Bioenergetics, the origins of complexity, and the
ascent of man
Douglas C. Wallace1
Organized Research Unit for Molecular and Mitochondrial Medicine and Genetics and Departments of Ecology and Evolutionary Biology, Biological
Chemistry, and Pediatrics, University of California, Irvine, CA 92697-3940
Complex structures are generated and maintained through energy
flux. Structures embody information, and biological information is
stored in nucleic acids. The progressive increase in biological com-
generating power of energy flow plus the information-accumulating
capacity of DNA, winnowed by natural selection. Consequently, the
most important component of the biological environment is energy
reproduction. Animals can exploit and adapt to available energy
resources at three levels. They can evolve different anatomical forms
through nuclear DNA (nDNA) mutations permitting exploitation of
alternative energy reservoirs, resulting in new species. They can
evolve modified bioenergetic physiologies within a species, primarily
through the high mutation rate of mitochondrial DNA (mtDNA)–
getic environments. They can alter the epigenomic regulation of the
thousands of dispersed bioenergetic genes via mitochondrially gen-
erated high-energy intermediates permitting individual accommoda-
tion to short-term environmental energetic fluctuations. Because
variation often involves sequence changes in bioenergetic genes,
most commonly mtDNA mutations, plus changes in the expression
of bioenergetic genes mediated by the epigenome. Consequently,
common nDNA polymorphisms in anatomical genes may represent
only a fraction of the genetic variation associated with the common
billion years of information generation by energy flow, accumulated
and preserved in DNA and edited by natural selection.
evolution|mitochondria|natural selection|human origins|common
greater complexity. Yet, throughoutthe more than 3.5billion years
of biological evolution (3), life has generated ever more complex
are its implications for the ascent of man?
Bioenergetics and the Origin of Biological Complexity
In a thermodynamically isolated system, complex structures decay
energy through the system generates and sustains structural com-
On Earth, the flux of energy through the biosphere is relatively
constant. If the flow of energy were the only factor generating
complexity, complexitywouldsoonachieve a steadystatebetween
the production and decay of structure. Biology is not static, be-
cause the information embedded in biological structures can be
encoded and duplicated by informational molecules, DNA and
RNA. Therefore, biological complexity increases because a por-
tion of the information generated by energy flow through each
generation is added to the accumulated information stores from
previous generations. The increasingly complex information can
then be used to recreate the more complex structures, as long as
there is sufficient energy flow (Mathematical Formulations).
The flow of energy through biological structures permits them to
reproduce, thus duplicating their DNA. In the process of DNA
copying, errors occur. The duplicated mutant DNA changes the
physiology and structure of the progeny. These progeny must com-
pete for the available energy resources within the environment.
Those that are more effective at acquiring and/or expending the
available energy will sustain their energy flux and thus survive and
is the interplay between the organizing principle of energy flow, the
accumulation of information in nucleic acids, and the winnowing of
that information to optimize the use of the available energy flux for
information propagation (Mathematical Formulations).
During the origin of life, biomolecular systems interacted di-
rectly with energy flux, resulting in the formation and polymeri-
zation of ribonucleic acids and their subsequent conformational
changes to form catalysts to facilitate biochemical reactions (6).
within nucleic acids. Subsequently, systems evolved by which the
proteins permitting more complex structures.
Today, the primary energy source for terrestrial life is the flux of
energy photons are collected by plant chloroplasts, descendants of
symbiotic cyanobacteria, and the energy used to split water to hy-
flows in the form of reducing equivalents through the biosphere.
reducingequivalents.Carbohydrate breakdownproducts thenenter
mitochondria strip the hydrogens off the hydrocarbons and react
themwith oxygento generate water,releasingthe storedenergy(7).
plus the information storage capacity of nucleic acids, winnowed
by natural selection, that continually drives biology to increased
complexity. Dobzhansky argued that, “Nothing in biology makes
and the ascent of man, we must understand how energy flows
through the biosphere, creating the environment; how this energy
flow increases biological information; and how the edited in-
formation results in complexity and thus man.
This paper results from the Arthur M. Sackler Colloquium of the National Academy of
Sciences, “In the Light of Evolution IV: The Human Condition,” held December 10–12,
2009, at the Arnold and Mabel Beckman Center of the National Academies of Sciences
andEngineeringinIrvine, CA.Thecompleteprogramand audiofilesofmostpresentations
are available on the NAS Web site at www.nasonline.org/SACKLER_Human_Condition.
The author declares no conflict of interest.
This article is a PNAS Direct Submission.
| May 11, 2010
| vol. 107
| suppl. 2
Energy and the Environment: Three Levels of Bioenergetics
From this analysis, it is clear that the central aspect of an organ-
ism’s “environment” is energy flow. The energy environment of
a biological system is the balance between the energy available to
a system and the demands made on the biological systems’ energy
supply for survival and reproduction. As life is about the preser-
vation and transmission of information, reproduction is the
Organisms within the biosphere interface with energy flux at
three levels: (i) the source of and requirement for the energy
available to a species within its niche, the energy reservoir (ii);
the regional differences in energy requirements and availability
of subpopulations within a species, the energy environment; and
(iii) the short-term fluctuations in energy availability and
demands made on the individual during life by biological and
environmental cycles, the energy fluctuations (Fig. 1).
and its capacity to survive to reproduce within that niche. In most
available takes animals in the range of tens of thousands to hun-
dreds of thousands of years. So mutations in anatomical genes
anatomical structures to exploit the energy reservoir are in place,
then purifying selection maintains those structures as long as the
energy reservoir is stable and can support the species’ population.
As anatomy is controlled by developmental genes, and as these
genes are located on the chromosomes, nuclear DNA (nDNA)
mutations are required to create a new species. The time that it
takes for the necessary anatomical mutations to accumulate for
speciation is determined by the nDNA mutation rate. For multi-
cellular animals, the nDNA gene mutation rate is low, and hence
the accumulation of adaptive nDNA mutations is slow.
For different subpopulations of a species, the energy environ-
ment can differ due to alternative climatic zones, differences in
availability and type of calories, and differing demands on energy
resources. These differences can result from migration, climatic
change, changes in predation or parasitism, and so forth. Such
Bioenergetic genes are distributed throughout the genome and
include hundreds to thousands of nDNA-encoded bioenergetic
genes plus dozens of mtDNA-encoded bioenergetic genes. The
mtDNA bioenergetic genes are the most functionally important
because they are central to mitochondrial energy production. The
mtDNA genes also have a much higher mutation rate than nDNA
genes. Thus, adaptive bioenergetic mtDNA mutations arise in
populations within hundreds to thousands of years and permit
rapid physiological adaptation to changes in the regional energy
environment. As regional subpopulations become established,
additional nDNA mutations in bioenergetic genes arise to further
solidify thephysiological changes (8,9). Overlonger time periods,
anatomical mutations can be added leading toward speciation.
An individual’s energy environment fluctuates in cycles through-
out its life. These cycles can occur over the individual’s life span
in response to seasons, occur monthly relative to the reproductive
cycle,or recurdaily basedonactivity andfeeding.Allofthese cyclic
changes require reversible alterations in bioenergetic physiology,
which cannot be achieved through static genetic changes.
Cyclic changes that occur over tens of years require moderate
stability. These are achieved through epigenomic changes: modifi-
cation of DNA by methylation or of histones through phosphoryla-
tion, acetylation, and methylation. Shorter-term reversible changes
are accomplished through modulation of transcription factors and
be cued to changes in the energetic environment. Therefore, cyclic
including ATP for phosphorylation, acetyl-CoA for acetylation,
NAD+for Sirtuin-mediated deacetylation, S-adenosylmethionine
(SAM) for methylation, oxidation-reduction (redox) state for thiol-
disulfide regulation, and reactive oxygen species (ROS) for driving
oxidative reactions (10).
Energy Reservoirs and Speciation
selection, numerous examples have been reported of anatomical
changes associated with speciation. The earliest report of ana-
tomical changes associated with exploitation of alternative energy
resources was that of Darwin’s Galapagos finches, discussed by
Darwin and Gould before the Geological Society of London in
January 1839. More recently, the change in beak size of these
finches has been attributed in part to changes in calmodulin ex-
pression (11). Comparable studies have continued for more than
a hundred years, culiminating in the recent report that pelvic loss
the Pituitary homeobox transcription factor 1 (Pitx1) gene (12).
Although these studies confirm the importance of anatomical
adaptations that are required for a species to occupy a new bio-
Protein + DNA Modifications
Chromatin + Signaling
High Energy Substrates
z i tnauQ
c i t e
v i t a t i tna
c i t en
energy resources and demands. The primary contributor to the biological
environment is the flux of energy through the biosphere. The dichotomy
between structure and energy in eukaryotics results from the symbiotic or-
igin of the eukaryotic cell involving the proto-mitochondrion and the proto-
nucleus-cytosol. The mitochondrion became specialized in energy pro-
duction and retained core genes for controlling energy production within
the mtDNA. The nuclear-cytosol became specialized in structure with the
accrual of the developmental genes in the nDNA. Because growth and re-
production must be coordinated with the availability of energy, the status of
the energetic flux through the cellular bioenergetic systems, particularly the
mitochondrion, came to be communicated to the nucleus-cytosol by alter-
ations in the nDNA chromatin, the epigenome, and cytosol signal trans-
duction systems, based on the production and availability of high energy
intermediates, reducing equivalents, and ROS produced primarily by the
mitochondrion. As a consequence, biological systems interface with the
energy environment at three levels: the species level in which nDNA gene
variation alters anatomical forms to exploit different environmental energy
reservoirs, the species population level in which primarily mtDNA bio-
energetic genetic variation permits adaptation to long-term regional dif-
ferences in the niche energetic environment, and the individual level in
which high-energy intermediates reflecting cyclic changes in environmental
energetics drive the modification of the epigenome and the signal trans-
duction pathways. [Reproduced with permission from ref. 44 (Copyright
2009, Cold Spring Harbor Laboratory Press).]
Three hypothesized levels of eukaryotic animal cell adaptation to
| www.pnas.org/cgi/doi/10.1073/pnas.0914635107 Wallace
Energy Environments and Subpopulation Radiation
To understand the radiation of subpopulations of a species, it is
necessary to study the intraspecific variation of a single species
that occupies a wide range of regional energetic environments.
The best studied species in this regard is Homo sapiens.
A striking feature of the radiation of mammalian and primate
genomic elements is that mtDNA sequences show a much greater
sequence evolution rate than do nDNA sequences (13–15). This
and regional variation ofhuman mtDNAs (16).The mtDNA genes
of all animals encode the core proteins of OXPHOS, so mtDNA
mutations directly affect bioenergetic physiology and provide the
ideal genetic system for adaptation to changes in regional
Mitochondrial Bioenergetics and the mtDNA. Theuniquecapacityof
origin of the eukaryotic cell. Current theory postulates that a gly-
colytic motile microorganism, the proto-nucleus-cytosol, formed
an association with an oxidative α-protobacterium, the proto-
rise in atmospheric oxygen generated by free-living cyanobacteria.
As the symbiosis matured, the two organisms consolidated their
metabolic pathways and exchanged genes, natural selection enrich-
ing for more efficient forms. During the ensuing intersymbiont re-
organization, most of the genes of the mitochondrial genome were
nuclear-cytosol bioenergetic genes. Ultimately, one genetic and
metabolic combination was sufficiently energetically efficient to
permit the advent of multicellularity. In this proto-multicellular
eukaryote, 98% of the protein coding genes of the mitochondrial
polypeptide genes for mitochondrial growth, reproduction, and
metabolism plus ≈80 polypeptide genes for OXPHOS (7, 17, 18).
The mtDNAs of multicellular animals all retained roughly the
same13OXPHOSpolypeptide genes.These includeseven (ND1,
[cytochrome b (cytb)] of the 11 subunits of complex III, three
and 8) of the ≈16 subunits of complex V. Animal mtDNAs also
retain the rRNAs and tRNAs genes for mitochondrial protein
synthesis and a control region for regulating mtDNA replication
and transcription (7, 17, 18).
Carbohydrates and fats are metabolized through the mitochon-
and β-oxidation pathways. These pathways strip the reducing
equivalents off of the hydrocarbons and transfer them to mito-
chondrial NAD+and FAD. The resulting reducing equivalents
(electrons) are transferred from NADH + H+and FADH2to
complexes I and II, respectively, initiating the electron transport
and complex IV to reduce 1/2 O2into H2O. The energy that is re-
leasedastheelectrons pass throughcomplexes I,III,andIVisused
to transport protons out across the mitochondrial inner membrane
used by the ATP synthase, complex V, to condense ADP + Pi to
ATP, the ATP being exported to the cytosol by the adenine nucle-
otide translocators (ANTs). ΔP can also be used to drive many
other functions including the import of cytosolic Ca2+into the mi-
tochondrial matrix (7, 17, 18).
If excess electrons accumulate in complexes I and III and CoQ,
a potent oxidizing agent. Mitochondrial O2.−can be converted to
(MnSOD) or the intermembrane space Cu/ZnSOD. The H2O2
can acquire an additional electron, producing the highly reactive
hydroxyl radical (·OH), or can be reduced to water by glutathione
·OH) are primarily of mitochondrial origin (7, 17, 18).
The mitochondrion also incorporates a self-destruct system, the
mitochondrial permeability transition pore (mtPTP). The mtPTP
or an increase in mitochondrial matrix Ca2+level or ROS toxicity.
The efficiency by which OXPHOS generates ATP is called the
complexes I, III, and IV convert the oxidation of reducing equiv-
alents into ΔP and the efficiency by which complex V converts ΔP
into ATP. A tightly coupled OXPHOS system maximizes ATP
generation per calorie burned. A less coupled system must burn
more calories for the same amount of ATP, resulting in a higher
caloric intake and greater heat production (7).
All of the proton translocating complexes of OXPHOS (com-
plexes I, III, IV, and V) must be balanced to ensure that one
complex is not disproportionately permeable to protons and thus
shorts ΔP. This is achieved by having the core electron and proton
transport genes retained on a single piece of nonrecombining
DNA, the exclusively maternally inherited mtDNA. This requires
that each new mutation be tested by natural selection in the con-
mtDNA Variation in Adaptation and Disease. Because each cell has
hundreds of mitochondria and thousands mtDNAs, new mtDNA
mtDNAs, heteroplasmy. The percentage of mutant and normal
mtDNAscan beunequallydistributed atcytokinesis, suchthat the
percentage of mutant mtDNAs can drift during successive mitotic
and meiotic cell divisions, replicative segregation.
As the percentage of deleterious mtDNA mutations increases,
the energy output of the cell declines until it drops below the min-
imum energy output required for that cell type to function and
symptoms ensue, the bioenergetic threshold. To date, more than
200 pathogenic mtDNA mutations have been identified, and these
cause all of the symptoms seen in the common metabolic and de-
generative disease including diabetes and metabolic syndrome,
cardiomyopathy, renal dysfunction, and hepatic failure. Mutations
in the mtDNA also contribute to cancer and aging (7, 17).
mutations are very common. The frequency of recognized mito-
chondrial diseases is already estimated at 1/4,000–1/5,000 (19),
and the de novo mtDNA mutation rate observed in cord blood, as
assessed through 15 known pathogenic mutations, has been
reported as 1 in 200 (20). Given the high mtDNA mutation rate
and the great importance and conservation of the mtDNA genes,
encompasses a selective system that systematically eliminates
those proto-oocyes that harbor the most severely deleterious
mtDNA mutations (21, 22). Consequently, only oocytes with
mildly deleterious, neutral, or beneficial mtDNA variants are
ovulated and can be transmitted into the next generation. New
mtDNA variants are constantly being introduced into animal
populations, thus modifying individual energy metabolism. These
variants provide the physiological variability required for sub-
populations to adjust to new regional energetic environments.
As an mtDNA harboring an adaptive mutation becomes
enriched in a new energy environment, additional neutral or ad-
regional maternal lineage. This creates distinctive branches of the
mtDNA tree, each a cluster of related mtDNA haplotypes known
mutations is finite, the same adaptive mutations have been ob-
served repeatedly on different mtDNA backgrounds around the
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| suppl. 2
world. This convergent evolution confirms that these mtDNA
mutations are adaptive.
Each regional indigenous human population has its own dis-
tinctive mtDNAs. African mtDNAs belong to macrohaplogroup
L, which encompasses the greatest mtDNA sequence diversity
implying an African origin for the mtDNA tree (23–25). Of all of
the African mtDNA variants, only two mtDNAs successfully left
AfricaandcolonizedEurasia, founding macrohaplogroupsM and
European-specific lineages H, I, J, Uk, T, U, V, W, and X. Both
macrohaplogroups M and N radiated into Asia, generating
Bering land bridge to colonize the Americas (7, 16).
variation permitted humans to live in different climatic zones, per-
haps through regulation of OXPHOS coupling efficiency and thus
thermal regulation (7). Accordingly, mtDNA variation but not
In mtDNAs harboring the two founder macrohaplogroup N mis-
and ATP6 nucleotide 8701 (amino acid change A59T), several mi-
to change mitochondrial transcription and copy number (28).
Although mild mtDNA mutations may be adaptive in one local
energy environment, the same mutation might be maladaptive in
another energy environment. Consistent with this conjecture,
for a wide range of common metabolic and degenerative diseases
and to influence various cancers and longevity (17, 29).
Once a subpopulation has become established in a region
through adaptive mtDNA mutations, additional mutations can
arise in nDNA bioenergetic genes to further enhance physio-
logical adaptation and contribute to speciation (8). Examples of
such variants in human populations include polymorphisms in
the nDNA-encoded mitochondrial uncoupling protein genes
(30–33) and in the bioenergetic transcription factor genes for the
peroxisome-proliferator-activated receptor γ (PPARγ) (34) and
PPARγ-coactivator 1α (PCG-1α) (35, 36). These polymorphic
genes have also been found to be risk factors for obesity and
diabetes in certain populations. In large-scale population studies
that cut across regional energy environments, the associations
with PPARγ and PGC-1α are lost (37–40). This paradox may
result from the mixing of populations from different energy
environments which harbor alternative region-specific adaptive
genetic variants, such that the impact of each individual regional
variant is averaged out.
Energy Fluctuation and Cyclic Adaptation
Individual adjustments to cyclic changes in the energy environ-
ment must be reversible. Therefore, cyclic changes cannot be due
to DNA sequence changes, but must be due to changes in bio-
energetic gene expression. Relevant cyclic bioenergetic changes
encompass a wide temporal range from intergenerational effects
to daily fluctuations. The more long-term cyclic modulations
occur as epigenomic changes at the chromatin level, whereas the
shorter-term changes involve alterations of transcription factors,
signal transduction pathways, and protein activation.
Epigenomic Regulation of Bioenergetics. Because the primary en-
vironmental variable is energetics, and because the bioenergetic
genes are dispersed across the chromosomes and mtDNA,
responses to environmental fluctuation must involve pan genomic
regulation of bioenergetic genes. The modulation of the epi-
genome by intracellular concentrations of high-energy inter-
the environment and the modulation of cellular gene expression.
When calories were abundant, the organism must grow and re-
produce, which requires the up-regulation of gene expression.
When calories were limiting, the organism must become quies-
cent, requiring the shutdown of gene expression (10).
Epigenomic regulation occurs at the chromatin level. The
nDNA is packaged in nucleosomes encompassing 146–147 base
pairs of DNA wrapped around a complex of two copies each of
histones H2A, H2B, H3, and H4. The amino-terminal tails of the
histones are positively charged, such that they bind electrostati-
cally to the phosphate backbone of the DNA and inhibit tran-
by kinases using ATP, or acetylated by histone acetyltransferases
(HAT) using acetyl-CoA, the positive charges are neutralized, the
affinity of the histone tails to DNA is reduced, and the chromatin
tails by methyltransferases using SAM can also modulate the af-
finity of proteins for DNA.
ATP is generated by both glycolysis and OXPHOS when caloric
reducing equivalents are prevalent. Mammalian cell acetyl-CoA is
generated primarily in the mitochondrion during pryruvate or fatty
acid oxidation. Within the mitochondrion, the acetyl-CoA is con-
verted to citrate by condensation with oxaloacetate (OAA) via cit-
rate synthetase. Citrate can be exported into the cytosol, where itis
cleaved back to acetyl-CoA and OAA by ATP-citrate lyase (10).
Mitochondrial acetyl-CoA can also be exported out of the mito-
chondrion as acetylcarnitine by the carnitine/acylcarnitine acetyl-
translocase. In the cytosol, acetylcarnitine reverts back into acetyl-
CoA for use in histone acetylation (41).
SAMisproduced inthecytosol by thereactionL-methionine +
ATP. ATP is generated by the mitochondrion and glycolysis,
whereas the methyl groups to convert homocystine to methionine
come from the mitochondrion. Therefore, all of the primary sub-
strates for chromatin modification are produced by the bio-
energetic pathways, which in turn are fueled by the availability of
calories in the environment (10).
the facts that pathogenic mtDNA mutations result in symptoms
similar to those attributed to the epigenomic disease and that sev-
eral epigenomic diseases have been associated with mitochondrial
dysfunction. Epigenomic diseases affect imprinting, methylation,
and chromatin organization (42). The epigenome can regulate
dispersed bioenergetic genes in either the cis configuration for ad-
jacent genes or in the trans configuration for dispersed genes. Cur-
rent knowledge about chromatin organization suggests that the cis
regulation occurs with chromatin loop domains and that trans reg-
ulation occurs by diffusible trans acting factors or by bringing to-
gether dispersed genes into transcriptional islands, in part through
shared enhancer sequences (10).
Imprinting diseases generally involve cis-acting epigenetic
defects. In Angelman and Prader-Willi syndromes, the perturba-
tion of cell function involves genetic inactivation of the active al-
lele on chromosome 15q11–13 in the context of an inactive
imprinted allele on the opposite chrosomome. The pathophysi-
ology of Angelman syndrome apprears to be mitochondrial, as
analysis of an Angelman murine model has revealed that the
hippocampal neurons have a reduced synaptic vesicle density and
shrunken mitochondria and the brain has a partial defect in
OXPHOS complexes II + III (10).
The pathophysiology of Beckwith-Wiedemann syndrome and
Wilm’s tumor may also involve bioenergetic dysfunction. Both of
these diseases are associated with loss of imprinting (LOI) on
chromosome 11q15.5 within a chromatin loop domain encom-
passing the insulin-like growth factor 2 (IGF2) gene. IGF2 may
act through the PI3K-Akt-FOXO pathway to modulate energy
metabolism (10, 42).
Rett syndrome and the laminopathies may be epigenomic dis-
eases that act in trans to affect mitochondrial function. Rett syn-
(MeCP2), which binds tomeCpG islands throughout the chromo-
somes (43). As abnormal mitochondria and mitochondrial func-
tion have been reported in several Rett patient studies, loss of
MeCP2 might disrupt the coordinate regulation of nDNA energy
gene expression (10). The laminopathies are caused by mutations
in the laminin A/C gene (LMNA), which disrupt the nuclear ar-
LMNA gene have been found to produce similar phenotypes to
those found in mtDNA mutations and a study of cells harboring
LMNA mutations revealed mitochondrial defects. Therefore,
various epigenomic defects may affect mitochondrial function
implying that an important function of the epigenome is to co-
ordinate the expression of the dispersed bioenergetic genes (10).
Bioenergetic Regulation of Signal Transduction and Metabolism. To
respond to more rapid energy environment fluctuations, animal
cells modify transcription factors and signal transduction systems
via high energy intermediates. High and low blood sugar results in
the secretion of insulin by the pancreatic α cells and glucagon by
the pancreatic β cells, respectively. Insulin binds to the insulin
receptor, which signals, through phosphatidyl-inositol 3 kinase
(PI3K) and Akt/PKB, to phosphorylate and inactivate the FOXO
transcription factor. When not phosphorylated, FOXO binds to
the PCG-1α promoter and increases PGC-1α expression, which
presence of glucose, FOXO is inactivated, OXPHOS is down-
regulated, and glycolysis is favored. In the absence of glucose
FOXO is active and OXPHOS is up-regulated to burn fat. Simi-
larly, glucacon binds to the glucagon receptor to activate adeny-
lylcyclase, and the resulting cAMP activates protein kinase A
PGC-1α promoter and up-regulates OXPHOS. Low glucose thus
doubly induces OXPHOS by inhibiting insulin signaling and en-
hancing glucagon signaling (7).
mTORC1 is also modulated by AMP kinase, which is activated by
reductions in high-energy phosphates. Virtually every signal trans-
duction pathway is modulated by ATP-mediated phosphorylation,
so almost all cellular processes are regulated by the availability of
high-energy intermediates (10, 18).
Changes in cellular redox state are also important in regulating
through the nucleus-cytosol, and on to the other cellular compart-
ments. Reducing equivalents enter the mitochondrion as NADH +
H+at −250 mV and flow through the ETC and other cellular
pathways down to oxygen at +600 mV. The importance of the sub-
cellular redox status is illustrated by the class III histone deacetylase
Sirt1. Sirt1 removes acetyl groups from proteins in the presence of
NAD+via the reaction: acetyl-lysine + NAD+→ lysine + nicotin-
amide + 2′-O-acetyl-ADP ribose. Although the oxidized NAD+is
a required coreactant, the reduced form of NAD+, NADH + H+,
cannot be used by Sirt1. Therefore, deacetylation is coupled to the
cellular redox state. The FOXO and PGC-1α transcription factors
are inactivated by acetyl-CoA–mediated acetylation. They can be
reactivated by deacetylation by Sirt1 + NAD+. When glucose is
process of generating pyruvate. The pyruvate is converted to acetyl-
the cytosol, and is used to acetylate and inactivate PGC-1α and
FOXO. Because the cytosolic NAD+is reduced to NADH + H+,
Sirt1 cannot deacetylation FOXO and PGC-1α and OXPHOS is
inhibited whereas glycolysis is favored. By contrast, when fatty acids
and ketone bodies (acetoacetate and β-hydroxybutyrate) are me-
cytosolic NAD+remains oxidized. The combination of Sirt1 +
NAD+then deacetylates and activates the FOXO and PGC-1α
transcription factors, up-regulating OXPHOS to oxidize fats and
The redox regulation of cellular metabolism goes far beyond its
the NADHis oxidizedvia the ETC usingO2to generateΔP,but the
redox state of a portion of the NADH + H+is increased by the
nicotinamide nucleoside transydrogenase (Nnt), using energy from
NADPH + H+with a redox potential of −405 mV. Mitochondrial
NADPH + H+can then drive the reduction of oxidized glutathione
(GS-SG) to reduced glutathione (2GSH), and GSH can act through
radicals. NADPH + H+also provides reducing equivalents for mi-
tochondrial thioredoxin-2(SH)2/SS [Trx2(SH)2/SS], to drive perox-
idoxins to reduce radical species and to mediate the modulation of
the redox status of thiol-disulfides of an array of mitochondrial
enzymes directly regulating their activity (18, 45).
To a limited extent, the reducing equivalents of mitochondrial
NADH + H+and NADPH + H+can also be transferred to the
via the mitochondrial inner membrane aspartate–malate shuttle.
Mitochondrial NADPH + H+can be exported to the cytosol via
cytosolic malic enzyme to pyruvate in association with the re-
duction of NADP+to NADPH + H+. Cytosolic NADPH + H+
The cytosolic NADPH + H+redox state is approximately
−393 mV. This can drive cytosolic glutathione reductase and
associated glutathione peroxidases to buffer cytosolic ROS and
the glutaredoxins to regulate the redox status of proteins. Cyto-
solic NADPH + H+also determines the redox status of the cy-
tosolic and nuclear thioredoxin-1(SH)2/SS [Trx1(SH)2/SS]. Trx1
(SH)2/SS donates reducing equivalents to cytosolic peroxidoxins
to control radicals, and to the thiol/disulfides of enzymes and
transcription factors to regulate their activity. Trx1(SH)2/SS di-
rectly regulates proteins such as Oct-4, but also regulates the
redox status of the bifunctional apurinic/apyrimidinic endonu-
clease/redox factor-1(APE/ Ref1Red/Ox). The redox state of APE/
Ref1Red/Ox, in turn, modulates the activity of a variety of tran-
scription factors including activator protein–1 (AP1, c-Jun), NF-
E2–related factor–2 (Nrf2), NF-κB, p53, glucocorticoid receptor
(GR), estrogen receptor (ER), and hypoxia-inducible factor–1α
(HIF-1α) (18, 45).
Mitochondrially modulated ROS production also regulates the
threonine kinases, multiple phosphatases, and NFκB-mediated cy-
tension directly regulate the activation of the HIF-1α transcription
factor. HIF-1α is constitutively synthesized but is inactivated in the
presence of high O2by hydroxylation via prolylhydroxylase domain
production can inhibit PHD2 activity, stabilizing HIF-1α. HIF-1α
together with HIF-1β then act as a transcription factor to induce the
expression of glycolytic enzymes and vascularization and hemato-
poietic factors, alter the oxygen affinity of OXPHOS complex IV by
inducing subunit COX4-2 and the mitochondrial LON protease to
degrade subunit COX4-1, induce pyruvate dehydrogenase (PDH)
regulates virtually every aspect of cellular growth, differentiation,
quiescence, and death.
Bioenergetics and the Ascent of Man
This energetic-information hypothesis on the origin of biological
complexity has fundamental implications for the ascent of man.
Since Vesalius’ anatomical catalog published over 450 years ago,
| May 11, 2010
| vol. 107
| suppl. 2
Western medicine has taken a predominantly anatomical perspec-
tive of medicine, the anatomical paradigm of disease. Similarly,
since the discovery of the Mendelian laws of inheritance about 150
years ago, it has been assumed that all genes are inherited in
anatomicalgenes are chromosomal andthus also Mendelian,these
two paradigms provided an internally consistent perspective on bi-
ology and medicine for 100 years. The anatomical and Mendelian
paradigms of medicine have produced many advances, such as un-
derstanding the molecular basis of diseases resulting from severely
deleterious nDNA mutations in structural genes. Because of these
successes, it has been assumed that if a disease Mendelizes it is ge-
netic and if it does not it is “complex,” the later implying an in-
Medicine pertains exclusively to humans, a single species.
Consequently, the most important variables in intraspecific ad-
aptation to local environmental changes, which are primarily en-
ergetic, should be alterations in bioenergetic genes, either genetic
or epigenetic. Mutations in the mtDNA are more common than
nDNA mutations and epigenomic changes can rapidly change the
expression of bioenergetic genes. Efforts to explain common
“complex” diseases like diabetes based exclusively on the analysis
to be relatively unproductive, as has been the case. In reality,
common diseases may not be particularly “complex,” they may
simply be energetic and non-Mendelian.
The discovery that the mammalian ovary harbors a selective
system to eliminate the most deleterious mtDNA mutations
explains why the high mtDNA mutation rate does not drive mam-
malian populations to extinction from overwhelming mtDNA ge-
netic load. Since the mtDNA only encodes OXPHOS genes and
selection can monitor the physiological consequences of mito-
chondrial OXPHOS defects within proto-oocytes and eliminate
those with the most severe bioenergetic aberrations.
expressed in the gametes, so gametes harboring severely delete-
rious developmental mutations cannot be phenotypically identi-
fied and eliminated within the gonads. Purifying selection of
deleterious nDNA mutations must occur postconception, at the
individual organism level. This greatly increases the genetic load
and energy wastage caused by deleterious nDNA mutations. To
avoid introduction of too many deleterious nDNA mutations into
the population, the nDNA mutation rate must be kept low. Still,
the nDNA mutation rate cannot be zero, as maintaining this level
offidelity wouldbetoo energyexpensiveandwouldalsoeliminate
the capacity of organisms to adapt to new energy reservoirs. Ge-
netic load then places an upper limit on the combination of the
nDNA mutation rate and the genetic target size, the amount of
protein coding information in the organism’s genome. In animal
species, a steady state may have been achieved between nDNA
mutation rate and gene target size when the genome complexity
reached that of the invertebrates. This may explain why the
number of protein coding genes is similar between Caenorhabditis
elegans, Drosophila melanogaster, Mus musculus, and Homo sapi-
ens, and that most of the increased structural complexity in ver-
tebrates has been achieved by alternative splicing and elaboration
nDNA constraints and the direct interface between organismal
bioenergetics and changes in the energetic environment, the
dominant mechanism for intraspecific adaptation to environ-
mental change occurs through bioenergetics.
gene information that can be added to the nuclear genomes of
higher animals, the flux of energy through the biosphere is contin-
ually adding information to the environment. Much of this physical
and biological information is too transient to be of value to future
animal generations and thus is not stored in DNA. The present
Still, this informationisofbenefit forthesurvival and reproduction
store the information to the use of DNA to build structures that
could store transient information. These short-term information
storage and retrieval systems ultimately became the brain.
The brain’s information is lost when the individual dies. Yet,
some of this information may be beneficial to the individual’s
relatives and descendants, requiring that this information be
transmitted between related individuals. This provided the im-
petus for the evolution of language and learning, leading to
culture, libraries, and computers.
Toward the end of their lives, Darwin and Wallace became es-
tranged. Darwin argued that natural selection was sufficient to
that natural selection alone was insufficient to explain the exis-
tence of complex structures such as the human brain. From the
bioenergetic perspective, Wallace’s reservations were justified,
as complexity can be generated only through the information-
generating power of energy flow and the cumulative information
for these systems to amass sufficient information to generate the
human brain. Thus the missing concept that Wallace sought to
explain the ascent of man is the interaction between energtics
According to the second law of thermodynamics, an energetically
isolated system will move toward equilibrium in association with
increased disorder or entropy (S), ΔA = ΔU – TΔS, where A is
Helmholtz free energy (energy for useful work), U is the total
energy of the system, and T is the absolute temperature. In a sys-
tem in which T is constant, disorder increases (ΔS is +) as ΔA
declines, provided ΔU is constant. However, in a system where
energy flows through the system, such that an equal quantity of
(U) remains constant but the energy to perform work (ΔA) and
thus produce change is increased. If ΔA becomes greater than U,
then ΔS becomes –, disorder decreases, and the system becomes
more ordered, which is the case for biological systems.
With sufficient information (I), any system can be described.
The greater the disorder of a system (larger the S) the greater
the information that is necessary for its description, S = kiI, were
I is information and ki is a constant. However, energy flow
generates structure, the nature of which is determined by the
inherent properties of the system. To describe a system requires
the information to describe the physical properties of the system,
I(p), and the information inherent in the system that permits the
creation of the ordered aspects of the system, I(o). By analogy, to
describe a glass of ice water requires information about the
physical properties of the ice and water but also information
about the inherent properties of H2O that cause dipole inter-
actions and crystalline lattice formation.
The information to describe the entire system is related to the
energy of the entire system, U, and encompasses both the physical
information embodied in A is I(a) = I(p)a+ I(o)a. In a physically
U, I(u), and the information content of the system decays. To
maintain a steady state structure, additional energy must be added
to A, through energy flux (Ef). This flow of energy will generate
Ef = k5I(ef). This information is then added to the usable in-
([k1I(p)u+ k2I(o)u] – [k3I(p)a+ k4I(o)a+ k5I(ef)])/T.
| www.pnas.org/cgi/doi/10.1073/pnas.0914635107 Wallace
If the system is to avoid decay, Ef must generate information,
I(a). In a complex system that does not decay (ΔS is zero or nega-
tive), A = k3I(p)a+ k4I(o)a+ k5I(ef) ≥ k1I(p)u+ k2I(o)u= U.
Consequently, if k5I(ef) > [k1I(p)u+ k2I(o)u] – [k3I(p)a+ k4I(o)a],
then information and order increase within the system.
Because the flux of energy across the Earth’s surface, Ef, is
roughly constant, the amount of organizing information from Ef
must also be constant. Hence, if this were the only factor, the
biosphere would quickly come to stasis. The reason that this
does not occur is because information pertaining to the ordering
of the system, I(o), can be accumulated, using an appropriate
information storage and retrieval system. In biology, this in-
formation storage system is nucleic acids, I(na). Therefore, in the
biosphere a portion of I(ef), I(o)u, and I(o)aare retained as I
(na): I(ef)na, I(o)na(u), and I(o)na(a). Hence, I(ef)na+ I(o)na(a)
must be > I(o)na(u)for the biosphere to continually increase
The nucleic acid information present in the biosphere today,
I(na), is the sum of the total nucleic acid information that has
formed over 3.5 billion years of terrestrial biology, I(na)t, minus
that portion of the total information that has been removed by
natural selection or cataclysm, I(na)e. I(na) = I(na)t– I(na)e.
The nucleic acid information in today’s biosphere, I(na), divided
by the sum of the energy flux through the biosphere over the past
3.5 billion years, represents the average efficiency by which en-
ergy flux has been converted into conserved biological in-
formation on Earth.
ACKNOWLEDGMENTS. This work was supported by National Institutes of
Health Grants NS21328, AG24373, DK73691, AG13154, and AG16573;
California Institute for Regenerative Medicine Comprehensive Grant RC1-
00353-1; and a Doris Duke Clinical Interfaces Award 2005.
1. Darwin CR, Wallace AR (1858) On the tendency of species to form varieties; and on
the perpetuation of varieties and species by natural means of selection. J Proc Linnean
Soc Lond Zool 3:46–50.
2. Darwin C (1859) On the Origin of Species by Means of Natural Selection, or the
Preservation of Favoured Races in the Struggle for Life (John Murray of Albemarle
3. Simpson S (2003) Questioning the oldest signs of life. Sci Am 288:70–77.
4. Morowitz HJ (1968) Energy Flow in Biology, Biological Organization as a Problem in
Thermal Physics (Academic, New York).
5. Rubí JM (2008) The long arm of the second law. Sci Am 299:62–67.
6. Ricardo A, Szostak JW (2009) Origin of life on earth. Sci Am 301:54–61.
7. Wallace DC (2007) Why do we still have a maternally inherited mitochondrial DNA?
Insights from evolutionary medicine. Annu Rev Biochem 76:781–821.
8. Mishmar D, et al. (2006) Adaptive selection of mitochondrial complex I subunits
during primate radiation. Gene 378:11–18.
9. Lane N (2009) Biodiversity: On the origin of bar codes. Nature 462:272–274.
10. Wallace DC, Fan W (2010) Energetics, epigenetics, mitochondrial genetics. Mito-
11. Abzhanov A, et al. (2006) The calmodulin pathway and evolution of elongated beak
morphology in Darwin’s finches. Nature 442:563–567.
12. Chan YF, et al. (2010) Adaptive evolution of pelvic reduction in sticklebacks by
recurrent deletion of a Pitx1 enhancer. Science 327:302–305.
13. Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of
primates: Tempo and mode of evolution. J Mol Evol 18:225–239.
14. Neckelmann N, Li K, Wade RP, Shuster R, Wallace DC (1987) cDNA sequence of
a human skeletal muscle ADP/ATP translocator: Lack of a leader peptide, divergence
from a fibroblast translocator cDNA, and coevolution with mitochondrial DNA genes.
Proc Natl Acad Sci USA 84:7580–7584.
15. Wallace DC, et al. (1987) Sequence analysis of cDNAs for the human and bovine ATP
synthase beta subunit: Mitochondrial DNA genes sustain seventeen times more
mutations. Curr Genet 12:81–90.
16. Wallace DC, Lott MT, Procaccio V (2007) Emery and Rimoin’s Principles and Practice of
Medical Genetics, eds Rimoin DL, Connor JM, Pyeritz RE, Korf BR (Churchill
Livingstone Elsevier, Philadelphia), 5th Ed, pp 194–298.
17. Wallace DC (2005) A mitochondrial paradigm of metabolic and degenerative diseases,
aging, and cancer: A dawn for evolutionary medicine. Annu Rev Genet 39:359–407.
18. Wallace DC, Fan W, Procaccio V (2010) Mitochondrial energetics and therapeutics.
Annu Rev Pathol 5:297–348.
19. Schaefer AM, et al. (2008) Prevalence of mitochondrial DNA disease in adults. Ann
20. Elliott HR, Samuels DC, Eden JA, Relton CL, Chinnery PF (2008) Pathogenic
mitochondrial DNA mutations are common in the general population. Am J Hum
21. Fan W, et al. (2008) A mouse model of mitochondrial disease reveals germline
selection against severe mtDNA mutations. Science 319:958–962.
22. Stewart JB, et al. (2008) Strong purifying selection in transmission of mammalian
mitochondrial DNA. PLoS Biol 6:0063–0071.
23. Johnson MJ, Wallace DC, Ferris SD, Rattazzi MC, Cavalli-Sforza LL (1983) Radiation of
human mitochondria DNA types analyzed by restriction endonuclease cleavage
patterns. J Mol Evol 19:255–271.
24. Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution.
25. Merriwether DA, et al. (1991) The structure of human mitochondrial DNA variation.
J Mol Evol 33:543–555.
26. Balloux F, Handley LJ, Jombart T, Liu H, Manica A (2009) Climate shaped the
worldwide distribution of human mitochondrial DNA sequence variation. Proc Biol Sci
27. Kazuno AA, et al. (2006) Identification of mitochondrial DNA polymorphisms that
alter mitochondrial matrix pH and intracellular calcium dynamics. PLoS Genet 2:
28. Suissa S, et al. (2009) Ancient mtDNA genetic variants modulate mtDNA transcription
and replication. PLoS Genet 5:e1000474.
29. Wallace DC, Fan W (2009) The pathophysiology of mitochondrial disease as modeled
in the mouse. Genes Dev 23:1714–1736.
30. Villarroya F, Iglesias R, Giralt M (2006) PPARs in the control of uncoupling proteins
gene expression. PPAR Res 2007:1–12.
31. Nakano T, et al. (2006) A/G heterozygote of the A-3826G polymorphism in the UCP-1
gene has higher BMI than A/A and G/G homozygote in young Japanese males. J Med
32. Bulotta A, et al. (2005) The common -866G/A polymorphism in the promoter region of
the UCP-2 gene is associated with reduced risk of type 2 diabetes in Caucasians from
Italy. J Clin Endocrinol Metab 90:1176–1180.
33. Cha MH, Shin HD, Kim KS, Lee BH, Yoon Y (2006) The effects of uncoupling protein 3
haplotypes on obesity phenotypes and very low-energy diet-induced changes among
overweight Korean female subjects. Metabolism 55:578–586.
34. Altshuler D, et al. (2000) The common PPARgamma Pro12Ala polymorphism is
associated with decreased risk of type 2 diabetes. Nat Genet 26:76–80.
35. Ek J, et al. (2001) Mutation analysis of peroxisome proliferator-activated receptor-
gamma coactivator-1 (PGC-1) and relationships of identified amino acid polymor-
phisms to type II diabetes mellitus. Diabetologia 44:2220–2226.
36. Muller YL, Bogardus C, Pedersen O, Baier L (2003) A Gly482Ser missense mutation in
the peroxisome proliferator-activated receptor gamma coactivator-1 is associated
with altered lipid oxidation and early insulin secretion in Pima Indians. Diabetes 52:
37. Saxena R, et al., Diabetes Genetics Initiative of Broad Institute of Harvard and MIT,
Lund University, and Novartis Institutes of BioMedical Research (2007) Genome-wide
association analysis identifies loci for type 2 diabetes and triglyceride levels. Science
38. Zeggini E, et al., Wellcome Trust Case Control Consortium (WTCCC) (2007) Replication
of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes.
39. Scott LJ, et al. (2007) A genome-wide association study of type 2 diabetes in Finns
detects multiple susceptibility variants. Science 316:1341–1345.
40. Sladek R, et al. (2007) A genome-wide association study identifies novel risk loci for
type 2 diabetes. Nature 445:881–885.
41. Madiraju P, Pande SV, Prentki M, Madiraju SR (2009) Mitochondrial acetylcarnitine
provides acetyl groups for nuclear histone acetylation. Epigenetics 4:399–403.
42. Feinberg AP (2007) Phenotypic plasticity and the epigenetics of human disease.
43. Loat CS, et al. (2008) Methyl-CpG-binding protein 2 polymorphisms and vulnerability
to autism. Genes Brain Behav 7:754–760.
44. Wallace DC (2009) Mitochondria, bioenergetics, and the epigenome in eukaryotic and
human evolution. Cold Spring Harb Symp Quant Biol, ePub ahead of print, http://
45. Kemp M, Go YM, Jones DP (2008) Nonequilibrium thermodynamics of thiol/disulfide
redox systems: A perspective on redox systems biology. Free Radic Biol Med 44:
46. Semenza GL (2008) Mitochondrial autophagy: Life and breath of the cell. Autophagy
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