COMMENTARY

COMMENTARY

Energetics and population genetics at the

root of eukaryotic cellular and
genomic complexity
Eugene V. Koonin1
National Center for Biotechnology Information, National Library of Medicine, National
Institutes of Health, Bethesda, MD 20894

In PNAS, Lynch and Marinov provide detailed estimates of the energy cost associated
with the addition of new coding or noncoding
sequences to prokaryotic and eukaryotic genomes (1). The amount of ATP that is
expended at each step of information transfer
is derived from the known biochemistry of
these processes and an extensive collection of
data on gene expression, as well as nucleic acid
and protein decay for diverse organisms. The
energy cost is then transformed into fitness

cost via a simple, intuitive notion that fitness

cost is proportional to the fraction of the total
energy expenditure of a cell that is attributable
to the maintenance of a given sequence.
The laws of thermodynamics dictate that
the stability and expansion of any physical
system including, naturally, evolution of living
organisms, are constrained by the adequate
energy availability. Under the laws of population genetics that are deeply analogous to
the laws of thermodynamics (2), the efficacy

Fig. 1. Cellular organization-driven evolutionary scenario of eukaryogenesis. Eukaryogenesis is represented by three

stages: 1, -proteobacterium engulfed by a Loki-like archaeon becomes the proto-mitochondrial endosymbiont; excess energy production; 2, excess energy production leads to cell enlargement accompanied by intracellular compartmentalization (emergence of endomembranes) and a drop in Ne; 3, expansion and remodeling of the genome
including insertion of endosymbiont DNA (both genes and introns) accompanied by shrinking of the endosymbiont
genome and linearization of the chromosomes; further evolution of intracellular organization including the origin of
the nucleus from the endomembranes, conceivably, as a protective device against translation of aberrant, introncontaining transcripts (14). The cellular complexity of the Loki-like putative host of the endosymbiont is unknown; the
figure only includes some inferences from the gene repertoire of the Lokiarchaeon. Abbreviations: CC, circular
chromosome; CS, cytoskeleton; EM, endomembranes; LC, linear chromosomes; N, nucleus.

www.pnas.org/cgi/doi/10.1073/pnas.1520869112

of selection in an evolving population is determined by the effective population size. In

small populations, only mutations with a large
phenotypic effect (selection coefficient) cross
the barrier imposed by the genetic drift and
are either eliminated from the population
or fixed (depending on the sign of the selection coefficient), whereas in large populations,
even mutations with a slight deleterious or
beneficial effect are subject to efficient selection (3). Although this is rarely addressed in
explicit terms, any evolutionary scenario can
be considered seriously if and only if it falls
within both the energetic and the populationgenetic constraints (4).
Lynch and Marinov (1) show that the fitness cost of a new sequence negatively scales
with the cell size, which is readily understandable because the energy cost does not necessarily strongly depend on the cell size, whereas
the total energy expenditure is proportional to
the cell volume. For a new sequence to be
detected and eliminated by purifying selection from a haploid population, its cost
should exceed 1/Ne (where Ne is effective
population size). The estimates of Lynch
and Marinov clearly show that this threshold is exceeded in prokaryotes, which accordingly cannot fix even a short sequence
unless it provides a significant selective advantage, but not in eukaryotes that cannot
eliminate a gene unless it is translated.
Therefore, genome expansion in eukaryotes
is possible under a neutral evolutionary regime and does not require any significant
increase in energy production.
Energetic considerations appear to be particularly relevant when it comes to the origin
of eukaryotes (eukaryogenesis), one of the
major transitions in the evolution of cellular
life that resulted in an unprecedented increase in the complexity of the cellular organization and genome architecture (5). All
extant eukaryotic cells possess mitochondria,
the power-generating membranous organelles
Author contributions: E.V.K. wrote the paper.
The author declares no conflict of interest.
See companion article on page 15690 in issue 51 of volume 112.
1

Email: koonin@ncbi.nlm.nih.gov.

PNAS | December 29, 2015 | vol. 112 | no. 52 | 1577715778

that evolved from -proteobacterial endosymbionts, or degenerated derivatives of the mitochondria, such as hydrogenosomes (5, 6).
By inference, the last eukaryotic common ancestor already carried mitochondria. Lane and
Martin have argued that the boost in energy
production provided by the acquisition of
(proto)mitochondria was a prerequisite for
the evolution of the eukaryotic cell and, in
particular, the complexification and drastic
remodeling of the genome that accompanied
eukaryogenesis (7, 8). In addition to the sheer
expansion, this genomic transformation included insertion of multiple introns into
the protein-coding genes, disruption of
operons, and linearization of chromosomes, which became possible thanks to
the recruitment of the telomerase from a
prokaryotic mobile element (9). The estimates of Lynch and Marinov (1) show that in
and by itself the eukaryotic genome expansion
did not require the energy production boost
from the mitochondria.
Does this demonstration imply that the
acquisition of mitochondria was not the
key factor, possibly a prerequisite, of eukaryogenesis? Not at all. The estimates indicate
that eukaryotes can acquire DNA sequences
of considerable length effectively for free,
or put another way, are unable to eliminate
invading DNA. This feature of eukaryotic
biology apparently is a result of the synergistic effects of the large cell size that is
characteristic of eukaryotes and results in
the low fitness cost of new sequences (the
energy expenditure for the maintenance of a
new sequence is negligible compared with
the total energy budget of a eukaryotic but
not a prokaryotic cell) and the small population size that limits the power of selection (1).
However, these estimates provide no clue as to
how these intrinsic features of eukaryotic cells
that seem to be prerequisites for the genome
expansion could have emerged in the first
place. Unlike genome expansion, increase of
the cell size does require substantial amounts
of extra energy per cell, which becomes problematic if only because the efficacy of membrane energetics [the only highly efficient form
of biological energy conversion (10)] scales
with the square of the cell diameter, whereas
the cell volume obviously scales with the cube
of the same. Membrane-bound energy-transforming organelles (i.e., mitochondria) offer
the best known solution. In a broad agreement
with the hypothesis of Lane and Martin (8,
10), the contribution of mitochondria to energy production could have enabled the drastic
enlargement of the cells in the population that
acquired the endosymbiont.
The large cell size in the primordial eukaryotic lineage leading to the last eukaryotic
15778 | www.pnas.org/cgi/doi/10.1073/pnas.1520869112

(11, 12). Nevertheless, it appears likely that

picoeukaryotes independently emerged via
reductive evolution in different lines of descent. Furthermore, early cell enlargement
triggered by the mitochondria would be
accompanied by a drop in Ne [given the
apparently universal inverse correlation
between the size of a cell or an organism
and effective population size (3)], which
would create the niche for genome expansion and remodeling.
The role of mitochondria in eukaryogenesis
seems to extend far beyond the boost to
energy production. Given the fundamental differences in the structure of
the membrane phospholipids in archaea
on the one hand, and bacteria and eukaryotes on the other hand (13), it appears
likely that the mitochondria spawned
the proliferation of the eukaryotic endomembranes, including the endoplasmic reticulum and the nuclear envelope along with
the replacement of the plasma membrane
with the bacterial version (14). Furthermore,
because of the continuous lysis of the endosymbionts inside the evolving chimeric
cell, the constant release of the endosymbiont DNA most likely triggered genome

remodeling, via insertion of self-splicing

group II introns into the host genes and
transfer of numerous endosymbiont genes
to the host genome (9, 14).
If the establishment of endosymbiosis that
led to the emergence of eukaryotes was a
singular occurrence, we may never know the
actual chain of events. Nevertheless, analysis
of energetic and population-genetic requirements for various evolutionary novelties,
along with more specific biological evidence,
constrain the possibilities and limit the space
of plausible evolutionary scenarios. The
above considerations suggest that, in the
case of eukaryogenesis, evolution of cellular
organization could have been the primary
driver of genomic innovations, not the other
way around (Fig. 1). The recent discovery of
Lokiarchaeota (Loki), the archaeal sister group
of eukaryotes that are indistinguishable from
other archaea in terms of genome size and
architecture but encode a variety of proteins
indicative of complex intracellular organization, in particular an advanced cytoskeleton
(1518), appears best compatible with
the possibility that the host of the
proto-mitochondrial endosymbiont was an
archaeon, albeit one with an unusually
elaborate intracellular organization (Fig. 1).
Engulfment and domestication of an
-proteobacterium by a Loki-like archaeon
could have led to substantially increased energy production per (chimeric) cell, which
would trigger cell enlargement accompanied
by intracellular compartmentalization. As
shown by the estimates of Lynch and
Marinov, a small population of large cells
would have been conducive to the capture
of substantial amounts of new DNA (1).
Together with the onslaught of the endosymbiont DNA, this condition could have
led to genome remodeling and expansion,
molding the eukaryotic genomes (Fig. 1).

1 Lynch M, Marinov GK (2015) The bioenergetic costs of a gene.

Proc Natl Acad Sci USA 112(51):1569015695.
2 Sella G, Hirsh AE (2005) The application of statistical physics to
evolutionary biology. Proc Natl Acad Sci USA 102(27):
95419546.
3 Lynch M (2007) The Origins of Genome Architecture (Sinauer
Associates, Sunderland, MA).
4 Lynch M (2007) The frailty of adaptive hypotheses for the origins
of organismal complexity. Proc Natl Acad Sci USA 104(Suppl 1):
85978604.
5 Embley TM, Martin W (2006) Eukaryotic evolution, changes and
challenges. Nature 440(7084):623630.
6 van der Giezen M (2009) Hydrogenosomes and mitosomes: Conservation
and evolution of functions. J Eukaryot Microbiol 56(3):221231.
7 Lane N (2011) Energetics and genetics across the prokaryoteeukaryote divide. Biol Direct 6:35.
8 Lane N, Martin W (2010) The energetics of genome complexity.
Nature 467(7318):929934.
9 Koonin EV (2006) The origin of introns and their role in
eukaryogenesis: A compromise solution to the introns-early versus
introns-late debate? Biol Direct 1:22.

10 Lane N (2015) The Vital Question: Energy, Evolution, and the

Origins of Complex Life (WW Norton & Company, London).
11 Vaulot D, Eikrem W, Viprey M, Moreau H (2008) The diversity of
small eukaryotic phytoplankton (< or =3 microm) in marine
ecosystems. FEMS Microbiol Rev 32(5):795820.
12 Massana R (2011) Eukaryotic picoplankton in surface oceans.
Annu Rev Microbiol 65:91110.
13 Lombard J, Lpez-Garca P, Moreira D (2012) The early evolution
of lipid membranes and the three domains of life. Nat Rev Microbiol
10(7):507515.
14 Martin W, Koonin EV (2006) Introns and the origin of nucleuscytosol compartmentalization. Nature 440(7080):4145.
15 Spang A, et al. (2015) Complex archaea that bridge the
gap between prokaryotes and eukaryotes. Nature 521(7551):
173179.
16 Saw JH, et al. (2015) Exploring microbial dark matter to resolve
the deep archaeal ancestry of eukaryotes. Philos Trans R Soc Lond B
Biol Sci 370(1678):20140328.
17 Koonin EV (2015) Archaeal ancestors of eukaryotes: Not so
elusive any more. BMC Biol 13:84.
18 Embley TM, Williams TA (2015) Evolution: Steps on the road
to eukaryotes. Nature 521(7551):169170.

common ancestor is not a certainty. Indeed,

numerous, phylogenetically diverse picoeukaryotes with cell sizes barely exceeding the
typical prokaryotic size are known to exist

As shown by the estimates of Lynch and

Marinov, a small population of large cells
would have been conducive to the capture of
substantial amounts of
new DNA.

Koonin