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Xu S, Lee I, Kwon SJ, Kim E, Nevo L, Straight L, Murata H, Matyjaszewski K, Dordick JS. Split fluorescent protein-mediated multimerization of cell wall binding domain for highly sensitive and selective bacterial detection. N Biotechnol 2024; 82:54-64. [PMID: 38750815 DOI: 10.1016/j.nbt.2024.05.004] [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: 01/28/2024] [Revised: 04/22/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
Cell wall peptidoglycan binding domains (CBDs) of cell lytic enzymes, including bacteriocins, autolysins and bacteriophage endolysins, enable highly selective bacterial binding, and thus, have potential as biorecognition molecules for nondestructive bacterial detection. Here, a novel design for a self-complementing split fluorescent protein (FP) complex is proposed, where a multimeric FP chain fused with specific CBDs ((FP-CBD)n) is assembled inside the cell, to improve sensitivity by enhancing the signal generated upon Staphylococcus aureus or Bacillus anthracis binding. Flow cytometry shows enhanced fluorescence on the cell surface with increasing FP stoichiometry and surface plasmon resonance reveals nanomolar binding affinity to isolated peptidoglycan. The breadth of function of these complexes is demonstrated through the use of CBD modularity and the ability to attach enzymatic detection modalities. Horseradish peroxidase-coupled (FP-CBD)n complexes generate a catalytic amplification, with the degree of amplification increasing as a function of FP length, reaching a limit of detection (LOD) of 103 cells/droplet (approximately 0.1 ng S. aureus or B. anthracis) within 15 min on a polystyrene surface. These fusion proteins can be multiplexed for simultaneous detection. Multimeric split FP-CBD fusions enable use as a biorecognition molecule with enhanced signal for use in bacterial biosensing platforms.
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Affiliation(s)
- Shirley Xu
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Inseon Lee
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Eunsol Kim
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Liv Nevo
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Lorelli Straight
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Hironobu Murata
- Department of Chemistry, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, USA
| | | | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA; Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA.
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Zheng T, Zhang C. Engineering strategies and challenges of endolysin as an antibacterial agent against Gram-negative bacteria. Microb Biotechnol 2024; 17:e14465. [PMID: 38593316 PMCID: PMC11003714 DOI: 10.1111/1751-7915.14465] [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: 01/22/2024] [Revised: 03/09/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024] Open
Abstract
Bacteriophage endolysin is a novel antibacterial agent that has attracted much attention in the prevention and control of drug-resistant bacteria due to its unique mechanism of hydrolysing peptidoglycans. Although endolysin exhibits excellent bactericidal effects on Gram-positive bacteria, the presence of the outer membrane of Gram-negative bacteria makes it difficult to lyse them extracellularly, thus limiting their application field. To enhance the extracellular activity of endolysin and facilitate its crossing through the outer membrane of Gram-negative bacteria, researchers have adopted physical, chemical, and molecular methods. This review summarizes the characterization of endolysin targeting Gram-negative bacteria, strategies for endolysin modification, and the challenges and future of engineering endolysin against Gram-negative bacteria in clinical applications, to promote the application of endolysin in the prevention and control of Gram-negative bacteria.
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Affiliation(s)
- Tianyu Zheng
- Bathurst Future Agri‐Tech InstituteQingdao Agricultural UniversityQingdaoChina
| | - Can Zhang
- College of Veterinary MedicineQingdao Agricultural UniversityQingdaoChina
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Sui B, Wang X, Zhao T, Zhen J, Ren H, Liu W, Zhang X, Zhang C. Design, Screening, and Characterization of Engineered Phage Endolysins with Extracellular Antibacterial Activity against Gram-Negative Bacteria. Appl Environ Microbiol 2023; 89:e0058123. [PMID: 37338346 PMCID: PMC10370328 DOI: 10.1128/aem.00581-23] [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: 04/07/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023] Open
Abstract
Phage-encoded endolysins are emerging antibacterial agents based on their ability to efficiently degrade peptidoglycan on Gram-positive bacteria, but the envelope characteristics of Gram-negative bacteria limit their application. Engineering modifications of endolysins can improve the optimization of their penetrative and antibacterial properties. This study constructed a screening platform to screen for engineered Artificial-Bp7e (Art-Bp7e) endolysins with extracellular antibacterial activity against Escherichia coli. An oligonucleotide of 20 repeated NNK codons was inserted upstream of the endolysin gene Bp7e to construct a chimeric endolysin library in the pColdTF vector. The chimeric Art-Bp7e proteins were expressed by transforming the plasmid library into E. coli BL21 and released by chloroform fumigation, and the protein activities were evaluated by the spotting method and the colony-counting method to screen for promising proteins. Sequence analysis showed that all screened proteins with extracellular activities had a chimeric peptide with a positive charge and an α-helical structure. Also, a representative protein, Art-Bp7e6, was further characterized. It exhibited broad antibacterial activity against E. coli (7/21), Salmonella enterica serovar Enteritidis (4/10), Pseudomonas aeruginosa (3/10), and even Staphylococcus aureus (1/10). In the transmembrane process, the chimeric peptide of Art-Bp7e6 depolarized the host cell envelope, increased the permeability of the cell, and facilitated the movement of Art-Bp7e6 across the envelope to hydrolyze the peptidoglycan. In conclusion, the screening platform successfully screened for chimeric endolysins with extracellular antibacterial activities against Gram-negative bacteria, which provides methodological support for the further screening of engineered endolysins with high extracellular activities against Gram-negative bacteria. Also, the established platform showed broad application prospects and can be used to screen various proteins. IMPORTANCE The presence of the envelope in Gram-negative bacteria limits the use of phage endolysins, and engineering endolysins is an efficient way to optimize their penetrative and antibacterial properties. We built a platform for endolysin engineering and screening. A random peptide was fused with the phage endolysin Bp7e to construct a chimeric endolysin library, and engineered Artificial-Bp7e (Art-Bp7e) endolysins with extracellular activity against Gram-negative bacteria were successfully screened from the library. The purposeful Art-Bp7e had a chimeric peptide with an abundant positive charge and an α-helical structure, which led Bp7e to acquire the ability for the extracellular lysis of Gram-negative bacteria and showed a broad lysis spectrum. The platform provides a huge library capacity without the limitations of reported proteins or peptides. It can be utilized for the further screening of optimal endolysins against Gram-negative bacteria as well as for the screening of additional proteins with specific modifications.
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Affiliation(s)
- Bingrui Sui
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xinrui Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Tianyi Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Jianyu Zhen
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xiaoxuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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Endolysins of bacteriophage vB_Sal-S-S10 can naturally lyse Salmonella enteritidis. BMC Vet Res 2022; 18:410. [PMID: 36411417 PMCID: PMC9677904 DOI: 10.1186/s12917-022-03514-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The holin-endolysin lysis system plays an essential role in the phage life cycle. Endolysins are promising alternatives to antibiotics, and have been successfully used against Gram-positive bacteria. However, a few endolysins can externally lyse Gram-negative bacteria, due to the inaccessible peptidoglycan layer covered by the envelope. RESULTS This study investigated the lysis system of a new Siphoviridae bacteriophage vB_Sal-S-S10 (S10), which, that was isolated from broiler farms, was found to be able to infect 51.4% (37/72) of tested S. enteritidis strains. Phage S10 genome had a classic holin-endolysin lysis system, except that one holin and one endolysin gene were functionally annotated. The orf 22 adjacent to the lysis cassette was identified as a new endolysin gene. Antibacterial activity assays showed that holin had an intracellular penetrating activity against S. enteritidis 35; both endolysins acted on the cell envelope of S. enteritidis 35 and showed a natural extracellular antibacterial activity, leading to a ~ 1 log titer decrease in 30 min. Protein characterization of lysin1 and lysin2 revealed that the majority of the N-terminus and the C-terminus were hydrophobic amino acids or positively charged. CONCLUSION In this study, a new Salmonella phage vB_Sal-S-S10 (S10) was characterized and showed an ideal development prospect. Phage S10 has a classic holin-endolysin lysis system, carrying an overlapping holin-lysin gene and a novel lysin gene. Both endolysins coded by lysin genes could externally lyse S. enteritidis. The natural extracellular antibacterial character of endolysins would provide necessary information for the development of engineering endolysin as the antibiotic alternative against the infection with multidrug-resistant gram-negative bacteria.
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Yin Y, Wang X, Mou Z, Ren H, Zhang C, Zou L, Liu H, Liu W, Liu Z. Characterization and genome analysis of Pseudomonas aeruginosa phage vB_PaeP_Lx18 and the antibacterial activity of its lysozyme. Arch Virol 2022; 167:1805-1817. [PMID: 35716268 DOI: 10.1007/s00705-022-05472-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/30/2022] [Indexed: 11/25/2022]
Abstract
A lytic Pseudomonas aeruginosa phage, vB_PaeP_Lx18 (Lx18), was isolated from the sewage of a dairy farm. Biological characterization revealed that Lx18 was stable from 40 °C to 60 °C and over a wide range of pH values from 4 to 10. It was able to lyse 63.6% (21/33) of the P. aeruginosa strains tested and was able to reduce and disperse biofilms, with a biofilm reduction rate of 76.8%. Whole-genome sequencing showed that Lx18 is a dsDNA virus with a genome of 42,735 bp and G+C content of 62.16%. The genome contains 54 open reading frames (ORFs), 28 of which have known functions, including DNA replication and modification, transcriptional regulation, structural and packaging proteins, and host cell lysis. No virulence or tRNA genes were identified. Phylogenetic analysis showed that phage Lx18 belongs to the genus Phikmvvirus. The lysozyme of Lx18, Lys18, was cloned and expressed. The combined action of Lys18 and ethylenediaminetetraacetic acid (EDTA) had antibacterial activity against Pseudomonas aeruginosa. The study of phage Lx18 and its lysozyme will provide basic information for further research on the treatment of Pseudomonas aeruginosa infections.
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Affiliation(s)
- Yin Yin
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, 266109, China
| | - Xinwei Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, 266109, China
| | - Zehua Mou
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, 266109, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, 266109, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, 266109, China
| | - Ling Zou
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, 266109, China
| | - Huanqi Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, 266109, China.
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, 266109, China.
| | - Zongzhu Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, 266109, China
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Kim J, Chae JP, Kim GH, Kim JW, Lee NG, Moon JO, Yoon SS. Isolation, characterization, and genomic analysis of the novel T4-like bacteriophage ΦCJ20. Food Sci Biotechnol 2021; 30:735-744. [PMID: 34123469 DOI: 10.1007/s10068-021-00906-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/26/2021] [Accepted: 03/12/2021] [Indexed: 11/29/2022] Open
Abstract
Pathogenic Escherichia coli infections have been consistently reported annually. The basic characteristics and genome of the newly isolated ΦCJ20 from swine feces was analyzed. To determine basic characteristics, dotting assays and double-layer agar assays were conducted. Bacteriophage particles were analyzed via transmission electron microscopy. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis was performed to determine the sizes of major structural proteins. The complete genome of the phage was analyzed. Bacteriophage particles were identified as Myoviridae, with a head measuring 110.57 ± 1.89 nm and a contractile tail measuring 107.97 ± 3.20 nm and were found to infect E. coli. Major structural proteins of ΦCJ20 showed two well-pronounced bands of approximately 53.6 and 70.9 kDa. The genome size of ΦCJ20 was 169,884 bp, and 118 of 307 open reading frames were annotated. This study provides a baseline for the development of E. coli infection treatment strategies. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-021-00906-y.
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Affiliation(s)
- Jaegon Kim
- Department of Biological Science and Technology, Yonsei University, 1 Yeonsedae-gil, Heungeop-myeon, Wonju-si, Gangwon-do 26493 Republic of Korea
| | - Jong Pyo Chae
- Institute of Biotechnology, CJ CheilJedang, Suwon, Gyeonggi-do 16495 Republic of Korea
| | - Gyeong-Hwuii Kim
- Department of Biological Science and Technology, Yonsei University, 1 Yeonsedae-gil, Heungeop-myeon, Wonju-si, Gangwon-do 26493 Republic of Korea
| | - Jae-Won Kim
- Institute of Biotechnology, CJ CheilJedang, Suwon, Gyeonggi-do 16495 Republic of Korea
| | - Na-Gyeong Lee
- Department of Biological Science and Technology, Yonsei University, 1 Yeonsedae-gil, Heungeop-myeon, Wonju-si, Gangwon-do 26493 Republic of Korea
| | - Jun-Ok Moon
- Institute of Biotechnology, CJ CheilJedang, Suwon, Gyeonggi-do 16495 Republic of Korea
| | - Sung-Sik Yoon
- Department of Biological Science and Technology, Yonsei University, 1 Yeonsedae-gil, Heungeop-myeon, Wonju-si, Gangwon-do 26493 Republic of Korea
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Sui B, Qi X, Wang X, Ren H, Liu W, Zhang C. Characterization of a Novel Bacteriophage swi2 Harboring Two Lysins Can Naturally Lyse Escherichia coli. Front Microbiol 2021; 12:670799. [PMID: 34113331 PMCID: PMC8185280 DOI: 10.3389/fmicb.2021.670799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/22/2021] [Indexed: 11/21/2022] Open
Abstract
The novel virulent Siphoviridae bacteriophage swi2 was isolated from a pig farm, and its biological characteristics, genome architecture, and infection-related properties were characterized. Phage swi2 has a high titer of 1.01 × 1012 PFU/mL with good tolerance to UV rays and remains stable in the pH range of 6–10 and at temperatures less than 50°C. One-step growth analysis revealed that phage swi2 had a 25 min latent period with a large burst size (1,000 PFU/cell). The biological characteristics indicated that swi2 had good host infectivity and effective lytic activities. The genome of phage swi2 is composed of 47,611 bp with a G + C content of 46.50%. Eighty-nine orfs were predicted, and only 18 of them have known functions. No virulence genes or drug resistance genes were found in the genome. Genome sequence comparison of phage swi2 showed that there were a total of 10 homologous phages in the database with low similarity (less than 92.51% nucleotide identity and 66% query coverage). The predicted host lysis-related genes of phage swi2 consist of one holin, two endolysins, and Rz/Rz1 equivalents. Antibacterial activity assays showed that both endolysins could naturally reduce the host Escherichia coli 51 titers by -1 log unit both in vitro and in vivo, EDTA showed no obvious synergistic action, and holin had no lytic effects on the host cell. These results provide necessary information for the development of antibiotic alternatives for the treatment of multidrug-resistant Escherichia coli infection.
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Affiliation(s)
- Bingrui Sui
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, China
| | - Xin Qi
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, China
| | - Xiaoxue Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Shandong, China
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