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Multidisciplinary Methods for Screening Toxic Proteins from Phages and Their Potential Molecular Targets

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Phage Engineering and Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2793))

Abstract

This chapter presents a comprehensive methodology for the identification, characterization, and functional analyses of potentially toxic hypothetical proteins of unknown function (toxHPUFs) in phages. The methods begin with in vivo toxicity verification of toxHPUFs in bacterial hosts, utilizing conventional drop tests and following growth curves. Computational methods for structural and functional predictions of toxHPUFs are outlined, incorporating the use of tools such as Phyre2, HHpred, and AlphaFold2. To ascertain potential targets, a comparative genomic approach is described using bioinformatics toolkits for sequence alignment and functional annotation. Moreover, steps are provided to predict protein–protein interactions and visualizing these using PyMOL. The culmination of these methods equips researchers with an effective pipeline to identify and analyze toxHPUFs and their potential targets, laying the groundwork for future experimental confirmations.

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Acknowledgement

The authors would like to thank professors Abram Aertsen and Rob Lavigne from KU Leuven, Belgium, for the time-lapse microscopy as shown in Fig. 2. This research was funded by the Academy of Finland (grant number 288701) and by Jane and Aatos Erkko Foundation to M.S. (Decision 2016). X.W. received a personal grant from the Jane and Aatos Erkko Foundation (grant number 200050).

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Authors and Affiliations

  1. Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland

    Xing Wan & Mikael Skurnik

  2. Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland

    Xing Wan

Authors
  1. Xing Wan
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  2. Mikael Skurnik
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Corresponding author

Correspondence to Xing Wan .

Editor information

Editors and Affiliations

  1. Cellular Signaling Laboratory International Research, Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China

    Huan Peng

  2. College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China

    Jianfeng Liu

  3. Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA

    Irene A. Chen

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© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Wan, X., Skurnik, M. (2024). Multidisciplinary Methods for Screening Toxic Proteins from Phages and Their Potential Molecular Targets. In: Peng, H., Liu, J., Chen, I.A. (eds) Phage Engineering and Analysis. Methods in Molecular Biology, vol 2793. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3798-2_15

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  • DOI: https://doi.org/10.1007/978-1-0716-3798-2_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3797-5

  • Online ISBN: 978-1-0716-3798-2

  • eBook Packages: Springer Protocols

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