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Letting Escherichia Coli Teach Me about Genome Engineering

By Shapiro, James A. | Genetics, December 2009 | Go to article overview

Letting Escherichia Coli Teach Me about Genome Engineering

Shapiro, James A., Genetics


A career of following unplanned observations has serendipitously led to a deep appreciation of the capacity that bacterial cells have for restructuring their genomes in a biologically responsive manner. Routine characterization of spontaneous mutations in the gal operon guided the discovery that bacteria transpose DNA segments into new genome sites. A failed project to fuse λ sequences to a lacZ reporter ultimately made it possible to demonstrate how readily Escherichia coli generated rearrangements necessary for in vivo cloning of chromosomal fragments into phage genomes. Thinking about the molecular mechanism of IS1 and phage Mu transposition unexpectedly clarified how transposable elements mediate large-scale rearrangements of the bacterial genome. Following up on lab lore about long delays needed to obtain Mu-mediated lacZ protein fusions revealed a striking connection between physiological stress and activation of DNA rearrangement functions. Examining the fate of Mudlac DNA in sectored colonies showed that these same functions are subject to developmental control, like controlling elements in maize. All these experiences confirmed Barbara McClintock's view that cells frequently respond to stimuli by restructuring their genomes and provided novel insights into the natural genetic engineering processes involved in evolution.

THIS article is the reminiscence of a bacterial geneticist studying the processes of mutation and DNA rearrangements. I want toemphasizehowmy experience was full of surprises and unplanned discoveries that took me ever deeper into the mechanisms and regulation of natural genetic engineering by Escherichia coli cells.

For the benefit of youngermolecular geneticists, there are at least three points to be made. First, you can find something truly novel only when you do not know exactly what you are looking for. If the experiment comes out just as you planned, you have not really learned anything you did not already know or suspect.

Second, routine characterization of your experimental material is critical because it will tell you where your understanding is incomplete-but only when the characterizations do not come out as you expect. In other words, it can be a good thing if an experimental result does not fit your expectations.

Third, science will inevitably lead us in the future to think about the subjects that we are studying in ways that we cannot currently predict. When I began my research, we thought we understood the basics of genome expression and mutation because we knew about DNA, RNA polymerase, and the triplet code for amino acids. The worlds of transcriptional regulation beyond simple repressor-operator models, signal transduction, chromatin formatting, transcript processing, protein modifications, and regulatory RNAs were all in the future. In my particular field, the molecular basis of genetic change, discoveries about mobile genetic elements, reverse transcription, programmed genome rearrangements, and other aspects of what I call "natural genetic engineering" were yet to be made.

The following account relates my own experimental journey into a new way of thinking about the molecular and cellular basis of genetic change. After detailing the journey, I will explain why and how I believe that this newmode of thought is likely to influence our ideas about evolution, the most basic of biological subjects.

I would be remiss if I did not acknowledge the powerful influence of Barbara McClintock on my thinking. After meeting her in 1976, I realized that she possessed an unmatched depth of experience about all aspects of biology, from natural history to the current status of molecular genetics. We engaged in a 16-year dialogue up to her death in 1992 (Shapiro 1992c). Only after many years did I finally come to appreciate the wisdom of her insistence that the ability of cells to sense and respond to "genome shock" was just as important in determining what happens to their genomes as are the biochemical mechanisms that they use in repairing and restructuring DNA molecules (McClintock 1984).

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Letting Escherichia Coli Teach Me about Genome Engineering


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