Parallel Genomics Uncover Novel Enterococcal-Bacteriophage Interactions

• Published in: mBio Vol. 11; no. 2
• Main Authors: Chatterjee, Anushila, Willett, Julia L E, Nguyen, Uyen Thy, Monogue, Brendan, Palmer, Kelli L, Dunny, Gary M, Duerkop, Breck A
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 03-03-2020
• Subjects: Alleles; antibiotic resistance; bacteriophages; Bacteriophages - physiology; Biological Evolution; DNA Mismatch Repair; DNA Replication; DNA Transposable Elements; Enterococcus; Enterococcus - physiology; Enterococcus - virology; Gene Expression Profiling; Gene Expression Regulation; Genomics - methods; Microbial Interactions; Molecular Biology and Physiology; Mutation; RNA-Seq; Tn-Seq; transposons; Enterococcus; RNA-Seq; antibiotic resistance; Tn-Seq; bacteriophages; transposons; phage-bacterium interactions
• ISSN: 2161-2129; 2150-7511
• DOI: 10.1128/mBio.03120-19

Bacteriophages (phages) have been proposed as alternative therapeutics for the treatment of multidrug-resistant bacterial infections. However, there are major gaps in our understanding of the molecular events in bacterial cells that control how bacteria respond to phage predation. Using the model organism
, we used two distinct genomic approaches, namely, transposon library screening and RNA sequencing, to investigate the interaction of
with a virulent phage. We discovered that a transcription factor encoding a LytR family response regulator controls the expression of enterococcal polysaccharide antigen (
) genes that are involved in phage infection and bacterial fitness. In addition, we discovered that DNA mismatch repair mutants rapidly evolve phage adsorption deficiencies, underpinning a molecular basis for
mutation during phage infection. Transcriptomic profiling of phage-infected
revealed broad transcriptional changes influencing viral replication and progeny burst size. We also demonstrate that phage infection alters the expression of bacterial genes associated with intra- and interbacterial interactions, including genes involved in quorum sensing and polymicrobial competition. Together, our results suggest that phage predation has the potential to influence complex microbial behavior and may dictate how bacteria respond to external environmental stimuli. These responses could have collateral effects (positive or negative) on microbial communities, such as the host microbiota, during phage therapy.
We lack fundamental understanding of how phage infection influences bacterial gene expression and, consequently, how bacterial responses to phage infection affect the assembly of polymicrobial communities. Using parallel genomic approaches, we have discovered novel transcriptional regulators and metabolic genes that influence phage infection. The integration of whole-genome transcriptomic profiling during phage infection has revealed the differential regulation of genes important for group behaviors and polymicrobial interactions. Our work suggests that therapeutic phages could more broadly influence bacterial community composition outside their intended host targets.