Student Theses and Dissertations

Sri Ram

Date of Award

2008

Document Type

Thesis

Degree Name

Doctor of Philosophy (PhD)

RU Laboratory

Leibler Laboratory

Abstract

The genomic mutation rate of wild-type Escherichia coli is 3 􀵈 10􀬿􀬷 per generation, a value that is shared by many DNA-based microbes and viruses. A majority of clinical isolates of E. coli also have a mutation rate that is close to the wild-type value. These findings raise the possibility that the observed mutation rate is constrained by some universal evolutionary forces. In many laboratory settings, however, strains with high mutation rate (mutator strains) have been shown to outcompete otherwise isogenic wildtype cells. These results have been explained by positing that mutators offer a short-term benefit in the form of increased probability of generation of beneficial mutations. Yet, given that a majority of non-neutral mutations are deleterious, there is a long-term cost associated with high mutation rates. This thesis explores the idea that one form of the long-term cost involves the fixation of deleterious mutations when rare beneficial mutations sweep through large asexual populations. Our simulations suggest that this is indeed the case at high mutation rates (~200-fold higher than the wild-type mutation rate), but the deleterious effects are expected to be quite small (~1%). Detection of such effects requires the measurement of mean fitness of large populations with high precision and high frequency. Towards this end, we constructed an apparatus that combines bioluminescence based growth rate measurements with techniques for long-term microbial culture for recording of growth rate dynamics of luminescent Escherichia coli. After a comparison of several culture media, we found that the reproducibility of growth rate measurements is the best in LB. In LB, growth rates can be measured every 65 min (~3.5 generations) and with an overall precision of ~2.7%. Instrumental errors are estimated to contribute only 0.3% to the overall precision. We show that the apparatus can be used to detect small changes in growth rates by measuring the sensitivity of growth rate to temperature changes as small as 0.3 °C. We also show that precision can be maintained in long-term measurements of growth rates. We are now poised to evaluate the deleterious effects of high mutation rates in our apparatus.

Comments

A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for The degree of Doctor of Philosophy

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