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Article

Structure and Topology Prediction of Phage Adhesion Devices Using AlphaFold2: The Case of Two Oenococcus oeni Phages

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Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, CEDEX 09, 13288 Marseille, France
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Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, CEDEX 09, 13288 Marseille, France
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Author to whom correspondence should be addressed.
Academic Editor: James Garnett
Microorganisms 2021, 9(10), 2151; https://doi.org/10.3390/microorganisms9102151
Received: 16 September 2021 / Revised: 5 October 2021 / Accepted: 11 October 2021 / Published: 14 October 2021
(This article belongs to the Special Issue Siphophages Infecting Food Processing Bacteria)
Lactic acid bacteria (LAB) are important microorganisms in food fermentation. In the food industry, bacteriophages (phages or bacterial viruses) may cause the disruption of LAB-dependent processes with product inconsistencies and economic losses. LAB phages use diverse adhesion devices to infect their host, yet the overall picture of host-binding mechanisms remains incomplete. Here, we aimed to determine the structure and topology of the adhesion devices of two lytic siphophages, OE33PA and Vinitor162, infecting the wine bacteria Oenococcus oeni. These phages possess adhesion devices with a distinct composition and morphology and likely use different infection mechanisms. We primarily used AlphaFold2, an algorithm that can predict protein structure with unprecedented accuracy, to obtain a 3D model of the adhesion devices’ components. Using our prior knowledge of the architecture of the LAB phage host-binding machineries, we also reconstituted the topology of OE33PA and Vinitor162 adhesion devices. While OE33PA exhibits original structures in the assembly of its bulky adhesion device, Vinitor162 harbors several carbohydrate-binding modules throughout its long and extended adhesion device. Overall, these results highlight the ability of AlphaFold2 to predict protein structures and illustrate its great potential in the study of phage structures and host-binding mechanisms. View Full-Text
Keywords: AlphaFold2; Oenococcus oeni; Siphoviridae; bacteriophages; protein structure; protein modelling AlphaFold2; Oenococcus oeni; Siphoviridae; bacteriophages; protein structure; protein modelling
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MDPI and ACS Style

Goulet, A.; Cambillau, C. Structure and Topology Prediction of Phage Adhesion Devices Using AlphaFold2: The Case of Two Oenococcus oeni Phages. Microorganisms 2021, 9, 2151. https://doi.org/10.3390/microorganisms9102151

AMA Style

Goulet A, Cambillau C. Structure and Topology Prediction of Phage Adhesion Devices Using AlphaFold2: The Case of Two Oenococcus oeni Phages. Microorganisms. 2021; 9(10):2151. https://doi.org/10.3390/microorganisms9102151

Chicago/Turabian Style

Goulet, Adeline, and Christian Cambillau. 2021. "Structure and Topology Prediction of Phage Adhesion Devices Using AlphaFold2: The Case of Two Oenococcus oeni Phages" Microorganisms 9, no. 10: 2151. https://doi.org/10.3390/microorganisms9102151

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