We’ve been talking about phage recombination recently. Rosies posted a series of posts on her blog about phage recombination, and I’ve been doing some reading on the subject to familiarize myself. Fortuanesly a new this week in microbiology(twim episode 6) covered the topic of bacteriophages, albeit mostly from a clinical perspective

Phage recombination increases 100 fold in competent cells. This is from the 1991 sxy-1 paper. I wasn’t sure if this meant that phage recombination increases 100 fold after 100 minutes in MIV, or if phage recombination increases 100 fold in cells that are actually competent. I did a quick reread and it’s the former. If phage recombination has more to do with the cell state under competence, as the lower levels of phage recombination in competence gene knockouts indicate, rather than starvation conditions, the congression of phage recombination should be roughly identical to the the congression of chromosomal recombination. Phage recombination in actually competent cells should be higher than 100 fold in all MIV cells, and maybe could be a good standard to compare chromosomal recombination hotspots to(we don’t know much yet about how much recombination is really going on)

Testing this seems like it should be easy, but it might be prohibitively difficult. Isolating only competent cells is simple, just using the old antibiotic marker method, but spotting plaques requires lawns and using an antibitoic marker prohibits lawns. A lot more cells would have to be plated, the vast majority of which would be dead. adding the antibiotic and regrowing the cells to a good density would get rid of that problem, but would defeat the purpose of testing phage recombination in competent cells.

A bit of a theoretical thought, a bit related to the work i did in Ohio on selfish genetic elements. Haemophilus preferentially takes up DNA with an uptake signal sequence, AAGTGCGGT.  Could a phage exploit this pathway into the cell, could a virus in this system simply be a DNA sequence ? I talked to Rosie about it today. An undergrad had done a project a while back, A HI phage has multiple USS(although at a slightly lower density than the HI genome), to see if it could get into the bacteria that way, and it can. But I was thinking more  of a virus that only existed as DNA, relied entierly on competence for entry and didn’t code for a capsid, rather than a possible alternative entry way for a traditional phage. If it existed it could also be a tool for the lab, as it would be a phage that only infected competent cells

However when DNA is taken up by competent cells 1 strand is always degraded. This means that a phage that enters this way can only be lytic if anouther complementary strand is taken up at the same time and the two bind together, a rare sequence of events. A lysogenic phage can enter and recombine into the chromosome like any other type of DNA with homology. Maybe this could be an explanation to why one strand is degraded immediately, to protect the cell from phages exploiting this entryway(Do other naturally competent bacteria with also degraded one strand? Does having uptake specificity matter?)

Anouther thing I was interested in is bald spots. It’s a phenomenum we sometimes see when plating high densities on agar plates, large waxy areas where colonies don’t grow with odd shaped boundaries. I can’t find anything on this at all, nothing in published journals or even a simple google search. They are notoriously inconsistent, they can’t be replicated by just plating high densities. Rosie believes it has something to do with the high densities, as cells lyse they release toxins that cause neighboring cells to lyse creating a chain reaction resulting in these bald spots. I’d like to know if the bald spots are infectious/communicable, if scrapings from a baldspot is added to a  culture/plate would it spread. It’s not at all related to our research/funding however, so I need to look for a potential masters project elsewhere.

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