Assay for determing uptake specificity

I was thinking about an unresolved question about competence, is it for food or sex? Specifically I was wondering if uptake specificity changes depending on the the conditions that cause competence to be induced. Uptake specificity is the fact that our bacteria will take up DNA with this little USS motif many times more readily than DNA without it, and this motif is found littered all other the HI genome. If uptake was used for both sex and food sometimes, maybe under conditions of purine starvation cells would be less picky about specificity and willing to grab any random strands, rather than at times of great sex opportunities such as high density late log cultures where their goal would rely more on the USS(maybe especially if they were growing alongside anouther strain/bacteria?)

 

A simple test would be growing the cells through different conditions and transforming with 2 different antibiotic DNA markers, one with a USS site and one without, and compare the transformation frequencies. If specificty changes then the ratio of USS/non USS DNA transformation frequencies should also change.

 

A complication could be that if cells were doing something special when they were starved, losing their specificity requirements, they could also do something like digesting DNA more rapidly before it has a chance to translocated and recombine, muddying up any clear result on changing ratios. Is DNA digestion itself influenced by USS sites?(hmm maybe I should test if my ComM- DprA- mutants, strains lacking proteins that bind onto taken up DNA and protect it from degradation, have different phenotypes compared to WT when given USS and non-USS DNA)

 

I wonder if the labs microarray data shows any difference for competence regulon induction when bact is under different competence conditions.

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2 Comments (+add yours?)

  1. Rosie Redfield
    Mar 05, 2011 @ 07:08:28

    Nice idea! And easy to test! Do we have markers you could use – one with a very close USS and one without? Ideally also the same markers with the USS reversed.

    Reply

    • dnogas
      Mar 05, 2011 @ 10:22:25

      I’m not sure, we definitely have markers with USS and I think we have ones without, but really they should be for the same antibiotic cassette and as you said very close. Maybe a randomized sequence for one instead of USS? If we don’t I can’t imagine it being terribly difficult to make/obtain. I’ll check(ask) on Monday

      Sunita was telling me about how vibrio cholerae has two homologs of sxy/tfox, one with an uncharacterized function. Do you have any speculation what it could be doing?

      I found something you might be interested in, a paper by a NASA scientist claiming to have found extraterrestrial microbial life in a meteorite. Here’s the link
      http://journalofcosmology.com/Life100.html

      “Official Statement from Dr. Rudy Schild, Center for Astrophysics, Harvard-Smithsonian, Editor-in-Chief, Journal of Cosmology. We believe Dr. Hoover’s careful analysis provides definitive evidence of ancient microbial life on astral bodies some of which may predate the origin of Earth and this solar system.
      Dr. Richard Hoover is a highly respected scientist and astrobiologist with a prestigious record of accomplishment at NASA. Given the controversial nature of his discovery, we have invited 100 experts and have issued a general invitation to over 5000 scientists from the scientific community to review the paper and to offer their critical analysis. Our intention is to publish the commentaries, both pro and con, alongside Dr. Hoover’s paper. In this way, the paper will have received a thorough vetting, and all points of view can be presented. No other paper in the history of science has undergone such a thorough analysis, and no other scientific journal in the history of science has made such a profoundly important paper available to the scientific community, for comment, before it is published. We believe the best way to advance science, is to promote debate and discussion.”

      I can’t weigh in on the science, but it looks like they are going about it the right way.

      Reply

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