From:    Tim Ikeda
To:      All                                    Msg #64, Jun-07-93 11:01AM
Subject: Re: the role of mutation in evolution

Organization: /etc/organization
From: timi@chloroplast.Berkeley.EDU ( Tim Ikeda)
Message-ID: <1v039d$h17@agate.berkeley.edu>
Newsgroups: talk.origins

Chris Colby (colby@bu-bio.bu.edu):
>>The vast majority of mutants with any phenotypic effect are
>>deleterious and are flushed from the gene pool.

Mark Isaak (isaak@aurora.com):
M>I know I've asked this before, but I've forgotten the answer.
M>How vast is "vast," and how do you know?

Chris:
>I don't know if anyone has come up with a number for this. I
>would suspect that it would be species and context dependent.
>
>I know that the average fitness change in mutations (that do
>change fitness) has been measured, there was a Nature paper
>about a year or two ago. I suppose someone who did chemostats
>or large yeast populations could measure this if they wanted.
>
>Grow a large population of organisms grown from two clones,
>each identical except carrying a unique neutral genetic marker. Check
>the frequency of these two genotypes frequently. When one starts
>to change rapidly and increase towards one, you can infer that a
>"good" (in this specific context) mutation has occurred somewhere
>in the genome of one of these organisms and it is reproducing faster
>than the other organisms.
>
>Divide this one mutation, by all the mutations that have occurred in
>the population (if you know the population size through time and the
>average mutation rate, you could figure it out.) Repeat a bunch
>of times.
>
>Maybe this has been done and I just don't know the paper.
> [...]

Experiments roughly similar to what you mentioned have been done in E. coli
by Dean, Dykhuizen and Hartl (Probably because E. coli still has the best
understood metabolism and genetics of any  organism).  They started with
metabolic control theory to ask how changes in the different enzyme
activities of a metabolic pathway might affect the overall flux through
that pathway.  This way, they were able to model how different mutations in
pathway enzymes may affect the fitness of an organism.  So for a pathway
catalyzed by the enzymes, A, B, and C, below:

       A          B          C
   w ----->  x  ----->  y  ----->  product z

One should be able calculate how changes in the rates of any of the enzymes
will affect the rate at which product "z" is made.  If the enzyme "C" is
saturated with "y" under normal conditions, meaning that the step from
y --> z can't go any faster, then any mutations which increase the speeds
of enzymes "A" and "B" won't allow product "z" to be made any faster.  So
in this case, you could say that enzyme-C has the highest "control
coefficient" because changes in C have the greatest effect on the
pathway's flux. Assuming that the kinetic parameters of all the enzymes
are determined, then the control coefficients for all the steps can be
calculated.

But what happens in the case where the flux through a pathway determines
how fast an organism can grow and reproduce?  What if product-z is
essential but substrate-x is limiting in the medium?  In their model
system, the researchers used the disaccharide, lactose, as the limiting
source of carbon in a liquid medium.  In E. coli, lactose passes passively
through the outer membrane of the cell and then is actively transported
through the inner membrane by *lac permease* (encoded by the gene, lacY).
Once inside the cell, *beta-galactosidase* (encoded by the gene, lacZ),
splits the lactose into glucose and galactose, which then enter the cell's
central metabolism.  If the flux of lactose through this pathway is what
sets the growth rate of a particular strain, then mutations affecting the
pathway's enzymes could affect the strain's fitness (at least with respect
to growth on lactose).

In the first step of the experiments, the activities of the lac permeases
and beta-galactosidases from numerous natural isolates of E. coli were
assayed. Individually, wide variations in the enzyme activities were found
among the isolates.  Next, the authors constructed strains which were
identical in all respects except for their lacY or lacZ genes -- which were
taken from the different E. coli isolates -- and then forced the strains to
compete in pairs under conditions where lactose was held limiting (Strains
also carried harmless marker genes which allowed the workers to identify
and count the numbers of each strain in the culture). The rate at which one
strain could outgrow another in chemostatic culture (nutrient limited),
indicated how each of the mutant alleles contributed to the relative
fitness of the strain.  What the researchers found was that despite large
variations in enzyme activities, relatively small effects on fitness were
observed.  Why was this?

Metabolic modeling showed that a 100% increase in beta-galactosidase
activity would cause less than a 1% increase in the overall flux through
the pathway.  The lac permease has a little bit more control -- 100% in
activity produces an 8% increase in flux.  As it turned out, the relative
effects of lacZ and lacY mutations on the flux through the pathway matched
these calculated fitness values.  This suggests that the lactose catabolic
pathways in most of the natural E. coli isolates are already optimized for
growth on lactose -- That further improvement means working at the point of
diminishing returns.  But where does all the genetic variation in lacY and
lacZ leave natural selection if, as shown, most of the variation has a
largely neutral effect on fitness?

As reviewed by Richard E. Lenski (Current Biology 1993, Vol. 3, No. 2, pp.
121-123):
"More generally, Hartl, Dykhuizen and Dean, have proposed a sort of `grand
unification' of selectionist and neutralist positions by arguing that the
neutrality of many enzyme variants may be the consequence of past selection
coupled with fundamental contraints on biochemical kinetics.  That is,
selection in the past has tended to increase the biochemical activity of
these enzymes to the point of decreasing returns, such that further
increases in activity translate into even smaller improvements in fitness.
But they do not regard the neutral variation that remains as completely
unimportant for adaptive evolution.  Rather, they hypothesize that
variation which is neutral in an organism's historical environment provides
a source of variation, or a latent potential for selection, if the
prevailing environment should change.  That is, variations in biochemical
activity that are essentially invisible to natural selection (because thay
are at the point of diminishing returns) may be subject to strong selection
in other environments, where enzyme activities are well away from the point
of diminishing returns.  Thus, according to this hypothesis, long periods
of selection in a relatively constant environment can beget neutrality,
whereas environmental changes may precipitate selection among formerly
neutral variants.

In a forthcoming paper, Silva and Dykhuizen take this work an important
step further, by testing explicitly whether selection among lac operons
[T.I. note - lacZ and lacY form part of this lac operon] from naturally
occurring isolates of E. coli is more intense in novel environments.  In
addition to lactose, several other sugars are substrates for the lac-
encoded beta-galactosidase, including lactulose, galactosyl-arabinose and
methyl-galactopyranoside. [...]  However, whereas lactose is commonly found
in the environments that E. coli inhabits, these other sugars are
encountered rarely if ever.  The prediction is that variation among the lac
operons from nature in performance on these rarely encountered sugars
should be greater than variation in performance on lactose. [...goes on to
mention that Silva and Dykhuizen (1993) show that selection turns out to be
greater for growth on many of these rarer sugars than for lactose...]"

Assorted refs:

DL Hartl, DE Dykhuizen, AM Dean: Limits of adaptation: The evolution of
selective neutrality. Genetics 1985, 111:655-647.

DL Hartl, DE Dykhuizen: The neutral theory and the molecular basis of
preadaptation. In `Population Genetics and Molecular Evolution' - T Ohta,
K Aoki, eds. Berlin: Springer-Verlag; 1985:107-124.

AM Dean, DE Dykhuizen, DL Hartl: Fitness as a function of beta-
galactosidase activity in Escherichia coli. Genet. Res. 1986, 48:1-8.

AM Dean: Selection and neutrality in lactose operons of Escherichia coli.
Genetics 1989, 123:441-454.

DE Dykhuizen, AM Dean: Enzyme activity and fitness: Evolution in solution.
Trends. Ecol. Evol. 1990, 5:257-262.

PJN Silva, DE Dykhuizen: The increased potential for selection of the lac
operon of Escherichia coli. Evolution 1993, 47:in press.

FWIW

Regards,
Tim Ikeda
(timi@mendel.berkeley.edu)