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Gyger J, Torrens G, Cava F, Bernhardt TG, Fumeaux C. A potential space-making role in cell wall biogenesis for SltB1and DacB revealed by a beta-lactamase induction phenotype in Pseudomonas aeruginosa. mBio 2024; 15:e0141924. [PMID: 38920394 PMCID: PMC11253642 DOI: 10.1128/mbio.01419-24] [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: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024] Open
Abstract
Pseudomonas aeruginosa encodes the beta-lactamase AmpC, which promotes resistance to beta-lactam antibiotics. Expression of ampC is induced by anhydro-muropeptides (AMPs) released from the peptidoglycan (PG) cell wall upon beta-lactam treatment. AmpC can also be induced via genetic inactivation of PG biogenesis factors such as the endopeptidase DacB that cleaves PG crosslinks. Mutants in dacB occur in beta-lactam-resistant clinical isolates of P. aeruginosa, but it has remained unclear why DacB inactivation promotes ampC induction. Similarly, the inactivation of lytic transglycosylase (LT) enzymes such as SltB1 that cut PG glycans has also been associated with ampC induction and beta-lactam resistance. Given that LT enzymes are capable of producing AMP products that serve as ampC inducers, this latter observation has been especially difficult to explain. Here, we show that ampC induction in sltB1 or dacB mutants requires another LT enzyme called MltG. In Escherichia coli, MltG has been implicated in the degradation of nascent PG strands produced upon beta-lactam treatment. Accordingly, in P. aeruginosa sltB1 and dacB mutants, we detected the MltG-dependent production of pentapeptide-containing AMP products that are signatures of nascent PG degradation. Our results therefore support a model in which SltB1 and DacB use their PG-cleaving activity to open space in the PG matrix for the insertion of new material. Thus, their inactivation mimics low-level beta-lactam treatment by reducing the efficiency of new PG insertion into the wall, causing the degradation of some nascent PG material by MltG to produce the ampC-inducing signal. IMPORTANCE Inducible beta-lactamases like the ampC system of Pseudomonas aeruginosa are a common determinant of beta-lactam resistance among gram-negative bacteria. The regulation of ampC is elegantly tuned to detect defects in cell wall synthesis caused by beta-lactam drugs. Studies of mutations causing ampC induction in the absence of drug therefore promise to reveal new insights into the process of cell wall biogenesis in addition to aiding our understanding of how resistance to beta-lactam antibiotics arises in the clinic. In this study, the ampC induction phenotype for mutants lacking a glycan-cleaving enzyme or an enzyme that cuts cell wall crosslinks was used to uncover a potential role for these enzymes in making space in the wall matrix for the insertion of new material during cell growth.
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Affiliation(s)
- Joël Gyger
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gabriel Torrens
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Umea, Sweden
- Department of Molecular Biology, Science for Life Laboratory (SciLifeLab), Umeå University, Umeå, Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Umea, Sweden
- Department of Molecular Biology, Science for Life Laboratory (SciLifeLab), Umeå University, Umeå, Sweden
| | - Thomas G. Bernhardt
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Coralie Fumeaux
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
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2
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Li B, Srivastava S, Shaikh M, Mereddy G, Garcia MR, Shah A, Ofori-Anyinam N, Chu T, Cheney N, Yang JH. Bioenergetic stress potentiates antimicrobial resistance and persistence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603336. [PMID: 39026737 PMCID: PMC11257553 DOI: 10.1101/2024.07.12.603336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Antimicrobial resistance (AMR) is a global health crisis and there is an urgent need to better understand AMR mechanisms. Antibiotic treatment alters several aspects of bacterial physiology, including increased ATP utilization, carbon metabolism, and reactive oxygen species (ROS) formation. However, how the "bioenergetic stress" induced by increased ATP utilization affects treatment outcomes is unknown. Here we utilized a synthetic biology approach to study the direct effects of bioenergetic stress on antibiotic efficacy. We engineered a genetic system that constitutively hydrolyzes ATP or NADH in Escherichia coli. We found that bioenergetic stress potentiates AMR evolution via enhanced ROS production, mutagenic break repair, and transcription-coupled repair. We also find that bioenergetic stress potentiates antimicrobial persistence via potentiated stringent response activation. We propose a unifying model that antibiotic-induced antimicrobial resistance and persistence is caused by antibiotic-induced. This has important implications for preventing or curbing the spread of AMR infections.
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3
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Son JE, Park SH, Choi U, Lee CR. Lytic transglycosylase repertoire diversity enables intrinsic antibiotic resistance and daughter cell separation in Escherichia coli under acidic stress. Antimicrob Agents Chemother 2024; 68:e0037224. [PMID: 38884456 PMCID: PMC11232391 DOI: 10.1128/aac.00372-24] [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: 03/07/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
Peptidoglycan (PG) is an important architectural element that imparts physical toughness and rigidity to the bacterial envelope. It is also a dynamic structure that undergoes continuous turnover or autolysis. Escherichia coli possesses redundant PG degradation enzymes responsible for PG turnover; however, the advantage afforded by the existence of numerous PG degradation enzymes remains incompletely understood. In this study, we elucidated the physiological roles of MltE and MltC, members of the lytic transglycosylase (LTG) family that catalyze the cleavage of glycosidic bonds between disaccharide subunits within PG strands. MltE and MltC are acidic LTGs that exhibit increased enzymatic activity and protein levels under acidic pH conditions, respectively, and deletion of these two LTGs results in a pronounced growth defect at acidic pH. Furthermore, inactivation of these two LTGs induces increased susceptibility at acidic pH against various antibiotics, particularly vancomycin, which seems to be partially caused by elevated membrane permeability. Intriguingly, inactivation of these LTGs induces a chaining morphology, indicative of daughter cell separation defects, only under acidic pH conditions. Simultaneous deletion of PG amidases, known contributors to daughter cell separation, exacerbates the chaining phenotype at acidic pH. This suggests that the two LTGs may participate in the cleavage of glycan strands between daughter cells under acidic pH conditions. Collectively, our findings highlight the role of LTG repertoire diversity in facilitating bacterial survival and antibiotic resistance under stressful conditions.
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Affiliation(s)
- Ji Eun Son
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Si Hyoung Park
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Umji Choi
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
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4
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Jang H, Kim CM, Hong E, Park HH. Fully closed conformation of penicillin-binding protein revealed by structure of PBP2 from Acinetobacter baumannii. Biochem Biophys Res Commun 2024; 729:150368. [PMID: 38986258 DOI: 10.1016/j.bbrc.2024.150368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Penicillin-binding protein 2 (PBP2), a vital protein involved in bacterial cell-wall synthesis, serves a target for β-lactam antibiotics. Acinetobacter baumannii is a pathogen notorious for multidrug resistance; therefore, exploration of PBPs is pivotal in the development of new antimicrobial strategies. In this study, the tertiary structure of PBP2 from A. baumannii (abPBP2) was elucidated using X-ray crystallography. The structural analysis demonstrated notable movement in the head domain, potentially critical for its glycosyltransferase function, suggesting that abPBP2 assumes a fully closed conformation. Our findings offer valuable information for developing novel antimicrobial agents targeting abPBP2 that are applicable in combating multidrug-resistant infections.
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Affiliation(s)
- Hyunseok Jang
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Chang Min Kim
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea.
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5
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Singh PP, Pandey G, Murti Y, Gairola J, Mahajan S, Kandhari H, Tivari S, Srivastava V. Light-driven photocatalysis as an effective tool for degradation of antibiotics. RSC Adv 2024; 14:20492-20515. [PMID: 38946773 PMCID: PMC11208907 DOI: 10.1039/d4ra03431g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/22/2024] [Indexed: 07/02/2024] Open
Abstract
Antibiotic contamination has become a severe issue and a dangerous concern to the environment because of large release of antibiotic effluent into terrestrial and aquatic ecosystems. To try and solve these issues, a plethora of research on antibiotic withdrawal has been carried out. Recently photocatalysis has received tremendous attention due to its ability to remove antibiotics from aqueous solutions in a cost-effective and environmentally friendly manner with few drawbacks compared to traditional photocatalysts. Considerable attention has been focused on developing advanced visible light-driven photocatalysts in order to address these problems. This review provides an overview of recent developments in the field of photocatalytic degradation of antibiotics, including the doping of metals and non-metals into ultraviolet light-driven photocatalysts, the formation of new semiconductor photocatalysts, the advancement of heterojunction photocatalysts, and the building of surface plasmon resonance-enhanced photocatalytic systems.
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Affiliation(s)
- Praveen P Singh
- Department of Chemistry, United College of Engineering & Research Prayagraj U.P.-211010 India
| | - Geetika Pandey
- Department of Physics, Faculty of Science, United University Prayagraj-211012 India
| | - Yogesh Murti
- Institute of Pharmaceutical Research, GLA University Mathura-281406 India
| | - Jagriti Gairola
- School of Pharmacy, Graphic Era Hill University Clement Town Dehradun 248002 Uttarakhand India
- Department of Allied Sciences, Graphic Era (Deemed to be University) Clement Town Dehradun 248002 Uttarakhand India
| | - Shriya Mahajan
- Centre of Research Impact and Outcome, Chitkara University Rajpura-140417 Punjab India
| | - Harsimrat Kandhari
- Chitkara Centre for Research and Development, Chitkara University Himachal Pradesh-174103 India
| | - Shraddha Tivari
- Department of Chemistry, CMP Degree College, University of Allahabad Prayagraj U.P.-211002 India
| | - Vishal Srivastava
- Department of Chemistry, CMP Degree College, University of Allahabad Prayagraj U.P.-211002 India
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6
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Perez AJ, Lamanna MM, Bruce KE, Touraev MA, Page JE, Shaw SL, Tsui HCT, Winkler ME. Elongasome core proteins and class A PBP1a display zonal, processive movement at the midcell of Streptococcus pneumoniae. Proc Natl Acad Sci U S A 2024; 121:e2401831121. [PMID: 38875147 PMCID: PMC11194595 DOI: 10.1073/pnas.2401831121] [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: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 06/16/2024] Open
Abstract
Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus), have two spatially separated peptidoglycan (PG) synthase nanomachines that locate zonally to the midcell of dividing cells. The septal PG synthase bPBP2x:FtsW closes the septum of dividing pneumococcal cells, whereas the elongasome located on the outer edge of the septal annulus synthesizes peripheral PG outward. We showed previously by sm-TIRFm that the septal PG synthase moves circumferentially at midcell, driven by PG synthesis and not by FtsZ treadmilling. The pneumococcal elongasome consists of the PG synthase bPBP2b:RodA, regulators MreC, MreD, and RodZ, but not MreB, and genetically associated proteins Class A aPBP1a and muramidase MpgA. Given its zonal location separate from FtsZ, it was of considerable interest to determine the dynamics of proteins in the pneumococcal elongasome. We found that bPBP2b, RodA, and MreC move circumferentially with the same velocities and durations at midcell, driven by PG synthesis. However, outside of the midcell zone, the majority of these elongasome proteins move diffusively over the entire surface of cells. Depletion of MreC resulted in loss of circumferential movement of bPBP2b, and bPBP2b and RodA require each other for localization and circumferential movement. Notably, a fraction of aPBP1a molecules also moved circumferentially at midcell with velocities similar to those of components of the core elongasome, but for shorter durations. Other aPBP1a molecules were static at midcell or diffusing over cell bodies. Last, MpgA displayed nonprocessive, subdiffusive motion that was largely confined to the midcell region and less frequently detected over the cell body.
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Affiliation(s)
- Amilcar J. Perez
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Melissa M. Lamanna
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Kevin E. Bruce
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Marc A. Touraev
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Julia E. Page
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Sidney L. Shaw
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | | | - Malcolm E. Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
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Brissac T, Guyonnet C, Sadouni A, Hernández-Montoya A, Jacquemet E, Legendre R, Sismeiro O, Trieu-Cuot P, Lanotte P, Tazi A, Firon A. Coordinated regulation of osmotic imbalance by c-di-AMP shapes ß-lactam tolerance in Group B Streptococcus. MICROLIFE 2024; 5:uqae014. [PMID: 38993744 PMCID: PMC11238645 DOI: 10.1093/femsml/uqae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 07/13/2024]
Abstract
Streptococcus agalactiae is among the few pathogens that have not developed resistance to ß-lactam antibiotics despite decades of clinical use. The molecular basis of this long-lasting susceptibility has not been investigated, and it is not known whether specific mechanisms constrain the emergence of resistance. In this study, we first report ß-lactam tolerance due to the inactivation of the c-di-AMP phosphodiesterase GdpP. Mechanistically, tolerance depends on antagonistic regulation by the repressor BusR, which is activated by c-di-AMP and negatively regulates ß-lactam susceptibility through the BusAB osmolyte transporter and the AmaP/Asp23/GlsB cell envelope stress complex. The BusR transcriptional response is synergistic with the simultaneous allosteric inhibition of potassium and osmolyte transporters by c-di-AMP, which individually contribute to low-level ß-lactam tolerance. Genome-wide transposon mutagenesis confirms the role of GdpP and highlights functional interactions between a lysozyme-like hydrolase, the KhpAB RNA chaperone and the protein S immunomodulator in the response of GBS to ß-lactam. Overall, we demonstrate that c-di-AMP acts as a turgor pressure rheostat, coordinating an integrated response at the transcriptional and post-translational levels to cell wall weakening caused by ß-lactam activity, and reveal additional mechanisms that could foster resistance.
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Affiliation(s)
- Terry Brissac
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Cécile Guyonnet
- Université Paris Cité, Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique UMR8104, Team Bacteria and Perinatality, 75015, Paris, France
- Department of Bacteriology, French National Reference Center for Streptococci, Assistance Publique-Hôpitaux de Paris Hôpitaux Universitaires Paris Centre, Hôpital Cochin, 75005, Paris, France
- Fédération Hospitalo-Universitaire Fighting Prematurity, 75005, Paris, France
| | - Aymane Sadouni
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Ariadna Hernández-Montoya
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Elise Jacquemet
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015 Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015 Paris, France
| | - Odile Sismeiro
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Patrick Trieu-Cuot
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Philippe Lanotte
- Université de Tours, INRAE, UMR 1282 ISP, 3700, Tours, France
- CHRU de Tours, Service de Bactériologie-Virologie, 37044, Tours, France
| | - Asmaa Tazi
- Université Paris Cité, Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique UMR8104, Team Bacteria and Perinatality, 75015, Paris, France
- Department of Bacteriology, French National Reference Center for Streptococci, Assistance Publique-Hôpitaux de Paris Hôpitaux Universitaires Paris Centre, Hôpital Cochin, 75005, Paris, France
- Fédération Hospitalo-Universitaire Fighting Prematurity, 75005, Paris, France
| | - Arnaud Firon
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
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8
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Romano KP, Bagnall J, Warrier T, Sullivan J, Ferrara K, Orzechowski M, Nguyen P, Raines K, Livny J, Shoresh N, Hung D. Perturbation-Specific Transcriptional Mapping for unbiased target elucidation of antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.590978. [PMID: 38712067 PMCID: PMC11071498 DOI: 10.1101/2024.04.25.590978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The rising prevalence of antibiotic resistance threatens human health. While more sophisticated strategies for antibiotic discovery are being developed, target elucidation of new chemical entities remains challenging. In the post-genomic era, expression profiling can play an important role in mechanism-of-action (MOA) prediction by reporting on the cellular response to perturbation. However, the broad application of transcriptomics has yet to fulfill its promise of transforming target elucidation due to challenges in identifying the most relevant, direct responses to target inhibition. We developed an unbiased strategy for MOA prediction, called Perturbation-Specific Transcriptional Mapping (PerSpecTM), in which large-throughput expression profiling of wildtype or hypomorphic mutants, depleted for essential targets, enables a computational strategy to address this challenge. We applied PerSpecTM to perform reference-based MOA prediction based on the principle that similar perturbations, whether chemical or genetic, will elicit similar transcriptional responses. Using this approach, we elucidated the MOAs of three new molecules with activity against Pseudomonas aeruginosa by comparing their expression profiles to those of a reference set of antimicrobial compounds with known MOAs. We also show that transcriptional responses to small molecule inhibition resemble those resulting from genetic depletion of essential targets by CRISPRi by PerSpecTM, demonstrating proof-of-concept that correlations between expression profiles of small molecule and genetic perturbations can facilitate MOA prediction when no chemical entities exist to serve as a reference. Empowered by PerSpecTM, this work lays the foundation for an unbiased, readily scalable, systematic reference-based strategy for MOA elucidation that could transform antibiotic discovery efforts.
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9
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Wang W, Wang H, Zhang Z, Li W, Yin X, Long Y. Dual RNA sequencing during Trichoderma harzianum-Phytophthora capsici interaction reveals multiple biological processes involved in the inhibition and highlights the cell wall as a potential target. PEST MANAGEMENT SCIENCE 2024. [PMID: 38742618 DOI: 10.1002/ps.8160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Phytophthora capsici is a destructive oomycete pathogen, causing huge economic losses for agricultural production. The genus Trichoderma represents one of the most extensively researched categories of biocontrol agents, encompassing a diverse array of effective strains. The commercial biocontrol agent Trichoderma harzianum strain T-22 exhibits pronounced biocontrol effects against many plant pathogens, but its activity against P. capsici is not known. RESULTS T. harzianum T-22 significantly inhibited the growth of P. capsici mycelia and the culture filtrate of T-22 induced lysis of P. capsici zoospores. Electron microscopic analyses indicated that T-22 significantly modulated the ultrastructural composition of P. capsici, with a severe impact on the cell wall integrity. Dual RNA sequencing revealed multiple biological processes involved in the inhibition during the interaction between these two microorganisms. In particular, a marked upregulation of genes was identified in T. harzianum that are implicated in cell wall degradation or disruption. Concurrently, the presence of T. harzianum appeared to potentiate the susceptibility of P. capsici to cell wall biosynthesis inhibitors such as mandipropamid and dimethomorph. Further investigations showed that mandipropamid and dimethomorph could strongly inhibit the growth and development of P. capsici but had no impact on T. harzianum even at high concentrations, demonstrating the feasibility of combining T. harzianum and these cell wall synthesis inhibitors to combat P. capsici. CONCLUSION These findings provided enhanced insights into the biocontrol mechanisms against P. capsici with T. harzianum and evidenced compatibility between specific biological and chemical control strategies. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Weizhen Wang
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, People's Republic of China
| | - Haidong Wang
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, People's Republic of China
| | - Zhuzhu Zhang
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, People's Republic of China
| | - Wenzhi Li
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, People's Republic of China
| | - Xianhui Yin
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, People's Republic of China
| | - Youhua Long
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, People's Republic of China
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10
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Tao Y, Zheng D, Zou W, Guo T, Liao G, Zhou W. Targeting the cysteine biosynthesis pathway in microorganisms: Mechanism, structure, and drug discovery. Eur J Med Chem 2024; 271:116461. [PMID: 38691891 DOI: 10.1016/j.ejmech.2024.116461] [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: 02/01/2024] [Revised: 04/16/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
Owing to the global health crisis of resistant pathogenic infections, researchers are emphasizing the importance of novel prevention and control strategies. Existing antimicrobial drugs predominantly target a few pathways, and their widespread use has pervasively increased drug resistance. Therefore, it is imperative to develop new antimicrobial drugs with novel targets and chemical structures. The de novo cysteine biosynthesis pathway, one of the microbial metabolic pathways, plays a crucial role in pathogenicity and drug resistance. This pathway notably differs from that in humans, thereby representing an unexplored target for developing antimicrobial drugs. Herein, we have presented an overview of cysteine biosynthesis pathways and their roles in the pathogenicity of various microorganisms. Additionally, we have investigated the structure and function of enzymes involved in these pathways as well as have discussed drug design strategies and structure-activity relationships of the enzyme inhibitors. This review provides valuable insights for developing novel antimicrobials and offers new avenues to combat drug resistance.
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Affiliation(s)
- Ying Tao
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Dandan Zheng
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Wei Zou
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Ting Guo
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Guojian Liao
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China.
| | - Wei Zhou
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China.
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11
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Perez AJ, Lamanna MM, Bruce KE, Touraev MA, Page JE, Shaw SL, Tsui HCT, Winkler ME. Elongasome core proteins and class A PBP1a display zonal, processive movement at the midcell of Streptococcus pneumoniae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575112. [PMID: 38328058 PMCID: PMC10849506 DOI: 10.1101/2024.01.10.575112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus), have two spatially separated peptidoglycan (PG) synthase nanomachines that locate zonally to the midcell of dividing cells. The septal PG synthase bPBP2x:FtsW closes the septum of dividing pneumococcal cells, whereas the elongasome located on the outer edge of the septal annulus synthesizes peripheral PG outward. We showed previously by sm-TIRFm that the septal PG synthase moves circumferentially at midcell, driven by PG synthesis and not by FtsZ treadmilling. The pneumococcal elongasome consists of the PG synthase bPBP2b:RodA, regulators MreC, MreD, and RodZ, but not MreB, and genetically associated proteins Class A aPBP1a and muramidase MpgA. Given its zonal location separate from FtsZ, it was of considerable interest to determine the dynamics of proteins in the pneumococcal elongasome. We found that bPBP2b, RodA, and MreC move circumferentially with the same velocities and durations at midcell, driven by PG synthesis. However, outside of the midcell zone, the majority of these elongasome proteins move diffusively over the entire surface of cells. Depletion of MreC resulted in loss of circumferential movement of bPBP2b, and bPBP2b and RodA require each other for localization and circumferential movement. Notably, a fraction of aPBP1a molecules also moved circumferentially at midcell with velocities similar to those of components of the core elongasome, but for shorter durations. Other aPBP1a molecules were static at midcell or diffusing over cell bodies. Last, MpgA displayed non-processive, subdiffusive motion that was largely confined to the midcell region and less frequently detected over the cell body.
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12
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Marbun KT, Sugata M, Purnomo JS, Dikson, Mudana SO, Jan TT, Jo J. Genomic Characterization and Safety Assessment of Bifidobacterium breve BS2-PB3 as Functional Food. J Microbiol Biotechnol 2024; 34:871-879. [PMID: 38494884 DOI: 10.4014/jmb.2311.11031] [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: 11/21/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 03/19/2024]
Abstract
Our group had isolated Bifidobacterium breve strain BS2-PB3 from human breast milk. In this study, we sequenced the whole genome of B. breve BS2-PB3, and with a focus on its safety profile, various probiotic characteristics (presence of antibiotic resistance genes, virulence factors, and mobile elements) were then determined through bioinformatic analyses. The antibiotic resistance profile of B. breve BS2-PB3 was also evaluated. The whole genome of B. breve BS2-PB3 consisted of 2,268,931 base pairs with a G-C content of 58.89% and 2,108 coding regions. The average nucleotide identity and whole-genome phylogenetic analyses supported the classification of B. breve BS2-PB3. According to our in silico assessment, B. breve BS2-PB3 possesses antioxidant and immunomodulation properties in addition to various genes related to the probiotic properties of heat, cold, and acid stress, bile tolerance, and adhesion. Antibiotic susceptibility was evaluated using the Kirby-Bauer disk-diffusion test, in which the minimum inhibitory concentrations for selected antibiotics were subsequently tested using the Epsilometer test. B. breve BS2-PB3 only exhibited selected resistance phenotypes, i.e., to mupirocin (minimum inhibitory concentration/MIC >1,024 μg/ml), sulfamethoxazole (MIC >1,024 μg/ml), and oxacillin (MIC >3 μg/ml). The resistance genes against those antibiotics, i.e., ileS, mupB, sul4, mecC and ramA, were detected within its genome as well. While no virulence factor was detected, four insertion sequences were identified within the genome but were located away from the identified antibiotic resistance genes. In conclusion, B. breve BS2-PB3 demonstrated a sufficient safety profile, making it a promising candidate for further development as a potential functional food.
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Affiliation(s)
- Kristin Talia Marbun
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Marcelia Sugata
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Jonathan Suciono Purnomo
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Dikson
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Samuel Owen Mudana
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Tan Tjie Jan
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Juandy Jo
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
- Mochtar Riady Institute for Nanotechnology, Tangerang 15811, Indonesia
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13
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Sang M, Feng P, Chi LP, Zhang W. The biosynthetic logic and enzymatic machinery of approved fungi-derived pharmaceuticals and agricultural biopesticides. Nat Prod Rep 2024; 41:565-603. [PMID: 37990930 DOI: 10.1039/d3np00040k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Covering: 2000 to 2023The kingdom Fungi has become a remarkably valuable source of structurally complex natural products (NPs) with diverse bioactivities. Since the revolutionary discovery and application of the antibiotic penicillin from Penicillium, a number of fungi-derived NPs have been developed and approved into pharmaceuticals and pesticide agents using traditional "activity-guided" approaches. Although emerging genome mining algorithms and surrogate expression hosts have brought revolutionary approaches to NP discovery, the time and costs involved in developing these into new drugs can still be prohibitively high. Therefore, it is essential to maximize the utility of existing drugs by rational design and systematic production of new chemical structures based on these drugs by synthetic biology. To this purpose, there have been great advances in characterizing the diversified biosynthetic gene clusters associated with the well-known drugs and in understanding the biosynthesis logic mechanisms and enzymatic transformation processes involved in their production. We describe advances made in the heterogeneous reconstruction of complex NP scaffolds using fungal polyketide synthases (PKSs), non-ribosomal peptide synthetases (NRPSs), PKS/NRPS hybrids, terpenoids, and indole alkaloids and also discuss mechanistic insights into metabolic engineering, pathway reprogramming, and cell factory development. Moreover, we suggest pathways for expanding access to the fungal chemical repertoire by biosynthesis of representative family members via common platform intermediates and through the rational manipulation of natural biosynthetic machineries for drug discovery.
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Affiliation(s)
- Moli Sang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Peiyuan Feng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Lu-Ping Chi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Wei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
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14
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Hsu TW, Fang JM. Advances and prospects of analytic methods for bacterial transglycosylation and inhibitor discovery. Analyst 2024; 149:2204-2222. [PMID: 38517346 DOI: 10.1039/d3an01968c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
The cell wall is essential for bacteria to maintain structural rigidity and withstand external osmotic pressure. In bacteria, the cell wall is composed of peptidoglycan. Lipid II is the basic unit for constructing highly cross-linked peptidoglycan scaffolds. Transglycosylase (TGase) is the initiating enzyme in peptidoglycan synthesis that catalyzes the ligation of lipid II moieties into repeating GlcNAc-MurNAc polysaccharides, followed by transpeptidation to generate cross-linked structures. In addition to the transglycosylases in the class-A penicillin-binding proteins (aPBPs), SEDS (shape, elongation, division and sporulation) proteins are also present in most bacteria and play vital roles in cell wall renewal, elongation, and division. In this review, we focus on the latest analytical methods including the use of radioactive labeling, gel electrophoresis, mass spectrometry, fluorescence labeling, probing undecaprenyl pyrophosphate, fluorescence anisotropy, ligand-binding-induced tryptophan fluorescence quenching, and surface plasmon resonance to evaluate TGase activity in cell wall formation. This review also covers the discovery of TGase inhibitors as potential antibacterial agents. We hope that this review will give readers a better understanding of the chemistry and basic research for the development of novel antibiotics.
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Affiliation(s)
- Tse-Wei Hsu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
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15
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Elfadadny A, Ragab RF, AlHarbi M, Badshah F, Ibáñez-Arancibia E, Farag A, Hendawy AO, De los Ríos-Escalante PR, Aboubakr M, Zakai SA, Nageeb WM. Antimicrobial resistance of Pseudomonas aeruginosa: navigating clinical impacts, current resistance trends, and innovations in breaking therapies. Front Microbiol 2024; 15:1374466. [PMID: 38646632 PMCID: PMC11026690 DOI: 10.3389/fmicb.2024.1374466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/05/2024] [Indexed: 04/23/2024] Open
Abstract
Pseudomonas aeruginosa, a Gram-negative bacterium, is recognized for its adaptability and opportunistic nature. It poses a substantial challenge in clinical settings due to its complicated antibiotic resistance mechanisms, biofilm formation, and capacity for persistent infections in both animal and human hosts. Recent studies revealed a potential zoonotic transmission of P. aeruginosa between animals, the environment, and human populations which highlights awareness of this microbe. Implementation of the One Health approach, which underscores the connection between human, animal, and environmental health, we aim to offer a comprehensive perspective on the current landscape of P. aeruginosa management. This review presents innovative strategies designed to counteract P. aeruginosa infections. Traditional antibiotics, while effective in many cases, are increasingly compromised by the development of multidrug-resistant strains. Non-antibiotic avenues, such as quorum sensing inhibition, phage therapy, and nanoparticle-based treatments, are emerging as promising alternatives. However, their clinical application encounters obstacles like cost, side effects, and safety concerns. Effectively addressing P. aeruginosa infections necessitates persistent research efforts, advancements in clinical development, and a comprehension of host-pathogen interactions to deal with this resilient pathogen.
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Affiliation(s)
- Ahmed Elfadadny
- Laboratory of Internal Medicine, Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Japan
- Department of Internal Medicine, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Rokaia F. Ragab
- Laboratory of Internal Medicine, Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Japan
- Department of Biochemistry, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Maha AlHarbi
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Farhad Badshah
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Eliana Ibáñez-Arancibia
- PhD Program in Sciences Mentioning Applied Molecular and Cell Biology, La Frontera University, Temuco, Chile
- Laboratory of Engineering, Biotechnology and Applied Biochemistry – LIBBA, Department of Chemical Engineering, Faculty of Engineering and Science, La Frontera University, Temuco, Chile
- Department of Biological and Chemical Sciences, Faculty of Natural Resources, Catholic University of Temuco, Temuco, Chile
| | - Ahmed Farag
- Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Amin Omar Hendawy
- Department of Animal and Poultry Production, Faculty of Agriculture, Damanhour University, Damanhour, Egypt
| | - Patricio R. De los Ríos-Escalante
- Department of Biological and Chemical Sciences, Faculty of Natural Resources, Catholic University of Temuco, Temuco, Chile
- Nucleus of Environmental Sciences, Faculty of Natural Resources, Catholic University of Temuco, Temuco, Chile
| | - Mohamed Aboubakr
- Department of Pharmacology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Qaliobiya, Egypt
| | - Shadi A. Zakai
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wedad M. Nageeb
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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16
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Carbo CR, Faromiki OG, Nan B. A lytic transglycosylase connects bacterial focal adhesion complexes to the peptidoglycan cell wall. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588103. [PMID: 38617213 PMCID: PMC11014575 DOI: 10.1101/2024.04.04.588103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The Gram-negative bacterium Myxococcus xanthus glides on solid surfaces. Dynamic bacterial focal adhesion complexes (bFACs) convert proton motive force from the inner membrane into mechanical propulsion on the cell surface. It is unclear how the mechanical force transmits across the rigid peptidoglycan (PG) cell wall. Here we show that AgmT, a highly abundant lytic PG transglycosylase homologous to Escherichia coli MltG, couples bFACs to PG. Coprecipitation assay and single-particle microscopy reveal that the gliding motors fail to connect to PG and thus are unable to assemble into bFACs in the absence of an active AgmT. Heterologous expression of E. coli MltG restores the connection between PG and bFACs and thus rescues gliding motility in the M. xanthus cells that lack AgmT. Our results indicate that bFACs anchor to AgmT-modified PG to transmit mechanical force across the PG cell wall.
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Affiliation(s)
- Carlos Ramirez Carbo
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- The Genetics and Genomics Interdisciplinary Program, Texas A&M University, College Station, TX 77843, USA
- C. R. C and O. G. F. contribute equally to this work
| | - Olalekan G. Faromiki
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- C. R. C and O. G. F. contribute equally to this work
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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17
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Ahmed H, Böhmdorfer M, Eberl S, Jäger W, Zeitlinger M. Interspecies variability in protein binding of antibiotics basis for translational PK/PD studies-a case study using cefazolin. Antimicrob Agents Chemother 2024; 68:e0164723. [PMID: 38376186 PMCID: PMC10989014 DOI: 10.1128/aac.01647-23] [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: 12/14/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
For antimicrobial agents in particular, plasma protein binding (PPB) plays a pivotal role in deciphering key properties of drug candidates. Animal models are generally used in the preclinical development of new drugs to predict their effects in humans using translational pharmacokinetics/pharmacodynamics (PK/PD). Thus, we compared the protein binding (PB) of cefazolin as well as bacterial growth under various conditions in vitro. The PB extent of cefazolin was studied in human, bovine, and rat plasmas at different antibiotic concentrations in buffer and media containing 20-70% plasma or pure plasma using ultrafiltration (UF) and equilibrium dialysis (ED). Moreover, bacterial growth and time-kill assays were performed in Mueller Hinton Broth (MHB) containing various plasma percentages. The pattern for cefazolin binding to plasma proteins was found to be similar for both UF and ED. There was a significant decrease in cefazolin binding to bovine plasma compared to human plasma, whereas the pattern in rat plasma was more consistent with that in human plasma. Our growth curve analysis revealed considerable growth inhibition of Escherichia coli at 70% bovine or rat plasma compared with 70% human plasma or pure MHB. As expected, our experiments with cefazolin at low concentrations showed that E. coli grew slightly better in 20% human and rat plasma compared to MHB, most probably due to cefazolin binding to proteins in the plasma. Based on the example of cefazolin, our study highlights the interspecies differences of PB with potential impact on PK/PD. These findings should be considered before preclinical PK/PD data can be extrapolated to human patients.
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Affiliation(s)
- Hifza Ahmed
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | | | - Sabine Eberl
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Walter Jäger
- Department of Clinical Pharmacy, University of Vienna, Vienna, Austria
| | - Markus Zeitlinger
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
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18
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Razew A, Herail Q, Miyachiro M, Anoyatis-Pelé C, Bougault C, Dessen A, Arthur M, Simorre JP. Monitoring Drug-Protein Interactions in the Bacterial Periplasm by Solution Nuclear Magnetic Resonance Spectroscopy. J Am Chem Soc 2024; 146:9252-9260. [PMID: 38500259 DOI: 10.1021/jacs.4c00604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The rapid spread of antimicrobial resistance across bacterial pathogens poses a serious risk to the efficacy and sustainability of available treatments. This puts pressure on research concerning the development of new drugs. Here, we present an in-cell NMR-based research strategy to monitor the activity of the enzymes located in the periplasmic space delineated by the inner and outer membranes of Gram-negative bacteria. We demonstrate its unprecedented analytical power in monitoring in situ and in real time (i) the hydrolysis of β-lactams by β-lactamases, (ii) the interaction of drugs belonging to the β-lactam family with their essential targets, and (iii) the binding of inhibitors to these enzymes. We show that in-cell NMR provides a powerful analytical tool for investigating new drugs targeting the molecular components of the bacterial periplasm.
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Affiliation(s)
- Alicja Razew
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Quentin Herail
- INSERM, Sorbonne Université, Université Paris Cité, Paris, 75006, France
| | - Mayara Miyachiro
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | | | - Catherine Bougault
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Andrea Dessen
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Michel Arthur
- INSERM, Sorbonne Université, Université Paris Cité, Paris, 75006, France
| | - Jean-Pierre Simorre
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
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19
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Antillon SF, Bernhardt TG, Chamakura K, Young R. Physiological characterization of single-gene lysis proteins. J Bacteriol 2024; 206:e0038423. [PMID: 38426721 PMCID: PMC10955853 DOI: 10.1128/jb.00384-23] [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: 11/20/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Single-strand RNA (ssRNA) and single-strand DNA phages elicit host lysis using a single gene, in each case designated as sgl. Of the 11 identified Sgls, three have been shown to be specific inhibitors of different steps in the pathway that supplies lipid II to the peptidoglycan (PG) biosynthesis machinery. These Sgls have been called "protein antibiotics" because the lytic event is a septal catastrophe indistinguishable from that caused by cell wall antibiotics. Here, we designate these as type I Sgls. In this formalism, the other eight Sgls are assigned to type II, the best-studied of which is protein L of the paradigm F-specific ssRNA phage MS2. Comparisons have suggested that type II Sgls have four sequence elements distinguished by hydrophobic and polar character. Environmental metatranscriptomics has revealed thousands of new ssRNA phage genomes, each of which presumably has an Sgl. Here, we describe methods to distinguish type I and type II Sgls. Using phase contrast microscopy, we show that both classes of Sgls cause the formation of blebs prior to lysis, but the location of the blebs differs significantly. In addition, we show that L and other type II Sgls do not inhibit the net synthesis of PG, as measured by radio-labeling of PG. Finally, we provide direct evidence that the Sgl from Pseudomonas phage PP7 is a type I Sgl, in support of a recent report based on a genetic selection. This shows that the putative four-element sequence structure suggested for L is not a reliable discriminator for the operational characterization of Sgls. IMPORTANCE The ssRNA phage world has recently undergone a metagenomic expansion upward of a thousandfold. Each genome likely carries at least one single-gene lysis (sgl) cistron encoding a protein that single-handedly induces host autolysis. Here, we initiate an approach to segregate the Sgls into operational types based on physiological analysis, as a first step toward the alluring goal of finding many new ways to induce bacterial death and the attendant expectations for new antibiotic development.
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Affiliation(s)
- S. Francesca Antillon
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
| | - Thomas G. Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Karthik Chamakura
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
| | - Ry Young
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
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20
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Fang Y, Chen C, Cui B, Zhou D. Nanoscale zero-valent iron alleviate antibiotic resistance risk during managed aquifer recharge (MAR) by regulating denitrifying bacterial network. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133238. [PMID: 38134694 DOI: 10.1016/j.jhazmat.2023.133238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/05/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
The frequent occurrence of antibiotics in reclaimed water is concerning, in the case of managed aquifer recharge (MAR), it inevitably hinders further water purification and accelerates the evolutionary resistance in indigenous bacteria. In this study, we constructed two column reactors and nanoscale zero-valent iron (nZVI) amendment was applied for its effects on water quality variation, microbial community succession, and antibiotic resistance genes (ARGs) dissemination, deciphered the underlying mechanism of resistance risk reduction. Results showed that nZVI was oxidized to iron oxides in the sediment column, and total effluent iron concentration was within permissible limits. nZVI enhanced NO3--N removal by 15.5% through enriching denitrifying bacteria and genes, whereas made no effects on oxacillin (OXA) removal. In addition, nZVI exhibited a pivotal impact on ARGs and plasmids decreasing. Network analysis elucidated that the diversity and richness of ARG host declined with nZVI amendment. Denitrifying bacteria play a key role in suppressing horizontal gene transfer (HGT). The underlying mechanisms of inhibited HGT included the downregulated SOS response, the inhibited Type-Ⅳ secretion system and the weakened driving force. This study afforded vital insights into ARG spread control, providing a reference for future applications of nZVI in MAR.
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Affiliation(s)
- Yuanping Fang
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China
| | - Congli Chen
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China
| | - Bin Cui
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
| | - Dandan Zhou
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
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21
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Voedts H, Anoyatis-Pelé C, Langella O, Rusconi F, Hugonnet JE, Arthur M. (p)ppGpp modifies RNAP function to confer β-lactam resistance in a peptidoglycan-independent manner. Nat Microbiol 2024; 9:647-656. [PMID: 38443580 DOI: 10.1038/s41564-024-01609-w] [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: 02/21/2023] [Accepted: 01/16/2024] [Indexed: 03/07/2024]
Abstract
(p)ppGpp is a nucleotide alarmone that controls bacterial response to nutrient deprivation. Since elevated (p)ppGpp levels confer mecillinam resistance and are essential for broad-spectrum β-lactam resistance as mediated by the β-lactam-insensitive transpeptidase YcbB (LdtD), we hypothesized that (p)ppGpp might affect cell wall peptidoglycan metabolism. Here we report that (p)ppGpp-dependent β-lactam resistance does not rely on any modification of peptidoglycan metabolism, as established by analysis of Escherichia coli peptidoglycan structure using high-resolution mass spectrometry. Amino acid substitutions in the β or β' RNA polymerase (RNAP) subunits, alone or in combination with the CRISPR interference-mediated downregulation of three of seven ribosomal RNA operons, were sufficient for resistance, although β-lactams have no known impact on the RNAP or ribosomes. This implies that modifications of RNAP and ribosome functions are critical to prevent downstream effects of the inactivation of peptidoglycan transpeptidases by β-lactams.
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Affiliation(s)
- Henri Voedts
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
| | - Constantin Anoyatis-Pelé
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
| | - Olivier Langella
- GQE-Le Moulon/PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, Gif-sur-Yvette, France
| | - Filippo Rusconi
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
- GQE-Le Moulon/PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, Gif-sur-Yvette, France
| | - Jean-Emmanuel Hugonnet
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France.
| | - Michel Arthur
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France.
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22
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Islam MM, Saha S, Sahoo P, Mandal S. Endophytic Streptomyces sp. MSARE05 isolated from roots of Peanut plant produces a novel antimicrobial compound. J Appl Microbiol 2024; 135:lxae051. [PMID: 38419296 DOI: 10.1093/jambio/lxae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/18/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024]
Abstract
AIM This study aimed to isolate, endophytic Streptomyces sp. MSARE05 isolated from root of a peanut (Arachis hypogaea) inhibits the growth of other bacteria. The research focused on characterizing the strain and the antimicrobial compound. METHODS AND RESULTS The surface-sterilized peanut roots were used to isolate the endophytic bacterium Streptomyces sp. MSARE05. A small-scale fermentation was done to get the antimicrobial compound SM05 produced in highest amount in ISP-2 medium (pH 7) for 7 days at 30°C in shaking (180 rpm) condition. Extraction, purification, and chemical analysis of the antibacterial component revealed a novel class of antibiotics with a 485.54 Dalton molecular weight. The MIC was 0.4-0.8 µg ml-1 against the tested pathogens. It also inhibits multidrug-resistant (MDR) pathogens and Mycobacterium with 0.8-3.2 µg ml-1 MIC. SM05 was found to disrupt cell membrane of target pathogen as evident by significant leakage of intracellular proteins and nucleic acids. It showed synergistic activity with ampicillin, chloramphenicol, streptomycin, and kanamycin. CONCLUSIONS The new-class antimicrobial SM05 consisting naphthalene core moiety was effective against drug-resistant pathogens but non-cytotoxic to human cells. This study underscores the significance of endophytic Streptomyces as a source of innovative antibiotics, contributing to the ongoing efforts to combat antibiotic resistance.
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Affiliation(s)
- Md Majharul Islam
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Shrabani Saha
- The Molecular Recognition Laboratory, Department of Chemistry, Visva-Bharati University, Siksha Bhavana, Santiniketan, Birbhum 731235, India
| | - Prithidipa Sahoo
- The Molecular Recognition Laboratory, Department of Chemistry, Visva-Bharati University, Siksha Bhavana, Santiniketan, Birbhum 731235, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India
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23
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Marmont LS, Orta AK, Baileeves BWA, Sychantha D, Fernández-Galliano A, Li YE, Greene NG, Corey RA, Stansfeld PJ, Clemons WM, Bernhardt TG. Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa. Nat Microbiol 2024; 9:763-775. [PMID: 38336881 PMCID: PMC10914600 DOI: 10.1038/s41564-024-01603-2] [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: 08/01/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024]
Abstract
Many bacterial surface glycans such as the peptidoglycan (PG) cell wall are built from monomeric units linked to a polyprenyl lipid carrier. How this limiting carrier is distributed among competing pathways has remained unclear. Here we describe the isolation of hyperactive variants of Pseudomonas aeruginosa MraY, the enzyme that forms the first lipid-linked PG precursor. These variants result in the elevated production of the final PG precursor lipid II in cells and are hyperactive in vitro. The activated MraY variants have substitutions that map to a cavity on the extracellular side of the dimer interface, far from the active site. Our structural and molecular dynamics results suggest that this cavity is a binding site for externalized lipid II. Overall, our results support a model in which excess externalized lipid II allosterically inhibits MraY, providing a feedback mechanism that prevents the sequestration of lipid carrier in the PG biogenesis pathway.
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Affiliation(s)
- Lindsey S Marmont
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Michael DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Anna K Orta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Becca W A Baileeves
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - David Sychantha
- Michael DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Ana Fernández-Galliano
- Michael DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Yancheng E Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Neil G Greene
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, USA
| | - Robin A Corey
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Bristol, UK
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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24
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Finina BF, Mersha AK. Nano-enabled antimicrobial thin films: design and mechanism of action. RSC Adv 2024; 14:5290-5308. [PMID: 38357038 PMCID: PMC10866018 DOI: 10.1039/d3ra07884a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
Antimicrobial thin films are types of protective coatings that are applied to surfaces such as medical devices, food packaging materials, water-resistant coatings, and other systems. These films prevent and reduce the spread of microbial organisms, including bacteria, fungi, and viruses. Antimicrobial thin films can be prepared from a variety of nanostructured materials including metal nanoparticles, metal oxides, plant materials, enzymes, bacteriocins and polymers. Their antimicrobial mechanism varies mostly based on the types of active agents from which the film is made of. Antimicrobial thin films are becoming increasingly popular microbial treatment methods due to their advantages such as enhanced stability, reduced toxicity levels, extended effectiveness over time and broad spectrum antimicrobial action without side effects on human health or the environment. This popularity and enhanced performance is mainly due to the extended possibility of film designs. Thin films offer convenient formulation methods which makes them suitable for commercial practices aiming at high turnover rates along with residential applications requiring frequent application cycles. This review focuses on recent developments in the possible processing methods and design approaches for assembling the various types of antimicrobial materials into nanostructured thin film-based delivery systems, along with mechanisms of action against microbes.
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Affiliation(s)
- Bilisuma Fekadu Finina
- Department of Industrial Chemistry, Addis Ababa Science and Technology University Addis Ababa Ethiopia
- Department of Chemistry, Kotebe University of Education Addis Ababa Ethiopia
| | - Anteneh Kindu Mersha
- Department of Industrial Chemistry, Addis Ababa Science and Technology University Addis Ababa Ethiopia
- Nanotechnology Center of Excellence, Addis Ababa Science and Technology University Addis Ababa Ethiopia
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25
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Ronneau S, Michaux C, Giorgio RT, Helaine S. Intoxication of antibiotic persisters by host RNS inactivates their efflux machinery during infection. PLoS Pathog 2024; 20:e1012033. [PMID: 38421944 PMCID: PMC10903880 DOI: 10.1371/journal.ppat.1012033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
The host environment is of critical importance for antibiotic efficacy. By impacting bacterial machineries, stresses encountered by pathogens during infection promote the formation of phenotypic variants that are transiently insensitive to the action of antibiotics. It is assumed that these recalcitrant bacteria-termed persisters-contribute to antibiotic treatment failure and relapsing infections. Recently, we demonstrated that host reactive nitrogen species (RNS) transiently protect persisters against the action of β-lactam antibiotics by delaying their regrowth within host cells. Here, we discovered that RNS intoxication of persisters also collaterally sensitizing them to fluoroquinolones during infection, explaining the higher efficiency of fluoroquinolones against intramacrophage Salmonella. By reducing bacterial respiration and the proton-motive force, RNS inactivate the AcrAB efflux machinery of persisters, facilitating the accumulation of fluoroquinolones intracellularly. Our work shows that target inactivity is not the sole reason for Salmonella persisters to withstand antibiotics during infection, with active efflux being a major contributor to survival. Thus, understanding how the host environment impacts persister physiology is critical to optimize antibiotics efficacy during infection.
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Affiliation(s)
- Séverin Ronneau
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Charlotte Michaux
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rachel T. Giorgio
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sophie Helaine
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
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26
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Kaul M, Meher SK, Nallamotu KC, Reddy M. Glycan strand cleavage by a lytic transglycosylase, MltD contributes to the expansion of peptidoglycan in Escherichia coli. PLoS Genet 2024; 20:e1011161. [PMID: 38422114 DOI: 10.1371/journal.pgen.1011161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 03/12/2024] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Peptidoglycan (PG) is a protective sac-like exoskeleton present in most bacterial cell walls. It is a large, covalently crosslinked mesh-like polymer made up of many glycan strands cross-bridged to each other by short peptide chains. Because PG forms a continuous mesh around the bacterial cytoplasmic membrane, opening the mesh is critical to generate space for the incorporation of new material during its expansion. In Escherichia coli, the 'space-making activity' is known to be achieved by cleavage of crosslinks between the glycan strands by a set of redundant PG endopeptidases whose absence leads to rapid lysis and cell death. Here, we demonstrate a hitherto unknown role of glycan strand cleavage in cell wall expansion in E. coli. We find that overexpression of a membrane-bound lytic transglycosylase, MltD that cuts the glycan polymers of the PG sacculus rescues the cell lysis caused by the absence of essential crosslink-specific endopeptidases, MepS, MepM and MepH. We find that cellular MltD levels are stringently controlled by two independent regulatory pathways; at the step of post-translational stability by a periplasmic adaptor-protease complex, NlpI-Prc, and post-transcriptionally by RpoS, a stationary-phase specific sigma factor. Further detailed genetic and biochemical analysis implicated a role for MltD in cleaving the nascent uncrosslinked glycan strands generated during the expansion of PG. Overall, our results show that the combined activity of PG endopeptidases and lytic transglycosylases is necessary for successful expansion of the cell wall during growth of a bacterium.
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Affiliation(s)
- Moneca Kaul
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Suraj Kumar Meher
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Krishna Chaitanya Nallamotu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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27
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Lewis K. Streptonigrin kills bacteria by stealth. Proc Natl Acad Sci U S A 2024; 121:e2320942121. [PMID: 38227663 PMCID: PMC10823159 DOI: 10.1073/pnas.2320942121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Affiliation(s)
- Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA02115
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28
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Halawa EM, Fadel M, Al-Rabia MW, Behairy A, Nouh NA, Abdo M, Olga R, Fericean L, Atwa AM, El-Nablaway M, Abdeen A. Antibiotic action and resistance: updated review of mechanisms, spread, influencing factors, and alternative approaches for combating resistance. Front Pharmacol 2024; 14:1305294. [PMID: 38283841 PMCID: PMC10820715 DOI: 10.3389/fphar.2023.1305294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
Antibiotics represent a frequently employed therapeutic modality for the management of bacterial infections across diverse domains, including human health, agriculture, livestock breeding, and fish farming. The efficacy of antibiotics relies on four distinct mechanisms of action, which are discussed in detail in this review, along with accompanying diagrammatic illustrations. Despite their effectiveness, antibiotic resistance has emerged as a significant challenge to treating bacterial infections. Bacteria have developed defense mechanisms against antibiotics, rendering them ineffective. This review delves into the specific mechanisms that bacteria have developed to resist antibiotics, with the help of diagrammatic illustrations. Antibiotic resistance can spread among bacteria through various routes, resulting in previously susceptible bacteria becoming antibiotic-resistant. Multiple factors contribute to the worsening crisis of antibiotic resistance, including human misuse of antibiotics. This review also emphasizes alternative solutions proposed to mitigate the exacerbation of antibiotic resistance.
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Affiliation(s)
- Esraa M. Halawa
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
| | - Mohamed Fadel
- Department of Microbial Chemistry, Biotechnology Research Institute, National Research Centre, Dokki, Cairo, Egypt
| | - Mohammed W. Al-Rabia
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Clinical Laboratories-Diagnostic Immunology Division, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Ali Behairy
- Department of Pharmacology, Faculty of Medicine, Benha University, Benha, Egypt
| | - Nehal A. Nouh
- Department of Microbiology, Medicine Program, Batterjee Medical College, Jeddah, Saudi Arabia
- Inpatient Pharmacy, Mansoura University Hospitals, Mansoura, Egypt
| | - Mohamed Abdo
- Department of Animal Histology and Anatomy, School of Veterinary Medicine, Badr University in Cairo (BUC), Badr City, Egypt
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Rada Olga
- Department of Biology and Plant Protection, Faculty of Agriculture, University of Life Sciences “King Michael I” from Timișoara, Timișoara, Romania
| | - Liana Fericean
- Department of Biology and Plant Protection, Faculty of Agriculture, University of Life Sciences “King Michael I” from Timișoara, Timișoara, Romania
| | - Ahmed M. Atwa
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Egyptian Russian University, Cairo, Egypt
| | - Mohammad El-Nablaway
- Department of Medical Biochemistry, Faculty of Medicine, Mansoura University, Mansoura, Egypt
- Department of Basic Medical Sciences, College of Medicine, AlMaarefa University, Riyadh, Saudi Arabia
| | - Ahmed Abdeen
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
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29
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Maffei E, Woischnig AK, Burkolter MR, Heyer Y, Humolli D, Thürkauf N, Bock T, Schmidt A, Manfredi P, Egli A, Khanna N, Jenal U, Harms A. Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication. Nat Commun 2024; 15:175. [PMID: 38168031 PMCID: PMC10761892 DOI: 10.1038/s41467-023-44157-3] [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: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Bacteriophages are ubiquitous viral predators that have primarily been studied using fast-growing laboratory cultures of their bacterial hosts. However, microbial life in nature is mostly in a slow- or non-growing, dormant state. Here, we show that diverse phages can infect deep-dormant bacteria and suspend their replication until the host resuscitates ("hibernation"). However, a newly isolated Pseudomonas aeruginosa phage, named Paride, can directly replicate and induce the lysis of deep-dormant hosts. While non-growing bacteria are notoriously tolerant to antibiotic drugs, the combination with Paride enables the carbapenem meropenem to eradicate deep-dormant cultures in vitro and to reduce a resilient bacterial infection of a tissue cage implant in mice. Our work might inspire new treatments for persistent bacterial infections and, more broadly, highlights two viral strategies to infect dormant bacteria (hibernation and direct replication) that will guide future studies on phage-host interactions.
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Affiliation(s)
- Enea Maffei
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | - Anne-Kathrin Woischnig
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Marco R Burkolter
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | - Yannik Heyer
- Biozentrum, University of Basel, Basel, Switzerland
| | - Dorentina Humolli
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | | | - Thomas Bock
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University and University Hospital of Basel, Basel, Switzerland
| | - Nina Khanna
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
| | - Alexander Harms
- Biozentrum, University of Basel, Basel, Switzerland.
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland.
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30
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Wu H, Wang T, Liang Y, Chen L, Li Z. Self-assembled and dynamic bond crosslinked herb-polysaccharide hydrogel with anti-inflammation and pro-angiogenesis effects for burn wound healing. Colloids Surf B Biointerfaces 2024; 233:113639. [PMID: 37951186 DOI: 10.1016/j.colsurfb.2023.113639] [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: 08/02/2023] [Revised: 10/16/2023] [Accepted: 11/06/2023] [Indexed: 11/13/2023]
Abstract
Excessive inflammation and defective angiogenesis can affect burn wound healing. Recently, naturally derived substances with anti-inflammatory and proangiogenic properties have attracted public attention. The design and fabrication of naturally derived substance-based bioactive hydrogels as wound dressings are of interest and important for regulating the complex microenvironment of the wound bed. Herein, we developed a hydrogel by self-assembling a natural herb (glycyrrhizic acid, GA) dynamic Schiff base crosslinking of hyaluronic acid derivatives and integrating deferoxamine (DFO). The naturally derived herbal GA endowed the bioactive hydrogel with a native anti-inflammatory capability. The introduction of dynamic bond crosslinking improved the hydrogel stability. In addition, dynamic crosslinking is conducive for integrating the naturally-derived DFO, delivering it to the wound site, and promoting angiogenesis. Rheological tests, injectability, degradation behavior, and drug release performance demonstrated the enhanced stability of the hydrogel and sustained release of DFO. Cytotoxicity, cell proliferation, and cell migration tests suggested that the hydrogel was biocompatible. Further, the hydrogel exerted anti-inflammatory and angiogenic effects and accelerated burn wound healing in rats. Therefore, the proposed hydrogel has the potential to be a natural, herb-based, bioactive dressing for burn wound management.
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Affiliation(s)
- Hongfu Wu
- Dongguan Key Laboratory of Stem Cell and Regenerative Tissue Engineering, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
| | - Tao Wang
- Department of Surgery, The Third Hospital of Guangdong Medical University (Longjiang Hospital of Shunde District), Foshan 528318, China
| | - Yinru Liang
- Dongguan Key Laboratory of Stem Cell and Regenerative Tissue Engineering, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
| | - Liji Chen
- Dongguan Key Laboratory of Stem Cell and Regenerative Tissue Engineering, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
| | - Ziyi Li
- Dongguan Key Laboratory of Stem Cell and Regenerative Tissue Engineering, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; The Second Clinical Medical College, Guangdong Medical University, Dongguan 523808, China.
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31
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Alamán-Zárate MG, Rady BJ, Evans CA, Pian B, Greetham D, Marecos-Ortiz S, Dickman MJ, Lidbury IDEA, Lovering AL, Barstow BM, Mesnage S. Unusual 1-3 peptidoglycan cross-links in Acetobacteraceae are made by L,D-transpeptidases with a catalytic domain distantly related to YkuD domains. J Biol Chem 2024; 300:105494. [PMID: 38006948 PMCID: PMC10727944 DOI: 10.1016/j.jbc.2023.105494] [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: 11/02/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023] Open
Abstract
Peptidoglycan is an essential component of the bacterial cell envelope that contains glycan chains substituted by short peptide stems. Peptide stems are polymerized by D,D-transpeptidases, which make bonds between the amino acid in position four of a donor stem and the third residue of an acceptor stem (4-3 cross-links). Some bacterial peptidoglycans also contain 3-3 cross-links that are formed by another class of enzymes called L,D-transpeptidases which contain a YkuD catalytic domain. In this work, we investigate the formation of unusual bacterial 1-3 peptidoglycan cross-links. We describe a version of the PGFinder software that can identify 1-3 cross-links and report the high-resolution peptidoglycan structure of Gluconobacter oxydans (a model organism within the Acetobacteraceae family). We reveal that G. oxydans peptidoglycan contains peptide stems made of a single alanine as well as several dipeptide stems with unusual amino acids at their C-terminus. Using a bioinformatics approach, we identified a G. oxydans mutant from a transposon library with a drastic reduction in 1-3 cross-links. Through complementation experiments in G. oxydans and recombinant protein production in a heterologous host, we identify an L,D-transpeptidase enzyme with a domain distantly related to the YkuD domain responsible for these non-canonical reactions. This work revisits the enzymatic capabilities of L,D-transpeptidases, a versatile family of enzymes that play a key role in bacterial peptidoglycan remodelling.
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Affiliation(s)
- Marcel G Alamán-Zárate
- Molecular Microbiology, Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Brooks J Rady
- Molecular Microbiology, Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Caroline A Evans
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, UK
| | - Brooke Pian
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, USA
| | - Darren Greetham
- Molecular Microbiology, Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Sabrina Marecos-Ortiz
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, USA
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, UK
| | - Ian D E A Lidbury
- Molecular Microbiology, Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Buz M Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, USA
| | - Stéphane Mesnage
- Molecular Microbiology, Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, UK.
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32
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Galley NF, Greetham D, Alamán-Zárate MG, Williamson MP, Evans CA, Spittal WD, Buddle JE, Freeman J, Davis GL, Dickman MJ, Wilcox MH, Lovering AL, Fagan RP, Mesnage S. Clostridioides difficile canonical L,D-transpeptidases catalyze a novel type of peptidoglycan cross-links and are not required for beta-lactam resistance. J Biol Chem 2024; 300:105529. [PMID: 38043796 PMCID: PMC10792238 DOI: 10.1016/j.jbc.2023.105529] [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: 10/13/2023] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea worldwide with significant morbidity and mortality. This organism is naturally resistant to several beta-lactam antibiotics that inhibit the polymerization of peptidoglycan, an essential component of the bacteria cell envelope. Previous work has revealed that C. difficile peptidoglycan has an unusual composition. It mostly contains 3-3 cross-links, catalyzed by enzymes called L,D-transpeptidases (Ldts) that are poorly inhibited by beta-lactams. It was therefore hypothesized that peptidoglycan polymerization by these enzymes could underpin antibiotic resistance. Here, we investigated the catalytic activity of the three canonical Ldts encoded by C. difficile (LdtCd1, LdtCd2, and LdtCd3) in vitro and explored their contribution to growth and antibiotic resistance. We show that two of these enzymes catalyze the formation of novel types of peptidoglycan cross-links using meso-diaminopimelic acid both as a donor and an acceptor, also observed in peptidoglycan sacculi. We demonstrate that the simultaneous deletion of these three genes only has a minor impact on both peptidoglycan structure and resistance to beta-lactams. This unexpected result therefore implies that the formation of 3-3 peptidoglycan cross-links in C. difficile is catalyzed by as yet unidentified noncanonical Ldt enzymes.
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Affiliation(s)
- Nicola F Galley
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Darren Greetham
- School of Biosciences, University of Sheffield, Sheffield, UK
| | | | | | - Caroline A Evans
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - William D Spittal
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; Healthcare Associated Infections Research Group, Leeds Institute of Medical Research University of Leeds, Leeds, UK
| | | | - Jane Freeman
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; Healthcare Associated Infections Research Group, Leeds Institute of Medical Research University of Leeds, Leeds, UK
| | - Georgina L Davis
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; Healthcare Associated Infections Research Group, Leeds Institute of Medical Research University of Leeds, Leeds, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; Healthcare Associated Infections Research Group, Leeds Institute of Medical Research University of Leeds, Leeds, UK
| | | | - Robert P Fagan
- School of Biosciences, University of Sheffield, Sheffield, UK
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33
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Bersani M, Failla M, Vascon F, Gianquinto E, Bertarini L, Baroni M, Cruciani G, Verdirosa F, Sannio F, Docquier JD, Cendron L, Spyrakis F, Lazzarato L, Tondi D. Structure-Based Optimization of 1,2,4-Triazole-3-Thione Derivatives: Improving Inhibition of NDM-/VIM-Type Metallo-β-Lactamases and Synergistic Activity on Resistant Bacteria. Pharmaceuticals (Basel) 2023; 16:1682. [PMID: 38139809 PMCID: PMC10747250 DOI: 10.3390/ph16121682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
The worldwide emergence and dissemination of Gram-negative bacteria expressing metallo-β-lactamases (MBLs) menace the efficacy of all β-lactam antibiotics, including carbapenems, a last-line treatment usually restricted to severe pneumonia and urinary tract infections. Nonetheless, no MBL inhibitor is yet available in therapy. We previously identified a series of 1,2,4-triazole-3-thione derivatives acting as micromolar inhibitors of MBLs in vitro, but devoid of synergistic activity in microbiological assays. Here, via a multidisciplinary approach, including molecular modelling, synthesis, enzymology, microbiology, and X-ray crystallography, we optimized this series of compounds and identified low micromolar inhibitors active against clinically relevant MBLs (NDM-1- and VIM-type). The best inhibitors increased, to a certain extent, the susceptibility of NDM-1- and VIM-4-producing clinical isolates to meropenem. X-ray structures of three selected inhibitors in complex with NDM-1 elucidated molecular recognition at the base of potency improvement, confirmed in silico predicted orientation, and will guide further development steps.
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Affiliation(s)
- Matteo Bersani
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Mariacristina Failla
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Filippo Vascon
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy; (F.V.); (L.C.)
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Laura Bertarini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy;
| | - Massimo Baroni
- Kinetic Business Centre, Molecular Discovery Ltd., Elstree, Borehamwood, Hertfordshire WD6 4PJ, UK;
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, Università Degli Studi di Perugia, Via Elce di Sotto, 06132 Perugia, Italy;
| | - Federica Verdirosa
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy; (F.V.); (F.S.); (J.-D.D.)
| | - Filomena Sannio
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy; (F.V.); (F.S.); (J.-D.D.)
| | - Jean-Denis Docquier
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy; (F.V.); (F.S.); (J.-D.D.)
- Laboratoire de Bactériologie Moléculaire, Centre d’Ingénierie des Protéines-InBioS, Université de Liège, B-4000 Liège, Belgium
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy; (F.V.); (L.C.)
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Loretta Lazzarato
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy;
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Anirudhan A, Iryani MTM, Andriani Y, Sorgeloos P, Tan MP, Wong LL, Mok WJ, Ming W, Yantao L, Lau CC, Sung YY. The effects of Pandanus tectorius leaf extract on the resistance of White-leg shrimp Penaeus vannamei towards pathogenic Vibrio parahaemolyticus. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 4:100101. [PMID: 37397801 PMCID: PMC10313901 DOI: 10.1016/j.fsirep.2023.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/08/2023] [Accepted: 06/03/2023] [Indexed: 07/04/2023] Open
Abstract
Pandanus tectorius leaf extract effect on the White-leg shrimp Penaeus vannamei tolerance against Vibrio parahaemolyticus were investigated in this study. Thirty shrimp post-larvae measured at approximately 1 cm were exposed for 24 h to 0.5, 1, 2, 3, 4, 5 and 6 g/L leaf extract and subsequently observed for survival and immune-related genes expression (Hsp70, ProPO, peroxinectin, penaeidin, crustin and transglutaminase), followed by determination of their tolerance and histological tissue profiles upon Vibrio challenge. Survival of shrimps treated with 6 g/L of leaf extract improved by up to 95% to controls. Hsp70, crustin, and prophenoloxidase mRNA levels were observed to be 8.5, 10.4, and 1.5-fold higher, respectively. Histopathological analysis of the hepatopancreas and the muscle tissues revealed major tissue degeneration in Vibrio-challenged shrimps but not in shrimps primed with P. tectorius leaf extract. Of all the dose examined, the best pathogen resistance results were obtained with a 24 h incubation of shrimp in 6 g/L P. tectorius methanolic leaf extract. The tolerance towards V. parahaemolyticus might be associated with the increased regulation of Hsp70, prophenoloxidase and crustin upon exposure to the extract, all immune-related proteins essential for pathogen elimination in Penaeid shrimp. The present study primarily demonstrated that P. tectorius leaf extract is a viable alternative for enhancing P. vannamei post-larvae resistance against V. parahaemolyticus, a major bacterial pathogen in aquaculture.
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Affiliation(s)
- Anupa Anirudhan
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Mat Taib Mimi Iryani
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Yosie Andriani
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Patrick Sorgeloos
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Laboratory of Aquaculture and Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Campus Coupure - Blok F, Ghent University, Coupure Links 653, Gent B-9000, Belgium
| | - Min Pau Tan
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Li Lian Wong
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- UMT-OUC Joint Academic Center for Marine Studies, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Wen Jye Mok
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- UMT-OUC Joint Academic Center for Marine Studies, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Wang Ming
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Academic Center for Marine Studies, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Liang Yantao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Academic Center for Marine Studies, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Cher Chien Lau
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Yeong Yik Sung
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- UMT-OUC Joint Academic Center for Marine Studies, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
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Pahlavan F, Moosavi SS, Zolghadr AR, Iranpoor N. Electronic origins of the stereochemistry in β-lactam formed through the Staudinger reaction catalyzed by a nucleophile. RSC Adv 2023; 13:33654-33667. [PMID: 38020014 PMCID: PMC10653035 DOI: 10.1039/d3ra05286a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
This paper evaluates the electronic effects of molecular substituents on the stereoselectivity of the umpolung Staudinger catalytic reaction. This is especially important because experimental studies on constructing the β-lactam ring, a core structure of most antibiotics, through catalyzed Staudinger reactions have been massively progressing over the last century. Yet, there is a necessity for an in-depth understanding of the reaction mechanisms to help chemists, working on the well-established discoveries, improve these to optimize the stereoselectivity and yield of synthetic methods. Access to practical and effective advancements in forming optically pure β-lactam is paramount in the field of medical chemistry. This paper specifically investigates how changing the N-protecting group in the imine fragment can switch the stereoselectivity of the PPY-catalyzed Staudinger reaction. To do so, we employed the density functional theory (DFT) for geometry optimization and electronic analysis at the B3LYP/6-31G(d) level of theory to examine and compare the role of N-tosyl (N-Ts) and N-triflyl (N-Tf) imine on the mechanism pathways, i.e., imine-first or ketene-first, and stereochemistry of the reaction, i.e., cis or trans β-lactam. Our results show that the reaction mechanism pathway cannot be simply switched from ketene-first to imine-first by changing the substituent on the imine nitrogen atom, which is contrary to the reported experimental results, and both imines go through the ketene-first mechanism with different stereochemistries, which is cis selective for imine-Ts and trans selective for imine-Tf. Based on electronic analyses, the reversal in diastereoselectivity in the N-triflyl imine system could be attributed to the charge transfers and electron-density distribution over the transition states. Therefore, the cis/trans selectivity of the PPY-catalyzed Staudinger reaction could be effectively controlled by the electronic characteristics of the molecular substituents in the reactants. A N-protecting group in imine with a more electron-withdrawing nature seems to accelerate the stereo-determining step, ring closure, and increase the stabilization charge transfers in the transition state, leading to a preference for trans β-lactam formation. It seems that using a N-substituent with a higher electron-withdrawing nature can initially activate the imine by the nucleophilic catalyst in competition with ketene, i.e., imine-first versus ketene-first. These results can provide an insight into select proper substituents for the fragments to synthesis β-lactam with a desired stereochemistry. Also, a comprehensive comparison was performed between calculations with and without dispersion.
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Affiliation(s)
- Farideh Pahlavan
- Department of Chemistry, School of Science, Shiraz University Shiraz 71454 Iran
| | | | - Amin Reza Zolghadr
- Department of Chemistry, School of Science, Shiraz University Shiraz 71454 Iran
| | - Nasser Iranpoor
- Department of Chemistry, School of Science, Shiraz University Shiraz 71454 Iran
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36
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Mack AR, Kumar V, Taracila MA, Mojica MF, O'Shea M, Schinabeck W, Silver G, Hujer AM, Papp-Wallace KM, Chen S, Haider S, Caselli E, Prati F, van den Akker F, Bonomo RA. Natural protein engineering in the Ω-loop: the role of Y221 in ceftazidime and ceftolozane resistance in Pseudomonas-derived cephalosporinase. Antimicrob Agents Chemother 2023; 67:e0079123. [PMID: 37850746 PMCID: PMC10648885 DOI: 10.1128/aac.00791-23] [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: 06/19/2023] [Accepted: 08/07/2023] [Indexed: 10/19/2023] Open
Abstract
A wide variety of clinically observed single amino acid substitutions in the Ω-loop region have been associated with increased minimum inhibitory concentrations and resistance to ceftazidime (CAZ) and ceftolozane (TOL) in Pseudomonas-derived cephalosporinase and other class C β-lactamases. Herein, we demonstrate the naturally occurring tyrosine to histidine substitution of amino acid 221 (Y221H) in Pseudomonas-derived cephalosporinase (PDC) enables CAZ and TOL hydrolysis, leading to similar kinetic profiles (k cat = 2.3 ± 0.2 µM and 2.6 ± 0.1 µM, respectively). Mass spectrometry of PDC-3 establishes the formation of stable adducts consistent with the formation of an acyl enzyme complex, while spectra of E219K (a well-characterized, CAZ- and TOL-resistant comparator) and Y221H are consistent with more rapid turnover. Thermal denaturation experiments reveal decreased stability of the variants. Importantly, PDC-3, E219K, and Y221H are all inhibited by avibactam and the boronic acid transition state inhibitors (BATSIs) LP06 and S02030 with nanomolar IC50 values and the BATSIs stabilize all three enzymes. Crystal structures of PDC-3 and Y221H as apo enzymes and complexed with LP06 and S02030 (1.35-2.10 Å resolution) demonstrate ligand-induced conformational changes, including a significant shift in the position of the sidechain of residue 221 in Y221H (as predicted by enhanced sampling well-tempered metadynamics simulations) and extensive hydrogen bonding between the enzymes and BATSIs. The shift of residue 221 leads to the expansion of the active site pocket, and molecular docking suggests substrates orientate differently and make different intermolecular interactions in the enlarged active site compared to the wild-type enzyme.
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Affiliation(s)
- Andrew R. Mack
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Vijay Kumar
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Magdalena A. Taracila
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Maria F. Mojica
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Margaret O'Shea
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - William Schinabeck
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Galen Silver
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Andrea M. Hujer
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Krisztina M. Papp-Wallace
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Shuang Chen
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, England, United Kingdom
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, England, United Kingdom
- UCL Centre for Advanced Research Computing, University College London, London, England, United Kingdom
| | - Emilia Caselli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Robert A. Bonomo
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
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37
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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38
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Liu X, den Blaauwen T. NlpI-Prc Proteolytic Complex Mediates Peptidoglycan Synthesis and Degradation via Regulation of Hydrolases and Synthases in Escherichia coli. Int J Mol Sci 2023; 24:16355. [PMID: 38003545 PMCID: PMC10671308 DOI: 10.3390/ijms242216355] [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: 10/16/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Balancing peptidoglycan (PG) synthesis and degradation with precision is essential for bacterial growth, yet our comprehension of this intricate process remains limited. The NlpI-Prc proteolytic complex plays a crucial but poorly understood role in the regulation of multiple enzymes involved in PG metabolism. In this paper, through fluorescent D-amino acid 7-hydroxycoumarincarbonylamino-D-alanine (HADA) labeling and immunolabeling assays, we have demonstrated that the NlpI-Prc complex regulates the activity of PG transpeptidases and subcellular localization of PBP3 under certain growth conditions. PBP7 (a PG hydrolase) and MltD (a lytic transglycosylase) were confirmed to be negatively regulated by the NlpI-Prc complex by an in vivo degradation assay. The endopeptidases, MepS, MepM, and MepH, have consistently been demonstrated as redundantly essential "space makers" for nascent PG insertion. However, we observed that the absence of NlpI-Prc complex can alleviate the lethality of the mepS mepM mepH mutant. A function of PG lytic transglycosylases MltA and MltD as "space makers" was proposed through multiple gene deletions. These findings unveil novel roles for NlpI-Prc in the regulation of both PG synthesis and degradation, shedding light on the previously undiscovered function of lytic transglycosylases as "space makers" in PG expansion.
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Affiliation(s)
| | - Tanneke den Blaauwen
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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39
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Witek K, Kaczor A, Żesławska E, Podlewska S, Marć MA, Czarnota-Łydka K, Nitek W, Latacz G, Tejchman W, Bischoff M, Jacob C, Handzlik J. Chalcogen-Varied Imidazolone Derivatives as Antibiotic Resistance Breakers in Staphylococcus aureus Strains. Antibiotics (Basel) 2023; 12:1618. [PMID: 37998820 PMCID: PMC10669504 DOI: 10.3390/antibiotics12111618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
In this study, a search for new therapeutic agents that may improve the antibacterial activity of conventional antibiotics and help to successfully overcome methicillin-resistant Staphylococcus aureus (MRSA) infections has been conducted. The purpose of this work was to extend the scope of our preliminary studies and to evaluate the adjuvant potency of new derivatives in a set of S. aureus clinical isolates. The study confirmed the high efficacy of piperazine derivatives of 5-arylideneimidazol-4-one (7-9) tested previously, and it enabled the authors to identify even more efficient modulators of bacterial resistance among new analogs. The greatest capacity to enhance oxacillin activity was determined for 1-benzhydrylpiperazine 5-spirofluorenehydantoin derivative (13) which, at concentrations as low as 0.0625 mM, restores the effectiveness of β-lactam antibiotics against MRSA strains. In silico studies showed that the probable mechanism of action of 13 is related to the binding of the molecule with the allosteric site of PBP2a. Interestingly, thiazole derivatives tested were shown to act as both oxacillin and erythromycin conjugators in S. aureus isolates, suggesting a complex mode of action (i.e., influence on the Msr(A) efflux pump). This high enhancer activity indicates the high potential of imidazolones to become commercially available antibiotic adjuvants.
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Affiliation(s)
- Karolina Witek
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
- Department of Pharmaceutical Microbiology, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
- Bioorganic Chemistry, School of Pharmacy, University of Saarland, Campus B2.1, D-66123 Saarbrüecken, Germany;
- Institute of Medical Microbiology and Hygiene, Saarland University, D-66421 Homburg, Germany;
| | - Aneta Kaczor
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
| | - Ewa Żesławska
- Institute of Biology and Earth Sciences, Pedagogical University of Krakow, Podchorążych 2, 30-084 Krakow, Poland; (E.Ż.); (W.T.)
| | - Sabina Podlewska
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
- Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Krakow, Poland
| | - Małgorzata Anna Marć
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
| | - Kinga Czarnota-Łydka
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
- Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, Św. Łazarza 15, 31-530 Krakow, Poland
| | - Wojciech Nitek
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland;
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
| | - Waldemar Tejchman
- Institute of Biology and Earth Sciences, Pedagogical University of Krakow, Podchorążych 2, 30-084 Krakow, Poland; (E.Ż.); (W.T.)
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, D-66421 Homburg, Germany;
| | - Claus Jacob
- Bioorganic Chemistry, School of Pharmacy, University of Saarland, Campus B2.1, D-66123 Saarbrüecken, Germany;
| | - Jadwiga Handzlik
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
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Antillon SF, Bernhardt TG, Chamakura K, Young R. Physiological characterization of single gene lysis proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562596. [PMID: 37905155 PMCID: PMC10614894 DOI: 10.1101/2023.10.16.562596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Until recently only 11 distinct Sgls (single gene lysis proteins) have been experimentally identified. Of these, three have been shown to be specific inhibitors of different steps in the pathway that supplies Lipid II to the peptidoglycan (PG) biosynthesis machinery: Qβ A2 inhibits MurA, ϕX174 E inhibits MraY, and Lys from coliphage M inhibits MurJ. These Sgls have been called "protein antibiotics" because the lytic event is a septal catastrophe indistinguishable from that caused by cell wall antibiotics. Here we propose to designate these as members of type I Sgls, to distinguish them from another Sgl, the L protein of the paradigm ssRNA phage MS2. Although none of the other distinct Sgls have significant sequence similarity to L, alignments suggested the presence of four domains distinguished by hydrophobic and polar character. The simplest notion is that these other Sgls have the same autolytic mechanism and, based on this, constitute type II. Although the number of experimentally confirmed Sgls has not changed, recent environmental metagenomes and metatranscriptomes have revealed thousands of new ssRNA phage genomes, each of which presumably has at least one Sgl gene. Here we report on methods to distinguish type I and type II Sgls. Using phase-contrast microscopy, we show that both classes of Sgls cause the formation of blebs prior to lysis, but the location of the blebs differs significantly. In addition, we show that L and other type II Sgls do not inhibit net synthesis of PG, as measured by incorporation of 3[H]-diaminopimelic acid. Finally, we provide support for the unexpected finding by Adler and colleagues that the Sgl from Pseudomonas phage PP7 is a type I Sgl, as determined by the two methods. This shows that the sharing the putative 4-domain structure suggested for L is not a reliable discriminator for operational characterization of Sgls. Overall, this study establishes new ways to rapidly classify novel Sgls and thus may facilitate the identification of new cell envelope targets that will help generate new antibiotics.
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Affiliation(s)
- S Francesca Antillon
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, United States
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, TX, 77843-2128, United States
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
- HHMI, Chevy Chase, MD 20815
| | - Karthik Chamakura
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, United States
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, TX, 77843-2128, United States
| | - Ry Young
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, United States
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, TX, 77843-2128, United States
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41
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Yan YH, Zhang TT, Li R, Wang SY, Wei LL, Wang XY, Zhu KR, Li SR, Liang GQ, Yang ZB, Yang LL, Qin S, Li GB. Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-β-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding. J Med Chem 2023; 66:13746-13767. [PMID: 37791640 DOI: 10.1021/acs.jmedchem.3c01189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Metallo-β-lactamases (MBLs) are zinc-dependent enzymes capable of hydrolyzing all bicyclic β-lactam antibiotics, posing a great threat to public health. However, there are currently no clinically approved MBL inhibitors. Despite variations in their active sites, MBLs share a common catalytic mechanism with carbapenems, forming similar reaction species and hydrolysates. We here report the development of 2-aminothiazole-4-carboxylic acids (AtCs) as broad-spectrum MBL inhibitors by mimicking the anchor pharmacophore features of carbapenem hydrolysate binding. Several AtCs manifested potent activity against B1, B2, and B3 MBLs. Crystallographic analyses revealed a common binding mode of AtCs with B1, B2, and B3 MBLs, resembling binding observed in the MBL-carbapenem product complexes. AtCs restored Meropenem activity against MBL-producing isolates. In the murine sepsis model, AtCs exhibited favorable synergistic efficacy with Meropenem, along with acceptable pharmacokinetics and safety profiles. This work offers promising lead compounds and a structural basis for the development of potential drug candidates to combat MBL-mediated antimicrobial resistance.
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Affiliation(s)
- Yu-Hang Yan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Ting-Ting Zhang
- School of Pharmaceutical Sciences, Institute of Drug Discovery and Development, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou 450001, China
| | - Rong Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Si-Yao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Liu-Liu Wei
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xin-Yue Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Kai-Rong Zhu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Shan-Rui Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Guo-Qing Liang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Zeng-Bao Yang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Ling-Ling Yang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Institute of Drug Discovery and Development, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou 450001, China
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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Zheng M, Lupoli TJ. Counteracting antibiotic resistance enzymes and efflux pumps. Curr Opin Microbiol 2023; 75:102334. [PMID: 37329679 DOI: 10.1016/j.mib.2023.102334] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/17/2023] [Indexed: 06/19/2023]
Abstract
Bacterial pathogens are constantly evolving new resistance mechanisms against antibiotics; hence, strategies to potentiate existing antibiotics or combat mechanisms of resistance using adjuvants are always in demand. Recently, inhibitors have been identified that counteract enzymatic modification of the drugs isoniazid and rifampin, which have implications in the study of multi-drug-resistant mycobacteria. A wealth of structural studies on efflux pumps from diverse bacteria has also fueled the design of new small-molecule and peptide-based agents to prevent the active transport of antibiotics. We envision that these findings will inspire microbiologists to apply existing adjuvants to clinically relevant resistant strains, or to use described platforms to discover novel antibiotic adjuvant scaffolds.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA.
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43
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Ago R, Tahara YO, Yamaguchi H, Saito M, Ito W, Yamasaki K, Kasai T, Okamoto S, Chikada T, Oshima T, Osaka I, Miyata M, Niki H, Shiomi D. Relationship between the Rod complex and peptidoglycan structure in Escherichia coli. Microbiologyopen 2023; 12:e1385. [PMID: 37877652 PMCID: PMC10561026 DOI: 10.1002/mbo3.1385] [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: 08/28/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Peptidoglycan for elongation in Escherichia coli is synthesized by the Rod complex, which includes RodZ. Although various mutant strains of the Rod complex have been isolated, the relationship between the activity of the Rod complex and the overall physical and chemical structures of the peptidoglycan have not been reported. We constructed a RodZ mutant, termed RMR, and analyzed the growth rate, morphology, and other characteristics of cells producing the Rod complexes containing RMR. The growth and morphology of RMR cells were abnormal, and we isolated suppressor mutants from RMR cells. Most of the suppressor mutations were found in components of the Rod complex, suggesting that these suppressor mutations increase the integrity and/or the activity of the Rod complex. We purified peptidoglycan from wild-type, RMR, and suppressor mutant cells and observed their structures in detail. We found that the peptidoglycan purified from RMR cells had many large holes and different compositions of muropeptides from those of WT cells. The Rod complex may be a determinant not only for the whole shape of peptidoglycan but also for its highly dense structure to support the mechanical strength of the cell wall.
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Affiliation(s)
- Risa Ago
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Yuhei O. Tahara
- Graduate School of ScienceOsaka Metropolitan UniversityOsakaJapan
- The OMU Advanced Research Center for Natural Science and TechnologyOsaka Metropolitan UniversityOsakaJapan
| | - Honoka Yamaguchi
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Motoya Saito
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Wakana Ito
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Kaito Yamasaki
- Department of Pharmaceutical Engineering, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Taishi Kasai
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Sho Okamoto
- Microbial Physiology Laboratory, Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
| | - Taiki Chikada
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Taku Oshima
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Issey Osaka
- Department of Pharmaceutical Engineering, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Makoto Miyata
- Graduate School of ScienceOsaka Metropolitan UniversityOsakaJapan
- The OMU Advanced Research Center for Natural Science and TechnologyOsaka Metropolitan UniversityOsakaJapan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
- Department of GeneticsThe Graduate University for Advanced Studies, SOKENDAIMishimaShizuokaJapan
| | - Daisuke Shiomi
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
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Zhu H, Peng N, Liang X, Yang S, Cai S, Chen Z, Yang Y, Wang J, Wang Y. Synthesis, properties and mechanism of carbon dots-based nano-antibacterial materials. Biomed Mater 2023; 18:062002. [PMID: 37722396 DOI: 10.1088/1748-605x/acfada] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/18/2023] [Indexed: 09/20/2023]
Abstract
Antibiotics play an important role in the treatment of diseases, but bacterial resistance caused by their widespread and unreasonable use has become an urgent problem in clinical treatment. With the rapid advancement of nanoscience and nanotechnology, the development of nanomedicine has been transformed into a new approach to the problem of bacterial resistance. As a new type of carbon-based nanomaterial, carbon dots (CDs) have attracted the interest of antibacterial researchers due to their ease of preparation, amphiphilicity, facile surface functionalization, and excellent optical properties, among other properties. This article reviewed the synthesis methods and properties of various CDs and their composites in order to highlight the advancements in the field of CDs-based antibacterial agents. Then we focused on the relationship between the principal properties of CDs and the antibacterial mechanism, including the following: (1) the physical damage caused by the small size, amphiphilicity, and surface charge of CDs. (2) Photogenerated electron transfer characteristics of CDs that produce reactive oxygen species (ROS) in themselves or in other compounds. The ability of ROS to oxidize can lead to the lipid peroxidation of cell membranes, as well as damage proteins and DNA. (3) The nano-enzyme properties of CDs can catalyze reactions that generate ROS. (4) Synergistic antibacterial effect of CDs and antibiotics or other nanocomposites. Finally, we look forward to the challenges that CDs-based nanocomposites face in practical antibacterial applications and propose corresponding solutions to further expand the application potential of nanomaterials in the treatment of infectious diseases, particularly drug-resistant bacterial infections.
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Affiliation(s)
- Haimei Zhu
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, People's Republic of China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, People's Republic of China
| | - Nannan Peng
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, People's Republic of China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, People's Republic of China
| | - Xiao Liang
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, People's Republic of China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, People's Republic of China
| | - Song Yang
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, People's Republic of China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, People's Republic of China
| | - Shenghao Cai
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, People's Republic of China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, People's Republic of China
| | - Zifan Chen
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, People's Republic of China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, People's Republic of China
| | - Yang Yang
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, People's Republic of China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, People's Republic of China
| | - Jingmin Wang
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, People's Republic of China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, People's Republic of China
| | - Yongzhong Wang
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, People's Republic of China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, People's Republic of China
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45
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Fang Y, Yang G, Wu X, Qin B, Xie Y, Zhuang L. Sub-MIC antibiotics affect microbial ferrihydrite reduction by extracellular membrane vesicles. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131876. [PMID: 37379597 DOI: 10.1016/j.jhazmat.2023.131876] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Environmental concentrations of antibiotics, usually below MIC, have significant biological effects on bacterial cells. Sub-MIC antibiotics exposure induces bacteria to produce outer membrane vesicles (OMVs). Recently, OMVs is discovered as a novel pathway for dissimilatory iron reducing bacteria (DIRB) to mediate extracellular electron transfer (EET). Whether and how the antibiotic-induced OMVs modulate iron oxides reduction by DIRB have not been studied. This study showed the sub-MIC antibiotics (ampicillin or ciprofloxacin) increased OMVs secretion in Geobacter sulfurreducens, and the antibiotic-induced OMVs contained more redox active cytochromes facilitating iron oxides reduction, especially for the ciprofloxacin-induced OMVs. Deduced from a combination of electron microscopy and proteomic analysis, the influence of ciprofloxacin on SOS response triggered prophage induction and led to the formation of outer-inner membrane vesicles (OIMVs) in, which was a first report in Geobacter species. While ampicillin disrupting cell membrane integrity resulted in more formation of classic OMVs from outer membrane blebbing. The results indicated that the different structure and composition of vesicles were responsible for the antibiotic-dependent regulation on iron oxides reduction. This newly identified regulation on EET-mediated redox reactions by sub-MIC antibiotics expands our knowledge about the impact of antibiotics on microbial processes or "non-target" organisms.
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Affiliation(s)
- Yanlun Fang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
| | - Xian Wu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Baoli Qin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yiqiao Xie
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
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46
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Zhang H, Venkatesan S, Ng E, Nan B. Coordinated peptidoglycan synthases and hydrolases stabilize the bacterial cell wall. Nat Commun 2023; 14:5357. [PMID: 37660104 PMCID: PMC10475089 DOI: 10.1038/s41467-023-41082-3] [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: 04/01/2022] [Accepted: 08/21/2023] [Indexed: 09/04/2023] Open
Abstract
Peptidoglycan (PG) defines cell shape and protects bacteria against osmotic stress. The growth and integrity of PG require coordinated actions between synthases that insert new PG strands and hydrolases that generate openings to allow the insertion. However, the mechanisms of their coordination remain elusive. Moenomycin that inhibits a family of PG synthases known as Class-A penicillin-binding proteins (aPBPs), collapses rod shape despite aPBPs being non-essential for rod-like morphology in the bacterium Myxococcus xanthus. Here, we demonstrate that inhibited PBP1a2, an aPBP, accelerates the degradation of cell poles by DacB, a hydrolytic PG peptidase. Moenomycin promotes the binding between DacB and PG and thus reduces the mobility of DacB through PBP1a2. Conversely, DacB also regulates the distribution and dynamics of aPBPs. Our findings clarify the action of moenomycin and suggest that disrupting the coordination between PG synthases and hydrolases could be more lethal than eliminating individual enzymes.
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Affiliation(s)
- Huan Zhang
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Srutha Venkatesan
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Emily Ng
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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47
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Alberge F, Lakey BD, Schaub RE, Dohnalkova AC, Lemmer KC, Dillard JP, Noguera DR, Donohue TJ. A previously uncharacterized divisome-associated lipoprotein, DalA, is needed for normal cell division in Rhodobacterales. mBio 2023; 14:e0120323. [PMID: 37389444 PMCID: PMC10470522 DOI: 10.1128/mbio.01203-23] [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: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
The bacterial cell envelope is a key subcellular compartment with important roles in antibiotic resistance, nutrient acquisition, and cell morphology. We seek to gain a better understanding of proteins that contribute to the function of the cell envelope in Alphaproteobacteria. Using Rhodobacter sphaeroides, we show that a previously uncharacterized protein, RSP_1200, is an outer membrane (OM) lipoprotein that non-covalently binds peptidoglycan (PG). Using a fluorescently tagged version of this protein, we find that RSP_1200 undergoes a dynamic repositioning during the cell cycle and is enriched at the septum during cell division. We show that the position of RSP_1200 mirrors the location of FtsZ rings, leading us to propose that RSP_1200 is a newly identified component of the R. sphaeroides' divisome. Additional support for this hypothesis includes the co-precipitation of RSP_1200 with FtsZ, the Pal protein, and several predicted PG L,D-transpeptidases. We also find that a ∆RSP_1200 mutation leads to defects in cell division, sensitivity to PG-active antibiotics, and results in the formation of OM protrusions at the septum during cell division. Based on these results, we propose to name RSP_1200 DalA (for division-associated lipoprotein A) and postulate that DalA serves as a scaffold to position or modulate the activity of PG transpeptidases that are needed to form envelope invaginations during cell division. We find that DalA homologs are present in members of the Rhodobacterales order within Alphaproteobacteria. Therefore, we propose that further analysis of this and related proteins will increase our understanding of the macromolecular machinery and proteins that participate in cell division in Gram-negative bacteria. IMPORTANCE Multi-protein complexes of the bacterial cell envelope orchestrate key processes like growth, division, biofilm formation, antimicrobial resistance, and production of valuable compounds. The subunits of these protein complexes are well studied in some bacteria, and differences in their composition and function are linked to variations in cell envelope composition, shape, and proliferation. However, some envelope protein complex subunits have no known homologs across the bacterial phylogeny. We find that Rhodobacter sphaeroides RSP_1200 is a newly identified lipoprotein (DalA) and that loss of this protein causes defects in cell division and changes the sensitivity to compounds, affecting cell envelope synthesis and function. We find that DalA forms a complex with proteins needed for cell division, binds the cell envelope polymer peptidoglycan, and colocalizes with enzymes involved in the assembly of this macromolecule. The analysis of DalA provides new information on the cell division machinery in this and possibly other Alphaproteobacteria.
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Affiliation(s)
- François Alberge
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Bryan D. Lakey
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan E. Schaub
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alice C. Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Joseph P. Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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48
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Fivenson EM, Rohs PDA, Vettiger A, Sardis MF, Torres G, Forchoh A, Bernhardt TG. A role for the Gram-negative outer membrane in bacterial shape determination. Proc Natl Acad Sci U S A 2023; 120:e2301987120. [PMID: 37607228 PMCID: PMC10469335 DOI: 10.1073/pnas.2301987120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/21/2023] [Indexed: 08/24/2023] Open
Abstract
The cell envelope of Gram-negative bacteria consists of three distinct layers: the cytoplasmic membrane, a cell wall made of peptidoglycan (PG), and an asymmetric outer membrane (OM) composed of phospholipid in the inner leaflet and lipopolysaccharide (LPS) glycolipid in the outer leaflet. The PG layer has long been thought to be the major structural component of the envelope protecting cells from osmotic lysis and providing them with their characteristic shape. In recent years, the OM has also been shown to be a load-bearing layer of the cell surface that fortifies cells against internal turgor pressure. However, whether the OM also plays a role in morphogenesis has remained unclear. Here, we report that changes in LPS synthesis or modification predicted to strengthen the OM can suppress the growth and shape defects of Escherichia coli mutants with reduced activity in a conserved PG synthesis machine called the Rod complex (elongasome) that is responsible for cell elongation and shape determination. Evidence is presented that OM fortification in the shape mutants restores the ability of MreB cytoskeletal filaments to properly orient the synthesis of new cell wall material by the Rod complex. Our results are therefore consistent with a role for the OM in the propagation of rod shape during growth in addition to its well-known function as a diffusion barrier promoting the intrinsic antibiotic resistance of Gram-negative bacteria.
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Affiliation(s)
- Elayne M. Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Patricia D. A. Rohs
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Andrea Vettiger
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Marios F. Sardis
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Grasiela Torres
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Alison Forchoh
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Thomas G. Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- HHMI, Chevy Chase, MD20815
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49
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Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S, Belenky P. Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis. Microbiol Spectr 2023; 11:e0237623. [PMID: 37439681 PMCID: PMC10434222 DOI: 10.1128/spectrum.02376-23] [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: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/14/2023] Open
Abstract
Antibiotic-induced gut microbiome dysbiosis (AID) is known to be influenced by host dietary composition. However, how and when diet modulates gut dysbiosis remains poorly characterized. Thus, here, we utilize a multi-omics approach to characterize how a diet supplemented with oats, a rich source of microbiota-accessible carbohydrates, or dextrose impacts amoxicillin-induced changes to gut microbiome structure and transcriptional activity. We demonstrate that oat administration during amoxicillin challenge provides greater protection from AID than the always oats or recovery oats diet groups. In particular, the group in which oats were provided at the time of antibiotic exposure induced the greatest protection against AID while the other oat diets saw greater effects after amoxicillin challenge. The oat diets likewise reduced amoxicillin-driven elimination of Firmicutes compared to the dextrose diet. Functionally, gut communities fed dextrose were carbohydrate starved and favored respiratory metabolism and consequent metabolic stress management while oat-fed communities shifted their transcriptomic profile and emphasized antibiotic stress management. The metabolic trends were exemplified when assessing transcriptional activity of the following two common gut commensal bacteria: Akkermansia muciniphila and Bacteroides thetaiotaomicron. These findings demonstrate that while host diet is important in shaping how antibiotics effect the gut microbiome composition and function, diet timing may play an even greater role in dietary intervention-based therapeutics. IMPORTANCE We utilize a multi-omics approach to demonstrate that diets supplemented with oats, a rich source of microbiota-accessible carbohydrates, are able to confer protection against antibiotic-induced dysbiosis (AID). Our findings affirm that not only is host diet important in shaping antibiotics effects on gut microbiome composition and function but also that the timing of these diets may play an even greater role in managing AID. This work provides a nuanced perspective on dietary intervention against AID and may be informative on preventing AID during routine antibiotic treatment.
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Affiliation(s)
- Stephen K. Costa
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Katherine Antosca
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Chapman N. Beekman
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Rachel L. Peterson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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50
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Izquierdo-Martinez A, Billini M, Miguel-Ruano V, Hernández-Tamayo R, Richter P, Biboy J, Batuecas MT, Glatter T, Vollmer W, Graumann PL, Hermoso JA, Thanbichler M. DipM controls multiple autolysins and mediates a regulatory feedback loop promoting cell constriction in Caulobacter crescentus. Nat Commun 2023; 14:4095. [PMID: 37433794 DOI: 10.1038/s41467-023-39783-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Proteins with a catalytically inactive LytM-type endopeptidase domain are important regulators of cell wall-degrading enzymes in bacteria. Here, we study their representative DipM, a factor promoting cell division in Caulobacter crescentus. We show that the LytM domain of DipM interacts with multiple autolysins, including the soluble lytic transglycosylases SdpA and SdpB, the amidase AmiC and the putative carboxypeptidase CrbA, and stimulates the activities of SdpA and AmiC. Its crystal structure reveals a conserved groove, which is predicted to represent the docking site for autolysins by modeling studies. Mutations in this groove indeed abolish the function of DipM in vivo and its interaction with AmiC and SdpA in vitro. Notably, DipM and its targets SdpA and SdpB stimulate each other's recruitment to midcell, establishing a self-reinforcing cycle that gradually increases autolytic activity as cytokinesis progresses. DipM thus coordinates different peptidoglycan-remodeling pathways to ensure proper cell constriction and daughter cell separation.
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Affiliation(s)
- Adrian Izquierdo-Martinez
- Department of Biology, University of Marburg, Marburg, Germany
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Maria Billini
- Department of Biology, University of Marburg, Marburg, Germany
| | - Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Rogelio Hernández-Tamayo
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Pia Richter
- Department of Biology, University of Marburg, Marburg, Germany
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - María T Batuecas
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Timo Glatter
- Mass Spectrometry and Proteomics Facility, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Peter L Graumann
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, Germany.
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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