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Why do bacteria take up only one DNA strand?

People who disagree with us about the nutritional importance of DNA for bacteria very often cite the degradation of one DNA strand at the cell surface. Like almost all (maybe all) other competent bacteria, H. influenzae initially binds double-stranded DNA, but brings only one of the two strands across the inner membrane into the cytoplasm. The other strand is degraded to nucleotides in the periplasm. In Gram-positive bacteria the degradation also occurs at the surface, before the remaining DNA strand is transported into the cytoplasm, and the released nucleotides are found in the culture medium.

(Hmm, aside, I must go back and check the old literature, to see if it's the nucleotides or only the phosphates that are found in the medium. This is significant because we know that the phosphate must be removed from each nucleotide before it can be taken up. No, they used tritiated thymidine, so the label was in the bases.)

If bacteria were taking up DNA for its nucleotides, they argue, the bacteria would certainly not discard all of one strand, thus getting only half the ncleotides they would get if they took up both strands. Therefore DNA must be taken up for its genetic information. My usual response to this (usually ignored) is to point out that the bacteria have efficient uptake systems for nucleotides (actually nucleosides = nucleotides with their phosphates removed), and any nucleotides produced at the cell surface are likely to be taken up by these systems rather than 'discarded'. The same people happily accept that bacteria secrete nucleases to obtain nucleotides from environmental DNA, a process much more strongly limited by diffusion, so they should find this convincing.

But today I've thought of another response, which is to bounce the 'discard = waste' argument right back. If bacteria are taking DNA up for its genetic information, then surely it is wasteful to take up only one strand. Although only a single DNA strand usually participates in a single recombination event, many strands are degraded by cytoplasmic nucleases before they can recombine at all. Others recombine, but the new genetic information they contain is lost through mismatch correction. Surely it would be better to take up both strands and give each a chance to recombine, effectively doubling the probability that the cell will get the new genetic information.

2 comments:

  1. Two additional thoughts on why bacteria might not want to take up intact dsDNA (not sure what the likelihood is of two complementary ssDNA sequences rehybridizing inside the cell if taken in separately, but at the same site):

    1. ssDNA avoids most restriction endonucleases. This would help facilitate recombination with interspecific bacterial DNA, if that's the sort of thing the bacterium would "want" to do.

    2. better exclusion of parasites (mostly plasmids, since I can't imagine a whole, unencapsidated phage genome could get in by naturally competent cells). Taking up ssDNA means the plasmid is less likely to become a functional dsDNA permanent resident than if the bacterium took it in already double-stranded. There are some very petite plasmids out there, including linear ones, so their 'genome' sizes might be capable of being taken up by competent bacteria.

    But these ideas might already be widely expressed the literature... this is not my area of expertise.

    ReplyDelete
  2. Restriction systems can differ even between close relatives (same species). The ssDNA effect probably isn't important for plasmids (the need-a-free-end effect takes care of them) but it certainly does limit phage 'transfection.

    ReplyDelete

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