Chapter 1
How
Should We Think About Evolution in the Age of Genomics?
James A. Shapiro
Dept.
Biochemistry and Molecular Biology, University of Chicago,
Gordon Center for
Integrative Science W123B, 979 E. 57t Street, Chicago, IL
60637, USA jsha@uchicago.edu
ABSTRACT
Eibi Nevo’s
research highlights the
complexity of evolutionary responses to ecological
parameters. This important
work pioneered a growing awareness of the multiple levels of
biological
activity and organismal interactions that contribute to
evolutionary change. In
large measure, our current understanding of adaptive
innovation is based on the
newly acquired ability to track the details of evolutionary
processes through
genome analysis. Genomics has unambiguously demonstrated the
importance of cell
fusion, symbiosis, interspecific hybridization, genome
restructuring involving
mobile DNA elements, and the many forms of infectious
heredity all to be major
contributors to the appearance of organisms with novel
adaptive
characteristics. In addition, genomics has confirmed
interspecific
hybridization as a major stimulus to the rapid emergence of
new taxa among
sexually reproducing organisms. The work of Eibi and many
other scientists has
shown that ecology can trigger and influence all these
different modes of hereditary
change. We must recognize that genomic analyses have
provided 21st
Century evolutionary scientists with such a rich variety of
documented paths to
inherited novelty that it has become impossible to formulate
a comprehensive
theory of evolutionary change. Thus, an important part of
the future in
evolution science will be to adapt Eibi’s wisdom by devising
synthetic
Evolution Canyons as complex experimental microcosms, where
we can rigorously
study the principles governing ecological and biological
interactions in
adaptive innovation. Hopefully, those interactive principles
will make it
possible to integrate information from genomic analysis into
a coherent picture
of evolution as a biological response to ecological change.
KEY
WORDS: Cell
fusion; symbiosis; interspecific
hybridization; mobile DNA elements; infectious heredity;
horizontal DNA
transfer; virosphere; genome restructuring; ecological
triggers; synthetic
Evolution Canyons
Background: Tribute
to a unique
evolutionary biologist
This 90th Jubilee
Symposium and book, New Horizons in Evolution, pay tribute to Eviatar Nevo, a prolific
pioneer best known today
for his work at Evolution Canyon, where two distinct
ecologies sit side-by-side
[1]. Exploiting this special geography, Eibi and
his many colleagues
have been able to observe the effects of ecological
differences on real-time
processes of evolutionary change of numerous species from
microbes to mammals
at the population [2-4],
organismal [5, 6],
karyotypic [7] and molecular levels [8].
Eibi’s research highlights the
complexity of
evolutionary responses to ecological parameters using the
most up-to-date tools
available. In particular, he has documented the impacts of
ecological stresses [9] on specific processes that bring about
adaptive genome change: DNA
repair [10], mutation [8], chromosome rearrangements [11], amplification and movement of repetitive and
mobile DNA elements [12-14].
Eibi’s extremely broad documentation
of how real-world
ecological challenges integrate with genome change
operations presents us with
an opportunity to reconsider the basic principles of
evolutionary biology in
the age of genomics. Does our contemporary knowledge of how
genomes change in
the course of evolution confirm traditional principles
established in the 19th
and 20th Centuries? Or does that body of
information force us to
adopt a new, more contemporary set of principles? This paper
will argue in
favor of the latter position, based on contemporary
empirical data cited in a
pair of recent reviews [15, 16] and
also posted under various headings on my University of
Chicago web page (online
link 1 – the online links are listed before the references
after the main text
before the references).
Basic
principles of
evolutionary change necessary to encompass Eibi’s work
Traditional evolutionary theory in
the 19th
and early 20th Centuries focused on accidental
changes in isolated
genomes. Under the principle of “Descent with Modification,”
evolutionary
biologists had to explain where and how hereditary changes
took place. Each
species was assumed to have its own genome, comprising the
nuclear chromosomes.
The nuclear genome was isolated from the genomes of other
species by sexual
incompatibility (the Bateson-Dobzhansky-Muller model [17]) and from life history events by the Weismann
Barrier between the
soma and the germline [18, 19]. Within these isolated genomes, hereditary
changes were assumed to
occur by random accidents in the course of germline
reproduction. When DNA was
identified as the molecular carrier of genetic information,
the random accident
theory was updated to unavoidable copying errors in the
course of DNA
replication [20, 21].
The traditional perspective did not
allow any
possibilities for ecological inputs, like those Eibi’s
research has documented,
into the process of hereditary variation. Today, of course,
we can see that the
“isolationist” view of hereditary determination was
unjustifiably restrictive
in several fundamental ways. The second half of the 20th
Century
made us aware of many biochemical processes of hereditary
change, ranging from
the active movement of mobile DNA elements in the genomes of
maize and all
other organisms (online link 2) [22] to DNA transfer, repair, rearrangement and
mutator functions
(online link 3) [23, 24]. Like all physiological activities (and as
Eibi’s research demonstrates
so well), these molecular “Natural Genetic Engineering”
(NGE) processes of DNA
change are subject to cellular regulation (online link 4)
and operate in a
manner that is sensitive to ecological inputs (online link
5). As we shall see
below, genomic analysis has documented important
evolutionary adaptations that
result from NGE action.
In addition to the regulated
physiological processes
that alter DNA molecules, we now have overwhelming evidence
that genomes are
not as isolated from each other or from the environment as
traditional theories
assumed [16]. There are multiple forms of “infectious
heredity” understood in
its broadest sense (online link 6) [25]. All organisms reproduce in the presence of
abundant environmental
DNA as well as a staggering density of viruses, vesicles and
other forms of
enclosed DNA molecules. Multiple mechanisms exist for cells
of different
organisms to exchange DNA molecules, and there is abundant
genomic data that
adaptive horizontal DNA transfers have occurred across
virtually all taxonomic
boundaries. Moreover, as we shall discuss shortly, there is
no question that
cell fusions can combine unrelated genomes in a single
hereditary lineage to
form modified or new kinds of organisms, including the first
mitochondrion-bearing ancestor of all eukaryotes. The
reproductive boundaries
between species are not as absolute as once assumed, and we
shall see that
mating across species boundaries is a major stimulus to
evolutionary innovation
in sexually reproducing organisms.
The Weissman Barrier soma-germline
separation is also
not absolute, as some exponents of traditional theory have
claimed. Such a
barrier cannot exist in cells that proliferate by vegetative
multiplication,
such as all prokaryotes and lower unicellular eukaryotes,
where there is a
direct hereditary connection between “somatic” and
“germline” cells. Even in
unicellular eukaryotes that undergo sexual differentiation
and reproduction,
vegetative cells are the direct precursors of spores and
gametes. The same cell
lineage connection exists between soma and germline in
plants. Since flowers
containing plant sexual organs develop out of somatic
tissues, the genomic
consequences of life history events can be incorporated into
pollen and ovules
that merge to form the next generation. Only in animals,
where germline cells
separate from somatic tissues early in multicellular
development, is formation
of a Weismann Barrier a realistic possibility. Nonetheless,
we now know about
processes of macromolecular transport in animals which
facilitate the transfer
of somatically acquired genomic information to animal sperm
cells [26].
From the foregoing summary, we can
see that discoveries
based on genomic data provide us a 21st Century
picture of
ecologically sensitive evolutionary processes that coincides
with what Eibi’s
amazingly productive research has revealed.
Cell
fusions produced
foundational evolutionary innovations
The deepest
evolutionary divides among living organisms are the
separation of all cells
into three distinct lineages: Bacteria,
Archaea and Eukarya [27, 28]. It
is a salutary reminder of the power of genomic analysis and
of the capacity for
new data to transform our understanding of fundamental
evolution principles to
recognize that our knowledge of Archaea
as a distinct cell type only dates from analysis of
ribosomal RNA sequences in
1977, less than 50 years ago [29, 30]. The
same kind of early genomic evidence made it clear that the
mitochondrion of the
earliest known eukaryotic ancestor descended from an
endosymbiotic
Gram-negative Proteobacterium
[31-34].
Parallel sequence analysis confirmed the evolutionary
origins of
light-harvesting plastid organelles in a wide range of
algae, plants and other
photosynthetic eukaryotes as descendants of endosymbiotic cyanobacteria (online link 8).
Fossil and genomic
data tell us that both Bacteria and Archaea are the
most ancient cell
lineages (dating from > 3.4 GYA) and that the primordial
symbiogenetic event
in evolution of Eukarya
occurred
approximately 1.6-1.8 GYA, as the Earth’s atmosphere was
accumulating a
significant concentration of molecular oxygen (O2),
following the
evolution of oxygenic photosynthesis in cyanobacteria
[35-37]. The
O2 concentration is important because the best
genomic evidence
indicates that the host cell in the primordial symbiogenesis
was an anaerobic archaeal
cell encoding many proteins once considered to be exclusive
to eukaryotes [35, 38-41].
Since Proteobacteria
are aerobic and
contemporary mitochondria are the loci of oxidative
energy-yielding metabolism
in eukaryotic cells, it is evident that acquisition of an
aerobic endosymbiont
would provide a significant metabolic advantage to an
anaerobic host cell in an
environment with a growing atmospheric O2
concentration.
During the course
of transformation from an independent cell to a subcellular
organelle in the proto-eukaryotic
cell, the endosymbiont Proteobacterium
underwent a series of major changes in genome content
(online link 9). In all
eukaryotes, mitochondrial DNA coding content is only a
fraction of that in Proteobacteria.
The largest
mitochondrial genome encodes only 100 protein and RNA
molecules compared to
over 800 for the smallest Proteobacterium
cell. A typical animal mitochondrion like ours encodes only
37 molecules [42]. DNA containing the vast majority of bacterial
coding sequences
required for mitochondrial maintenance and metabolism
transferred to the
nuclear genome of the evolving eukaryotic host cells. The
resulting
nuclear-encoded mitochondrial proteins are synthesized like
other eukaryotic
proteins and imported into the mitochondrion organelle by
newly evolved protein
transport systems. Since overall genome size, physical DNA
structure, and
coding content differs greatly between the mitochondria in
the cells of various
eukaryotic lineages, it is clear that mitochondrial genome
evolution has
involved an ongoing and complex series of
taxonomically-specific DNA
restructuring processes [32].
Although sequence data
indicates that the symbiogenetic event originating
mitochondrial evolution
appears to have been unique, multiple cell fusion events
have transferred
plastids encoding photosynthetic capabilities to diverse
eukaryotic lineages
(online link 10). The oldest one involved a common
cyanobacterial progenitor of
the different plastids in four distinct groups of organisms:
green algae (Chlorophyta),
red algae (Rhodophyta),
blue-gray algae (Glaucophyta),
and green plants (Embryophyta).
Such a cyanobacterial fusion
is called a “primary symbiogenesis,” and there has been a
second, much more
recent primary symbiogenesis of a distinct species of
cyanobacteria creating a
single photosynthetic amoeba, Paulinella
chromatophora. Further “secondary” symbiogenetic
events have occurred when
a photosynthetic eukaryote, generally one of the algae, has
fused with a
non-photosynthetic eukaryote cell type to create a novel
photosynthetic lineage
[43]. If the product of a secondary photosynthetic
fusion merges with
another non-photosynthetic lineage, that creates a
“tertiary” symbiogenesis.
Many of the most important
photosynthetic organisms on
Earth, such as diatoms, have resulted from these secondary
and tertiary
symbiogeneses. Clearly, photosynthetic cell fusions have
occurred over a
prolonged period of evolutionary time and are quite likely
to be taking place
now. As with mitochondria, there has been significant DNA
transfer from
plastids to the nuclear genome, and plastid-specific protein
transport has
evolved to incorporate into the plastids nuclear-encoded
proteins needed for
photosynthesis. Also similar to mitochondria, there are
lineage-specific
differences in plastid DNA content, physical DNA structures,
and coding
capacities. In cases of secondary and tertiary
symbiogenesis, there are also
significant rearrangements and losses of nuclear DNA from
the eukaryotic
endosymbionts.
In addition to these various cases of
photosynthetic
symbiogenesis, there are numerous other cases of cell
fusions and endosymbiosis
that have profound adaptive significance [44-46].
Bacteria can invade other bacteria as well as virtually all
kinds of eukaryotic
cells [47, 48]. A smaller
number of endosymbiotic Archaea have been documented, but
more cases will
doubtless appear as genomic analysis comes to bear on more
types of organisms
from other parts of the biosphere. Eukaryotic microbes can
become endosymbionts
of other eukaryotes, just as they do in secondary and
tertiary photosynthetic
fusions [49]. The adaptive significance of these
endosymbiotic relationships
involve various adaptive characteristics, such as synthesis
of important
nutrients (vitamins, amino acids, etc.), utilization of
particular food sources
(e.g., digestion of plant polymers), or protection against
predators or
infectious agents [45, 50].
So-called “obligate” endosymbiosis occurs when the cell
fusion becomes
essential for reproduction of the host organism or the
endosymbiont (often due
to genome reduction, similar to what occurred in
mitochondria and plastids) [51, 52].
Microbiomes
and holobionts
Besides cell fusions,
microbes and multicellular organisms establish important
symbiotic
relationships simply by growing in close proximity or by the
microbes
colonizing the cells or interior cavities of major organ
systems, like the
intestine (online link 11). Each multicellular organism has
its own
“microbiome,” the generic term for all the associated
microorganisms [53]. The microbes interact biochemically with each
other and with the
multicellular host in ways that affect the overall
phenotype.
Different organs or regions of a
single host can have
distinct microbiome compositions with unique phenotypic
consequences. In
plants, for example, the microbiomes on leaves and roots are
dramatically
different and play radically different roles in transport of
nutrients and
responses to biotic and abiotic stresses [54]. Of particular importance for all plants and
animals is the role a
healthy microbiome at each site plays in blocking infection
by microbial pathogens.
The microbiome plays important roles
in many adaptive
phenotypes. We are becoming familiar with discussions of how
the “human
microbiome” (usually meaning the intestinal microbiome)
affects our health and
well-being, metabolism and digestion, pregnancy, immune
responses, and even
mood and states of mind. Microbiome species synthesize
critical nutrients for
the macroscopic holobiont host, ranging from amino acids in
aphids [55] to a
wide range of essential metabolites in primitive marine
animals [56] to signaling molecules that affect functioning
of our own
metabolic, neural and innate immune systems [57]. In Drosophila,
the
intestinal microbiome affects growth factor signaling and
morphogenesis [58], volatile pheromone production and social
attraction [59], and neuropeptide synthesis and locomotor
behavior [60].
Clearly, the adaptive properties of
the host plus its
microbiome result from expression of microbial as well as
host genomes.
Typically, the protein coding capacity of the total
microbiome genome is far
more diverse than that of the host genome [61]. In our
own case, the human gut microbiome is estimated to encode
from 3.3 to 9.9
million distinct proteins, or 150 – 450 times greater than
the basic
nucleus-encoded human proteome.
From an evolutionary point of view,
the recognition of
microbiome contributions to whole organism phenotypes poses
a definitional
challenge. What is the evolving entity? In order to deal
with this question,
the terms “holobiont” and “hologenome” were invented to
describe the evolving
entity and its genetic endowment [62-64]. A
holobiont is composed of a multicellular plant or animal
together with its
associated microbiome, and this terminology has been widely
adopted in the
relevant literature. Holobiont heredity differs radically
from Mendelian
principles and has been described as far more similar to
schemes proposed by
Lamarck [65] and Darwin (“gemmules”) [66]. Frequently, microbiome components are
transmitted horizontally to
the oocyte (pre- or post-fertilization) or developing embryo
by maternal
tissues [67, 68], but
horizontal transmission also occurs paternally [69, 70]. It
is safe to say that our knowledge of trans-generational
microbiome maintenance
is very partial and requires a great deal of further
research [71].
Because of their composite natures,
holobionts can
rapidly evolve complex adaptive phenotypes by acquisition or
loss of microbiome
constituents, outcomes not achievable simply by changes to
the host genome. In Drosophila,
mosquitoes and other
invertebrates, acquisition of bacterial endosymbionts from
the Wolbachia
group affects a variety of
important characteristics, such as resistance to viruses and
parasites, and
also frequently generates mating incompatibility between
colonized and Wolbachia-free
hosts [50, 72, 73].
Since mating incompatibility between two populations is
often the first step of
divergence into separate species, Wolbachia
entry into the microbiome has been characterized as
stimulating “speciation by
symbiosis” [74].
Interspecific
hybridization
Cell fusions are an
essential feature of sexual reproduction. Contrary to the
idealized assumption
of complete reproductive isolation between different
species, there is abundant
genomic evidence of mating between related but distinct
microbial, plant and
animal species, including real-time observations (online
link 12).
Interspecific matings are ecologically sensitive because
their frequency will
increase when mating population sizes decline and
conspecific mates become
harder to find.
The consequences of
interspecific mating are high levels of genome instability
(such as chromosome
rearrangements, activation of mobile DNA elements, whole
genome duplications –
online link 13) and the formation of novel species with
phenotypic traits that
are more than simple mixtures of characters from the two
parents. This kind of hybrid
speciation was long ago characterized as “Cataclysmic
Evolution” by the
distinguished evolutionary biologist G. Ledyard Stebbins [75]. Typically, the karyotype of the hybrid
species contains a diploid
number equal to the sum of the chromosomes in the two
parental species. The
increase in chromosome number results from the whole genome
duplications
necessary for the initial hybrid to undergo successful
meiosis.
Although hybrid
speciation was long known to occur in plants and serve as
the source of useful
agricultural crop species, its importance in animals was not
appreciated before
genomics provided evidence for many hybrid species. Of
particular interest are
Darwin’s finches in the Galapagos Islands, an important
evolutionary model
cited by Darwin [76], and freshwater cichlid fishes that have
become models for rapid
speciation and phenotypic diversification [77-79]. In
the case of the Galapagos finches, it is worthwhile noting
that interspecific
hybridization has also been followed in real time by
Rosemary and Peter Grant
and colleagues, who have documented abrupt changes in beak
morphology in hybrid
birds rather than the gradual changes postulated by Darwin [80-82].
Protein
evolution.
Ever since the
articulation of the “one gene – one protein” hypothesis in
the middle of the 20th
Century [83], the formation of new protein sequences to
execute novel functions
has been seen as central to adaptive evolutionary change.
With the identification
of DNA as the genetic material and the elucidation of the
coding relationships
between genomic DNA and the sequence of amino acids in each
protein [84, 85], protein evolution was widely assumed to occur
largely by a gradual
succession of single amino acid substitutions due to random
mutations in the
underlying DNA code. However, DNA sequencing and genomic
comparisons led to a
number of unexpected insights which indicated that protein
evolution involves
far more active cellular DNA manipulation than initially
believed.
Proteins as
systems. The first pair of
insights concerned the organization of protein molecules and
of the DNA that
encodes them. Most proteins consist of structurally and
functionally
independent “domains” joined together, often connected by
short linker peptides
[86, 87]. Different
proteins are generally similar to each other in one or more
domains but not in
others. Because each domain has specific functional
characteristics, the
overall activity of a given protein is determined by the
integration of its
various domains into a functional system. This means that
proteins can evolve
functionally by amplifying, acquiring and rearranging their
domain contents to
generate novel combinations [88-94].
Mechanistically, amplifying and
rearranging domains
occurs by joining together distinct DNA coding regions, not
by mutational
changes altering particular amino acids. DNA joining
involves many distinct
biochemical processes and proteins that have to be
coordinated and synthesized
at the same time. Frequently, domain rearrangements involve
mobile DNA NGE
functions (online link 14).
While many domains are shared across
broad phylogenetic
distances, patterns of multi-domain architectures are
specific to each taxon [95, 96].
Domain organization indicates that the primary object of
evolutionary change is
often the domain rather than the whole protein [96-100].
There are protein domain databases [101, 102], and
it is common practice in contemporary comparative genomics
to describe a coding
region and its cognate protein product by its domain
content. One major
question in protein evolution involves the sources of new
domain architectures [103].
Domain loss and the appearance of novel kinds of domains are
genomic signatures
at the emergence of major new taxonomic groups [104].
Coding sequences
in pieces. When DNA
sequencing was applied to
mammalian regions encoding well-known proteins, a surprising
result emerged.
The sequences for a single polypeptide chain were not
continuous but consisted
of a series of expressed DNA elements (“exons”) encoding
segments of the chain
separated by intervening DNA elements (“introns”) [105, 106]. The intron-exon coding pattern is widespread
among eukaryotes. In
the process of protein synthesis, introns are “spliced” from
the primary
transcript to form the continuously coding mRNA that is
translated on the ribosomes
[107]. Although some introns are self-splicing
ribozymes [108], splicing generally takes place on a complex
“spliceosome”
organelle [109].
There are multiple ways that the
exon-intron-exon
protein coding structure contributes to protein diversity
and evolution. In
coding region transcripts with multiple exons and introns,
not all splicing
events necessarily produce only a single combination of
joined exons.
“Alternative splicing” that creates different combinations
of exons from a
single pre-mRNA transcript enhances an organism’s protein
repertoire [110].
Regulation of alternative splicing means that different
conditions can control
the expression of distinct proteins from a single coding
region [111-113]. In
many organisms, there is even “trans-splicing,” where exons
from two different
pre-mRNA transcripts can be joined together to produce
hybrid proteins encoded
by two different coding regions [114, 115].
Since the sequences of exon-intron boundaries are important
determinants of
where and when splicing events occur, one way that novel
protein architectures
evolve is by changes in splicing patterns rather than by
alteration of amino
acid coding sequences [116, 117].
By and large, there is a good (but
not absolute)
correspondence between exons and protein domains [118]. This means that protein evolution by domain
rearrangement often
involves mobilizing the corresponding exons, sometimes with
associated introns,
into new genomic sites. Since it is easier to mobilize a
domain coding sequence
that is isolated as one exon (or several exons in series),
split coding regions
facilitate functional protein evolution [119]. It has been documented that the requisite DNA
restructuring events
often involve the DNA rearrangement activities associated
with mobile DNA
elements (online link 14).
Another
major
question in protein evolution concerns the origins of new
domains. It turns out
that novel protein coding sequences have a variety of
sources in both “coding”
and “non-coding” DNA sequences (online link 15). The ability
of supposedly
“non-coding” genetic elements to contribute to protein
coding came as a
surprise to many evolutionary theorists, who called such
elements “selfish or
junk DNA” [120-122]. In
2001, it was first established that repetitive mobile DNA
elements contribute
directly to many protein coding sequences [123]. Since then, repetitive mobile DNA elements
have proven to be a
rich source for the origination of exons encoding novel
domains, often by acquiring
novel splicing signals so that previously intronic segments
form new exons
(online link 16) [124].
Combined with the above-cited
capacity of mobile DNA
elements to help mobilize exon rearrangements, it appears
from their role as
substrates for novel domain coding sequences that the mobile
DNA component of
various genomes serve as major facilitators of protein
evolution. We will see
below that mobile DNA elements play a parallel role in the
evolution of
regulatory and transcription networks for complex
adaptations in advanced plant
and animal species. These discoveries show that once poorly
understood
so-called “junk DNA” elements can play important roles in
evolution.
Recognizing the validity of that statement should serve as
an object lesson
about how dangerous it is to misinterpret unexpected
observations (in this
case, the abundance of repetitive DNA in genomes of advanced
organisms) and base
broad generalizations upon our ignorance rather than our
understanding.
Horizontal
DNA transfers
An important and
unexpected aspect of rapid evolutionary adaptation first
became evident when
antibiotics were widely used to combat bacterial infections
following World War
II. Rather than acquire resistance by mutation, the
mechanism well-documented
by laboratory experiments, the vast majority of resistant
bacteria isolated in
clinical settings were found to contain genetic elements
encoding high levels
of resistance that were able to transmit that resistance to
other,
phylogenetically distant strains of bacteria, thereby
helping to explain the
rapid spread of antibiotic resistance (online link 17).
These “resistance
transfer factors” (R-factors) encoded various resistance
mechanisms that
included chemical inactivation of specific antibiotics,
antibiotic removal from
the host bacterium, and modification of the cellular targets
of antibiotic
action. Many R-factors combined coding information for
multiple activities
conferring resistance to several antibiotics at once [125].
Interbacterial transmission became
known as a form of
“infective heredity” [126-128] and
provided a virtually instantaneous way of acquiring new
adaptive traits. No
extended process of developing a new character was
necessary. Since the new
genetic information came from another cell, infective
heredity constituted a
“horizontal transfer” of genetic information, quite distinct
from the normal
vertical transmission from ancestral cells. Over time, it
became evident that
many different kinds of adaptive traits in bacteria (and
later in archaea) are
subject to horizontal transfer, such as metabolic pathways,
surface attachment
structures, virulence factors, ability to establish
symbiotic relationships,
and synthesis of lethal compounds attacking unrelated
bacteria [129-134].
Horizontal transfer became so universal a feature of
bacterial genetics that
some scientists proposed the concept of a shared pan-genome
which individual
strains of bacteria sampled freely according to the demands
of the ecological
niches they inhabited [135].
With the advent of widespread DNA
sequence analysis, the
protein-coding complement of many eukaryotic genomes was
established.
Comparisons of these coding sequences helped define the
phylogenetic
relationships of various species by their protein
repertoires. While these
relationships were largely consistent with shared ancestries
and protein
diversification across the generations (including the
emergence of novel
proteins and domains), there were also instances of
protein-coding sequences appearing
in lineages that were absent from the genomes of ancestral
species but highly similar
to those of unrelated organisms, often from a completely
different domain of
life. These “misplaced” coding sequences must have been
acquired by horizontal
DNA transfer either directly or indirectly from their
original source. Multiple
cellular mechanisms exist for horizontal DNA transfer
(online link 18), but the
genomic data provide no indication of how any particular
transfer actually
occurred.
Horizontal DNA transfers have been
documented across
virtually all taxonomic boundaries (online link 19). They
involve many
important adaptive traits. For example, both Bdelloid
rotifers (a class of microscopic
animal) and herbivorous nematode worms have acquired coding
sequences from
bacteria and fungi on multiple occasions that allow them to
synthesize enzymes
to break down otherwise indigestible plant polymers [136-139].
Since different rotifers have acquired hundreds of distinct
bacterial and
fungal sequences, it is clear that horizontal DNA
acquisition by these tiny
animals has comprised ongoing molecular incorporations [138]. The ability to short-circuit the process of
protein adaptation and
immediately extend the organism’s range of food resources
illustrates the kind
of evolutionary advantage conferred by cellular capacities
for DNA uptake and
genome integration.
Horizontal transfers can involve DNA
segments encoding
whole proteins or only encoding one or more individual
domains. In either case,
the transfers involve the introduction of new domains into a
distant lineage
and set up conditions for the evolution of novel domain
architectures in
multiple proteins [140, 141]. In
this way, horizontal transfer can initiate the evolution of
new protein
families and the specialized adaptive traits they support.
Examples include the
proliferation of plant cell wall destabilizing proteins
following transfer of
expansin domains from plants to bacteria and fungi [142], interacting domains and regulatory networks
in oomycetes
(filamentous fungus-like water molds) [143], and the “effector” proteins with eukaryotic
domains that Legionella
bacteria inject into target
cells to commandeer host functions during infection [144-147].
Major adaptive changes have been
found to involve
horizontal DNA transfers. One such change is the use of
bacterial sequences to
foster the emergence from thermophilic ancestors of new
Archaeal lineages
capable of growth under mesophilic conditions [148, 149].
Another recently documented case is the ability of
autotrophic and osmotrophic
eukaryotic lineages to assimilate environmental nitrate as
their sole source of
metabolic nitrogen [150].
Although the precise mechanism of
horizontal DNA
transfer is indeterminate for any particular case, the kinds
of interactions
that occur throughout the biosphere provide us with multiple
potential paths
for this kind of genomic exchange [16]. One of the most important, the ubiquity of
genomic information
protected inside virus capsids, is our next topic.
The
virosphere as an
evolutionary R & D sector (online link 20)
Viruses are the
most abundant biological entities on planet Earth [151]. They are found at astonishing concentrations
in the soil, in
bodies of water (~1010 per liter), and in the
atmosphere (falling at
~109 per square meter per day) [152, 153]. In
addition to viruses, there are a variety of virus-like
particles (VLPs) that
contain nucleic acids but not viral genomes [154]. Among the VLPs are dedicated DNA transport
particles called “gene
transfer agents” (GTAs) [155]. While these viral and virus-like agents
inject DNA or RNA into
cells that have surface receptors, which limits their range
of target cells,
some have been documented to participate in cross-species
DNA transfers. VLP
donors capable of transferring genetic information to
mesophilic E. coli
and B. subtilis bacteria have been reported to
include microbial mats
of hyperthermophilic bacteria from hot springs and marine
bacteria from the
oceans [156, 157].
Viruses, and especially the
bacteriophages which infect
bacteria, are the most numerous reservoirs of protein coding
sequences on
planet Earth. These coding sequences can be divided into two
groups with quite
distinct evolutionary potentials:
(1)
The first group includes sequences encoding proteins similar
to
those found in cells that participate in established
metabolic routines,
ranging from the different steps of alternative
photosynthesis systems to
various forms of intracellular energy metabolism, phosphate
recycling,
apoptosis (programmed cell death), cell surface structures,
virulence and
infectivity [154, 158].
These reservoirs of established cell physiology functions
can be utilized to
repair damaged cells or to extend the metabolic capabilities
of an organism
adapting to novel ecological circumstances. [159-162]
(2) The second group consists of
uniquely viral protein
coding information that cells do not possess and which,
therefore, have the
potential to initiate the evolution of entirely new types of
cellular proteins [163]. Over 90% of all unique coding sequences in
the genomic databases occur
in viral genomes [164]. Since they are unique, they do not exist in
cells. When one of
these unique sequences is exapted by a cell (often for a
function related to
its source, like anti-virus defense), a novel protein
sequence and structure
appears in the genome. This new motif is then available to
combine with other
protein domains or mutate to a new functionality and thus
generate a capability
which did not previously exist, either in the virosphere or
cellular realm.
This creative capability is part of what makes the
virosphere an evolutionary R
and D domain of life. In this vein, retroviruses have been
cited as source of
new genes in vertebrates [165].
Virus particle capsids naturally
break down over time
and liberate their nucleic acid cargos into the environment.
The virosphere is
thus a major contributor to the free DNA molecules present
in all ecologies.
Many types of cells have been found to be capable of taking
up DNA from their
surroundings and incorporating it into their genomes (online
link 6): Archaea,
“competent” bacteria with dedicated DNA import complexes,
yeast, red algae and
invertebrate and vertebrate sperm. Under experimental
conditions, DNA
“transformation” has further been extended to cultured
animal cells, suggesting
that similar processes may occur under natural conditions.
The role of viruses
as sources of environmental DNA for uptake has recently been
demonstrated in
experiments with so-called “super-spreader” bacteriophages
that transfer
plasmid DNA from E.
coli bacteria to
unrelated phage-resistant Streptococcus
pneumonia bacteria competent for DNA import [166]