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de Crécy-Lagard V, Jaroch M. Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity. Trends Microbiol 2020; 29:41-53. [PMID: 32718697 DOI: 10.1016/j.tim.2020.06.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 01/21/2023]
Abstract
Modified nucleotides in tRNA are critical components of the translation apparatus, but their importance in the process of translational regulation had until recently been greatly overlooked. Two breakthroughs have recently allowed a fuller understanding of the importance of tRNA modifications in bacterial physiology. One is the identification of the full set of tRNA modification genes in model organisms such as Escherichia coli K12. The second is the improvement of available analytical tools to monitor tRNA modification patterns. The role of tRNA modifications varies greatly with the specific modification within a given tRNA and with the organism studied. The absence of these modifications or reductions can lead to cell death or pleiotropic phenotypes or may have no apparent visible effect. By linking translation through their decoding functions to metabolism through their biosynthetic pathways, tRNA modifications are emerging as important components of the bacterial regulatory toolbox.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Marshall Jaroch
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
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2
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Siadat SD, Khaledi A, Shahcheraghi F, Rashki S, Arfaatabar M. Molecular diversity of hpd gene in clinical isolates of Haemophilus influenzae. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2019.100556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Missoury S, Plancqueel S, Li de la Sierra-Gallay I, Zhang W, Liger D, Durand D, Dammak R, Collinet B, van Tilbeurgh H. The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification. Nucleic Acids Res 2018; 46:5850-5860. [PMID: 29741707 PMCID: PMC6009658 DOI: 10.1093/nar/gky323] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/09/2018] [Accepted: 04/17/2018] [Indexed: 12/25/2022] Open
Abstract
The universal N6-threonylcarbamoyladenosine (t6A) modification at position A37 of ANN-decoding tRNAs is essential for translational fidelity. In bacteria the TsaC enzyme first synthesizes an l-threonylcarbamoyladenylate (TC-AMP) intermediate. In cooperation with TsaB and TsaE, TsaD then transfers the l-threonylcarbamoyl-moiety from TC-AMP onto tRNA. We determined the crystal structure of the TsaB-TsaE-TsaD (TsaBDE) complex of Thermotoga maritima in presence of a non-hydrolysable AMPCPP. TsaE is positioned at the entrance of the active site pocket of TsaD, contacting both the TsaB and TsaD subunits and prohibiting simultaneous tRNA binding. AMPCPP occupies the ATP binding site of TsaE and is sandwiched between TsaE and TsaD. Unexpectedly, the binding of TsaE partially denatures the active site of TsaD causing loss of its essential metal binding sites. TsaE interferes in a pre- or post-catalytic step and its binding to TsaBD is regulated by ATP hydrolysis. This novel binding mode and activation mechanism of TsaE offers good opportunities for antimicrobial drug development.
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Affiliation(s)
- Sophia Missoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Stéphane Plancqueel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Wenhua Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Raoudha Dammak
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR7590 CNRS/Sorbonne-Université, UPMC, Paris, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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4
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Colameco S, Elliot MA. Non-coding RNAs as antibiotic targets. Biochem Pharmacol 2016; 133:29-42. [PMID: 28012959 DOI: 10.1016/j.bcp.2016.12.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023]
Abstract
Antibiotics inhibit a wide range of essential processes in the bacterial cell, including replication, transcription, translation and cell wall synthesis. In many instances, these antibiotics exert their effects through association with non-coding RNAs. This review highlights many classical antibiotic targets (e.g. rRNAs and the ribosome), explores a number of emerging targets (e.g. tRNAs, RNase P, riboswitches and small RNAs), and discusses the future directions and challenges associated with non-coding RNAs as antibiotic targets.
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Affiliation(s)
- Savannah Colameco
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Marie A Elliot
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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5
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Thiaville PC, Iwata-Reuyl D, de Crécy-Lagard V. Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t(6)A), a universal modification of tRNA. RNA Biol 2015; 11:1529-39. [PMID: 25629598 PMCID: PMC4615747 DOI: 10.4161/15476286.2014.992277] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tRNA modification field has a rich literature covering biochemical analysis going back more than 40 years, but many of the corresponding genes were only identified in the last decade. In recent years, comparative genomic-driven analysis has allowed for the identification of the genes and subsequent characterization of the enzymes responsible for N6-threonylcarbamoyladenosine (t6A). This universal modification, located in the anticodon stem-loop at position 37 adjacent to the anticodon of tRNAs, is found in nearly all tRNAs that decode ANN codons. The t6A biosynthesis enzymes and synthesis pathways have now been identified, revealing both a core set of enzymes and kingdom-specific variations. This review focuses on the elucidation of the pathway, diversity of the synthesis genes, and proposes a new nomenclature for t6A synthesis enzymes.
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Affiliation(s)
- Patrick C Thiaville
- a Genetics and Genomics Graduate Program ; University of Florida ; Gainesville , FL USA
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6
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Thiaville PC, El Yacoubi B, Köhrer C, Thiaville JJ, Deutsch C, Iwata-Reuyl D, Bacusmo JM, Armengaud J, Bessho Y, Wetzel C, Cao X, Limbach PA, RajBhandary UL, de Crécy-Lagard V. Essentiality of threonylcarbamoyladenosine (t(6)A), a universal tRNA modification, in bacteria. Mol Microbiol 2015; 98:1199-221. [PMID: 26337258 DOI: 10.1111/mmi.13209] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2015] [Indexed: 02/06/2023]
Abstract
Threonylcarbamoyladenosine (t(6)A) is a modified nucleoside universally conserved in tRNAs in all three kingdoms of life. The recently discovered genes for t(6)A synthesis, including tsaC and tsaD, are essential in model prokaryotes but not essential in yeast. These genes had been identified as antibacterial targets even before their functions were known. However, the molecular basis for this prokaryotic-specific essentiality has remained a mystery. Here, we show that t(6)A is a strong positive determinant for aminoacylation of tRNA by bacterial-type but not by eukaryotic-type isoleucyl-tRNA synthetases and might also be a determinant for the essential enzyme tRNA(Ile)-lysidine synthetase. We confirm that t(6)A is essential in Escherichia coli and a survey of genome-wide essentiality studies shows that genes for t(6)A synthesis are essential in most prokaryotes. This essentiality phenotype is not universal in Bacteria as t(6)A is dispensable in Deinococcus radiodurans, Thermus thermophilus, Synechocystis PCC6803 and Streptococcus mutans. Proteomic analysis of t(6)A(-) D. radiodurans strains revealed an induction of the proteotoxic stress response and identified genes whose translation is most affected by the absence of t(6)A in tRNAs. Thus, although t(6)A is universally conserved in tRNAs, its role in translation might vary greatly between organisms.
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Affiliation(s)
- Patrick C Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.,Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL, 32610, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.,Institut de Génétique et Microbiologie, Université of Paris-Sud, Orsay, France
| | - Basma El Yacoubi
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jennifer J Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Chris Deutsch
- Department of Chemistry, Portland State University, Portland, OR, 97297, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, OR, 97297, USA
| | - Jo Marie Bacusmo
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Jean Armengaud
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory 'Innovative technologies for Detection and Diagnostics', Bagnols-sur-Cèze, F-30200, France
| | - Yoshitaka Bessho
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Institute of Physics, Academia Sinica, 128 Sec. 2, Academia Rd., Nankang, Taipei, 11529, Taiwan
| | - Collin Wetzel
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Uttam L RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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7
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Abstract
A powerful early approach to evaluating the druggability of proteins involved determining the hit rate in NMR-based screening of a library of small compounds. Here, we show that a computational analog of this method, based on mapping proteins using small molecules as probes, can reliably reproduce druggability results from NMR-based screening and can provide a more meaningful assessment in cases where the two approaches disagree. We apply the method to a large set of proteins. The results show that, because the method is based on the biophysics of binding rather than on empirical parametrization, meaningful information can be gained about classes of proteins and classes of compounds beyond those resembling validated targets and conventionally druglike ligands. In particular, the method identifies targets that, while not druggable by druglike compounds, may become druggable using compound classes such as macrocycles or other large molecules beyond the rule-of-five limit.
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Affiliation(s)
- Dima Kozakov
- Department of Applied Mathematics & Statistics, Stony Brook University , Stony Brook, New York 11794, United States
| | - David R Hall
- Acpharis Inc. , Holliston, Massachusetts 01746, United States
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8
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Nett M. Genome mining: concept and strategies for natural product discovery. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2014; 99:199-245. [PMID: 25296440 DOI: 10.1007/978-3-319-04900-7_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Hashimoto C, Hashimoto M, Honda H, Kato JI. Effects on IS1 transposition frequency of a mutation in the ygjD gene involved in an essential tRNA modification in Escherichia coli. FEMS Microbiol Lett 2013; 347:140-8. [PMID: 23909935 DOI: 10.1111/1574-6968.12227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 07/30/2013] [Accepted: 07/30/2013] [Indexed: 12/01/2022] Open
Abstract
The YgjD protein is essential for the synthesis of the universal tRNA modification, N(6) -threonylcarbamoyladenosine (t(6) A), which is necessary for the decoding of ANN codons. We isolated a suppressor (ygjDsup ) of the ygjD(ts) mutant by its permissive growth at high temperature in Escherichia coli. Resequencing of the ygjDsup mutant genome showed the presence of a complicated chromosome rearrangement, an inverse insertion of a large duplicated region (c. 450 kb) into a small deleted region. The temperature-resistant growth associated with ygjDsup was due to the presence of multicopy suppressor genes, yjeE and groL, of the ygjD(ts) mutation in the duplicated region. This DNA rearrangement was not simply mediated by IS1 transposition, but the duplicated region was flanked by IS1. We showed that the frequency of IS1 transposition was increased in ygjD(ts) mutants. The transposase of IS1 is coded for by the insB gene, and its translation occurs through a frameshift of a ribosome translating upstream of the insA gene. We showed that this frameshifting frequency was increased by the ygjD(ts) mutation. These results indicated that the mutation of the gene for tRNA modification, t(6) A, affected IS1 transposition.
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Affiliation(s)
- Chika Hashimoto
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
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10
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Wecke T, Mascher T. Antibiotic research in the age of omics: from expression profiles to interspecies communication. J Antimicrob Chemother 2011; 66:2689-704. [DOI: 10.1093/jac/dkr373] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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11
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Miller CH, O'Toole RF. Navigating tuberculosis drug discovery with target-based screening. Expert Opin Drug Discov 2011; 6:839-54. [DOI: 10.1517/17460441.2011.586999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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12
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Comess KM, Sun C, Abad-Zapatero C, Goedken ER, Gum RJ, Borhani DW, Argiriadi M, Groebe DR, Jia Y, Clampit JE, Haasch DL, Smith HT, Wang S, Song D, Coen ML, Cloutier TE, Tang H, Cheng X, Quinn C, Liu B, Xin Z, Liu G, Fry EH, Stoll V, Ng TI, Banach D, Marcotte D, Burns DJ, Calderwood DJ, Hajduk PJ. Discovery and characterization of non-ATP site inhibitors of the mitogen activated protein (MAP) kinases. ACS Chem Biol 2011; 6:234-44. [PMID: 21090814 DOI: 10.1021/cb1002619] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Inhibition of protein kinases has validated therapeutic utility for cancer, with at least seven kinase inhibitor drugs on the market. Protein kinase inhibition also has significant potential for a variety of other diseases, including diabetes, pain, cognition, and chronic inflammatory and immunologic diseases. However, as the vast majority of current approaches to kinase inhibition target the highly conserved ATP-binding site, the use of kinase inhibitors in treating nononcology diseases may require great selectivity for the target kinase. As protein kinases are signal transducers that are involved in binding to a variety of other proteins, targeting alternative, less conserved sites on the protein may provide an avenue for greater selectivity. Here we report an affinity-based, high-throughput screening technique that allows nonbiased interrogation of small molecule libraries for binding to all exposed sites on a protein surface. This approach was used to screen both the c-Jun N-terminal protein kinase Jnk-1 (involved in insulin signaling) and p38α (involved in the formation of TNFα and other cytokines). In addition to canonical ATP-site ligands, compounds were identified that bind to novel allosteric sites. The nature, biological relevance, and mode of binding of these ligands were extensively characterized using two-dimensional (1)H/(13)C NMR spectroscopy, protein X-ray crystallography, surface plasmon resonance, and direct enzymatic activity and activation cascade assays. Jnk-1 and p38α both belong to the MAP kinase family, and the allosteric ligands for both targets bind similarly on a ledge of the protein surface exposed by the MAP insertion present in the CMGC family of protein kinases and distant from the active site. Medicinal chemistry studies resulted in an improved Jnk-1 ligand able to increase adiponectin secretion in human adipocytes and increase insulin-induced protein kinase PKB phosphorylation in human hepatocytes, in similar fashion to Jnk-1 siRNA and to rosiglitazone treatment. Together, the data suggest that these new ligand series bind to a novel, allosteric, and physiologically relevant site and therefore represent a unique approach to identify kinase inhibitors.
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Affiliation(s)
- Kenneth M. Comess
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Chaohong Sun
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Cele Abad-Zapatero
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Eric R. Goedken
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Rebecca J. Gum
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - David W. Borhani
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Maria Argiriadi
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Duncan R. Groebe
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Yong Jia
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Jill E. Clampit
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Deanna L. Haasch
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Harriet T. Smith
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Sanyi Wang
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Danying Song
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Michael L. Coen
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Timothy E. Cloutier
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Hua Tang
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Xueheng Cheng
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Christopher Quinn
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Bo Liu
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Zhili Xin
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Gang Liu
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Elizabeth H. Fry
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Vincent Stoll
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Teresa I. Ng
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - David Banach
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Doug Marcotte
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - David J. Burns
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - David J. Calderwood
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
| | - Philip J. Hajduk
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, United States
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Karst JC, Foucher AE, Campbell TL, Di Guilmi AM, Stroebel D, Mangat CS, Brown ED, Jault JM. The ATPase activity of an 'essential' Bacillus subtilis enzyme, YdiB, is required for its cellular function and is modulated by oligomerization. MICROBIOLOGY-SGM 2009; 155:944-956. [PMID: 19246765 DOI: 10.1099/mic.0.021543-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Characterization of 'unknown' proteins is one of the challenges of the post-genomic era. Here, we report a study of Bacillus subtilis YdiB, which belongs to an uncharted class of bacterial P-loop ATPases. Precise deletion of the ydiB gene yielded a mutant with much reduced growth rate compared to the wild-type strain. In vitro, purified YdiB was in equilibrium among different forms, monomers, dimers and oligomers, and this equilibrium was strongly affected by salts; high concentrations of NaCl favoured the monomeric over the oligomeric form of the enzyme. Interestingly, the ATPase activity of the monomer was about three times higher than that of the oligomer, and the monomer showed a K(m) of about 60 microM for ATP and a V(max) of about 10 nmol min(-1) (mg protein)(-1) (k(cat) approximately 10 h(-1)). This low ATPase activity was shown to be specific to YdiB because mutation of an invariant lysine residue in the P-loop motif (K41A) strongly attenuated this rate. This mutant was unable to restore a normal growth phenotype when introduced into a conditional knockout strain for ydiB, showing that the ATPase activity of YdiB is required for the in vivo function of the protein. Oligomerization was also observed with the purified YjeE from Escherichia coli, a YdiB orthologue, suggesting that this property is shared by all members of this family of ATPases. Importantly, dimers of YdiB were also observed in a B. subtilis extract, or when stabilized by formaldehyde cross-linking for YjeE from E. coli, suggesting that oligomerization might regulate the function of this new class of proteins in vivo.
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Affiliation(s)
- Johanna C Karst
- Institut de Biologie Structurale, UMR 5075 Université Joseph Fourier/CEA/CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Anne-Emmanuelle Foucher
- Institut de Biologie Structurale, UMR 5075 Université Joseph Fourier/CEA/CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Tracey L Campbell
- Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
| | - Anne-Marie Di Guilmi
- Institut de Biologie Structurale, UMR 5075 Université Joseph Fourier/CEA/CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - David Stroebel
- Institut de Biologie Structurale, UMR 5075 Université Joseph Fourier/CEA/CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Chand S Mangat
- Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
| | - Eric D Brown
- Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
| | - Jean-Michel Jault
- Institut de Biologie Structurale, UMR 5075 Université Joseph Fourier/CEA/CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
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14
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Known Bioactive Small Molecules Probe the Function of a Widely Conserved but Enigmatic Bacterial ATPase, YjeE. ACTA ACUST UNITED AC 2008; 15:1287-95. [DOI: 10.1016/j.chembiol.2008.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 09/30/2008] [Accepted: 10/14/2008] [Indexed: 11/22/2022]
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15
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Self-Purificatory Ganga Water Facilitates Death of Pathogenic Escherichia coli O157:H7. Curr Microbiol 2008; 58:25-9. [DOI: 10.1007/s00284-008-9260-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 07/25/2008] [Accepted: 08/25/2008] [Indexed: 11/27/2022]
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