Biology Reference
In-Depth Information
these three lines of evidence point to a series of surprisingly
simple principles behind life's ability to produce novel and
beneficial phenotypes, i.e., its innovability.
Here, I will first devote three short sections to three
central classes of systems and their phenotypes. Changes in
these systems are the foundations of most, if not all
evolutionary innovations. These system classes are meta-
bolic networks, regulatory circuits, and molecules such as
proteins and RNA. Subsequently, I will suggest how one
can study phenotypic variability systematically in these
system classes. The next section explains two fundamental
concepts, that of a genotype space and the phenotypes
therein, for these system classes. The two sections after that
summarize recent evidence that these system classes share
two organizational features of genotype space that facilitate
phenotypic variability and evolutionary innovation. These
are the existence of genotype networks (to be defined
further below) and of a great phenotypic diversity in
different neighborhoods of genotype space. The next
section explains how these concepts can help explain the
origins of evolutionary innovations. A final section
suggests why system classes as different as these can share
such similarities, and especially the existence of genotype
networks. The reason is that systems in these classes typi-
cally operate in changing environments, which endows
them with robustness to environmental change, but also to
genetic change. The existence of genotype networks is
a consequence of such robustness.
I emphasize that the principles I discuss here by no
means negate the importance of other factors, such as
environmental change, phenotypic plasticity, multi-
functionality of biological systems, epigenetic change,
gene duplication, and gradual evolution from simple to
complex systems, for the ability to bring forth variable
phenotypes
[15
organisms to survive on new sources of food. Prokaryotes
are the undisputed masters of such innovations. They are
able to survive on sources of carbon and energy that are
bizarre and toxic (to us), including methane, hydrogen gas,
crude oil, antibiotics, and xenobiotic chemicals
[22
24]
.
The likely reason why many metabolic innovations
occur in prokaryotes is the ability of prokaryotes to
exchange genes through a variety of mechanism
[25,26]
.
Horizontal gene transfer can transform the genome of
a prokaryote on short evolutionary timescales, such that
even different strains of the same bacterial species may
differ in hundreds of genes. Such horizontal gene transfer is
the cause of many evolutionary innovations. A candidate
example involves the prokaryote Sphingomonas chlor-
ophenolica, which is able to metabolize the toxic xenobi-
otic compound pentachlorophenol. It does so through
a sequence of four chemical reactions
[27]
, none of which
is new to S. chlorophenolica. Two of them are involved in
degrading naturally occurring chlorinated compounds in
other organisms. Two others are involved in the metabolism
of the common amino acid tyrosine
[27]
. The innovation in
S. chlorophenolica's metabolism is the combination of
these reactions. Such new combinations of reactions can be
easily achieved through horizontal
e
transfer of enzyme
coding genes.
Prokaryotes may be the most prolific metabolic inno-
vators, but metabolic innovations also occur in the evolu-
tion of higher, multicellular organisms. An example is the
urea cycle, an innovation that occurred during the evolution
of land-living animals. It allows animals to dispose of
ammonia, a waste product of their metabolism that is toxic
to cells, by converting it into urea that is excreted in urine.
The urea cycle consists of five metabolic reactions, none of
which are new to their carrier. Individually, they are
widespread in many organisms. Four of these reactions are
involved in the biosynthesis of arginine, and the fifth is
involved in the degradation of arginine
[28]
. What is new is
the combination of these five reactions into a metabolic
cycle, a major innovation of biological waste management.
20]
. The principles I discuss are comple-
mentary to other factors, and may even help clarify the role
these factors play in phenotypic variability. They do not
only apply to qualitatively new phenotypes, but also to
beneficial quantitative changes in existing phenotypes
e
e
evolutionary adaptations, in the jargon of evolutionary
biologists. A more comprehensive treatment can be found
elsewhere
[10]
.
REGULATORY CIRCUITS AND THEIR
INNOVATIONS
Regulation is a process that changes the activity of genes
and their products. It can affect transcription, translation,
post-translational modification, transport, as well as several
other aspects of gene and protein function. Among all the
known modes of regulation, transcriptional regulation is
perhaps the most prominent
[29
METABOLIC NETWORKS AND THEIR
INNOVATIONS
Large-scale metabolic networks are systems of hundreds to
more than 1000 chemical reactions that are at work in every
organism
[21]
. Their most fundamental task is to transform
sources of chemical elements and energy into a chemical
form that is useful to the organism. Evolutionary innova-
tions in metabolism fall into multiple categories. An
especially prominent category concerns traits that allow
33]
. The reason is that
most modes of regulation ultimately affect the regulation of
transcription. Transcriptional regulation is thus a backbone
of regulatory processes inside an organism. Transcriptional
regulation involves specialized proteins called transcription
e
