1
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Zhang P, Liu Z. Structural insights into the transporting and catalyzing mechanism of DltB in LTA D-alanylation. Nat Commun 2024; 15:3404. [PMID: 38649359 PMCID: PMC11035591 DOI: 10.1038/s41467-024-47783-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
DltB, a model member of the Membrane-Bound O-AcylTransferase (MBOAT) superfamily, plays a crucial role in D-alanylation of the lipoteichoic acid (LTA), a significant component of the cell wall of gram-positive bacteria. This process stabilizes the cell wall structure, influences bacterial virulence, and modulates the host immune response. Despite its significance, the role of DltB is not well understood. Through biochemical analysis and cryo-EM imaging, we discover that Streptococcus thermophilus DltB forms a homo-tetramer on the cell membrane. We further visualize DltB in an apo form, in complex with DltC, and in complex with its inhibitor amsacrine (m-AMSA). Each tetramer features a central hole. The C-tunnel of each protomer faces the intratetramer interface and provides access to the periphery membrane. Each protomer binds a DltC without changing the tetrameric organization. A phosphatidylglycerol (PG) molecule in the substrate-binding site may serve as an LTA carrier. The inhibitor m-AMSA bound to the L-tunnel of each protomer blocks the active site. The tetrameric organization of DltB provides a scaffold for catalyzing D-alanyl transfer and regulating the channel opening and closing. Our findings unveil DltB's dual function in the D-alanylation pathway, and provide insight for targeting DltB as a anti-virulence antibiotic.
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Affiliation(s)
- Pingfeng Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
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2
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Cacace E, Kim V, Varik V, Knopp M, Tietgen M, Brauer-Nikonow A, Inecik K, Mateus A, Milanese A, Mårli MT, Mitosch K, Selkrig J, Brochado AR, Kuipers OP, Kjos M, Zeller G, Savitski MM, Göttig S, Huber W, Typas A. Systematic analysis of drug combinations against Gram-positive bacteria. Nat Microbiol 2023; 8:2196-2212. [PMID: 37770760 PMCID: PMC10627819 DOI: 10.1038/s41564-023-01486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
Drug combinations can expand options for antibacterial therapies but have not been systematically tested in Gram-positive species. We profiled ~8,000 combinations of 65 antibacterial drugs against the model species Bacillus subtilis and two prominent pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Thereby, we recapitulated previously known drug interactions, but also identified ten times more novel interactions in the pathogen S. aureus, including 150 synergies. We showed that two synergies were equally effective against multidrug-resistant S. aureus clinical isolates in vitro and in vivo. Interactions were largely species-specific and synergies were distinct from those of Gram-negative species, owing to cell surface and drug uptake differences. We also tested 2,728 combinations of 44 commonly prescribed non-antibiotic drugs with 62 drugs with antibacterial activity against S. aureus and identified numerous antagonisms that might compromise the efficacy of antimicrobial therapies. We identified even more synergies and showed that the anti-aggregant ticagrelor synergized with cationic antibiotics by modifying the surface charge of S. aureus. All data can be browsed in an interactive interface ( https://apps.embl.de/combact/ ).
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Affiliation(s)
- Elisabetta Cacace
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Vladislav Kim
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Vallo Varik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Michael Knopp
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manuela Tietgen
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | | | - Kemal Inecik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Alessio Milanese
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
- Department of Biology, Institute of Microbiology, and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Karin Mitosch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Joel Selkrig
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
| | - Ana Rita Brochado
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Molecular Biology and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Georg Zeller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Stephan Göttig
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
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3
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Jeong GJ, Khan F, Tabassum N, Cho KJ, Kim YM. Controlling biofilm and virulence properties of Gram-positive bacteria by targeting wall teichoic acid and lipoteichoic acid. Int J Antimicrob Agents 2023; 62:106941. [PMID: 37536571 DOI: 10.1016/j.ijantimicag.2023.106941] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023]
Abstract
Wall teichoic acid (WTA) and lipoteichoic acid (LTA) are structural components of Gram-positive bacteria's peptidoglycan and cell membrane, which are mostly anionic glycopolymers. WTA confers numerous physiological, virulence, and pathogenic features to bacterial pathogens. It controls cell shape, cell division, and the localisation of autolytic enzymes and ion homeostasis. In the context of virulence and pathogenicity, it aids bacterial cell attachment and colonisation and protects against the host defence system and antibiotics. Having such a broad function in pathogenic bacteria's lifecycle, WTA/LTA become one of the potential targets for antibacterial agents to reduce bacterial infection in the host. The number of reports for targeting the WTA/LTA pathway has risen, mostly by focusing on three distinct targets: antivirulence targets, β-lactam potentiator targets, and essential targets. The current review looked at the role of WTA/LTA in biofilm development and virulence in a range of Gram-positive pathogenic bacteria. Furthermore, alternate strategies, such as the application of natural and synthetic compounds that target the WTA/LTA pathway, have been thoroughly discussed. Moreover, the application of nanomaterials and a combination of drugs have also been discussed as a viable method for targeting the WTA/LTA in numerous Gram-positive bacteria. In addition, a future perspective for controlling bacterial infection by targeting the WTA/LTA is proposed.
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Affiliation(s)
- Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
| | - Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Kyung-Jin Cho
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
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4
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Schultz BJ, Snow ED, Walker S. Mechanism of D-alanine transfer to teichoic acids shows how bacteria acylate cell envelope polymers. Nat Microbiol 2023; 8:1318-1329. [PMID: 37308592 PMCID: PMC10664464 DOI: 10.1038/s41564-023-01411-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/17/2023] [Indexed: 06/14/2023]
Abstract
Bacterial cell envelope polymers are often modified with acyl esters that modulate physiology, enhance pathogenesis and provide antibiotic resistance. Here, using the D-alanylation of lipoteichoic acid (Dlt) pathway as a paradigm, we have identified a widespread strategy for how acylation of cell envelope polymers occurs. In this strategy, a membrane-bound O-acyltransferase (MBOAT) protein transfers an acyl group from an intracellular thioester onto the tyrosine of an extracytoplasmic C-terminal hexapeptide motif. This motif shuttles the acyl group to a serine on a separate transferase that moves the cargo to its destination. In the Dlt pathway, here studied in Staphylococcus aureus and Streptococcus thermophilus, the C-terminal 'acyl shuttle' motif that forms the crucial pathway intermediate is found on a transmembrane microprotein that holds the MBOAT protein and the other transferase together in a complex. In other systems, found in both Gram-negative and Gram-positive bacteria as well as some archaea, the motif is fused to the MBOAT protein, which interacts directly with the other transferase. The conserved chemistry uncovered here is widely used for acylation throughout the prokaryotic world.
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Affiliation(s)
- Bailey J Schultz
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Eric D Snow
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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5
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Coupland CE, Ansell TB, Sansom MSP, Siebold C. Rocking the MBOAT: Structural insights into the membrane bound O-acyltransferase family. Curr Opin Struct Biol 2023; 80:102589. [PMID: 37040671 DOI: 10.1016/j.sbi.2023.102589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 04/13/2023]
Abstract
The membrane-bound O-acyltransferase (MBOAT) superfamily catalyses the transfer of acyl chains to substrates implicated in essential cellular functions. Aberrant function of MBOATs is associated with various diseases and MBOATs are promising drug targets. There has been recent progress in structural characterisation of MBOATs, advancing our understanding of their functional mechanism. Integrating information across the MBOAT family, we characterise a common MBOAT fold and provide a blueprint for substrate and inhibitor engagement. This work provides context for the diverse substrates, mechanisms, and evolutionary relationships of protein and small-molecule MBOATs. Further work should aim to characterise MBOATs, as inherently lipid-associated proteins, within their membrane environment.
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Affiliation(s)
- Claire E Coupland
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - T Bertie Ansell
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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6
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Stone MC, Mychack A, Coe KA, Walker S. Combining Signal Peptidase and Lipoprotein Processing Inhibitors Overcomes Ayr Resistance in Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0011523. [PMID: 37097175 PMCID: PMC10190671 DOI: 10.1128/aac.00115-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/30/2023] [Indexed: 04/26/2023] Open
Abstract
Antibiotic resistance in bacterial pathogens is an ongoing public health concern. The arylomycins are a class of natural product antibiotics that target the type I signal peptidase, which carries out the terminal step in protein secretion. Here, we used transposon sequencing (Tn-Seq) to profile the effects of the optimized arylomycin derivative G0775 in Staphylococcus aureus. Our transposon libraries include both upregulation and inactivation mutants, allowing us to identify resistance mechanisms and targets for synergism. We identified several cell envelope pathways that, when inactivated, sensitize S. aureus to the arylomycin G0775. These pathways include the lipoprotein processing pathway, and we have shown that inhibitors of this pathway synergize with G0775 even though lipoprotein processing is nonessential in S. aureus. Moreover, we found that blocking this pathway completely reverses Ayr resistance, which is a major resistance mechanism to arylomycins, including G0775. Our Tn-Seq data also showed that upregulation of mprF and several other genes is protective against G0775. Because a subset of these genes was previously found in a Tn-Seq profile of the clinically important antibiotic daptomycin, we tested a set of daptomycin-nonsusceptible clinical isolates with gain-of-function mutations in mprF for susceptibility to arylomycin G0775. Despite structural and mechanistic differences between these antibiotics, we observed similar decreases in susceptibility. Taken together, our results highlight how Tn-Seq profiles that include both gene inactivation and upregulation can identify targets, antibiotic resistance mechanisms, and strategies to overcome resistance.
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Affiliation(s)
- Madeleine C. Stone
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Aaron Mychack
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathryn A. Coe
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
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7
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Abstract
Almost all bactericidal drugs require bacterial replication and/or metabolic activity for their killing activity. When these processes are inhibited by bacteriostatic antibiotics, bacterial killing is significantly reduced. One notable exception is the lipopeptide antibiotic daptomycin, which has been reported to efficiently kill growth-arrested bacteria. However, these studies employed only short periods of growth arrest (<1 h), which may not fully represent the duration of growth arrest that can occur in vivo. We found that a growth inhibitory concentration of the protein synthesis inhibitor tetracycline led to a time-dependent induction of daptomycin tolerance in S. aureus, with an approximately 100,000-fold increase in survival after 16 h of growth arrest, relative to exponential-phase bacteria. Daptomycin tolerance required glucose and was associated with increased production of the cell wall polymers peptidoglycan and wall-teichoic acids. However, while the accumulation of peptidoglycan was required for daptomycin tolerance, only a low abundance of wall teichoic acid was necessary. Therefore, whereas tolerance to most antibiotics occurs passively due to a lack of metabolic activity and/or replication, daptomycin tolerance arises via active cell wall remodelling. IMPORTANCE Understanding why antibiotics sometimes fail to cure infections is fundamental to improving treatment outcomes. This is a major challenge when it comes to Staphylococcus aureus because this pathogen causes several different chronic or recurrent infections. Previous work has shown that a lack of replication, as often occurs during infection, makes bacteria tolerant of most bactericidal antibiotics. However, one antibiotic that has been reported to kill nonreplicating bacteria is daptomycin. In this work, we show that the growth arrest of S. aureus does in fact lead to daptomycin tolerance, but it requires time, nutrients, and biosynthetic pathways, making it distinct from other types of antibiotic tolerance that occur in nonreplicating bacteria.
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8
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Lee W. Construction of high-density transposon mutant library of Staphylococcus aureus using bacteriophage ϕ11. J Microbiol 2022; 60:1123-1129. [PMID: 36422842 DOI: 10.1007/s12275-022-2476-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Transposon mutant libraries are an important resource to study bacterial metabolism and pathogenesis. The fitness analysis of mutants in the libraries under various growth conditions provides important clues to study the physiology and biogenesis of structural components of a bacterial cell. A transposon library in conjunction with next-generation sequencing techniques, collectively named transposon sequencing (Tn-seq), enables high-throughput genome profiling and synthetic lethality analysis. Tn-seq has also been used to identify essential genes and to study the mode of action of antibacterials. To construct a high-density transposon mutant library, an efficient delivery system for transposition in a model bacterium is essential. Here, I describe a detailed protocol for generating a high-density phage-based transposon mutant library in a Staphylococcus aureus strain, and this protocol is readily applicable to other S. aureus strains including USA300 and MW2.
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Affiliation(s)
- Wonsik Lee
- Department of Pharmacy, School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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9
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Zhou J, Cai Y, Liu Y, An H, Deng K, Ashraf MA, Zou L, Wang J. Breaking down the cell wall: Still an attractive antibacterial strategy. Front Microbiol 2022; 13:952633. [PMID: 36212892 PMCID: PMC9544107 DOI: 10.3389/fmicb.2022.952633] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Since the advent of penicillin, humans have known about and explored the phenomenon of bacterial inhibition via antibiotics. However, with changes in the global environment and the abuse of antibiotics, resistance mechanisms have been selected in bacteria, presenting huge threats and challenges to the global medical and health system. Thus, the study and development of new antimicrobials is of unprecedented urgency and difficulty. Bacteria surround themselves with a cell wall to maintain cell rigidity and protect against environmental insults. Humans have taken advantage of antibiotics to target the bacterial cell wall, yielding some of the most widely used antibiotics to date. The cell wall is essential for bacterial growth and virulence but is absent from humans, remaining a high-priority target for antibiotic screening throughout the antibiotic era. Here, we review the extensively studied targets, i.e., MurA, MurB, MurC, MurD, MurE, MurF, Alr, Ddl, MurI, MurG, lipid A, and BamA in the cell wall, starting from the very beginning to the latest developments to elucidate antimicrobial screening. Furthermore, recent advances, including MraY and MsbA in peptidoglycan and lipopolysaccharide, and tagO, LtaS, LspA, Lgt, Lnt, Tol-Pal, MntC, and OspA in teichoic acid and lipoprotein, have also been profoundly discussed. The review further highlights that the application of new methods such as macromolecular labeling, compound libraries construction, and structure-based drug design will inspire researchers to screen ideal antibiotics.
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Affiliation(s)
- Jingxuan Zhou
- The People’s Hospital of China Three Gorges University, Yichang, Hubei, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Yi Cai
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Ying Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Haoyue An
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Kaihong Deng
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Muhammad Awais Ashraf
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Lili Zou
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Jun Wang
- The People’s Hospital of China Three Gorges University, Yichang, Hubei, China
- *Correspondence: Jun Wang,
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10
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Malachowa N, McGuinness W, Kobayashi SD, Porter AR, Shaia C, Lovaglio J, Smith B, Rungelrath V, Saturday G, Scott DP, Falugi F, Missiakas D, Schneewind O, DeLeo FR. Toward Optimization of a Rabbit Model of Staphylococcus aureus (USA300) Skin and Soft Tissue Infection. Microbiol Spectr 2022; 10:e0271621. [PMID: 35389241 PMCID: PMC9045089 DOI: 10.1128/spectrum.02716-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/22/2022] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus remains a leading cause of skin and soft tissue infections (SSTIs) globally. In the United States, many of these infections are caused by isolates classified as USA300. Our understanding of the success of USA300 as a human pathogen is due in part to data obtained from animal infection models, including rabbit SSTI models. These animal models have been used to study S. aureus virulence and pathogenesis and to gain an enhanced understanding of the host response to infection. Although significant knowledge has been gained, the need to use a relatively high inoculum of USA300 (1 × 108 to 5 × 108 CFU) is a caveat of these infection models. As a step toward addressing this issue, we created mutations in USA300 that mimic those found in S. aureus strains with naturally occurring rabbit tropism-namely, single nucleotide polymorphisms in dltB and/or deletion of rot. We then developed a rabbit SSTI model that utilizes an inoculum of 106 USA300 CFU to cause reproducible disease and tested whether primary SSTI protects rabbits against severe reinfection caused by the same strain. Although there was modest protection against severe reinfection, primary infection and reinfection with rabbit-tropic USA300 strains failed to increase the overall level of circulating anti-S. aureus antibodies significantly. These findings provide additional insight into the host response to S. aureus. More work is needed to further develop a low-inoculum infection model that can be used to better test the potential of new therapeutics or vaccine target antigens. IMPORTANCE Animal models of S. aureus infection are important for evaluating bacterial pathogenesis and host immune responses. These animal infection models are often used as an initial step in the testing of vaccine antigens and new therapeutics. The extent to which animal models of S. aureus infection approximate human infections remains a significant consideration for translation of results to human clinical trials. Although significant progress has been made with rabbit models of S. aureus infection, one concern is the high inoculum needed to cause reproducible disease. Here, we generated USA300 strains that have tropism for rabbits and developed a rabbit SSTI model that uses fewer CFU than previous models.
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Affiliation(s)
- Natalia Malachowa
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Will McGuinness
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Scott D. Kobayashi
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Adeline R. Porter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Carl Shaia
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Jamie Lovaglio
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Brian Smith
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Viktoria Rungelrath
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Greg Saturday
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Dana P. Scott
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Fabiana Falugi
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | | | - Olaf Schneewind
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Frank R. DeLeo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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11
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Zhang Y, Zhang Y, Chen C, Cheng H, Deng X, Li D, Bai B, Yu Z, Deng Q, Guo J, Wen Z. Antibacterial activities and action mode of anti-hyperlipidemic lomitapide against Staphylococcus aureus. BMC Microbiol 2022; 22:114. [PMID: 35473561 PMCID: PMC9040290 DOI: 10.1186/s12866-022-02535-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/18/2022] [Indexed: 11/27/2022] Open
Abstract
Background The increasing emergence of multidrug-resistant Gram-positive bacterial infections necessitates new antibacterial agents with novel mechanisms of action that can be used to treat these infections. Lomitapide has been approved by FDA for years in reducing levels of low-density lipoprotein (LDL) in cases of familial hypercholesterolemia, whereas the antibacterial effect of lomitapide remains elusive. In this study, the inhibitory activities of lomitapide against Gram-positive bacteria were the first time explored. Quantitative proteomics analysis was then applied to investigate the mechanisms of action of lomitapide. Results The minimum inhibitory concentration (MIC) values of lomitapide against Gram-positive bacteria including both methicillin sensitive and resistant Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Enterococcus faecium, and Streptococcus agalactiae were range 12.5–50 μM. Moreover, lomitapide also inhibited anti-biofilm activity against clinical S. aureus isolates. A total of 106 proteins with > 1.5-fold changes in expression were identified upon 1/2 × MIC lomitapide exposure, including 83 up-regulated proteins and 23 down-regulated proteins. Based on bioinformatics analysis, the expression of cell wall damage response proteins including two-component system VraS/VraR, lipoteichoic acid (LPA) D-alanylnation related proteins D-alanyl carrier protein (dltC) and carrier protein ligase (dltA), methionine sulfoxide reductases (mrsA1 and mrsB) were up-regulated. Moreover, the expression of SaeS and multiple fibrinogen-binding proteins (SAOUHSC_01110, FnBPB, SAOUHSC_02802, SdrC, SdrD) which were involved in the bacterial adhesion and biofilm formation, was inhibited by lomitapide. Furthermore, VraS/VraR deletion mutant (ΔvraSR) showed an enhanced lomitapide sensitivity phenotype. Conclusion Lomitapide displayed broad antimicrobial activities against Gram-positive bacteria. The antibacterial effect of lomitapide may be caused by cell wall destruction, while the anti-biofilm activity may be related to the inhibition of surface proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02535-9.
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Affiliation(s)
- Yufang Zhang
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated Hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.,Class of Biological Science, Futian District, Shenzhen College of International Education, No. 3 Antuoshan 6th Rd, Shenzhen, 518040, China
| | - Yiying Zhang
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated Hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Chengchun Chen
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated Hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Hang Cheng
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated Hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Xiangbin Deng
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated Hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Duoyun Li
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated Hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Bing Bai
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated Hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Zhijian Yu
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated Hospital of Guangdong Medical University, Shenzhen, 518052, China.,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Qiwen Deng
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated Hospital of Guangdong Medical University, Shenzhen, 518052, China. .,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.
| | - Jie Guo
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated Hospital of Guangdong Medical University, Shenzhen, 518052, China. .,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.
| | - Zewen Wen
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th affiliated Hospital of Guangdong Medical University, Shenzhen, 518052, China. .,Quality Control Center of Hospital Infection Management of Shenzhen, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.
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12
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Ong ZX, Kannan B, Becker DL. Exploiting transposons in the study of Staphylococcus aureus pathogenesis and virulence. Crit Rev Microbiol 2022; 49:297-317. [PMID: 35438613 DOI: 10.1080/1040841x.2022.2052794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The opportunistic pathogen Staphylococcus aureus has an extremely complex relationship with humans. While the bacteria can exist as a commensal in many, it can cause a wide range of diseases and infections when turned pathogenic. Its presence is a determinant of chronicity and poor prognosis in numerous diseases, and its genomic plasticity causes S. aureus antimicrobial resistance to be one of the most dire contemporary medical problems to solve. Genetic manipulation of S. aureus has led to numerous findings that are vital in the fight against its pathogenesis. The utilisation of transposon mutant libraries for the systematic inspection of the S. aureus genome led to many landmark discoveries pertaining to the bacteria's pathogenicity, antimicrobial resistance acquisition, and virulence regulation. In this review, we describe mutant libraries, and their significant contributions, from various S. aureus strains created with commonly used transposons. The general workflow for the construction of libraries will be presented, along with a discussion of the challenges of undertaking the task of large-scale library construction. As the accessibility of transposon mutant library construction, screening, and analysis increases, this genetic tool could be further exploited in the study of the S. aureus genome.
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Affiliation(s)
- Zi Xin Ong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Skin Research Institute, Singapore.,Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore
| | - Bavani Kannan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Skin Research Institute, Singapore
| | - David L Becker
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Skin Research Institute, Singapore
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13
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Wang J, Zhang Q, Han J, Zhao Y, Zhao C, Yan B, Dai C, Wu L, Wen Y, Zhang Y, Leng D, Wang Z, Yang X, He S, Bo X. Computational methods, databases and tools for synthetic lethality prediction. Brief Bioinform 2022; 23:6555403. [PMID: 35352098 PMCID: PMC9116379 DOI: 10.1093/bib/bbac106] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/15/2022] [Accepted: 03/02/2022] [Indexed: 12/17/2022] Open
Abstract
Synthetic lethality (SL) occurs between two genes when the inactivation of either gene alone has no effect on cell survival but the inactivation of both genes results in cell death. SL-based therapy has become one of the most promising targeted cancer therapies in the last decade as PARP inhibitors achieve great success in the clinic. The key point to exploiting SL-based cancer therapy is the identification of robust SL pairs. Although many wet-lab-based methods have been developed to screen SL pairs, known SL pairs are less than 0.1% of all potential pairs due to large number of human gene combinations. Computational prediction methods complement wet-lab-based methods to effectively reduce the search space of SL pairs. In this paper, we review the recent applications of computational methods and commonly used databases for SL prediction. First, we introduce the concept of SL and its screening methods. Second, various SL-related data resources are summarized. Then, computational methods including statistical-based methods, network-based methods, classical machine learning methods and deep learning methods for SL prediction are summarized. In particular, we elaborate on the negative sampling methods applied in these models. Next, representative tools for SL prediction are introduced. Finally, the challenges and future work for SL prediction are discussed.
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Affiliation(s)
- Jing Wang
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Qinglong Zhang
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Junshan Han
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yanpeng Zhao
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Caiyun Zhao
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Bowei Yan
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Chong Dai
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Lianlian Wu
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yuqi Wen
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yixin Zhang
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Dongjin Leng
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Zhongming Wang
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiaoxi Yang
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Song He
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
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14
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Muscato J, Morris HG, Mychack A, Rajagopal M, Baidin V, Hesser AR, Lee W, İnecik K, Wilson LJ, Kraml CM, Meredith TC, Walker S. Rapid Inhibitor Discovery by Exploiting Synthetic Lethality. J Am Chem Soc 2022; 144:3696-3705. [PMID: 35170959 PMCID: PMC9012225 DOI: 10.1021/jacs.1c12697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Synthetic lethality occurs when inactivation of two genes is lethal but inactivation of either single gene is not. This phenomenon provides an opportunity for efficient compound discovery. Using differential growth screens, one can identify biologically active compounds that selectively inhibit proteins within the synthetic lethal network of any inactivated gene. Here, based purely on synthetic lethalities, we identified two compounds as the only possible inhibitors of Staphylococcus aureus lipoteichoic acid (LTA) biosynthesis from a screen of ∼230,000 compounds. Both compounds proved to inhibit the glycosyltransferase UgtP, which assembles the LTA glycolipid anchor. UgtP is required for β-lactam resistance in methicillin-resistant S. aureus (MRSA), and the inhibitors restored sensitivity to oxacillin in a highly resistant S. aureus strain. As no other compounds were pursued as possible LTA glycolipid assembly inhibitors, this work demonstrates the extraordinary efficiency of screens that exploit synthetic lethality to discover compounds that target specified pathways. The general approach should be applicable not only to other bacteria but also to eukaryotic cells.
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Affiliation(s)
- Jacob
D. Muscato
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Heidi G. Morris
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Aaron Mychack
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mithila Rajagopal
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States,Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Vadim Baidin
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Anthony R. Hesser
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Wonsik Lee
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kemal İnecik
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Laura J. Wilson
- Lotus
Separations LLC, B20 Frick Chemistry Laboratory, Princeton, New Jersey 08544, United States
| | - Christina M. Kraml
- Lotus
Separations LLC, B20 Frick Chemistry Laboratory, Princeton, New Jersey 08544, United States
| | - Timothy C. Meredith
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Suzanne Walker
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States,Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States,
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15
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Ferraro NJ, Kim S, Im W, Pires MM. Systematic Assessment of Accessibility to the Surface of Staphylococcus aureus. ACS Chem Biol 2021; 16:2527-2536. [PMID: 34609132 DOI: 10.1021/acschembio.1c00604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proteins from bacterial foes, antimicrobial peptides, and host immune proteins must navigate past a dense layer of bacterial surface biomacromolecules to reach the peptidoglycan (PG) layer of Gram-positive bacteria. A subclass of molecules (e.g., antibiotics with intracellular targets) also must permeate through the PG (in a molecular sieving manner) to reach the cytoplasmic membrane. Despite the biological and therapeutic importance of surface accessibility, systematic analyses in live bacterial cells have been lacking. We describe a live cell fluorescence assay that is robust, shows a high level of reproducibility, and reports on the permeability of molecules to and within the PG scaffold. Moreover, our study shows that teichoic acids impede the permeability of molecules of a wide range of sizes and chemical composition.
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Affiliation(s)
- Noel J. Ferraro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Seonghoon Kim
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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16
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Coupri D, Verneuil N, Hartke A, Liebaut A, Lequeux T, Pfund E, Budin-Verneuil A. Inhibition of d-alanylation of teichoic acids overcomes resistance of methicillin-resistant Staphylococcus aureus. J Antimicrob Chemother 2021; 76:2778-2786. [PMID: 34450626 PMCID: PMC8521394 DOI: 10.1093/jac/dkab287] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022] Open
Abstract
Background MRSA are high-priority multidrug-resistant pathogens. Although there are still some antibiotics active against MRSA, continuous efforts to discover new antibiotics and treatment strategies are needed because resistance to these new drugs has already been reported. Objectives Here we explore if d-alanylation of teichoic acids (TAs) mediated by the dlt operon gene products might be a druggable target to overcome β-lactam-resistance of MRSA. Methods MICs and bactericidal effects of several β-lactam antibiotics were monitored in a panel of clinical MRSA strains with genetic or chemically induced deficiency in d-alanylation of TAs. Efficiency of the chemical inhibitor to rescue MRSA-infected larvae of Galleria mellonella as well as its ability to prevent or eradicate biofilms of S. aureus were analysed. Results Genetic inactivation of the Dlt system or its chemical inhibition re-sensitizes MRSA to β-lactams. Among the 13 strains, the most pronounced effect was obtained using the inhibitor with imipenem, reducing the median MIC from 16 to 0.25 mg/L. This combination was also bactericidal in some strains and significantly protected G. mellonella larvae from lethal MRSA infections. Finally, inactivation of d-alanylation potentiated the effect of imipenem on inhibition and/or eradication of biofilm. Conclusions Our combined results show that highly efficient inhibitors of d-alanylation of TAs targeting enzymes of the Dlt system should be promising therapeutic adjuvants, especially in combination with carbapenems, for restoring the therapeutic efficacy of this class of antibiotics against MRSA.
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Affiliation(s)
| | | | - Axel Hartke
- Normandie Univ, UNICAEN, U2RM, 14000 Caen, France
| | | | - Thierry Lequeux
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd. du Maréchal Juin, 14050 Caen, France
| | - Emmanuel Pfund
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd. du Maréchal Juin, 14050 Caen, France
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17
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Apostolos AJ, Ferraro NJ, Dalesandro BE, Pires MM. SaccuFlow: A High-Throughput Analysis Platform to Investigate Bacterial Cell Wall Interactions. ACS Infect Dis 2021; 7:2483-2491. [PMID: 34291914 DOI: 10.1021/acsinfecdis.1c00255] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Bacterial cell walls are formidable barriers that protect bacterial cells against external insults and oppose internal turgor pressure. While cell wall composition is variable across species, peptidoglycan is the principal component of all cell walls. Peptidoglycan is a mesh-like scaffold composed of cross-linked strands that can be heavily decorated with anchored proteins. The biosynthesis and remodeling of peptidoglycan must be tightly regulated by cells because disruption to this biomacromolecule is lethal. This essentiality is exploited by the human innate immune system in resisting colonization and by a number of clinically relevant antibiotics that target peptidoglycan biosynthesis. Evaluation of molecules or proteins that interact with peptidoglycan can be a complicated and, typically, qualitative effort. We have developed a novel assay platform (SaccuFlow) that preserves the native structure of bacterial peptidoglycan and is compatible with high-throughput flow cytometry analysis. We show that the assay is facile and versatile as demonstrated by its compatibility with sacculi from Gram-positive bacteria, Gram-negative bacteria, and mycobacteria. Finally, we highlight the utility of this assay to assess the activity of sortase A from Staphylococcus aureus against potential antivirulence agents.
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Affiliation(s)
- Alexis J. Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Noel J. Ferraro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Brianna E. Dalesandro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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18
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Zhu M, Tse MW, Weller J, Chen J, Blainey PC. The future of antibiotics begins with discovering new combinations. Ann N Y Acad Sci 2021; 1496:82-96. [PMID: 34212403 PMCID: PMC8290516 DOI: 10.1111/nyas.14649] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/20/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
Antibiotic resistance is a worldwide and growing clinical problem. With limited drug development in the antibacterial space, combination therapy has emerged as a promising strategy to combat multidrug‐resistant bacteria. Antibacterial combinations can improve antibiotic efficacy and suppress antibacterial resistance through independent, synergistic, or even antagonistic activities. Combination therapies are famously used to treat viral and mycobacterial infections and cancer. However, antibacterial combinations are only now emerging as a common treatment strategy for other bacterial infections owing to challenges in their discovery, development, regulatory approval, and commercial/clinical deployment. Here, we focus on discovery—where the sheer scale of combinatorial chemical spaces represents a significant challenge—and discuss how combination therapy can impact the treatment of bacterial infections. Despite these challenges, recent advancements, including new in silico methods, theoretical frameworks, and microfluidic platforms, are poised to identify the new and efficacious antibacterial combinations needed to revitalize the antibacterial drug pipeline.
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Affiliation(s)
- Meilin Zhu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Megan W Tse
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Juliane Weller
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Julie Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, Massachusetts
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19
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Yuan T, Werman JM, Sampson NS. The pursuit of mechanism of action: uncovering drug complexity in TB drug discovery. RSC Chem Biol 2021; 2:423-440. [PMID: 33928253 PMCID: PMC8081351 DOI: 10.1039/d0cb00226g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022] Open
Abstract
Whole cell-based phenotypic screens have become the primary mode of hit generation in tuberculosis (TB) drug discovery during the last two decades. Different drug screening models have been developed to mirror the complexity of TB disease in the laboratory. As these culture conditions are becoming more and more sophisticated, unraveling the drug target and the identification of the mechanism of action (MOA) of compounds of interest have additionally become more challenging. A good understanding of MOA is essential for the successful delivery of drug candidates for TB treatment due to the high level of complexity in the interactions between Mycobacterium tuberculosis (Mtb) and the TB drug used to treat the disease. There is no single "standard" protocol to follow and no single approach that is sufficient to fully investigate how a drug restrains Mtb. However, with the recent advancements in -omics technologies, there are multiple strategies that have been developed generally in the field of drug discovery that have been adapted to comprehensively characterize the MOAs of TB drugs in the laboratory. These approaches have led to the successful development of preclinical TB drug candidates, and to a better understanding of the pathogenesis of Mtb infection. In this review, we describe a plethora of efforts based upon genetic, metabolomic, biochemical, and computational approaches to investigate TB drug MOAs. We assess these different platforms for their strengths and limitations in TB drug MOA elucidation in the context of Mtb pathogenesis. With an emphasis on the essentiality of MOA identification, we outline the unmet needs in delivering TB drug candidates and provide direction for further TB drug discovery.
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Affiliation(s)
- Tianao Yuan
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
| | - Joshua M. Werman
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
| | - Nicole S. Sampson
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
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20
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Fisher JF, Mobashery S. β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium. Chem Rev 2021; 121:3412-3463. [PMID: 33373523 PMCID: PMC8653850 DOI: 10.1021/acs.chemrev.0c01010] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biological diversity of the unicellular bacteria-whether assessed by shape, food, metabolism, or ecological niche-surely rivals (if not exceeds) that of the multicellular eukaryotes. The relationship between bacteria whose ecological niche is the eukaryote, and the eukaryote, is often symbiosis or stasis. Some bacteria, however, seek advantage in this relationship. One of the most successful-to the disadvantage of the eukaryote-is the small (less than 1 μm diameter) and nearly spherical Staphylococcus aureus bacterium. For decades, successful clinical control of its infection has been accomplished using β-lactam antibiotics such as the penicillins and the cephalosporins. Over these same decades S. aureus has perfected resistance mechanisms against these antibiotics, which are then countered by new generations of β-lactam structure. This review addresses the current breadth of biochemical and microbiological efforts to preserve the future of the β-lactam antibiotics through a better understanding of how S. aureus protects the enzyme targets of the β-lactams, the penicillin-binding proteins. The penicillin-binding proteins are essential enzyme catalysts for the biosynthesis of the cell wall, and understanding how this cell wall is integrated into the protective cell envelope of the bacterium may identify new antibacterials and new adjuvants that preserve the efficacy of the β-lactams.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
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21
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Rosiana S, Zhang L, Kim GH, Revtovich AV, Uthayakumar D, Sukumaran A, Geddes-McAlister J, Kirienko NV, Shapiro RS. Comprehensive genetic analysis of adhesin proteins and their role in virulence of Candida albicans. Genetics 2021; 217:iyab003. [PMID: 33724419 PMCID: PMC8045720 DOI: 10.1093/genetics/iyab003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/31/2020] [Indexed: 12/14/2022] Open
Abstract
Candida albicans is a microbial fungus that exists as a commensal member of the human microbiome and an opportunistic pathogen. Cell surface-associated adhesin proteins play a crucial role in C. albicans' ability to undergo cellular morphogenesis, develop robust biofilms, colonize, and cause infection in a host. However, a comprehensive analysis of the role and relationships between these adhesins has not been explored. We previously established a CRISPR-based platform for efficient generation of single- and double-gene deletions in C. albicans, which was used to construct a library of 144 mutants, comprising 12 unique adhesin genes deleted singly, and every possible combination of double deletions. Here, we exploit this adhesin mutant library to explore the role of adhesin proteins in C. albicans virulence. We perform a comprehensive, high-throughput screen of this library, using Caenorhabditis elegans as a simplified model host system, which identified mutants critical for virulence and significant genetic interactions. We perform follow-up analysis to assess the ability of high- and low-virulence strains to undergo cellular morphogenesis and form biofilms in vitro, as well as to colonize the C. elegans host. We further perform genetic interaction analysis to identify novel significant negative genetic interactions between adhesin mutants, whereby combinatorial perturbation of these genes significantly impairs virulence, more than expected based on virulence of the single mutant constituent strains. Together, this study yields important new insight into the role of adhesins, singly and in combinations, in mediating diverse facets of virulence of this critical fungal pathogen.
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Affiliation(s)
- Sierra Rosiana
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON NIG 2W1, Canada
| | - Liyang Zhang
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Grace H Kim
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON NIG 2W1, Canada
| | | | - Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON NIG 2W1, Canada
| | - Arjun Sukumaran
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON NIG 2W1, Canada
| | | | | | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON NIG 2W1, Canada
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Wu X, Han J, Gong G, Koffas MAG, Zha J. Wall teichoic acids: physiology and applications. FEMS Microbiol Rev 2020; 45:6019871. [DOI: 10.1093/femsre/fuaa064] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/01/2020] [Indexed: 12/21/2022] Open
Abstract
ABSTRACT
Wall teichoic acids (WTAs) are charged glycopolymers containing phosphodiester-linked polyol units and represent one of the major components of Gram-positive cell envelope. WTAs have important physiological functions in cell division, gene transfer, surface adhesion, drug resistance and biofilm formation, and are critical virulence factors and vital determinants in mediating cell interaction with and tolerance to environmental factors. Here, we first briefly introduce WTA structure, biosynthesis and its regulation, and then summarize in detail four major physiological roles played by WTAs, i.e. WTA-mediated resistance to antimicrobials, virulence to mammalian cells, interaction with bacteriolytic enzymes and regulation of cell metabolism. We also review the applications of WTAs in these fields that are closely related to the human society, including antibacterial drug discovery targeting WTA biosynthesis, development of vaccines and antibodies regarding WTA-mediated pathogenicity, specific and sensitive detection of pathogens in food using WTAs as a surface epitope and regulation of WTA-related pathways for efficient microbial production of useful compounds. We also point out major problems remaining in these fields, and discuss some possible directions in the future exploration of WTA physiology and applications.
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Affiliation(s)
- Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Jing Han
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Guoli Gong
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Mattheos A G Koffas
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
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23
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Pickering AC, Fitzgerald JR. The Role of Gram-Positive Surface Proteins in Bacterial Niche- and Host-Specialization. Front Microbiol 2020; 11:594737. [PMID: 33193271 PMCID: PMC7658395 DOI: 10.3389/fmicb.2020.594737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/05/2020] [Indexed: 11/25/2022] Open
Abstract
Gram-positive bacterial pathogens have an array of proteins on their cell surface that mediate interactions with the host environment. In particular, bacterial cell wall-associated (CWA) proteins play key roles in both colonization and pathogenesis. Furthermore, some CWA proteins promote specialization for host-species or mediate colonization of specific anatomical niches within a host. In this mini review, we provide examples of the many ways by which major pathogens, such as Staphylococci, Streptococci and Listeria monocytogenes, utilize CWA proteins for both host- and niche-specialization. We describe different biological mechanisms mediated by CWA proteins including: the acquisition of iron from hemoglobin in the bloodstream, adherence to and invasion of host cells, and innate immune evasion through binding to the plasma proteins fibrinogen, immunoglobulin G, and complement. We also discuss the limitations of using animal models for understanding the role of specific CWA proteins in host-specialization and how transformative technologies, such as CRISPR-Cas, offer tremendous potential for developing transgenic models that simulate the host environment of interest. Improved understanding of the role of CWA proteins in niche- or host-specificity will allow the design of new therapeutic approaches which target key host–pathogen interactions underpinning Gram-positive bacterial infections.
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Affiliation(s)
- Amy C Pickering
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh, United Kingdom
| | - J Ross Fitzgerald
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh, United Kingdom
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24
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Hesser AR, Matano LM, Vickery CR, Wood BM, Santiago AG, Morris HG, Do T, Losick R, Walker S. The length of lipoteichoic acid polymers controls Staphylococcus aureus cell size and envelope integrity. J Bacteriol 2020; 202:JB.00149-20. [PMID: 32482719 PMCID: PMC8404710 DOI: 10.1128/jb.00149-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/22/2020] [Indexed: 02/08/2023] Open
Abstract
The opportunistic pathogen Staphylococcus aureus is protected by a cell envelope that is crucial for viability. In addition to peptidoglycan, lipoteichoic acid (LTA) is an especially important component of the S. aureus cell envelope. LTA is an anionic polymer anchored to a glycolipid in the outer leaflet of the cell membrane. It was known that deleting the gene for UgtP, the enzyme that makes this glycolipid anchor, causes cell growth and division defects. In Bacillus subtilis, growth abnormalities from the loss of ugtP have been attributed to both the absence of the encoded protein and to the loss of its products. Here, we show that growth defects in S. aureus ugtP deletion mutants are due to the long, abnormal LTA polymer that is produced when the glycolipid anchor is missing from the outer leaflet of the membrane. Dysregulated cell growth leads to defective cell division, and these phenotypes are corrected by mutations in the LTA polymerase, ltaS, that reduce polymer length. We also show that S. aureus mutants with long LTA are sensitized to cell wall hydrolases, beta-lactam antibiotics, and compounds that target other cell envelope pathways. We conclude that control of LTA polymer length is important for S. aureus physiology and promotes survival under stressful conditions, including antibiotic stress.IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of community- and hospital-acquired infections and is responsible for a large fraction of deaths caused by antibiotic-resistant bacteria. S. aureus is surrounded by a complex cell envelope that protects it from antimicrobial compounds and other stresses. Here we show that controlling the length of an essential cell envelope polymer, lipoteichoic acid, is critical for controlling S. aureus cell size and cell envelope integrity. We also show that genes involved in LTA length regulation are required for resistance to beta-lactam antibiotics in MRSA. The proteins encoded by these genes may be targets for combination therapy with an appropriate beta-lactam.
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Affiliation(s)
- Anthony R Hesser
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Leigh M Matano
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - B McKay Wood
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ace George Santiago
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Heidi G Morris
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Truc Do
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
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25
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Sharma R, Gal L, Garmyn D, Bisaria VS, Sharma S, Piveteau P. Evidence of Biocontrol Activity of Bioinoculants Against a Human Pathogen, Listeria monocytogenes. Front Microbiol 2020; 11:350. [PMID: 32218775 PMCID: PMC7078112 DOI: 10.3389/fmicb.2020.00350] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/17/2020] [Indexed: 11/13/2022] Open
Abstract
Due to rhizodeposits and various microbial interactions, the rhizosphere is an extremely dynamic system, which provides a conductive niche not only for bacteria beneficial to plants but also for those that might pose a potential threat to humans. The importance of bioinoculants as biocontrol agents to combat phytopathogens has been widely recognized. However, little information exists with respect to their role in inhibiting human pathogens in the rhizosphere. The present study is an attempt to understand the impact of an established bacterial consortium, Azotobacter chroococcum, Bacillus megaterium, and Pseudomonas fluorescens, on the survivability of Listeria monocytogenes in the rhizosphere of Cajanus cajan and Festuca arundinacea. An experiment conducted in Hoagland's medium in the presence of C. cajan demonstrated that the presence of bioinoculants impaired growth of L. monocytogenes compared to that observed in their absence. On the other hand, in the presence of F. arundinacea, no significant differences were observed in the population dynamics of L. monocytogenes in the presence or absence of the bioinoculants. Agar plate assay through cross streak method revealed the inhibition of L. monocytogenes by bioinoculants. Potential bioactive compounds were identified by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). These results suggest that agricultural amendments can act as protective agents against human pathogens while enforcing plant growth promotion.
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Affiliation(s)
- Richa Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Laurent Gal
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne – Franche-Comté, Dijon, France
| | - Dominique Garmyn
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne – Franche-Comté, Dijon, France
| | - V. S. Bisaria
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Pascal Piveteau
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne – Franche-Comté, Dijon, France
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26
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Smitten KL, Fairbanks SD, Robertson CC, Bernardino de la Serna J, Foster SJ, Thomas JA. Ruthenium based antimicrobial theranostics - using nanoscopy to identify therapeutic targets and resistance mechanisms in Staphylococcus aureus. Chem Sci 2020; 11:70-79. [PMID: 32110358 PMCID: PMC7012045 DOI: 10.1039/c9sc04710g] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
In previous studies we reported that specific dinuclear RuII complexes are particularly active against pathogenic Gram-negative bacteria and, unusually for this class of compounds, appeared to display lowered activity against Gram-positive bacteria. With the aim of identifying resistance mechanisms specific to Gram-positive bacteria, the uptake and antimicrobial activity of the lead complex against Staphylococcus aureus SH1000 and other isolates, including MRSA was investigated. This revealed differential, strain specific, sensitivity to the complex. Exploiting the inherent luminescent properties of the RuII complex, super-resolution STED nanoscopy was used to image its initial interaction with S. aureus and confirm its cellular internalization. Membrane damage assays and transmission electron microscopy confirm that the complex disrupts the bacterial membrane structure before internalization, which ultimately results in a small amount of DNA damage. A known resistance mechanism against cationic antimicrobials in Gram-positive bacteria involves increased expression of the mprF gene as this results in an accumulation of positively charged lysyl-phosphatidylglycerol on the outer leaflet of the cytoplasmic membrane that electrostatically repel cationic species. Consistent with this model, it was found that an mprF deficient strain was particularly susceptible to treatment with the lead complex. More detailed co-staining studies also revealed that the complex was more active in S. aureus strains missing, or with altered, wall teichoic acids.
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Affiliation(s)
- Kirsty L Smitten
- Department of Chemistry , University of Sheffield , Sheffield S10 2TN , UK . ;
- The Florey Institute and Department of Molecular Biology and Biotechnology , University of Sheffield , S10 2TN , UK
| | - Simon D Fairbanks
- Department of Chemistry , University of Sheffield , Sheffield S10 2TN , UK . ;
| | - Craig C Robertson
- Department of Chemistry , University of Sheffield , Sheffield S10 2TN , UK . ;
| | - Jorge Bernardino de la Serna
- National Heart and Lung Institute , Faculty of Medicine , Imperial College London , South Kensington Campus , London SW7 2AZ , UK
- Research Complex at Harwell , Rutherford Appleton Laboratory , Central Laser Facility , United Kingdom Research and Innovation , OX11 0FA , UK
| | - Simon J Foster
- The Florey Institute and Department of Molecular Biology and Biotechnology , University of Sheffield , S10 2TN , UK
| | - Jim A Thomas
- Department of Chemistry , University of Sheffield , Sheffield S10 2TN , UK . ;
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27
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Coe KA, Lee W, Stone MC, Komazin-Meredith G, Meredith TC, Grad YH, Walker S. Multi-strain Tn-Seq reveals common daptomycin resistance determinants in Staphylococcus aureus. PLoS Pathog 2019; 15:e1007862. [PMID: 31738809 PMCID: PMC6934316 DOI: 10.1371/journal.ppat.1007862] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 12/27/2019] [Accepted: 09/24/2019] [Indexed: 01/30/2023] Open
Abstract
Antibiotic-resistant Staphylococcus aureus remains a leading cause of antibiotic resistance-associated mortality in the United States. Given the reality of multi-drug resistant infections, it is imperative that we establish and maintain a pipeline of new compounds to replace or supplement our current antibiotics. A first step towards this goal is to prioritize targets by identifying the genes most consistently required for survival across the S. aureus phylogeny. Here we report the first direct comparison of multiple strains of S. aureus via transposon sequencing. We show that mutant fitness varies by strain in key pathways, underscoring the importance of using more than one strain to differentiate between core and strain-dependent essential genes. We treated the libraries with daptomycin to assess whether the strain-dependent differences impact pathways important for survival. Despite baseline differences in gene importance, several pathways, including the lipoteichoic acid pathway, consistently promote survival under daptomycin exposure, suggesting core vulnerabilities that can be exploited to resensitize daptomycin-nonsusceptible isolates. We also demonstrate the merit of using transposons with outward-facing promoters capable of overexpressing nearby genes for identifying clinically-relevant gain-of-function resistance mechanisms. Together, the daptomycin vulnerabilities and resistance mechanisms support a mode of action with wide-ranging effects on the cell envelope and cell division. This work adds to a growing body of literature demonstrating the nuanced insights gained by comparing Tn-Seq results across multiple bacterial strains. Antibiotic-resistant Staphylococcus aureus kills thousands of people every year in the United States alone. To stay ahead of the looming threat of multidrug-resistant infections, we must continue to develop new antibiotics and find ways to make our current repertoire of antibiotics more effective, including by finding pairs of compounds that perform best when administered together. In the age of next-generation sequencing, we can now use transposon sequencing to find potential targets for new antibiotics on a genome-wide scale, identified as either essential genes or genes that positively influence survival in the presence of an antibiotic. In this work, we created a compendium of genes that are essential across a range of S. aureus strains, as well as those that are important for growth in the presence of the antibiotic daptomycin. The results will be a resource for researchers working to develop the next generation of antibiotic therapies.
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Affiliation(s)
- Kathryn A. Coe
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Wonsik Lee
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Madeleine C. Stone
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gloria Komazin-Meredith
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
| | - Timothy C. Meredith
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- * E-mail: (TCM); (YHG); (SW)
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (TCM); (YHG); (SW)
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (TCM); (YHG); (SW)
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28
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Wang X, Chen J, Wang W, Jaunarajs A, Wang X. Tryptoline-based benzothiazoles re-sensitize MRSA to β-lactam antibiotics. Bioorg Med Chem 2019; 27:115095. [PMID: 31521461 DOI: 10.1016/j.bmc.2019.115095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 01/03/2023]
Abstract
Resistance-modifying agents (RMAs) offer a promising solution to combat bacterial antibiotic resistance. Here we report the discovery and structure-activity relationships of a new class of RMAs with a novel tryptoline-based benzothiazole scaffold. Our most potent compound in this series (4ad) re-sensitizes multiple MRSA strains to cephalosporins at low concentrations (2 μg/mL) and has low mammalian cytotoxicity with a half growth inhibitory concentration (GI50) > 100 μg/mL in human cervical carcinoma (HeLa) cells. In addition, the same core scaffold with different substitutions also gives good antibacterial activity against MRSA.
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Affiliation(s)
- Xinfeng Wang
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
| | - Jinsen Chen
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
| | - Wei Wang
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
| | - Anna Jaunarajs
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
| | - Xiang Wang
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States.
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29
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Coupri D, Budin-Verneuil A, Hartke A, Benachour A, Léger L, Lequeux T, Pfund E, Verneuil N. Genetic and pharmacological inactivation of d-alanylation of teichoic acids sensitizes pathogenic enterococci to β-lactams. J Antimicrob Chemother 2019; 74:3162-3169. [DOI: 10.1093/jac/dkz322] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/20/2019] [Accepted: 06/28/2019] [Indexed: 01/23/2023] Open
Abstract
AbstractBackgroundEnterococci intrinsically resistant to cephalosporins represent a major cause of healthcare-associated infections, and the emergence of MDR makes therapeutic approaches particularly challenging.ObjectivesTeichoic acids are cell wall glycopolymers present in Gram-positive bacteria. Teichoic acids can be modified by d-alanylation, which requires four proteins encoded by the dltABCD operon. Our objective was to evaluate the Dlt system as a druggable target to treat enterococcal infections.MethodsThe susceptibility of a d-alanylation-deficient strain of Enterococcus faecalis to β-lactam antibiotics individually and/or in combination was analysed. Moreover, a DltA inhibitor was synthesized to test pharmacological inhibition of d-alanylation in vivo and in host using the animal model Galleria mellonella with different clinical isolates of E. faecalis and Enterococcus faecium.ResultsMost cephalosporins used as mono treatment had no impact on survival of the parental strain, but were slightly lethal for the dltA mutant of E. faecalis. Addition of a very low concentration of amoxicillin significantly increased killing of the dltA mutant under these conditions. The most spectacular effect was obtained with a combination of cefotaxime (1 mg/L) and amoxicillin (0.03 mg/L). In the presence of the inhibitor, the WT strain was as susceptible to this combination treatment as the dltA mutant. This molecule associated with the antibiotics was also effective in killing other E. faecalis clinical isolates and successfully prevented death of Galleria infected with either E. faecalis or E. faecium.ConclusionsThe combined results support the potential usefulness of the Dlt system as a target to potentiate antibiotic combination therapies for the treatment of drug-resistant enterococci.
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Affiliation(s)
| | | | - Axel Hartke
- Normandie Université, UNICAEN, U2RM, Caen, France
| | | | - Loïc Léger
- Normandie Université, UNICAEN, U2RM, Caen, France
| | - Thierry Lequeux
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd du Maréchal Juin, Caen, France
| | - Emmanuel Pfund
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique UMR 6507, ENSICAEN, UNICAEN, CNRS, 6 Bd du Maréchal Juin, Caen, France
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30
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Tet38 of Staphylococcus aureus Binds to Host Cell Receptor Complex CD36-Toll-Like Receptor 2 and Protects from Teichoic Acid Synthesis Inhibitors Tunicamycin and Congo Red. Infect Immun 2019; 87:IAI.00194-19. [PMID: 31010815 DOI: 10.1128/iai.00194-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/14/2019] [Indexed: 02/06/2023] Open
Abstract
Using an affinity column retention assay, we showed that the purified Tet38 membrane transporter of Staphylococcus aureus bound specifically to host cell CD36 and to the complex CD36-Toll-like receptor 2 (TLR-2), but not to TLR-2 alone or TLR-2 and S. aureus lipoteichoic acid (LTA). We tested the effect of LTA on the internalization of S. aureus tet38 mutant QT7 versus RN6390 by A549 epithelial cells. Addition of anti-LTA antibody to the bacteria prior to adding to A549 cells reduced internalization of QT7 2-fold compared to that with nonspecific antibody treatment. QT7 internalized 4- to 6-fold less than RN6390 with or without anti-LTA antibody. These data suggested that Tet38 and LTA were independently involved in the invasion process. The wall teichoic acid (WTA) inhibitor tunicamycin had an 8-fold decrease in activity with overexpression of tet38 and a 2-fold increase in activity in QT7 (tet38). Reserpine (an inhibitor of efflux pumps) reduced the effect of tet38 overexpression on tunicamycin resistance 4-fold. In addition, tet38 affected growth in the presence of LTA inhibitor Congo red, with overexpression increasing growth and deletion of tet38 reducing growth. In conclusion, Tet38 contributes to S. aureus invasion of A549 via direct binding to CD36 of the complex CD36-TLR-2, and LTA independently bound to TLR-2. The reduction of tunicamycin resistance in the presence of reserpine and the survival ability of the tet38 overexpressor in the presence of Congo red suggest that Tet38 can also protect the synthesis of LTA and WTA in S. aureus against their inhibitors, possibly functioning as an efflux pump.
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31
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Jeong S, Kim HY, Kim AR, Yun CH, Han SH. Propionate Ameliorates Staphylococcus aureus Skin Infection by Attenuating Bacterial Growth. Front Microbiol 2019; 10:1363. [PMID: 31275281 PMCID: PMC6591440 DOI: 10.3389/fmicb.2019.01363] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023] Open
Abstract
Staphylococcus aureus causes various diseases including skin and soft tissue infections, pneumonia, gastroenteritis, and sepsis. Antibiotic-resistant S. aureus such as methicillin-resistant S. aureus (MRSA) and multidrug-resistant S. aureus is a serious threat in healthcare-associated settings and in the communities. In this study, we investigated the effects of short-chain fatty acids, metabolites produced by commensal bacteria, on the growth of S. aureus both in vitro and in vivo. Sodium propionate (NaP) most potently inhibited the growth of MRSA and multidrug-resistant clinical isolates. Of note, only NaP, but not sodium acetate (NaA) or sodium butyrate (NaB), ameliorated MRSA skin infection, significantly lowering bacterial load, excessive cytokine production, and the size and weight of abscesses approximately by twofold. In addition, interestingly, S. aureus deficient of lipoteichoic acids (LTA) or wall teichoic acids (WTA), which are important in bacterial physiology and antimicrobial susceptibility, was more susceptible to NaP than the wild-type. Furthermore, S. aureus deficient of D-alanine motifs common in LTA and WTA was more susceptible to NaP, its growth being almost completely inhibited. Concordantly, MRSA treated with an inhibitor of D-alanylation on LTA and WTA was more susceptible to NaP, and co-treatment of NaP and a D-alanylation inhibitor further decreased the pathology of MRSA skin infection. Collectively, these results demonstrate that NaP ameliorates MRSA skin infection by attenuating the growth of S. aureus, and suggest an alternative combination treatment strategy against S. aureus infection.
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Affiliation(s)
- Soyoung Jeong
- Department of Oral Microbiology and Immunology, DRI, and BK21 Plus Program, School of Dentistry, Seoul National University, Seoul, South Korea
| | - Hyun Young Kim
- Department of Oral Microbiology and Immunology, DRI, and BK21 Plus Program, School of Dentistry, Seoul National University, Seoul, South Korea
| | - A Reum Kim
- Department of Oral Microbiology and Immunology, DRI, and BK21 Plus Program, School of Dentistry, Seoul National University, Seoul, South Korea
| | - Cheol-Heui Yun
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Seung Hyun Han
- Department of Oral Microbiology and Immunology, DRI, and BK21 Plus Program, School of Dentistry, Seoul National University, Seoul, South Korea
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32
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Sun Q, Wang Y, Fan J, Li Z, Zhang J, Wang L, Fan X, Ji M, Zhu M, Dai J, Ma H, Jin G, Hu Z, Shen H. Association of expression quantitative trait loci for long noncoding RNAs with lung cancer risk in Asians. Mol Carcinog 2019; 58:1303-1313. [DOI: 10.1002/mc.23013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/09/2019] [Accepted: 03/20/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Qi Sun
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Yuzhuo Wang
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Jingyi Fan
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Zhihua Li
- Department of Thoracic SurgeryFirst Affiliated Hospital of Nanjing Medical UniversityNanjing China
| | - Jiahui Zhang
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Lijuan Wang
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Xikang Fan
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Mengmeng Ji
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjing China
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Sambamoorthy G, Sinha H, Raman K. Evolutionary design principles in metabolism. Proc Biol Sci 2019; 286:20190098. [PMID: 30836874 PMCID: PMC6458322 DOI: 10.1098/rspb.2019.0098] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/14/2019] [Indexed: 12/28/2022] Open
Abstract
Microorganisms are ubiquitous and adapt to various dynamic environments to sustain growth. These adaptations accumulate, generating new traits forming the basis of evolution. Organisms adapt at various levels, such as gene regulation, signalling, protein-protein interactions and metabolism. Of these, metabolism forms the integral core of an organism for maintaining the growth and function of a cell. Therefore, studying adaptations in metabolic networks is crucial to understand the emergence of novel metabolic capabilities. Metabolic networks, composed of enzyme-catalysed reactions, exhibit certain repeating paradigms or design principles that arise out of different selection pressures. In this review, we discuss the design principles that are known to exist in metabolic networks, such as functional redundancy, modularity, flux coupling and exaptations. We elaborate on the studies that have helped gain insights highlighting the interplay of these design principles and adaptation. Further, we discuss how evolution plays a role in exploiting such paradigms to enhance the robustness of organisms. Looking forward, we predict that with the availability of ever-increasing numbers of bacterial, archaeal and eukaryotic genomic sequences, novel design principles will be identified, expanding our understanding of these paradigms shaped by varied evolutionary processes.
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Affiliation(s)
- Gayathri Sambamoorthy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
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Wood BM, Santa Maria JP, Matano LM, Vickery CR, Walker S. A partial reconstitution implicates DltD in catalyzing lipoteichoic acid d-alanylation. J Biol Chem 2018; 293:17985-17996. [PMID: 30237166 PMCID: PMC6240853 DOI: 10.1074/jbc.ra118.004561] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/27/2018] [Indexed: 12/19/2022] Open
Abstract
Modifications to the Gram-positive bacterial cell wall play important roles in antibiotic resistance and pathogenesis, but the pathway for the d-alanylation of teichoic acids (DLT pathway), a ubiquitous modification, is poorly understood. The d-alanylation machinery includes two membrane proteins of unclear function, DltB and DltD, which are somehow involved in transfer of d-alanine from a carrier protein inside the cell to teichoic acids on the cell surface. Here, we probed the role of DltD in the human pathogen Staphylococcus aureus using both cell-based and biochemical assays. We first exploited a known synthetic lethal interaction to establish the essentiality of each gene in the DLT pathway for d-alanylation of lipoteichoic acid (LTA) and confirmed this by directly detecting radiolabeled d-Ala-LTA both in cells and in vesicles prepared from mutant strains of S. aureus We developed a partial reconstitution of the pathway by using cell-derived vesicles containing DltB, but no other components of the d-alanylation pathway, and showed that d-alanylation of previously formed lipoteichoic acid in the DltB vesicles requires the presence of purified and reconstituted DltA, DltC, and DltD, but not of the LTA synthase LtaS. Finally, based on the activity of DltD mutants in cells and in our reconstituted system, we determined that Ser-70 and His-361 are essential for d-alanylation activity, and we propose that DltD uses a catalytic dyad to transfer d-alanine to LTA. In summary, we have developed a suite of assays for investigating the bacterial DLT pathway and uncovered a role for DltD in LTA d-alanylation.
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Affiliation(s)
- B McKay Wood
- From the Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115
| | - John P Santa Maria
- From the Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Leigh M Matano
- From the Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Christopher R Vickery
- From the Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Suzanne Walker
- From the Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115.
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35
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Klobucar K, Brown ED. Use of genetic and chemical synthetic lethality as probes of complexity in bacterial cell systems. FEMS Microbiol Rev 2018; 42:4563584. [PMID: 29069427 DOI: 10.1093/femsre/fux054] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/23/2017] [Indexed: 12/22/2022] Open
Abstract
Different conditions and genomic contexts are known to have an impact on gene essentiality and interactions. Synthetic lethal interactions occur when a combination of perturbations, either genetic or chemical, result in a more profound fitness defect than expected based on the effect of each perturbation alone. Synthetic lethality in bacterial systems has long been studied; however, during the past decade, the emerging fields of genomics and chemical genomics have led to an increase in the scale and throughput of these studies. Here, we review the concepts of genomics and chemical genomics in the context of synthetic lethality and their revolutionary roles in uncovering novel biology such as the characterization of genes of unknown function and in antibacterial drug discovery. We provide an overview of the methodologies, examples and challenges of both genetic and chemical synthetic lethal screening platforms. Finally, we discuss how to apply genetic and chemical synthetic lethal approaches to rationalize the synergies of drugs, screen for new and improved antibacterial therapies and predict drug mechanism of action.
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Affiliation(s)
- Kristina Klobucar
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St West, Hamilton, ON L8N 3Z5, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St West, Hamilton, ON L8N 3Z5, Canada
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36
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Abstract
Membrane-bound O-acyltransferases (MBOATs) are a superfamily of integral transmembrane enzymes that are found in all kingdoms of life1. In bacteria, MBOATs modify protective cell-surface polymers. In vertebrates, some MBOAT enzymes-such as acyl-coenzyme A:cholesterol acyltransferase and diacylglycerol acyltransferase 1-are responsible for lipid biosynthesis or phospholipid remodelling2,3. Other MBOATs, including porcupine, hedgehog acyltransferase and ghrelin acyltransferase, catalyse essential lipid modifications of secreted proteins such as Wnt, hedgehog and ghrelin, respectively4-10. Although many MBOAT proteins are important drug targets, little is known about their molecular architecture and functional mechanisms. Here we present crystal structures of DltB, an MBOAT responsible for the D-alanylation of cell-wall teichoic acid in Gram-positive bacteria11-16, both alone and in complex with the D-alanyl donor protein DltC. DltB contains a ring of 11 peripheral transmembrane helices, which shield a highly conserved extracellular structural funnel extending into the middle of the lipid bilayer. The conserved catalytic histidine residue is located at the bottom of this funnel and is connected to the intracellular DltC through a narrow tunnel. Mutation of either the catalytic histidine or the DltC-binding site of DltB abolishes the D-alanylation of lipoteichoic acid and sensitizes the Gram-positive bacterium Bacillus subtilis to cell-wall stress, which suggests cross-membrane catalysis involving the tunnel. Structure-guided sequence comparison among DltB and vertebrate MBOATs reveals a conserved structural core and suggests that MBOATs from different organisms have similar catalytic mechanisms. Our structures provide a template for understanding structure-function relationships in MBOATs and for developing therapeutic MBOAT inhibitors.
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37
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Romaniuk JAH, Cegelski L. Peptidoglycan and Teichoic Acid Levels and Alterations in Staphylococcus aureus by Cell-Wall and Whole-Cell Nuclear Magnetic Resonance. Biochemistry 2018; 57:3966-3975. [PMID: 29806458 PMCID: PMC6309457 DOI: 10.1021/acs.biochem.8b00495] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gram-positive bacteria surround themselves with a multilayered macromolecular cell wall that is essential to cell survival and serves as a major target for antibiotics. The cell wall of Staphylococcus aureus is composed of two major structural components, peptidoglycan (PG) and wall teichoic acid (WTA), together creating a heterogeneous and insoluble matrix that poses a challenge to quantitative compositional analysis. Here, we present 13C cross polarization magic angle spinning solid-state nuclear magnetic resonance (NMR) spectra of intact cell walls, purified PG, and purified WTA. The spectra reveal the clear molecular differences in the two polymers and enable quantification of PG and WTA in isolated cell walls, an attractive alternative to estimating teichoic acid content from a phosphate analysis of completely pyrolyzed cell walls. Furthermore, we discovered that unique PG and WTA spectral signatures could be identified in whole-cell NMR spectra and used to compare PG and WTA levels among intact bacterial cell samples. The distinguishing whole-cell 13C NMR contributions associated with PG include the GlcNAc-MurNAc sugar carbons and glycyl α-carbons. WTA contributes carbons from the phosphoribitol backbone. Distinguishing 15N spectral signatures include glycyl amide nitrogens in PG and the esterified d-alanyl amine nitrogens in WTA. 13C NMR analysis was performed with samples at natural abundance and included 10 whole-cell sample comparisons. Changes consistent with altered PG and WTA content were detected in whole-cell spectra of bacteria harvested at different growth times and in cells treated with tunicamycin. This use of whole-cell NMR provides quantitative parameters of composition in the context of whole-cell activity.
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Affiliation(s)
| | - Lynette Cegelski
- Stanford University, Department of Chemistry, 380 Roth Way, Stanford CA 94305
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38
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Lee W, Do T, Zhang G, Kahne D, Meredith TC, Walker S. Antibiotic Combinations That Enable One-Step, Targeted Mutagenesis of Chromosomal Genes. ACS Infect Dis 2018. [PMID: 29534563 DOI: 10.1021/acsinfecdis.8b00017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Targeted modification of bacterial chromosomes is necessary to understand new drug targets, investigate virulence factors, elucidate cell physiology, and validate results of -omics-based approaches. For some bacteria, reverse genetics remains a major bottleneck to progress in research. Here, we describe a compound-centric strategy that combines new negative selection markers with known positive selection markers to achieve simple, efficient one-step genome engineering of bacterial chromosomes. The method was inspired by the observation that certain nonessential metabolic pathways contain essential late steps, suggesting that antibiotics targeting a late step can be used to select for the absence of genes that control flux into the pathway. Guided by this hypothesis, we have identified antibiotic/counterselectable markers to accelerate reverse engineering of two increasingly antibiotic-resistant pathogens, Staphylococcus aureus and Acinetobacter baumannii. For S. aureus, we used wall teichoic acid biosynthesis inhibitors to select for the absence of tarO and for A. baumannii, we used colistin to select for the absence of lpxC. We have obtained desired gene deletions, gene fusions, and promoter swaps in a single plating step with perfect efficiency. Our method can also be adapted to generate markerless deletions of genes using FLP recombinase. The tools described here will accelerate research on two important pathogens, and the concept we outline can be readily adapted to any organism for which a suitable target pathway can be identified.
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Affiliation(s)
- Wonsik Lee
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Truc Do
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Ge Zhang
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Timothy C. Meredith
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
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39
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Salt-Induced Stress Stimulates a Lipoteichoic Acid-Specific Three-Component Glycosylation System in Staphylococcus aureus. J Bacteriol 2018; 200:JB.00017-18. [PMID: 29632092 DOI: 10.1128/jb.00017-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/03/2018] [Indexed: 01/01/2023] Open
Abstract
Lipoteichoic acid (LTA) in Staphylococcus aureus is a poly-glycerophosphate polymer anchored to the outer surface of the cell membrane. LTA has numerous roles in cell envelope physiology, including regulating cell autolysis, coordinating cell division, and adapting to environmental growth conditions. LTA is often further modified with substituents, including d-alanine and glycosyl groups, to alter cellular function. While the genetic determinants of d-alanylation have been largely defined, the route of LTA glycosylation and its role in cell envelope physiology have remained unknown, in part due to the low levels of basal LTA glycosylation in S. aureus We demonstrate here that S. aureus utilizes a membrane-associated three-component glycosylation system composed of an undecaprenol (Und) N-acetylglucosamine (GlcNAc) charging enzyme (CsbB; SAOUHSC_00713), a putative flippase to transport loaded substrate to the outside surface of the cell (GtcA; SAOUHSC_02722), and finally an LTA-specific glycosyltransferase that adds α-GlcNAc moieties to LTA (YfhO; SAOUHSC_01213). We demonstrate that this system is specific for LTA with no cross recognition of the structurally similar polyribitol phosphate containing wall teichoic acids. We show that while wild-type S. aureus LTA has only a trace of GlcNAcylated LTA under normal growth conditions, amounts are raised upon either overexpressing CsbB, reducing endogenous d-alanylation activity, expressing the cell envelope stress responsive alternative sigma factor SigB, or by exposure to environmental stress-inducing culture conditions, including growth media containing high levels of sodium chloride.IMPORTANCE The role of glycosylation in the structure and function of Staphylococcus aureus lipoteichoic acid (LTA) is largely unknown. By defining key components of the LTA three-component glycosylation pathway and uncovering stress-induced regulation by the alternative sigma factor SigB, the role of N-acetylglucosamine tailoring during adaptation to environmental stresses can now be elucidated. As the dlt and glycosylation pathways compete for the same sites on LTA and induction of glycosylation results in decreased d-alanylation, the interplay between the two modification systems holds implications for resistance to antibiotics and antimicrobial peptides.
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40
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Santiago M, Lee W, Fayad AA, Coe KA, Rajagopal M, Do T, Hennessen F, Srisuknimit V, Müller R, Meredith TC, Walker S. Genome-wide mutant profiling predicts the mechanism of a Lipid II binding antibiotic. Nat Chem Biol 2018; 14:601-608. [PMID: 29662210 PMCID: PMC5964011 DOI: 10.1038/s41589-018-0041-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 02/27/2018] [Indexed: 12/11/2022]
Abstract
Identifying targets of antibacterial compounds remains a challenging step in antibiotic development. We have developed a two-pronged functional genomics approach to predict mechanism of action that uses mutant fitness data from antibiotic-treated transposon libraries containing both upregulation and inactivation mutants. We treated a Staphylococcus aureus transposon library containing 690,000 unique insertions with 32 antibiotics. Upregulation signatures, identified from directional biases in insertions, revealed known molecular targets and resistance mechanisms for the majority of these. Because single gene upregulation does not always confer resistance, we used a complementary machine learning approach to predict mechanism from inactivation mutant fitness profiles. This approach suggested the cell wall precursor Lipid II as the molecular target of the lysocins, a mechanism we have confirmed. We conclude that docking to membrane-anchored Lipid II precedes the selective bacteriolysis that distinguishes these lytic natural products, showing the utility of our approach for nominating antibiotic mechanism of action.
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Affiliation(s)
- Marina Santiago
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Wonsik Lee
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Antoine Abou Fayad
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Kathryn A Coe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Mithila Rajagopal
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Truc Do
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Fabienne Hennessen
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Veerasak Srisuknimit
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.
| | - Timothy C Meredith
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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41
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Vickery CR, Wood BM, Morris HG, Losick R, Walker S. Reconstitution of Staphylococcus aureus Lipoteichoic Acid Synthase Activity Identifies Congo Red as a Selective Inhibitor. J Am Chem Soc 2018; 140:876-879. [PMID: 29300473 PMCID: PMC5856125 DOI: 10.1021/jacs.7b11704] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Lipoteichoic acid (LTA) is an anionic surface polymer that is essential for normal growth of Staphylococcus aureus, making the LTA polymerase, LTA synthase (LtaS), a proposed drug target for combating Staphylococcal infections. LtaS is a polytopic membrane protein with five membrane-spanning helices and an extracellular domain, and it uses phosphatidylglycerol to assemble a glycerol phosphate chain on a glycosylated diacylglycerol membrane anchor. We report here the first reconstitution of LtaS polymerization activity and show that the azo dye Congo red inhibits this enzyme both in vitro and in cells. Related azo dyes and the previously reported LtaS inhibitor 1771 have weak or no in vitro inhibitory activity. Synthetic lethality with mutant strains known to be nonviable in the absence of LTA confirms selective inhibition by Congo red. As the only validated LtaS inhibitor, Congo red can serve as a probe to understand how inhibiting lipoteichoic acid biosynthesis affects cell physiology and may also guide the discovery of more potent inhibitors for use in treating S. aureus infections.
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Affiliation(s)
- Christopher R. Vickery
- Department of Microbiology and Immunobiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - B. McKay Wood
- Department of Microbiology and Immunobiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Heidi G. Morris
- Department of Microbiology and Immunobiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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42
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RgpF Is Required for Maintenance of Stress Tolerance and Virulence in Streptococcus mutans. J Bacteriol 2017; 199:JB.00497-17. [PMID: 28924033 DOI: 10.1128/jb.00497-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 09/12/2017] [Indexed: 02/01/2023] Open
Abstract
Bacterial cell wall dynamics have been implicated as important determinants of cellular physiology, stress tolerance, and virulence. In Streptococcus mutans, the cell wall is composed primarily of a rhamnose-glucose polysaccharide (RGP) linked to the peptidoglycan. Despite extensive studies describing its formation and composition, the potential roles for RGP in S. mutans biology have not been well investigated. The present study characterizes the impact of RGP disruption as a result of the deletion of rgpF, the gene encoding a rhamnosyltransferase involved in the construction of the core polyrhamnose backbone of RGP. The ΔrgpF mutant strain displayed an overall reduced fitness compared to the wild type, with heightened sensitivities to various stress-inducing culture conditions and an inability to tolerate acid challenge. The loss of rgpF caused a perturbation of membrane-associated functions known to be critical for aciduricity, a hallmark of S. mutans acid tolerance. The proton gradient across the membrane was disrupted, and the ΔrgpF mutant strain was unable to induce activity of the F1Fo ATPase in cultures grown under low-pH conditions. Further, the virulence potential of S. mutans was also drastically reduced following the deletion of rgpF The ΔrgpF mutant strain produced significantly less robust biofilms, indicating an impairment in its ability to adhere to hydroxyapatite surfaces. Additionally, the ΔrgpF mutant lost competitive fitness against oral peroxigenic streptococci, and it displayed significantly attenuated virulence in an in vivoGalleria mellonella infection model. Collectively, these results highlight a critical function of the RGP in the maintenance of overall stress tolerance and virulence traits in S. mutansIMPORTANCE The cell wall of Streptococcus mutans, the bacterium most commonly associated with tooth decay, is abundant in rhamnose-glucose polysaccharides (RGP). While these structures are antigenically distinct to S. mutans, the process by which they are formed and the enzymes leading to their construction are well conserved among streptococci. The present study describes the consequences of the loss of RgpF, a rhamnosyltransferase involved in RGP construction. The deletion of rgpF resulted in severe ablation of the organism's overall fitness, culminating in significantly attenuated virulence. Our data demonstrate an important link between the RGP and cell wall physiology of S. mutans, affecting critical features used by the organism to cause disease and providing a potential novel target for inhibiting the pathogenesis of S. mutans.
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43
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Santa Maria JP, Park Y, Yang L, Murgolo N, Altman MD, Zuck P, Adam G, Chamberlin C, Saradjian P, Dandliker P, Boshoff HIM, Barry CE, Garlisi C, Olsen DB, Young K, Glick M, Nickbarg E, Kutchukian PS. Linking High-Throughput Screens to Identify MoAs and Novel Inhibitors of Mycobacterium tuberculosis Dihydrofolate Reductase. ACS Chem Biol 2017; 12:2448-2456. [PMID: 28806050 DOI: 10.1021/acschembio.7b00468] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Though phenotypic and target-based high-throughput screening approaches have been employed to discover new antibiotics, the identification of promising therapeutic candidates remains challenging. Each approach provides different information, and understanding their results can provide hypotheses for a mechanism of action (MoA) and reveal actionable chemical matter. Here, we describe a framework for identifying efficacy targets of bioactive compounds. High throughput biophysical profiling against a broad range of targets coupled with machine learning was employed to identify chemical features with predicted efficacy targets for a given phenotypic screen. We validate the approach on data from a set of 55 000 compounds in 24 historical internal antibacterial phenotypic screens and 636 bacterial targets screened in high-throughput biophysical binding assays. Models were built to reveal the relationships between phenotype, target, and chemotype, which recapitulated mechanisms for known antibacterials. We also prospectively identified novel inhibitors of dihydrofolate reductase with nanomolar antibacterial efficacy against Mycobacterium tuberculosis. Molecular modeling provided structural insight into target-ligand interactions underlying selective killing activity toward mycobacteria over human cells.
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Affiliation(s)
- John P. Santa Maria
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Yumi Park
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Lihu Yang
- Department of Chemistry, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Nicholas Murgolo
- Department of Information & Analytics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Michael D. Altman
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Paul Zuck
- Research Science, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Greg Adam
- Department of Pharmacology, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Chad Chamberlin
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Saradjian
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Dandliker
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Helena I. M. Boshoff
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Clifton E. Barry
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Charles Garlisi
- Department of Pharmacology, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - David B. Olsen
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Katherine Young
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Meir Glick
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Elliott Nickbarg
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter S. Kutchukian
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
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44
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Matano LM, Morris HG, Hesser AR, Martin SES, Lee W, Owens TW, Laney E, Nakaminami H, Hooper D, Meredith TC, Walker S. Antibiotic That Inhibits the ATPase Activity of an ATP-Binding Cassette Transporter by Binding to a Remote Extracellular Site. J Am Chem Soc 2017; 139:10597-10600. [PMID: 28727445 DOI: 10.1021/jacs.7b04726] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibiotic-resistant strains of Staphylococcus aureus pose a major threat to human health and there is an ongoing need for new antibiotics to treat resistant infections. In a high throughput screen (HTS) of 230 000 small molecules designed to identify bioactive wall teichoic acid (WTA) inhibitors, we identified one hit, which was expanded through chemical synthesis into a small panel of potent compounds. We showed that these compounds target TarG, the transmembrane component of the two-component ATP-binding cassette (ABC) transporter TarGH, which exports WTA precursors to the cell surface for attachment to peptidoglycan. We purified, for the first time, a WTA transporter and have reconstituted ATPase activity in proteoliposomes. We showed that this new compound series inhibits TarH-catalyzed ATP hydrolysis even though the binding site maps to TarG near the opposite side of the membrane. These are the first ABC transporter inhibitors shown to block ATPase activity by binding to the transmembrane domain. The compounds have potential as therapeutic agents to treat S. aureus infections, and purification of the transmembrane transporter will enable further development.
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Affiliation(s)
- Leigh M Matano
- Department of Microbiology and Immunobiology, Harvard University , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Heidi G Morris
- Department of Microbiology and Immunobiology, Harvard University , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Anthony R Hesser
- Department of Microbiology and Immunobiology, Harvard University , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Sara E S Martin
- Department of Microbiology and Immunobiology, Harvard University , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Wonsik Lee
- Department of Microbiology and Immunobiology, Harvard University , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Tristan W Owens
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Emaline Laney
- Department of Microbiology and Immunobiology, Harvard University , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Hidemasa Nakaminami
- Division of Infectious Diseases, Massachusetts General Hospital , 55 Fruit Street, Boston, Massachusetts 02114, United States
| | - David Hooper
- Division of Infectious Diseases, Massachusetts General Hospital , 55 Fruit Street, Boston, Massachusetts 02114, United States
| | - Timothy C Meredith
- Department of Biochemistry and Molecular Biology, Pennsylvania State University , 206 South Frear Laboratory, University Park, Pennsylvania 16802, United States
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard University , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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45
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Schaefer K, Matano LM, Qiao Y, Kahne D, Walker S. In vitro reconstitution demonstrates the cell wall ligase activity of LCP proteins. Nat Chem Biol 2017; 13:396-401. [PMID: 28166208 DOI: 10.1038/nchembio.2302] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 12/01/2016] [Indexed: 02/02/2023]
Abstract
Sacculus is a peptidoglycan (PG) matrix that protects bacteria from osmotic lysis. In Gram-positive organisms, the sacculus is densely functionalized with glycopolymers important for survival, but the way in which assembly occurs is not known. In Staphylococcus aureus, three LCP (LytR-CpsA-Psr) family members have been implicated in attaching the major glycopolymer wall teichoic acid (WTA) to PG, but ligase activity has not been demonstrated for these or any other LCP proteins. Using WTA and PG substrates produced chemoenzymatically, we show that all three proteins can transfer WTA precursors to nascent PGs, establishing that LCP proteins are PG-glycopolymer ligases. Although all S. aureus LCP proteins have the capacity to attach WTA to PG, we show that their cellular functions are not redundant. Strains lacking lcpA have phenotypes similar to those of WTA-null strains, indicating that this is the most important WTA ligase. This work provides a foundation for studying how LCP enzymes participate in cell wall assembly.
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Affiliation(s)
- Kaitlin Schaefer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Leigh M Matano
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Yuan Qiao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Suzanne Walker
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
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46
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Antibacterial New Target Discovery: Sentinel Examples, Strategies, and Surveying Success. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2016_31] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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47
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New antibiotics from Nature’s chemical inventory. Bioorg Med Chem 2016; 24:6227-6252. [DOI: 10.1016/j.bmc.2016.09.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023]
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48
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Dos Santos BS, da Silva LCN, da Silva TD, Rodrigues JFS, Grisotto MAG, Correia MTDS, Napoleão TH, da Silva MV, Paiva PMG. Application of Omics Technologies for Evaluation of Antibacterial Mechanisms of Action of Plant-Derived Products. Front Microbiol 2016; 7:1466. [PMID: 27729901 PMCID: PMC5037136 DOI: 10.3389/fmicb.2016.01466] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 09/01/2016] [Indexed: 01/15/2023] Open
Abstract
In the face of increasing bacterial resistance to antibiotics currently in use, the search for new antimicrobial agents has received a boost in recent years, with natural products playing an important role in this field. In fact, several methods have been proposed to investigate the antibacterial activities of natural products. However, given that the ultimate aim is future therapeutic use as novel drugs, it is extremely necessary to elucidate their modes of action, stating the molecular effects in detail, and identifying their targets in the bacterial cell. This review analyzes the application of “omics technologies” to understand the antibacterial mechanisms of bioactive natural products, to stimulate research interest in this area and promote scientific collaborations. Some studies have been specifically highlighted herein by examining their procedures and results (targeted proteins and metabolic pathways). These approaches have the potential to provide new insights into our comprehension of antimicrobial resistance/susceptibility, creating new perspectives for the struggle against bacteria, and leading to the development of novel products in the future.
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Affiliation(s)
- Bruno S Dos Santos
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco Pernambuco, Brazil
| | - Luís C N da Silva
- Programa de Pós-graduação em Biologia Parasitária, Universidade CEUMA Maranhão, Brazil
| | - Túlio D da Silva
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de PernambucoPernambuco, Brazil; Centro de Tecnologias Estratégicas do NordestePernambuco, Brazil
| | - João F S Rodrigues
- Programa de Pós-graduação em Biologia Parasitária, Universidade CEUMA Maranhão, Brazil
| | - Marcos A G Grisotto
- Programa de Pós-graduação em Biologia Parasitária, Universidade CEUMAMaranhão, Brazil; Instituto Florence de Ensino SuperiorMaranhão, Brazil
| | - Maria T Dos Santos Correia
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco Pernambuco, Brazil
| | - Thiago H Napoleão
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco Pernambuco, Brazil
| | - Márcia V da Silva
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco Pernambuco, Brazil
| | - Patrícia M G Paiva
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco Pernambuco, Brazil
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49
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Zhu Y, Cleaver L, Wang W, Podoll JD, Walls S, Jolly A, Wang X. Tetracyclic indolines as a novel class of β-lactam-selective resistance-modifying agent for MRSA. Eur J Med Chem 2016; 125:130-142. [PMID: 27657810 DOI: 10.1016/j.ejmech.2016.09.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/04/2016] [Accepted: 09/09/2016] [Indexed: 01/11/2023]
Abstract
Antibiotic-resistant bacterial infections have seen a marked increase in recent years, while antibiotic discovery has waned. Resistance-modifying agents (RMA) offer an intriguing alternative strategy to fight against resistant bacteria. Here we report the discovery, antibiotic profiling, and structure-activity relationships of a novel class of RMAs, tetracyclic indolines. These selectively potentiate β-lactam antibiotics in methicillin-resistant Staphylococcus aureus (MRSA) without antibacterial or β-lactamase inhibitory activity on their own. The most potent analogue, 6a, showed strong potentiation of amoxicillin/clavulanic acid in a variety of hospital-acquired and community-acquired MRSA strains with low mammalian toxicity. These compounds may be further developed to extend the clinic life span of β-lactam antibiotics.
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Affiliation(s)
- Yugen Zhu
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Lakota Cleaver
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Jessica D Podoll
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Shane Walls
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Austin Jolly
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Xiang Wang
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
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50
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Biofilms 2015: Multidisciplinary Approaches Shed Light into Microbial Life on Surfaces. J Bacteriol 2016; 198:2553-63. [PMID: 26977109 DOI: 10.1128/jb.00156-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The 7th ASM Conference on Biofilms was held in Chicago, Illinois, from 24 to 29 October 2015. The conference provided an international forum for biofilm researchers across academic and industry platforms, and from different scientific disciplines, to present and discuss new findings and ideas. The meeting covered a wide range of topics, spanning environmental sciences, applied biology, evolution, ecology, physiology, and molecular biology of the biofilm lifestyle. This report summarizes the presentations with regard to emerging biofilm-related themes.
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