In the Light of Evolution Volume III: Two Centuries of Darwin (2009) / Chapter Skim
Currently Skimming:
8 In the Light of Directed Evolution: Pathways of Adaptive Protein Evolution--Jesse D. Bloom and Frances H. Arnold
8 In the Light of Directed Evolution: Pathways of Adaptive Protein Evolution--Jesse D. Bloom and Frances H. Arnold
Pages 149-164
The Chapter Skim interface presents what we've algorithmically identified as the most significant single chunk of text within every page in the chapter.
Select key terms on the right to highlight them within pages of the chapter.
From page 149... ...
Functionally neutral mutations can enhance a protein's stability, thereby increasing its tolerance for subsequent functionally beneficial but destabilizing mutations. They can also lead to changes in "promiscuous" func tions that are not currently under selective pressure, but can sub sequently become the starting points for the adaptive evolution of new functions.
|
From page 150... ...
First, natural proteins evolve through a combination of neutral genetic drift and functionally selected substitutions. Although probably every evolutionary biologist would acknowledge the existence of both types of substitutions, their relative prevalence is debated with often startling vehemence (Gillespie, 1984; Blum, 1992)
|
From page 151... ...
. The results of these experiments offer substantial insight into the possible pathways of adaptive protein evolution and the interplay between adaptive and neutral mutations.
|
From page 152... ...
Arnold FiGUre 8.1 schematic outline of a typical directed evolution experiment. The re searcher begins with the gene for the parent protein.
|
From page 153... ...
such screening is nonetheless sufficient to examine most of the possible individual mutations to a parent protein, because a 200-aa protein possesses only 19 × 200 = 3,800 unique single mutants (even fewer are accessible via single nucleotide changes)
|
From page 154... ...
Arnold how beneficial mutations arise, rather than on how these mutations would actually spread in a naturally evolving population. AN EXAMPLE OF DIRECTED EVOLUTION: CONVERTING A CYTOCHROME P450 FATTY ACID HYDROXYLASE INTO A PROPANE HYDROXYLASE As an example of protein adaptation via directed evolution, we describe how the substrate specificity of a cytochrome P450 enzyme was dramatically altered (Fasan et al., 2007, 2008)
|
From page 155... ...
The exception is the step indicated by the arrow, where stabilizing mutations were intentionally selected to recover some of the lost stability. Data are taken from zpq9990981650002.c.eps Fasan et al.
|
From page 156... ...
Arnold Many Desirable Protein Properties Can Be Improved Incrementally, Through Single Mutations Perhaps the most surprising result from directed evolution experiments is simply how effectively random mutation and selection are able to enhance target protein properties. in most cases where the researcher has been able to devise a high-throughput and sensitive screening assay, it has proved possible to find mutations that improve function (usually a catalytic activity or binding affinity)
|
From page 157... ...
Much of the Epistatic Coupling Between Mutations Is Simply Explained in Terms of Protein Stability, Which Can Underlie Variation in Both Mutational Robustness and Evolvability The fact that most proteins can be engineered through sequential single mutations must not be interpreted to indicate that epistatic coupling between mutations does not exist. Both directed evolution and retro A B FiGUre 8.3 Fitness landscapes and neutral networks.
|
From page 158... ...
. The role of stability compensation in adaptive evolution was demonstrated in a study showing that a naturally occurring antibiotic-resistance enzyme acquired activity on new antibiotics by pairing a stabilizing mutation with one or more catalytically beneficial but destabilizing mutations (Wang et al., 2002)
|
From page 159... ...
But in a directed evolution experiment, the process can be expedited by intentional selection for stabilizing mutations, as was done in the cytochrome P450 experiment described above. Adaptive Protein Evolution Relies Heavily on the Prevalence of Promiscuous Functions, and Protein Promiscuity in Turn Fluctuates with Neutral Mutations Directed protein evolution experiments have demonstrated that once a biochemical function is present at even a low level, it can usually be
|
From page 160... ...
Actually performing neutral evolution in the laboratory may be of limited engineering value because of the considerable experimental effort required to accumulate a substantial number of substitutions. But protein engineers routinely screen and recombine naturally occurring protein homologs (Crameri et al., 1998; landwehr et al., 2007)
|
From page 161... ...
in addition, laboratory evolution experiments usually impose a very strong selection for the target protein property, such that mutations that benefit the target property may be selected even to the detriment of other properties. The fact that laboratory evolution tends to impose fewer pleiotropic constraints and stronger positive selection means that it almost certainly overestimates the frequency of neutral and beneficial mutations relative to natural evolution.
|
From page 162... ...
selectively neutral mutations that increase stability can promote evolvability by allowing for subsequent beneficial but destabilizing mutations (Bloom et al., 2006) , whereas neutral mutations that alter promiscuous activities (Amitai et al., 2007; Bloom et al., 2007c)
|
From page 163... ...
. natural evolution does not so deliberately exploit the potential benefits of neutral mutations, but genetic drift and preexisting diversity may play a similarly important role in natural adaptive evolution.
|
Key Terms
This material may be derived from roughly machine-read images, and so is provided only to facilitate research.
More
information on Chapter Skim is available.