Proteomics Analysis of a Phage‐Bacterium Interaction Reveals Both Hijacking and Suppression of Host Metabolic Processes

Abstract

The potential for phages to serve as both therapeutic agents and in broad applications ranging from food bio‐preservation, wastewater treatment, and disease diagnosis, has led to renewed interest in the study of phage‐bacteria interactions. Phages attack their hosts by hijacking its molecular machinery and using it for its own replication, subsequently shutting off the host macromolecular synthesis. Not much is known about how this mechanism occurs, however, especially at the translational level. In this study, label‐free tandem mass spectrometry based quantitative proteomics and qPCR assay of phage Ochi17‐infected Mycobacterium smegmatis suggested that shutoff of the host macromolecular synthesis also involves suppression of its resistance mechanisms. A total of 2,188 proteins were identified in the analysis, with 299 significantly up‐regulated proteins and 135 down‐regulated proteins. The results indicated phage Ochi17 DNA integration into the host’s genome, and a consequent hijack and suppression of the host’s energy metabolic processes and antibiotic resistance mechanisms as seen in the significant enrichment of proteins involved in homologous recombination, transcriptional factors, ribosomal proteins, amino acid (arginine, proline, and histidine) metabolism, and oxidoreductase activities. Majority of the proteins were found to be part of the host’s energy metabolic processes. With these results, we propose that phages counter their host defensive response by suppressing these responses in addition to evolving new attack strategies. We also reported the expression of 59 phage proteins (54%) expressed during the interaction. This study provides the first global proteome investigation and characterization of any phage‐infected bacteria with respect to the host bacterium response. These Results would serve as a rich source for further molecular studies of phage‐bacteria interactions in elucidating contributions of individual proteins, and in engineering phages that can overcome various defense strategies employed by host bacteria.Support or Funding InformationThis work was supported by the Biotechnology Innovation and Regulatory Science (BIRS) Center, Purdue University.