1
|
Qin J, Hong Y, Totsika M. Determining glycosyltransferase functional order via lethality due to accumulated O-antigen intermediates, exemplified with Shigella flexneri O-antigen biosynthesis. Appl Environ Microbiol 2024; 90:e0220323. [PMID: 38747588 PMCID: PMC11218652 DOI: 10.1128/aem.02203-23] [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: 12/07/2023] [Accepted: 04/09/2024] [Indexed: 06/19/2024] Open
Abstract
The O antigen (OAg) polysaccharide is one of the most diverse surface molecules of Gram-negative bacterial pathogens. The structural classification of OAg, based on serological typing and sequence analysis, is important in epidemiology and the surveillance of outbreaks of bacterial infections. Despite the diverse chemical structures of OAg repeating units (RUs), the genetic basis of RU assembly remains poorly understood and represents a major limitation in assigning gene functions in polysaccharide biosynthesis. Here, we describe a genetic approach to interrogate the functional order of glycosyltransferases (GTs). Using Shigella flexneri as a model, we established an initial glycosyltransferase (IT)-controlled system, which allows functional order allocation of the subsequent GT in a 2-fold manner as follows: (i) first, by reporting the growth defects caused by the sequestration of UndP through disruption of late GTs and (ii) second, by comparing the molecular sizes of stalled OAg intermediates when each putative GT is disrupted. Using this approach, we demonstrate that for RfbF and RfbG, the GT involved in the assembly of S. flexneri backbone OAg RU, RfbG, is responsible for both the committed step of OAg synthesis and the third transferase for the second L-Rha. We also show that RfbF functions as the last GT to complete the S. flexneri OAg RU backbone. We propose that this simple and effective genetic approach can be also extended to define the functional order of enzymatic synthesis of other diverse polysaccharides produced both by Gram-negative and Gram-positive bacteria.IMPORTANCEThe genetic basis of enzymatic assembly of structurally diverse O antigen (OAg) repeating units (RUs) in Gram-negative pathogens is poorly understood, representing a major limitation in our understanding of gene functions for the synthesis of bacterial polysaccharides. We present a simple genetic approach to confidently assign glycosyltransferase (GT) functions and the order in which they act during assembly of the OAg RU. We employed this approach to determine the functional order of GTs involved in Shigella flexneri OAg assembly. This approach can be generally applied in interrogating GT functions encoded by other bacterial polysaccharides to advance our understanding of diverse gene functions in the biosynthesis of polysaccharides, key knowledge in advancing biosynthetic polysaccharide production.
Collapse
Affiliation(s)
- Jilong Qin
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Yaoqin Hong
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Max Planck Queensland Centre, Queensland University of Technology, Brisbane City, Queensland, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Max Planck Queensland Centre, Queensland University of Technology, Brisbane City, Queensland, Australia
| |
Collapse
|
2
|
Zhang P, Zhang B, Ji Y, Jiao J, Zhang Z, Tian C. Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome. MLIFE 2024; 3:277-290. [PMID: 38948139 PMCID: PMC11211677 DOI: 10.1002/mlf2.12132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/20/2024] [Accepted: 04/24/2024] [Indexed: 07/02/2024]
Abstract
Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function, while accessory genes are dispensable, particularly in nutrient-rich environments. However, this assumption is seldom tested genetically within the pangenome context. In this study, we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for Sinorhizobium strains with a canonical open pangenome. To evaluate the robustness of fitness category assignment, Tn-seq data for three independent mutant libraries per strain were analyzed by three methods, which indicates that the Hidden Markov Model (HMM)-based method is most robust to variations between mutant libraries and not sensitive to data size, outperforming the Bayesian and Monte Carlo simulation-based methods. Consequently, the HMM method was used to classify the fitness category. Fitness genes, categorized as essential (ES), advantage (GA), and disadvantage (GD) genes for growth, are enriched in core genes, while nonessential genes (NE) are over-represented in accessory genes. Accessory ES/GA genes showed a lower fitness effect than core ES/GA genes. Connectivity degrees in the cofitness network decrease in the order of ES, GD, and GA/NE. In addition to accessory genes, 1599 out of 3284 core genes display differential essentiality across test strains. Within the pangenome core, both shared quasi-essential (ES and GA) and strain-dependent fitness genes are enriched in similar functional categories. Our analysis demonstrates a considerable fuzzy essential zone determined by cofitness connectivity degrees in Sinorhizobium pangenome and highlights the power of the cofitness network in understanding the genetic basis of ever-increasing prokaryotic pangenome data.
Collapse
Affiliation(s)
- Pan Zhang
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
- Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Biliang Zhang
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
- State Key Laboratory of Livestock and Poultry Biotechnology Breeding, and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yuan‐Yuan Ji
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
| | - Jian Jiao
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
| | - Ziding Zhang
- State Key Laboratory of Livestock and Poultry Biotechnology Breeding, and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Chang‐Fu Tian
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Jacinto-Méndez D, Granados-Ramírez CG, Carbajal-Tinoco MD. KCD: A prediction web server of knowledge-based circular dichroism. Protein Sci 2024; 33:e4967. [PMID: 38532692 DOI: 10.1002/pro.4967] [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: 10/14/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/28/2024]
Abstract
We present a web server that predicts the far-UV circular dichroism (CD) spectra of proteins by utilizing their three-dimensional (3D) structures from the Protein Data Bank (PDB). The main algorithm is based on the classical theory of optical activity together with a set of atomic complex polarizabilities, which are obtained from the analysis of a series of synchrotron radiation CD spectra and their related 3D structures from the PDB. The results of our knowledge-based CD method (KCD) are in good agreement with measured spectra that could include the effect of D-amino acids. Our method also delivers some of the most accurate predictions, in comparison with the calculated spectra from well-established models. Specifically, using a metric of closeness based on normalized absolute deviations between experimental and calculated spectra, the mean values for a series of 57 test proteins give the following figures for such models: 0.26 KCD, 0.27 PDBMD2CD, 0.30 SESCA, and 0.47 DichroCalc. From another point of view, it is worth mentioning the remarkable capabilities of the recent approaches based on artificial intelligence, which can precisely predict the native structure of proteins. The structure of proteins, however, is flexible and can be modified by a diversity of environmental factors such as interactions with other molecules, mechanical stresses, variations of temperature, pH, or ionic strength. Experimental CD spectra together with reliable predictions can be utilized to assess eventual secondary structural changes. A similar kind of evaluation can be done for the case of an incomplete protein structure that has been reconstructed by using different approaches. The KCD method can be freely accessed from: https://kcd.cinvestav.mx/.
Collapse
Affiliation(s)
- Damián Jacinto-Méndez
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City, Mexico
| | | | | |
Collapse
|
5
|
Tan Z, Tezuka T, Ohnishi Y. Identification of a putative cell wall-hydrolyzing amidase involved in sporangiospore maturation in Actinoplanes missouriensis. J Bacteriol 2024; 206:e0045623. [PMID: 38426722 PMCID: PMC10955841 DOI: 10.1128/jb.00456-23] [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: 12/31/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Actinoplanes missouriensis is a filamentous bacterium that differentiates into terminal sporangia, each containing a few hundred spores. Previously, we reported that a cell wall-hydrolyzing N-acetylglucosaminidase, GsmA, is required for the maturation process of sporangiospores in A. missouriensis; sporangia of the gsmA null mutant (ΔgsmA) strain released chains of 2-20 spores under sporangium dehiscence-inducing conditions. In this study, we identified and characterized a putative cell wall hydrolase (AsmA) that is also involved in sporangiospore maturation. AsmA was predicted to have a signal peptide for the general secretion pathway and an N-acetylmuramoyl-l-alanine amidase domain. The transcript level of asmA increased during the early stages of sporangium formation. The asmA null mutant (ΔasmA) strain showed phenotypes similar to those of the wild-type strain, but sporangia of the ΔgsmAΔasmA double mutant released longer spore chains than those from the ΔgsmA sporangia. Furthermore, a weak interaction between AsmA and GsmA was detected in a bacterial two-hybrid assay using Escherichia coli as the host. Based on these results, we propose that AsmA is an enzyme that hydrolyzes peptidoglycan at septum-forming sites to separate adjacent spores during sporangiospore maturation in cooperation with GsmA in A. missouriensis.IMPORTANCEActinoplanes missouriensis produces sporangiospores as dormant cells. The spores inside the sporangia are assumed to be formed from prespores generated by the compartmentalization of intrasporangium hyphae via septation. Previously, we identified GsmA as a cell wall hydrolase responsible for the separation of adjacent spores inside sporangia. However, we predicted that an additional cell wall hydrolase(s) is inevitably involved in the maturation process of sporangiospores because the sporangia of the gsmA null mutant strain released not only tandemly connected spore chains (2-20 spores) but also single spores. In this study, we successfully identified a putative cell wall hydrolase (AsmA) that is involved in sporangiospore maturation in A. missouriensis.
Collapse
Affiliation(s)
- Zhuwen Tan
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
6
|
Koatale P, Welling MM, Ndlovu H, Kgatle M, Mdanda S, Mdlophane A, Okem A, Takyi-Williams J, Sathekge MM, Ebenhan T. Insights into Peptidoglycan-Targeting Radiotracers for Imaging Bacterial Infections: Updates, Challenges, and Future Perspectives. ACS Infect Dis 2024; 10:270-286. [PMID: 38290525 PMCID: PMC10862554 DOI: 10.1021/acsinfecdis.3c00443] [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: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 02/01/2024]
Abstract
The unique structural architecture of the peptidoglycan allows for the stratification of bacteria as either Gram-negative or Gram-positive, which makes bacterial cells distinguishable from mammalian cells. This classification has received attention as a potential target for diagnostic and therapeutic purposes. Bacteria's ability to metabolically integrate peptidoglycan precursors during cell wall biosynthesis and recycling offers an opportunity to target and image pathogens in their biological state. This Review explores the peptidoglycan biosynthesis for bacteria-specific targeting for infection imaging. Current and potential radiolabeled peptidoglycan precursors for bacterial infection imaging, their development status, and their performance in vitro and/or in vivo are highlighted. We conclude by providing our thoughts on how to shape this area of research for future clinical translation.
Collapse
Affiliation(s)
- Palesa
C. Koatale
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Mick M. Welling
- Interventional
Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Honest Ndlovu
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Mankgopo Kgatle
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Sipho Mdanda
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Amanda Mdlophane
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Ambrose Okem
- Department
of Anaesthesia, School of Clinical Medicine, University of Witwatersrand, 2050 Johannesburg, South Africa
| | - John Takyi-Williams
- Pharmacokinetic
and Mass Spectrometry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mike M. Sathekge
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Thomas Ebenhan
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
- DSI/NWU Pre-clinical
Drug Development Platform, North West University, 2520 Potchefstroom, South Africa
| |
Collapse
|
7
|
Tang Y, Yang G, Ma Y, Huang D, Zhai W, Fodjo EK, Zhang X, Li S, Zhang W, Shi Y, Kong C. Development, validation, and implementation of an ultratrace analysis method for the determination of moenomycin A, in aquatic animal products. Anal Bioanal Chem 2024; 416:745-757. [PMID: 37812219 DOI: 10.1007/s00216-023-04965-4] [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: 08/02/2023] [Revised: 09/09/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023]
Abstract
Moenomycin A, an antimicrobial growth promoter widely used as an additive in aquaculture feedstuffs, has been restricted for use in the European Union and China due to its potential risk of promoting resistant strains of pathogenic bacteria and causing residues in aquatic animal products. Although methods for analyzing moenomycin A in feedstuffs have been developed, no established method exists for aquatic matrices. In this study, we present, for the first time, a sensitive and validated high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method for the determination of moenomycin A in aquatic animal products. Samples were extracted using methanol and purified with the QuEChERS method employing C18 sorbent. The aliquot was dried under a nitrogen stream, reconstituted with methanol-water solvent, and analyzed by HPLC-MS/MS. The developed method exhibited good linearity (r2 > 0.995) over a wide concentration range (1-100 μg/L) and a low limit of detection (1 µg/kg). Average recoveries ranged between 70 and 110% at spiked concentrations of 1, 50, and 100 μg/kg, with associated intra- and inter-day relative standard deviations of 1.25 to 7.32% (n = 6) and 2.91 to 10.08% (n = 3), for different representative aquatic animal production, respectively. To the best of our knowledge, this is the first reported HPLC-MS/MS method for the quantification of moenomycin A in aquatic animal products. The new approach was effectively employed in the analysis of moenomycin A across various aquatic samples.
Collapse
Affiliation(s)
- Yunyu Tang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Jungong 300, Shanghai, 200090, People's Republic of China
| | - Guangxin Yang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Jungong 300, Shanghai, 200090, People's Republic of China
| | - Yingqing Ma
- Shanghai Center of Agri-Product Quality and Safety, Xinfu Middle Road 1528, No.28, Shanghai, 201708, People's Republic of China
| | - Dongmei Huang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Jungong 300, Shanghai, 200090, People's Republic of China.
| | - Wenlei Zhai
- Institute of Quality Standard and Testing Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Essy Kouadio Fodjo
- Laboratory of Constitution and Reaction of Matter, UFR SSMT, Université Felix Houphouet Boigny, 22 BP 582 Abidjan 22, Abidjan, Côte d'Ivoire
| | - Xuan Zhang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Jungong 300, Shanghai, 200090, People's Republic of China
| | - Siman Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Jungong 300, Shanghai, 200090, People's Republic of China
| | - Weiyi Zhang
- Shanghai Center of Agri-Product Quality and Safety, Xinfu Middle Road 1528, No.28, Shanghai, 201708, People's Republic of China.
| | - Yongfu Shi
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Jungong 300, Shanghai, 200090, People's Republic of China
| | - Cong Kong
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Jungong 300, Shanghai, 200090, People's Republic of China.
| |
Collapse
|
8
|
Li X, Ma Z, Tang Q, Gui Z, Zhang B, Sun G, Li J, Li J, Li M, Li X, Ma H, Ye X. 8-octyl berberine combats Staphylococcus aureus by preventing peptidoglycan synthesis. Eur J Pharm Sci 2023; 191:106602. [PMID: 37806408 DOI: 10.1016/j.ejps.2023.106602] [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: 08/01/2023] [Revised: 09/14/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
Staphylococcus aureus is an important pathogenic bacterium responsible for various organ infections. The serious side effects and the development of antibiotic resistance have rendered the antibiotic therapy against S. aureus increasingly challenging, emphasizing the pressing need for the exploration of novel therapeutic agents. Our research has uncovered the promising antimicrobial properties of 8-octyl berberine (OBBR), a novel compound derived from berberine (BBR), against S. aureus. OBBR exhibited a minimum inhibitory concentration (MIC) of 1.0 μg/mL, which closely approximated that of levofloxacin. Intriguingly, a multipassage resistance assay demonstrated that the MIC of OBBR against S. aureus remained relatively stable, while levofloxacin exhibited a 4-fold increase over 20 days, suggesting that OBBR was less prone to inducing resistance. Mechanistically, our investigation, employing Zeta potential measurements, flow cytometry, scanning electron microscopy, and transmission electron microscopy, unveiled that OBBR induced morphological alterations in the bacteria. Furthermore, it disrupted the bacterial cell wall and membrane by altering membrane potential and compromising membrane integrity. These actions culminated in bacterial disintegration and apoptosis. Transcriptomic analysis shed light on significant downregulation of gene ontology terms, predominantly associated with membranes. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis implicated OBBR in disturbing peptidoglycan biosynthesis, with the membrane protein MraY emerging as a potential target for OBBR's action against S. aureus. Notably, experiments involving the overexpression of MraY confirmed OBBR's inhibitory effect on peptidoglycan synthesis. Furthermore, molecular docking and cellular thermal shift assay revealed OBBR's direct interaction with MraY, potentially leading to the inhibition of the enzymatic activity of MraY and, consequently, impeding peptidoglycan synthesis. In summary, OBBR, by targeting MraY and inhibiting peptidoglycan synthesis, emerges as a promising alternative antibiotic against S. aureus, offering potential advantages in terms of limited drug resistance development.
Collapse
Affiliation(s)
- Xiaoduo Li
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China; Department of Clinical Laboratory, AnShun City People's Hospital, Guizhou 561000, China
| | - Zhengcai Ma
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qin Tang
- College of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, 400715, China
| | - Zhenwei Gui
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Biao Zhang
- Department of Clinical Laboratory, AnShun City People's Hospital, Guizhou 561000, China
| | - Guang Sun
- Department of Clinical Laboratory, AnShun City People's Hospital, Guizhou 561000, China
| | - Jingwei Li
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Juan Li
- College of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, 400715, China
| | - Mengmeng Li
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xuegang Li
- College of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, 400715, China
| | - Hang Ma
- College of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, 400715, China.
| | - Xiaoli Ye
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
9
|
Alsenani TA, Viviani SL, Papp-Wallace KM, Bonomo RA, van den Akker F. Exploring avibactam and relebactam inhibition of Klebsiella pneumoniae carbapenemase D179N variant: role of the Ω loop-held deacylation water. Antimicrob Agents Chemother 2023; 67:e0035023. [PMID: 37750722 PMCID: PMC10583681 DOI: 10.1128/aac.00350-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/27/2023] [Indexed: 09/27/2023] Open
Abstract
Klebsiella pneumoniae carbapenemase-2 (KPC-2) presents a clinical threat as this β-lactamase confers resistance to carbapenems. Recent variants of KPC-2 in clinical isolates contribute to concerning resistance phenotypes. Klebsiella pneumoniae expressing KPC-2 D179Y acquired resistance to the ceftazidime/avibactam combination affecting both the β-lactam and the β-lactamase inhibitor yet has lowered minimum inhibitory concentrations for all other β-lactams tested. Furthermore, Klebsiella pneumoniae expressing the KPC-2 D179N variant also manifested resistance to ceftazidime/avibactam yet retained its ability to confer resistance to carbapenems although significantly reduced. This structural study focuses on the inhibition of KPC-2 D179N by avibactam and relebactam and expands our previous analysis that examined ceftazidime resistance conferred by D179N and D179Y variants. Crystal structures of KPC-2 D179N soaked with avibactam and co-crystallized with relebactam were determined. The complex with avibactam reveals avibactam making several hydrogen bonds, including with the deacylation water held in place by Ω loop. These results could explain why the KPC-2 D179Y variant, which has a disordered Ω loop, has a decreased affinity for avibactam. The relebactam KPC-2 D179N complex revealed a new orientation of the diazabicyclooctane (DBO) intermediate with the scaffold piperidine ring rotated ~150° from the standard DBO orientation. The density shows relebactam to be desulfated and present as an imine-hydrolysis intermediate not previously observed. The tetrahedral imine moiety of relebactam interacts with the deacylation water. The rotated relebactam orientation and deacylation water interaction could potentially contribute to KPC-mediated DBO fragmentation. These results elucidate important differences that could aid in the design of novel β-lactamase inhibitors.
Collapse
Affiliation(s)
- T. A. Alsenani
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - S. L. Viviani
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - K. M. Papp-Wallace
- Clinical Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, North liberty, Iowa, USA
| | - R. A. Bonomo
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Clinical Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, North liberty, Iowa, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, 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
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - F. van den Akker
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| |
Collapse
|
10
|
Brogan AP, Habib C, Hobbs SJ, Kranzusch PJ, Rudner DZ. Bacterial SEAL domains undergo autoproteolysis and function in regulated intramembrane proteolysis. Proc Natl Acad Sci U S A 2023; 120:e2310862120. [PMID: 37756332 PMCID: PMC10556640 DOI: 10.1073/pnas.2310862120] [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: 06/27/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Gram-positive bacteria use SigI/RsgI-family sigma factor/anti-sigma factor pairs to sense and respond to cell wall defects and plant polysaccharides. In Bacillus subtilis, this signal transduction pathway involves regulated intramembrane proteolysis (RIP) of the membrane-anchored anti-sigma factor RsgI. However, unlike most RIP signaling pathways, site-1 cleavage of RsgI on the extracytoplasmic side of the membrane is constitutive and the cleavage products remain stably associated, preventing intramembrane proteolysis. The regulated step in this pathway is their dissociation, which is hypothesized to involve mechanical force. Release of the ectodomain enables intramembrane cleavage by the RasP site-2 protease and activation of SigI. The constitutive site-1 protease has not been identified for any RsgI homolog. Here, we report that RsgI's extracytoplasmic domain has structural and functional similarities to eukaryotic SEA domains that undergo autoproteolysis and have been implicated in mechanotransduction. We show that site-1 proteolysis in B. subtilis and Clostridial RsgI family members is mediated by enzyme-independent autoproteolysis of these SEA-like domains. Importantly, the site of proteolysis enables retention of the ectodomain through an undisrupted β-sheet that spans the two cleavage products. Autoproteolysis can be abrogated by relief of conformational strain in the scissile loop, in a mechanism analogous to eukaryotic SEA domains. Collectively, our data support the model that RsgI-SigI signaling is mediated by mechanotransduction in a manner that has striking parallels with eukaryotic mechanotransducive signaling pathways.
Collapse
Affiliation(s)
- Anna P. Brogan
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Cameron Habib
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Samuel J. Hobbs
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA02115
| | - Philip J. Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA02115
| | - David Z. Rudner
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| |
Collapse
|
11
|
Chen LM, de Bruin S, Pronk M, Sousa DZ, van Loosdrecht MCM, Lin Y. Sialylation and Sulfation of Anionic Glycoconjugates Are Common in the Extracellular Polymeric Substances of Both Aerobic and Anaerobic Granular Sludges. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13217-13225. [PMID: 37604486 PMCID: PMC10483923 DOI: 10.1021/acs.est.2c09586] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/14/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
Anaerobic and aerobic granular sludge processes are widely applied in wastewater treatment. In these systems, microorganisms grow in dense aggregates due to the production of extracellular polymeric substances (EPS). This study investigates the sialylation and sulfation of anionic glyconconjugates in anaerobic and aerobic granular sludges collected from full-scale wastewater treatment processes. Size exclusion chromatography revealed a wide molecular weight distribution (3.5 to >5500 kDa) of the alkaline-extracted EPS. The high-molecular weight fraction (>5500 kDa), comprising 16.9-27.4% of EPS, was dominant with glycoconjugates. Mass spectrometry analysis and quantification assays identified nonulosonic acids (NulOs, e.g., bacterial sialic acids) and sulfated groups contributing to the negative charge in all EPS fractions. NulOs were predominantly present in the high-molecular weight fraction (47.2-84.3% of all detected NulOs), while sulfated glycoconjugates were distributed across the molecular weight fractions. Microorganisms, closely related to genera found in the granular sludge communities, contained genes responsible for NulO and sulfate group synthesis or transfer. The similar distribution patterns of sialylation and sulfation of the anionic glycoconjugates in the EPS samples indicate that these two glycoconjugate modifications commonly occur in the EPS of aerobic and anaerobic granular sludges.
Collapse
Affiliation(s)
- Le Min Chen
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Stefan de Bruin
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mario Pronk
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
- Royal
HaskoningDHV, Laan 1914
35, Amersfoort 3800 AL, The Netherlands
| | - Diana Z. Sousa
- Laboratory
of Microbiology, Wageningen University &
Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Mark C. M. van Loosdrecht
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Yuemei Lin
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| |
Collapse
|
12
|
Kant R, Jha P, Saluja D, Chopra M. Identification of novel inhibitors of Neisseria gonorrhoeae MurI using homology modeling, structure-based pharmacophore, molecular docking, and molecular dynamics simulation-based approach. J Biomol Struct Dyn 2023; 41:7433-7446. [PMID: 36106953 DOI: 10.1080/07391102.2022.2121943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
Abstract
MurI is one of the most significant role players in the biosynthesis of the peptidoglycan layer in Neisseria gonorrhoeae (Ng). We attempted to highlight the structural and functional relationship between Ng-MurI and D-glutamate to design novel molecules targeting this interaction. The three-dimensional (3D) model of the protein was constructed by homology modeling and the quality and consistency of generated model were assessed. The binding site of the protein was identified by molecular docking studies and a pharmacophore was identified using the interactions of the control ligand. The structure-based pharmacophore model was validated and employed for high-throughput virtual screening and molecular docking to identify novel Ng-MurI inhibitors. Finally, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with the substrate glutamate and novel molecules facilitated us to confirm the stability of the protein-ligand docked complexes. The 100 ns MD simulations of the potential lead compounds with protein confirmed that the modeled complexes were stable. This study identifies novel potential compounds with good fitness and docking scores, which made the interactions of biological significance within the protein active site. Hence, the identified compounds may act as new leads to design and develop Ng-MurI inhibitors.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ravi Kant
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research & Delhi School of Public Health, IoE, University of Delhi, Delhi, India
| | - Prakash Jha
- Laboratory of Molecular Modeling and Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Daman Saluja
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research & Delhi School of Public Health, IoE, University of Delhi, Delhi, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| |
Collapse
|
13
|
Brogan AP, Habib C, Hobbs SJ, Kranzusch PJ, Rudner DZ. Bacterial SEAL domains undergo autoproteolysis and function in regulated intramembrane proteolysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546760. [PMID: 37425962 PMCID: PMC10327162 DOI: 10.1101/2023.06.27.546760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Gram-positive bacteria use SigI/RsgI-family sigma factor/anti-sigma factor pairs to sense and respond to cell wall defects and plant polysaccharides. In Bacillus subtilis this signal transduction pathway involves regulated intramembrane proteolysis (RIP) of the membrane-anchored anti-sigma factor RsgI. However, unlike most RIP signaling pathways, site-1 cleavage of RsgI on the extracytoplasmic side of the membrane is constitutive and the cleavage products remain stably associated, preventing intramembrane proteolysis. The regulated step in this pathway is their dissociation, which is hypothesized to involve mechanical force. Release of the ectodomain enables intramembrane cleavage by the RasP site-2 protease and activation of SigI. The constitutive site-1 protease has not been identified for any RsgI homolog. Here, we report that RsgI's extracytoplasmic domain has structural and functional similarities to eukaryotic SEA domains that undergo autoproteolysis and have been implicated in mechanotransduction. We show that site-1 proteolysis in B. subtilis and Clostridial RsgI family members is mediated by enzyme-independent autoproteolysis of these SEA-like (SEAL) domains. Importantly, the site of proteolysis enables retention of the ectodomain through an undisrupted ß-sheet that spans the two cleavage products. Autoproteolysis can be abrogated by relief of conformational strain in the scissile loop, in a mechanism analogous to eukaryotic SEA domains. Collectively, our data support the model that RsgI-SigI signaling is mediated by mechanotransduction in a manner that has striking parallels with eukaryotic mechanotransducive signaling pathways. SIGNIFICANCE SEA domains are broadly conserved among eukaryotes but absent in bacteria. They are present on diverse membrane-anchored proteins some of which have been implicated in mechanotransducive signaling pathways. Many of these domains have been found to undergo autoproteolysis and remain noncovalently associated following cleavage. Their dissociation requires mechanical force. Here, we identify a family of bacterial SEA-like (SEAL) domains that arose independently from their eukaryotic counterparts but have structural and functional similarities. We show these SEAL domains autocleave and the cleavage products remain stably associated. Importantly, these domains are present on membrane-anchored anti-sigma factors that have been implicated in mechanotransduction pathways analogous to those in eukaryotes. Our findings suggest that bacterial and eukaryotic signaling systems have evolved a similar mechanism to transduce mechanical stimuli across the lipid bilayer.
Collapse
Affiliation(s)
- Anna P. Brogan
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
| | - Cameron Habib
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
| | - Samuel J. Hobbs
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Philip J. Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115
| | - David Z. Rudner
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
| |
Collapse
|
14
|
Kadhim BA, Alqaseer K, Al-Ganahi SA. Identification and characterization of a novel lytic peptidoglycan transglycosylase (MltC) in Shigella dysenteriae. Braz J Microbiol 2023:10.1007/s42770-023-00957-9. [PMID: 36973582 DOI: 10.1007/s42770-023-00957-9] [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: 11/14/2022] [Accepted: 03/20/2023] [Indexed: 03/29/2023] Open
Abstract
Shigellosis remains a worldwide health problem due to the lack of vaccines and the emergence of antibiotic-resistant strains. Shigella (S.) dysenteriae has rigid peptidoglycan (PG), and its tight regulation of biosynthesis and remodeling is essential for bacterial integrity. Lytic transglycosylases are highly conserved PG autolysins in bacteria that play essential roles in bacterial growth. However, their precise functions are obscure. We aimed to identify, clone, and express MltC, a unique autolysin in Escherichia (E.) coli C41 strain. The purification of recombinant MltC protein was performed using affinity chromatography and size-exclusion chromatography methods. The PG enzymatic activity of MltC was investigated using Zymogram and Fluorescein isothiocyanate (FITC)-labeled PG assays. Also, we aimed to detect its localization in bacterial fractions (cytoplasm and membrane) by western blot using specific polyclonal anti-MltC antibodies and its probable partners using immunoprecipitation and mass spectrometry applications. Purified MltC showed autolysin activity. Native MltC showed various locations in S. dysenteriae cells during different growth phases. In the Lag and early stationary phases, MltC was not found in cytoplasm and membrane fractions. However, it was detected in cytoplasm and membrane fractions during the exponential phase. In the late stationary phase, MltC was expressed in the membrane fraction only. Different candidate protein partners of MltC were identified that could be essential for bacterial growth and pathogenicity. This is the first study to suggest that MltC is indeed autolysin and could be a new drug target for the treatment of shigellosis by understanding its biological functions.
Collapse
Affiliation(s)
- Baleegh A Kadhim
- Department of Biology, College of Science, University of Al-Qadisiyah, Al Diwaniyah, Iraq.
| | - Kawther Alqaseer
- Department of Basic Science, College of Nursing, University of Kufa, Kufa, Iraq
| | - Sura A Al-Ganahi
- Department of Biology, College of Science, University of Al-Qadisiyah, Al Diwaniyah, Iraq
| |
Collapse
|
15
|
Syeddan SA. Research Methodology and Mechanisms of Action of Current Orthopaedic Implant Coatings. J Long Term Eff Med Implants 2023; 33:51-66. [PMID: 36734927 DOI: 10.1615/jlongtermeffmedimplants.2022040062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Orthopedic implants are crucial interventions that are gaining greater importance in modern medicine to restore function to commonly affected joints. Each implantation carries the risk of implant-associated infection and loosening of the implant due to improper integration with soft tissue. Coating strategies have been developed to aid the growth of bone into the implant (osteointegration) and prevent biofilm formation to avoid infection. In this review, primary articles highlighting recent developments and advancements in orthopedic implant coating will be presented. Additionally, the methodology of the articles will be critiqued based on this research criteria: establishment of function on a theoretical basis, validation of coating function, and potential next steps/improvements based on results. A theoretical basis based on understanding the mechanisms at play of these various coatings allows for systems to be developed to tackle the tasks of osteointegration, subversion of infection, and avoidance of cytotoxicity. The current state of research methodology in coating design focuses too heavily on either osteointegration or the prevention of infection, thus, future development in medical implant coating needs to investigate the creation of a coating that accomplishes both tasks. Additionally, next steps and improvements to systems need to be better highlighted to move forward when problems arise within a system. Research currently showcasing new coatings is performed primarily in vitro and in vivo. More clinical trials need to be performed to highlight long-term sustainability, the structural integrity, and the safety of the implant.
Collapse
|
16
|
Schalich K, Rajagopala S, Das S, O’Connell R, Yan F. Intestinal epithelial cell-derived components regulate transcriptome of Lactobacillus rhamnosus GG. Front Microbiol 2023; 13:1051310. [PMID: 36687654 PMCID: PMC9846326 DOI: 10.3389/fmicb.2022.1051310] [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: 09/22/2022] [Accepted: 11/24/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction Intestinal epithelial cells (IECs) provide the frontline responses to the gut microbiota for maintaining intestinal homeostasis. Our previous work revealed that IEC-derived components promote the beneficial effects of a commensal and probiotic bacterium, Lactobacillus rhamnosus GG (LGG). This study aimed to elucidate the regulatory effects of IEC-derived components on LGG at the molecular level. Methods Differential gene expression in LGG cultured with IEC-derived components at the timepoint between the exponential and stationary phase was studied by RNA sequencing and functional analysis. Results The transcriptomic profile of LGG cultured with IEC-derived components was significantly different from that of control LGG, with 231 genes were significantly upregulated and 235 genes significantly down regulated (FDR <0.05). The Clusters of Orthologous Groups (COGs) and Gene Ontology (GO) analysis demonstrated that the predominant genes enriched by IEC-derived components are involved in nutrient acquisition, including transporters for amino acids, metals, and sugars, biosynthesis of amino acids, and in the biosynthesis of cell membrane and cell wall, including biosynthesis of fatty acid and lipoteichoic acid. In addition, genes associated with cell division and translation are upregulated by IEC-derived components. The outcome of the increased transcription of these genes is supported by the result that IEC-derived components significantly promoted LGG growth. The main repressed genes are associated with the metabolism of amino acids, purines, carbohydrates, glycerophospholipid, and transcription, which may reflect regulation of metabolic mechanisms in response to the availability of nutrients in bacteria. Discussion These results provide mechanistic insight into the interactions between the gut microbiota and the host.
Collapse
Affiliation(s)
- Kasey Schalich
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Seesandra Rajagopala
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Suman Das
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Ryan O’Connell
- Department of Pathology, University of Utah, Salt Lake City, UT, United States
| | - Fang Yan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States,*Correspondence: Fang Yan,
| |
Collapse
|
17
|
Sass P. Antibiotics: Precious Goods in Changing Times. Methods Mol Biol 2023; 2601:3-26. [PMID: 36445576 DOI: 10.1007/978-1-0716-2855-3_1] [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] [Indexed: 06/16/2023]
Abstract
Antibiotics represent a first line of defense of diverse microorganisms, which produce and use antibiotics to counteract natural enemies or competitors for nutritional resources in their nearby environment. For antimicrobial activity, nature has invented a great variety of antibiotic modes of action that involve the perturbation of essential bacterial structures or biosynthesis pathways of macromolecules such as the bacterial cell wall, DNA, RNA, or proteins, thereby threatening the specific microbial lifestyle and eventually even survival. However, along with highly inventive modes of antibiotic action, nature also developed a comparable set of resistance mechanisms that help the bacteria to circumvent antibiotic action. Microorganisms have evolved specific adaptive responses that allow to appropriately react to the presence of antimicrobial agents, thereby ensuring survival during antimicrobial stress. In times of rapid development and spread of antibiotic (multi-)resistance, new resistance-breaking strategies to counteract bacterial infections are desperately needed. This chapter is an update to Chapter 1 of the first edition of this book and intends to give an overview of common antibiotics and their target pathways. It will also present examples for new antibiotics with novel modes of action, illustrating that nature's repertoire of innovative new antimicrobial agents has not been fully exploited yet, and we still might find new drugs that help to evade established antimicrobial resistance strategies.
Collapse
Affiliation(s)
- Peter Sass
- Interfaculty Institute for Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany.
| |
Collapse
|
18
|
Nakaya T, Yabe M, Mashalidis EH, Sato T, Yamamoto K, Hikiji Y, Katsuyama A, Shinohara M, Minato Y, Takahashi S, Horiuchi M, Yokota SI, Lee SY, Ichikawa S. Synthesis of macrocyclic nucleoside antibacterials and their interactions with MraY. Nat Commun 2022; 13:7575. [PMID: 36539416 PMCID: PMC9768162 DOI: 10.1038/s41467-022-35227-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
The development of new antibacterial drugs with different mechanisms of action is urgently needed to address antimicrobial resistance. MraY is an essential membrane enzyme required for bacterial cell wall synthesis. Sphaerimicins are naturally occurring macrocyclic nucleoside inhibitors of MraY and are considered a promising target in antibacterial discovery. However, developing sphaerimicins as antibacterials has been challenging due to their complex macrocyclic structures. In this study, we construct their characteristic macrocyclic skeleton via two key reactions. Having then determined the structure of a sphaerimicin analogue bound to MraY, we use a structure-guided approach to design simplified sphaerimicin analogues. These analogues retain potency against MraY and exhibit potent antibacterial activity against Gram-positive bacteria, including clinically isolated drug resistant strains of S. aureus and E. faecium. Our study combines synthetic chemistry, structural biology, and microbiology to provide a platform for the development of MraY inhibitors as antibacterials against drug-resistant bacteria.
Collapse
Affiliation(s)
- Takeshi Nakaya
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan
| | - Miyuki Yabe
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan
| | - Ellene H. Mashalidis
- grid.26009.3d0000 0004 1936 7961Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710 USA ,grid.410513.20000 0000 8800 7493Present Address: Pfizer Global Research & Development, Eastern Point Road, Groton, CT 06340 USA
| | - Toyotaka Sato
- grid.39158.360000 0001 2173 7691Laboratory of Veterinary Hygiene, School/Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818 Japan ,grid.39158.360000 0001 2173 7691Graduate School of Infectious Diseases, Hokkaido University, Sapporo, 060-0818 Japan
| | - Kazuki Yamamoto
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan ,grid.39158.360000 0001 2173 7691Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan
| | - Yuta Hikiji
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan
| | - Akira Katsuyama
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan ,grid.39158.360000 0001 2173 7691Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan ,grid.39158.360000 0001 2173 7691Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Sapporo, Japan
| | - Motoko Shinohara
- grid.256115.40000 0004 1761 798XDepartment of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192 Japan
| | - Yusuke Minato
- grid.256115.40000 0004 1761 798XDepartment of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192 Japan
| | - Satoshi Takahashi
- grid.470107.5Division of Laboratory Medicine, Sapporo Medical University Hospital, South-1, West-16, Chuo-ku, Sapporo, 060-8543 Japan ,grid.263171.00000 0001 0691 0855Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, South-1, West-16, Chuo-ku, Sapporo, 060-8543 Japan
| | - Motohiro Horiuchi
- grid.39158.360000 0001 2173 7691Laboratory of Veterinary Hygiene, School/Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818 Japan ,grid.39158.360000 0001 2173 7691Graduate School of Infectious Diseases, Hokkaido University, Sapporo, 060-0818 Japan
| | - Shin-ichi Yokota
- grid.263171.00000 0001 0691 0855Department of Microbiology, Sapporo Medical University School of Medicine, South-1, West-17, Chuo-ku, Sapporo, 060-8556 Japan
| | - Seok-Yong Lee
- grid.26009.3d0000 0004 1936 7961Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710 USA
| | - Satoshi Ichikawa
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan ,grid.39158.360000 0001 2173 7691Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan ,grid.39158.360000 0001 2173 7691Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Sapporo, Japan
| |
Collapse
|
19
|
Edwards BD, Field SK. The Struggle to End a Millennia-Long Pandemic: Novel Candidate and Repurposed Drugs for the Treatment of Tuberculosis. Drugs 2022; 82:1695-1715. [PMID: 36479687 PMCID: PMC9734533 DOI: 10.1007/s40265-022-01817-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2022] [Indexed: 12/12/2022]
Abstract
This article provides an encompassing review of the current pipeline of putative and developed treatments for tuberculosis, including multidrug-resistant strains. The review has organized each compound according to its site of activity. To provide context, mention of drugs within current recommended treatment regimens is made, thereafter followed by discussion on recently developed and upcoming molecules at established and novel targets. The review is designed to provide a clinically applicable understanding of the compounds that are deemed most currently relevant, including those already under clinical study and those that have shown promising pre-clinical results. An extensive review of the efficacy and safety data for key contemporary drugs already incorporated into treatment regimens, such as bedaquiline, pretomanid, and linezolid, is provided. The three levels of the bacterial cell wall (mycolic acid, arabinogalactan, and peptidoglycan layers) are highlighted and important compounds designed to target each layer are delineated. Amongst others, the highly optimistic and potent anti-mycobacterial activity of agents such as BTZ-043, PBTZ 169, and OPC-167832 are emphasized. The evolving spectrum of oxazolidinones, such as sutezolid, delpazolid, and TBI-223, all aiming to exceed the efficacy achieved with linezolid yet offer a safer alternative to the potential toxicity, are reviewed. New and exciting prospective agents with novel mechanisms of impact against TB, including 3-aminomethyl benzoxaboroles and telacebec, are underscored. We describe new diaryloquinolines in development, striving to build on the immense success of bedaquiline. Finally, we discuss some of these compounds that have shown encouraging additive or synergistic benefit when used in combination, providing some promise for the future in treating this ancient scourge.
Collapse
Affiliation(s)
- Brett D Edwards
- Division of Infectious Diseases and Tuberculosis Services, Alberta Health Services, Department of Medicine, Cumming School of Medicine, University of Calgary, Peter Lougheed Centre, 3500, 26 Avenue NE, Calgary, AB, T1Y6J4, Canada.
| | - Stephen K Field
- Division of Infectious Diseases and Tuberculosis Services, Alberta Health Services, Department of Medicine, Cumming School of Medicine, University of Calgary, Peter Lougheed Centre, 3500, 26 Avenue NE, Calgary, AB, T1Y6J4, Canada
| |
Collapse
|
20
|
Chen X, Li Y, Bai K, Gu M, Xu X, Jiang N, Chen Y, Li J, Luo L. Class A Penicillin-Binding Protein C Is Responsible for Stress Response by Regulation of Peptidoglycan Assembly in Clavibacter michiganensis. Microbiol Spectr 2022; 10:e0181622. [PMID: 36040162 PMCID: PMC9603630 DOI: 10.1128/spectrum.01816-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/12/2022] [Indexed: 12/31/2022] Open
Abstract
The cell wall peptidoglycan of bacteria is essential for their survival and shape development. The penicillin-binding proteins (PBPs) are responsible for the terminal stage of peptidoglycan assembly. It has been shown that PBPC, a member of class A high-molecular-weight PBP, played an important role in morphology maintenance and stress response in Clavibacter michiganensis. Here, we reported the stress response strategies under viable but nonculturable (VBNC) state and revealed the regulation of peptidoglycan assembly by PBPC in C. michiganensis cells. Using atomic force microscopy imaging, we found that peptidoglycan of C. michiganensis cells displayed a relatively smooth and dense surface, whereas ΔpbpC was characterized by a "ridge-and-groove" surface, which was more distinctive after Cu2+ treatment. The peptidoglycan layer of wild type cells exhibited a significant increase in thickness and slight increase in cross-linkage following Cu2+ treatment. Compared with wild type, the thickness and cross-linkage of peptidoglycan decreased during log phase in ΔpbpC cells, but the peptidoglycan cross-linkage increased significantly under Cu2+ stress, while the thickness did not change. It is noteworthy that the above changes in the peptidoglycan layer resulted in a significant increase in the accumulation of amylase and exopolysaccharide in ΔpbpC. This study elucidates the role of PBPC in Gram-positive rod-shaped plant pathogenic bacterium in response to environmental stimuli by regulating the assembling of cell wall peptidoglycan, which is significant in understanding the survival of C. michiganensis under stress and the field epidemiology of tomato bacterial canker disease. IMPORTANCE Peptidoglycan of cell walls in bacteria is a cross-linked and meshlike scaffold that provides strength to withstand the external pressure. The increased cross-linkage in peptidoglycan and altered structure in VBNC cells endowed the cell wall more resistant to adversities. Here we systematically evaluated the stress response strategies in Gram-positive rod-shaped bacterium C. michiganensis log phase cells and revealed a significant increase of peptidoglycan thickness and slight increase of cross-linkage after Cu2+ treatment. Most strikingly, knocking-out of PBPC leads to a significant increase in cross-linking of peptidoglycan in response to Cu2+ treatment. Understanding the stress resistance mechanism and survival strategy of phytopathogenic bacteria is the basis of exploring bacterial physiology and disease epidemiology.
Collapse
Affiliation(s)
- Xing Chen
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, People’s Republic of China
| | - Yao Li
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, People’s Republic of China
| | - Kaihong Bai
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, People’s Republic of China
| | - Meng Gu
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, People’s Republic of China
| | - Xiaoli Xu
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, People’s Republic of China
| | - Na Jiang
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, People’s Republic of China
| | - Yu Chen
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, People’s Republic of China
| | - Jianqiang Li
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, People’s Republic of China
| | - Laixin Luo
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, People’s Republic of China
| |
Collapse
|
21
|
Iwicka E, Hajtuch J, Dzierzbicka K, Inkielewicz-Stepniak I. Muramyl dipeptide-based analogs as potential anticancer compounds: Strategies to improve selectivity, biocompatibility, and efficiency. Front Oncol 2022; 12:970967. [PMID: 36237313 PMCID: PMC9551026 DOI: 10.3389/fonc.2022.970967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/22/2022] [Indexed: 11/14/2022] Open
Abstract
According to the WHO, cancer is the second leading cause of death in the world. This is an important global problem and a major challenge for researchers who have been trying to find an effective anticancer therapy. A large number of newly discovered compounds do not exert selective cytotoxic activity against tumorigenic cells and have too many side effects. Therefore, research on muramyl dipeptide (MDP) analogs has attracted interest due to the urgency for finding more efficient and safe treatments for oncological patients. MDP is a ligand of the cytosolic nucleotide-binding oligomerization domain 2 receptor (NOD2). This molecule is basic structural unit that is responsible for the immune activity of peptidoglycans and exhibits many features that are important for modern medicine. NOD2 is a component of the innate immune system and represents a promising target for enhancing the innate immune response as well as the immune response against cancer cells. For this reason, MDP and its analogs have been widely used for many years not only in the treatment of immunodeficiency diseases but also as adjuvants to support improved vaccine delivery, including for cancer treatment. Unfortunately, in most cases, both the MDP molecule and its synthesized analogs prove to be too pyrogenic and cause serious side effects during their use, which consequently exclude them from direct clinical application. Therefore, intensive research is underway to find analogs of the MDP molecule that will have better biocompatibility and greater effectiveness as anticancer agents and for adjuvant therapy. In this paper, we review the MDP analogs discovered in the last 10 years that show promise for antitumor therapy. The first part of the paper compiles the achievements in the field of anticancer vaccine adjuvant research, which is followed by a description of MDP analogs that exhibit promising anticancer and antiproliferative activity and their structural changes compared to the original MDP molecule.
Collapse
Affiliation(s)
- Eliza Iwicka
- Department of Pharmaceutical Pathophysiology, Medical University of Gdansk, Gdansk, Poland
| | - Justyna Hajtuch
- Department of Pharmaceutical Pathophysiology, Medical University of Gdansk, Gdansk, Poland
| | - Krystyna Dzierzbicka
- Department of Organic Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Iwona Inkielewicz-Stepniak
- Department of Pharmaceutical Pathophysiology, Medical University of Gdansk, Gdansk, Poland
- *Correspondence: Iwona Inkielewicz-Stepniak,
| |
Collapse
|
22
|
Lin P, Crooks DR, Linehan WM, Fan TWM, Lane AN. Resolving Enantiomers of 2-Hydroxy Acids by Nuclear Magnetic Resonance. Anal Chem 2022; 94:12286-12291. [PMID: 36040304 PMCID: PMC9539631 DOI: 10.1021/acs.analchem.2c00490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biologically important 2-hydroxy carboxylates such as lactate, malate, and 2-hydroxyglutarate exist in two enantiomeric forms that cannot be distinguished under achiral conditions. The D and L (or R, S) enantiomers have different biological origins and functions, and therefore, there is a need for a simple method for resolving, identifying, and quantifying these enantiomers. We have adapted and improved a chiral derivatization technique for nuclear magnetic resonance (NMR), which needs no chromatography for enantiomer resolution, with greater than 90% overall recovery. This method was developed for 2-hydroxyglutarate (2HG) to produce diastereomers resolvable by column chromatography. We have applied the method to lactate, malate, and 2HG. The limit of quantification was determined to be about 1 nmol for 2HG with coefficients of variation of less than 5%. We also demonstrated the method on an extract of a renal carcinoma bearing an isocitrate dehydrogenase-2 (IDH2) variant that produces copious quantities of 2HG and showed that it is the D enantiomer that was exclusively produced. We also demonstrated in the same experiment that the lactate produced in the same sample was the L enantiomer.
Collapse
Affiliation(s)
- Penghui Lin
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536, United States
| |
Collapse
|
23
|
Xu H, Fu N, Zheng J, Sohail M, Zhang X. Mn-doped bimetallic synergistic catalysis boosts for enzymatic phosphorylation of N-Acetylglucosamine/ N-Acetylgalactosamine and their derivatives. Bioorg Chem 2022; 128:106041. [PMID: 35907378 DOI: 10.1016/j.bioorg.2022.106041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/04/2022] [Accepted: 07/16/2022] [Indexed: 11/02/2022]
Abstract
Metal-organic frameworks (MOFs), as advanced enzyme immobilization platforms for improving biocatalysis and protein biophysics, are rarely investigated as solid supports in the enzymatic synthesis of carbohydrate and derivatives, which can be attributed to the complex biochemical reaction mechanisms and the adverse interactions between the high polarity of substrate sugars, glycoenzymes and traditional MOFs. Here, we introduced divalent metal ion Mn2+ into MOF to prepare bimetallic MOF microreactor that encapsulated N-acetylhexosamine 1-Kinase (NahK), a critical anomeric kinase involved in the enzymatic synthesis of sugar nucleotide. The introduced Mn ions not only adjusted the microstructure of MOFs, but also participated in the enzymatic catalysis as cofactor, thus facilitated the N-acetylglucosamine/ N-acetylgalactosamine (GlcNAc/GalNAc) phosphorylation. The Mn-doped NahK@Zn-metal organic material (MOM), integrated with high catalytic activity, high stability, and high recoverability, solved the issues of immobilization related to glucokinase activity. These features significantly improved the operability and reduced the processing cost, assuring industrial application prospects for sugar nucleotides synthesis.
Collapse
Affiliation(s)
- Han Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Wenyuan Road 1, Nanjing 210023, China
| | - Ninghua Fu
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jie Zheng
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Muhammad Sohail
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Wenyuan Road 1, Nanjing 210023, China
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Wenyuan Road 1, Nanjing 210023, China.
| |
Collapse
|
24
|
Rimal B, Senzani S, Ealand C, Lamichhane G, Kana B, Kim SJ. Peptidoglycan compositional analysis of Mycobacterium smegmatis using high-resolution LC-MS. Sci Rep 2022; 12:11061. [PMID: 35773428 PMCID: PMC9247062 DOI: 10.1038/s41598-022-15324-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/22/2022] [Indexed: 11/21/2022] Open
Abstract
Peptidoglycan (PG) is the exoskeleton of bacterial cells and is required for their viability, growth, and cell division. Unlike most bacteria, mycobacteria possess an atypical PG characterized by a high degree of unique linkages and chemical modifications which most likely serve as important determinants of virulence and pathogenesis in mycobacterial diseases. Despite this important role, the chemical composition and molecular architecture of mycobacterial PG have yet to be fully determined. Here we determined the chemical composition of PG from Mycobacterium smegmatis using high-resolution liquid chromatography-mass spectrometry. Purified cell walls from the stationary phase were digested with mutanolysin and compositional analysis was performed on 130 muropeptide ions that were identified using an in silico PG library. The relative abundance for each muropeptide ion was measured by integrating the extracted-ion chromatogram. The percentage of crosslink per PG subunit was measured at 45%. While both 3→3 and 4→3 transpeptide cross-linkages were found in PG dimers, a high abundance of 3→3 linkages was found associated with the trimers. Approximately 43% of disaccharides in the PG of M. smegmatis showed modifications by acetylation or deacetylation. A significant number of PG trimers are found with a loss of 41.00 amu that is consistent with N-deacetylation, whereas the dimers show a gain of 42.01 amu corresponding to O-acetylation of the PG disaccharides. This suggests a possible role of PG acetylation in the regulation of cell wall homeostasis in M. smegmatis. Collectively, these data report important novel insights into the ultrastructure of mycobacterial PG.
Collapse
Affiliation(s)
- Binayak Rimal
- Institute of Biomedical Studies, Baylor University, Waco, TX, 76798, USA.,Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Sibusiso Senzani
- National Health Laboratory Service, Faculty of Health Sciences, DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand, Johannesburg, 2001, South Africa
| | - Christopher Ealand
- National Health Laboratory Service, Faculty of Health Sciences, DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand, Johannesburg, 2001, South Africa
| | - Gyanu Lamichhane
- Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Bavesh Kana
- National Health Laboratory Service, Faculty of Health Sciences, DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand, Johannesburg, 2001, South Africa.
| | - Sung Joon Kim
- Department of Chemistry, Howard University, Chemistry Building, 525 College Street, Washington, DC, 20059, USA.
| |
Collapse
|
25
|
Della-Felice F, de Andrade Bartolomeu A, Pilli RA. The phosphate ester group in secondary metabolites. Nat Prod Rep 2022; 39:1066-1107. [PMID: 35420073 DOI: 10.1039/d1np00078k] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2000 to mid-2021The phosphate ester is a versatile, widespread functional group involved in a plethora of biological activities. Its presence in secondary metabolites, however, is relatively rare compared to other functionalities and thus is part of a rather unexplored chemical space. Herein, the chemistry of secondary metabolites containing the phosphate ester group is discussed. The text emphasizes their structural diversity, biological and pharmacological profiles, and synthetic approaches employed in the phosphorylation step during total synthesis campaigns, covering the literature from 2000 to mid-2021.
Collapse
Affiliation(s)
- Franco Della-Felice
- Institute of Chemistry, University of Campinas (UNICAMP), P.O. Box 6154, CEP 13083-970 Campinas, Sao Paulo, Brazil.,Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain.
| | | | - Ronaldo Aloise Pilli
- Institute of Chemistry, University of Campinas (UNICAMP), P.O. Box 6154, CEP 13083-970 Campinas, Sao Paulo, Brazil
| |
Collapse
|
26
|
An Interplay of Multiple Positive and Negative Factors Governs Methicillin Resistance in Staphylococcus aureus. Microbiol Mol Biol Rev 2022; 86:e0015921. [PMID: 35420454 PMCID: PMC9199415 DOI: 10.1128/mmbr.00159-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The development of resistance to β-lactam antibiotics has made Staphylococcus aureus a clinical burden on a global scale. MRSA (methicillin-resistant S. aureus) is commonly known as a superbug. The ability of MRSA to proliferate in the presence of β-lactams is attributed to the acquisition of mecA, which encodes the alternative penicillin binding protein, PBP2A, which is insensitive to the antibiotics. Most MRSA isolates exhibit low-level β-lactam resistance, whereby additional genetic adjustments are required to develop high-level resistance. Although several genetic factors that potentiate or are required for high-level resistance have been identified, how these interact at the mechanistic level has remained elusive. Here, we discuss the development of resistance and assess the role of the associated components in tailoring physiology to accommodate incoming mecA.
Collapse
|
27
|
Amino acid profile, phytochemical composition and antimicrobial activities of edible tropical bolete mushroom (Phlebopus colossus (R. Heim) Singer). JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2022. [DOI: 10.1007/s11694-022-01331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
28
|
Ma J, Li K, Gu S. Selective strategies for antibacterial regulation of nanomaterials. RSC Adv 2022; 12:4852-4864. [PMID: 35425473 PMCID: PMC8981418 DOI: 10.1039/d1ra08996j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
Recalcitrant bacterial infection, as a worldwide challenge, causes large problems for human health and is attracting great attention. The excessive antibiotic-dependent treatment of infections is prone to induce antibiotic resistance. A variety of unique nanomaterials provide an excellent toolkit for killing bacteria and preventing drug resistance. It is of great importance to summarize the design rules of nanomaterials for inhibiting the growth of pathogenic bacteria. We completed a review involving the strategies for regulating antibacterial nanomaterials. First, we discuss the antibacterial manipulation of nanomaterials, including the interaction between the nanomaterial and the bacteria, the damage of the bacterial structure, and the inactivation of biomolecules. Next, we identify six main factors for controlling the antibacterial activity of nanomaterials, including their element composition, size dimensions, surface charge, surface topography, shape selection and modification density. Every factor possesses a preferable standard for maximizing antibacterial activity, providing universal rules for antibacterial regulation of nanomaterials. We hope this comprehensive review will help researchers to precisely design and synthesize nanomaterials, developing intelligent antibacterial agents to address bacterial infections.
Collapse
Affiliation(s)
- Jinliang Ma
- College of Food and Bioengineering, Henan University of Science and Technology Luoyang Henan 471023 China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Kexin Li
- College of Food and Bioengineering, Henan University of Science and Technology Luoyang Henan 471023 China
| | - Shaobin Gu
- College of Food and Bioengineering, Henan University of Science and Technology Luoyang Henan 471023 China
| |
Collapse
|
29
|
Sahoo J, De M. Gram-Selective Antibacterial Activity of Mixed-Charge 2D-MoS2. J Mater Chem B 2022; 10:4588-4594. [DOI: 10.1039/d2tb00361a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Development of nanomaterial-based antibiotics can be the most potent alternative due to the increasing resistance against conventional antibiotics. But one of the important parameters in development of antibacterial agent is...
Collapse
|
30
|
Sassine J, Pazos M, Breukink E, Vollmer W. Lytic transglycosylase MltG cleaves in nascent peptidoglycan and produces short glycan strands. Cell Surf 2021; 7:100053. [PMID: 34036206 PMCID: PMC8135044 DOI: 10.1016/j.tcsw.2021.100053] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/17/2021] [Accepted: 04/26/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria encase their cytoplasmic membrane with peptidoglycan (PG) to maintain the shape of the cell and protect it from bursting. The enlargement of the PG layer is facilitated by the coordinated activities of PG synthesising and -cleaving enzymes. In Escherichia coli, the cytoplasmic membrane-bound lytic transglycosylase MltG associates with PG synthases and was suggested to terminate the polymerisation of PG glycan strands. Using pull-down and surface plasmon resonance, we detected interactions between MltG from Bacillus subtilis and two PG synthases; the class A PBP1 and the class B PBP2B. Using in vitro PG synthesis assays with radio-labelled or fluorophore-labelled B. subtilis-type and/or E. coli-type lipid II, we showed that both, BsMltG and EcMltG, are lytic tranglycosylases and that their activity is higher during ongoing glycan strand polymerisation. MltG competed with the transpeptidase activity of class A PBPs, but had no effect on their glycosyltransferase activity, and produced glycan strands with a length of 7 disaccharide units from cleavage in the nascent strands. We hypothesize that MltG cleaves the nascent strands to produce short glycan strands that are used in the cell for a yet unknown process.
Collapse
Affiliation(s)
- Jad Sassine
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Manuel Pazos
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre of Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
31
|
Diaminopimelic acid and its analogues: Synthesis and biological perspective. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
32
|
Seok J, Hong J, Park J, Kim KJ. Structural analysis of the peptidoglycan editing factor PdeF from Bacillus cereus ATCC 14579. Biochem Biophys Res Commun 2021; 583:43-48. [PMID: 34735878 DOI: 10.1016/j.bbrc.2021.10.051] [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: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022]
Abstract
The coding gene for peptidoglycan editing factor (pdeF) is located in the division and cell wall (dcw) cluster, and encodes a protein that has an editing function for misplaced amino acids in peptidoglycan in E. coli. In this study, we determined the crystal structure of PdeF from Bacillus cereus (BcPdeF) at a 1.60 Å resolution. BcPdeF exists as a monomer in solution and consists of two domains: a core domain containing a Pfam motif DUF152 and a smaller subdomain. The X-ray fluorescence spectrum of BcPdeF crystal elucidated that the protein has a Zn2+ ion in its active site and the metal ion was coordinated by two histidine and one cysteine residue. We also performed docking calculations of the N-acetylmuramate (MurNAc)-L-Ser-D-iGlu ligand in the BcPdeF structure and revealed the substrate binding mode of the enzyme. Furthermore, structural comparisons between BcPdeF and human fatty acid metabolism-immunity nexus (FAMIN), which also contains the DUF152 motif in its core domain, provided a structural basis how the two structurally similar proteins have completely different physiological functions.
Collapse
Affiliation(s)
- Jihye Seok
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jiyeon Hong
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jiyoung Park
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea.
| |
Collapse
|
33
|
Harki EM. Biophysical and thermodynamic studies of sulfur and selenium analogues of threonine in gas and solution phases. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-021-02854-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
34
|
Wittlin S, Mäser P. From Magic Bullet to Magic Bomb: Reductive Bioactivation of Antiparasitic Agents. ACS Infect Dis 2021; 7:2777-2786. [PMID: 34472830 DOI: 10.1021/acsinfecdis.1c00118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Paul Ehrlich coined the term "magic bullet" to describe how a drug kills the parasite inside its human host without harming the host itself. Ehrlich concluded that the drug must have a greater affinity to the parasite than to human cells. Today, the specificity of drug action is understood in terms of the drug target. An ideal target is a protein that is essential for the proliferation of the pathogen but absent in human cells. Examples are the enzymes of folate synthesis or of the nonmevalonate pathway in the malaria parasites. However, there are other ways how a drug can kill selectively. Of particular relevance is the specific activation of a prodrug inside the pathogen but not in the host, as this is how the current frontrunners of parasite chemotherapy work. Artemisinins for malaria, fexinidazole for human African trypanosomiasis, benznidazole for Chagas' disease, metronidazole for intestinal protozoa: these molecules are "magic bombs" that are triggered selectively. They are prodrugs that need to be activated by chemical reduction, i.e., the acquisition of an electron, which occurs in the parasite. Such a mode of action is shared by the novel antimalarial peroxides arterolane and artefenomel, which are activated by reduction of the endoperoxide bond with ferrous heme as the likely electron donor, a metabolic end-product of Plasmodium falciparum. Here we provide an overview on the molecular basis of selectivity of antiparasitic drug action with particular reference to the ozonides, the new generation of antimalarial peroxides designed by Jonathan Vennerstrom.
Collapse
Affiliation(s)
- Sergio Wittlin
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland
- University of Basel, 4001 Basel, Switzerland
| | - Pascal Mäser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland
- University of Basel, 4001 Basel, Switzerland
| |
Collapse
|
35
|
Abstract
Most bacteria are protected from environmental offenses by a cell wall consisting of strong yet elastic peptidoglycan. The cell wall is essential for preserving bacterial morphology and viability, and thus the enzymes involved in the production and turnover of peptidoglycan have become preferred targets for many of our most successful antibiotics. In the past decades, Vibrio cholerae, the gram-negative pathogen causing the diarrheal disease cholera, has become a major model for understanding cell wall genetics, biochemistry, and physiology. More than 100 articles have shed light on novel cell wall genetic determinants, regulatory links, and adaptive mechanisms. Here we provide the first comprehensive review of V. cholerae's cell wall biology and genetics. Special emphasis is placed on the similarities and differences with Escherichia coli, the paradigm for understanding cell wall metabolism and chemical structure in gram-negative bacteria.
Collapse
Affiliation(s)
- Laura Alvarez
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-90187, Sweden;
| | - Sara B Hernandez
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-90187, Sweden;
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-90187, Sweden;
| |
Collapse
|
36
|
Harki E. Biophysical study of selenocysteine and selenomethionine in the gas and solution phases. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
37
|
Affiliation(s)
- Guozhi Xiao
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany University of Chinese Academy of Science Chinese Academy of Sciences 132 Lanhei Road Kunming 650201 China
| | - Haiqing He
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany University of Chinese Academy of Science Chinese Academy of Sciences 132 Lanhei Road Kunming 650201 China
| |
Collapse
|
38
|
Knoll KE, Lindeque Z, Adeniji AA, Oosthuizen CB, Lall N, Loots DT. Elucidating the Antimycobacterial Mechanism of Action of Ciprofloxacin Using Metabolomics. Microorganisms 2021; 9:microorganisms9061158. [PMID: 34071153 PMCID: PMC8228629 DOI: 10.3390/microorganisms9061158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 12/21/2022] Open
Abstract
In the interest of developing more effective and safer anti-tuberculosis drugs, we used a GCxGC-TOF-MS metabolomics research approach to investigate and compare the metabolic profiles of Mtb in the presence and absence of ciprofloxacin. The metabolites that best describe the differences between the compared groups were identified as markers characterizing the changes induced by ciprofloxacin. Malic acid was ranked as the most significantly altered metabolite marker induced by ciprofloxacin, indicative of an inhibition of the tricarboxylic acid (TCA) and glyoxylate cycle of Mtb. The altered fatty acid, myo-inositol, and triacylglycerol metabolism seen in this group supports previous observations of ciprofloxacin action on the Mtb cell wall. Furthermore, the altered pentose phosphate intermediates, glycerol metabolism markers, glucose accumulation, as well as the reduction in the glucogenic amino acids specifically, indicate a flux toward DNA (as well as cell wall) repair, also supporting previous findings of DNA damage caused by ciprofloxacin. This study further provides insights useful for designing network whole-system strategies for the identification of possible modes of action of various drugs and possibly adaptations by Mtb resulting in resistance.
Collapse
Affiliation(s)
- Kirsten E. Knoll
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Zander Lindeque
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Adetomiwa A. Adeniji
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Carel B. Oosthuizen
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
| | - Namrita Lall
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Du Toit Loots
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
- Correspondence: ; Tel.: +27-(0)18-299-1818
| |
Collapse
|
39
|
Nivedita PS, Shettar AK, Joy HH. Applications of Polysaccharides in Nutrition and Medicine. POLYSACCHARIDES 2021. [DOI: 10.1002/9781119711414.ch30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
|
40
|
Bacterial Resistance to Antimicrobial Agents. Antibiotics (Basel) 2021; 10:antibiotics10050593. [PMID: 34067579 PMCID: PMC8157006 DOI: 10.3390/antibiotics10050593] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial pathogens as causative agents of infection constitute an alarming concern in the public health sector. In particular, bacteria with resistance to multiple antimicrobial agents can confound chemotherapeutic efficacy towards infectious diseases. Multidrug-resistant bacteria harbor various molecular and cellular mechanisms for antimicrobial resistance. These antimicrobial resistance mechanisms include active antimicrobial efflux, reduced drug entry into cells of pathogens, enzymatic metabolism of antimicrobial agents to inactive products, biofilm formation, altered drug targets, and protection of antimicrobial targets. These microbial systems represent suitable focuses for investigation to establish the means for their circumvention and to reestablish therapeutic effectiveness. This review briefly summarizes the various antimicrobial resistance mechanisms that are harbored within infectious bacteria.
Collapse
|
41
|
Kieswetter NS, Ozturk M, Jones SS, Senzani S, Chengalroyen MD, Brombacher F, Kana B, Guler R. Deletion of N-acetylmuramyl-L-alanine amidases alters the host immune response to Mycobacterium tuberculosis infection. Virulence 2021; 12:1227-1238. [PMID: 33980132 PMCID: PMC8128173 DOI: 10.1080/21505594.2021.1914448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Peptidoglycan (PG), a heteropolysaccharide component of the mycobacterial cell wall can be shed during tuberculosis infection with immunomodulatory consequences. As such, changes in PG structure are expected to have important implications on disease progression and host responses during infection with Mycobacterium tuberculosis. Mycobacterial amidases have important roles in remodeling of PG during cell division and are implicated in susceptibility to antibiotics. However, their role in modulating host immunity remains unknown. We assessed the bacterial burden and host immune responses to M. tuberculosis mutants defective for either one of two PG N-acetylmuramyl-L-alanine amidases, Ami1 and Ami4, in bone marrow-derived macrophages (BMDM) and C57BL/6 mice. In infected BMDM, the single deletion of both genes resulted in increased proinflammatory cytokine responses. In mice, infection with the Δami1 mutant led to differential induction of pro-inflammatory cytokines and chemokines, decreased cellular recruitment and reduced lung pathology during the acute phase of the infection. While increased proinflammatory cytokines production was observed in BMDM infected with the Δami4 mutant, these effects did not prevail in mice. Infection using the Δami1 and Δami4 Mtb mutants showed that these genes are dispensable for intracellular mycobacterial growth in macrophages and mycobacterial burden in mice. These findings suggest that both Ami1 and Ami4 in M. tuberculosis are not essential for mycobacterial growth within the host. In summary, we show that amidases are important for modulating host immunity during Mtb infection in murine macrophages and mice.
Collapse
Affiliation(s)
- Nathan Scott Kieswetter
- Cape Town Component, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mumin Ozturk
- Cape Town Component, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shelby-Sara Jones
- Cape Town Component, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sibusiso Senzani
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Melissa Dalcina Chengalroyen
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Frank Brombacher
- Cape Town Component, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Bavesh Kana
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Reto Guler
- Cape Town Component, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
42
|
ddcP, pstB, and excess D-lactate impact synergism between vancomycin and chlorhexidine against Enterococcus faecium 1,231,410. PLoS One 2021; 16:e0249631. [PMID: 33831063 PMCID: PMC8031426 DOI: 10.1371/journal.pone.0249631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/22/2021] [Indexed: 11/19/2022] Open
Abstract
Vancomycin-resistant enterococci (VRE) are important nosocomial pathogens that cause life-threatening infections. To control hospital-associated infections, skin antisepsis and bathing utilizing chlorhexidine is recommended for VRE patients in acute care hospitals. Previously, we reported that exposure to inhibitory chlorhexidine levels induced the expression of vancomycin resistance genes in VanA-type Enterococcus faecium. However, vancomycin susceptibility actually increased for VanA-type E. faecium in the presence of chlorhexidine. Hence, a synergistic effect of the two antimicrobials was observed. In this study, we used multiple approaches to investigate the mechanism of synergism between chlorhexidine and vancomycin in the VanA-type VRE strain E. faecium 1,231,410. We generated clean deletions of 7 of 11 pbp, transpeptidase, and carboxypeptidase genes in this strain (ponA, pbpF, pbpZ, pbpA, ddcP, ldtfm, and vanY). Deletion of ddcP, encoding a membrane-bound carboxypeptidase, altered the synergism phenotype. Furthermore, using in vitro evolution, we isolated a spontaneous synergy escaper mutant and utilized whole genome sequencing to determine that a mutation in pstB, encoding an ATPase of phosphate-specific transporters, also altered synergism. Finally, addition of excess D-lactate, but not D-alanine, enhanced synergism to reduce vancomycin MIC levels. Overall, our work identified factors that alter chlorhexidine and vancomycin synergism in a model VanA-type VRE strain.
Collapse
|
43
|
Regulated cleavage of glycan strands by the murein hydrolase SagB in S. aureus involves a direct interaction with LyrA (SpdC). J Bacteriol 2021; 203:JB.00014-21. [PMID: 33593946 PMCID: PMC8092163 DOI: 10.1128/jb.00014-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
LyrA (SpdC), a homologue of eukaryotic CAAX proteases that act on prenylated substrates, has been implicated in the assembly of several pathways of the envelope of Staphylococcus aureus. We described earlier the Lysostaphin resistance (Lyr) and Staphylococcal protein A display (Spd) phenotypes associated with loss of the lyrA (spdC) gene. However, a direct contribution to the assembly of pentaglycine crossbridges, the target of lysostaphin cleavage in S. aureus peptidoglycan, or of Staphylococcal protein A attachment to peptidoglycan could not be attributed directly to LyrA (SpdC). These two processes are catalyzed by the Fem factors and Sortase A, respectively. To gain insight into the function of LyrA (SpdC), here we use affinity chromatography and LC-MS/MS analysis and report that LyrA interacts with SagB. SagB cleaves glycan strands of peptidoglycan to achieve physiological length. Similar to sagB peptidoglycan, lyrA peptidoglycan contains extended glycan strands. Purified lyrA peptidoglycan can still be cleaved to physiological length by SagB in vitro LyrA does not modify or cleave peptidoglycan, it also does not modify or stabilize SagB. The membrane bound domain of LyrA is sufficient to support SagB activity but predicted 'CAAX enzyme' catalytic residues in this domain are dispensable. We speculate that LyrA exerts its effect on bacterial prenyl substrates, specifically undecaprenol-bound peptidoglycan substrates of SagB, to help control glycan length. Such an activity also explains the Lyr and Spd phenotypes observed earlier.IMPORTANCE Peptidoglycan is assembled on the trans side of the plasma membrane from lipid II precursors into glycan chains that are crosslinked at stem peptides. In S. aureus, SagB, a membrane-associated N-acetylglucosaminidase, cleaves polymerized glycan chains to their physiological length. Deletion of sagB is associated with longer glycan strands in peptidoglycan, altered protein trafficking and secretion in the envelope, and aberrant excretion of cytosolic proteins. It is not clear whether SagB, with its single transmembrane segment, serves as the molecular ruler of glycan chains or whether other factors modulate its activity. Here, we show that LyrA (SpdC), a protein of the CAAX type II prenyl endopeptidase family, modulates SagB activity via interaction though its transmembrane domain.
Collapse
|
44
|
Multiple concurrent and convergent stages of genome reduction in bacterial symbionts across a stink bug family. Sci Rep 2021; 11:7731. [PMID: 33833268 PMCID: PMC8032781 DOI: 10.1038/s41598-021-86574-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Nutritional symbioses between bacteria and insects are prevalent and diverse, allowing insects to expand their feeding strategies and niches. A common consequence of long-term associations is a considerable reduction in symbiont genome size likely influenced by the radical shift in selective pressures as a result of the less variable environment within the host. While several of these cases can be found across distinct insect species, most examples provide a limited view of a single or few stages of the process of genome reduction. Stink bugs (Pentatomidae) contain inherited gamma-proteobacterial symbionts in a modified organ in their midgut and are an example of a long-term nutritional symbiosis, but multiple cases of new symbiont acquisition throughout the history of the family have been described. We sequenced the genomes of 11 symbionts of stink bugs with sizes that ranged from equal to those of their free-living relatives to less than 20%. Comparative genomics of these and previously sequenced symbionts revealed initial stages of genome reduction including an initial pseudogenization before genome reduction, followed by multiple stages of progressive degeneration of existing metabolic pathways likely to impact host interactions such as cell wall component biosynthesis. Amino acid biosynthesis pathways were retained in a similar manner as in other nutritional symbionts. Stink bug symbionts display convergent genome reduction events showing progressive changes from a free-living bacterium to a host-dependent symbiont. This system can therefore be used to study convergent genome evolution of symbiosis at a scale not previously available.
Collapse
|
45
|
EslB Is Required for Cell Wall Biosynthesis and Modification in Listeria monocytogenes. J Bacteriol 2021; 203:JB.00553-20. [PMID: 33229460 PMCID: PMC7847544 DOI: 10.1128/jb.00553-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
The ABC transporter EslABC is associated with the intrinsic lysozyme resistance of Listeria monocytogenes. However, the exact role of the transporter in this process and in the physiology of L. monocytogenes is unknown. Lysozyme is an important component of the innate immune system. It functions by hydrolyzing the peptidoglycan (PG) layer of bacteria. The human pathogen Listeria monocytogenes is intrinsically lysozyme resistant. The peptidoglycan N-deacetylase PgdA and O-acetyltransferase OatA are two known factors contributing to its lysozyme resistance. Furthermore, it was shown that the absence of components of an ABC transporter, referred to here as EslABC, leads to reduced lysozyme resistance. How its activity is linked to lysozyme resistance is still unknown. To investigate this further, a strain with a deletion in eslB, coding for a membrane component of the ABC transporter, was constructed in L. monocytogenes strain 10403S. The eslB mutant showed a 40-fold reduction in the MIC to lysozyme. Analysis of the PG structure revealed that the eslB mutant produced PG with reduced levels of O-acetylation. Using growth and autolysis assays, we showed that the absence of EslB manifests in a growth defect in media containing high concentrations of sugars and increased endogenous cell lysis. A thinner PG layer produced by the eslB mutant under these growth conditions might explain these phenotypes. Furthermore, the eslB mutant had a noticeable cell division defect and formed elongated cells. Microscopy analysis revealed that an early cell division protein still localized in the eslB mutant, indicating that a downstream process is perturbed. Based on our results, we hypothesize that EslB affects the biosynthesis and modification of the cell wall in L. monocytogenes and is thus important for the maintenance of cell wall integrity. IMPORTANCE The ABC transporter EslABC is associated with the intrinsic lysozyme resistance of Listeria monocytogenes. However, the exact role of the transporter in this process and in the physiology of L. monocytogenes is unknown. Using different assays to characterize an eslB deletion strain, we found that the absence of EslB affects not only lysozyme resistance but also endogenous cell lysis, cell wall biosynthesis, cell division, and the ability of the bacterium to grow in media containing high concentrations of sugars. Our results indicate that EslB is, by means of a yet-unknown mechanism, an important determinant for cell wall integrity in L. monocytogenes.
Collapse
|
46
|
Olademehin O, Kim SJ, Shuford KL. Molecular Dynamics Simulation of Atomic Interactions in the Vancomycin Binding Site. ACS OMEGA 2021; 6:775-785. [PMID: 33458529 PMCID: PMC7808135 DOI: 10.1021/acsomega.0c05353] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Vancomycin is a glycopeptide antibiotic produced by Amycolaptopsis orientalis used to treat serious infections by Gram-positive pathogens including methicillin-resistant Staphylococcus aureus. Vancomycin inhibits cell wall biosynthesis by targeting lipid II, which is the membrane-bound peptidoglycan precursor. The heptapeptide aglycon structure of vancomycin binds to the d-Ala-d-Ala of the pentapeptide stem structure in lipid II. The third residue of vancomycin aglycon is asparagine, which is not directly involved in the dipeptide binding. Nonetheless, asparagine plays a crucial role in substrate recognition, as the vancomycin analogue with asparagine substituted by aspartic acid (VD) shows a reduction in antibacterial activities. To characterize the function of asparagine, binding of vancomycin and its aspartic-acid-substituted analogue VD to l-Lys-d-Ala-d-Ala and l-Lys-d-Ala-d-Lac was investigated using molecular dynamic simulations. Binding interactions were analyzed using root-mean-square deviation (RMSD), two-dimensional (2D) contour plots, hydrogen bond analysis, and free energy calculations of the complexes. The analysis shows that the aspartate substitution introduced a negative charge to the binding cleft of VD, which altered the aglycon conformation that minimized the repulsive lone pair interaction in the binding of a depsipeptide. Our findings provide new insight for the development of novel glycopeptide antibiotics against the emerging vancomycin-resistant pathogens by chemical modification at the third residue in vancomycin to improve its binding affinity to the d-Ala-d-Lac-terminated peptidoglycan in lipid II found in vancomycin-resistant enterococci and vancomycin-resistant S. aureus.
Collapse
Affiliation(s)
- Olatunde
P. Olademehin
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sung Joon Kim
- Department
of Chemistry, Howard University, Washington, District of
Columbia 20059, United
States
| | - Kevin L. Shuford
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| |
Collapse
|
47
|
Lyratzakis A, Valsamidis G, Kanavaki I, Nikolaki A, Rupprecht F, Langer JD, Tsiotis G. Proteomic Characterization of the Pseudomonas sp. Strain phDV1 Response to Monocyclic Aromatic Compounds. Proteomics 2020; 21:e2000003. [PMID: 33108051 DOI: 10.1002/pmic.202000003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 10/13/2020] [Indexed: 11/06/2022]
Abstract
The degradation of aromatic compounds comprises an important step in the removal of pollutants and re-utilization of plastics and other non-biological polymers. Here, Pseudomonas sp. strain phDV1, a gram-negative bacterium that is selected for its ability to degrade aromatic compounds is studied. In order to understand how the aromatic compounds and their degradation products are reintroduced in the metabolism of the bacteria and the systematic/metabolic response of the bacterium to the new carbon source, the proteome of this strain is analyzed in the presence of succinate, phenol, and o-, m-, and p-cresol as the sole carbon source. As a reference proteome, the bacteria are grown in succinate and then compared with the respective proteomes of bacteria grown on phenol and different cresols. In total, 2295 proteins are identified; 1908 proteins are used for quantification between different growth conditions. The carbon source affects the synthesis of enzymes related to aromatic compound degradation and in particular the enzyme involved in the meta-pathway of monocyclic aromatic compounds degradation. In addition, proteins involved in the production of polyhydroxyalkanoate (PHA), an attractive biomaterial, show higher abundance in the presence of monocyclic aromatic compounds. The results provide, for the first time, comprehensive information on the proteome response of this strain to monocyclic aromatic compounds.
Collapse
Affiliation(s)
- Alexandros Lyratzakis
- Division of Biochemistry, Department of Chemistry, University of Crete, Voutes, Heraklion, GR-71003, Greece
| | - Giannis Valsamidis
- Division of Biochemistry, Department of Chemistry, University of Crete, Voutes, Heraklion, GR-71003, Greece
| | - Iliana Kanavaki
- Division of Biochemistry, Department of Chemistry, University of Crete, Voutes, Heraklion, GR-71003, Greece
| | - Antigoni Nikolaki
- Division of Biochemistry, Department of Chemistry, University of Crete, Voutes, Heraklion, GR-71003, Greece
| | - Fiona Rupprecht
- Max Planck Institute for Brain Research, Max-von-Laue-Straße 4, Frankfurt am Main, D-60438, Germany.,Max Planck Institute for Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, D-60438, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, Max-von-Laue-Straße 4, Frankfurt am Main, D-60438, Germany.,Max Planck Institute for Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, D-60438, Germany
| | - Georgios Tsiotis
- Division of Biochemistry, Department of Chemistry, University of Crete, Voutes, Heraklion, GR-71003, Greece
| |
Collapse
|
48
|
Qiao M, Li B, Ji Y, Lin L, Linhardt R, Zhang X. Synthesis of selected unnatural sugar nucleotides for biotechnological applications. Crit Rev Biotechnol 2020; 41:47-62. [PMID: 33153306 DOI: 10.1080/07388551.2020.1844623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Sugar nucleotides are the principal building blocks for the synthesis of most complex carbohydrates and are crucial intermediates in carbohydrate metabolism. Uridine diphosphate (UDP) monosaccharides are among the most common sugar nucleotide donors and are transferred to glycosyl acceptors by glycosyltransferases or synthases in glycan biosynthetic pathways. These natural nucleotide donors have great biological importance, however, the synthesis and application of unnatural sugar nucleotides that are not available from in vivo biosynthesis are not well explored. In this review, we summarize the progress in the preparation of unnatural sugar nucleotides, in particular, the widely studied UDP-GlcNAc/GalNAc analogs. We focus on the "two-block" synthetic pathway that is initiated from monosaccharides, in which the first block is the synthesis of sugar-1-phosphate and the second block is the diphosphate bond formation. The biotechnological applications of these unnatural sugar nucleotides showing their physiological and pharmacological potential are discussed.
Collapse
Affiliation(s)
- Meng Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yuan Ji
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Lei Lin
- School of Environment, Nanjing Normal University, Nanjing, China
| | - Robert Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.,Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| |
Collapse
|
49
|
Gontero D, Veglia AV, Bracamonte AG. In flow metal-enhanced fluorescence for biolabelling and biodetection. Photochem Photobiol Sci 2020; 19:1168-1188. [PMID: 32677642 DOI: 10.1039/d0pp00145g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Escherichia coli bacteria were determined by in flow cytometry with laser excitation and fluorescence detection applying ultraluminescent core-shell nanoparticles based on Metal Enhanced Fluorescence (MEF). Core-shell nanoparticles consisted of a 40 nm core modified with a silica spacer grafted with Rhodamine B (RhB). The electromagnetic field in the near field of the core surface enhanced the fluorescence of RhB by plasmonic and fluorophore coupling. The hydrophilic silica spacer allowed the non-covalent interaction with the polar E. coli surface and thus ultraluminescent bacteria biolabelling was developed. Clearly, well defined and bright bacteria imaging was recorded by Laser Fluorescence Microscopy based on the non-covalent deposition of the ultraluminescent nano-emitters. Using these nano-labellers, it was possible to detect labelled E. coli by in flow cytometry. Higher values of Side-scattered light (SSC) and Forward-scattered light (FSC), and number of fluorescent event detections, were observed for labelled bacteria compared to those non-labelled. The sensitivity of the methodology was evaluated by varying bacteria concentration and acceptable analytical figures of merit were determined. Applying this methodology we could quantify E. coli from a synthetic real sample of fortified water. Similar results were obtained by bacteria counting with Laser Fluorescence Microscopy and with a cell-bacteria counter.
Collapse
Affiliation(s)
- Daniela Gontero
- Laboratorio de Análisis Clínicos y Bacteriológicos, Clínica de la Familia II, 5850, Río Tercero, Córdoba, Argentina
| | - Alicia V Veglia
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5000, Córdoba, Argentina
| | - A Guillermo Bracamonte
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5000, Córdoba, Argentina. .,Departement de chimie and Centre d'optique, photonique et laser (COPL), Université Laval, Québec, QC, Canada.
| |
Collapse
|
50
|
Gao Y, Liu Y, Ma F, Sun M, Mu G, Tuo Y. Global transcriptomic and proteomics analysis of Lactobacillus plantarum Y44 response to 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress. J Proteomics 2020; 226:103903. [PMID: 32682107 DOI: 10.1016/j.jprot.2020.103903] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/23/2020] [Accepted: 07/11/2020] [Indexed: 12/22/2022]
Abstract
Our previous study demonstrated that Lactobacillus plantarum Y44 exhibited antioxidant activity. However, the physiological characteristics of L. plantarum Y44 exposure to oxidative stress was not clear. In this research, the differentially expressed proteins and genes in L. plantarum Y44 under 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress at different concentrations were studied by using integrated transcriptomic and proteomic methods. Under 100 mM AAPH stress condition, 1139 differentially expressed genes (DEGs, 546 up-regulated and 593 down-regulated) and 329 differentially expressed proteins (DEPs, 127 up-regulated and 202 down-regulated) were observed. Under 200 mM AAPH stress condition, 1526 DEGs (751 up-regulated and 775 down-regulated) and 382 DEPs (139 up-regulated and 243 down-regulated) were observed. Overall, we found that L. plantarum Y44 fought against AAPH induced oxidative stress by up-regulating antioxidant enzymes and DNA repair proteins, such as ATP-dependent DNA helicase RuvA, adenine DNA glycosylase, single-strand DNA-binding protein SSB, DNA-binding ferritin-like protein DPS, thioredoxin reductase, protein-methionine-S-oxide reductase and glutathione peroxidase. Additionally, cell envelope composition of L. plantarum Y44 was highly remodeled by accelerating peptidoglycan and teichoic-acid (LTA) biosynthesis and modulating the fatty acids (FA) composition to achieve a higher ratio of unsaturated/saturated fatty acids (UFAs/SFAs) against AAPH stress. Moreover, metabolism processes including carbohydrate metabolism, amino acid biosynthesis, and nucleotide metabolism altered to respond to AAPH-induced damage. Altogether, our findings allow us to facilitate a better understanding of L. plantarum Y44 against oxidative stress. SIGNIFICANCE: This study represents an integrated proteomic and transcriptomic analysis of Lactobacillus plantarum Y44 response to 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress. Differentially expressed proteins and genes were identified between the proteome and transcriptome of L. plantarum Y44 under different AAPH stress. AAPH-induced response of L. plantarum Y44 appears to be primarily based on ROS scavenging, DNA repair, highly remodeled cell surface and specific metabolic processes. The knowledge about these proteomes and transcriptomes provides significant insights into the oxidative stress response of Lactobacillus plantarum.
Collapse
Affiliation(s)
- Yuan Gao
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Yujun Liu
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China
| | - Fenglian Ma
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Mengying Sun
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Guangqing Mu
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China.
| | - Yanfeng Tuo
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China.
| |
Collapse
|