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Nakonieczna A, Topolska-Woś A, Łobocka M. New bacteriophage-derived lysins, LysJ and LysF, with the potential to control Bacillus anthracis. Appl Microbiol Biotechnol 2024; 108:76. [PMID: 38194144 PMCID: PMC10776502 DOI: 10.1007/s00253-023-12839-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/10/2024]
Abstract
Bacillus anthracis is an etiological agent of anthrax, a severe zoonotic disease that can be transmitted to people and cause high mortalities. Bacteriophages and their lytic enzymes, endolysins, have potential therapeutic value in treating infections caused by this bacterium as alternatives or complements to antibiotic therapy. They can also be used to identify and detect B. anthracis. Endolysins of two B. anthracis Wbetavirus phages, J5a and F16Ba which were described by us recently, differ significantly from the best-known B. anthracis phage endolysin PlyG from Wbetavirus genus bacteriophage Gamma and a few other Wbetavirus genus phages. They are larger than PlyG (351 vs. 233 amino acid residues), contain a signal peptide at their N-termini, and, by prediction, have a different fold of cell binding domain suggesting different structural basis of cell epitope recognition. We purified in a soluble form the modified versions of these endolysins, designated by us LysJ and LysF, respectively, and depleted of signal peptides. Both modified endolysins could lyse the B. anthracis cell wall in zymogram assays. Their activity against the living cells of B. anthracis and other species of Bacillus genus was tested by spotting on the layers of bacteria in soft agar and by assessing the reduction of optical density of bacterial suspensions. Both methods proved the effectiveness of LysJ and LysF in killing the anthrax bacilli, although the results obtained by each method differed. Additionally, the lytic efficiency of both proteins was different, which apparently correlates with differences in their amino acid sequence. KEY POINTS: • LysJ and LysF are B. anthracis-targeting lysins differing from lysins studied so far • LysJ and LysF could be overproduced in E. coli in soluble and active forms • LysJ and LysF are active in killing cells of B. anthracis virulent strains.
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Affiliation(s)
- Aleksandra Nakonieczna
- Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Center, 24-100, Puławy, Poland.
| | | | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
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Interrogation of the contribution of (endo)lysin domains to tune their bacteriolytic efficiency provides a novel clue to design superior antibacterials. Int J Biol Macromol 2022; 223:1042-1053. [PMID: 36370862 DOI: 10.1016/j.ijbiomac.2022.11.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
Abstract
Bacteriophage-derived endolysins and bacterial autolysins (hereinafter lysins) represent a completely new class of efficient antibacterials. They prevent the development of bacterial resistance and help protect commensal microbiota, producing cell wall lysis. Here we have investigated whether the acquisition of enzymatic active domains (EADs) and cell wall binding domains (CWBDs) of balancing efficiencies could be a way of tuning natural lysin activity. The concept was applied to produce a chimeric lysin of superior antibacterial capacity using the endolysin Skl and the major pneumococcal autolysin LytA. Combination of the Skl EAD and the cell wall choline-binding domain (CBD) of LytA in the chimera QSLA increased the bacterial killing by 2 logs or more compared to parental enzymes at an equal concentration and extended the substrate range to resistant and emergent pneumococci and other pathogens of the mitis group. Contrarily, QLAS, containing LytA EAD and Skl CBD, was inactive against all tested strains, although domain structures were preserved and hydrolysis of purified cell walls maintained in both chimeras. As a whole, our study provides a novel clue to design superior lysins to fight multidrug-resistant pathogens based on domain selection, and a powerful in-vivo active lysin (QSLA) with promising therapeutic perspectives.
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Razew A, Schwarz JN, Mitkowski P, Sabala I, Kaus-Drobek M. One fold, many functions-M23 family of peptidoglycan hydrolases. Front Microbiol 2022; 13:1036964. [PMID: 36386627 PMCID: PMC9662197 DOI: 10.3389/fmicb.2022.1036964] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/05/2022] [Indexed: 12/02/2023] Open
Abstract
Bacterial cell walls are the guards of cell integrity. They are composed of peptidoglycan that provides rigidity to sustain internal turgor and ensures isolation from the external environment. In addition, they harbor the enzymatic machinery to secure cell wall modulations needed throughout the bacterial lifespan. The main players in this process are peptidoglycan hydrolases, a large group of enzymes with diverse specificities and different mechanisms of action. They are commonly, but not exclusively, found in prokaryotes. Although in most cases, these enzymes share the same molecular function, namely peptidoglycan hydrolysis, they are leveraged to perform a variety of physiological roles. A well-investigated family of peptidoglycan hydrolases is M23 peptidases, which display a very conserved fold, but their spectrum of lytic action is broad and includes both Gram- positive and Gram- negative bacteria. In this review, we summarize the structural, biochemical, and functional studies concerning the M23 family of peptidases based on literature and complement this knowledge by performing large-scale analyses of available protein sequences. This review has led us to gain new insight into the role of surface charge in the activity of this group of enzymes. We present relevant conclusions drawn from the analysis of available structures and indicate the main structural features that play a crucial role in specificity determination and mechanisms of latency. Our work systematizes the knowledge of the M23 family enzymes in the context of their unique antimicrobial potential against drug-resistant pathogens and presents possibilities to modulate and engineer their features to develop perfect antibacterial weapons.
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Affiliation(s)
| | | | | | - Izabela Sabala
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Kaus-Drobek
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
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Influence of NaCl and pH on lysostaphin catalytic activity, cell binding, and bacteriolytic activity. Appl Microbiol Biotechnol 2022; 106:6519-6534. [DOI: 10.1007/s00253-022-12173-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/02/2022]
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Specific Isolation of Clostridium botulinum Group I Cells by Phage Lysin Cell Wall Binding Domain with the Aid of S-Layer Disruption. Int J Mol Sci 2022; 23:ijms23158391. [PMID: 35955526 PMCID: PMC9368847 DOI: 10.3390/ijms23158391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 02/05/2023] Open
Abstract
Clostridium botulinum is a notorious pathogen that raises health and food safety concerns by producing the potent botulinum neurotoxin and causing botulism, a potentially fatal neuroparalytic disease in humans and animals. Efficient methods for the identification and isolation of C. botulinum are warranted for laboratory diagnostics of botulism and for food safety risk assessment. The cell wall binding domains (CBD) of phage lysins are recognized by their high specificity and affinity to distinct types of bacteria, which makes them promising for the development of diagnostic tools. We previously identified CBO1751, which is the first antibotulinal phage lysin showing a lytic activity against C. botulinum Group I. In this work, we assessed the host specificity of the CBD of CBO1751 and tested its feasibility as a probe for the specific isolation of C. botulinum Group I strains. We show that the CBO1751 CBD specifically binds to C. botulinum Group I sensu lato (including C. sporogenes) strains. We also demonstrate that some C. botulinum Group I strains possess an S-layer, the disruption of which by an acid glycine treatment is required for efficient binding of the CBO1751 CBD to the cells of these strains. We further developed CBO1751 CBD-based methods using flow cytometry and magnetic separation to specifically isolate viable cells of C. botulinum Group I. These methods present potential for applications in diagnostics and risk assessment in order to control the botulism hazard.
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Nakonieczna A, Rutyna P, Fedorowicz M, Kwiatek M, Mizak L, Łobocka M. Three Novel Bacteriophages, J5a, F16Ba, and z1a, Specific for Bacillus anthracis, Define a New Clade of Historical Wbeta Phage Relatives. Viruses 2022; 14:v14020213. [PMID: 35215807 PMCID: PMC8878798 DOI: 10.3390/v14020213] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus anthracis is a potent biowarfare agent, able to be highly lethal. The bacteria dwell in the soil of certain regions, as natural flora. Bacteriophages or their lytic enzymes, endolysins, may be an alternative for antibiotics and other antibacterials to fight this pathogen in infections and to minimize environmental contamination with anthrax endospores. Upon screening environmental samples from various regions in Poland, we isolated three new siphophages, J5a, F16Ba, and z1a, specific for B. anthracis. They represent new species related to historical anthrax phages Gamma, Cherry, and Fah, and to phage Wbeta of Wbetavirus genus. We show that the new phages and their closest relatives, phages Tavor_SA, Negev_SA, and Carmel_SA, form a separate clade of the Wbetavirus genus, designated as J5a clade. The most distinctive feature of J5a clade phages is their cell lysis module. While in the historical phages it encodes a canonical endolysin and a class III holin, in J5a clade phages it encodes an endolysin with a signal peptide and two putative holins. We present the basic characteristic of the isolated phages. Their comparative genomic analysis indicates that they encode two receptor-binding proteins, of which one may bind a sugar moiety of B. anthracis cell surface.
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Affiliation(s)
- Aleksandra Nakonieczna
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
- Correspondence: (A.N.); (M.Ł.)
| | - Paweł Rutyna
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Magdalena Fedorowicz
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Magdalena Kwiatek
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Lidia Mizak
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106 Warsaw, Poland
- Correspondence: (A.N.); (M.Ł.)
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Glucose Decoration on Wall Teichoic Acid Is Required for Phage Adsorption and InlB-Mediated Virulence in Listeria ivanovii. J Bacteriol 2021; 203:e0013621. [PMID: 34096780 PMCID: PMC8297528 DOI: 10.1128/jb.00136-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Listeria ivanovii (Liv) is an intracellular Gram-positive pathogen that primarily infects ruminants but also occasionally causes enteric infections in humans. Albeit rare, this bacterium possesses the capacity to cross the intestinal epithelium of humans, similar to its more frequently pathogenic cousin, Listeria monocytogenes (Lmo). Recent studies in Lmo have shown that specific glycosyl modifications on the cell wall-associated glycopolymers (termed wall teichoic acid [WTA]) of Lmo are responsible for bacteriophage adsorption and retention of the major virulence factor internalin B (InlB). However, the relationship between InlB and WTA in Liv remains unclear. Here, we report the identification of the unique gene liv1070, which encodes a putative glucosyltransferase in the polycistronic WTA gene cluster of the Liv WSLC 3009 genome. We found that in-frame deletion of liv1070 led to loss of the glucose substitution on WTA, as revealed by ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) analysis. Interestingly, the glucose-deficient mutant became resistant to phage B025 infection due to an inability of the phage to adsorb to the bacterial surface, a binding process mediated by the receptor-binding protein B025_Gp17. As expected, deletion of liv1070 led to loss of InlB retention on the bacterial cell wall, which corresponded to a drastic decrease in cellular invasion. Genetic complementation of liv1070 restored the characteristic phenotypes, including glucose decoration, phage adsorption, and cellular invasion. Taken together, our data demonstrate that an interplay between phage, bacteria, and host cells also exists in Listeria ivanovii, suggesting that the trade-off between phage resistance and virulence attenuation may be a general feature in the genus Listeria. IMPORTANCE Listeria ivanovii is a Gram-positive bacterial pathogen known to cause enteric infection in rodents and ruminants and occasionally in immunocompromised humans. Recent investigations revealed that in its better-known cousin Listeria monocytogenes, strains develop resistance to bacteriophage attack due to loss of glycosylated surface receptors, which subsequently results in disconnection of one of the bacterium's major virulence factors, InlB. However, the situation in L. ivanovii remains unclear. Here, we show that L. ivanovii acquires phage resistance following deletion of a unique glycosyltransferase. This deletion also leads to dysfunction of InlB, making the resulting strain unable to invade host cells. Overall, this study suggests that the interplay between phage, bacteria, and the host may be a feature common to the genus Listeria.
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Cañada FJ, Canales Á, Valverde P, de Toro BF, Martínez-Orts M, Phillips PO, Pereda A. Conformational and Structural characterization of carbohydrates and their interactions studied by NMR. Curr Med Chem 2021; 29:1147-1172. [PMID: 34225601 DOI: 10.2174/0929867328666210705154046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/30/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.
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Affiliation(s)
- Francisco Javier Cañada
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Pablo Valverde
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Beatriz Fernández de Toro
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Mónica Martínez-Orts
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Paola Oquist Phillips
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Amaia Pereda
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
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Broendum SS, Williams DE, Hayes BK, Kraus F, Fodor J, Clifton BE, Geert Volbeda A, Codee JDC, Riley BT, Drinkwater N, Farrow KA, Tsyganov K, Heselpoth RD, Nelson DC, Jackson CJ, Buckle AM, McGowan S. High avidity drives the interaction between the streptococcal C1 phage endolysin, PlyC, with the cell surface carbohydrates of Group A Streptococcus. Mol Microbiol 2021; 116:397-415. [PMID: 33756056 DOI: 10.1111/mmi.14719] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 01/03/2023]
Abstract
Endolysin enzymes from bacteriophage cause bacterial lysis by degrading the peptidoglycan cell wall. The streptococcal C1 phage endolysin PlyC, is the most potent endolysin described to date and can rapidly lyse group A, C, and E streptococci. PlyC is known to bind the Group A streptococcal cell wall, but the specific molecular target or the binding site within PlyC remain uncharacterized. Here we report for the first time, that the polyrhamnose backbone of the Group A streptococcal cell wall is the binding target of PlyC. We have also characterized the putative rhamnose binding groove of PlyC and found four key residues that were critical to either the folding or the cell wall binding action of PlyC. Based on our results, we suggest that the interaction between PlyC and the cell wall may not be a high-affinity interaction as previously proposed, but rather a high avidity one, allowing for PlyC's remarkable lytic activity. Resistance to our current antibiotics is reaching crisis levels and there is an urgent need to develop the antibacterial agents with new modes of action. A detailed understanding of this potent endolysin may facilitate future developments of PlyC as a tool against the rise of antibiotic resistance.
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Affiliation(s)
- Sebastian S Broendum
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, Australia.,Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Daniel E Williams
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Brooke K Hayes
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Felix Kraus
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - James Fodor
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia.,Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Ben E Clifton
- Research School of Chemistry, Australian National University, Acton, ACT, Australia
| | - Anne Geert Volbeda
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Jeroen D C Codee
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Blake T Riley
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia.,Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, USA
| | - Nyssa Drinkwater
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Kylie A Farrow
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Kirill Tsyganov
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia.,Monash Bioinformatics Platform, Monash University, Melbourne, VIC, Australia
| | - Ryan D Heselpoth
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, MD, USA
| | - Daniel C Nelson
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, MD, USA
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Acton, ACT, Australia
| | - Ashley M Buckle
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, Australia
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