Discovery, structural characteristics and evolutionary analyses of functional domains in Acinetobacter baumannii phage tail fiber/spike proteins
Abstract Background The global rise in multidrug-resistant Acinetobacter baumannii infections poses a significant healthcare challenge. Bacteriophage offer a promising alternative to antibiotics for treating A. baumannii infections. Phage tail fiber and spike proteins are essential for host recognit...
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2025-02-01
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| Online Access: | https://doi.org/10.1186/s12866-025-03790-2 |
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| author | Shenshen Liu Tao Lei Yujing Tan Xiaoyi Huang Wenxin Zhao Huanhuan Zou Jianhui Su Ji Zeng Haiyan Zeng |
| author_facet | Shenshen Liu Tao Lei Yujing Tan Xiaoyi Huang Wenxin Zhao Huanhuan Zou Jianhui Su Ji Zeng Haiyan Zeng |
| author_sort | Shenshen Liu |
| collection | DOAJ |
| description | Abstract Background The global rise in multidrug-resistant Acinetobacter baumannii infections poses a significant healthcare challenge. Bacteriophage offer a promising alternative to antibiotics for treating A. baumannii infections. Phage tail fiber and spike proteins are essential for host recognition, with some exhibiting depolymerase activity that aids in degrading the bacterial cell wall, facilitating infection. Detailed studies of the functional domains responsible for depolymerase activity and receptor-binding in phage tail fiber/spike proteins are a crucial step toward developing effective phage treatments. Results A total of 32 functional domains were identified across 313 tail fiber and spike proteins from 204 publicly available Acinetobacter baumannii phages using InterPro and AlphaFold3. Domains associated with depolymerase function were Pectin lyase-like domain (PLD), phage_tailspike_middle domain (PTMD), Transglycosidases domain (TGD), and SGNH hydrolase domain (SHD). These domains were primarily found in phages from the Autographiviridae family, specifically within the Friunavirus genus. The predominant PLD domain displayed high variability, with its sequence conserved only in a 25-amino-acid region among two closely related fiber/spike protein lineages. All enzymatic domains exhibit high sequence diversity yet retain structural stability, which is essential for enzymatic function. As for receptor-binding domains, four types of pyocin_knob domains (PKD) were initially identified, characterized by unique β-sheet and α-helix configurations. Each type of PKD exhibited distinct potential receptor-binding sites, primarily located within the α-helix region, and was closely associated with the Obolenskvirus genus, as well as the Autographiviridae and Straboviridae families. The G3DSA:2.60.40.3940 domain, exhibiting minor structural variations, was predominantly found in phages of the Obolenskvirus genus. Additionally, a novel Obo-β-sandwich structure, identified as a potential receptor-binding domain, was discovered within Obolenskvirus genus cluster. The structural diversity of these receptor-binding domains accounts for their interactions with various receptors. Conclusions This research deepens the understanding of the relationship between A. baumannii phage genera and the functional domains within their tail fiber/spike proteins, emphasizing the compatibility between structural characteristics and functional roles. The data obtained could serve as a reference for the targeted modification of phages or their tail fiber/spike proteins, enhancing their therapeutic applications. |
| format | Article |
| id | doaj-art-44484dff469b475fa56cbd33126645ad |
| institution | OA Journals |
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| publishDate | 2025-02-01 |
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| series | BMC Microbiology |
| spelling | doaj-art-44484dff469b475fa56cbd33126645ad2025-08-20T02:13:19ZengBMCBMC Microbiology1471-21802025-02-0125111710.1186/s12866-025-03790-2Discovery, structural characteristics and evolutionary analyses of functional domains in Acinetobacter baumannii phage tail fiber/spike proteinsShenshen Liu0Tao Lei1Yujing Tan2Xiaoyi Huang3Wenxin Zhao4Huanhuan Zou5Jianhui Su6Ji Zeng7Haiyan Zeng8School of Biomedical and Pharmaceutical Sciences, Guangdong University of TechnologySchool of Public Health, Xiangnan UniversitySchool of Biomedical and Pharmaceutical Sciences, Guangdong University of TechnologySchool of Biomedical and Pharmaceutical Sciences, Guangdong University of TechnologySchool of Biomedical and Pharmaceutical Sciences, Guangdong University of TechnologySchool of Biomedical and Pharmaceutical Sciences, Guangdong University of TechnologySchool of Biomedical and Pharmaceutical Sciences, Guangdong University of TechnologySchool of Biomedical and Pharmaceutical Sciences, Guangdong University of TechnologySchool of Biomedical and Pharmaceutical Sciences, Guangdong University of TechnologyAbstract Background The global rise in multidrug-resistant Acinetobacter baumannii infections poses a significant healthcare challenge. Bacteriophage offer a promising alternative to antibiotics for treating A. baumannii infections. Phage tail fiber and spike proteins are essential for host recognition, with some exhibiting depolymerase activity that aids in degrading the bacterial cell wall, facilitating infection. Detailed studies of the functional domains responsible for depolymerase activity and receptor-binding in phage tail fiber/spike proteins are a crucial step toward developing effective phage treatments. Results A total of 32 functional domains were identified across 313 tail fiber and spike proteins from 204 publicly available Acinetobacter baumannii phages using InterPro and AlphaFold3. Domains associated with depolymerase function were Pectin lyase-like domain (PLD), phage_tailspike_middle domain (PTMD), Transglycosidases domain (TGD), and SGNH hydrolase domain (SHD). These domains were primarily found in phages from the Autographiviridae family, specifically within the Friunavirus genus. The predominant PLD domain displayed high variability, with its sequence conserved only in a 25-amino-acid region among two closely related fiber/spike protein lineages. All enzymatic domains exhibit high sequence diversity yet retain structural stability, which is essential for enzymatic function. As for receptor-binding domains, four types of pyocin_knob domains (PKD) were initially identified, characterized by unique β-sheet and α-helix configurations. Each type of PKD exhibited distinct potential receptor-binding sites, primarily located within the α-helix region, and was closely associated with the Obolenskvirus genus, as well as the Autographiviridae and Straboviridae families. The G3DSA:2.60.40.3940 domain, exhibiting minor structural variations, was predominantly found in phages of the Obolenskvirus genus. Additionally, a novel Obo-β-sandwich structure, identified as a potential receptor-binding domain, was discovered within Obolenskvirus genus cluster. The structural diversity of these receptor-binding domains accounts for their interactions with various receptors. Conclusions This research deepens the understanding of the relationship between A. baumannii phage genera and the functional domains within their tail fiber/spike proteins, emphasizing the compatibility between structural characteristics and functional roles. The data obtained could serve as a reference for the targeted modification of phages or their tail fiber/spike proteins, enhancing their therapeutic applications.https://doi.org/10.1186/s12866-025-03790-2Acinetobacter baumanniiPhageTail fiberTail spikeDepolymerasePectin lyase-like |
| spellingShingle | Shenshen Liu Tao Lei Yujing Tan Xiaoyi Huang Wenxin Zhao Huanhuan Zou Jianhui Su Ji Zeng Haiyan Zeng Discovery, structural characteristics and evolutionary analyses of functional domains in Acinetobacter baumannii phage tail fiber/spike proteins BMC Microbiology Acinetobacter baumannii Phage Tail fiber Tail spike Depolymerase Pectin lyase-like |
| title | Discovery, structural characteristics and evolutionary analyses of functional domains in Acinetobacter baumannii phage tail fiber/spike proteins |
| title_full | Discovery, structural characteristics and evolutionary analyses of functional domains in Acinetobacter baumannii phage tail fiber/spike proteins |
| title_fullStr | Discovery, structural characteristics and evolutionary analyses of functional domains in Acinetobacter baumannii phage tail fiber/spike proteins |
| title_full_unstemmed | Discovery, structural characteristics and evolutionary analyses of functional domains in Acinetobacter baumannii phage tail fiber/spike proteins |
| title_short | Discovery, structural characteristics and evolutionary analyses of functional domains in Acinetobacter baumannii phage tail fiber/spike proteins |
| title_sort | discovery structural characteristics and evolutionary analyses of functional domains in acinetobacter baumannii phage tail fiber spike proteins |
| topic | Acinetobacter baumannii Phage Tail fiber Tail spike Depolymerase Pectin lyase-like |
| url | https://doi.org/10.1186/s12866-025-03790-2 |
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