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Karalia S, Meena VK, Kumar V. Deciphering structural variation upon biotinylation of biotin carboxyl carrier protein domain in Streptococcus pneumoniae. Int J Biol Macromol 2024:133580. [PMID: 38960227 DOI: 10.1016/j.ijbiomac.2024.133580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/26/2024] [Accepted: 06/29/2024] [Indexed: 07/05/2024]
Abstract
Streptococcus pneumoniae is a leading cause of community-acquired pneumonia and is responsible for acute invasive and non-invasive infections. Fight against pneumococcus is currently hampered by insufficient vaccine coverage and rising antimicrobial resistance, making the research necessary on novel drug targets. High-throughput mutagenesis has shown that acetyl-CoA carboxylase (ACC) is an essential enzyme in S. pneumoniae which converts acetyl-CoA to malonyl-CoA, a key step in fatty acid biosynthesis. ACC has four subunits; Biotin carboxyl carrier protein (BCCP), Biotin carboxylase (BC), Carboxyl transferase subunit α and β. Biotinylation of S. pneumoniae BCCP (SpBCCP) is required for the activation of ACC complex. In this study, we have biophysically characterized the apo- and holo- biotinylating domain of SpBCCP80. We have performed 2D and 3D NMR experiments to analyze the changes in amino acid residues upon biotinylation of SpBCCP80. Further, we used NMR backbone chemical shift assignment data for bioinformatical analyses to determine the secondary and tertiary structure of proteins. We observed major changes in AMKVM motif and thumb region of SpBCCP80 upon biotinylation. Overall, this work provides structural insight into the apo- to holo- conversion of SpBCCP80 which can be further used as a drug target against S. pneumoniae.
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Affiliation(s)
- Shivani Karalia
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej, 1958 Frederiksberg C, Denmark; NMR-II Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India.
| | - Vinod Kumar Meena
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, Brussels, -1050, Belgium; NMR-II Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India.
| | - Vijay Kumar
- NMR-II Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
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2
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Smoczynski J, Yared MJ, Meynier V, Barraud P, Tisné C. Advances in the Structural and Functional Understanding of m 1A RNA Modification. Acc Chem Res 2024. [PMID: 38331425 PMCID: PMC10882958 DOI: 10.1021/acs.accounts.3c00568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
ConspectusRNA modification is a co- or post-transcriptional process by which specific nucleotides are chemically altered by enzymes after their initial incorporation into the RNA chain, expanding the chemical and functional diversity of RNAs. Our understanding of RNA modifications has changed dramatically in recent years. In the past decade, RNA methyltransferases (MTases) have been highlighted in numerous clinical studies and disease models, modifications have been found to be dynamically regulated by demodification enzymes, and significant technological advances have been made in the fields of RNA sequencing, mass spectrometry, and structural biology. Among RNAs, transfer RNAs (tRNAs) exhibit the greatest diversity and density of post-transcriptional modifications, which allow for potential cross-talks and regulation during their incorporation. N1-methyladenosine (m1A) modification is found in tRNAs at positions 9, 14, 16, 22, 57, and 58, depending on the tRNA and organism.Our laboratory has used and developed a large panel of tools to decipher the different mechanisms used by m1A tRNA MTases to recognize and methylate tRNA. We have solved the structures of TrmI from Thermus thermophilus (m1A58), TrmK from Bacillus subtilis (m1A22), and human TRMT10C (m1A9). These MTases do not share the same structure or organization to recognize tRNAs, but they all modify an adenosine, forming a non-Watson-Crick (WC) interaction. For TrmK, nuclear magnetic resonance (NMR) chemical shift mapping of the binding interface between TrmK and tRNASer was invaluable to build a TrmK/tRNA model, where both domains of TrmK participate in the binding of a full-length L-shaped tRNA and where the non-WC purine 13-A22 base pair positions the A22 N1-atom close to the methyl of the S-adenosyl-l-methionine (SAM) TrmK cofactor. For TRMT10C, cryoEM structures showed the MTase poised to N1-methylate A9 or G9 in tRNA and revealed different steps of tRNA maturation, where TRMT10C acts as a tRNA binding platform for sequential docking of each maturation enzyme. This work confers a role for TRMT10C in tRNA quality control and provides a framework to understand the link between mitochondrial tRNA maturation dysfunction and diseases.Methods to directly detect the incorporation of modifications during tRNA biosynthesis are rare and do not provide easy access to the temporality of their introduction. To this end, we have introduced time-resolved NMR to monitor tRNA maturation in the cellular environment. Combined with genetic and biochemical approaches involving the synthesis of specifically modified tRNAs, our methodology revealed that some modifications are incorporated in a defined sequential order, controlled by cross-talks between modification events. In particular, a strong modification circuit, namely Ψ55 → m5U54 → m1A58, controls the modification process in the T-arm of yeast elongator tRNAs. Conversely, we showed that m1A58 is efficiently introduced on unmodified initiator tRNAiMet without the need of any prior modification. Two distinct pathways are therefore followed for m1A58 incorporation in elongator and initiator tRNAs.We are undoubtedly entering an exciting period for the elucidation of the functions of RNA modifications and the intricate mechanisms by which modification enzymes identify and alter their RNA substrates. These are promising directions for the field of epitranscriptomics.
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Affiliation(s)
- Jakub Smoczynski
- Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique, IBPC, Expression Génétique Microbienne, Paris 75005, France
| | - Marcel-Joseph Yared
- Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique, IBPC, Expression Génétique Microbienne, Paris 75005, France
| | - Vincent Meynier
- Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique, IBPC, Expression Génétique Microbienne, Paris 75005, France
| | - Pierre Barraud
- Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique, IBPC, Expression Génétique Microbienne, Paris 75005, France
| | - Carine Tisné
- Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique, IBPC, Expression Génétique Microbienne, Paris 75005, France
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3
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Lenoir C, Pelletier A, Manuse S, Millat H, Ducret A, Galinier A, Doan T, Grangeasse C. The morphogenic protein CopD controls the spatio-temporal dynamics of PBP1a and PBP2b in Streptococcus pneumoniae. mBio 2023; 14:e0141123. [PMID: 37728370 PMCID: PMC10653890 DOI: 10.1128/mbio.01411-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE Penicillin-binding proteins (PBPs) are essential for proper bacterial cell division and morphogenesis. The genome of Streptococcus pneumoniae encodes for two class B PBPs (PBP2x and 2b), which are required for the assembly of the peptidoglycan framework and three class A PBPs (PBP1a, 1b and 2a), which remodel the peptidoglycan mesh during cell division. Therefore, their activities should be finely regulated in space and time to generate the pneumococcal ovoid cell shape. To date, two proteins, CozE and MacP, are known to regulate the function of PBP1a and PBP2a, respectively. In this study, we describe a novel regulator (CopD) that acts on both PBP1a and PBP2b. These findings provide valuable information for understanding bacterial cell division. Furthermore, knowing that ß-lactam antibiotic resistance often arises from PBP mutations, the characterization of such a regulator represents a promising opportunity to develop new strategies to resensitize resistant strains.
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Affiliation(s)
- Cassandra Lenoir
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Anaïs Pelletier
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Sylvie Manuse
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Hugo Millat
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR, Aix-Marseille Université, CNRS, Marseille, France
| | - Thierry Doan
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, UMR, Aix-Marseille Université, Marseille, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
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4
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Naha A, Haeusser DP, Margolin W. Anchors: A way for FtsZ filaments to stay membrane bound. Mol Microbiol 2023; 120:525-538. [PMID: 37503768 PMCID: PMC10593102 DOI: 10.1111/mmi.15067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 07/29/2023]
Abstract
Most bacteria use the tubulin homolog FtsZ to organize their cell division. FtsZ polymers initially assemble into mobile complexes that circle around a ring-like structure at the cell midpoint, followed by the recruitment of other proteins that will constrict the cytoplasmic membrane and synthesize septal peptidoglycan to divide the cell. Despite the need for FtsZ polymers to associate with the membrane, FtsZ lacks intrinsic membrane binding ability. Consequently, FtsZ polymers have evolved to interact with the membrane through adaptor proteins that both bind FtsZ and the membrane. Here, we discuss recent progress in understanding the functions of these FtsZ membrane tethers. Some, such as FtsA and SepF, are widely conserved and assemble into varied oligomeric structures bound to the membrane through an amphipathic helix. Other less-conserved proteins, such as EzrA and ZipA, have transmembrane domains, make extended structures, and seem to bind to FtsZ through two separate interactions. This review emphasizes that most FtsZs use multiple membrane tethers with overlapping functions, which not only attach FtsZ polymers to the membrane but also organize them in specific higher-order structures that can optimize cell division activity. We discuss gaps in our knowledge of these concepts and how future studies can address them.
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Affiliation(s)
- Arindam Naha
- Department of Microbiology and Molecular Genetics, UTHealth-Houston, Houston, TX 77030, USA
| | - Daniel P. Haeusser
- Department of Microbiology and Molecular Genetics, UTHealth-Houston, Houston, TX 77030, USA
- Department of Biology, Canisius College, Buffalo, NY 14208, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, UTHealth-Houston, Houston, TX 77030, USA
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5
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Wilkinson AJ, Ooi N, Finlayson J, Lee VE, Lyth D, Maskew KS, Newman R, Orr D, Ansell K, Birchall K, Canning P, Coombs P, Fusani L, McIver E, Pisco J, Ireland PM, Jenkins C, Norville IH, Southern SJ, Cowan R, Hall G, Kettleborough C, Savage VJ, Cooper IR. Evaluating the druggability of TrmD, a potential antibacterial target, through design and microbiological profiling of a series of potent TrmD inhibitors. Bioorg Med Chem Lett 2023; 90:129331. [PMID: 37187252 DOI: 10.1016/j.bmcl.2023.129331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023]
Abstract
The post-transcriptional modifier tRNA-(N1G37) methyltransferase (TrmD) has been proposed to be essential for growth in many Gram-negative and Gram-positive pathogens, however previously reported inhibitors show only weak antibacterial activity. In this work, optimisation of fragment hits resulted in compounds with low nanomolar TrmD inhibition incorporating features designed to enhance bacterial permeability and covering a range of physicochemical space. The resulting lack of significant antibacterial activity suggests that whilst TrmD is highly ligandable, its essentiality and druggability are called into question.
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Affiliation(s)
- Andrew J Wilkinson
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK.
| | - Nicola Ooi
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Jonathan Finlayson
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Victoria E Lee
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - David Lyth
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Kathryn S Maskew
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Rebecca Newman
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - David Orr
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Keith Ansell
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Kristian Birchall
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Peter Canning
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Peter Coombs
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Lucia Fusani
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Ed McIver
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - João Pisco
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Philip M Ireland
- CBR division, Dstl Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
| | | | | | | | - Richard Cowan
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 7RH, UK
| | - Gareth Hall
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 7RH, UK
| | | | - Victoria J Savage
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Ian R Cooper
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
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6
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Rahimova R, Nogaret P, Huteau V, Gelin M, Clément DA, Labesse G, Pochet S, Blanc-Potard AB, Lionne C. Structure-based design, synthesis and biological evaluation of a NAD + analogue targeting Pseudomonas aeruginosa NAD kinase. FEBS J 2023; 290:482-501. [PMID: 36036789 PMCID: PMC10087438 DOI: 10.1111/febs.16604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 02/05/2023]
Abstract
Multidrug resistance is a major public health problem that requires the urgent development of new antibiotics and therefore the identification of novel bacterial targets. The activity of nicotinamide adenine dinucleotide kinase, NADK, is essential in all bacteria tested so far, including many human pathogens that display antibiotic resistance leading to the failure of current treatments. Inhibiting NADK is therefore a promising and innovative antibacterial strategy since there is currently no drug on the market targeting this enzyme. Through a fragment-based drug design approach, we have recently developed a NAD+ -competitive inhibitor of NADKs, which displayed in vivo activity against Staphylococcus aureus. Here, we show that this compound, a di-adenosine derivative, is inactive against the NADK enzyme from the Gram-negative bacteria Pseudomonas aeruginosa (PaNADK). This lack of activity can be explained by the crystal structure of PaNADK, which was determined in complex with NADP+ in this study. Structural analysis led us to design and synthesize a benzamide adenine dinucleoside analogue, active against PaNADK. This novel compound efficiently inhibited PaNADK enzymatic activity in vitro with a Ki of 4.6 μm. Moreover, this compound reduced P. aeruginosa infection in vivo in a zebrafish model.
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Affiliation(s)
- Rahila Rahimova
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS UMR 5048, INSERM U1054, France
| | - Pauline Nogaret
- Laboratory of Pathogen Host Interactions (LPHI), Université de Montpellier, CNRS UMR 5235, France
| | - Valérie Huteau
- Unité de Chimie Biologique Epigénétique, Institut Pasteur, Université Paris Cité, CNRS UMR3523, France
| | - Muriel Gelin
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS UMR 5048, INSERM U1054, France
| | - David A Clément
- Unité de Chimie Biologique Epigénétique, Institut Pasteur, Université Paris Cité, CNRS UMR3523, France
| | - Gilles Labesse
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS UMR 5048, INSERM U1054, France
| | - Sylvie Pochet
- Unité de Chimie Biologique Epigénétique, Institut Pasteur, Université Paris Cité, CNRS UMR3523, France
| | | | - Corinne Lionne
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS UMR 5048, INSERM U1054, France
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7
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Sweeney P, Galliford A, Kumar A, Raju D, Krishna NB, Sutherland E, Leo CJ, Fisher G, Lalitha R, Muthuraj L, Sigamani G, Oehler V, Synowsky S, Shirran SL, Gloster TM, Czekster CM, Kumar P, da Silva RG. Structure, dynamics, and molecular inhibition of the Staphylococcus aureus m 1A22-tRNA methyltransferase TrmK. J Biol Chem 2022; 298:102040. [PMID: 35595101 PMCID: PMC9190014 DOI: 10.1016/j.jbc.2022.102040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022] Open
Abstract
The enzyme m1A22-tRNA methyltransferase (TrmK) catalyzes the transfer of a methyl group to the N1 of adenine 22 in bacterial tRNAs. TrmK is essential for Staphylococcus aureus survival during infection but has no homolog in mammals, making it a promising target for antibiotic development. Here, we characterize the structure and function of S. aureus TrmK (SaTrmK) using X-ray crystallography, binding assays, and molecular dynamics simulations. We report crystal structures for the SaTrmK apoenzyme as well as in complexes with methyl donor SAM and co-product product SAH. Isothermal titration calorimetry showed that SAM binds to the enzyme with favorable but modest enthalpic and entropic contributions, whereas SAH binding leads to an entropic penalty compensated for by a large favorable enthalpic contribution. Molecular dynamics simulations point to specific motions of the C-terminal domain being altered by SAM binding, which might have implications for tRNA recruitment. In addition, activity assays for SaTrmK-catalyzed methylation of A22 mutants of tRNALeu demonstrate that the adenine at position 22 is absolutely essential. In silico screening of compounds suggested the multifunctional organic toxin plumbagin as a potential inhibitor of TrmK, which was confirmed by activity measurements. Furthermore, LC-MS data indicated the protein was covalently modified by one equivalent of the inhibitor, and proteolytic digestion coupled with LC-MS identified Cys92 in the vicinity of the SAM-binding site as the sole residue modified. These results identify a cryptic binding pocket of SaTrmK, laying a foundation for future structure-based drug discovery.
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Affiliation(s)
- Pamela Sweeney
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK
| | - Ashleigh Galliford
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK
| | | | - Dinesh Raju
- Kcat Enzymatic Private Limited, Bangalore, India
| | | | - Emmajay Sutherland
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK
| | - Caitlin J Leo
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK
| | - Gemma Fisher
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK
| | | | | | | | - Verena Oehler
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK
| | - Silvia Synowsky
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK
| | - Sally L Shirran
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK
| | - Tracey M Gloster
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK
| | - Clarissa M Czekster
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK
| | - Pravin Kumar
- Kcat Enzymatic Private Limited, Bangalore, India.
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK.
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8
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Kumar S, Mollo A, Kahne D, Ruiz N. The Bacterial Cell Wall: From Lipid II Flipping to Polymerization. Chem Rev 2022; 122:8884-8910. [PMID: 35274942 PMCID: PMC9098691 DOI: 10.1021/acs.chemrev.1c00773] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The peptidoglycan (PG) cell wall is an extra-cytoplasmic glycopeptide polymeric structure that protects bacteria from osmotic lysis and determines cellular shape. Since the cell wall surrounds the cytoplasmic membrane, bacteria must add new material to the PG matrix during cell elongation and division. The lipid-linked precursor for PG biogenesis, Lipid II, is synthesized in the inner leaflet of the cytoplasmic membrane and is subsequently translocated across the bilayer so that the PG building block can be polymerized and cross-linked by complex multiprotein machines. This review focuses on major discoveries that have significantly changed our understanding of PG biogenesis in the past decade. In particular, we highlight progress made toward understanding the translocation of Lipid II across the cytoplasmic membrane by the MurJ flippase, as well as the recent discovery of a novel class of PG polymerases, the SEDS (shape, elongation, division, and sporulation) glycosyltransferases RodA and FtsW. Since PG biogenesis is an effective target of antibiotics, these recent developments may lead to the discovery of much-needed new classes of antibiotics to fight bacterial resistance.
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Affiliation(s)
- Sujeet Kumar
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Aurelio Mollo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
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9
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Perez AJ, Villicana JB, Tsui HCT, Danforth ML, Benedet M, Massidda O, Winkler ME. FtsZ-Ring Regulation and Cell Division Are Mediated by Essential EzrA and Accessory Proteins ZapA and ZapJ in Streptococcus pneumoniae. Front Microbiol 2021; 12:780864. [PMID: 34938281 PMCID: PMC8687745 DOI: 10.3389/fmicb.2021.780864] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
The bacterial FtsZ-ring initiates division by recruiting a large repertoire of proteins (the divisome; Z-ring) needed for septation and separation of cells. Although FtsZ is essential and its role as the main orchestrator of cell division is conserved in most eubacteria, the regulators of Z-ring presence and positioning are not universal. This study characterizes factors that regulate divisome presence and placement in the ovoid-shaped pathogen, Streptococcus pneumoniae (Spn), focusing on FtsZ, EzrA, SepF, ZapA, and ZapJ, which is reported here as a partner of ZapA. Epi-fluorescence microscopy (EFm) and high-resolution microscopy experiments showed that FtsZ and EzrA co-localize during the entire Spn cell cycle, whereas ZapA and ZapJ are late-arriving divisome proteins. Depletion and conditional mutants demonstrate that EzrA is essential in Spn and required for normal cell growth, size, shape homeostasis, and chromosome segregation. Moreover, EzrA(Spn) is required for midcell placement of FtsZ-rings and PG synthesis. Notably, overexpression of EzrA leads to the appearance of extra Z-rings in Spn. Together, these observations support a role for EzrA as a positive regulator of FtsZ-ring formation in Spn. Conversely, FtsZ is required for EzrA recruitment to equatorial rings and for the organization of PG synthesis. In contrast to EzrA depletion, which causes a bacteriostatic phenotype in Spn, depletion of FtsZ results in enlarged spherical cells that are subject to LytA-dependent autolysis. Co-immunoprecipitation and bacterial two-hybrid assays show that EzrA(Spn) is in complexes with FtsZ, Z-ring regulators (FtsA, SepF, ZapA, MapZ), division proteins (FtsK, StkP), and proteins that mediate peptidoglycan synthesis (GpsB, aPBP1a), consistent with a role for EzrA at the interface of cell division and PG synthesis. In contrast to the essentiality of FtsZ and EzrA, ZapA and SepF have accessory roles in regulating pneumococcal physiology. We further show that ZapA interacts with a non-ZapB homolog, named here as ZapJ, which is conserved in Streptococcus species. The absence of the accessory proteins, ZapA, ZapJ, and SepF, exacerbates growth defects when EzrA is depleted or MapZ is deleted. Taken together, these results provide new information about the spatially and temporally distinct proteins that regulate FtsZ-ring organization and cell division in Spn.
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Affiliation(s)
- Amilcar J Perez
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - Jesus Bazan Villicana
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - Ho-Ching T Tsui
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - Madeline L Danforth
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - Mattia Benedet
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Orietta Massidda
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Malcolm E Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
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10
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Bekaert M, Goffin N, McMillan S, Desbois AP. Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines. Front Microbiol 2021; 12:755801. [PMID: 34745063 PMCID: PMC8564382 DOI: 10.3389/fmicb.2021.755801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/24/2021] [Indexed: 01/04/2023] Open
Abstract
Essential genes in bacterial pathogens are potential drug targets and vaccine candidates because disrupting their function is lethal. The development of new antibiotics, in addition to effective prevention measures such as vaccination, contributes to addressing the global problem of bacterial antibiotic resistance. The aim of this present study was to determine the essential genes of Vibrio anguillarum, a bacterial pathogen of aquatic animals, as a means to identify putative targets for novel drugs and to assist the prioritisation of potential vaccine candidates. Essential genes were characterised by a Tn-seq approach using the TnSC189 mariner transposon to construct a library of 52,662 insertion mutants. In total, 329 essential genes were identified, with 34.7% found within the core genome of this species; each of these genes represents a strong potential drug target. Seven essential gene products were predicted to reside in the cell membrane or be released extracellularly, thus serving as putative vaccine candidates. Comparison to essential gene data from five other studies of Vibrio species revealed 13 proteins to be conserved across the studies, while 25 genes were specific to V. anguillarum and not found to be essential in the other Vibrio spp. This study provides new information on the essential genes of Vibrio species and the methodology may be applied to other pathogens to guide the development of new drugs and vaccines, which will assist efforts to counter antibiotic resistance.
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Affiliation(s)
- Michaël Bekaert
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Nikki Goffin
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Stuart McMillan
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Andrew P Desbois
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
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11
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Briggs NS, Bruce KE, Naskar S, Winkler ME, Roper DI. The Pneumococcal Divisome: Dynamic Control of Streptococcus pneumoniae Cell Division. Front Microbiol 2021; 12:737396. [PMID: 34737730 PMCID: PMC8563077 DOI: 10.3389/fmicb.2021.737396] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/15/2021] [Indexed: 12/14/2022] Open
Abstract
Cell division in Streptococcus pneumoniae (pneumococcus) is performed and regulated by a protein complex consisting of at least 14 different protein elements; known as the divisome. Recent findings have advanced our understanding of the molecular events surrounding this process and have provided new understanding of the mechanisms that occur during the division of pneumococcus. This review will provide an overview of the key protein complexes and how they are involved in cell division. We will discuss the interaction of proteins in the divisome complex that underpin the control mechanisms for cell division and cell wall synthesis and remodelling that are required in S. pneumoniae, including the involvement of virulence factors and capsular polysaccharides.
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Affiliation(s)
- Nicholas S. Briggs
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Kevin E. Bruce
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - Souvik Naskar
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Malcolm E. Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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12
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Bonavita R, Laukkanen MO. Common Signal Transduction Molecules Activated by Bacterial Entry into a Host Cell and by Reactive Oxygen Species. Antioxid Redox Signal 2021; 34:486-503. [PMID: 32600071 DOI: 10.1089/ars.2019.7968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Significance: An increasing number of pathogens are acquiring resistance to antibiotics. Efficient antimicrobial drug regimens are important even for the most advanced therapies, which range from cutting-edge invasive clinical protocols, such as robotic surgeries, to the treatment of harmless bacterial diseases and to minor scratches to the skin. Therefore, there is an urgent need to survey alternative antimicrobial drugs that can reinforce or replace existing antibiotics. Recent Advances: Bacterial proteins that are critical for energy metabolism, promising novel anticancer thiourea derivatives, and the use of synthetic molecules that increase the sensitivity of currently used antibiotics are among the recently discovered antimicrobial drugs. Critical Issues: In the development of new drugs, serious consideration should be given to the previous bacterial evolutionary selection caused by antibiotics, by the high proliferation rate of bacteria, and by the simple prokaryotic structure of bacteria. Future Directions: The survey of drug targets has mainly focused on bacterial proteins, although host signaling molecules involved in the treatment of various pathologies may have unknown antimicrobial characteristics. Recent data have suggested that small molecule inhibitors might enhance the effect of antibiotics, for example, by limiting bacterial entry into host cells. Phagocytosis, the mechanism by which host cells internalize pathogens through β-actin cytoskeletal rearrangement, induces calcium signaling, small GTPase activation, and phosphorylation of the phosphatidylinositol 3-kinase-serine/threonine-specific protein kinase B pathway. Antioxid. Redox Signal. 34, 486-503.
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Affiliation(s)
- Raffaella Bonavita
- Experimental Institute of Endocrinology and Oncology G. Salvatore, IEOS CNR, Naples, Italy
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13
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Luo H, Lin Y, Liu T, Lai FL, Zhang CT, Gao F, Zhang R. DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools. Nucleic Acids Res 2021; 49:D677-D686. [PMID: 33095861 PMCID: PMC7779065 DOI: 10.1093/nar/gkaa917] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/30/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022] Open
Abstract
Essential genes refer to genes that are required by an organism to survive under specific conditions. Studies of the minimal-gene-set for bacteria have elucidated fundamental cellular processes that sustain life. The past five years have seen a significant progress in identifying human essential genes, primarily due to the successful use of CRISPR/Cas9 in various types of human cells. DEG 15, a new release of the Database of Essential Genes (www.essentialgene.org), has provided major advancements, compared to DEG 10. Specifically, the number of eukaryotic essential genes has increased by more than fourfold, and that of prokaryotic ones has more than doubled. Of note, the human essential-gene number has increased by more than tenfold. Moreover, we have developed built-in analysis modules by which users can perform various analyses, such as essential-gene distributions between bacterial leading and lagging strands, sub-cellular localization distribution, enrichment analysis of gene ontology and KEGG pathways, and generation of Venn diagrams to compare and contrast gene sets between experiments. Additionally, the database offers customizable BLAST tools for performing species- and experiment-specific BLAST searches. Therefore, DEG comprehensively harbors updated human-curated essential-gene records among prokaryotes and eukaryotes with built-in tools to enhance essential-gene analysis.
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Affiliation(s)
- Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Yan Lin
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Tao Liu
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Fei-Liao Lai
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Chun-Ting Zhang
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Ren Zhang
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA
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14
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Murgas CJ, Green SP, Forney AK, Korba RM, An SS, Kitten T, Lucas HR. Intracellular Metal Speciation in Streptococcus sanguinis Establishes SsaACB as Critical for Redox Maintenance. ACS Infect Dis 2020; 6:1906-1921. [PMID: 32329608 DOI: 10.1021/acsinfecdis.0c00132] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Streptococcus sanguinis is an oral commensal bacterium, but it can colonize pre-existing heart valve vegetations if introduced into the bloodstream, leading to infective endocarditis. Loss of Mn- or Fe-cofactored virulence determinants are thought to result in weakening of this bacterium. Indeed, intracellular Mn accumulation mediated by the lipoprotein SsaB, a component of the SsaACB transporter complex, has been shown to promote virulence for endocarditis and O2 tolerance. To delineate intracellular metal-ion abundance and redox speciation within S. sanguinis, we developed a protocol exploiting two spectroscopic techniques, Inductively coupled plasma-optical emission spectrometry (ICP-OES) and electron paramagnetic resonance (EPR) spectroscopy, to respectively quantify total intracellular metal concentrations and directly measure redox speciation of Fe and Mn within intact whole-cell samples. Addition of the cell-permeable siderophore deferoxamine shifts the oxidation states of accessible Fe and Mn from reduced-to-oxidized, as verified by magnetic moment calculations, aiding in the characterization of intracellular metal pools and metal sequestration levels for Mn2+ and Fe. We have applied this methodology to S. sanguinis and an SsaACB knockout strain (ΔssaACB), indicating that SsaACB mediates both Mn and Fe uptake, directly influencing the metal-ion pools available for biological inorganic pathways. Mn supplementation of ΔssaACB returns total intracellular Mn to wild-type levels, but it does not restore wild-type redox speciation or distribution of metal cofactor availability for either Mn or Fe. Our results highlight the biochemical basis for S. sanguinis oxidative resistance, revealing a dynamic role for SsaACB in controlling redox homeostasis by managing the intracellular Fe/Mn composition and distribution.
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Affiliation(s)
- Cody J. Murgas
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Shannon P. Green
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Ashley K. Forney
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Rachel M. Korba
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Seon-Sook An
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Todd Kitten
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Heather R. Lucas
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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15
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Hou YM, Masuda I, Foster LJ. tRNA methylation: An unexpected link to bacterial resistance and persistence to antibiotics and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1609. [PMID: 32533808 DOI: 10.1002/wrna.1609] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 02/02/2023]
Abstract
A major threat to public health is the resistance and persistence of Gram-negative bacteria to multiple drugs during antibiotic treatment. The resistance is due to the ability of these bacteria to block antibiotics from permeating into and accumulating inside the cell, while the persistence is due to the ability of these bacteria to enter into a nonreplicating state that shuts down major metabolic pathways but remains active in drug efflux. Resistance and persistence are permitted by the unique cell envelope structure of Gram-negative bacteria, which consists of both an outer and an inner membrane (OM and IM, respectively) that lay above and below the cell wall. Unexpectedly, recent work reveals that m1 G37 methylation of tRNA, at the N1 of guanosine at position 37 on the 3'-side of the tRNA anticodon, controls biosynthesis of both membranes and determines the integrity of cell envelope structure, thus providing a novel link to the development of bacterial resistance and persistence to antibiotics. The impact of m1 G37-tRNA methylation on Gram-negative bacteria can reach further, by determining the ability of these bacteria to exit from the persistence state when the antibiotic treatment is removed. These conceptual advances raise the possibility that successful targeting of m1 G37-tRNA methylation can provide new approaches for treating acute and chronic infections caused by Gram-negative bacteria. This article is categorized under: Translation > Translation Regulation RNA Processing > RNA Editing and Modification RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Leonard J Foster
- Department of Biochemistry & Molecular Biology, and Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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16
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Bu QT, Li YP, Xie H, Wang J, Li ZY, Chen XA, Mao XM, Li YQ. Comprehensive dissection of dispensable genomic regions in Streptomyces based on comparative analysis approach. Microb Cell Fact 2020; 19:99. [PMID: 32375781 PMCID: PMC7204314 DOI: 10.1186/s12934-020-01359-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/29/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Large-scale genome reduction has been performed to significantly improve the performance of microbial chassis. Identification of the essential or dispensable genes is pivotal for genome reduction to avoid synthetic lethality. Here, taking Streptomyces as an example, we developed a combinatorial strategy for systematic identification of large and dispensable genomic regions in Streptomyces based on multi-omics approaches. RESULTS Phylogenetic tree analysis revealed that the model strains including S. coelicolor A3(2), S. albus J1074 and S. avermitilis MA-4680 were preferred reference for comparative analysis of candidate genomes. Multiple genome alignment suggested that the Streptomyces genomes embodied highly conserved core region and variable sub-telomeric regions, and may present symmetric or asymmetric structure. Pan-genome and functional genome analyses showed that most conserved genes responsible for the fundamental functions of cell viability were concentrated in the core region and the vast majority of abundant genes were dispersed in the sub-telomeric regions. These results suggested that large-scale deletion can be performed in sub-telomeric regions to greatly streamline the Streptomyces genomes for developing versatile chassis. CONCLUSIONS The integrative approach of comparative genomics, functional genomics and pan-genomics can not only be applied to perform a multi-tiered dissection for Streptomyces genomes, but also work as a universal method for systematic analysis of removable regions in other microbial hosts in order to generate more miscellaneous and versatile chassis with minimized genome for drug discovery.
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Affiliation(s)
- Qing-Ting Bu
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Yue-Ping Li
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
| | - Huang Xie
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Jue Wang
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Zi-Yue Li
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
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17
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Disruption of the cpsE and endA Genes Attenuates Streptococcus pneumoniae Virulence: Towards the Development of a Live Attenuated Vaccine Candidate. Vaccines (Basel) 2020; 8:vaccines8020187. [PMID: 32326482 PMCID: PMC7349068 DOI: 10.3390/vaccines8020187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/27/2020] [Accepted: 04/07/2020] [Indexed: 12/15/2022] Open
Abstract
The majority of deaths due to Streptococcus pneumoniae infections are in developing countries. Although polysaccharide-based pneumococcal vaccines are available, newer types of vaccines are needed to increase vaccine affordability, particularly in developing countries, and to provide broader protection across all pneumococcal serotypes. To attenuate pneumococcal virulence with the aim of engineering candidate live attenuated vaccines (LAVs), we constructed knockouts in S. pneumoniae D39 of one of the capsular biosynthetic genes, cpsE that encodes glycosyltransferase, and the endonuclease gene, endA, that had been implicated in the uptake of DNA from the environment as well as bacterial escape from neutrophil-mediated killing. The cpsE gene knockout significantly lowered peak bacterial density, BALB/c mice nasopharyngeal (NP) colonisation but increased biofilm formation when compared to the wild-type D39 strain as well as the endA gene knockout mutant. All constructed mutant strains were able to induce significantly high serum and mucosal antibody response in BALB/c mice. However, the cpsE-endA double mutant strain, designated SPEC, was able to protect mice from high dose mucosal challenge of the D39 wild-type. Furthermore, SPEC showed 23-fold attenuation of virulence compared to the wild-type. Thus, the cpsE-endA double-mutant strain could be a promising candidate for further development of a LAV for S. pneumoniae.
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18
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Recent development in acetyl-CoA carboxylase inhibitors and their potential as novel drugs. Future Med Chem 2020; 12:533-561. [PMID: 32048880 DOI: 10.4155/fmc-2019-0312] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Acetyl-CoA carboxylase (ACC), a critical enzyme in the regulation of fatty acid synthesis and metabolism, has emerged as an attractive target for a plethora of emerging diseases, such as diabetes mellitus, nonalcoholic fatty liver disease, cancer, bacterial infections and so on. With decades of efforts in medicinal chemistry, significant progress has been made toward the design and discovery of a considerable number of inhibitors of this enzyme. In this review, we not only clarify the role of ACC in emerging diseases, but also summarize recent developments of potent ACC inhibitors and discuss their molecular mechanisms of action and potentials as novel drugs as well as future perspectives toward the design and discovery of novel ACC inhibitors.
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19
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Dégut C, Roovers M, Barraud P, Brachet F, Feller A, Larue V, Al Refaii A, Caillet J, Droogmans L, Tisné C. Structural characterization of B. subtilis m1A22 tRNA methyltransferase TrmK: insights into tRNA recognition. Nucleic Acids Res 2019; 47:4736-4750. [PMID: 30931478 PMCID: PMC6511850 DOI: 10.1093/nar/gkz230] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/04/2019] [Accepted: 03/26/2019] [Indexed: 12/21/2022] Open
Abstract
1-Methyladenosine (m1A) is a modified nucleoside found at positions 9, 14, 22 and 58 of tRNAs, which arises from the transfer of a methyl group onto the N1-atom of adenosine. The yqfN gene of Bacillus subtilis encodes the methyltransferase TrmK (BsTrmK) responsible for the formation of m1A22 in tRNA. Here, we show that BsTrmK displays a broad substrate specificity, and methylates seven out of eight tRNA isoacceptor families of B. subtilis bearing an A22. In addition to a non-Watson–Crick base-pair between the target A22 and a purine at position 13, the formation of m1A22 by BsTrmK requires a full-length tRNA with intact tRNA elbow and anticodon stem. We solved the crystal structure of BsTrmK showing an N-terminal catalytic domain harbouring the typical Rossmann-like fold of Class-I methyltransferases and a C-terminal coiled-coil domain. We used NMR chemical shift mapping to drive the docking of BstRNASer to BsTrmK in complex with its methyl-donor cofactor S-adenosyl-L-methionine (SAM). In this model, validated by methyltransferase activity assays on BsTrmK mutants, both domains of BsTrmK participate in tRNA binding. BsTrmK recognises tRNA with very few structural changes in both partner, the non-Watson–Crick R13–A22 base-pair positioning the A22 N1-atom close to the SAM methyl group.
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Affiliation(s)
- Clément Dégut
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | | | - Pierre Barraud
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, CNRS, Univ. Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Franck Brachet
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - André Feller
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Valéry Larue
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Abdalla Al Refaii
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Joël Caillet
- Laboratoire d'Expression génétique microbienne, CNRS, Univ. Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, CNRS, Univ. Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
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20
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Li Y, Zhong W, Koay AZ, Ng HQ, Nah Q, Wong YH, Hill J, Lescar J, Dedon PC, Kang C. Backbone resonance assignment for the full length tRNA-(N 1G37) methyltransferase of Pseudomonas aeruginosa. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:327-332. [PMID: 31175551 DOI: 10.1007/s12104-019-09900-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) plays important roles in translation, making it an important target for the development of new antibacterial compounds. TrmD comprises two domains with the N-terminal domain binding to the S-adenosyl-L-methionine (SAM) cofactor and the C-terminal domain critical for tRNA binding. Bacterial TrmD is functional as a dimer. Here we report the backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa. Most resonances were assigned and the secondary structure for each amino acid was determined according to the assigned backbone resonances. The availability of the assignment will be valuable for exploring molecular interactions of TrmD with ligands, inhibitors and tRNA.
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Affiliation(s)
- Yan Li
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, People's Republic of China
| | - Wenhe Zhong
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Ann Zhufang Koay
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Hui Qi Ng
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Qianhui Nah
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Yee Hwa Wong
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jeffrey Hill
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Peter C Dedon
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - CongBao Kang
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore.
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21
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Muraminomicins, novel ester derivatives: in vitro and in vivo antistaphylococcal activity. J Antibiot (Tokyo) 2019; 72:956-969. [DOI: 10.1038/s41429-019-0235-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 08/09/2019] [Accepted: 08/29/2019] [Indexed: 11/08/2022]
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22
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Ulrych A, Petráčková D, Goldová J, Buriánková K, Doubravová L, Branny P. PynA is a pyrimidine 5'-nucleotidase that functions as an antimutator protein in Streptococcus pneumoniae. FEBS J 2019; 287:267-283. [PMID: 31437335 DOI: 10.1111/febs.15049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/18/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023]
Abstract
Streptococcus pneumoniae is a Gram-positive bacterium that is a major agent of community-acquired bacterial pneumonia, meningitis and sepsis. Although the mismatch repair function of S. pneumoniae has been assigned to the hexA-hexB gene products, an enzyme capable of the direct elimination of noncanonical nucleotides from the cytoplasm has not been described for this bacterium. Our results show that Spr1057, a protein with previously unknown function, is involved in the inactivation of mutagenic pyrimidine nucleotides and was accordingly designated PynA (pyrimidine nucleotidase A). Biochemical assays confirmed the phosphatase activity of the recombinant enzyme and revealed its metal ion dependence for optimal enzyme activity. We demonstrated that PynA forms a homodimer with higher in vitro activity towards noncanonical 5-fluoro-2'-deoxyuridine monophosphate than towards canonical thymidine monophosphate. Furthermore, we showed via in vivo assays that PynA protects cells against noncanonical pyrimidine derivatives such as 5-fluoro-2'-deoxyuridine and prevents the incorporation of the potentially mutagenic 5-bromo-2'-deoxyuridine (5-BrdU) into DNA. Fluctuation analysis performed under S. pneumoniae exposure to 5-BrdU revealed that the pynA null strain accumulates random mutations with high frequency, resulting in a 30-fold increase in the mutation rate. The data support a model in which PynA, a protein conserved in other Gram-positive bacteria, functions as a house-cleaning enzyme by selectively eliminating noncanonical nucleotides and maintaining the purity of dNTP pools, similar to the YjjG protein described for Escherichia coli.
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Affiliation(s)
- Aleš Ulrych
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
| | - Denisa Petráčková
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Goldová
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
| | - Karolína Buriánková
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
| | - Linda Doubravová
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Branny
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
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23
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Pelletier A, Freton C, Gallay C, Trouve J, Cluzel C, Franz-Wachtel M, Macek B, Jault JM, Grangeasse C, Guiral S. The Tyrosine-Autokinase UbK Is Required for Proper Cell Growth and Cell Morphology of Streptococcus pneumoniae. Front Microbiol 2019; 10:1942. [PMID: 31551943 PMCID: PMC6733980 DOI: 10.3389/fmicb.2019.01942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/07/2019] [Indexed: 12/11/2022] Open
Abstract
Protein phosphorylation is a key post-translational modification required for many cellular functions of the bacterial cell. Recently, we identified a new protein-kinase, named UbK, in Bacillus subtilis that belongs to a new family of protein-kinases widespread in bacteria. In this study, we analyze the function of UbK in Streptococcus pneumoniae. We show that UbK displays a tyrosine-kinase activity and autophosphorylates on a unique tyrosine in vivo. To get insights into its cellular role, we constructed a set of pneumococcal ubk mutants. Using conventional and electron microscopy, we show that the ubk deficient strain, as well as an ubk catalytic dead mutant, display both severe cell-growth and cell-morphology defects. The same defects are observed with a mutant mimicking permanent phosphorylation of UbK whereas they are not detected for a mutant mimicking defective autophosphorylation of UbK. Moreover, we find that UbK phosphorylation promotes its ability to hydrolyze ATP. These observations show that the hydrolysis of ATP by UbK serves not only for its autophosphorylation but also for a distinct purpose essential for the optimal cell growth and cell-morphogenesis of the pneumococcus. We thus propose a model in which the autophosphorylation/dephosphorylation of UbK regulates its cellular function through a negative feedback loop.
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Affiliation(s)
- Anaïs Pelletier
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Clément Gallay
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Jennyfer Trouve
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Caroline Cluzel
- Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, UMR 5305 CNRS/Université Lyon 1, Lyon, France
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Sébastien Guiral
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
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24
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Helal AM, Sayed AM, Omara M, Elsebaei MM, Mayhoub AS. Peptidoglycan pathways: there are still more! RSC Adv 2019; 9:28171-28185. [PMID: 35530449 PMCID: PMC9071014 DOI: 10.1039/c9ra04518j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 08/22/2019] [Indexed: 11/21/2022] Open
Abstract
The discovery of 3rd and 4th generations of currently existing classes of antibiotics has not hindered bacterial resistance, which is escalating at an alarming global level. This review follows WHO recommendations through implementing new criteria for newly discovered antibiotics. These recommendations focus on abandoning old scaffolds and hitting new targets. In light of these recommendations, this review discusses seven bacterial proteins that no commercial antibiotics have targeted yet, alongside their reported chemical scaffolds.
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Affiliation(s)
- Ahmed M Helal
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Ahmed M Sayed
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mariam Omara
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mohamed M Elsebaei
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Abdelrahman S Mayhoub
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
- University of Science and Technology, Zewail City of Science and Technology Giza Egypt
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25
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Xiang Z, Li Z, Ren Z, Zeng J, Peng X, Li Y, Li J. EzrA, a cell shape regulator contributing to biofilm formation and competitiveness in Streptococcus mutans. Mol Oral Microbiol 2019; 34:194-208. [PMID: 31287946 DOI: 10.1111/omi.12264] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/28/2019] [Accepted: 07/03/2019] [Indexed: 02/05/2023]
Abstract
Bacterial cell division is initiated by tubulin homologue FtsZ that assembles into a ring structure at mid-cell to facilitate cytokinesis. EzrA has been identified to be implicated in FtsZ-ring dynamics and cell wall biosynthesis during cell division of Bacillus subtilis and Staphylococcus aureus, the model rod and cocci. However, its role in pathogenic streptococci remains largely unknown. Here, the role of EzrA was investigated in Streptococcus mutans, the primary etiological agent of human dental caries, by constructing an ezrA in-frame deletion mutant. Our data showed that the ezrA mutant was slow-growing with a shortened length and extended width round cell shape compared to the wild type, indicating a delay in cell division with abnormalities of peptidoglycan biosynthesis. Additionally, FtsZ irregularly localized in dividing ezrA mutant cells forming angled division planes, potentially contributing to an aberrant cell shape. Furthermore, investigation using single-species cariogenic biofilm model revealed that deletion of ezrA resulted in defective biofilm formation with less extracellular polysaccharides and altered three-dimensional biofilm architecture. Unexpectedly, in a dual-species ecological model, the ezrA mutant exhibited substantially lower tolerance for H2 O2 and reduced competitiveness against one commensal species, Streptococcus sanguinis. Taken together, these results demonstrate that EzrA plays a key role in regulating cell division and maintaining a normal morphology in S. mutans and is required for its robust biofilm formation/interspecies competition. Therefore, EzrA protein represents a potential therapeutic target in the development of drugs controlling dental caries and other biofilm-related diseases.
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Affiliation(s)
- Zhenting Xiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Zongbo Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Zhi Ren
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jumei Zeng
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xian Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
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26
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Lin Y, Zhang FZ, Xue K, Gao YZ, Guo FB. Identifying Bacterial Essential Genes Based on a Feature-Integrated Method. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1274-1279. [PMID: 28212095 DOI: 10.1109/tcbb.2017.2669968] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Essential genes are those genes of an organism that are considered to be crucial for its survival. Identification of essential genes is therefore of great significance to advance our understanding of the principles of cellular life. We have developed a novel computational method, which can effectively predict bacterial essential genes by extracting and integrating homologous features, protein domain feature, gene intrinsic features, and network topological features. By performing the principal component regression (PCR) analysis for Escherichia coli MG1655, we established a classification model with the average area under curve (AUC) value of 0.992 in ten times 5-fold cross-validation tests. Furthermore, when employing this new model to a distantly related organism-Streptococcus pneumoniae TIGR4, we still got a reliable AUC value of 0.788. These results indicate that our feature-integrated approach could have practical applications in accurately investigating essential genes from broad bacterial species, and also provide helpful guidelines for the minimal cell.
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27
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Oerum S, Catala M, Atdjian C, Brachet F, Ponchon L, Barraud P, Iannazzo L, Droogmans L, Braud E, Ethève-Quelquejeu M, Tisné C. Bisubstrate analogues as structural tools to investigate m 6A methyltransferase active sites. RNA Biol 2019; 16:798-808. [PMID: 30879411 PMCID: PMC6546350 DOI: 10.1080/15476286.2019.1589360] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/24/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
RNA methyltransferases (MTases) catalyse the transfer of a methyl group to their RNA substrates using most-often S-adenosyl-L-methionine (SAM) as cofactor. Only few RNA-bound MTases structures are currently available due to the difficulties in crystallising RNA:protein complexes. The lack of complex structures results in poorly understood RNA recognition patterns and methylation reaction mechanisms. On the contrary, many cofactor-bound MTase structures are available, resulting in well-understood protein:cofactor recognition, that can guide the design of bisubstrate analogues that mimic the state at which both the substrate and the cofactor is bound. Such bisubstrate analogues were recently synthesized for proteins monomethylating the N6-atom of adenine (m6A). These proteins include, amongst others, RlmJ in E. coli and METLL3:METT14 and METTL16 in human. As a proof-of-concept, we here test the ability of the bisubstrate analogues to mimic the substrate:cofactor bound state during catalysis by studying their binding to RlmJ using differential scanning fluorimetry, isothermal titration calorimetry and X-ray crystallography. We find that the methylated adenine base binds in the correct pocket, and thus these analogues could potentially be used broadly to study the RNA recognition and catalytic mechanism of m6A MTases. Two bisubstrate analogues bind RlmJ with micro-molar affinity, and could serve as starting scaffolds for inhibitor design against m6A RNA MTases. The same analogues cause changes in the melting temperature of the m1A RNA MTase, TrmK, indicating non-selective protein:compound complex formation. Thus, optimization of these molecular scaffolds for m6A RNA MTase inhibition should aim to increase selectivity, as well as affinity.
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Affiliation(s)
- Stephanie Oerum
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Marjorie Catala
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Colette Atdjian
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Franck Brachet
- Institut de Biologie Physico-Chimique, IBPC, CNRS, Paris, France
| | - Luc Ponchon
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris, France
| | - Pierre Barraud
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), Gosselies, Belgium
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Carine Tisné
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
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28
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Li Y, Zhong W, Koay AZ, Ng HQ, Koh-Stenta X, Nah Q, Lim SH, Larsson A, Lescar J, Hill J, Dedon PC, Kang C. Backbone resonance assignment for the N-terminal region of bacterial tRNA-(N 1G37) methyltransferase. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:49-53. [PMID: 30298375 DOI: 10.1007/s12104-018-9849-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/15/2018] [Indexed: 06/08/2023]
Abstract
Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) is an important antibacterial target due to its essential role in translation. TrmD has two domains connected with a flexible linker. The N-terminal domain (NTD) of TrmD contains the S-adenosyl-L-methionine (SAM) cofactor binding site and the C-terminal domain is critical for tRNA binding. Here we report the backbone NMR resonance assignments for NTD of Pseudomonas aeruginosa TrmD. Its secondary structure was determined based on the assigned resonances. Relaxation analysis revealed that NTD existed as dimers in solution. NTD also exhibited thermal stability in solution. Its interactions with SAM and other compounds suggest it can be used for evaluating SAM competitive inhibitors by NMR.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, People's Republic of China
| | - Wenhe Zhong
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Ann Zhufang Koay
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Xiaoying Koh-Stenta
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Qianhui Nah
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Siau Hoi Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Experimental Biotherapeutics Centre, 30 Biopolis Street, #08-01 Matrix, Singapore, 138671, Singapore
| | - Andreas Larsson
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore.
| | - Peter C Dedon
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - CongBao Kang
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore.
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29
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Han X, Sun R, Sandalova T, Achour A. Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis in Streptococcus pneumoniae. Open Biol 2019; 8:rsob.170248. [PMID: 29669826 PMCID: PMC5936713 DOI: 10.1098/rsob.170248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/23/2018] [Indexed: 11/28/2022] Open
Abstract
Spr1654 from Streptococcus pneumoniae plays a key role in the production of unusual sugars, presumably functioning as a pyridoxal-5′-phosphate (PLP)-dependent aminotransferase. Spr1654 was predicted to catalyse the transferring of amino group to form the amino sugar 2-acetamido-4-amino-2, 4, 6-trideoxygalactose moiety (AATGal), representing a crucial step in biosynthesis of teichoic acids in S. pneumoniae. We have determined the crystal structures of the apo-, PLP- and PMP-bound forms of Spr1654. Spr1654 forms a homodimer, in which each monomer contains one active site. Using spectrophotometry and based on absorbance profiles of PLP- and PMP-formed enzymes, our results indicate that l-glutamate is most likely the preferred amino donor. Structural superposition of the crystal structures of Spr1654 on previously determined structures of other sugar aminotransferases in complex with glutamate and/or UDP-activated sugar allowed us to identify key Spr1654 residues for ligand binding and catalysis. The crystal structures of Spr1654 and in complex with PLP and PMP can direct the future rational design of novel therapeutic compounds against S. pneumoniae.
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Affiliation(s)
- Xiao Han
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden .,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
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30
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Bousis S, Setyawati I, Diamanti E, Slotboom DJ, Hirsch AKH. Energy-Coupling Factor Transporters as Novel Antimicrobial Targets. ADVANCED THERAPEUTICS 2019. [DOI: 10.1002/adtp.201800066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Spyridon Bousis
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
- Department of Pharmacy; Saarland University; Saarbrücken, Campus Building E8.1 66123 Saarbrücken Germany
| | - Inda Setyawati
- Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
- Department of Biochemistry; Bogor Agricultural University; Dramaga 16680 Bogor Indonesia
| | - Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
| | - Dirk J. Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
- Department of Biochemistry; Bogor Agricultural University; Dramaga 16680 Bogor Indonesia
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
- Department of Pharmacy; Saarland University; Saarbrücken, Campus Building E8.1 66123 Saarbrücken Germany
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31
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Biosynthetic and Synthetic Strategies for Assembling Capuramycin-Type Antituberculosis Antibiotics. Molecules 2019; 24:molecules24030433. [PMID: 30691073 PMCID: PMC6384614 DOI: 10.3390/molecules24030433] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/22/2019] [Accepted: 01/22/2019] [Indexed: 01/29/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) has recently surpassed HIV/AIDS as the leading cause of death by a single infectious agent. The standard therapeutic regimen against tuberculosis (TB) remains a long, expensive process involving a multidrug regimen, and the prominence of multidrug-resistant (MDR), extensively drug-resistant (XDR), and totally drug-resistant (TDR) strains continues to impede treatment success. An underexplored class of natural products—the capuramycin-type nucleoside antibiotics—have been shown to have potent anti-TB activity by inhibiting bacterial translocase I, a ubiquitous and essential enzyme that functions in peptidoglycan biosynthesis. The present review discusses current literature concerning the biosynthesis and chemical synthesis of capuramycin and analogs, seeking to highlight the potential of the capuramycin scaffold as a favorable anti-TB therapeutic that warrants further development.
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32
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Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes. PLoS Comput Biol 2018; 14:e1006556. [PMID: 30444863 PMCID: PMC6283598 DOI: 10.1371/journal.pcbi.1006556] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 12/06/2018] [Accepted: 10/09/2018] [Indexed: 01/13/2023] Open
Abstract
Essential metabolic reactions are shaping constituents of metabolic networks, enabling viable and distinct phenotypes across diverse life forms. Here we analyse and compare modelling predictions of essential metabolic functions with experimental data and thereby identify core metabolic pathways in prokaryotes. Simulations of 15 manually curated genome-scale metabolic models were integrated with 36 large-scale gene essentiality datasets encompassing a wide variety of species of bacteria and archaea. Conservation of metabolic genes was estimated by analysing 79 representative genomes from all the branches of the prokaryotic tree of life. We find that essentiality patterns reflect phylogenetic relations both for modelling and experimental data, which correlate highly at the pathway level. Genes that are essential for several species tend to be highly conserved as opposed to non-essential genes which may be conserved or not. The tRNA-charging module is highlighted as ancestral and with high centrality in the networks, followed closely by cofactor metabolism, pointing to an early information processing system supplied by organic cofactors. The results, which point to model improvements and also indicate faults in the experimental data, should be relevant to the study of centrality in metabolic networks and ancient metabolism but also to metabolic engineering with prokaryotes. If we tried to list every known chemical reaction within an organism–human, plant or even bacteria–we would get quite a long and confusing read. But when this information is represented in so-called genome-scale metabolic networks, we have the means to access computationally each of those reactions and their interconnections. Some parts of the network have alternatives, while others are unique and therefore can be essential for growth. Here, we simulate growth and compare essential reactions and genes for the simplest type of unicellular species–prokaryotes–to understand which parts of their metabolism are universally essential and potentially ancestral. We show that similar patterns of essential reactions echo phylogenetic relationships (this makes sense, as the genome provides the building plan for the enzymes that perform those reactions). Our computational predictions correlate strongly with experimental essentiality data. Finally, we show that a crucial step of protein synthesis (tRNA charging) and the synthesis and transformation of small molecules that enzymes require (cofactors) are the most essential and conserved parts of metabolism in prokaryotes. Our results are a step further in understanding the biology and evolution of prokaryotes but can also be relevant in applied studies including metabolic engineering and antibiotic design.
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33
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The Role of Pneumococcal Virulence Factors in Ocular Infectious Diseases. Interdiscip Perspect Infect Dis 2018; 2018:2525173. [PMID: 30538741 PMCID: PMC6257906 DOI: 10.1155/2018/2525173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/07/2018] [Indexed: 12/24/2022] Open
Abstract
Streptococcus pneumoniae is a gram-positive, facultatively anaerobic pathogen that can cause severe infections such as pneumonia, meningitis, septicemia, and middle ear infections. It is also one of the top pathogens contributing to bacterial keratitis and conjunctivitis. Though two pneumococcal vaccines exist for the prevention of nonocular diseases, they do little to fully prevent ocular infections. This pathogen has several virulence factors that wreak havoc on the conjunctiva, cornea, and intraocular system. Polysaccharide capsule aids in the evasion of host complement system. Pneumolysin (PLY) is a cholesterol-dependent cytolysin that acts as pore-forming toxin. Neuraminidases assist in adherence and colonization by exposing cell surface receptors to the pneumococcus. Zinc metalloproteinases contribute to evasion of the immune system and disease severity. The main purpose of this review is to consolidate the multiple studies that have been conducted on several pneumococcal virulence factors and the role each plays in conjunctivitis, keratitis, and endophthalmitis.
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Morlot C, Straume D, Peters K, Hegnar OA, Simon N, Villard AM, Contreras-Martel C, Leisico F, Breukink E, Gravier-Pelletier C, Le Corre L, Vollmer W, Pietrancosta N, Håvarstein LS, Zapun A. Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae. Nat Commun 2018; 9:3180. [PMID: 30093673 PMCID: PMC6085368 DOI: 10.1038/s41467-018-05602-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/17/2018] [Indexed: 11/08/2022] Open
Abstract
The universality of peptidoglycan in bacteria underlies the broad spectrum of many successful antibiotics. However, in our times of widespread resistance, the diversity of peptidoglycan modifications offers a variety of new antibacterials targets. In some Gram-positive species such as Streptococcus pneumoniae, Staphylococcus aureus, or Mycobacterium tuberculosis, the second residue of the peptidoglycan precursor, D-glutamate, is amidated into iso-D-glutamine by the essential amidotransferase MurT/GatD complex. Here, we present the structure of this complex at 3.0 Å resolution. MurT has central and C-terminal domains similar to Mur ligases with a cysteine-rich insertion, which probably binds zinc, contributing to the interface with GatD. The mechanism of amidation by MurT is likely similar to the condensation catalyzed by Mur ligases. GatD is a glutaminase providing ammonia that is likely channeled to the MurT active site through a cavity network. The structure and assay presented here constitute a knowledge base for future drug development studies.
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Affiliation(s)
- Cécile Morlot
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | - Daniel Straume
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom
| | - Olav A Hegnar
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Nolwenn Simon
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | - Anne-Marie Villard
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | | | - Francisco Leisico
- Departamento de Química, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, 3584, The Netherlands
| | - Christine Gravier-Pelletier
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Laurent Le Corre
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom
| | - Nicolas Pietrancosta
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Leiv Sigve Håvarstein
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - André Zapun
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France.
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Huang YY, Sun YH, Huang N, Liu XX, Yan J, Sun AH. Sublethal β-lactam antibiotics induce PhpP phosphatase expression and StkP kinase phosphorylation in PBP-independent β-lactam antibiotic resistance of Streptococcus pneumoniae. Biochem Biophys Res Commun 2018; 503:2000-2008. [PMID: 30135012 DOI: 10.1016/j.bbrc.2018.07.148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 07/30/2018] [Indexed: 12/16/2022]
Abstract
StkP and PhpP of Streptococcus pneumoniae have been confirmed to compose a signaling couple, in which the former is a serine/threonine (Ser/Thr) kinase while the latter was annotated as a phosphotase. StkP has been reported to be involved in penicillin-binding protein (PBP)-independent penicillin resistance of S. pneumoniae. However, the enzymatic characterization of PhpP and the role of PhpP in StkP-PhpP couple remain poorly understood. Here we showed that 1/4 minimal inhibitory concentration (MIC) of penicillin (PCN) or cefotaxime (CTX), the representatives of β-lactam antibiotics, could induce the expression of stkP and phpP genes and phosphorylation of StkP in PCN/CTX-sensitive strain ATCC6306 and three isolates of S. pneumoniae (MICs: 0.02-0.5 μg/ml). The product of phpP gene hydrolyzed PP2C type Ser/Thr phosphotase-specific RRA (pT)VA phosphopeptide substrate with the Km and Kcat values of 277.35 μmoL/L and 0.71 S-1, and the hydrolytic activity was blocked by sodium fluoride, a PP2C type Ser/Thr phosphatase inhibitor. The phosphorylation levels of StkP in the four phpP gene-knockout (ΔphpP) mutants were significantly higher than that in the wild-type strains. In particular, the MICs of PCN and CTX against the ΔphpP mutants were significantly elevated as 4-16 μg/ml. Therefore, our findings confirmed that sublethal PCN and CTX act as environmental inducers to cause the increase of phpP and stkP gene expression and StkP phosphorylation. PhpP is a PP2C type Ser/Thr protein phosphatase responsible for dephosphorylation of StkP. Knockout of the phpP gene results in a high level of StkP phosphorylation and PBP-independent PCN/CTX resistance of S. pneumoniae.
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Affiliation(s)
- Yan-Ying Huang
- Faculty of Basic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, PR China; Department of Pathology, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, 310003, PR China.
| | - Yan-Hong Sun
- Department of Laboratory Medicine, The Children's Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310052, PR China.
| | - Nan Huang
- College of Medical Technology, Zhang Chinese Medical University, Hangzhou, Zhejiang, 310053, PR China.
| | - Xiao-Xiang Liu
- Faculty of Basic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, PR China.
| | - Jie Yan
- Division of Basic Medical Microbiology, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, PR China; Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, PR China.
| | - Ai-Hua Sun
- Faculty of Basic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, PR China.
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Hering J, Dunevall E, Ek M, Brändén G. Structural basis for selective inhibition of antibacterial target MraY, a membrane-bound enzyme involved in peptidoglycan synthesis. Drug Discov Today 2018; 23:1426-1435. [DOI: 10.1016/j.drudis.2018.05.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/13/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022]
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Ferrándiz MJ, Carreño D, Ayora S, de la Campa AG. HU of Streptococcus pneumoniae Is Essential for the Preservation of DNA Supercoiling. Front Microbiol 2018; 9:493. [PMID: 29662473 PMCID: PMC5890176 DOI: 10.3389/fmicb.2018.00493] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/02/2018] [Indexed: 01/11/2023] Open
Abstract
The histone-like protein HU is a conserved nucleoid-associated protein that is involved in the maintenance of the bacterial chromosome architecture. It is the only known nucleoid-associated protein in Streptococcus pneumoniae, but it has not been studied. The pneumococcal gene encoding this protein, hlp, is shown herein to be essential for cell viability. Its disruption was only possible either when it was duplicated in the chromosome and its expression induced from the P Zn promoter, or when hlp was cloned into a plasmid under the control of the inducible P mal promoter. In vitro assays indicated that pneumococcal HU shows a preference for binding to supercoiled DNA rather than to linear or nicked DNA. In vivo experiments in which the amount of HU was manipulated showed a relationship between the amount of HU and the level of DNA supercoiling. A twofold reduction in the amount of HU triggered a 21% increase in DNA relaxation in untreated cells. However, in cells treated with novobiocin, a drug that relaxes DNA by inhibiting DNA gyrase, a 35% increase in DNA relaxation was observed, instead of the expected 20% in cells with a constitutive HU amount. Conversely, a fourfold HU increase caused only 14% of DNA relaxation in the presence of novobiocin. Taken together, these results support an essential role for HU in the maintenance of DNA supercoiling in S. pneumoniae.
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Affiliation(s)
- María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - David Carreño
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Ayora
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Zhang X, Cui J, Wu Y, Wang H, Wang J, Qiu Y, Mo Y, He Y, Zhang X, Yin Y, Xu W. Streptococcus pneumoniae Attenuated Strain SPY1 with an Artificial Mineral Shell Induces Humoral and Th17 Cellular Immunity and Protects Mice against Pneumococcal Infection. Front Immunol 2018; 8:1983. [PMID: 29375585 PMCID: PMC5768616 DOI: 10.3389/fimmu.2017.01983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae is a major pathogen leading to substantial morbidity and mortality in children under 5 years of age. Vaccination is an effective strategy to prevent S. pneumoniae infection. SPY1 is a pneumococcal vaccine candidate strain obtained in our previous study. To improve its stability and immunogencity, in this study, we constructed the SPY1ΔlytA strain that lacks autolysin activity and was coated with an artificial exterior surface calcium phosphate shell by in situ mineralization. The resulting strain SPY1ΔlytACaPi displayed enhanced thermal stability enabling storage at 37°C for 1 week. Furthermore, mucosal and subcutaneous immunization with the SPY1ΔlytACaPi strain induced better protective effects than SPY1ΔlytA in anti-colonization after challenging with 19F and anti-invasion by D39 in mice. Subcutaneous immunization with SPY1ΔlytACaPi elicited higher IgG level while mucosal immunization primarily elicited an immune response which is supposed to be related to Th17 cells. Taken together, the mineralized strain may be a promising candidate for an attenuated S. pneumoniae vaccine.
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Affiliation(s)
- Xinyuan Zhang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Jingjing Cui
- Department of Clinical Laboratory, Chongqing Hospital for Women and Children, Chongqing, China
| | - Yingying Wu
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Hong Wang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Jian Wang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yulan Qiu
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yunjun Mo
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yujuan He
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Xuemei Zhang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yibing Yin
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Wenchun Xu
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
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Abstract
Gene essentiality is a founding concept of genetics with important implications in both fundamental and applied research. Multiple screens have been performed over the years in bacteria, yeasts, animals and more recently in human cells to identify essential genes. A mounting body of evidence suggests that gene essentiality, rather than being a static and binary property, is both context dependent and evolvable in all kingdoms of life. This concept of a non-absolute nature of gene essentiality changes our fundamental understanding of essential biological processes and could directly affect future treatment strategies for cancer and infectious diseases.
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40
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Krumholz EW, Libourel IGL. Thermodynamic Constraints Improve Metabolic Networks. Biophys J 2017; 113:679-689. [PMID: 28793222 DOI: 10.1016/j.bpj.2017.06.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 05/24/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022] Open
Abstract
In pursuit of establishing a realistic metabolic phenotypic space, the reversibility of reactions is thermodynamically constrained in modern metabolic networks. The reversibility constraints follow from heuristic thermodynamic poise approximations that take anticipated cellular metabolite concentration ranges into account. Because constraints reduce the feasible space, draft metabolic network reconstructions may need more extensive reconciliation, and a larger number of genes may become essential. Notwithstanding ubiquitous application, the effect of reversibility constraints on the predictive capabilities of metabolic networks has not been investigated in detail. Instead, work has focused on the implementation and validation of the thermodynamic poise calculation itself. With the advance of fast linear programming-based network reconciliation, the effects of reversibility constraints on network reconciliation and gene essentiality predictions have become feasible and are the subject of this study. Networks with thermodynamically informed reversibility constraints outperformed gene essentiality predictions compared to networks that were constrained with randomly shuffled constraints. Unconstrained networks predicted gene essentiality as accurately as thermodynamically constrained networks, but predicted substantially fewer essential genes. Networks that were reconciled with sequence similarity data and strongly enforced reversibility constraints outperformed all other networks. We conclude that metabolic network analysis confirmed the validity of the thermodynamic constraints, and that thermodynamic poise information is actionable during network reconciliation.
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Affiliation(s)
- Elias W Krumholz
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota
| | - Igor G L Libourel
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota; Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota; Genome Craft, Saint Paul, Minnesota.
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41
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Liu X, Gallay C, Kjos M, Domenech A, Slager J, van Kessel SP, Knoops K, Sorg RA, Zhang JR, Veening JW. High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae. Mol Syst Biol 2017; 13:931. [PMID: 28490437 PMCID: PMC5448163 DOI: 10.15252/msb.20167449] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Genome‐wide screens have discovered a large set of essential genes in the opportunistic human pathogen Streptococcus pneumoniae. However, the functions of many essential genes are still unknown, hampering vaccine development and drug discovery. Based on results from transposon sequencing (Tn‐seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting 348 potentially essential genes by CRISPR interference (CRISPRi) and show a growth phenotype for 254 of them (73%). Using high‐content microscopy screening, we searched for essential genes of unknown function with clear phenotypes in cell morphology upon CRISPRi‐based depletion. We show that SPD_1416 and SPD_1417 (renamed to MurT and GatD, respectively) are essential for peptidoglycan synthesis, and that SPD_1198 and SPD_1197 (renamed to TarP and TarQ, respectively) are responsible for the polymerization of teichoic acid (TA) precursors. This knowledge enabled us to reconstruct the unique pneumococcal TA biosynthetic pathway. CRISPRi was also employed to unravel the role of the essential Clp‐proteolytic system in regulation of competence development, and we show that ClpX is the essential ATPase responsible for ClpP‐dependent repression of competence. The CRISPRi library provides a valuable tool for characterization of pneumococcal genes and pathways and revealed several promising antibiotic targets.
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Affiliation(s)
- Xue Liu
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands.,Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Clement Gallay
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Morten Kjos
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Arnau Domenech
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Jelle Slager
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Sebastiaan P van Kessel
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Kèvin Knoops
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Robin A Sorg
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands .,Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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42
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Hou YM, Matsubara R, Takase R, Masuda I, Sulkowska JI. TrmD: A Methyl Transferase for tRNA Methylation With m 1G37. Enzymes 2017; 41:89-115. [PMID: 28601227 DOI: 10.1016/bs.enz.2017.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
TrmD is an S-adenosyl methionine (AdoMet)-dependent methyl transferase that synthesizes the methylated m1G37 in tRNA. TrmD is specific to and essential for bacterial growth, and it is fundamentally distinct from its eukaryotic and archaeal counterpart Trm5. TrmD is unusual by using a topological protein knot to bind AdoMet. Despite its restricted mobility, the TrmD knot has complex dynamics necessary to transmit the signal of AdoMet binding to promote tRNA binding and methyl transfer. Mutations in the TrmD knot block this intramolecular signaling and decrease the synthesis of m1G37-tRNA, prompting ribosomes to +1-frameshifts and premature termination of protein synthesis. TrmD is unique among AdoMet-dependent methyl transferases in that it requires Mg2+ in the catalytic mechanism. This Mg2+ dependence is important for regulating Mg2+ transport to Salmonella for survival of the pathogen in the host cell. The strict conservation of TrmD among bacterial species suggests that a better characterization of its enzymology and biology will have a broad impact on our understanding of bacterial pathogenesis.
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Affiliation(s)
- Ya-Ming Hou
- Thomas Jefferson University, Philadelphia, PA, United States.
| | - Ryuma Matsubara
- Thomas Jefferson University, Philadelphia, PA, United States
| | - Ryuichi Takase
- Thomas Jefferson University, Philadelphia, PA, United States
| | - Isao Masuda
- Thomas Jefferson University, Philadelphia, PA, United States
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Abstract
To date, about 90 post-transcriptional modifications have been reported in tRNA expanding their chemical and functional diversity. Methylation is the most frequent post-transcriptional tRNA modification that can occur on almost all nitrogen sites of the nucleobases, on the C5 atom of pyrimidines, on the C2 and C8 atoms of adenosine and, additionally, on the oxygen of the ribose 2′-OH. The methylation on the N1 atom of adenosine to form 1-methyladenosine (m1A) has been identified at nucleotide position 9, 14, 22, 57, and 58 in different tRNAs. In some cases, these modifications have been shown to increase tRNA structural stability and induce correct tRNA folding. This review provides an overview of the currently known m1A modifications, the different m1A modification sites, the biological role of each modification, and the enzyme responsible for each methylation in different species. The review further describes, in detail, two enzyme families responsible for formation of m1A at nucleotide position 9 and 58 in tRNA with a focus on the tRNA binding, m1A mechanism, protein domain organisation and overall structures.
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The genome of serotype VI Streptococcus agalactiae serotype VI and comparative analysis. Gene 2017; 597:59-65. [DOI: 10.1016/j.gene.2016.10.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 10/12/2016] [Accepted: 10/19/2016] [Indexed: 01/21/2023]
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45
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Ulrych A, Holečková N, Goldová J, Doubravová L, Benada O, Kofroňová O, Halada P, Branny P. Characterization of pneumococcal Ser/Thr protein phosphatase phpP mutant and identification of a novel PhpP substrate, putative RNA binding protein Jag. BMC Microbiol 2016; 16:247. [PMID: 27776484 PMCID: PMC5078927 DOI: 10.1186/s12866-016-0865-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reversible protein phosphorylation catalyzed by protein kinases and phosphatases is the primary mechanism for signal transduction in all living organisms. Streptococcus pneumoniae encodes a single Ser/Thr protein kinase, StkP, which plays a role in virulence, stress resistance and the regulation of cell wall synthesis and cell division. However, the role of its cognate phosphatase, PhpP, is not well defined. RESULTS Here, we report the successful construction of a ΔphpP mutant in the unencapsulated S. pneumoniae Rx1 strain and the characterization of its phenotype. We demonstrate that PhpP negatively controls the level of protein phosphorylation in S. pneumoniae both by direct dephosphorylation of target proteins and by dephosphorylation of its cognate kinase, StkP. Catalytic inactivation or absence of PhpP resulted in the hyperphosphorylation of StkP substrates and specific phenotypic changes, including sensitivity to environmental stresses and competence deficiency. The morphology of the ΔphpP cells resembled the StkP overexpression phenotype and conversely, overexpression of PhpP resulted in cell elongation mimicking the stkP null phenotype. Proteomic analysis of the phpP knock-out strain permitted identification of a novel StkP/PhpP substrate, Spr1851, a putative RNA-binding protein homologous to Jag. Here, we show that pneumococcal Jag is phosphorylated on Thr89. Inactivation of jag confers a phenotype similar to the phpP mutant strain. CONCLUSIONS Our results suggest that PhpP and StkP cooperatively regulate cell division of S. pneumoniae and phosphorylate putative RNA binding protein Jag.
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Affiliation(s)
- Aleš Ulrych
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Nela Holečková
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Jana Goldová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Linda Doubravová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Prague, Czech Republic.
| | - Oldřich Benada
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Olga Kofroňová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Petr Halada
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Pavel Branny
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Prague, Czech Republic.
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Dégut C, Barraud P, Larue V, Tisné C. Backbone resonance assignments of the m1A22 tRNA methyltransferase TrmK from Bacillus subtilis. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:253-257. [PMID: 27098549 DOI: 10.1007/s12104-016-9680-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/12/2016] [Indexed: 06/05/2023]
Abstract
RNA modification is a post-transcriptional process by which certain nucleotides are altered after their initial incorporation into an RNA chain. Transfer RNAs (tRNAs) is the most heavily modified class of RNA molecules. These modifications expand the chemical and functional diversity of tRNAs and enhance their structural stability. To date, more than 100 modifications have been identified, the majority of which are specific from one domain of life. However, few modifications are extensively present in the three domains of life. Among those, the m(1)A nucleotide, which consists in the methylation at position 1 of the adenine aromatic ring, is found in tRNAs and ribosomal RNAs. In tRNAs, the m(1)A modification occurs at position 9, 14, 22, 57 and 58. The enzyme TrmK catalyzes the m(1)A formation at position 22. Here we report the backbone (1)H, (15)N and (13)C chemical shift assignments of TrmK from Bacillus subtilis obtained by heteronuclear multidimensional NMR spectroscopy as well as its secondary structure in solution as predicted by TALOS+. These assignments of TrmK pave the way for interaction studies with its tRNA substrates.
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Affiliation(s)
- Clément Dégut
- Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Pierre Barraud
- Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006, Paris, France.
| | - Valéry Larue
- Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Carine Tisné
- Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006, Paris, France.
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Cleverley RM, Rismondo J, Lockhart-Cairns MP, Van Bentum PT, Egan AJ, Vollmer W, Halbedel S, Baldock C, Breukink E, Lewis RJ. Subunit Arrangement in GpsB, a Regulator of Cell Wall Biosynthesis. Microb Drug Resist 2016; 22:446-60. [PMID: 27257764 PMCID: PMC5111876 DOI: 10.1089/mdr.2016.0050] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
GpsB, a key regulator of cell division in Gram-positive bacteria, interacts with a key peptidoglycan synthase at the cell division septum, the penicillin binding protein PBP1 (a.k.a. PonA). Bacillus subtilis GpsB has been reported to interact with other components of the cell division machinery, including EzrA, MreC, and PrkC. In this study, we report an analysis of the arrangement of subunits in Listeria monocytogenes GpsB by small-angle X-ray scattering. The resulting model has an elongated shape with residues critical for interaction with PBP1 and the cell membrane clustered at one end of the molecule. Mutations that destabilize the hexameric assembly of the wild-type protein have a gpsB null phenotype, indicating that oligomerization is critical for the correct function of GpsB. We suggest a model in which a single GpsB hexamer can interact with multiple PBP1 molecules and can therefore influence the arrangement of PBP1 molecules within the cell division machinery, a dynamic multiprotein complex called the divisome, consistent with a role for GpsB in modulating the synthesis of the cell wall.
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Affiliation(s)
- Robert M. Cleverley
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Jeanine Rismondo
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Michael P. Lockhart-Cairns
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Wellcome Trust Centre for Cell Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Paulien T. Van Bentum
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Utrecht, the Netherlands
| | - Alexander J.F. Egan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Clair Baldock
- Wellcome Trust Centre for Cell Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Utrecht, the Netherlands
| | - Richard J. Lewis
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
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Elhenawy W, Davis RM, Fero J, Salama NR, Felman MF, Ruiz N. The O-Antigen Flippase Wzk Can Substitute for MurJ in Peptidoglycan Synthesis in Helicobacter pylori and Escherichia coli. PLoS One 2016; 11:e0161587. [PMID: 27537185 PMCID: PMC4990322 DOI: 10.1371/journal.pone.0161587] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/08/2016] [Indexed: 11/19/2022] Open
Abstract
The peptidoglycan (PG) cell wall is an essential component of the cell envelope of most bacteria. Biogenesis of PG involves a lipid-linked disaccharide-pentapeptide intermediate called lipid II, which must be translocated across the cytoplasmic membrane after it is synthesized in the inner leaflet of this bilayer. Accordingly, it has been demonstrated that MurJ, the proposed lipid II flippase in Escherichia coli, is required for PG biogenesis, and thereby viability. In contrast, MurJ is not essential in Bacillus subtilis because this bacterium produces AmJ, an unrelated protein that is functionally redundant with MurJ. In this study, we investigated why MurJ is not essential in the prominent gastric pathogen, Helicobacter pylori. We found that in this bacterium, Wzk, the ABC (ATP-binding cassette) transporter that flips the lipid-linked O- or Lewis- antigen precursors across the inner membrane, is redundant with MurJ for cell viability. Heterologous expression of wzk in E. coli also suppresses the lethality caused by the loss of murJ. Furthermore, we show that this cross-species complementation is abolished when Wzk is inactivated by mutations that target a domain predicted to be required for ATPase activity. Our results suggest that Wzk can flip lipid II, implying that Wzk is the flippase with the most relaxed specificity for lipid-linked saccharides ever identified.
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Affiliation(s)
- Wael Elhenawy
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
| | - Rebecca M. Davis
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, United States of America
| | - Jutta Fero
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States of America
| | - Nina R. Salama
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States of America
| | - Mario F. Felman
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, United States of America
- * E-mail:
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Al-Dabbagh B, Olatunji S, Crouvoisier M, El Ghachi M, Blanot D, Mengin-Lecreulx D, Bouhss A. Catalytic mechanism of MraY and WecA, two paralogues of the polyprenyl-phosphate N-acetylhexosamine 1-phosphate transferase superfamily. Biochimie 2016; 127:249-57. [DOI: 10.1016/j.biochi.2016.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 06/07/2016] [Indexed: 10/21/2022]
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Peters K, Pipo J, Schweizer I, Hakenbeck R, Denapaite D. Promoter Identification and Transcription Analysis of Penicillin-Binding Protein Genes in Streptococcus pneumoniae R6. Microb Drug Resist 2016; 22:487-98. [PMID: 27409661 PMCID: PMC5036317 DOI: 10.1089/mdr.2016.0084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Penicillin-binding proteins (PBPs) are membrane-associated enzymes, which are involved in the last two steps of peptidoglycan biosynthesis, and some of them are key players in cell division. Furthermore, they are targets of β-lactams, the most widely used antibiotics. Nevertheless, very little is known about the expression and regulation of PBP genes. Using transcriptional mapping, we now determined the promoter regions of PBP genes from the laboratory strain Streptococcus pneumoniae R6 and examined the expression profile of these six promoters. The extended −10 region is highly conserved and complies with a σA-type promoter consensus sequence. In contrast, the −35 region is poorly conserved, indicating the possibility for differential PBP regulation. All PBP promoters were constitutively expressed and highly active during the exponential and early stationary growth phase. However, the individual expression of PBP promoters varied approximately fourfold, with pbp1a being the highest and pbp3 the lowest. Furthermore, the deletion of one nucleotide in the spacer region of the PBP3 promoter reduced pbp3 expression ∼10-fold. The addition of cefotaxime above the minimal inhibitory concentration (MIC) did not affect PBP expression in the penicillin-sensitive R6 strain. No evidence for regulation of S. pneumoniae PBP genes was obtained.
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Affiliation(s)
- Katharina Peters
- Department of Microbiology, University of Kaiserslautern , Kaiserslautern, Germany
| | - Julia Pipo
- Department of Microbiology, University of Kaiserslautern , Kaiserslautern, Germany
| | - Inga Schweizer
- Department of Microbiology, University of Kaiserslautern , Kaiserslautern, Germany
| | - Regine Hakenbeck
- Department of Microbiology, University of Kaiserslautern , Kaiserslautern, Germany
| | - Dalia Denapaite
- Department of Microbiology, University of Kaiserslautern , Kaiserslautern, Germany
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