Genome Sequence of the Bacteriophage CL31 and Interaction with the Host Strain Corynebacterium glutamicum ATCC 13032.

Max Hünnefeld,Julia Frunzke,Vikas Sharma,Ulrike Viets,Aël Hardy,Astrid Wirtz

doi:10.3390/v13030495

Abstract

In this study, we provide a comprehensive analysis of the genomic features of the phage CL31 and the infection dynamics with the biotechnologically relevant host strain Corynebacterium glutamicum ATCC 13032. Genome sequencing and annotation of CL31 revealed a 45-kbp genome composed of 72 open reading frames, mimicking the GC content of its host strain (54.4%). An ANI-based distance matrix showed the highest similarity of CL31 to the temperate corynephage Φ16. While the C. glutamicum ATCC 13032 wild type strain showed only mild propagation of CL31, a strain lacking the cglIR-cglIIR-cglIM restriction-modification system was efficiently infected by this phage. Interestingly, the prophage-free strain C. glutamicum MB001 featured an even accelerated amplification of CL31 compared to the ∆resmod strain suggesting a role of cryptic prophage elements in phage defense. Proteome analysis of purified phage particles and transcriptome analysis provide important insights into structural components of the phage and the response of C. glutamicum to CL31 infection. Isolation and sequencing of CL31-resistant strains revealed SNPs in genes involved in mycolic acid biosynthesis suggesting a role of this cell envelope component in phage adsorption. Altogether, these results provide an important basis for further investigation of phage-host interactions in this important biotechnological model organism.

Highlights

The Gram-positive actinobacterium Corynebacterium glutamicum represents an important biotechnological platform strain used for the production of amino acids at million tons scale, as well as for the production of organic acids, polymer precursors, and proteins [1]
This study focuses on the phage CL31, which was first identified in 1985 by Yeh and colleagues as a phage infecting C. glutamicum ATCC 15059 [19]
The present study provides a comprehensive analysis of the genomic features of phage CL31 and the infection of the host strain C. glutamicum ATCC 13032

Summary

Introduction

The Gram-positive actinobacterium Corynebacterium glutamicum represents an important biotechnological platform strain used for the production of amino acids at million tons scale, as well as for the production of organic acids, polymer precursors, and proteins [1]. This study focuses on derivatives of the model strain C. glutamicum ATCC 13032 (NCBI accession number BX927147) [2]. The genome of this strain includes three cryptic prophages, of which two (CGP1 and 2) are small and highly degenerated, while the third one (CGP3) was shown to be still inducible [3]. Besides the wild type strain C. glutamicum ATCC 13032, this study includes two derivative strains: a strain lacking the resmod system (∆resmod) and the prophage-free variant MB001 [6]. Phages can serve as a source of important molecular biology tools and fully adapted modulators, which can be harnessed for metabolic engineering and synthetic biology applications [7,8]

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