James A. Shapiro: Can Cells Bias Natural Genetic Engineering Toward Useful Evolutionary Outcomes?

A few blogs ago I asked, “Where, in fact, do ‘the good ones’ really come from?” By “good ones” I meant useful genome changes in evolution. This question stimulated some debate about whether it was possible to distinguish good changes from bad changes before they occur.

In the abstract, this may seem an overwhelmingly difficult problem. But if we think a bit about the highly organized state of the genome and non-random natural genetic engineering, biasing changes toward “good ones” becomes more conceivable.

I have already discussed purposeful, targeted changes in the immune system. The immune system illustrates how efficiently cells can target DNA restructuring by recognizing specific sequences and coupling DNA changes to transcription (copying DNA sequence into RNA).

Some evolutionists object that a somatic process like antibody synthesis provides no model for germline changes in evolution. So let’s examine natural genetic engineering events in microbial cells. We’ll look at mobile genetic elements targeted in ways that increase their evolutionary potential.

Mobile genetic elements come in many forms. Some operate purely as DNA. Others make an RNA copy and reverse transcribe it back into DNA as it inserts at a new location. Elements that move, or transpose, to multiple new locations are called “transposons” or “retrotransposons” (if they use an RNA intermediate).

Other mobile elements only insert in particular locations by a process called “site-specific” recombination. In bacterial evolution, this process is used in specialized structures called “integrons” that capture casettes containing protein coding sequences for antibiotic resistance, pathogenicity, and other functions.

What all mobile elements share are proteins that aid them to cut and splice DNA chains so that they can construct novel sequences, much as human genetic engineers do in their test tubes. These proteins have various names, such as “recombinase,” “transposase,” and “integrase.” It is the specificity of the cutting reactions involving these proteins that determines where a mobile element moves in the genome.

One fascinating case of highly biased integration is the bacterial transposon Tn7. Tn7 has two specialized proteins to target its transposition. The TnsD protein directs Tn7 to insert into a special “attTn7” site in the chromosomes of many bacterial species where it does not disrupt any host functions and so causes no deleterious effects.

Another, more interesting protein, TnsE, directs Tn7 to insert into replicating DNA molecules. The reason this is important is that transmissible plasmids replicate their DNA as they transfer from one cell to another. TnsE targeting to plasmids in transit to new cells thus enhances the spread of Tn7 and the resistances it carries to many different kinds of bacteria.

Tn7 carries its antibiotic resistance determinants in an integron. Integrons and their recombinase proteins are likewise specialized to participate in plasmid spreading through bacterial populations. Plasmids enter new cells as single-stranded DNA. We learned just in 2005 that integron site-specific recombinases are special in operating on single-stranded DNA, not double-stranded molecules like previously studied recombinases. Moreover, integron recombinase synthesis is triggered by the entrance of single-stranded DNA into a cell. So integron activity is intimately linked in more than one way to plasmid transfer.

Among eukaryotic microbes, retrotransposons show targeting that strongly biases them against disrupting the densely packed coding sequences in their genomes. The integrase proteins of retrotransposons in budding yeast Saccharomyces cerevisiaea, fission yeast Schizosaccharomyces pombe, and the slime mold Dictyostelium discoideum all bind to transcription factors (proteins involved in controlling transcription) so that they insert upstream of the functional DNA coding sequence. In this way, they can change regulation of the transcribed sequence without damaging the protein coding capacity of the cell.

The interactions involve a variety of transcription factors. In Saccharomyces, for example, the Ty1 and Ty3 retrotransposons target sites upstream of RNA polymerase III transcripts (95 to 98 percent of all inserts). The Ty1 integrase binds to TFIIIB subunit Bdp1p, and Ty3 integrase binds to the TFIIIB and TFIIIC factors.

The TRE-5A element of Dictyostileum discoideum belongs to a different class of retrotransposons from Ty3 and uses a different reverse transcription and integration mechanism. Nonetheless, its integration protein also interacts with TFIIIB and TFIIIC transcription factors and shows a similar preference for inserting upstream of RNA polymerase III start sites.

Two more Saccharomyces retrotransposons (Ty2 and Ty4) show the same target preferences as Ty1 and Ty4, but the protein affinities of their integrases are unknown. In contrast, the integrase of the Ty5 retrotransposon binds the Sir4 chromatin silencing protein and targets Ty5 insertions to epigenetically silenced regions of the genome, where they have minimal impact.

In Schizosaccharomyces pombe, theTf1 integrase binds to a transcriptional activator, Atf1p, and targets insertions upstream of RNA polymerase II transcription start sites. The Tfi insertions are not uniform for all RNA polymerase II start sites; they favor those activated by stress responses. The researchers who found this specificity hypothesized, “This targeting of stress response genes coupled with the ability of Tf1 to regulate the expression of adjacent genes suggests Tf1 may improve the survival of S. pombe when cells are exposed to environmental stress.”

In a future blog, we’ll leave the realm of microbes and discuss mobile elements in the germlines of insects and vertebrates, where the story is much the same. The DNA mobility machinery interacts with transcription factors or other proteins to target many mobile elements to sites where they do no damage.

For now we have two answers and a mystery:

  1. Where do the good ones come from? From natural genetic engineering.
  2. Can natural genetic engineering be biased toward positive results? Definitely.
  3. How far can positive biasing extend toward producing complex novelties? We don’t have an answer to that one yet. We need more research (the subject of yet another blog).

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