Background: The evolutionary arms race between bacterial viruses (phages) and bacteria in many ways shape their interactions. To avoid predation by phages, bacteria have evolved defense systems such as CRISPR-Cas and restriction modifications (RM) to protect themselves against invading nucleic acids. However, phages have evolved elaborate counter-defense mechanisms in order to circumvent these systems, including DNA modifications. However, very little is currently known about the biological consequences of these DNA modifications, which of systems they can bypass etc.

Aim and Experimental Approach: To assess the biological consequences of DNA modifications, we would like to compare different parameters important to the phage life cycle, such as burst size and host range between a wild-type phage, and a modification deficient mutant. To do this, we will employ both cutting-edge techniques based on 3rd

generation sequencing to detect DNA modifications and CRISPR-Cas9-mediated site-specific mutagenesisto generate phage mutants, before finally performing biological assays to determine the effects on biological parameters of the phages.

Importance: With the resurgence of phages as potential candidates for treating diseases in

humans and as alternatives to pesticides in agriculture, it will be imperative to understand

the interactions between phages and bacteria in detail, so that we can employ them in a more

informed manner.

Techniques: DNA work, phage and bacterial genetics, 2nd and 3rd generation sequencing,

molecular microbiology, phage characterization, CRISPR-Cas9 genome editing, Gibson assembly.

Supervisors: Prof. Lars Hestbjerg Hansen (lhha@plen.ku.dk), Assistant Prof. Witold Kot

(wk@plen.ku.dk)

Reading:

1.Hutinet G, Kot W, Cui L, at al. (2019): 7-Deazaguanine modifications protect phage DNA from host restriction systems. Nat Commun. 10(1):1-12

2.Kot W, Olsen N, Nielsen TK, at al. (2020): Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs. Nucleic Acids Res. 48(18):10383-10396. 

3.Gao L, Altae-Tran H, Böhning F,  at al. (2020): Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science. 369, 1077-1084.