1
|
Kajsikova M, Kajsik M, Bocanova L, Papayova K, Drahovska H, Bukovska G. Endolysin EN572-5 as an alternative to treat urinary tract infection caused by Streptococcus agalactiae. Appl Microbiol Biotechnol 2024; 108:79. [PMID: 38189950 PMCID: PMC10774192 DOI: 10.1007/s00253-023-12949-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/13/2023] [Accepted: 11/26/2023] [Indexed: 01/09/2024]
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) is an opportunistic pathogen causing urinary tract infection (UTI). Endolysin EN572-5 was identified in prophage KMB-572-E of the human isolate Streptococcus agalactiae KMB-572. The entire EN572-5 gene was cloned into an expression vector and the corresponding recombinant protein EN572-5 was expressed in Escherichia coli in a soluble form, isolated by affinity chromatography, and characterized. The isolated protein was highly active after 30 min incubation in a temperature range of - 20 °C to 37 °C and in a pH range of 5.5-8.0. The endolysin EN572-5 lytic activity was tested on different Streptococcus spp. and Lactobacillus spp. The enzyme lysed clinical GBS (n = 31/31) and different streptococci (n = 6/8), and also exhibited moderate lytic activity against UPEC (n = 4/4), but no lysis of beneficial vaginal lactobacilli (n = 4) was observed. The ability of EN572-5 to eliminate GBS during UTI was investigated using an in vitro model of UPSA. After the administration of 3 μM EN572-5, a nearly 3-log decrease of urine bacterial burden was detected within 3 h. To date, no studies have been published on the use of endolysins against S. agalactiae during UTI. KEY POINTS: • A lytic protein, EN572-5, from a prophage of a human GBS isolate has been identified. • This protein is easily produced, simple to prepare, and stable after lyophilization. • The bacteriolytic activity of EN572-5 was demonstrated for the first time in human urine.
Collapse
Affiliation(s)
- Maria Kajsikova
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Michal Kajsik
- Comenius University Science Park, Ilkovicova 8, 841 04, Bratislava, Slovakia
| | - Lucia Bocanova
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Kristina Papayova
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Hana Drahovska
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 841 15, Bratislava, Slovakia
| | - Gabriela Bukovska
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Mokhtari S, Li Y, Saris PEJ, Takala TM. Analysis of the cell wall binding domain in bacteriocin-like lysin LysL from Lactococcus lactis LAC460. Arch Microbiol 2024; 206:336. [PMID: 38954047 PMCID: PMC11219366 DOI: 10.1007/s00203-024-04066-5] [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: 03/27/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Wild-type Lactococcus lactis strain LAC460 secretes prophage-encoded bacteriocin-like lysin LysL, which kills some Lactococcus strains, but has no lytic effect on the producer. LysL carries two N-terminal enzymatic active domains (EAD), and an unknown C-terminus without homology to known domains. This study aimed to determine whether the C-terminus of LysL carries a cell wall binding domain (CBD) for target specificity of LysL. The C-terminal putative CBD region of LysL was fused with His-tagged green fluorescent protein (HGFPuv). The HGFPuv_CBDlysL gene fusion was ligated into the pASG-IBA4 vector, and introduced into Escherichia coli. The fusion protein was produced and purified with affinity chromatography. To analyse the binding of HGFPuv_CBDLysL to Lactococcus cells, the protein was mixed with LysL-sensitive and LysL-resistant strains, including the LysL-producer LAC460, and the fluorescence of the cells was analysed. As seen in fluorescence microscope, HGFPuv_CBDLysL decorated the cell surface of LysL-sensitive L. cremoris MG1614 with green fluorescence, whereas the resistant L. lactis strains LM0230 and LAC460 remained unfluorescent. The fluorescence plate reader confirmed the microscopy results detecting fluorescence only from four tested LysL-sensitive strains but not from 11 tested LysL-resistant strains. Specific binding of HGFPuv_CBDLysL onto the LysL-sensitive cells but not onto the LysL-resistant strains indicates that the C-terminus of LysL contains specific CBD. In conclusion, this report presents experimental evidence of the presence of a CBD in a lactococcal phage lysin. Moreover, the inability of HGFPuv_CBDLysL to bind to the LysL producer LAC460 may partly explain the host's resistance to its own prophage lysin.
Collapse
Affiliation(s)
- Samira Mokhtari
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
| | - Yanru Li
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Per E J Saris
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Timo M Takala
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| |
Collapse
|
4
|
Nakonieczna A, Abramowicz K, Kwiatek M, Kowalczyk E. Lysins as a powerful alternative to combat Bacillus anthracis. Appl Microbiol Biotechnol 2024; 108:366. [PMID: 38850320 PMCID: PMC11162388 DOI: 10.1007/s00253-024-13194-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024]
Abstract
This review gathers all, to the best of our current knowledge, known lysins, mainly bacteriophage-derived, that have demonstrated activity against Bacillus anthracis strains. B. anthracis is a spore-forming, toxin-producing bacteria, naturally dwelling in soil. It is best known as a potential biowarfare threat, an etiological agent of anthrax, and a severe zoonotic disease. Anthrax can be treated with antibiotics (ciprofloxacin, penicillin, doxycycline); however, their administration may take up even to 60 days, and different factors can compromise their effectiveness. Bacterial viruses, bacteriophages (phages), are natural enemies of bacteria and use their lytic enzymes, endolysins (lysins), to specifically kill bacterial cells. Harnessing the potential of lysins to combat bacterial infections holds promise for diminishing antibiotic usage and, consequently, addressing the escalating antibiotic resistance in bacteria. In this context, we list the lysins with the activity against B. anthracis, providing a summary of their lytic properties in vitro and the outcomes observed in animal models. Bacillus cereus strain ATCC 4342/RSVF1, a surrogate for B. anthracis, was also included as a target bacteria. KEY POINTS: • More than a dozen different B. anthracis lysins have been identified and studied. • They fall into three blocks regarding their amino acid sequence similarity and most of them are amidases. • Lysins could be used in treating B. anthracis infections.
Collapse
Affiliation(s)
- Aleksandra Nakonieczna
- Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Center, Puławy, 24-100, Poland.
| | - Karolina Abramowicz
- Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Center, Puławy, 24-100, Poland
| | - Magdalena Kwiatek
- Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Center, Puławy, 24-100, Poland
| | | |
Collapse
|
5
|
Shymialevich D, Błażejak S, Średnicka P, Cieślak H, Ostrowska A, Sokołowska B, Wójcicki M. Biological Characterization and Genomic Analysis of Three Novel Serratia- and Enterobacter-Specific Virulent Phages. Int J Mol Sci 2024; 25:5944. [PMID: 38892136 PMCID: PMC11172527 DOI: 10.3390/ijms25115944] [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: 04/29/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Due to the high microbiological contamination of raw food materials and the increase in the incidence of multidrug-resistant bacteria, new methods of ensuring microbiological food safety are being sought. One solution may be to use bacteriophages (so-called phages) as natural bacterial enemies. Therefore, the aim of this study was the biological and genomic characterization of three newly isolated Serratia- and Enterobacter-specific virulent bacteriophages as potential candidates for food biocontrol. Serratia phage KKP_3708 (vB_Sli-IAFB_3708), Serratia phage KKP_3709 (vB_Sma-IAFB_3709), and Enterobacter phage KKP_3711 (vB_Ecl-IAFB_3711) were isolated from municipal sewage against Serratia liquefaciens strain KKP 3654, Serratia marcescens strain KKP 3687, and Enterobacter cloacae strain KKP 3684, respectively. The effect of phage addition at different multiplicity of infection (MOI) rates on the growth kinetics of the bacterial hosts was determined using a Bioscreen C Pro growth analyzer. The phages retained high activity in a wide temperature range (from -20 °C to 60 °C) and active acidity values (pH from 3 to 12). Based on transmission electron microscopy (TEM) imaging and whole-genome sequencing (WGS), the isolated bacteriophages belong to the tailed bacteriophages from the Caudoviricetes class. Genomic analysis revealed that the phages have linear double-stranded DNA of size 40,461 bp (Serratia phage KKP_3708), 67,890 bp (Serratia phage KKP_3709), and 113,711 bp (Enterobacter phage KKP_3711). No virulence, toxins, or antibiotic resistance genes were detected in the phage genomes. The lack of lysogenic markers indicates that all three bacteriophages may be potential candidates for food biocontrol.
Collapse
Affiliation(s)
- Dziyana Shymialevich
- Culture Collection of Industrial Microorganisms—Microbiological Resources Center, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland; (D.S.); (H.C.)
| | - Stanisław Błażejak
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS–SGGW), Nowoursynowska 166 Str., 02-776 Warsaw, Poland;
| | - Paulina Średnicka
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland;
| | - Hanna Cieślak
- Culture Collection of Industrial Microorganisms—Microbiological Resources Center, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland; (D.S.); (H.C.)
| | - Agnieszka Ostrowska
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences (WULS–SGGW), Ciszewskiego 8 Str., 02-786 Warsaw, Poland;
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland;
| | - Michał Wójcicki
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland;
| |
Collapse
|
6
|
Vander Elst N. Bacteriophage-derived endolysins as innovative antimicrobials against bovine mastitis-causing streptococci and staphylococci: a state-of-the-art review. Acta Vet Scand 2024; 66:20. [PMID: 38769566 PMCID: PMC11106882 DOI: 10.1186/s13028-024-00740-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/05/2024] [Indexed: 05/22/2024] Open
Abstract
Bacteriophage-encoded endolysins, peptidoglycan hydrolases breaking down the Gram-positive bacterial cell wall, represent a groundbreaking class of novel antimicrobials to revolutionize the veterinary medicine field. Wild-type endolysins exhibit a modular structure, consisting of enzymatically active and cell wall-binding domains, that enable genetic engineering strategies for the creation of chimeric fusion proteins or so-called 'engineered endolysins'. This biotechnological approach has yielded variants with modified lytic spectrums, introducing new possibilities in antimicrobial development. However, the discovery of highly similar endolysins by different groups has occasionally resulted in the assignment of different names that complicate a straightforward comparison. The aim of this review was to perform a homology-based comparison of the wild-type and engineered endolysins that have been characterized in the context of bovine mastitis-causing streptococci and staphylococci, grouping homologous endolysins with ≥ 95.0% protein sequence similarity. Literature is explored by homologous groups for the wild-type endolysins, followed by a chronological examination of engineered endolysins according to their year of publication. This review concludes that the wild-type endolysins encountered persistent challenges in raw milk and in vivo settings, causing a notable shift in the field towards the engineering of endolysins. Lead candidates that display robust lytic activity are nowadays selected from screening assays that are performed under these challenging conditions, often utilizing advanced high-throughput protein engineering methods. Overall, these recent advancements suggest that endolysins will integrate into the antibiotic arsenal over the next decade, thereby innovating antimicrobial treatment against bovine mastitis-causing streptococci and staphylococci.
Collapse
Affiliation(s)
- Niels Vander Elst
- Department of Neuroscience, Karolinska Institutet, Biomedicum 7D, Solnavägen 9, 17165, Solna, Stockholm, Sweden.
| |
Collapse
|
7
|
Li X, Shangguan W, Yang X, Hu X, Li Y, Zhao W, Feng M, Feng J. Influence of Lipopolysaccharide-Interacting Peptides Fusion with Endolysin LysECD7 and Fatty Acid Derivatization on the Efficacy against Acinetobacter baumannii Infection In Vitro and In Vivo. Viruses 2024; 16:760. [PMID: 38793641 PMCID: PMC11125741 DOI: 10.3390/v16050760] [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: 03/18/2024] [Revised: 04/26/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Acinetobacter baumannii has developed multiple drug resistances, posing a significant threat to antibiotic efficacy. LysECD7, an endolysin derived from phages, could be a promising therapeutic agent against multi-drug resistance A. baumannii. In this study, in order to further enhance the antibacterial efficiency of the engineered LysECD7, a few lipopolysaccharide-interacting peptides (Li5, MSI594 and Li5-MSI) were genetically fused with LysECD7. Based on in vitro antibacterial activity, the fusion protein Lys-Li5-MSI was selected for further modifications aimed at extending its half-life. A cysteine residue was introduced into Lys-Li5-MSI through mutation (Lys-Li5-MSIV12C), followed by conjugation with a C16 fatty acid chain via a protonation substitution reaction(V12C-C16). The pharmacokinetic profile of V12C-C16 exhibited a more favorable characteristic in comparison to Lys-Li5-MSI, thereby resulting in enhanced therapeutic efficacy against lethal A. baumannii infection in mice. The study provides valuable insights for the development of novel endolysin therapeutics and proposes an alternative therapeutic strategy for combating A. baumannii infections.
Collapse
Affiliation(s)
- Xiaowan Li
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | | | - Xiaoqian Yang
- Chia Tai Tianqing Pharmaceutical Group Co., Ltd., Nanjing 210046, China
| | - Xiaoyue Hu
- China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Yanan Li
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Wenjie Zhao
- China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Meiqing Feng
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jun Feng
- China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| |
Collapse
|
8
|
Alreja AB, Appel AE, Zhu JC, Riley SP, Gonzalez-Juarbe N, Nelson DC. SP-CHAP, an endolysin with enhanced activity against biofilm pneumococci and nasopharyngeal colonization. mBio 2024; 15:e0006924. [PMID: 38470268 PMCID: PMC11005408 DOI: 10.1128/mbio.00069-24] [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: 01/12/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Streptococcus pneumoniae (Spn), a Gram-positive bacterium, is responsible for causing a wide variety of invasive infections. The emergence of multi-drug antibiotic resistance has prompted the search for antimicrobial alternatives. Phage-derived peptidoglycan hydrolases, known as endolysins, are an attractive alternative. In this study, an endolysin active against Spn, designated SP-CHAP, was cloned, produced, purified, biochemically characterized, and evaluated for its antimicrobial properties. Cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domains are widely represented in bacteriophage endolysins but have never previously been reported for pneumococcal endolysins. Here, we characterize the first pneumococcal endolysin with a CHAP catalytic domain. SP-CHAP was antimicrobial against all Spn serovars tested, including capsular and capsule-free pneumococci, and it was found to be more active than the most widely studied pneumococcal endolysin, Cpl-1, while not affecting various oral or nasal commensal organisms tested. SP-CHAP was also effective in eradicating Spn biofilms at concentrations as low as 1.56 µg/mL. In addition, a Spn mouse nasopharyngeal colonization model was employed, which showed that SP-CHAP caused a significant reduction in Spn colony-forming units, even more than Cpl-1. These results indicate that SP-CHAP may represent a promising alternative to combating Spn infections. IMPORTANCE Considering the high rates of pneumococcal resistance reported for several antibiotics, alternatives are urgently needed. In the present study, we report a Streptococcus pneumoniae-targeting endolysin with even greater activity than Cpl-1, the most characterized pneumococcal endolysin to date. We have employed a combination of biochemical and microbiological assays to assess the stability and lytic potential of SP-CHAP and demonstrate its efficacy on pneumococcal biofilms in vitro and in an in vivo mouse model of colonization. Our findings highlight the therapeutic potential of SP-CHAP as an antibiotic alternative to treat Streptococcus pneumoniae infections.
Collapse
Affiliation(s)
- Adit B. Alreja
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Amanda E. Appel
- Department of Infectious Diseases and Genomic Medicine, J. Craig Venter Institute, Rockville, Maryland, USA
| | - Jinyi C. Zhu
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Sean P. Riley
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Norberto Gonzalez-Juarbe
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
- Department of Infectious Diseases and Genomic Medicine, J. Craig Venter Institute, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Daniel C. Nelson
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| |
Collapse
|
9
|
Soontarach R, Srimanote P, Voravuthikunchai SP, Chusri S. Antibacterial and Anti-Biofilm Efficacy of Endolysin LysAB1245 against a Panel of Important Pathogens. Pharmaceuticals (Basel) 2024; 17:155. [PMID: 38399370 PMCID: PMC10893532 DOI: 10.3390/ph17020155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Infections caused by antibiotic-resistant bacteria pose a significant global challenge. This study explores the antibacterial effects of a bacteriophage-derived endolysin, LysAB1245, against important pathogens, including Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus. We determined the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) for all tested isolates. A time-kill study was conducted to evaluate the reduction in bacterial survival following treatment with LysAB1245. Additionally, the effects of LysAB1245 on P. aeruginosa K1455 and methicillin-resistant S. aureus (MRSA) NPRC 001R-formed biofilms were investigated. The MIC and MBC of LysAB1245 against all the tested isolates ranged from 4.68 to 9.36 µg/mL and 4.68 to 18.72 µg/mL, respectively. The time-kill study demonstrated more than a 4 log CFU/mL (99.99%) reduction in bacterial survival within 6 h of LysAB1245 treatment at 2MIC. LysAB1245 (1/8-1/2MIC) treatment significantly reduced biofilms formed by P. aeruginosa and MRSA in a concentration-dependent manner. Furthermore, scanning electron and confocal laser scanning microscopy confirmed the potential inhibition effects on 3-day established biofilms formed on abiotic surfaces upon treatment with LysAB1245 at 2MIC. The findings indicate that endolysin LysAB1245 could be employed as a new alternative therapeutic antibacterial and anti-biofilm agent for combating biofilm-related infections.
Collapse
Affiliation(s)
- Rosesathorn Soontarach
- Center of Antimicrobial Biomaterial Innovation-Southeast Asia, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand; (R.S.); (S.P.V.)
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Potjanee Srimanote
- Graduate in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathum Thani 12121, Thailand;
| | - Supayang Piyawan Voravuthikunchai
- Center of Antimicrobial Biomaterial Innovation-Southeast Asia, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand; (R.S.); (S.P.V.)
| | - Sarunyou Chusri
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| |
Collapse
|
10
|
Pantiora PD, Georgakis ND, Premetis GE, Labrou NE. Metagenomic analysis of hot spring soil for mining a novel thermostable enzybiotic. Appl Microbiol Biotechnol 2024; 108:163. [PMID: 38252132 PMCID: PMC10803476 DOI: 10.1007/s00253-023-12979-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024]
Abstract
The misuse and overuse of antibiotics have contributed to a rapid emergence of antibiotic-resistant bacterial pathogens. This global health threat underlines the urgent need for innovative and novel antimicrobials. Endolysins derived from bacteriophages or prophages constitute promising new antimicrobials (so-called enzybiotics), exhibiting the ability to break down bacterial peptidoglycan (PG). In the present work, metagenomic analysis of soil samples, collected from thermal springs, allowed the identification of a prophage-derived endolysin that belongs to the N-acetylmuramoyl-L-alanine amidase type 2 (NALAA-2) family and possesses a LysM (lysin motif) region as a cell wall binding domain (CWBD). The enzyme (Ami1) was cloned and expressed in Escherichia coli, and its bactericidal and lytic activity was characterized. The results indicate that Ami1 exhibits strong bactericidal and antimicrobial activity against a broad range of bacterial pathogens, as well as against isolated peptidoglycan (PG). Among the examined bacterial pathogens, Ami1 showed highest bactericidal activity against Staphylococcus aureus sand Staphylococcus epidermidis cells. Thermostability analysis revealed a melting temperature of 64.2 ± 0.6 °C. Overall, these findings support the potential that Ami1, as a broad spectrum antimicrobial agent, could be further assessed as enzybiotic for the effective treatment of bacterial infections. KEY POINTS: • Metagenomic analysis allowed the identification of a novel prophage endolysin • The endolysin belongs to type 2 amidase family with lysin motif region • The endolysin displays high thermostability and broad bactericidal spectrum.
Collapse
Affiliation(s)
- Panagiota D Pantiora
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Nikolaos D Georgakis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Georgios E Premetis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece.
| |
Collapse
|
11
|
Samir S. Molecular Machinery of the Triad Holin, Endolysin, and Spanin: Key Players Orchestrating Bacteriophage-Induced Cell Lysis and their Therapeutic Applications. Protein Pept Lett 2024; 31:85-96. [PMID: 38258777 DOI: 10.2174/0109298665181166231212051621] [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: 09/06/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 01/24/2024]
Abstract
Phage therapy, a promising alternative to combat multidrug-resistant bacterial infections, harnesses the lytic cycle of bacteriophages to target and eliminate bacteria. Key players in this process are the phage lysis proteins, including holin, endolysin, and spanin, which work synergistically to disrupt the bacterial cell wall and induce lysis. Understanding the structure and function of these proteins is crucial for the development of effective therapies. Recombinant versions of these proteins have been engineered to enhance their stability and efficacy. Recent progress in the field has led to the approval of bacteriophage-based therapeutics as drugs, paving the way for their clinical use. These proteins can be combined in phage cocktails or combined with antibiotics to enhance their activity against bacterial biofilms, a common cause of treatment failure. Animal studies and clinical trials are being conducted to evaluate the safety and efficacy of phage therapy in humans. Overall, phage therapy holds great potential as a valuable tool in the fight against multidrug- resistant bacteria, offering hope for the future of infectious disease treatment.
Collapse
Affiliation(s)
- Safia Samir
- Department of Biochemistry and Molecular Biology, Theodor Bilharz Research Institute, Giza, Egypt
| |
Collapse
|
12
|
Dorosky RJ, Lola SL, Brown HA, Schreier JE, Dreher-Lesnick SM, Stibitz S. Characterization of Lactobacilli Phage Endolysins and Their Functional Domains-Potential Live Biotherapeutic Testing Reagents. Viruses 2023; 15:1986. [PMID: 37896764 PMCID: PMC10610939 DOI: 10.3390/v15101986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Phage endolysin-specific binding characteristics and killing activity support their potential use in biotechnological applications, including potency and purity testing of live biotherapeutic products (LBPs). LBPs contain live organisms, such as lactic acid bacteria (LAB), and are intended for use as drugs. Our approach uses the endolysin cell wall binding domains (CBD) for LBP potency assays and the endolysin killing activity for purity assays. CBDs of the following five lactobacilli phage lysins were characterized: CL1, Jlb1, Lj965, LL-H, and ΦJB. They exhibited different bindings to 27 LAB strains and were found to bind peptidoglycan or surface polymers. Flow cytometry based on CBD binding was used to enumerate viable counts of two strains in the mixture. CL1-lys, jlb1-lys, and ΦJB-lys and their enzymatic domains (EADs) exhibited cell wall digestive activity and lytic activity against LAB. Jlb1-EAD and ΦJB-EAD were more sensitive than their respective hololysins to buffer pH and NaCl changes. The ΦJB-EAD exhibited stronger lytic activity than ΦJB-lys, possibly due to ΦJB-CBD-mediated sequestration of ΦJB-lys by cell debris. CBD multiplex assays indicate that these proteins may be useful LBP potency reagents, and the lytic activity suggests that CL1-lys, jlb1-lys, and ΦJB-lys and their EADs are good candidates for LBP purity reagent development.
Collapse
Affiliation(s)
- Robert J. Dorosky
- Office of Vaccines Research and Review, Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Stephanie L. Lola
- Office of Vaccines Research and Review, Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Haleigh A. Brown
- Office of Vaccines Research and Review, Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Jeremy E. Schreier
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - Sheila M. Dreher-Lesnick
- Office of Vaccines Research and Review, Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Scott Stibitz
- Office of Vaccines Research and Review, Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| |
Collapse
|
13
|
Mikoulinskaia GV, Prokhorov DA, Chernyshov SV, Sitnikova DS, Arakelian AG, Uversky VN. Conservative Tryptophan Residue in the Vicinity of an Active Site of the M15 Family l,d-Peptidases: A Key Element in the Catalysis. Int J Mol Sci 2023; 24:13249. [PMID: 37686055 PMCID: PMC10487532 DOI: 10.3390/ijms241713249] [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: 07/27/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Bioinformatics analysis of the sequences of orthologous zinc-containing peptidases of the M15_C subfamily revealed the presence of a conserved tryptophan residue near the active site, which is not involved in the formation of the protein core. Site-directed mutagenesis of this Trp114/109 residue using two representatives of the family, l-alanoyl-d-glutamate peptidases of bacteriophages T5 (calcium-activated EndoT5) and RB49 (EndoRB49, without ion regulation) as examples, and further analysis of the 1H NMR spectra of the mutants showed that a decrease in the volume of the W → F → A residue leads to changes in the hydrophobic core and active center of the protein, and also decreases the affinity for regulatory Ca2+ in the EndoT5 mutants. The inactive T5W114A mutant lacks the ability to bind the substrate. In general, the conserved Trp114/109 residue, due to the spatial restrictions of its side chain, significantly affects the formation of the catalytically active form of the enzyme and is critical for catalysis.
Collapse
Affiliation(s)
- Galina V. Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
| | - Dmitry A. Prokhorov
- Institute of Theoretical and Experimental Biophysics, RAS, Institutskaya ul., 3, 142290 Pushchino, Moscow Region, Russia;
| | - Sergei V. Chernyshov
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
| | - Daria S. Sitnikova
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
| | - Arina G. Arakelian
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
- Institute of Theoretical and Experimental Biophysics, RAS, Institutskaya ul., 3, 142290 Pushchino, Moscow Region, Russia;
| | - Vladimir N. Uversky
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow Region, Russia
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| |
Collapse
|
14
|
Madani A, Krause B, Greene ER, Subramanian S, Mohr BP, Holton JM, Olmos JL, Xiong C, Sun ZZ, Socher R, Fraser JS, Naik N. Large language models generate functional protein sequences across diverse families. Nat Biotechnol 2023; 41:1099-1106. [PMID: 36702895 PMCID: PMC10400306 DOI: 10.1038/s41587-022-01618-2] [Citation(s) in RCA: 172] [Impact Index Per Article: 172.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/17/2022] [Indexed: 01/27/2023]
Abstract
Deep-learning language models have shown promise in various biotechnological applications, including protein design and engineering. Here we describe ProGen, a language model that can generate protein sequences with a predictable function across large protein families, akin to generating grammatically and semantically correct natural language sentences on diverse topics. The model was trained on 280 million protein sequences from >19,000 families and is augmented with control tags specifying protein properties. ProGen can be further fine-tuned to curated sequences and tags to improve controllable generation performance of proteins from families with sufficient homologous samples. Artificial proteins fine-tuned to five distinct lysozyme families showed similar catalytic efficiencies as natural lysozymes, with sequence identity to natural proteins as low as 31.4%. ProGen is readily adapted to diverse protein families, as we demonstrate with chorismate mutase and malate dehydrogenase.
Collapse
Affiliation(s)
- Ali Madani
- Salesforce Research, Palo Alto, CA, USA.
- Profluent Bio, San Francisco, CA, USA.
| | | | - Eric R Greene
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Subu Subramanian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Jose Luis Olmos
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | | |
Collapse
|
15
|
Barnett MJ, Pinheiro J, Keown JR, Biboy J, Gray J, Lucinescu IW, Vollmer W, Hirt RP, Simoes-Barbosa A, Goldstone DC. NlpC/P60 peptidoglycan hydrolases of Trichomonas vaginalis have complementary activities that empower the protozoan to control host-protective lactobacilli. PLoS Pathog 2023; 19:e1011563. [PMID: 37585473 PMCID: PMC10461829 DOI: 10.1371/journal.ppat.1011563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/28/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023] Open
Abstract
Trichomonas vaginalis is a human protozoan parasite that causes trichomoniasis, a prevalent sexually transmitted infection. Trichomoniasis is accompanied by a shift to a dysbiotic vaginal microbiome that is depleted of lactobacilli. Studies on co-cultures have shown that vaginal bacteria in eubiosis (e.g. Lactobacillus gasseri) have antagonistic effects on T. vaginalis pathogenesis, suggesting that the parasite might benefit from shaping the microbiome to dysbiosis (e.g. Gardnerella vaginalis among other anaerobes). We have recently shown that T. vaginalis has acquired NlpC/P60 genes from bacteria, expanding them to a repertoire of nine TvNlpC genes in two distinct clans, and that TvNlpCs of clan A are active against bacterial peptidoglycan. Here, we expand this characterization to TvNlpCs of clan B. In this study, we show that the clan organisation of NlpC/P60 genes is a feature of other species of Trichomonas, and that Histomonas meleagridis has sequences related to one clan. We characterized the 3D structure of TvNlpC_B3 alone and with the inhibitor E64 bound, probing the active site of these enzymes for the first time. Lastly, we demonstrated that TvNlpC_B3 and TvNlpC_B5 have complementary activities with the previously described TvNlpCs of clan A and that exogenous expression of these enzymes empower this mucosal parasite to take over populations of vaginal lactobacilli in mixed cultures. TvNlpC_B3 helps control populations of L. gasseri, but not of G. vaginalis, which action is partially inhibited by E64. This study is one of the first to show how enzymes produced by a mucosal protozoan parasite may contribute to a shift on the status of a microbiome, helping explain the link between trichomoniasis and vaginal dysbiosis. Further understanding of this process might have significant implications for treatments in the future.
Collapse
Affiliation(s)
- Michael J. Barnett
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jully Pinheiro
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jeremy R. Keown
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joe Gray
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Robert P. Hirt
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - David C. Goldstone
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| |
Collapse
|
16
|
Premetis GE, Stathi A, Papageorgiou AC, Labrou NE. Structural and functional features of a broad-spectrum prophage-encoded enzybiotic from Enterococcus faecium. Sci Rep 2023; 13:7450. [PMID: 37156923 PMCID: PMC10167349 DOI: 10.1038/s41598-023-34309-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
Multidrug-resistant (MDR) bacteria have become a growing threat to public health. The gram-positive Enterococcus faecium is classified by WHO as a high-priority pathogen among the global priority list of antibiotic-resistant bacteria. Peptidoglycan-degrading enzymes (PDEs), also known as enzybiotics, are useful bactericidal agents in the fight against resistant bacteria. In this work, a genome-based screening approach of the genome of E. faecium allowed the identification of a putative PDE gene with predictive amidase activity (EfAmi1; EC 3.5.1.28) in a prophage-integrated sequence. EfAmi1 is composed by two domains: a N-terminal Zn2+-dependent N-acetylmuramoyl-L-alanine amidase-2 (NALAA-2) domain and a C-terminal domain with unknown structure and function. The full-length gene of EfAmi1 was cloned and expressed as a 6xHis-tagged protein in E. coli. EfAmi1 was produced as a soluble protein, purified, and its lytic and antimicrobial activities were investigated using turbidity reduction and Kirby-Bauer disk-diffusion assays against clinically isolated bacterial pathogens. The crystal structure of the N-terminal amidase-2 domain was determined using X-ray crystallography at 1.97 Å resolution. It adopts a globular fold with several α-helices surrounding a central five-stranded β-sheet. Sequence comparison revealed a cluster of conserved amino acids that defines a putative binding site for a buried zinc ion. The results of the present study suggest that EfAmi1 displays high lytic and antimicrobial activity and may represent a promising new antimicrobial in the post-antibiotic era.
Collapse
Affiliation(s)
- Georgios E Premetis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, 11855, Athens, Greece
| | - Angeliki Stathi
- Department of Microbiology, "Aghia Sophia" Children's Hospital, 11527, Athens, Greece
| | | | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, 11855, Athens, Greece.
| |
Collapse
|
17
|
Wang JM, Seok SH, Yoon WS, Kim JH, Seo MD. Crystal structure of the engineered endolysin mtEC340M. Acta Crystallogr F Struct Biol Commun 2023; 79:105-110. [PMID: 37132476 PMCID: PMC10167747 DOI: 10.1107/s2053230x23002583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/17/2023] [Indexed: 05/04/2023] Open
Abstract
Endolysins produced by bacteriophages play essential roles in the release of phage progeny by degrading the peptidoglycan layers of the bacterial cell wall. Bacteriophage-encoded endolysins have emerged as a new class of antibacterial agents to combat surging antibiotic resistance. The crystal structure of mtEC340M, an engineered endolysin EC340 from the PBEC131 phage that infects Escherichia coli, was determined. The crystal structure of mtEC340M at 2.4 Å resolution consists of eight α-helices and two loops. The three active residues of mtEC340M were predicted by structural comparison with peptidoglycan-degrading lysozyme.
Collapse
Affiliation(s)
- Jee-Min Wang
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Seung-Hyeon Seok
- College of Pharmacy and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju, Jeju 63243, Republic of Korea
| | - Won-Su Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk 28160, Republic of Korea
| | - Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| |
Collapse
|
18
|
Construction and Activity Testing of a Modular Fusion Peptide against Enterococcus faecalis. Antibiotics (Basel) 2023; 12:antibiotics12020388. [PMID: 36830298 PMCID: PMC9951850 DOI: 10.3390/antibiotics12020388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
The emergence of antibiotic resistance in enterococci is a great concern encountered worldwide. Almost all enterococci exhibit significant levels of resistance to penicillin, ampicillin, semi-synthetic penicillin and most cephalosporins, primarily due to the expression of low-affinity penicillin-binding proteins. The development of new and novel antibacterial agents against enterococci is a significant need of the hour. In this research, we have constructed a modular peptide against Enterococcus faecalis. The enzymatic domain of the constructed peptide BP404 is from the bacteriocin BacL1 and the cell wall binding domain from endolysin PlyV12 of phage ϕ1. The protein BP404 was found to be active against two tested strains of Enterococcus faecalis, with a reduction in cell density amounting to 85% and 65%. The cell wall binding assay confirms the binding of the protein to Enterococcus faecalis, which was not seen towards the control strain Escherichia coli, invariably pointing to the specificity of BP404. To the best of our knowledge, this is one of the first instances of the development of a chimeric peptide against Enterococcus faecalis. This study points out that novel proteins can be genetically engineered against clinically relevant enterococci.
Collapse
|
19
|
Kim Y, Lee SM, Nong LK, Kim J, Kim SB, Kim D. Characterization of Klebsiella pneumoniae bacteriophages, KP1 and KP12, with deep learning-based structure prediction. Front Microbiol 2023; 13:990910. [PMID: 36762092 PMCID: PMC9902359 DOI: 10.3389/fmicb.2022.990910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/19/2022] [Indexed: 01/26/2023] Open
Abstract
Concerns over Klebsiella pneumoniae resistance to the last-line antibiotic treatment have prompted a reconsideration of bacteriophage therapy in public health. Biotechnological application of phages and their gene products as an alternative to antibiotics necessitates the understanding of their genomic context. This study sequenced, annotated, characterized, and compared two Klebsiella phages, KP1 and KP12. Physiological validations identified KP1 and KP12 as members of Myoviridae family. Both phages showed that their activities were stable in a wide range of pH and temperature. They exhibit a host specificity toward K. pneumoniae with a broad intraspecies host range. General features of genome size, coding density, percentage GC content, and phylogenetic analyses revealed that these bacteriophages are distantly related. Phage lytic proteins (endolysin, anti-/holin, spanin) identified by the local alignment against different databases, were subjected to further bioinformatic analyses including three-dimensional (3D) structure prediction by AlphaFold. AlphaFold models of phage lysis proteins were consistent with the published X-ray crystal structures, suggesting the presence of T4-like and P1/P2-like bacteriophage lysis proteins in KP1 and KP12, respectively. By providing the primary sequence information, this study contributes novel bacteriophages for research and development pipelines of phage therapy that ultimately, cater to the unmet clinical and industrial needs against K. pneumoniae pathogens.
Collapse
Affiliation(s)
- Youngju Kim
- Optipharm Inc., Cheongju-si, Chungcheongbuk-do, Republic of Korea,Department of Microbiology and Molecular Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jaehyung Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea,*Correspondence: Donghyuk Kim,
| |
Collapse
|
20
|
Bocanova L, Psenko M, Barák I, Halgasova N, Drahovska H, Bukovska G. A novel phage-encoded endolysin EN534-C active against clinical strain Streptococcus agalactiae GBS. J Biotechnol 2022; 359:48-58. [PMID: 36179792 DOI: 10.1016/j.jbiotec.2022.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022]
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) is primarily known as a major neonatal pathogen. In adults, these bacteria often colonize the gastrointestinal and urogenital tracts. Treatment of infections using antibiotics is often complicated by recurrences caused by multi-resistant streptococci. Endolysin EN534 from prophage A2 of human isolate Streptococcus agalactiae KMB-534 has a modular structure consisting of two terminal catalytic domains, amidase_3 and CHAP, and one central binding domain, LysM. The EN534 gene was cloned into an expression vector, and the corresponding recombinant protein EN534-C was expressed in Escherichia coli in a soluble form and isolated by affinity chromatography. The lytic activity of this endolysin was tested on cell wall substrates from different GBS serotypes, B. subtilis, L. jensenii, and E. coli. The enzyme lysed streptococci, but not beneficial vaginal lactobacilli. The isolated protein is stable in a temperature range of 20 °C to 37 °C. Calcium ions enhanced the activity of the enzyme in the pH range from 5.0 to 8.0. The exolytic activity of EN534-C was observed by time-lapse fluorescence microscopy on a S. agalactiae CCM 6187 substrate. Recombinant endolysin EN534-C may have the potential to become an antimicrobial agent for the treatment of S. agalactiae infections.
Collapse
Affiliation(s)
- Lucia Bocanova
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51 Bratislava, Slovakia
| | - Michal Psenko
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51 Bratislava, Slovakia
| | - Imrich Barák
- Department of Microbial Genetics, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51 Bratislava, Slovakia
| | - Nora Halgasova
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51 Bratislava, Slovakia
| | - Hana Drahovska
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 841 15 Bratislava, Slovakia
| | - Gabriela Bukovska
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51 Bratislava, Slovakia.
| |
Collapse
|
21
|
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]
|
22
|
The Mechanism of Bacterial Resistance and Potential Bacteriostatic Strategies. Antibiotics (Basel) 2022; 11:antibiotics11091215. [PMID: 36139994 PMCID: PMC9495013 DOI: 10.3390/antibiotics11091215] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 12/26/2022] Open
Abstract
Bacterial drug resistance is rapidly developing as one of the greatest threats to human health. Bacteria will adopt corresponding strategies to crack the inhibitory effect of antibiotics according to the antibacterial mechanism of antibiotics, involving the mutation of drug target, secreting hydrolase, and discharging antibiotics out of cells through an efflux pump, etc. In recent years, bacteria are found to constantly evolve new resistance mechanisms to antibiotics, including target protective protein, changes in cell morphology, and so on, endowing them with multiple defense systems against antibiotics, leading to the emergence of multi-drug resistant (MDR) bacteria and the unavailability of drugs in clinics. Correspondingly, researchers attempt to uncover the mystery of bacterial resistance to develop more convenient and effective antibacterial strategies. Although traditional antibiotics still play a significant role in the treatment of diseases caused by sensitive pathogenic bacteria, they gradually lose efficacy in the MDR bacteria. Therefore, highly effective antibacterial compounds, such as phage therapy and CRISPER-Cas precision therapy, are gaining an increasing amount of attention, and are considered to be the treatments with the moist potential with regard to resistance against MDR in the future. In this review, nine identified drug resistance mechanisms are summarized, which enhance the retention rate of bacteria under the action of antibiotics and promote the distribution of drug-resistant bacteria (DRB) in the population. Afterwards, three kinds of potential antibacterial methods are introduced, in which new antibacterial compounds exhibit broad application prospects with different action mechanisms, the phage therapy has been successfully applied to infectious diseases caused by super bacteria, and the CRISPER-Cas precision therapy as a new technology can edit drug-resistant genes in pathogenic bacteria at the gene level, with high accuracy and flexibility. These antibacterial methods will provide more options for clinical treatment, and will greatly alleviate the current drug-resistant crisis.
Collapse
|
23
|
Suárez CA, Carrasco ST, Brandolisio FNA, Abatangelo V, Boncompain CA, Peresutti-Bacci N, Morbidoni HR. Bioinformatic Analysis of a Set of 14 Temperate Bacteriophages Isolated from Staphylococcus aureus Strains Highlights Their Massive Genetic Diversity. Microbiol Spectr 2022; 10:e0033422. [PMID: 35880893 PMCID: PMC9430571 DOI: 10.1128/spectrum.00334-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022] Open
Abstract
Epidemiology and virulence studies of Staphylococcus aureus showed that temperate bacteriophages are one of the most powerful drivers for its evolution not only because of their abundance but also because of the richness of their genetic payload. Here, we report the isolation, genome sequencing, and bioinformatic analysis of 14 bacteriophages induced from lysogenic S. aureus strains from human or veterinary (cattle) origin. The bacteriophages belonged to the Siphoviridae family; were of similar genome size (40 to 45 kbp); and fell into clusters B2, B3, B5, and B7 according to a recent clustering proposal. One of the phages, namely, vB_SauS_308, was the most unusual one, belonging to the sparsely populated subcluster B7 but showing differences in protein family contents compared with the rest of the members. This phage contains a type I endolysin (one catalytic domain and noncanonical cell wall domain [CBD]) and a host recognition module lacking receptor binding protein, cell wall hydrolase, and tail fiber proteins. This phage also lacked virulence genes, which is opposite to what has been reported for subcluster B6 and B7 members. None of six phages, taken as representatives of each of the four subclusters, showed activity on coagulase-negative staphylococci (excepted for two Staphylococcus hominis strains in which propagation and a very slow adsorption rate were observed) nor transducing ability. Immunity tests on S. aureus RN4220 lysogens with each of these phages showed no cross immunity. IMPORTANCE To the best of our knowledge, this set of sequenced bacteriophages is the largest one in South America. Our report describes for the first time the utilization of MultiTwin software to analyze the relationship between phage protein families. Notwithstanding the fact that most of the genetic information obtained correlated with recently published information, due to their geographical origin, the reported analysis adds up to and confirms currently available knowledge of Staphylococcus aureus temperate bacteriophages in terms of phylogeny and role in host evolution.
Collapse
Affiliation(s)
- Cristian A. Suárez
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Soledad T. Carrasco
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Facundo N. A. Brandolisio
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Virginia Abatangelo
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carina A. Boncompain
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Natalia Peresutti-Bacci
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Héctor R. Morbidoni
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| |
Collapse
|
24
|
Biochemical Characterizations of the Putative Endolysin Ecd09610 Catalytic Domain from Clostridioides difficile. Antibiotics (Basel) 2022; 11:antibiotics11081131. [PMID: 36010000 PMCID: PMC9405191 DOI: 10.3390/antibiotics11081131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Clostridioides difficile is the major pathogen of pseudomembranous colitis, and novel antimicrobial agents are sought after for its treatment. Phage-derived endolysins with species-specific lytic activity have potential as novel antimicrobial agents. We surveyed the genome of C. difficile strain 630 and identified an endolysin gene, Ecd09610, which has an uncharacterized domain at the N-terminus and two catalytic domains that are homologous to glucosaminidase and endopeptidase at the C-terminus. Genes containing the two catalytic domains, the glucosaminidase domain and the endopeptidase domain, were cloned and expressed in Escherichia coli as N-terminal histidine-tagged proteins. The purified domain variants showed lytic activity almost specifically for C. difficile, which has a unique peptide bridge in its peptidoglycan. This species specificity is thought to depend on substrate cleavage activity rather than binding. The domain variants were thermostable, and, notably, the glucosaminidase domain remained active up to 100 °C. In addition, we determined the optimal pH and salt concentrations of these domain variants. Their properties are suitable for formulating a bacteriolytic enzyme as an antimicrobial agent. This lytic enzyme can serve as a scaffold for the construction of high lytic activity mutants with enhanced properties.
Collapse
|
25
|
Wong KY, Megat Mazhar Khair MH, Song AAL, Masarudin MJ, Chong CM, In LLA, Teo MYM. Endolysins against Streptococci as an antibiotic alternative. Front Microbiol 2022; 13:935145. [PMID: 35983327 PMCID: PMC9378833 DOI: 10.3389/fmicb.2022.935145] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/07/2022] [Indexed: 11/21/2022] Open
Abstract
Multi-drug resistance has called for a race to uncover alternatives to existing antibiotics. Phage therapy is one of the explored alternatives, including the use of endolysins, which are phage-encoded peptidoglycan hydrolases responsible for bacterial lysis. Endolysins have been extensively researched in different fields, including medicine, food, and agricultural applications. While the target specificity of various endolysins varies greatly between species, this current review focuses specifically on streptococcal endolysins. Streptococcus spp. causes numerous infections, from the common strep throat to much more serious life-threatening infections such as pneumonia and meningitis. It is reported as a major crisis in various industries, causing systemic infections associated with high mortality and morbidity, as well as economic losses, especially in the agricultural industry. This review highlights the types of catalytic and cell wall-binding domains found in streptococcal endolysins and gives a comprehensive account of the lytic ability of both native and engineered streptococcal endolysins studied thus far, as well as its potential application across different industries. Finally, it gives an overview of the advantages and limitations of these enzyme-based antibiotics, which has caused the term enzybiotics to be conferred to it.
Collapse
Affiliation(s)
- Kuan Yee Wong
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Megat Hamzah Megat Mazhar Khair
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Mas Jaffri Masarudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Chou Min Chong
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Selangor, Malaysia
| | - Lionel Lian Aun In
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
- Lionel Lian Aun In,
| | - Michelle Yee Mun Teo
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
- *Correspondence: Michelle Yee Mun Teo,
| |
Collapse
|
26
|
Costa SP, Nogueira CL, Cunha AP, Lisac A, Carvalho CM. Potential of bacteriophage proteins as recognition molecules for pathogen detection. Crit Rev Biotechnol 2022:1-18. [PMID: 35848817 DOI: 10.1080/07388551.2022.2071671] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Bacterial pathogens are leading causes of infections with high mortality worldwide having a great impact on healthcare systems and the food industry. Gold standard methods for bacterial detection mainly rely on culture-based technologies and biochemical tests which are laborious and time-consuming. Regardless of several developments in existing methods, the goal of achieving high sensitivity and specificity, as well as a low detection limit, remains unaccomplished. In past years, various biorecognition elements, such as antibodies, enzymes, aptamers, or nucleic acids, have been widely used, being crucial for the pathogens detection in different complex matrices. However, these molecules are usually associated with high detection limits, demand laborious and costly production, and usually present cross-reactivity. (Bacterio)phage-encoded proteins, especially the receptor binding proteins (RBPs) and cell-wall binding domains (CBDs) of endolysins, are responsible for the phage binding to the bacterial surface receptors in different stages of the phage lytic cycle. Due to their remarkable properties, such as high specificity, sensitivity, stability, and ability to be easily engineered, they are appointed as excellent candidates to replace conventional recognition molecules, thereby contributing to the improvement of the detection methods. Moreover, they offer several possibilities of application in a variety of detection systems, such as magnetic, optical, and electrochemical. Herein we provide a review of phage-derived bacterial binding proteins, namely the RBPs and CBDs, with the prospect to be employed as recognition elements for bacteria. Moreover, we summarize and discuss the various existing methods based on these proteins for the detection of nosocomial and foodborne pathogens.
Collapse
Affiliation(s)
- Susana P Costa
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,International Iberian Nanotechnology Laboratory, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores-Microsistemas e Nanotecnologias (INESC MN), IN-Institute of Nanoscience and Nanotechnolnology, Lisbon, Portugal
| | - Catarina L Nogueira
- International Iberian Nanotechnology Laboratory, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores-Microsistemas e Nanotecnologias (INESC MN), IN-Institute of Nanoscience and Nanotechnolnology, Lisbon, Portugal
| | - Alexandra P Cunha
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Ana Lisac
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Carla M Carvalho
- International Iberian Nanotechnology Laboratory, Braga, Portugal
| |
Collapse
|
27
|
Venturini C, Petrovic Fabijan A, Fajardo Lubian A, Barbirz S, Iredell J. Biological foundations of successful bacteriophage therapy. EMBO Mol Med 2022; 14:e12435. [PMID: 35620963 PMCID: PMC9260219 DOI: 10.15252/emmm.202012435] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/20/2022] Open
Abstract
Bacteriophages (phages) are selective viral predators of bacteria. Abundant and ubiquitous in nature, phages can be used to treat bacterial infections (phage therapy), including refractory infections and those resistant to antibiotics. However, despite an abundance of anecdotal evidence of efficacy, significant hurdles remain before routine implementation of phage therapy into medical practice, including a dearth of robust clinical trial data. Phage-bacterium interactions are complex and diverse, characterized by co-evolution trajectories that are significantly influenced by the environments in which they occur (mammalian body sites, water, soil, etc.). An understanding of the molecular mechanisms underpinning these dynamics is essential for successful clinical translation. This review aims to cover key aspects of bacterium-phage interactions that affect bacterial killing by describing the most relevant published literature and detailing the current knowledge gaps most likely to influence therapeutic success.
Collapse
Affiliation(s)
- Carola Venturini
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Aleksandra Petrovic Fabijan
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Alicia Fajardo Lubian
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Stefanie Barbirz
- Department of Medicine, Science Faculty, MSB Medical School Berlin, Berlin, Germany
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Westmead Hospital, Western Sydney Local Health District, Westmead, NSW, Australia
| |
Collapse
|
28
|
Characterization and complete genome analysis of a novel Escherichia phage, vB_EcoM-RPN242. Arch Virol 2022; 167:1675-1679. [DOI: 10.1007/s00705-022-05479-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/04/2022] [Indexed: 01/10/2023]
|
29
|
Phothichaisri W, Chankhamhaengdecha S, Janvilisri T, Nuadthaisong J, Phetruen T, Fagan RP, Chanarat S. Potential Role of the Host-Derived Cell-Wall Binding Domain of Endolysin CD16/50L as a Molecular Anchor in Preservation of Uninfected Clostridioides difficile for New Rounds of Phage Infection. Microbiol Spectr 2022; 10:e0236121. [PMID: 35377223 PMCID: PMC9045149 DOI: 10.1128/spectrum.02361-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/20/2022] [Indexed: 01/21/2023] Open
Abstract
Endolysin is a phage-encoded cell-wall hydrolase which degrades the peptidoglycan layer of the bacterial cell wall. The enzyme is often expressed at the late stage of the phage lytic cycle and is required for progeny escape. Endolysins of bacteriophage that infect Gram-positive bacteria often comprises two domains: a peptidoglycan hydrolase and a cell-wall binding domain (CBD). Although the catalytic domain of endolysin is relatively well-studied, the precise role of CBD is ambiguous and remains controversial. Here, we focus on the function of endolysin CBD from a recently isolated Clostridioides difficile phage. We found that the CBD is not required for lytic activity, which is strongly prevented by the surface layer of C. difficile. Intriguingly, hidden Markov model analysis suggested that the endolysin CBD is likely derived from the CWB2 motif of C. difficile cell-wall proteins but possesses a higher binding affinity to bacterial cell-wall polysaccharides. Moreover, the CBD forms a homodimer, formation of which is necessary for interaction with the surface saccharides. Importantly, endolysin diffusion and sequential cytolytic assays showed that CBD of endolysin is required for the enzyme to be anchored to post-lytic cell-wall remnants, suggesting its physiological roles in limiting diffusion of the enzyme, preserving neighboring host cells, and thereby enabling the phage progeny to initiate new rounds of infection. Taken together, this study provides an insight into regulation of endolysin through CBD and can potentially be applied for endolysin treatment against C. difficile infection. IMPORTANCE Endolysin is a peptidoglycan hydrolase encoded in a phage genome. The enzyme is attractive due to its potential use as antibacterial treatment. To utilize endolysin for the therapeutic propose, understanding of the fundamental role of endolysin becomes important. Here, we investigate the function of cell-wall binding domain (CBD) of an endolysin from a C. difficile phage. The domain is homologous to a cell-wall associating module of bacterial cell-wall proteins, likely acquired during phage-host coevolution. The interaction of CBD to bacterial cell walls reduces enzyme diffusion and thereby limits cell lysis of the neighboring bacteria. Our findings indicate that the endolysin is trapped to the cell-wall residuals through CBD and might serve as an advantage for phage replication. Thus, employing a CBD-less endolysin might be a feasible strategy for using endolysin for the treatment of C. difficile infection.
Collapse
Affiliation(s)
- Wichuda Phothichaisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jirayu Nuadthaisong
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tanaporn Phetruen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Robert P. Fagan
- School of Biosciences, Florey Institute, University of Sheffield, Sheffield, United Kingdom
| | - Sittinan Chanarat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Laboratory of Molecular Cell Biology, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| |
Collapse
|
30
|
Cernooka E, Rumnieks J, Zrelovs N, Tars K, Kazaks A. Diversity of the lysozyme fold: structure of the catalytic domain from an unusual endolysin encoded by phage Enc34. Sci Rep 2022; 12:5005. [PMID: 35322067 PMCID: PMC8943055 DOI: 10.1038/s41598-022-08765-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/10/2022] [Indexed: 12/02/2022] Open
Abstract
Endolysins are bacteriophage-encoded peptidoglycan-degrading enzymes with potential applications for treatment of multidrug-resistant bacterial infections. Hafnia phage Enc34 encodes an unusual endolysin with an N-terminal enzymatically active domain and a C-terminal transmembrane domain. The catalytic domain of the endolysin belongs to the conserved protein family PHA02564 which has no recognizable sequence similarity to other known endolysin types. Turbidity reduction assays indicate that the Enc34 enzyme is active against peptidoglycan from a variety of Gram-negative bacteria including the opportunistic pathogen Pseudomonas aeruginosa PAO1. The crystal structure of the catalytic domain of the Enc34 endolysin shows a distinctive all-helical architecture that distantly resembles the α-lobe of the lysozyme fold. Conserved catalytically important residues suggest a shared evolutionary history between the Enc34 endolysin and GH73 and GH23 family glycoside hydrolases and propose a molecular signature for substrate cleavage for a large group of peptidoglycan-degrading enzymes.
Collapse
Affiliation(s)
- Elina Cernooka
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, 1067, Latvia
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, 1067, Latvia
| | - Nikita Zrelovs
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, 1067, Latvia
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, 1067, Latvia.,Faculty of Biology, University of Latvia, Jelgavas 1, Riga, 1004, Latvia
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, 1067, Latvia.
| |
Collapse
|
31
|
Schuch R, Cassino C, Vila-Farres X. Direct Lytic Agents: Novel, Rapidly Acting Potential Antimicrobial Treatment Modalities for Systemic Use in the Era of Rising Antibiotic Resistance. Front Microbiol 2022; 13:841905. [PMID: 35308352 PMCID: PMC8928733 DOI: 10.3389/fmicb.2022.841905] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/28/2022] [Indexed: 12/19/2022] Open
Abstract
Direct lytic agents (DLAs) are novel antimicrobial compounds with unique mechanisms of action based on rapid cell wall destabilization and bacteriolysis. DLAs include two classes of purified polypeptides—lysins (peptidoglycan hydrolase enzymes) and amurins (outer membrane targeting peptides). Their intended use is to kill bacteria in a manner that is complimentary to and synergistic with traditional antibiotics without selection for DLA resistance. Lysins were originally described as having activity against Gram-positive pathogens and of those, exebacase, is the first to have advanced into Phase 3 of clinical development. Recently, both engineered and native DLAs have now been described with potent bactericidal activity against a range of Gram-negative pathogens, including multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii. Importantly, novel DLAs targeting Gram-negatives, including the lysin CF-370 and the amurin peptides, are active in biological matrices (blood/serum) and, as such, offer promise for therapeutic use as systemically administered agents for the treatment of life-threatening invasive infections. In this review, DLAs are discussed as potential new classes of antimicrobial biologics that can be used to treat serious systemic infections.
Collapse
|
32
|
Arenas T, Osorio A, Ginez LD, Camarena L, Poggio S. Bacterial cell-wall quantification by a modified low volume Nelson-Somogyi method and its use with different sugars. Can J Microbiol 2022; 68:295-302. [PMID: 35100051 DOI: 10.1139/cjm-2021-0238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The study of peptidoglycan binding proteins frequently requires in vitro binding assays in which the isolated peptidoglycan used as substrate has to be carefully quantified. Here we describe an easy and sensitive assay for the quantification of peptidoglycan based on a modified Nelson-Somogyi reducing sugar assay. We report the response of this assay to different common sugars and adapt its use to peptidoglycan samples that have been subjected to acid hydrolysis. This method showed a better sensitivity than the peptidoglycan quantification method based on the acid detection of diaminopimelic acid. The method described in this work besides being valuable in the characterization of peptidoglycan binding proteins, is also useful for quantification of reducing monosaccharides or of polysaccharides after acid or hydrolysis.
Collapse
Affiliation(s)
- Thelma Arenas
- Universidad Nacional Autónoma de México, 7180, Depto. Biología Molecular y Biotecnología, Ciudad de Mexico, Mexico;
| | - Aurora Osorio
- Universidad Nacional Autónoma de México, 7180, Depto. Biología Molecular y Biotecnología, Ciudad de Mexico, Mexico;
| | - Luis David Ginez
- National Autonomous University of Mexico, 7180, Molecular Biology and Biotechnology, Ciudad de Mexico, Mexico, 04510;
| | - Laura Camarena
- Universidad Nacional Autonoma de Mexico, 7180, Instituto de Investigaciones Biomédicas, Ciudad de Mexico, Ciudad de México, Mexico;
| | - Sebastian Poggio
- Universidad Nacional Autonoma de Mexico Instituto de Investigaciones Biomedicas, 61738, Biologia Molecular y Biotecnologia, Ciudad de Mexico, Ciudad de Mexico, Mexico;
| |
Collapse
|
33
|
Hong W, Nyaruaba R, Li X, Liu H, Yang H, Wei H. In-situ and Real-Time Monitoring of the Interaction Between Lysins and Staphylococcus aureus Biofilm by Surface Plasmon Resonance. Front Microbiol 2021; 12:783472. [PMID: 34917062 PMCID: PMC8670000 DOI: 10.3389/fmicb.2021.783472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/12/2021] [Indexed: 11/22/2022] Open
Abstract
Staphylococcus aureus can produce a multilayered biofilm embedded in extracellular polymeric matrix. This biofilm is difficult to remove, insensitive to antibiotics, easy to develop drug-resistant strains and causes enormous problems to environments and health. Phage lysin which commonly consists of a catalytic domain (CD) and a cell-wall binding domain (CBD) is a powerful weapon against bacterial biofilm. However, the real-time interaction between lysin and S. aureus biofilm is still not fully understood. In this study, we monitored the interactions of three lysins (ClyF, ClyC, PlySs2) against culture-on-chip S. aureus biofilm, in real-time, based on surface plasmon resonance (SPR). A typical SPR response curve showed that the lysins bound to the biofilm rapidly and the biofilm destruction started at a longer time. By using 1:1 binding model analysis, affinity constants (KD) for ClyF, ClyC, and PlySs2 were found to be 3.18 ± 0.127 μM, 1.12 ± 0.026 μM, and 15.5 ± 0.514 μM, respectively. The fact that ClyF and PlySs2 shared the same CBD but showed different affinity to S. aureus biofilm suggested that, not only CBD, but also CD affects the binding activity of the entire lysin. The SPR platform can be applied to improve our understanding on the complex interactions between lysins and bacterial biofilm including association (adsorption) and disassociation (destruction).
Collapse
Affiliation(s)
- Wei Hong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Raphael Nyaruaba
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohong Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huan Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
34
|
Danis-Wlodarczyk KM, Wozniak DJ, Abedon ST. Treating Bacterial Infections with Bacteriophage-Based Enzybiotics: In Vitro, In Vivo and Clinical Application. Antibiotics (Basel) 2021; 10:1497. [PMID: 34943709 PMCID: PMC8698926 DOI: 10.3390/antibiotics10121497] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Over the past few decades, we have witnessed a surge around the world in the emergence of antibiotic-resistant bacteria. This global health threat arose mainly due to the overuse and misuse of antibiotics as well as a relative lack of new drug classes in development pipelines. Innovative antibacterial therapeutics and strategies are, therefore, in grave need. For the last twenty years, antimicrobial enzymes encoded by bacteriophages, viruses that can lyse and kill bacteria, have gained tremendous interest. There are two classes of these phage-derived enzymes, referred to also as enzybiotics: peptidoglycan hydrolases (lysins), which degrade the bacterial peptidoglycan layer, and polysaccharide depolymerases, which target extracellular or surface polysaccharides, i.e., bacterial capsules, slime layers, biofilm matrix, or lipopolysaccharides. Their features include distinctive modes of action, high efficiency, pathogen specificity, diversity in structure and activity, low possibility of bacterial resistance development, and no observed cross-resistance with currently used antibiotics. Additionally, and unlike antibiotics, enzybiotics can target metabolically inactive persister cells. These phage-derived enzymes have been tested in various animal models to combat both Gram-positive and Gram-negative bacteria, and in recent years peptidoglycan hydrolases have entered clinical trials. Here, we review the testing and clinical use of these enzymes.
Collapse
Affiliation(s)
| | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA;
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
| |
Collapse
|
35
|
Sekiya H, Kamitori S, Nariya H, Matsunami R, Tamai E. Structural and biochemical characterization of the Clostridium perfringens-specific Zn 2+-dependent amidase endolysin, Psa, catalytic domain. Biochem Biophys Res Commun 2021; 576:66-72. [PMID: 34482025 DOI: 10.1016/j.bbrc.2021.08.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/27/2021] [Indexed: 11/19/2022]
Abstract
Phage-derived endolysins, enzymes that degrade peptidoglycans, have the potential to serve as alternative antimicrobial agents. Psa, which was identified as an endolysin encoded in the genome of Clostridium perfringens st13, was shown to specifically lyse C. perfringens. Psa has an N-terminal catalytic domain that is homologous to the Amidase_2 domain (PF01510), and a novel C-terminal cell wall-binding domain. Here, we determined the X-ray structure of the Psa catalytic domain (Psa-CD) at 1.65 Å resolution. Psa-CD has a typical Amidase_2 domain structure, consisting of a spherical structure with a central β-sheet surrounded by two α-helix groups. Furthermore, there is a Zn2+ at the center of Psa-CD catalytic reaction site, as well as a unique T-shaped substrate-binding groove consisting of two grooves on the molecule surface. We performed modeling study of the enzyme/substrate complex along with a mutational analysis, and demonstrated that the structure of the substrate-binding groove is closely related to the amidase activity. Furthermore, we proposed a Zn2+-mediated catalytic reaction mechanism for the Amidase_2 family, in which tyrosine constitutes part of the catalytic reaction site.
Collapse
Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Hirofumi Nariya
- Laboratory of Food Microbiology, Graduate School of Human Life Sciences Food and Nutritional Sciences, Jumonji University, 2-1-28, Kansawa, Niiza, Saitama, 352-8510, Japan
| | - Risa Matsunami
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan; Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan.
| |
Collapse
|
36
|
Rahman MU, Wang W, Sun Q, Shah JA, Li C, Sun Y, Li Y, Zhang B, Chen W, Wang S. Endolysin, a Promising Solution against Antimicrobial Resistance. Antibiotics (Basel) 2021; 10:1277. [PMID: 34827215 PMCID: PMC8614784 DOI: 10.3390/antibiotics10111277] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global crisis for human public health which threatens the effective prevention and control of ever-increasing infectious diseases. The advent of pandrug-resistant bacteria makes most, if not all, available antibiotics invalid. Meanwhile, the pipeline of novel antibiotics development stagnates, which prompts scientists and pharmacists to develop unconventional antimicrobials. Bacteriophage-derived endolysins are cell wall hydrolases which could hydrolyze the peptidoglycan layer from within and outside of bacterial pathogens. With high specificity, rapid action, high efficiency, and low risk of resistance development, endolysins are believed to be among the best alternative therapeutic agents to treat multidrug resistant (MDR) bacteria. As of now, endolysins have been applied to diverse aspects. In this review, we comprehensively introduce the structures and activities of endolysins and summarize the latest application progress of recombinant endolysins in the fields of medical treatment, pathogen diagnosis, food safety, and agriculture.
Collapse
Affiliation(s)
- Mujeeb ur Rahman
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Weixiao Wang
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China;
| | - Qingqing Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Junaid Ali Shah
- College of Life Sciences, Jilin University, Changchun 130012, China;
| | - Chao Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Yanmei Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Yuanrui Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Bailing Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China;
| | - Wei Chen
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China;
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| |
Collapse
|
37
|
Ramos-Vivas J, Superio J, Galindo-Villegas J, Acosta F. Phage Therapy as a Focused Management Strategy in Aquaculture. Int J Mol Sci 2021; 22:10436. [PMID: 34638776 PMCID: PMC8508683 DOI: 10.3390/ijms221910436] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022] Open
Abstract
Therapeutic bacteriophages, commonly called as phages, are a promising potential alternative to antibiotics in the management of bacterial infections of a wide range of organisms including cultured fish. Their natural immunogenicity often induces the modulation of a variated collection of immune responses within several types of immunocytes while promoting specific mechanisms of bacterial clearance. However, to achieve standardized treatments at the practical level and avoid possible side effects in cultivated fish, several improvements in the understanding of their biology and the associated genomes are required. Interestingly, a particular feature with therapeutic potential among all phages is the production of lytic enzymes. The use of such enzymes against human and livestock pathogens has already provided in vitro and in vivo promissory results. So far, the best-understood phages utilized to fight against either Gram-negative or Gram-positive bacterial species in fish culture are mainly restricted to the Myoviridae and Podoviridae, and the Siphoviridae, respectively. However, the current functional use of phages against bacterial pathogens of cultured fish is still in its infancy. Based on the available data, in this review, we summarize the current knowledge about phage, identify gaps, and provide insights into the possible bacterial control strategies they might represent for managing aquaculture-related bacterial diseases.
Collapse
Affiliation(s)
- José Ramos-Vivas
- Grupo de Investigación en Acuicultura, Universidad de Las Palmas de Gran Canaria, 35214 Las Palmas de Gran Canaria, Spain; (J.R.-V.); (F.A.)
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico
| | - Joshua Superio
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway;
| | | | - Félix Acosta
- Grupo de Investigación en Acuicultura, Universidad de Las Palmas de Gran Canaria, 35214 Las Palmas de Gran Canaria, Spain; (J.R.-V.); (F.A.)
| |
Collapse
|
38
|
Ho MKY, Zhang P, Chen X, Xia J, Leung SSY. Bacteriophage endolysins against gram-positive bacteria, an overview on the clinical development and recent advances on the delivery and formulation strategies. Crit Rev Microbiol 2021; 48:303-326. [PMID: 34478359 DOI: 10.1080/1040841x.2021.1962803] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Facing the increasing threat of multi-drug antimicrobial resistance (AMR), humans strive to search for antibiotic drug candidates and antibacterial alternatives from all possible places, from soils in remote areas to deep in the sea. In this "gold rush for antibacterials," researchers turn to the natural enemy of bacterial cells, bacteriophage (phages), and find them a rich source of weapons for AMR bacteria. Endolysins (lysins), the enzymes phages use to break the bacterial cells from within, have been shown to be highly selective and efficient in killing their target bacteria from outside while maintaining a low occurrence of bacterial resistance. In this review, we start with the structures and mechanisms of action of lysins against Gram-positive (GM+) bacteria. The developmental history of lysins is also outlined. Then, we detail the latest preclinical and clinical research on their safety and efficacy against GM+ bacteria, focusing on the formulation strategies of these enzymes. Finally, the challenges and potential hurdles are discussed. Notwithstanding these limitations, the trends in development indicate that the first, approved lysin drugs will be available soon in the near future. Overall, this review presents a timely summary of the current progress on lysins as antibacterial enzymes for AMR GM+ bacteria, and provides a guidebook for biomaterial researchers who are dedicating themselves to the battle against bacterial infections.
Collapse
Affiliation(s)
- Marco Kai Yuen Ho
- School of Pharmacy, The Chinese University of Hong Kong, Hong Kong, China
| | - Pengfei Zhang
- School of Pharmacy, The Chinese University of Hong Kong, Hong Kong, China
| | - Xi Chen
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, China
| | | |
Collapse
|
39
|
Yan J, Yang R, Yu S, Zhao W. The strategy of biopreservation of meat product against MRSA using lytic domain of lysin from Staphylococcus aureus bacteriophage. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.100967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
40
|
Batool N, Yoon S, Imdad S, Kong M, Kim H, Ryu S, Lee JH, Chaurasia AK, Kim KK. An Antibacterial Nanorobotic Approach for the Specific Targeting and Removal of Multiple Drug-Resistant Staphylococcus aureus. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100257. [PMID: 33838013 DOI: 10.1002/smll.202100257] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/06/2021] [Indexed: 06/12/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) causes diseases ranging from skin infections to lethal sepsis and has become a serious threat to human health due to multiple-drug resistance (MDR). Therefore, a resistance-free antibacterial therapy is necessary to overcome MDR MRSA infections. In this study, an antibacterial nanorobot (Ab-nanobot) is developed wherein a cell wall-binding domain (CBD)-endolysin, acting as a sensor, is covalently conjugated with an actuator consisting of an iron oxide/silica core-shell. The CBD-endolysin sensor shows an excellent specificity to detect, bind, and accumulate on the S. aureus USA300 cell surface even in a bacterial consortium, and in host cell infections. Ab-nanobot specifically captures and kills MRSA in response to medically approved radiofrequency (RF) electromagnetic stimulation (EMS) signal. When Ab-nanobot receives the RF-EMS signal on the cell surface, actuator induces cell death in MRSA with 99.999% removal within 20 min by cell-wall damage via generation of localized heat and reactive oxygen species. The in vivo efficacy of Ab-nanobot is proven using a mice subcutaneous skin infection model. Collectively, this study offers a nanomedical resistance-free strategy to overcome MDR MRSA infections by providing a highly specific nanorobot for S. aureus.
Collapse
Affiliation(s)
- Nayab Batool
- Department of Precision Medicine, Institute for Antimicrobial Resistance Research and Therapeutics, Graduate School of Basic Medical Sciences (GSBMS), Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Seokyoung Yoon
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Saba Imdad
- Department of Precision Medicine, Institute for Antimicrobial Resistance Research and Therapeutics, Graduate School of Basic Medical Sciences (GSBMS), Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Minsuk Kong
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul, 01811, South Korea
| | - Hun Kim
- Department of Precision Medicine, Institute for Antimicrobial Resistance Research and Therapeutics, Graduate School of Basic Medical Sciences (GSBMS), Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Akhilesh Kumar Chaurasia
- Department of Precision Medicine, Institute for Antimicrobial Resistance Research and Therapeutics, Graduate School of Basic Medical Sciences (GSBMS), Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Institute for Antimicrobial Resistance Research and Therapeutics, Graduate School of Basic Medical Sciences (GSBMS), Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
A Putative Amidase Endolysin Encoded by Clostridium perfringens St13 Exhibits Specific Lytic Activity and Synergizes with the Muramidase Endolysin Psm. Antibiotics (Basel) 2021; 10:antibiotics10030245. [PMID: 33804492 PMCID: PMC7999503 DOI: 10.3390/antibiotics10030245] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 01/21/2023] Open
Abstract
Clostridium perfringens is an often-harmful intestinal bacterium that causes various diseases ranging from food poisoning to life-threatening fulminant disease. Potential treatments include phage-derived endolysins, a promising family of alternative antimicrobial agents. We surveyed the genome of the C. perfringens st13 strain and identified an endolysin gene, psa, in the phage remnant region. Psa has an N-terminal catalytic domain that is homologous to the amidase_2 domain, and a C-terminal domain of unknown function. psa and gene derivatives encoding various Psa subdomains were cloned and expressed in Escherichia coli as N-terminal histidine-tagged proteins. Purified His-tagged full-length Psa protein (Psa-his) showed C. perfringens-specific lytic activity in turbidity reduction assays. In addition, we demonstrated that the uncharacterized C-terminal domain has cell wall-binding activity. Furthermore, cell wall-binding measurements showed that Psa binding was highly specific to C. perfringens. These results indicated that Psa is an amidase endolysin that specifically lyses C. perfringens; the enzyme’s specificity is highly dependent on the binding of the C-terminal domain. Moreover, Psa was shown to have a synergistic effect with another C. perfringens-specific endolysin, Psm, which is a muramidase that cleaves peptidoglycan at a site distinct from that targeted by Psa. The combination of Psa and Psm may be effective in the treatment and prevention of C. perfringens infections.
Collapse
|
43
|
Bhagwat A, Zhang F, Collins CH, Dordick JS. Influence of bacterial culture medium on peptidoglycan binding of cell wall lytic enzymes. J Biotechnol 2021; 330:27-34. [PMID: 33652073 DOI: 10.1016/j.jbiotec.2021.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/18/2021] [Indexed: 10/22/2022]
Abstract
The bacteriolysin lysostaphin (Lst) and endolysin PlyPH are potent modular lytic enzymes with activity against clinically-relevant Gram-positive Staphylococcus aureus and Bacillus cereus, respectively. Both enzymes possess an N-terminal catalytic domain and C-terminal binding domain, with the latter conferring significant enzyme specificity. Lst and PlyPH show reduced activity in the presence of bacterial growth-supporting conditions, such as complex media. Here, we hypothesize that Lst and PlyPH bind poorly to their targets in growth media, which may influence their use in antimicrobial applications in the food industry, as therapeutics, and for control of microbial communities. To this end, binding of isolated Lst and PlyPH binding domains to target bacteria was quantified in the presence of three increasingly complex media - phosphate buffered saline (PBS), defined growth medium (AAM) and undefined complex medium (TSB) by surface plasmon resonance (SPR) and flow cytometry. Evaluation of binding kinetics by SPR demonstrated that PlyPH binding was particularly sensitive to medium composition, with 8-fold lower association and 3.4-fold lower dissociation rate constants to B. cereus in TSB compared to PBS. Flow cytometry studies indicated a decrease in the binding-dependent fluorescent populations of S. aureus and B. cereus, for lysostaphin binding domain and PlyPH binding domain, respectively, in TSB compared to PBS. Enzyme binding behavior was consistent with the enzymes' catalytic activity in the three media, thereby suggesting that compromised enzyme binding could be responsible for poor activity in more complex growth media.
Collapse
Affiliation(s)
- Amala Bhagwat
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Cynthia H Collins
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States.
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States.
| |
Collapse
|
44
|
Xu X, Zhang D, Zhou B, Zhen X, Ouyang S. Structural and biochemical analyses of the tetrameric cell binding domain of Lys170 from enterococcal phage F170/08. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:721-729. [PMID: 33609147 DOI: 10.1007/s00249-021-01511-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/11/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
Lysins are a class of hydrolytic enzymes used by bacteriophages to target and cleave the peptidoglycan of bacterial cell walls during their lytic cycle. The lysins from bacteriophages that infect Gram-positive bacteria are typically monomeric and consist of one or two catalytic domains (CD) and a cell binding domain (CBD). However, multimeric lysins encoded by a single gene have also been reported, among which Lys170 from enterococcal phage F170/08 was one of the first identified. Here, we determined the crystal structure of Lys170 CBD at 1.40 Å resolution. The structure reveals that Lys170 CBDs assemble into a tetrameric functional unit and that each monomer folds into a three-stranded β-sheet core capped on each side by an α-helix. In addition, we identified key residues of Lys170 CBD involved in host cell binding. Our work provides a basis for designing highly efficient lysins targeting Enterococcus faecalis.
Collapse
Affiliation(s)
- Xiaolong Xu
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Dandan Zhang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,The Engineering Technology Research Center of Characteristic Medicinal Plants of Fujian, Ningde Normal University, Ningde, China
| | - Biao Zhou
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xiangkai Zhen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.
| |
Collapse
|
45
|
Lisboa J, Pereira C, Rifflet A, Ayala J, Terceti MS, Barca AV, Rodrigues I, Pereira PJB, Osorio CR, García-Del Portillo F, Gomperts Boneca I, do Vale A, Dos Santos NMS. A Secreted NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida Cleaves the Peptidoglycan of Potentially Competing Bacteria. mSphere 2021; 6:e00736-20. [PMID: 33536321 PMCID: PMC7860986 DOI: 10.1128/msphere.00736-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/08/2021] [Indexed: 11/20/2022] Open
Abstract
Peptidoglycan (PG) is a major component of the bacterial cell wall, forming a mesh-like structure enwrapping the bacteria that is essential for maintaining structural integrity and providing support for anchoring other components of the cell envelope. PG biogenesis is highly dynamic and requires multiple enzymes, including several hydrolases that cleave glycosidic or amide bonds in the PG. This work describes the structural and functional characterization of an NlpC/P60-containing peptidase from Photobacterium damselae subsp. piscicida (Phdp), a Gram-negative bacterium that causes high mortality of warm-water marine fish with great impact for the aquaculture industry. PnpA ( PhotobacteriumNlpC-like protein A) has a four-domain structure with a hydrophobic and narrow access to the catalytic center and specificity for the γ-d-glutamyl-meso-diaminopimelic acid bond. However, PnpA does not cleave the PG of Phdp or PG of several Gram-negative and Gram-positive bacterial species. Interestingly, it is secreted by the Phdp type II secretion system and degrades the PG of Vibrio anguillarum and Vibrio vulnificus This suggests that PnpA is used by Phdp to gain an advantage over bacteria that compete for the same resources or to obtain nutrients in nutrient-scarce environments. Comparison of the muropeptide composition of PG susceptible and resistant to the catalytic activity of PnpA showed that the global content of muropeptides is similar, suggesting that susceptibility to PnpA is determined by the three-dimensional organization of the muropeptides in the PG.IMPORTANCE Peptidoglycan (PG) is a major component of the bacterial cell wall formed by long chains of two alternating sugars interconnected by short peptides, generating a mesh-like structure that enwraps the bacterial cell. Although PG provides structural integrity and support for anchoring other components of the cell envelope, it is constantly being remodeled through the action of specific enzymes that cleave or join its components. Here, it is shown that Photobacterium damselae subsp. piscicida, a bacterium that causes high mortality in warm-water marine fish, produces PnpA, an enzyme that is secreted into the environment and is able to cleave the PG of potentially competing bacteria, either to gain a competitive advantage and/or to obtain nutrients. The specificity of PnpA for the PG of some bacteria and its inability to cleave others may be explained by differences in the structure of the PG mesh and not by different muropeptide composition.
Collapse
Affiliation(s)
- Johnny Lisboa
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Cassilda Pereira
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Aline Rifflet
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France
- INSERM Groupe Avenir, Paris, France
- CNRS, UMR "Integrated and Molecular Microbiology," Paris, France
| | - Juan Ayala
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mateus S Terceti
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alba V Barca
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Inês Rodrigues
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Pedro José Barbosa Pereira
- Biomolecular Structure Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Macromolecular Structure Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Carlos R Osorio
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco García-Del Portillo
- Laboratorio de Patógenos Bacterianos Intracelulares, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ivo Gomperts Boneca
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France
- INSERM Groupe Avenir, Paris, France
- CNRS, UMR "Integrated and Molecular Microbiology," Paris, France
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Nuno M S Dos Santos
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| |
Collapse
|
46
|
Binte Muhammad Jai HS, Dam LC, Tay LS, Koh JJW, Loo HL, Kline KA, Goh BC. Engineered Lysins With Customized Lytic Activities Against Enterococci and Staphylococci. Front Microbiol 2020; 11:574739. [PMID: 33324362 PMCID: PMC7724435 DOI: 10.3389/fmicb.2020.574739] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
The emergence of multidrug-resistant bacteria has made minor bacterial infections incurable with many existing antibiotics. Lysins are phage-encoded peptidoglycan hydrolases that have demonstrated therapeutic potential as a novel class of antimicrobials. The modular architecture of lysins enables the functional domains – catalytic domain (CD) and cell wall binding domain (CBD) – to be shuffled to create novel lysins. The CD is classically thought to be only involved in peptidoglycan hydrolysis whereas the CBD dictates the lytic spectrum of a lysin. While there are many studies that extended the lytic spectrum of a lysin by domain swapping, few have managed to introduce species specificity in a chimeric lysin. In this work, we constructed two chimeric lysins by swapping the CBDs of two parent lysins with different lytic spectra against enterococci and staphylococci. We showed that these chimeric lysins exhibited customized lytic spectra distinct from the parent lysins. Notably, the chimeric lysin P10N-V12C, which comprises a narrow-spectrum CD fused with a broad-spectrum CBD, displayed species specificity not lysing Enterococcus faecium while targeting Enterococcus faecalis and staphylococci. Such species specificity can be attributed to the narrow-spectrum CD of the chimeric lysin. Using flow cytometry and confocal microscopy, we found that the E. faecium cells that were treated with P10N-V12C are less viable with compromised membranes yet remained morphologically intact. Our results suggest that while the CBD is a major determinant of the lytic spectrum of a lysin, the CD is also responsible in the composition of the final lytic spectrum, especially when it pertains to species-specificity.
Collapse
Affiliation(s)
- Hana Sakina Binte Muhammad Jai
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore
| | - Linh Chi Dam
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore
| | - Lowella Servito Tay
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore
| | - Jodi Jia Wei Koh
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore
| | - Hooi Linn Loo
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore
| | - Kimberly A Kline
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Boon Chong Goh
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore
| |
Collapse
|
47
|
Sekiya H, Tamai E, Kawasaki J, Murakami K, Kamitori S. Structural and biochemical characterizations of the novel autolysin Acd24020 from Clostridioides difficile and its full-function catalytic domain as a lytic enzyme. Mol Microbiol 2020; 115:684-698. [PMID: 33140473 DOI: 10.1111/mmi.14636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/13/2020] [Accepted: 10/28/2020] [Indexed: 12/17/2022]
Abstract
Autolysin is a lytic enzyme that hydrolyzes peptidoglycans of the bacterial cell wall, with a catalytic domain and cell wall-binding (CWB) domains, to be involved in different physiological functions that require bacterial cell wall remodeling. We identified a novel autolysin, Acd24020, from Clostridioides (Clostridium) difficile (C. difficile), with an endopeptidase catalytic domain belonging to the NlpC/P60 family and three bacterial Src-homology 3 domains as CWB domains. The catalytic domain of Acd24020 (Acd24020-CD) exhibited C. difficile-specific lytic activity equivalent to Acd24020, indicating that Acd24020-CD has full-function as a lytic enzyme by itself. To elucidate the specific peptidoglycan-recognition and catalytic reaction mechanisms of Acd24020-CD, biochemical characterization, X-ray structure determination, a modeling study of the enzyme/substrate complex, and mutagenesis analysis were performed. Acd24020-CD has an hourglass-shaped substrate-binding groove across the molecule, which is responsible for recognizing the direct 3-4 cross-linking structure unique to C. difficile peptidoglycan. Based on the X-ray structure and modeling study, we propose a dynamic Cys/His catalyzing mechanism, in which the catalytic Cys299 and His354 residues dynamically change their conformations to complement each step of the enzyme catalytic reaction.
Collapse
Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan.,Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Japan
| | - Jurina Kawasaki
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Kaho Murakami
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Japan
| |
Collapse
|
48
|
Shen Y, Kalograiaki I, Prunotto A, Dunne M, Boulos S, Taylor NMI, Sumrall ET, Eugster MR, Martin R, Julian-Rodero A, Gerber B, Leiman PG, Menéndez M, Peraro MD, Cañada FJ, Loessner MJ. Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase. Chem Sci 2020; 12:576-589. [PMID: 34163788 PMCID: PMC8179006 DOI: 10.1039/d0sc04394j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3′O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. Our multidisciplinary approach tackled an extremely challenging protein–glycopolymer complex and delineated a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity. Combining genetic, biochemical and computational approaches, we elucidated the molecular mechanisms underlying the recognition of Listeria wall teichoic acid by bacteriophage-encoded SH3b repeats.![]()
Collapse
Affiliation(s)
- Yang Shen
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Ioanna Kalograiaki
- Centro de Investigaciones Biológicas, Margarita Salas, Consejo Superior de Investigaciones Científicas Ramiro de Maeztu 9 28040 Madrid Spain.,Centro de Investigación Biomédica en Red-Enfermedades Respiratorias (CIBERES) Avenida de Monforte de Lemos 3-5 28029 Madrid Spain
| | - Alessio Prunotto
- Laboratory for Biomolecular Modeling, EPFL IBI-SV Station 19 1015 Lausanne Switzerland
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Samy Boulos
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 9 8092 Zurich Switzerland
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen Blegdamsvej 3B Copenhagen 2200 Denmark
| | - Eric T Sumrall
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Marcel R Eugster
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Rebecca Martin
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Alicia Julian-Rodero
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Benjamin Gerber
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Petr G Leiman
- University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics 301 University Blvd Galveston TX 77555-0647 USA
| | - Margarita Menéndez
- Centro de Investigación Biomédica en Red-Enfermedades Respiratorias (CIBERES) Avenida de Monforte de Lemos 3-5 28029 Madrid Spain.,Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Cientificas Serrano 119 28006 Madrid Spain
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, EPFL IBI-SV Station 19 1015 Lausanne Switzerland
| | - Francisco Javier Cañada
- Centro de Investigaciones Biológicas, Margarita Salas, Consejo Superior de Investigaciones Científicas Ramiro de Maeztu 9 28040 Madrid Spain.,Centro de Investigación Biomédica en Red-Enfermedades Respiratorias (CIBERES) Avenida de Monforte de Lemos 3-5 28029 Madrid Spain
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| |
Collapse
|
49
|
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: 4.8] [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.
Collapse
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
| |
Collapse
|
50
|
Characterization of PlyB221 and PlyP32, Two Novel Endolysins Encoded by Phages Preying on the Bacillus cereus Group. Viruses 2020; 12:v12091052. [PMID: 32967292 PMCID: PMC7551664 DOI: 10.3390/v12091052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022] Open
Abstract
Endolysins are phage-encoded enzymes implicated in the breaching of the bacterial cell wall at the end of the viral cycle. This study focuses on the endolysins of Deep-Blue (PlyB221) and Deep-Purple (PlyP32), two phages preying on the Bacillus cereus group. Both enzymes exhibit a typical modular organization with an enzymatically active domain (EAD) located in the N-terminal and a cell wall binding domain (CBD) in the C-terminal part of the protein. In silico analysis indicated that the EAD domains of PlyB221 and PlyP32 are endowed with peptidase and muramidase activities, respectively, whereas in both proteins SH3 domains are involved in the CBD. To evaluate their antimicrobial properties and binding specificity, both endolysins were expressed and purified. PlyB221 and PlyP32 efficiently recognized and lysed all the tested strains from the B. cereus group. Biochemical characterization showed that PlyB221 activity was stable under a wide range of pHs (5–9), NaCl concentrations (up to 200 mM), and temperature treatments (up to 50 °C). Although PlyP32 activity was less stable than that of PlyB221, the endolysin displayed high activity at pH 6–7, NaCl concentration up to 100 mM and the temperature treatment up to 45 °C. Overall, PlyB221 and PlyP32 display suitable characteristics for the development of biocontrol and detection tools.
Collapse
|