1
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Sun WS, Torrens G, ter Beek J, Cava F, Berntsson RPA. Breaking barriers: pCF10 type 4 secretion system relies on a self-regulating muramidase to modulate the cell wall. mBio 2024; 15:e0048824. [PMID: 38940556 PMCID: PMC11323569 DOI: 10.1128/mbio.00488-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
Conjugative type 4 secretion systems (T4SSs) are the main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. To deliver the DNA substrate to recipient cells, it must cross the cell envelopes of both donor and recipient bacteria. In the T4SS from the enterococcal conjugative plasmid pCF10, PrgK is known to be the active cell wall degrading enzyme. It has three predicted extracellular hydrolase domains: metallo-peptidase (LytM), soluble lytic transglycosylase (SLT), and cysteine, histidine-dependent amidohydrolases/peptidases (CHAP). Here, we report the structure of the LytM domain and show that its active site is degenerate and lacks the active site metal. Furthermore, we show that only the predicted SLT domain is functional in vitro and that it unexpectedly has a muramidase instead of a lytic transglycosylase activity. While we did not observe any peptidoglycan hydrolytic activity for the LytM or CHAP domain, we found that these domains downregulated the SLT muramidase activity. The CHAP domain was also found to be involved in PrgK dimer formation. Furthermore, we show that PrgK interacts with PrgL, which likely targets PrgK to the rest of the T4SS. The presented data provides important information for understanding the function of Gram-positive T4SSs.IMPORTANCEAntibiotic resistance is a large threat to human health and is getting more prevalent. One of the major contributors to the spread of antibiotic resistance among different bacteria is type 4 secretion systems (T4SS). However, mainly T4SSs from Gram-negative bacteria have been studied in detail. T4SSs from Gram-positive bacteria, which stand for more than half of all hospital-acquired infections, are much less understood. The significance of our research is in identifying the function and regulation of a cell wall hydrolase, a key component of the pCF10 T4SS from Enterococcus faecalis. This system is one of the best-studied Gram-positive T4SSs, and this added knowledge aids in our understanding of horizontal gene transfer in E. faecalis as well as other medically relevant Gram-positive bacteria.
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Affiliation(s)
- Wei-Sheng Sun
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Gabriel Torrens
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Josy ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Ronnie P.-A. Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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2
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Kennedy NW, Comstock LE. Mechanisms of bacterial immunity, protection, and survival during interbacterial warfare. Cell Host Microbe 2024; 32:794-803. [PMID: 38870897 PMCID: PMC11216714 DOI: 10.1016/j.chom.2024.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024]
Abstract
Most bacteria live in communities, often with closely related strains and species with whom they must compete for space and resources. Consequently, bacteria have acquired or evolved mechanisms to antagonize competitors through the production of antibacterial toxins. Similar to bacterial systems that combat phage infection and mechanisms to thwart antibiotics, bacteria have also acquired and evolved features to protect themselves from antibacterial toxins. Just as there is a large body of research identifying and characterizing antibacterial proteins and toxin delivery systems, studies of bacterial mechanisms to resist and survive assault from competitors' weapons have also expanded tremendously. Emerging data are beginning to reveal protective processes and mechanisms that are as diverse as the toxins themselves. Protection against antibacterial toxins can be acquired by horizontal gene transfer, receptor or target alteration, induction of protective functions, physical barriers, and other diverse processes. Here, we review recent studies in this rapidly expanding field.
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Affiliation(s)
- Nolan W Kennedy
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Laurie E Comstock
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.
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3
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Espaillat A, Alvarez L, Torrens G, Ter Beek J, Miguel-Ruano V, Irazoki O, Gago F, Hermoso JA, Berntsson RPA, Cava F. A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha- and Betaproteobacteria. Nat Commun 2024; 15:1343. [PMID: 38351082 PMCID: PMC10864386 DOI: 10.1038/s41467-024-45620-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
The bacterial cell-wall peptidoglycan is made of glycan strands crosslinked by short peptide stems. Crosslinks are catalyzed by DD-transpeptidases (4,3-crosslinks) and LD-transpeptidases (3,3-crosslinks). However, recent research on non-model species has revealed novel crosslink types, suggesting the existence of uncharacterized enzymes. Here, we identify an LD-transpeptidase, LDTGo, that generates 1,3-crosslinks in the acetic-acid bacterium Gluconobacter oxydans. LDTGo-like proteins are found in Alpha- and Betaproteobacteria lacking LD3,3-transpeptidases. In contrast with the strict specificity of typical LD- and DD-transpeptidases, LDTGo can use non-terminal amino acid moieties for crosslinking. A high-resolution crystal structure of LDTGo reveals unique features when compared to LD3,3-transpeptidases, including a proline-rich region that appears to limit substrate access, and a cavity accommodating both glycan chain and peptide stem from donor muropeptides. Finally, we show that DD-crosslink turnover is involved in supplying the necessary substrate for LD1,3-transpeptidation. This phenomenon underscores the interplay between distinct crosslinking mechanisms in maintaining cell wall integrity in G. oxydans.
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Affiliation(s)
- Akbar Espaillat
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
- Chr. Hansen A/S, Microbial Physiology, R&D, 2970, Hoersholm, Denmark
| | - Laura Alvarez
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Gabriel Torrens
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Blas Cabrera", CSIC, Madrid, Spain
| | - Oihane Irazoki
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Federico Gago
- Department of Biomedical Sciences & IQM-CSIC Associate Unit, School of Medicine and Health Sciences, University of Alcalá, E-28805, Madrid, Alcalá de Henares, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Blas Cabrera", CSIC, Madrid, Spain
| | - Ronnie P-A Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden.
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4
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Gilmore MC, Yadav AK, Espaillat A, Gust AA, Williams MA, Brown PJB, Cava F. A peptidoglycan N-deacetylase specific for anhydroMurNAc chain termini in Agrobacterium tumefaciens. J Biol Chem 2024; 300:105611. [PMID: 38159848 PMCID: PMC10838918 DOI: 10.1016/j.jbc.2023.105611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024] Open
Abstract
During growth, bacteria remodel and recycle their peptidoglycan (PG). A key family of PG-degrading enzymes is the lytic transglycosylases, which produce anhydromuropeptides, a modification that caps the PG chains and contributes to bacterial virulence. Previously, it was reported that the polar-growing Gram-negative plant pathogen Agrobacterium tumefaciens lacks anhydromuropeptides. Here, we report the identification of an enzyme, MdaA (MurNAc deacetylase A), which specifically removes the acetyl group from anhydromuropeptide chain termini in A. tumefaciens, resolving this apparent anomaly. A. tumefaciens lacking MdaA accumulates canonical anhydromuropeptides, whereas MdaA was able to deacetylate anhydro-N-acetyl muramic acid in purified sacculi that lack this modification. As for other PG deacetylases, MdaA belongs to the CE4 family of carbohydrate esterases but harbors an unusual Cys residue in its active site. MdaA is conserved in other polar-growing bacteria, suggesting a possible link between PG chain terminus deacetylation and polar growth.
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Affiliation(s)
- Michael C Gilmore
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Akhilesh K Yadav
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India; Regulatory Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, Uttar Pradesh, India
| | - Akbar Espaillat
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Andrea A Gust
- Department of Plant Biochemistry, Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Michelle A Williams
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, USA
| | - Pamela J B Brown
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, USA
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden.
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5
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Orsini Delgado ML, Gamelas Magalhaes J, Morra R, Cultrone A. Muropeptides and muropeptide transporters impact on host immune response. Gut Microbes 2024; 16:2418412. [PMID: 39439228 PMCID: PMC11509177 DOI: 10.1080/19490976.2024.2418412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 10/04/2024] [Accepted: 10/10/2024] [Indexed: 10/25/2024] Open
Abstract
In bacteria, the cell envelope is the key element surrounding and protecting the bacterial content from mechanical or osmotic damages. It allows the selective interchanges of solutes, ions, cellular debris, and drugs between the cellular compartments and the external environment, thanks to the presence of transmembrane proteins called transporters. The major component of the cell envelope is the peptidoglycan, consisting of long linear glycan strands cross-linked by short peptide stems. During cell growth or under stress conditions, peptidoglycan fragments, the muropeptides, are released by bacteria and recognized by the host Pattern Recognition Receptor, promoting the activation of their innate defense mechanisms. The review sums up the salient aspects of microbiota-host interaction with a focus on the NOD-dependent immune response to bacterial peptidoglycan and on the accountability of muropeptide transporters in the crosstalk with the host and in antibiotic resistance. Furthermore, it retraces the discoveries and applications of microorganisms-derived components such as vaccines or vaccine adjuvants.
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6
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Alamán-Zárate MG, Rady BJ, Evans CA, Pian B, Greetham D, Marecos-Ortiz S, Dickman MJ, Lidbury IDEA, Lovering AL, Barstow BM, Mesnage S. Unusual 1-3 peptidoglycan cross-links in Acetobacteraceae are made by L,D-transpeptidases with a catalytic domain distantly related to YkuD domains. J Biol Chem 2024; 300:105494. [PMID: 38006948 PMCID: PMC10727944 DOI: 10.1016/j.jbc.2023.105494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023] Open
Abstract
Peptidoglycan is an essential component of the bacterial cell envelope that contains glycan chains substituted by short peptide stems. Peptide stems are polymerized by D,D-transpeptidases, which make bonds between the amino acid in position four of a donor stem and the third residue of an acceptor stem (4-3 cross-links). Some bacterial peptidoglycans also contain 3-3 cross-links that are formed by another class of enzymes called L,D-transpeptidases which contain a YkuD catalytic domain. In this work, we investigate the formation of unusual bacterial 1-3 peptidoglycan cross-links. We describe a version of the PGFinder software that can identify 1-3 cross-links and report the high-resolution peptidoglycan structure of Gluconobacter oxydans (a model organism within the Acetobacteraceae family). We reveal that G. oxydans peptidoglycan contains peptide stems made of a single alanine as well as several dipeptide stems with unusual amino acids at their C-terminus. Using a bioinformatics approach, we identified a G. oxydans mutant from a transposon library with a drastic reduction in 1-3 cross-links. Through complementation experiments in G. oxydans and recombinant protein production in a heterologous host, we identify an L,D-transpeptidase enzyme with a domain distantly related to the YkuD domain responsible for these non-canonical reactions. This work revisits the enzymatic capabilities of L,D-transpeptidases, a versatile family of enzymes that play a key role in bacterial peptidoglycan remodelling.
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Affiliation(s)
- Marcel G Alamán-Zárate
- Molecular Microbiology, Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Brooks J Rady
- Molecular Microbiology, Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Caroline A Evans
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, UK
| | - Brooke Pian
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, USA
| | - Darren Greetham
- Molecular Microbiology, Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Sabrina Marecos-Ortiz
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, USA
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, UK
| | - Ian D E A Lidbury
- Molecular Microbiology, Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Buz M Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, USA
| | - Stéphane Mesnage
- Molecular Microbiology, Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, UK.
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7
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Patel MH, Lu SY, Liu S, Skory CD. Novel endolysin LysMP for control of Limosilactobacillus fermentum contamination in small-scale corn mash fermentation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:144. [PMID: 37775769 PMCID: PMC10541714 DOI: 10.1186/s13068-023-02400-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
BACKGROUND Traditional bioethanol fermentation industries are not operated under strict sterile conditions and are prone to microbial contamination. Lactic acid bacteria (LAB) are often pervasive in fermentation tanks, competing for nutrients and producing inhibitory acids that have a negative impact on ethanol-producing yeast, resulting in decreased yields and stuck fermentations. Antibiotics are frequently used to combat contamination, but antibiotic stewardship has resulted in a shift to alternative antimicrobials. RESULTS We demonstrate that endolysin LysMP, a bacteriophage-encoded peptidoglycan hydrolase, is an effective method for controlling growth of LAB. The LysMP gene was synthesized based on the prophage sequence in the genome of Limosilactobacillus fermentum KGL7. Analysis of the recombinant enzyme expressed in E. coli and purified by immobilized metal chelate affinity chromatography (IMAC) showed an optimal lysis activity against various LAB species at pH 6, with stability from pH 4 to 8 and from 20 to 40 °C up to 48 h. Moreover, it retains more than 80% of its activity at 10% ethanol (v/v) for up to 48 h. When LysMP was added at 250 µg/mL to yeast corn mash fermentations containing L. fermentum, it reduced bacterial load by at least 4-log fold compared to the untreated controls and prevented stuck fermentation. In comparison, untreated controls with contamination increased from an initial bacterial load of 1.50 × 107 CFU/mL to 2.25 × 109 CFU/mL and 1.89 × 109 CFU/mL after 24 h and 48 h, respectively. Glucose in the treated samples was fully utilized, while untreated controls with contamination had more than 4% (w/v) remaining at 48 h. Furthermore, there was at least a fivefold reduction in lactic acid (0.085 M untreated contamination controls compared to 0.016 M treated), and a fourfold reduction in acetic acid (0.027 M untreated contamination controls vs. 0.007 M treated), when LysMP was used to treat contaminated corn mash fermentations. Most importantly, final ethanol yields increased from 6.3% (w/v) in untreated contamination samples to 9.3% (w/v) in treated contamination samples, an approximate 50% increase to levels comparable to uncontaminated controls 9.3% (w/v). CONCLUSION LysMP could be a good alternative to replace antibiotics for mitigation of LAB contamination in biofuel refineries.
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Affiliation(s)
- Maulik H Patel
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, USA
| | - Shao-Yeh Lu
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, 1815 N. University St, Peoria, IL, 61604-3902, USA.
| | - Siqing Liu
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, 1815 N. University St, Peoria, IL, 61604-3902, USA
| | - Christopher D Skory
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research Unit, 1815 N. University St, Peoria, IL, 61604-3902, USA
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8
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Qush A, Al Khatib HA, Rachid H, Al-Tamimi H, Al-Eshaq A, Al-Adwi S, Yassine HM, Kamareddine L. Intake of caffeine containing sugar diet remodels gut microbiota and perturbs Drosophila melanogaster immunity and lifespan. Microbes Infect 2023; 25:105149. [PMID: 37169244 DOI: 10.1016/j.micinf.2023.105149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/30/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
The diet-microbiome-immunity axis is one among the many arms that draw up the "we are what we intake" proclamation. As such, studies on the effect of food and beverage intake on the gut environment and microbiome and on modulating immunological responses and the host's susceptibility to pathogens are on the rise. A typical accompaniment in different sustenance we consume on daily basis is the trimethylxanthine alkaloid caffeine. Being a chief component in our regular aliment, a better understanding of the effect of caffeine containing food and beverages on our gut-microbiome-immunity axis and henceforth on our health is much needed. In this study, we shed more light on the effect of oral consumption of caffeine supplemented sugar diet on the gut environment, specifically on the gut microbiota, innate immunity and host susceptibility to pathogens using the Drosophila melanogaster model organism. Our findings reveal that the oral intake of a dose-specific caffeine containing sucrose/agarose sugar diet causes a significant alteration within the fly gut milieu demarcated by microbial dysbiosis and an elevation in the production of reactive oxygen species and expression of immune-deficiency (Imd) pathway-dependent antimicrobial peptide genes. The oral intake of caffeine containing sucrose/agarose sugar diet also renders the flies more susceptible to bacterial infection and shortens their lifespan in both infection and non-infection settings. Our findings set forth additional insight into the potentiality of diet to alter the gut milieu and highlight the importance of dietary control on health.
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Affiliation(s)
- Abeer Qush
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hebah A Al Khatib
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar; Biomedical Research Center, Qatar University, Doha, Qatar
| | - Hajar Rachid
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hend Al-Tamimi
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Alyaa Al-Eshaq
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Shaima Al-Adwi
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hadi M Yassine
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar; Biomedical Research Center, Qatar University, Doha, Qatar
| | - Layla Kamareddine
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar; Biomedical Research Center, Qatar University, Doha, Qatar.
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9
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Alberge F, Lakey BD, Schaub RE, Dohnalkova AC, Lemmer KC, Dillard JP, Noguera DR, Donohue TJ. A previously uncharacterized divisome-associated lipoprotein, DalA, is needed for normal cell division in Rhodobacterales. mBio 2023; 14:e0120323. [PMID: 37389444 PMCID: PMC10470522 DOI: 10.1128/mbio.01203-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
The bacterial cell envelope is a key subcellular compartment with important roles in antibiotic resistance, nutrient acquisition, and cell morphology. We seek to gain a better understanding of proteins that contribute to the function of the cell envelope in Alphaproteobacteria. Using Rhodobacter sphaeroides, we show that a previously uncharacterized protein, RSP_1200, is an outer membrane (OM) lipoprotein that non-covalently binds peptidoglycan (PG). Using a fluorescently tagged version of this protein, we find that RSP_1200 undergoes a dynamic repositioning during the cell cycle and is enriched at the septum during cell division. We show that the position of RSP_1200 mirrors the location of FtsZ rings, leading us to propose that RSP_1200 is a newly identified component of the R. sphaeroides' divisome. Additional support for this hypothesis includes the co-precipitation of RSP_1200 with FtsZ, the Pal protein, and several predicted PG L,D-transpeptidases. We also find that a ∆RSP_1200 mutation leads to defects in cell division, sensitivity to PG-active antibiotics, and results in the formation of OM protrusions at the septum during cell division. Based on these results, we propose to name RSP_1200 DalA (for division-associated lipoprotein A) and postulate that DalA serves as a scaffold to position or modulate the activity of PG transpeptidases that are needed to form envelope invaginations during cell division. We find that DalA homologs are present in members of the Rhodobacterales order within Alphaproteobacteria. Therefore, we propose that further analysis of this and related proteins will increase our understanding of the macromolecular machinery and proteins that participate in cell division in Gram-negative bacteria. IMPORTANCE Multi-protein complexes of the bacterial cell envelope orchestrate key processes like growth, division, biofilm formation, antimicrobial resistance, and production of valuable compounds. The subunits of these protein complexes are well studied in some bacteria, and differences in their composition and function are linked to variations in cell envelope composition, shape, and proliferation. However, some envelope protein complex subunits have no known homologs across the bacterial phylogeny. We find that Rhodobacter sphaeroides RSP_1200 is a newly identified lipoprotein (DalA) and that loss of this protein causes defects in cell division and changes the sensitivity to compounds, affecting cell envelope synthesis and function. We find that DalA forms a complex with proteins needed for cell division, binds the cell envelope polymer peptidoglycan, and colocalizes with enzymes involved in the assembly of this macromolecule. The analysis of DalA provides new information on the cell division machinery in this and possibly other Alphaproteobacteria.
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Affiliation(s)
- François Alberge
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Bryan D. Lakey
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan E. Schaub
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alice C. Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Joseph P. Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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10
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Figueroa-Cuilan WM, Irazoki O, Feeley M, Smith E, Nguyen T, Cava F, Goley ED. Quantitative analysis of morphogenesis and growth dynamics in an obligate intracellular bacterium. Mol Biol Cell 2023; 34:ar69. [PMID: 37017481 PMCID: PMC10295487 DOI: 10.1091/mbc.e23-01-0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/23/2023] [Accepted: 03/29/2023] [Indexed: 04/06/2023] Open
Abstract
Obligate intracellular bacteria of the order Rickettsiales include important human pathogens. However, our understanding of the biology of Rickettsia species is limited by challenges imposed by their obligate intracellular lifestyle. To overcome this roadblock, we developed methods to assess cell wall composition, growth, and morphology of Rickettsia parkeri, a human pathogen in the spotted fever group of the Rickettsia genus. Analysis of the cell wall of R. parkeri revealed unique features that distinguish it from free-living alphaproteobacteria. Using a novel fluorescence microscopy approach, we quantified R. parkeri morphology in live host cells and found that the fraction of the population undergoing cell division decreased over the course of infection. We further demonstrated the feasibility of localizing fluorescence fusions, for example, to the cell division protein ZapA, in live R. parkeri for the first time. To evaluate population growth kinetics, we developed an imaging-based assay that improves on the throughput and resolution of other methods. Finally, we applied these tools to quantitatively demonstrate that the actin homologue MreB is required for R. parkeri growth and rod shape. Collectively, a toolkit was developed of high-throughput, quantitative tools to understand growth and morphogenesis of R. parkeri that is translatable to other obligate intracellular bacteria.
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Affiliation(s)
- Wanda M. Figueroa-Cuilan
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Oihane Irazoki
- Laboratory for Molecular Infection Medicine, Umeå Center for Microbial Research, Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Marissa Feeley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Erika Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Trung Nguyen
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine, Umeå Center for Microbial Research, Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Erin D. Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
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11
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Onuma T, Yamauchi T, Kosakamoto H, Kadoguchi H, Kuraishi T, Murakami T, Mori H, Miura M, Obata F. Recognition of commensal bacterial peptidoglycans defines Drosophila gut homeostasis and lifespan. PLoS Genet 2023; 19:e1010709. [PMID: 37023169 PMCID: PMC10112789 DOI: 10.1371/journal.pgen.1010709] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/18/2023] [Accepted: 03/21/2023] [Indexed: 04/08/2023] Open
Abstract
Commensal microbes in animals have a profound impact on tissue homeostasis, stress resistance, and ageing. We previously showed in Drosophila melanogaster that Acetobacter persici is a member of the gut microbiota that promotes ageing and shortens fly lifespan. However, the molecular mechanism by which this specific bacterial species changes lifespan and physiology remains unclear. The difficulty in studying longevity using gnotobiotic flies is the high risk of contamination during ageing. To overcome this technical challenge, we used a bacteria-conditioned diet enriched with bacterial products and cell wall components. Here, we demonstrate that an A. persici-conditioned diet shortens lifespan and increases intestinal stem cell (ISC) proliferation. Feeding adult flies a diet conditioned with A. persici, but not with Lactiplantibacillus plantarum, can decrease lifespan but increase resistance to paraquat or oral infection of Pseudomonas entomophila, indicating that the bacterium alters the trade-off between lifespan and host defence. A transcriptomic analysis using fly intestine revealed that A. persici preferably induces antimicrobial peptides (AMPs), while L. plantarum upregulates amidase peptidoglycan recognition proteins (PGRPs). The specific induction of these Imd target genes by peptidoglycans from two bacterial species is due to the stimulation of the receptor PGRP-LC in the anterior midgut for AMPs or PGRP-LE from the posterior midgut for amidase PGRPs. Heat-killed A. persici also shortens lifespan and increases ISC proliferation via PGRP-LC, but it is not sufficient to alter the stress resistance. Our study emphasizes the significance of peptidoglycan specificity in determining the gut bacterial impact on healthspan. It also unveils the postbiotic effect of specific gut bacterial species, which turns flies into a "live fast, die young" lifestyle.
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Affiliation(s)
- Taro Onuma
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Toshitaka Yamauchi
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Hibiki Kadoguchi
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Takayuki Kuraishi
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Takumi Murakami
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Hiroshi Mori
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Fumiaki Obata
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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12
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Pseudomonas aeruginosa Alters Peptidoglycan Composition under Nutrient Conditions Resembling Cystic Fibrosis Lung Infections. mSystems 2022; 7:e0015622. [PMID: 35545925 PMCID: PMC9239049 DOI: 10.1128/msystems.00156-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Epidemic strains of Pseudomonas aeruginosa are highly virulent opportunistic pathogens with increased transmissibility and enhanced antimicrobial resistance. Understanding the cellular mechanisms behind this heightened virulence and resistance is critical. Peptidoglycan (PG) is an integral component of P. aeruginosa cells that is essential to its survival and a target for antimicrobials. Here, we examined the global PG composition of two P. aeruginosa epidemic strains, LESB58 and LESlike1, and compared them to the common laboratory strains PAO1 and PA14. We also examined changes in PG composition when the strains were cultured under nutrient conditions that resembled cystic fibrosis lung infections. We identified 448 unique muropeptides and provide the first evidence for stem peptides modified with O-methylation, meso-diaminopimelic acid (mDAP) deamination, and novel substitutions of mDAP residues within P. aeruginosa PG. Our results also present the first evidence for both d,l- and l,d-endopeptidase activity on the PG sacculus of a Gram-negative organism. The PG composition of the epidemic strains varied significantly when grown under conditions resembling cystic fibrosis (CF) lung infections, showing increases in O-methylated stem peptides and decreases in l,d-endopeptidase activity as well as an increased abundance of de-N-acetylated sugars and l,d-transpeptidase activity, which are related to bacterial virulence and antibiotic resistance, respectively. We also identified strain-specific changes where LESlike1 increased the addition of unique amino acids to the terminus of the stem peptide and LESB58 increased amidase activity. Overall, this study demonstrates that P. aeruginosa PG composition is primarily influenced by nutrient conditions that mimic the CF lung; however, inherent strain-to-strain differences also exist. IMPORTANCE Using peptidoglycomics to examine the global composition of the peptidoglycan (PG) allows insights into the enzymatic activity that functions on this important biopolymer. Changes within the PG structure have implications for numerous physiological processes, including virulence and antimicrobial resistance. The identification of highly unique PG modifications illustrates the complexity of this biopolymer in Pseudomonas aeruginosa. Analyzing the PG composition of clinical P. aeruginosa epidemic strains provides insights into the increased virulence and antimicrobial resistance of these difficult-to-eradicate infections.
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13
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Impact of crossbridge structure on peptidoglycan crosslinking: A synthetic stem peptide approach. Methods Enzymol 2022; 665:259-279. [PMID: 35379437 DOI: 10.1016/bs.mie.2021.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The bacterial cell wall, whose main component is peptidoglycan (PG), provides cellular rigidity and prevents lysis from osmotic pressure. Moreover, the cell wall is the main interface between the external environment and internal cellular components. Given its essentiality, many antibiotics target enzymes related to the biosynthesis of cell wall. Of these enzymes, transpeptidases (TPs) are central to proper cell wall assembly and their inactivation is the mechanism of action of many antibiotics including β-lactams. TPs are responsible for stitching together strands of PG to make the crosslinked meshwork of the cell wall. This chapter focuses on the use of solid-phase peptide synthesis to build PG analogs that become site-selectively incorporated into the cell wall of live bacterial cells. This method allows for the design of fluorescent handles on PG probes that will enable the interrogation of substrate preferences of TPs (e.g., amidation at the glutamic acid residue, crossbridge presence) by analyzing the level of probe incorporation within the native cell wall of live bacterial cells.
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14
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Sun L, Rogiers G, Courtin P, Chapot-Chartier MP, Bierne H, Michiels CW. AsnB Mediates Amidation of Meso-Diaminopimelic Acid Residues in the Peptidoglycan of Listeria monocytogenes and Affects Bacterial Surface Properties and Host Cell Invasion. Front Microbiol 2021; 12:760253. [PMID: 34721369 PMCID: PMC8554201 DOI: 10.3389/fmicb.2021.760253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/24/2021] [Indexed: 11/30/2022] Open
Abstract
A mutant of Listeria monocytogenes ScottA with a transposon in the 5' untranslated region of the asnB gene was identified to be hypersensitive to the antimicrobial t-cinnamaldehyde. Here, we report the functional characterization of AsnB in peptidoglycan (PG) modification and intracellular infection. While AsnB of Listeria is annotated as a glutamine-dependent asparagine synthase, sequence alignment showed that this protein is closely related to a subset of homologs that catalyze the amidation of meso-diaminopimelic acid (mDAP) residues in the peptidoglycan of other bacterial species. Structural analysis of peptidoglycan from an asnB mutant, compared to that of isogenic wild-type (WT) and complemented mutant strains, confirmed that AsnB mediates mDAP amidation in L. monocytogenes. Deficiency in mDAP amidation caused several peptidoglycan- and cell surface-related phenotypes in the asnB mutant, including formation of shorter but thicker cells, susceptibility to lysozyme, loss of flagellation and motility, and a strong reduction in biofilm formation. In addition, the mutant showed reduced invasion of human epithelial JEG-3 and Caco-2 cells. Analysis by immunofluorescence microscopy revealed that asnB inactivation abrogated the proper display at the listerial surface of the invasion protein InlA, which normally gets cross-linked to mDAP via its LPXTG motif. Together, this work shows that AsnB of L. monocytogenes, like several of its homologs in related Gram-positive bacteria, mediates the amidation of mDAP residues in the peptidoglycan and, in this way, affects several cell wall and cell surface-related properties. It also for the first time implicates the amidation of peptidoglycan mDAP residues in cell wall anchoring of InlA and in bacterial virulence.
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Affiliation(s)
- Lei Sun
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S) and Leuven Food Science and Nutrition Research Center (LFoRCe), KU Leuven, Leuven, Belgium
| | - Gil Rogiers
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S) and Leuven Food Science and Nutrition Research Center (LFoRCe), KU Leuven, Leuven, Belgium
| | - Pascal Courtin
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Hélène Bierne
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
| | - Chris W Michiels
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S) and Leuven Food Science and Nutrition Research Center (LFoRCe), KU Leuven, Leuven, Belgium
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15
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Formylglycine-generating enzyme-like proteins constitute a novel family of widespread type VI secretion system immunity proteins. J Bacteriol 2021; 203:e0028121. [PMID: 34398661 DOI: 10.1128/jb.00281-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Competition is a critical aspect of bacterial life, as it enables niche establishment and facilitates the acquisition of essential nutrients. Warfare between Gram-negative bacteria is largely mediated by the type VI secretion system (T6SS), a dynamic nanoweapon that delivers toxic effector proteins from an attacking cell to adjacent bacteria in a contact-dependent manner. Effector-encoding bacteria prevent self-intoxication and kin cell killing by the expression of immunity proteins, which prevent effector toxicity by specifically binding their cognate effector and either occluding its active site or preventing structural rearrangements necessary for effector activation. In this study, we investigate Tsi3, a previously uncharacterized T6SS immunity protein present in multiple strains of the human pathogen Acinetobacter baumannii. We show that Tsi3 is the cognate immunity protein of the antibacterial effector of unknown function Tse3. Our bioinformatic analyses indicate that Tsi3 homologs are widespread among Gram-negative bacteria, often encoded within T6SS effector-immunity modules. Surprisingly, we found that Tsi3 homologs are predicted to possess a characteristic formylglycine-generating enzyme (FGE) domain, which is present in various enzymatic proteins. Our data shows that Tsi3-mediated immunity is dependent on Tse3-Tsi3 protein-protein interactions and that Tsi3 homologs from various bacteria do not provide immunity against non-kin Tse3. Thus, we conclude that Tsi3 homologs are unlikely to be functional enzymes. Collectively, our work identifies FGE domain-containing proteins as important mediators of immunity against T6SS attacks and indicates that the FGE domain can be co-opted as a scaffold in multiple proteins to carry out diverse functions. Importance Despite the wealth of knowledge on the diversity of biochemical activities carried out by T6SS effectors, comparably little is known about the various strategies bacteria employ to prevent susceptibility to T6SS-dependent bacterial killing. Our work establishes a novel family of T6SS immunity proteins with a characteristic FGE domain. This domain is present in enzymatic proteins with various catalytic activities. Our characterization of Tsi3 expands the known functions carried out by FGE-like proteins to include defense during T6SS-mediated bacterial warfare. Moreover, it highlights the evolution of FGE domain-containing proteins to carry out diverse biological functions.
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16
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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17
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Modulation of Peptidoglycan Synthesis by Recycled Cell Wall Tetrapeptides. Cell Rep 2021; 31:107578. [PMID: 32348759 DOI: 10.1016/j.celrep.2020.107578] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/12/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022] Open
Abstract
The bacterial cell wall is made of peptidoglycan (PG), a polymer that is essential for the maintenance of cell shape and survival. During growth, bacteria remodel their PG, releasing fragments that are predominantly re-internalized and recycled. Here, we show that Vibrio cholerae recycles PG fragments modified with non-canonical d-amino acids (NCDAA), which lead to the accumulation of cytosolic PG tetrapeptides. We demonstrate that the accumulation of recycled tetrapeptides has two regulatory consequences for the cell wall: reduction of d,d-cross-linkage and reduction of PG synthesis. We further demonstrate that l,d-carboxypeptidases from five different species show a preferential activity for substrates containing canonical (d-alanine) versus non-canonical (d-methionine) d-amino acids, suggesting that the accumulation of intracellular tetrapeptides in NCDAA-rich environments is widespread. Collectively, this work reveals a regulatory role of NCDAA linking PG recycling and synthesis to promote optimal cell wall assembly and composition in the stationary phase.
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18
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Aliashkevich A, Howell M, Brown PJB, Cava F. d-canavanine affects peptidoglycan structure, morphogenesis and fitness in Rhizobiales. Environ Microbiol 2021; 23:5823-5836. [PMID: 33830599 DOI: 10.1111/1462-2920.15513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/25/2021] [Accepted: 04/06/2021] [Indexed: 02/02/2023]
Abstract
The bacterial cell wall is made of peptidoglycan (PG), a polymer that is essential for maintenance of cell shape and survival. Many bacteria alter their PG chemistry as a strategy to adapt their cell wall to external challenges. Therefore, identifying these environmental cues is important to better understand the interplay between microbes and their habitat. Here, we used the soil bacterium Pseudomonas putida to uncover cell wall modulators from plant extracts and found canavanine (CAN), a non-proteinogenic amino acid. We demonstrated that cell wall chemical editing by CAN is licensed by P. putida BSAR, a broad-spectrum racemase which catalyses production of dl-CAN from l-CAN, which is produced by many legumes. Importantly, d-CAN diffuses to the extracellular milieu thereby having a potential impact on other organisms inhabiting the same niche. Our results show that d-CAN alters dramatically the PG structure of Rhizobiales (e.g., Agrobacterium tumefaciens, Sinorhizobium meliloti), impairing PG crosslinkage and cell division. Using A. tumefaciens, we demonstrated that the detrimental effect of d-CAN is suppressed by a single amino acid substitution in the cell division PG transpeptidase penicillin binding protein 3a. Collectively, this work highlights the role of amino acid racemization in cell wall chemical editing and fitness.
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Affiliation(s)
- Alena Aliashkevich
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Matthew Howell
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65201, USA.,Department of Biology and Environmental Science, Westminster College, Fulton, MO, 65251, USA
| | - Pamela J B Brown
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65201, USA
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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19
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Class A Penicillin-Binding Protein-Mediated Cell Wall Synthesis Promotes Structural Integrity during Peptidoglycan Endopeptidase Insufficiency in Vibrio cholerae. mBio 2021; 12:mBio.03596-20. [PMID: 33824203 PMCID: PMC8092314 DOI: 10.1128/mbio.03596-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial cell wall is composed primarily of peptidoglycan (PG), a poly-aminosugar that is essential to sustain cell shape, growth, and structural integrity. PG is synthesized by class A/B penicillin-binding proteins (a/bPBPs) and shape, elongation, division, and sporulation (SEDS) proteins like RodA (as part of the Rod system cell elongation machinery) and degraded by "autolytic" enzymes to accommodate growth processes. It is thought that autolysins (particularly endopeptidases [EPs]) are required for PG synthesis and incorporation by creating gaps that are patched and paved by PG synthases, but the exact relationship between autolysins and PG synthesis remains incompletely understood. Here, we have probed the consequences of EP depletion for PG synthesis in the diarrheal pathogen Vibrio cholerae We found that EP depletion resulted in severe morphological and division defects, but these cells continued to increase in mass and aberrantly incorporated new cell wall material. Mass increase proceeded in the presence of Rod system inhibitors, but cells lysed upon inhibition of aPBPs, suggesting that aPBPs are required for structural integrity under these conditions. The Rod system, although not essential for the observed mass increase, remained functional even after prolonged EP depletion. Last, heterologous expression of an EP from Neisseria gonorrhoeae fully complemented growth and morphology of an EP-insufficient V. cholerae, highlighting the possibility that the PG synthases may not necessarily function via direct interaction with EPs. Overall, our findings suggest that during EP insufficiency in V. cholerae, aPBPs become essential for structural integrity while the Rod system is unable to promote proper cell expansion.IMPORTANCE Synthesis and turnover of the bacterial cell wall must be tightly coordinated to avoid structural integrity failure and cell death. Details of this coordination are poorly understood, particularly if and how cell wall turnover enzymes are required for the activity of the different cell wall synthesis machines, the aPBPs and the Rod system. Our results suggest that in Vibrio cholerae, one class of turnover enzymes, the endopeptidases, are necessary for proper cell elongation and division. aPBPs become essential for maintaining structural integrity during EP insufficiency, while the Rod system remains active but contributes little to cell expansion under these conditions. Our results suggest that aPBPs are more versatile than the Rod system in their ability to recognize cell wall gaps formed by autolysins other than the major endopeptidases, adding to our understanding of the coordination between autolysins and cell wall synthases. A detailed understanding of autolysin biology may promote the development of antibiotics that target these essential turnover processes.
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20
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Sibinelli-Sousa S, Hespanhol JT, Bayer-Santos E. Targeting the Achilles' Heel of Bacteria: Different Mechanisms To Break Down the Peptidoglycan Cell Wall during Bacterial Warfare. J Bacteriol 2021; 203:e00478-20. [PMID: 33139480 PMCID: PMC8088523 DOI: 10.1128/jb.00478-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteria commonly live in dense polymicrobial communities and compete for scarce resources. Consequently, they employ a diverse array of mechanisms to harm, inhibit, and kill their competitors. The cell wall is essential for bacterial survival by providing mechanical strength to resist osmotic stress. Because peptidoglycan is the major component of the cell wall and its synthesis is a complex multistep pathway that requires the coordinate action of several enzymes, it provides a target for rival bacteria, which have developed a large arsenal of antibacterial molecules to attack the peptidoglycan of competitors. These molecules include antibiotics, bacteriocins, and contact-dependent effectors that are either secreted into the medium or directly translocated into a target cell. In this minireview, we summarize the diversity of these molecules and highlight distinct mechanisms to disrupt the peptidoglycan, giving special attention to molecules that are known or have the potential to be used during interbacterial competitions.
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Affiliation(s)
- Stephanie Sibinelli-Sousa
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Julia Takuno Hespanhol
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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21
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Gilmore MC, Ritzl-Rinkenberger B, Cava F. An updated toolkit for exploring bacterial cell wall structure and dynamics. Fac Rev 2021; 10:14. [PMID: 33659932 PMCID: PMC7894271 DOI: 10.12703/r/10-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The bacterial cell wall is made primarily from peptidoglycan, a complex biomolecule which forms a bag-like exoskeleton that envelops the cell. As it is unique to bacteria and typically essential for their growth and survival, it represents one of the most successful targets for antibiotics. Although peptidoglycan has been studied intensively for over 50 years, the past decade has seen major steps in our understanding of this molecule because of the advent of new analytical and imaging methods. Here, we outline the most recent developments in tools that have helped to elucidate peptidoglycan structure and dynamics.
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Affiliation(s)
- Michael C Gilmore
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Barbara Ritzl-Rinkenberger
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
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22
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New approaches and techniques for bacterial cell wall analysis. Curr Opin Microbiol 2021; 60:88-95. [PMID: 33631455 DOI: 10.1016/j.mib.2021.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 12/17/2022]
Abstract
Peptidoglycan (PG) has remained for decades in the spotlight of the never-ending battle against pathogenic bacteria as this essential bacterial structure is one of the most successful targets for antibiotics. Most of our current understanding about the composition, architecture, and dynamics of the PG relies on techniques which have experienced great technological and methodological improvements in the past years. Here we summarize recent advances in these methods with the intention to furnish a valuable resource for both PG experts and newcomers.
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23
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Zhao D, Liu X, Zhang R, Huang X, Xiao X. Facile one-pot synthesis of multifunctional protamine sulfate-derived carbon dots for antibacterial applications and fluorescence imaging of bacteria. NEW J CHEM 2021. [DOI: 10.1039/d0nj04458j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
PS-carbon dots (CDs) were prepared by a microwave-assisted method using protamine sulfate (PS), and they have dual functions of antibacterial and bacterial imaging.
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Affiliation(s)
- Dan Zhao
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan 430074
- P. R. China
- National Demonstration Center for Experimental Ethnopharmacology Education (South-Central University for Nationalities)
| | - Xuemei Liu
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan 430074
- P. R. China
| | - Rui Zhang
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan 430074
- P. R. China
| | - Xianju Huang
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan 430074
- P. R. China
| | - Xincai Xiao
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan 430074
- P. R. China
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24
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García-Del Portillo F. Building peptidoglycan inside eukaryotic cells: A view from symbiotic and pathogenic bacteria. Mol Microbiol 2020; 113:613-626. [PMID: 32185832 PMCID: PMC7154730 DOI: 10.1111/mmi.14452] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/08/2019] [Accepted: 01/09/2020] [Indexed: 12/13/2022]
Abstract
The peptidoglycan (PG), as the exoskeleton of most prokaryotes, maintains a defined shape and ensures cell integrity against the high internal turgor pressure. These important roles have attracted researchers to target PG metabolism in order to control bacterial infections. Most studies, however, have been performed in bacteria grown under laboratory conditions, leading to only a partial view on how the PG is synthetized in natural environments. As a case in point, PG metabolism and its regulation remain poorly understood in symbiotic and pathogenic bacteria living inside eukaryotic cells. This review focuses on the PG metabolism of intracellular bacteria, emphasizing the necessity of more in vivo studies involving the analysis of enzymes produced in the intracellular niche and the isolation of PG from bacteria residing within eukaryotic cells. The review also points to persistent infections caused by some intracellular bacterial pathogens and the extent at which the PG could contribute to establish such physiological state. Based on recent evidences, I speculate on the idea that certain structural features of the PG may facilitate attenuation of intracellular growth. Lastly, I discuss recent findings in endosymbionts supporting a cooperation between host and bacterial enzymes to assemble a mature PG.
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25
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Crump GM, Zhou J, Mashayekh S, Grimes CL. Revisiting peptidoglycan sensing: interactions with host immunity and beyond. Chem Commun (Camb) 2020; 56:13313-13322. [PMID: 33057506 PMCID: PMC7642115 DOI: 10.1039/d0cc02605k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The interaction between host immunity and bacterial cells plays a pivotal role in a variety of human diseases. The bacterial cell wall component peptidoglycan (PG) is known to stimulate an immune response, which makes PG a distinctive recognition element for unveiling these complicated molecular interactions. Pattern recognition receptor (PRR) proteins are among the critical components of this system that initially recognize molecular patterns associated with microorganisms such as bacteria and fungi. These molecular patterns are mostly embedded in the bacterial or fungal cell wall structure and can be released and presented to the immune system in various situations. Nonetheless, detailed knowledge of this recognition is limited due to the diversity among the PG polymer and its fragments; the subsequent responses by multiple hosts add more complexity. Here, we discuss how our understanding of the role and molecular mechanisms of the well-studied PRR, the NOD-like receptors (NLRs), in the human immune system has evolved in recent years. We highlight the instances of other classes of proteins with similar behavior in the recognition of PG that have been identified in other microorganisms such as yeasts. These proteins are particularly interesting because a network of cellular interactions exists between human host cells, bacteria and yeast as a part of the normal human flora. To support our understanding of these interactions, we provide insight into the chemist's toolbox of peptidoglycan probes that aid in the investigations of the behaviors of these proteins and other biological contexts relevant to the sensing and recognition of peptidoglycan. The importance of these interactions in human health for the development of biomarkers and biotherapy is highlighted.
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Affiliation(s)
- Geneva Maddison Crump
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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Zhao D, Liu X, Zhang R, Xiao X, Li J. Preparation of two types of silver-doped fluorescent carbon dots and determination of their antibacterial properties. J Inorg Biochem 2020; 214:111306. [PMID: 33221600 DOI: 10.1016/j.jinorgbio.2020.111306] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/27/2020] [Accepted: 11/07/2020] [Indexed: 10/23/2022]
Abstract
The preparation and performance of doped antibacterial carbon dots (CDs) have been the research hotspot. In this paper, we report the preparation of two blue light-emitting silver-doped CDs, CD-1 and CD-2, through one- and two-step routes, respectively, by using polyethyleneimine, citric acid, and AgNO3 as raw materials. Both CDs exhibited excellent and broad-spectrum activity against gram-positive bacteria, gram-negative bacteria, and fungi. We compared the emission wavelength, surface group, particle size, chargeability, and element content of the two CDs through various characterization methods. CD-2 exhibiting longer emission wavelength, larger particle size, and higher silver content displayed higher antibacterial activity against microorganisms than CD-1. On the other hand, CDs exhibited varying antibacterial properties against different microorganisms because of differences in the cell wall structure of gram-positive bacteria (peptidoglycan), gram-negative bacteria (lipopolysaccharides), and fungi (chitin). Based on scanning electron microscopy observations, circular dichroism spectroscopy and agarose gel electrophoresis, we speculate that CDs exert antibacterial activity mainly through membrane disruption and their effect on intracellular DNA and proteins. At the same time, CDs have multicolor imaging capabilities of Staphylococcus aureus. The antibacterial activity and versatility of bioimaging make them more potential antibacterial agents than traditional agents.
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Affiliation(s)
- Dan Zhao
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, P. R. China; National Demonstration Center for Experimental Ethnopharmacology Education (South-Central University for Nationalities), Wuhan 430065, P. R. China.
| | - Xuemei Liu
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, P. R. China
| | - Rui Zhang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, P. R. China
| | - Xincai Xiao
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, P. R. China
| | - Jun Li
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, P. R. China
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Grishin AV, Karyagina AS, Vasina DV, Vasina IV, Gushchin VA, Lunin VG. Resistance to peptidoglycan-degrading enzymes. Crit Rev Microbiol 2020; 46:703-726. [PMID: 32985279 DOI: 10.1080/1040841x.2020.1825333] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The spread of bacterial strains resistant to commonly used antibiotics urges the development of novel antibacterial compounds. Ideally, these novel antimicrobials should be less prone to the development of resistance. Peptidoglycan-degrading enzymes are a promising class of compounds with a fundamentally different mode of action compared to traditionally used antibiotics. The difference in the mechanism of action implies differences both in the mechanisms of resistance and the chances of its emergence. To critically assess the potential of resistance development to peptidoglycan-degrading enzymes, we review the available evidence for the development of resistance to these enzymes in vitro, along with the known mechanisms of resistance to lysozyme, bacteriocins, autolysins, and phage endolysins. We conclude that genetic determinants of resistance to peptidoglycan-degrading enzymes are unlikely to readily emerge de novo. However, resistance to these enzymes would probably spread by the horizontal transfer between intrinsically resistant and susceptible species. Finally, we speculate that the higher cost of the therapeutics based on peptidoglycan degrading enzymes compared to classical antibiotics might result in less misuse, which in turn would lead to lower selective pressure, making these antibacterials less prone to resistance development.
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Affiliation(s)
- Alexander V Grishin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Anna S Karyagina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical and Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Daria V Vasina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Irina V Vasina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vladimir A Gushchin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir G Lunin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Lu SY, Bischoff KM, Rich JO, Liu S, Skory CD. Recombinant bacteriophage LysKB317 endolysin mitigates Lactobacillus infection of corn mash fermentations. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:157. [PMID: 32944073 PMCID: PMC7488000 DOI: 10.1186/s13068-020-01795-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Commercial ethanol fermentation facilities traditionally rely on antibiotics for bacterial contamination control. Here we demonstrate an alternative approach to treat contamination using a novel peptidoglycan hydrolase (LysKB317) isolated from a bacteriophage, EcoSau. This endolysin was specially selected against Lactobacillus strains that were isolated as contaminants from a fuel ethanol plant. The LysKB317 gene was recombinantly expressed in Escherichia coli as a 33 kDa purified enzyme. RESULTS In turbidity reduction assays, the recombinant enzyme was subjected to a panel of 32 bacterial strains and was active against 28 bacterial strains representing 1 species of Acetobacter, 8 species of Lactobacillus, 1 species of Pediococcus, 3 species of Streptococcus, and 1 species of Weissella. The activity of LysKB317 was optimal around pH 6, but it has broad activity and stability from pH 4.5-7.5 up to at least 48 h. Maximum activity was observed at 50 °C up to at least 72 h. In addition, LysKB317 was stable in 30% ethanol up to at least 72 h. In experimentally infected corn mash fermentations, 1 µM endolysin reduced bacterial load by 3-log fold change, while 0.01 µM reduced bacteria by 2-log fold change. Concentration of fermentation products (ethanol, residual glucose, lactic acid, and acetic acids) for infected cultures treated with ≥ 0.01 µM LysKB317 was similar to uncontaminated controls. CONCLUSION Exogenously added LysKB317 endolysin is functional in conditions typically found in fuel ethanol fermentations tanks and may be developed as an alternative to antibiotics for contamination control during fuel ethanol fermentations.
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Affiliation(s)
- Shao-Yeh Lu
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604-3902 USA
| | - Kenneth M. Bischoff
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604-3902 USA
| | - Joseph O. Rich
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604-3902 USA
- Agricultural Research Service, U.S. Department of Agriculture, Fort Collins, CO 80526 USA
| | - Siqing Liu
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604-3902 USA
| | - Christopher D. Skory
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604-3902 USA
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Le NH, Peters K, Espaillat A, Sheldon JR, Gray J, Di Venanzio G, Lopez J, Djahanschiri B, Mueller EA, Hennon SW, Levin PA, Ebersberger I, Skaar EP, Cava F, Vollmer W, Feldman MF. Peptidoglycan editing provides immunity to Acinetobacter baumannii during bacterial warfare. SCIENCE ADVANCES 2020; 6:eabb5614. [PMID: 32832672 PMCID: PMC7439305 DOI: 10.1126/sciadv.abb5614] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/09/2020] [Indexed: 05/02/2023]
Abstract
Peptidoglycan (PG) is essential in most bacteria. Thus, it is often targeted by various assaults, including interbacterial attacks via the type VI secretion system (T6SS). Here, we report that the Gram-negative bacterium Acinetobacter baumannii strain ATCC 17978 produces, secretes, and incorporates the noncanonical d-amino acid d-lysine into its PG during stationary phase. We show that PG editing increases the competitiveness of A. baumannii during bacterial warfare by providing immunity against peptidoglycan-targeting T6SS effectors from various bacterial competitors. In contrast, we found that d-Lys production is detrimental to pathogenesis due, at least in part, to the activity of the human enzyme d-amino acid oxidase (DAO), which degrades d-Lys producing H2O2 toxic to bacteria. Phylogenetic analyses indicate that the last common ancestor of A. baumannii had the ability to produce d-Lys. However, this trait was independently lost multiple times, likely reflecting the evolution of A. baumannii as a human pathogen.
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Affiliation(s)
- Nguyen-Hung Le
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, NE2 4AX Newcastle upon Tyne, UK
| | - Akbar Espaillat
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, 90187 Umeå, Sweden
| | - Jessica R. Sheldon
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Joe Gray
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gisela Di Venanzio
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Juvenal Lopez
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bardya Djahanschiri
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main 60438, Germany
| | - Elizabeth A. Mueller
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63105, USA
| | - Seth W. Hennon
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63105, USA
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main 60438, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Center (S-BIKF), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, 90187 Umeå, Sweden
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, NE2 4AX Newcastle upon Tyne, UK
| | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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Lesperance DN, Broderick NA. Microbiomes as modulators of Drosophila melanogaster homeostasis and disease. CURRENT OPINION IN INSECT SCIENCE 2020; 39:84-90. [PMID: 32339931 PMCID: PMC7302976 DOI: 10.1016/j.cois.2020.03.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/09/2020] [Accepted: 03/15/2020] [Indexed: 05/26/2023]
Abstract
Drosophila melanogaster harbors a simple gut microbial community, or microbiome, that regulates several facets of its physiology. As a result, the host employs multiple mechanisms of maintaining control over its microbiome in an effort to promote overall organismal homeostasis. Perturbations to the balance between microbiome and host can result in states of instability or disease, making maintenance of microbial homeostasis a fundamental physiologic aspect of D. melanogaster biology. While the interactions between microbes and their hosts can be direct, particularly in the context of immunity and gut renewal, effects resulting from indirect interactions, such as those between microbiota members, can be equally as important. This review highlights the major ways, in which D. melanogaster regulates microbial homeostasis, the consequences of disruptions to homeostasis, and the different mechanisms, by which the microbiome interacts with its host.
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Affiliation(s)
- Danielle Na Lesperance
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - Nichole A Broderick
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06296, USA.
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A Family of T6SS Antibacterial Effectors Related to l,d-Transpeptidases Targets the Peptidoglycan. Cell Rep 2020; 31:107813. [DOI: 10.1016/j.celrep.2020.107813] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/20/2020] [Accepted: 06/03/2020] [Indexed: 12/17/2022] Open
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Chu X, Wu F, Sun B, Zhang M, Song S, Zhang P, Wang Y, Zhang Q, Zhou N, Shen J. Genipin cross-linked carbon dots for antimicrobial, bioimaging and bacterial discrimination. Colloids Surf B Biointerfaces 2020; 190:110930. [PMID: 32146275 DOI: 10.1016/j.colsurfb.2020.110930] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/28/2020] [Accepted: 03/01/2020] [Indexed: 01/09/2023]
Abstract
Multifunctional carbon dots (CDs) present enormous potential in numerous applications and have attracted widespread attention for various applications in the biomedical field. Bacterial infection is a common health issue; the development of antibacterial materials with low toxicity and good biocompatibility is becoming more important. In this work, we synthesized a new type of nitrogen co-doped carbon dots-genipin covalent conjugate (N-CDs-GP) via hydrothermal methods. The microstructure and chemical composition of the N-CDs-GP were characterized. The biocompatibility, stability, antibacterial activity, and fluorescence performance of the N-CDs-GP were assessed. The results revealed that N-CDs-GP possessed high biocompatibility, high light stability, and broad antibacterial activity. Additionally, selective Gram-positive bacterial imaging by N-CDs-GP provided a more rapid method of bacterial detection. The N-CDs-GP have the potential to be applied as bioimaging and antibacterial agents and for bacterial discrimination.
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Affiliation(s)
- Xiaohong Chu
- Jiangsu Collaborative Innovation Center for Biological Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
| | - Fan Wu
- Jiangsu Collaborative Innovation Center for Biological Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
| | - Baohong Sun
- Jiangsu Collaborative Innovation Center for Biological Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
| | - Ming Zhang
- Jiangsu Collaborative Innovation Center for Biological Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Saijie Song
- Jiangsu Collaborative Innovation Center for Biological Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
| | - Pan Zhang
- Jiangsu Collaborative Innovation Center for Biological Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
| | - Yuli Wang
- Jiangsu Collaborative Innovation Center for Biological Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
| | - Qicheng Zhang
- Jiangsu Collaborative Innovation Center for Biological Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
| | - Ninglin Zhou
- Jiangsu Collaborative Innovation Center for Biological Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China; Nanjing Zhou Ninglin Advanced Materials Technology Company Limited, Nanjing 211505, China.
| | - Jian Shen
- Jiangsu Collaborative Innovation Center for Biological Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China.
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The role of bacterial cell envelope structures in acid stress resistance in E. coli. Appl Microbiol Biotechnol 2020; 104:2911-2921. [PMID: 32067056 DOI: 10.1007/s00253-020-10453-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/29/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
Abstract
Acid resistance (AR) is an indispensable mechanism for the survival of neutralophilic bacteria, such as Escherichia coli (E. coli) strains that survive in the gastrointestinal tract. E. coli acid tolerance has been extensively studied during past decades, with most studies focused on gene regulation and mechanisms. However, the role of cell membrane structure in the context of acid stress resistance has not been discussed in depth. Here, we provide a comprehensive review of the roles and mechanisms of the E. coli cell envelope from different membrane components, such as membrane proteins, fatty acids, chaperones, and proton-consuming systems, and particularly focus on the innovative effects revealed by recent studies. We hope that the information guides us to understand the bacterial survival strategies under acid stress and to further explore the AR regulatory mechanisms to prevent or treat E. coli and other related Gram-negative bacteria infection, or to enhance the AR of engineering E. coli.
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Muropeptides Stimulate Growth Resumption from Stationary Phase in Escherichia coli. Sci Rep 2019; 9:18043. [PMID: 31792329 PMCID: PMC6888817 DOI: 10.1038/s41598-019-54646-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 11/18/2019] [Indexed: 12/19/2022] Open
Abstract
When nutrients run out, bacteria enter a dormant metabolic state. This low or undetectable metabolic activity helps bacteria to preserve their scant reserves for the future needs, yet it also diminishes their ability to scan the environment for new growth-promoting substrates. However, neighboring microbial growth is a reliable indicator of a favorable environment and can thus serve as a cue for exiting dormancy. Here we report that for Escherichia coli and Pseudomonas aeruginosa this cue is provided by the basic peptidoglycan unit (i.e. muropeptide). We show that several forms of muropeptides from a variety of bacterial species can stimulate growth resumption of dormant cells and the sugar – peptide bond is crucial for this activity. These results, together with previous research that identifies muropeptides as a germination signal for bacterial spores, and their detection by mammalian immune cells, show that muropeptides are a universal cue for bacterial growth.
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Anderson EM, Sychantha D, Brewer D, Clarke AJ, Geddes-McAlister J, Khursigara CM. Peptidoglycomics reveals compositional changes in peptidoglycan between biofilm- and planktonic-derived Pseudomonas aeruginosa. J Biol Chem 2019; 295:504-516. [PMID: 31771981 DOI: 10.1074/jbc.ra119.010505] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
Peptidoglycan (PG) is a critical component of the bacterial cell wall and is composed of a repeating β-1,4-linked disaccharide of N-acetylglucosamine and N-acetylmuramic acid appended with a highly conserved stem peptide. In Gram-negative bacteria, PG is assembled in the cytoplasm and exported into the periplasm where it undergoes considerable maturation, modification, or degradation depending on the growth phase or presence of environmental stressors. These modifications serve important functions in diverse processes, including PG turnover, cell elongation/division, and antibiotic resistance. Conventional methods for analyzing PG composition are complex and time-consuming. We present here a streamlined MS-based method that combines differential analysis with statistical 1D annotation approaches to quantitatively compare PGs produced in planktonic- and biofilm-cultured Pseudomonas aeruginosa We identified a core assembly of PG that is present in high abundance and that does not significantly differ between the two growth states. We also identified an adaptive PG assembly that is present in smaller amounts and fluctuates considerably between growth states in response to physiological changes. Biofilm-derived adaptive PG exhibited significant changes compared with planktonic-derived PG, including amino acid substitutions of the stem peptide and modifications that indicate changes in the activity of amidases, deacetylases, and lytic transglycosylases. The results of this work also provide first evidence of de-N-acetylated muropeptides from P. aeruginosa The method developed here offers a robust and reproducible workflow for accurately determining PG composition in samples that can be used to assess global PG fluctuations in response to changing growth conditions or external stimuli.
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Affiliation(s)
- Erin M Anderson
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - David Sychantha
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - Dyanne Brewer
- Mass Spectrometry Facility, University of Guelph, Ontario N1G 2W1, Canada
| | - Anthony J Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - Jennifer Geddes-McAlister
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada; Mass Spectrometry Facility, University of Guelph, Ontario N1G 2W1, Canada.
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada; Mass Spectrometry Facility, University of Guelph, Ontario N1G 2W1, Canada.
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Mayer VMT, Hottmann I, Figl R, Altmann F, Mayer C, Schäffer C. Peptidoglycan-type analysis of the N-acetylmuramic acid auxotrophic oral pathogen Tannerella forsythia and reclassification of the peptidoglycan-type of Porphyromonas gingivalis. BMC Microbiol 2019; 19:200. [PMID: 31477019 PMCID: PMC6721243 DOI: 10.1186/s12866-019-1575-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/22/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Tannerella forsythia is a Gram-negative oral pathogen. Together with Porphyromonas gingivalis and Treponema denticola it constitutes the "red complex" of bacteria, which is crucially associated with periodontitis, an inflammatory disease of the tooth supporting tissues that poses a health burden worldwide. Due to the absence of common peptidoglycan biosynthesis genes, the unique bacterial cell wall sugar N-acetylmuramic acid (MurNAc) is an essential growth factor of T. forsythia to build up its peptidoglycan cell wall. Peptidoglycan is typically composed of a glycan backbone of alternating N-acetylglucosamine (GlcNAc) and MurNAc residues that terminates with anhydroMurNAc (anhMurNAc), and short peptides via which the sugar backbones are cross-linked to build up a bag-shaped network. RESULTS We investigated T. forsythia's peptidoglycan structure, which is an essential step towards anti-infective strategies against this pathogen. A new sensitive radioassay was developed which verified the presence of MurNAc and anhMurNAc in the cell wall of the bacterium. Upon digest of isolated peptidoglycan with endo-N-acetylmuramidase, exo-N-acetylglucosaminidase and muramyl-L-alanine amidase, respectively, peptidoglycan fragments were obtained. HPLC and mass spectrometry (MS) analyses revealed the presence of GlcNAc-MurNAc-peptides and the cross-linked dimer with retention-times and masses, respectively, equalling those of control digests of Escherichia coli and P. gingivalis peptidoglycan. Data were confirmed by tandem mass spectrometry (MS2) analysis, revealing the GlcNAc-MurNAc-tetra-tetra-MurNAc-GlcNAc dimer to contain the sequence of the amino acids alanine, glutamic acid, diaminopimelic acid (DAP) and alanine, as well as a direct cross-link between DAP on the third and alanine on the fourth position of the two opposite stem peptides. The stereochemistry of DAP was determined by reversed-phase HPLC after dabsylation of hydrolysed peptidoglycan to be of the meso-type. CONCLUSION T. forsythia peptidoglycan is of the A1γ-type like that of E. coli. Additionally, the classification of P. gingivalis peptidoglycan as A3γ needs to be revised to A1γ, due to the presence of meso-DAP instead of LL-DAP, as reported previously.
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Affiliation(s)
- Valentina M T Mayer
- Department of NanoBiotechnology, NanoGlycobiology unit, Universität für Bodenkultur Wien, Vienna, Austria
| | - Isabel Hottmann
- Department of Biology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls Universität, Tübingen, Germany
| | - Rudolf Figl
- Department of Chemistry, Institute of Biochemistry, Universität für Bodenkultur Wien, Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, Institute of Biochemistry, Universität für Bodenkultur Wien, Vienna, Austria
| | - Christoph Mayer
- Department of Biology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls Universität, Tübingen, Germany.
| | - Christina Schäffer
- Department of NanoBiotechnology, NanoGlycobiology unit, Universität für Bodenkultur Wien, Vienna, Austria.
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37
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Porfírio S, Carlson RW, Azadi P. Elucidating Peptidoglycan Structure: An Analytical Toolset. Trends Microbiol 2019; 27:607-622. [DOI: 10.1016/j.tim.2019.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/16/2019] [Accepted: 01/29/2019] [Indexed: 01/04/2023]
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38
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Abstract
The peptidoglycan sacculus is a net-like polymer that surrounds the cytoplasmic membrane in most bacteria. It is essential to maintain the bacterial cell shape and protect from turgor. The peptidoglycan has a basic composition, common to all bacteria, with species-specific variations that can modify its biophysical properties or the pathogenicity of the bacteria. The synthesis of peptidoglycan starts in the cytoplasm and the precursor lipid II is flipped across the cytoplasmic membrane. The new peptidoglycan strands are synthesised and incorporated into the pre-existing sacculus by the coordinated activities of peptidoglycan synthases and hydrolases. In the model organism Escherichia coli there are two complexes required for the elongation and division. Each of them is regulated by different proteins from both the cytoplasmic and periplasmic sides that ensure the well-coordinated synthesis of new peptidoglycan.
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39
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Bhinderwala F, Wase N, DiRusso C, Powers R. Combining Mass Spectrometry and NMR Improves Metabolite Detection and Annotation. J Proteome Res 2018; 17:4017-4022. [PMID: 30303385 DOI: 10.1021/acs.jproteome.8b00567] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite inherent complementarity, nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are routinely separately employed to characterize metabolomics samples. More troubling is the erroneous view that metabolomics is better served by exclusively utilizing MS. Instead, we demonstrate the importance of combining NMR and MS for metabolomics by using small chemical compound treatments of Chlamydomonas reinhardtii as an illustrative example. A total of 102 metabolites were detected (82 by gas chromatography-MS, 20 by NMR, and 22 by both techniques). Out of these, 47 metabolites of interest were identified: 14 metabolites were uniquely identified by NMR, and 16 metabolites were uniquely identified by GC-MS. A total of 17 metabolites were identified by both NMR and GC-MS. In general, metabolites identified by both techniques exhibited similar changes upon compound treatment. In effect, NMR identified key metabolites that were missed by MS and enhanced the overall coverage of the oxidative pentose phosphate pathway, Calvin cycle, tricarboxylic acid cycle, and amino acid biosynthetic pathways that informed on pathway activity in central carbon metabolism, leading to fatty-acid and complex-lipid synthesis. Our study emphasizes a prime advantage of combining multiple analytical techniques: the improved detection and annotation of metabolites.
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Affiliation(s)
- Fatema Bhinderwala
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States.,Nebraska Center for Integrated Biomolecular Communication , Lincoln , Nebraska 68588-0304 , United States
| | - Nishikant Wase
- Department of Biochemistry , University of Nebraska , Lincoln , Nebraska 68588-0664 , United States
| | - Concetta DiRusso
- Department of Biochemistry , University of Nebraska , Lincoln , Nebraska 68588-0664 , United States.,Nebraska Center for Integrated Biomolecular Communication , Lincoln , Nebraska 68588-0304 , United States
| | - Robert Powers
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States.,Nebraska Center for Integrated Biomolecular Communication , Lincoln , Nebraska 68588-0304 , United States
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40
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Yadav AK, Espaillat A, Cava F. Bacterial Strategies to Preserve Cell Wall Integrity Against Environmental Threats. Front Microbiol 2018; 9:2064. [PMID: 30233540 PMCID: PMC6127315 DOI: 10.3389/fmicb.2018.02064] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/13/2018] [Indexed: 12/18/2022] Open
Abstract
Bacterial cells are surrounded by an exoskeleton-like structure, the cell wall, composed primarily of the peptidoglycan (PG) sacculus. This structure is made up of glycan strands cross-linked by short peptides generating a covalent mesh that shapes bacteria and prevents their lysis due to their high internal osmotic pressure. Even though the PG is virtually universal in bacteria, there is a notable degree of diversity in its chemical structure. Modifications in both the sugars and peptides are known to be instrumental for bacteria to cope with diverse environmental challenges. In this review, we summarize and discuss the cell wall strategies to withstand biotic and abiotic environmental insults such as the effect of antibiotics targeting cell wall enzymes, predatory PG hydrolytic proteins, and PG signaling systems. Finally we will discuss the opportunities that species-specific PG variability might open to develop antimicrobial therapies.
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Affiliation(s)
- Akhilesh K Yadav
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Akbar Espaillat
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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41
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Principal coordinate analysis assisted chromatographic analysis of bacterial cell wall collection: A robust classification approach. Anal Biochem 2018; 550:8-14. [PMID: 29649471 DOI: 10.1016/j.ab.2018.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/08/2018] [Indexed: 11/20/2022]
Abstract
In the present work, Principal coordinate analysis (PCoA) is introduced to develop a robust model to classify the chromatographic data sets of peptidoglycan sample. PcoA captures the heterogeneity present in the data sets by using the dissimilarity matrix as input. Thus, in principle, it can even capture the subtle differences in the bacterial peptidoglycan composition and can provide a more robust and fast approach for classifying the bacterial collection and identifying the novel cell wall targets for further biological and clinical studies. The utility of the proposed approach is successfully demonstrated by analysing the two different kind of bacterial collections. The first set comprised of peptidoglycan sample belonging to different subclasses of Alphaproteobacteria. Whereas, the second set that is relatively more intricate for the chemometric analysis consist of different wild type Vibrio Cholerae and its mutants having subtle differences in their peptidoglycan composition. The present work clearly proposes a useful approach that can classify the chromatographic data sets of chromatographic peptidoglycan samples having subtle differences. Furthermore, present work clearly suggest that PCoA can be a method of choice in any data analysis workflow.
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42
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Ruscitto A, Sharma A. Peptidoglycan synthesis in Tannerella forsythia: Scavenging is the modus operandi. Mol Oral Microbiol 2018; 33:125-132. [PMID: 29247483 DOI: 10.1111/omi.12210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2017] [Indexed: 01/05/2023]
Abstract
Tannerella forsythia is a Gram-negative oral pathogen strongly associated with periodontitis. This bacterium has an absolute requirement for exogenous N-acetylmuramic acid (MurNAc), an amino sugar that forms the repeating disaccharide unit with amino sugar N-acetylglucosamine (GlcNAc) of the peptidoglycan backbone. In silico genome analysis indicates that T. forsythia lacks the key biosynthetic enzymes needed for the de novo synthesis of MurNAc, and so relies on alternative ways to meet its requirement for peptidoglycan biosynthesis. In the subgingival niche, the bacterium can acquire MurNAc and peptidoglycan fragments (muropeptides) released by the cohabiting bacteria during their cell wall breakdown associated with cell division. Tannerella forsythia is able to also use host sialic acid (Neu5Ac) in lieu of MurNAc or muropeptides for its survival during the biofilm growth. Evidence suggests that the bacterium might be able to shunt sialic acid into a metabolic pathway leading to peptidoglycan synthesis. In this review, we explore the mechanisms by which T. forsythia is able to scavenge MurNAc, muropeptide and sialic acid for its peptidoglycan synthesis, and the impact of these scavenging activities on pathogenesis.
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Affiliation(s)
| | - A Sharma
- Department of Oral Biology, University at Buffalo, Buffalo, NY, USA
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43
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Zhao H, Patel V, Helmann JD, Dörr T. Don't let sleeping dogmas lie: new views of peptidoglycan synthesis and its regulation. Mol Microbiol 2017; 106:847-860. [PMID: 28975672 DOI: 10.1111/mmi.13853] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 12/24/2022]
Abstract
Bacterial cell wall synthesis is the target for some of our most powerful antibiotics and has thus been the subject of intense research focus for more than 50 years. Surprisingly, we still lack a fundamental understanding of how bacteria build, maintain and expand their cell wall. Due to technical limitations, directly testing hypotheses about the coordination and biochemistry of cell wall synthesis enzymes or architecture has been challenging, and interpretation of data has therefore often relied on circumstantial evidence and implicit assumptions. A number of recent papers have exploited new technologies, like single molecule tracking and real-time, high resolution temporal mapping of cell wall synthesis processes, to address fundamental questions of bacterial cell wall biogenesis. The results have challenged established dogmas and it is therefore timely to integrate new data and old observations into a new model of cell wall biogenesis in rod-shaped bacteria.
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Affiliation(s)
- Heng Zhao
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Vaidehi Patel
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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44
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PG-Metrics: A chemometric-based approach for classifying bacterial peptidoglycan data sets and uncovering their subjacent chemical variability. PLoS One 2017; 12:e0186197. [PMID: 29040278 PMCID: PMC5645090 DOI: 10.1371/journal.pone.0186197] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 09/27/2017] [Indexed: 02/07/2023] Open
Abstract
Bacteria cells are protected from osmotic and environmental stresses by an exoskeleton-like polymeric structure called peptidoglycan (PG) or murein sacculus. This structure is fundamental for bacteria’s viability and thus, the mechanisms underlying cell wall assembly and how it is modulated serve as targets for many of our most successful antibiotics. Therefore, it is now more important than ever to understand the genetics and structural chemistry of the bacterial cell walls in order to find new and effective methods of blocking it for the treatment of disease. In the last decades, liquid chromatography and mass spectrometry have been demonstrated to provide the required resolution and sensitivity to characterize the fine chemical structure of PG. However, the large volume of data sets that can be produced by these instruments today are difficult to handle without a proper data analysis workflow. Here, we present PG-metrics, a chemometric based pipeline that allows fast and easy classification of bacteria according to their muropeptide chromatographic profiles and identification of the subjacent PG chemical variability between e.g. bacterial species, growth conditions and, mutant libraries. The pipeline is successfully validated here using PG samples from different bacterial species and mutants in cell wall proteins. The obtained results clearly demonstrated that PG-metrics pipeline is a valuable bioanalytical tool that can lead us to cell wall classification and biomarker discovery.
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45
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Shen Y, Boulos S, Sumrall E, Gerber B, Julian-Rodero A, Eugster MR, Fieseler L, Nyström L, Ebert MO, Loessner MJ. Structural and functional diversity in Listeria cell wall teichoic acids. J Biol Chem 2017; 292:17832-17844. [PMID: 28912268 DOI: 10.1074/jbc.m117.813964] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Indexed: 11/06/2022] Open
Abstract
Wall teichoic acids (WTAs) are the most abundant glycopolymers found on the cell wall of many Gram-positive bacteria, whose diverse surface structures play key roles in multiple biological processes. Despite recent technological advances in glycan analysis, structural elucidation of WTAs remains challenging due to their complex nature. Here, we employed a combination of ultra-performance liquid chromatography-coupled electrospray ionization tandem-MS/MS and NMR to determine the structural complexity of WTAs from Listeria species. We unveiled more than 10 different types of WTA polymers that vary in their linkage and repeating units. Disparity in GlcNAc to ribitol connectivity, as well as variable O-acetylation and glycosylation of GlcNAc contribute to the structural diversity of WTAs. Notably, SPR analysis indicated that constitution of WTA determines the recognition by bacteriophage endolysins. Collectively, these findings provide detailed insight into Listeria cell wall-associated carbohydrates, and will guide further studies on the structure-function relationship of WTAs.
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Affiliation(s)
- Yang Shen
- From the Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, CH-8092 Zurich,
| | - Samy Boulos
- the Laboratory of Food Biochemistry, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 9, CH-8092 Zurich
| | - Eric Sumrall
- From the Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, CH-8092 Zurich
| | - Benjamin Gerber
- From the Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, CH-8092 Zurich
| | - Alicia Julian-Rodero
- From the Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, CH-8092 Zurich
| | - Marcel R Eugster
- From the Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, CH-8092 Zurich
| | - Lars Fieseler
- the ZHAW School of Life Sciences and Facility Management, Einsiedlerstrasse 31, CH-8820 Wädenswil, and
| | - Laura Nyström
- the Laboratory of Food Biochemistry, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 9, CH-8092 Zurich
| | - Marc-Olivier Ebert
- the Laboratory of Organic Chemistry, ETH Zurich, Vladmimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Martin J Loessner
- From the Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, CH-8092 Zurich
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46
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Dik DA, Marous DR, Fisher JF, Mobashery S. Lytic transglycosylases: concinnity in concision of the bacterial cell wall. Crit Rev Biochem Mol Biol 2017. [PMID: 28644060 DOI: 10.1080/10409238.2017.1337705] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lytic transglycosylases (LTs) are bacterial enzymes that catalyze the non-hydrolytic cleavage of the peptidoglycan structures of the bacterial cell wall. They are not catalysts of glycan synthesis as might be surmised from their name. Notwithstanding the seemingly mundane reaction catalyzed by the LTs, their lytic reactions serve bacteria for a series of astonishingly diverse purposes. These purposes include cell-wall synthesis, remodeling, and degradation; for the detection of cell-wall-acting antibiotics; for the expression of the mechanism of cell-wall-acting antibiotics; for the insertion of secretion systems and flagellar assemblies into the cell wall; as a virulence mechanism during infection by certain Gram-negative bacteria; and in the sporulation and germination of Gram-positive spores. Significant advances in the mechanistic understanding of each of these processes have coincided with the successive discovery of new LTs structures. In this review, we provide a systematic perspective on what is known on the structure-function correlations for the LTs, while simultaneously identifying numerous opportunities for the future study of these enigmatic enzymes.
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Affiliation(s)
- David A Dik
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Daniel R Marous
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Jed F Fisher
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Shahriar Mobashery
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
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47
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Kumar K, Cava F. Constraint randomised non-negative factor analysis (CRNNFA): an alternate chemometrics approach for analysing the biochemical data sets. Analyst 2017; 142:1916-1928. [DOI: 10.1039/c7an00274b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present work introduces an alternate chemometrics approach constraint randomised non-negative factor analysis (CRNNFA) for analysing the bioanalytical data sets.
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Affiliation(s)
- Keshav Kumar
- Laboratory for Molecular Infection Medicine Sweden
- Department of Molecular Biology
- Umeå Centre for Microbial Research
- Umeå University
- 90187 Umeå
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden
- Department of Molecular Biology
- Umeå Centre for Microbial Research
- Umeå University
- 90187 Umeå
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