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Proteomic response to PhiX174 infection

ABSTRACT: Elucidating host-bacteriophage dynamics is an important approach to elucidating bacterial survival functions and responses to infection. The model bacteriophage φX174 endemically found amongst the human intestinal microbiota and has a long history of use in bacteriophage based research, however the common laboratory host’s response to infection lacks detailed investigation. In this study we have measured host Escherichia coli C122 proteomic and transcriptomic response to φX174 infection to fill this knowledge gap. We identify differentially expressed genes and proteins during phage induced lysis. We also use mass spectrometry to identify and quantify all φX174 proteins and over 1700 E. coli proteins enabling us to comprehensively map host pathways involved in φX174 infection. Most notably, in our dual omics investigation we observe significant host responses pertaining to membrane remodeling, cellular chaperone activity, and lipoprotein processing. We also highlight host small heat-shock proteins IbpA and IbpB as having fold-change inductions comparable to that of the phage proteins. Together, this study provides foundational and the first proteomic and transcriptomic data characterizing host response to Microviridae infection.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli

SUBMITTER: Bradley Wright

LAB HEAD: Mark P Molloy

PROVIDER: PXD021681 | Pride | 2021-04-08

REPOSITORIES: Pride

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Project description:Cyanobacteria are highly abundant in the oceans where they are constantly exposed to lytic viruses. Some viruses are restricted to a narrow host range while others infect a broad range of hosts. It is currently unknown whether broad-host range phages employ the same infection program, or regulate their program in a host-specific manner to accommodate for the different genetic makeup and defense systems of each host. Here we used a combination of microarray and RNA-seq analyses to investigate the interaction of three phylogentically distinct Synechococcus strains, WH7803, WH8102, and WH8109, with the broad-host range T4-like myovirus, Syn9, during infection. Strikingly, we found that the phage led a nearly identical expression program in the three hosts despite considerable differences in host gene content. On the other hand, host responses to infection involved mainly host-specific genes, suggesting variable attempts at defense against infection. A large number of responsive host genes were located in hypervariable genomic islands, substantiating genomic islands as a major axis of phage-bacteria interactions in cyanobacteria. Furthermore, transcriptome analyses and experimental determination of the complete phage promoter map revealed three temporally regulated modules and not two as previously thought for cyanophages. In contrast to T4, an extensive, previously unknown regulatory motif drives expression of early genes and host-like promoters drive middle-gene expression. These promoters are highly conserved among cyanophages and host-like middle promoters extend to other T4-like phages, indicating that the well-known mode of regulation in T4 is not the rule among the broad family of T4-like phages. We investigated the infection process and transcriptional program of the P-TIM40 cyanophage during infection of a Prochlorococcus NATL2A host. The results are discussed in conjunction with results obtained from the infection process for the Syn9 cyanophage in three different Synechococcus hosts: WH7803 (Dufresne et al. 2008), WH8102 (Palenik et al. 2003) and WH8109 (sequenced as part of this study).

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Proteomic response to PhiX174 infection

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