)
- Naresh C Bal
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210
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Giorgi L, Plateau P, O'Mahony G, Aubard C, Fromant M, Thureau A, Grøtli M, Blanquet S, Bontems F. NMR-Based Substrate Analog Docking to Escherichia coli Peptidyl-tRNA Hydrolase. J Mol Biol 2011; 412:619-33. [DOI: 10.1016/j.jmb.2011.06.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 05/06/2011] [Accepted: 06/15/2011] [Indexed: 11/27/2022]
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Pulavarti S, Jain A, Prakash Pathak P, Mahmood A, Arora A. Solution Structure and Dynamics of Peptidyl-tRNA Hydrolase from Mycobacterium tuberculosis H37Rv. J Mol Biol 2008; 378:165-77. [DOI: 10.1016/j.jmb.2008.02.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 01/15/2008] [Accepted: 02/14/2008] [Indexed: 11/28/2022]
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