Group Title: BMC Biology
Title: The Planetary biology of cytochrome P450 aromatases
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Title: The Planetary biology of cytochrome P450 aromatases
Physical Description: Book
Language: English
Creator: Gaucher, Eric
Graddy, Logan
Li, Tang
Simmen, Rosalia
Simmen, Frank
Schreiber, David
Liberles, David
Janis, Christine
Benner, Steven
Publisher: BMC Biology
Publication Date: 2004
 Notes
Abstract: BACKGROUND:Joining a model for the molecular evolution of a protein family to the paleontological and geological records (geobiology), and then to the chemical structures of substrates, products, and protein folds, is emerging as a broad strategy for generating hypotheses concerning function in a post-genomic world. This strategy expands systems biology to a planetary context, necessary for a notion of fitness to underlie (as it must) any discussion of function within a biomolecular system.RESULTS:Here, we report an example of such an expansion, where tools from planetary biology were used to analyze three genes from the pig Sus scrofa that encode cytochrome P450 aromatases–enzymes that convert androgens into estrogens. The evolutionary history of the vertebrate aromatase gene family was reconstructed. Transition redundant exchange silent substitution metrics were used to interpolate dates for the divergence of family members, the paleontological record was consulted to identify changes in physiology that correlated in time with the change in molecular behavior, and new aromatase sequences from peccary were obtained. Metrics that detect changing function in proteins were then applied, including KA/KS values and those that exploit structural biology. These identified specific amino acid replacements that were associated with changing substrate and product specificity during the time of presumed adaptive change. The combined analysis suggests that aromatase paralogs arose in pigs as a result of selection for Suoidea with larger litters than their ancestors, and permitted the Suoidea to survive the global climatic trauma that began in the Eocene.CONCLUSIONS:This combination of bioinformatics analysis, molecular evolution, paleontology, cladistics, global climatology, structural biology, and organic chemistry serves as a paradigm in planetary biology. As the geological, paleontological, and genomic records improve, this approach should become widely useful to make systems biology statements about high-level function for biomolecular systems.
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Research article

The planetary biology of cytochrome P450 aromatases
Eric A Gaucherl, Logan G Graddy2, Tang Lil, Rosalia CM Simmen3,
Frank A Simmen3, David R Schreiber', David A Liberles4, Christine M Janis5
and Steven A Benner*6


Address: 'Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville FL 32601-4256, USA, 2Department of Psychiatry, Duke
University Medical Center, Durham, NC 27708, USA, 3Department of Physiology & Biophysics, Medical Sciences & Children's Nutrition Center,
University of Arkansas, 1120 Marshall Street, Little Rock AR, 72202, USA, 4Computational Biology Unit, Bergen Center for Computational Science,
University of Bergen, 5020 Bergen, Norway, 5Ecology and Evolutionary Biology, Brown University, Providence RI 02912, USA and 6Department
of Chemistry, University of Florida, Gainesville FL 32611-7200, USA
Email: Eric A Gaucher gaucher@scinq.org; Logan G Graddy gradd001 @mc.duke.edu; Tang Li tang@scinq.org;
Rosalia CM Simmen simmenrosalia@uams.edu; Frank A Simmen simmenfranka@uams.edu; David R Schreiber schreiber@scinq.org;
David A Liberles liberles@cbu.uib.no; Christine M Janis ChristineJanis@brown.edu; Steven A Benner* benner@chem.ufl.edu
* Corresponding author



Published: 17 August 2004 Received: 12 February 2004
BMC Biology 2004, 2:19 doi:10.1186/1741-7007-2-19 Accepted: 17 August 2004
This article is available from: http://www.biomedcentral.com/1741-7007/2/19
2004 Gaucher et al; licensee BioMed Central Ltd.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.



Abstract
Background:Joining a model for the molecular evolution of a protein family to the paleontological
and geological records (geobiology), and then to the chemical structures of substrates, products,
and protein folds, is emerging as a broad strategy for generating hypotheses concerning function in
a post-genomic world. This strategy expands systems biology to a planetary context, necessary for
a notion of fitness to underlie (as it must) any discussion of function within a biomolecular system.
Results: Here, we report an example of such an expansion, where tools from planetary biology
were used to analyze three genes from the pig Sus scrofa that encode cytochrome P450
aromatases-enzymes that convert androgens into estrogens. The evolutionary history of the
vertebrate aromatase gene family was reconstructed. Transition redundant exchange silent
substitution metrics were used to interpolate dates for the divergence of family members, the
paleontological record was consulted to identify changes in physiology that correlated in time with
the change in molecular behavior, and new aromatase sequences from peccary were obtained.
Metrics that detect changing function in proteins were then applied, including KA/Ks values and
those that exploit structural biology. These identified specific amino acid replacements that were
associated with changing substrate and product specificity during the time of presumed adaptive
change. The combined analysis suggests that aromatase paralogs arose in pigs as a result of selection
for Suoidea with larger litters than their ancestors, and permitted the Suoidea to survive the global
climatic trauma that began in the Eocene.
Conclusions: This combination of bioinformatics analysis, molecular evolution, paleontology,
cladistics, global climatology, structural biology, and organic chemistry serves as a paradigm in
planetary biology. As the geological, paleontological, and genomic records improve, this approach
should become widely useful to make systems biology statements about high-level function for
biomolecular systems.



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Background
The emergence of complete genomes for many organisms,
including humans, has created the need for hypotheses
concerning the "function" of specific genes that encode
specific proteins. While "function" is interpreted by differ-
ent workers in different ways [1], Darwinian theory (by
axiom) requires that the term be connected to fitness; nat-
ural selection is the only mechanism admitted by theory
to generate functional behavior in a living system, macro
or molecular. This, in turn, implies that the hypotheses
about function have a "systems" component, including
the interaction of the protein with other proteins, their
impact on the physiology (defined broadly) of the cell
and organism, and the consequences of physiology in a
changing ecosystem in a planetary context [2].

Systems hypotheses can be supported by information
from many areas. Geology, paleontology, and genomics,
for example, provide three records that capture the natural
history of past life on Earth. At the same time, structural
biology, genetics, and organic chemistry describe the
structures, behaviors and reactivities of proteins that allow
them to support present life. It has been appreciated that
a combination of these six types of analysis provides
insights into functional behavior of proteins that cannot
be provided by any of these alone [2]. Over the long term,
we expect that the histories of the geosphere, the bio-
sphere, and the genosphere will converge to give a coher-
ent picture showing the relationship between life and the
planet that supports it. This picture will be based, how-
ever, on individual cases that serve as paradigms for mak-
ing the connection.

The aromatase family of proteins offers an interesting sys-
tem to illustrate the power of this combination as a way to
create hypotheses regarding protein function within a sys-
tem [3]. These hypotheses are not "proof", of course, but
are limiting in genomics-inspired biological experimenta-
tion, now that genomic data themselves are so abundant.

Aromatases are cytochrome P450-dependent enzymes
that use dioxygen to catalyze a multistep transformation
of an androgenic steroid (such as testosterone) to an estro-
genic steroid (such as estradiol) (Figure 1). The protein
plays a key role in normal vertebrate reproductive biol-
ogy-a role that appears to have arisen before fish and
tetrapods (land vertebrates, including mammals)
diverged some 375 million years ago [4]. Aromatase is
important in modem medicine as well, especially in
breast and other hormone-dependent cancers [5].

Different numbers of aromatase genes are found in differ-
ent vertebrates. Two aromatase genes are known in teleost
fish [6,7]. Only a single gene is known in the horse [8], rat
[9], and mouse [10]. Cattle have both a functional gene


and a pseudogene built from homologs of exons 2, 3, 5,
8, and 9 of their functional gene; these are interspersed
with a bovine repeat element [11,12]. In several mamma-
lian species, including humans and rabbits, a single gene
yields multiple forms of the mRNA for aromatase in dif-
ferent tissues via alternative splicing [13-16].

A still different phenomenology is observed in the pig (Sus
scrofa). Three different mRNA molecules had been
reported in different tissues from pig [17-21]. Compelling
evidence then emerged that the three variants of mRNA
identified in cDNA studies arose from three paralogous
genes [22], rather than from a single gene differentially
spliced [23]. This implies that the three aromatase para-
logs in pigs arose via gene duplications relatively recent in
geologic time.

Hypotheses relating to the function of the three aromatase
paralogs depend in part on when those duplications took
place. If they were very recent, the three genes might have
helped pigs adapt to domestication. If they pre-dated the
divergence of pigs and fish [6], they may have different
roles that are very fundamental to reproductive endo-
crinology in vertebrates. We apply here a series of tools to
generate better hypotheses concerning the aromatase fam-
ily of paralogs in swine.

Results
One strategy useful for understanding the function of
genes correlates events in their molecular evolution with
events occurring in the history of other genes in the same
and/or neighboring lineages, and with events recorded in
the geological and paleontological records [2]. We incor-
porated a tool to date the divergence of two or more genes
through an analysis of transitions at synonymous sites of
two-fold redundant coding systems, where the encoded
amino acid has been conserved [24]. This analysis exploits
the approach-to-equilibrium kinetic behavior displayed
by these sites. The analysis yields a transition redundant
exchange (TREx) distance for any gene pair where the syn-
onymous sites have not equilibrated.

To calibrate the silent TREx clock, inter-taxa histograms
relating pig (Sus scrofa) and ox (Bos taurus) were con-
structed for transitions at the silent sites of two-fold
redundant codon systems where the encoded amino acid
was conserved between the species [24]. The major peaks
associated with the separation of these two lineages was
observed at f2 = 0.87, corresponding to a TREx distance of
kt = 0.332. As the fossil record constrains the date of diver-
gence of these two lineages to be 60 + 5 Ma [25-27], and
the codon biases in modem Sus scrofa and Bos taurus
project an equilibrium value for f2 = 0.54 [24], the rate
constants for transitions at the TREx silent sites were



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testosterone


androstenedione


OH
SOH3C



OOH
OHOH
H2C


o0


19-oxo- H
testosterone


OH

19-nortestosterone H 0


OH

estradiol HO

HO HO
Figure I
Reactions catalyzed by aromatases on multiple androgenic substrates.


estimated to be ca. 2.8 x 10-9 transitions/silent site/year
during the time interval that separates these lineages.

Analogous f2 values were then obtained for other verte-
brate aromatase pairs, including fish vs. tetrapods (f2 =
0.56), birds versus mammals (f2 = 0.612), primates versus
ungulates (f2 = 0.823), and horses versus artiodactyls (f2 =
0.828). Assuming a time-invariant single lineage first


1-p3-hydroxy-
androstenedione





19-hydroxy-
androstenedione


19-oxo-
androstenedione




19-norandrostenedione





estrone


order rate constant of 3.6 x 10-9 changes/site/year and an
equilibrium f2 of 0.54, the corresponding dates of diver-
gence are calculated to be 435, 258, 67, and 65 Ma respec-
tively, with the oldest dates being the least precise. The last
three of these dates of divergence are similar to those sug-
gested by the paleontological record [28], within the error
of the calculation, which reflects the modest number of
characters used to calculate the f2 values. A tree for the


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1-p-hydroxy-
testosterone





19-hydroxy-
testosterone


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placental


53.9- 27.4- 26.2-
65.3 38.7 37.5
I I- I


Figure 2
Dating the pig duplication events. An evolutionary tree, fol-
lowing the topology of Figure 5, showing estimated TREx dis-
tances for individual branches calculated from reconstructed
ancestral sequences. The scale corresponds to evolutionary
time (in million years) estimated from the TREx's using a first
order rate constant for transitions of 3 x 10-9 changes per
base per year.





artiodactyl lineage was constructed from the correspond-
ing TREx distances (Figure 2). This was found to be con-
sistent with the tree constructed from other metrics.

The TREx clock is not widely used. It may, however, pro-
vide more accurate dates in regions where synonymous
transitions have not equilibrated than conventional
clocks that combine data from synonymous transitions
and synonymous transversions, or from non-synony-
mous changes. A comparison of different clocks will be
provided in detail elsewhere (Benner et al., in prepara-
tion). Briefly, the rate constants for transitions and trans-
versions are more different than the two rate constants for
purine-purine and pyrimidine-pyrimidine transitions.
Further, nucleotide frequencies can be used to calibrate
the end equilibrium points for two-fold redundant codon
systems directly, and this permits an "approach to equilib-
rium" formalism, well known in chemical kinetics, to be
applied [24,29-31].

From the tree, the TREx distances from the ancestor of
fetal and placental aromatase to the modern enzymes are
0.113-0.079 (using an endpoint of 0.54 to reflect equili-
bration at the silent sites), corresponding to a range in the
time of divergence of 26-38 Ma. The TREx distances from
the divergence of all of the porcine aromatases and the
modem forms ranges from 0.082-0.116, corresponding


to dates of divergence in the range of 27-39 Ma. This sug-
gests that the three aromatase paralogs diverged in the late
Eocene to mid Oligocene.

To further correlate the duplication of the genes with the
fossil record, genomic DNA was analyzed from relatives of
Sus scrofa. Both peccary and babirusa seminal plasma
(Tayassu pecari, from the Center for Reproduction of
Endangered Species, Zoological Society of San Diego; Bab-
yrousa babyrussa, from the Bronx Zoo, New York) was
probed by PCR (Polymerase Chain Reaction) amplifica-
tion using exon 4-specific primers [32]. Bands having the
sizes expected for the corresponding aromatases were
observed by agarose gel electrophoresis. Based on
sequence similarity, two isoforms of aromatase were
obtained from both peccary and babirusa as clones
derived from the PCR products (Figure 3). This establishes
that at least one of the duplications occurred before the
Tayassuidae (the peccaries) diverged from the Suidae (the
true pigs) ca. 35 Ma [33,34].

These data are consistent with an evolutionary model that
holds that the ancestor of pig and oxen (approximated in
the fossil record by Diacodexis, from the early Eocene ca.
55 Ma) [35] contained a single aromatase gene, and that
the paralogous genes in pig arose some 20 million years
later. This suggests that the paralogs in pig can be
explained neither in terms of the fundamentals of verte-
brate reproductive endocrinology, nor as a consequence
of swine domestication.

This does, however, suggest that the emergence of the aro-
matase paralogs was approximately contemporaneous
with the emergence of a litter in the Suoidea larger than
that found in the ancestral artiodactyl condition. While
ruminant and camelid artiodactyls have only one-two
young per litter, suoids in general have at least two young
per litter (as seen in peccaries) and most suines (true pigs)
routinely have three-four young (up to 12 in the domestic
pig, Sus). Note that there has long been the tacit assump-
tion that large litters in suoids represent the primitive arti-
odactyl condition. Large litters are primitive for mammals
in general, and because suoids are plesiomorphic in some
anatomical conditions relative to other artiodactyls (e.g.,
short legs, retention of four digits, bunodont cheek teeth),
they have been assumed to be plesiomorphic in other
respects.

Other data suggest that small litters are in fact the primi-
tive artiodactyl condition. Tragulids (mouse deer or chev-
rotains) are surviving small, primitive ruminants that are
not too dissimilar from Diacodexis in body form, but only
have one-two young per litter. Additionally, fossil record
data on pregnant oreodonts (an extinct group probably
related to the ruminant/camelid artiodactyl lineage, but


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Ovarian
Fetal

Placental

Peccaryl
Peccary2

Babyrousal
Babyrousa2


NHYTCRFGSKLGLECIGMHEKGIMFNNN
SHYTSRFGSKPGLQFIGMHEKGIIFNNN

SHYTSRFGSKPGLECIGMYEKGIIFNND

SHYTSRFGSKPGLQFIGMHEKGIIFNNN
-HYTSRFGSKLGLECIGMHEKGIIFNN-

-HYTSRFGSKPGLECIGMYEKGIIFNN-
-HYTCRFGSKLGLECIGMHEKGIMFNN-


*** *** ** **


*** **** ***


Figure 3
The amino acid alignment of exon 4 of two aromatase isoforms from both peccary and babirusa sequences with exon 4 of pig
aromatase isoforms ovarian, fetal, and placental. Asterisks represent conserved sites.


with a suoid-like plesiomorphic postcranial morphology)
shows that they also only had one-two young [36,371. A
cladogram of the Artiodactyla (Figure 4) illustrates the
probable acquisition of multiparous versus uniparous
reproductive strategies, and places the character of litters
with typically more than two members emerging just
before the divergence of Tayassuidae and Suidae.

The approximate correlation in time of the aromatase
divergence in Suoidea with the enlargement of litters in
Suoidea suggests, as a hypothesis, that the two are func-
tionally related. To expand on this hypothesis, we sought
genomic signatures of functional change within the aro-
matase paralogs. The number of non-synonymous
changes in the gene divided by the number of the synon-
ymous changes, normalized for the number of non-syn-
onymous and synonymous sites (the KA/Ks value),
strongly suggests functional change when the value is sig-
nificantly greater than unity [38,39], and is also an indica-
tor of hypothetical functional change when the value is
high on a branch of a tree relative to other branches of the
same tree [40-43]. KA/Ks values were reconstructed for
individual branches of the evolutionary tree derived from
the Darwin bioinformatics workbench (see Methods)
using a distance matrix and ancestral states constructed by
the method of Messier and Stewart [39]. The typical
branch in the aromatase evolutionary tree has a KA/Ks
value of 0.35. A higher KA/Ksvalue of 0.85 is found in the
episodes of evolution near when the pig aromatases
diverged. While a KA/Ks value of 0.85 does not require the
conclusion that positive selection occurred during the
emergence of these aromatase paralogs, an inference
based on the magnitude of KA/Ks in one branch, relative


to the KA/Ks value for typical branches [40-431, suggests
that adaptive changes occurred during the duplications of
the aromatase genes in pigs.

A complete maximum likelihood analysis of the aro-
matase gene family was performed using the PAUP and
PAML programs. The resulting tree, generated in PAUP, is
shown in Figure 5, with parameters estimated using
PAML. Once more, the generation of paralogs in the pig
was found to have occurred after the divergence of pigs
from oxen. A high KA/Ks value (0.93) was again found in
the divergence of the swine isoforms on the branch lead-
ing to the ancestor of the placental and embryonic
enzymes following their divergence from the pig ovarian
enzyme. The distribution of substitutions along this
branch is consistent with altered functional constraints for
the placental and embryonic enzymes compared with
their extinct and extant counterparts (Tables 1 and 2) [44].

We correlated the episode of rapid sequence change dur-
ing the emergence of the embryonic and placental para-
logs with the structural biology of aromatase. A homology
model of aromatase was built from progesterone 21-
hydroxylase from rabbit liver (coordinates from PDB file
1DT6) [45], a homologous cytochrome P450-dependent
monooxygenase. Residues undergoing replacement dur-
ing the episodes represented by branches in Figure 5
(branches 1-3) are highlighted in color on the 3D model
using a program in prototype with HyperChem (Figure 6).

Multiple features within the pattern of amino acid
replacement were apparent. First, the sites accepting
amino acid replacements in the branches with low KA/Ks


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SELENODONTIA
I I


SUIFORMES
SUOIDEA


Figure 4
Cladogram of the order Artiodactyla showing the extant families and some selected extinct ones. Ruminantia includes the
modern families Tragulidae, Giraffidae, Bovidae, Moschidae, and Cervidae, plus a number of extinct families. "Dichobunidae" is
a paraphyletic assemblage of primitive taxa considered broadly ancestral to the later families. The interrelationships of the fam-
ilies reflect the "traditional" relationship based on morphology [85]. Different arrangements based on molecular information
[86, 87] would alter the placement of the Camelidae and Hippopotamidae but would make no difference to the arguments pre-
sented here concerning the Suoidea. The interrelationships within the Suidae are based on information in several studies [32,
67, 88, 89]. Note that only a couple of extinct suid subfamilies are shown, and that only extant genera of Suinae are shown.
Thick, medium-thick and thin lines represent family or above, subfamily and genera, respectively.



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121


0.33 Pig placental

, 1, ,,i Pig fetal

'' Pig ovary

Ox

",4 Sheep

'', Horse


0.12 ** 0.08 Mouse

0.14 0.18 Rat

>2.0 0.15 Rabbit
** (3)
0.27 Human

0.03 Zebra finch
0.06E Chicken
0.05 Chicken


** I 0.16 Goldfish brain

0.06 Medaka
0.0941 Rainbow trout
0.41 Rainbow trout


0.10 Goldfish ovary

017 Zebrafish

%+f o


Figure 5
Phylogenetic tree for the 18 vertebrate aromatase genes.
Numbers above the branches represent the KA/K, ratios,
while numbers below indicate branches highlighted in Figure
6. Single and double asterisks represent bootstrap values of
95-99% and 100%, respectively. The following sequences
were used: Tilapia nilotica (rainbow trout), gi: 1613859, Oryzias
latipes medakaa), gi: 1786171, Danio rerio (zebrafish),
gi:2306966, Carassius auratus (goldfish, ovary), gi:2662330,
Ictalurus punctatus (catfish), gi:9 12802, Carassius auratus (gold-
fish, brain), gi:2662328, Sus scrofa (pig) placental, isoform 2,
gi: 1762232, Sus scrofa (pig) embryo, isoform 3, gi: 1244543,
Sus scrofa (pig) ovary, isoform I, gi: 1928957, Bos taurus (ox),
gi:665546, Equus caballus (horse), gi:2921277, Mus musculus
(mouse), gi:3046857, Rattus norvegicus (rat), gi:203804, Oryc-
tolagus cuniculus (rabbit), gi:2493381, Homo sapiens (human),
gi:28846, Gallus gallus (chicken), gi:211703, Poephila guttata
(zebra finch, ovary), gi:926845, Ovis aries (sheep), gi:7673985.


values (as represented by branch 2 in Figure 5) were typi-
cally scattered without any obvious pattern over the
surface of the protein. This is expected for neutral drift,
although an adaptive role for these replacements is not
excluded by this analysis.

In contrast, the distribution of sites accepting amino acid
replacements during the episode of rapid sequence
evolution of branch 1 (as indicated by a relatively high KA/
Ks value) involving pig paralogs was not random over the
protein surface. Rather, the sites are clustered near the sub-
strate binding pocket, and in a region of the surface
believed to contact the co-reductant protein, as identified
by mutagenesis experiments in the homolog [46,47].

The clustering of amino acid replacements near a sub-
strate binding site during an episode of rapid sequence
evolution suggests that the substrate specificity of the pro-
tein might be changing in correlation with a change in the
detailed physiological role of the protein. Recent reports
suggest that the substrate and product specificities of the
placental and embryonic enzymes are indeed different
from those of the ovarian enzyme [23,48-50]. Further,
synthesis of estrogen by the ovarian enzyme is more
dependent on the structure of the co-reductant than is the
placental enzyme [51]. Our in silicon analyses rationalize
these experimental observations from a structural per-
spective. The coupling of an evolutionary analysis to a
crystallographic analysis suggests that the amino acid
changes are functionally significant.

Discussion
Today, natural history holds some of the most intellectu-
ally challenging conundrums to ever fascinate the human
mind. Further, natural history offers biological chemists
the opportunity to place broad biological meaning on the
detailed analysis of the structure reactivity of isolated
biological molecules studied in a reductionist setting. To
do so, however, natural history must be connected to the
physical and molecular sciences, both in subject matter
and in culture.

In part to make this connection, natural historians have
sought to change the research paradigm in their field to
favor quantitative data directed towards the "proof" of
hypotheses over "story telling". Proving hypotheses is dif-
ficult in natural history (pace the philosophical reality that
no significant statement in empirical science can ever be
said to be "proven"). The events of interest (such as the
extinction of dinosaurs) are frequently distant in time, or
require a passing of time (as for speciation), making them
difficult to reproduce in a laboratory. The scale of the con-
cepts involved (species, environments, planets) also does
not lend these concepts to laboratory models and labora-
tory-controlled tests. Further, a reductionist approach,


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Table I: Frequency distributions of stem pig duplication substitutions versus substitutions on all other terrestrial vertebrate branches
Terrestrial vertebrates Non-synonymous substitutions Synonymous substitutions Totals

Stem pig duplicates (Branch 'I' in Figure 5) 23 9 32
Remaining branches 598 1449 2047
Totals 621 1458 2079

Fisher's exact test, P = 0.00000094784 [44].



Table 2: Frequency distributions of stem pig duplication substitutions versus substitutions within the Laurasiatheria subtree
Laurasiatheria subtree Non-synonymous substitutions Synonymous substitutions Totals


Stem pig duplicates (Branch 'I' in Figure 5)
Remaining branches
Totals

Fisher's exact test, P = 0.0056688 [44].


,- .. ..1 ,' 1
T^^4' '


I'"fy .


Branch (1)


Branch (2)


.



Branch (3) Reductase binding

Figure 6
The distribution of amino acid replacements on the tertiary
structure of cytochrome P450 homolog. Amino acid replace-
ments occurring along branches highlighted in Figure 5 are
shown in red. The substrate binding pocket and nicotinamide
co-factor are colored yellow and purple, respectively. The
sites that bind the co-reductant are highlighted in green for
reference.


even when available, will not necessarily generate data
that are relevant to the big issue that concerns the natural
historian. The emphasis on data and proof has amelio-
rated the worst excesses of storytelling in natural history,
with enormous positive impact.

Just as natural historians were purifying their field of sto-
rytelling, however, whole genome sequences began to
emerge. By dramatically increasing the quantity of chemi-
cal data concerning the molecular structures of proteins,
genomics changed the limiting steps in biochemical and
biomedical research. No longer was the typical researcher
attempting to solve an organic chemical or
biotechnological question (What is the sequence of my
protein? How do I express it at high levels to get the
sequence?) for a protein that had been selected for func-
tional reasons. Today, the typical researcher knows the
structure of many proteins, and wishes to select one for
expression and study based on a hypothesis about its
potential function.

Here, the fact that any definition of function, which must
make reference to fitness, requires some systems, ecologi-
cal, or planetary context, makes the natural historian a
natural source of hypotheses. Their full reductionist arma-
mentarium is available in the laboratory to test and
explore any hypothesis that the natural historian might
provide. The biomedical researchers may like some guid-
ance from the natural historian to narrow the broad selec-
tion, or to shorten the random walk, if only slightly.

For this purpose, the forswearing by natural historians of
storytelling has come at a most inopportune time. To the


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modem natural historian, creating hypothesis can easily
be regarded as "storytelling". They are reluctant to do so,
and may criticize as atavistic colleagues who do.

This has created a vacuum in the scientific community.
Very few laboratories exist that can draw upon an exper-
tise in natural history to generate stories that create
hypotheses for the researcher working in experimental
biochemistry and molecular biology.

This article is designed in part to illustrate how this vac-
uum might be filled. Here, we do not just tell a story based
on natural history, or even a story based on natural history
supplemented with physiology and molecular sequence
data. Rather, we show how the addition of other data,
including data from X-ray crystallography, can make a
story sufficiently rich that it can be viewed as being inter-
nally consistent with a wide range of independent data
drawn from independent sources. This creates a hypothe-
sis that is more than a story, even if it is less than proven.

With aromatase, the congruence of our different analyses
makes a compelling suggestion that the three aromatase
paralogs in pigs arose by two duplication events in the late
Eocene or early Oligocene. The emergence of the
aromatase paralogs corresponded approximately in time
to the emergence of larger litter size in suines. This implies
that the two duplication events are functionally related to
the larger litter sizes. This inference is consistent with the
physiological impact of estrogen synthesis by these para-
logs in Sus. Steroid production by the porcine embryo is
tightly controlled by the transient expression of aromatase
and 17-hydroxylase (P450C17) between days 10 and 13
[20,21,52]. In contrast, estrogen synthesis by the equine
embryo begins as early as day 6 and increases with
embryo age and diameter [52]. The estrogen produced by
the pig embryonic aromatase is believed to have an
impact on the mobility, spacing, and implantation of the
concept [52-56]. Adequate spacing would appear to be
required to manage a larger litter.

This is consistent with a structural biological analysis that
correlates specific amino acid replacements with specific
changes in the substrate and product specificity of the pro-
tein [57]. Interestingly, the substrate specificity of human
aromatase is reported to be more similar to that displayed
by the pig placental enzyme than the ovarian form
[48,49]. This is an unexpected similarity given that our
evolutionary analysis suggests a change in biochemical
function along the fetal/placental branch in the Suidae.

It should be noted that the hypothesis is supported by the
combination of data that individually would not have
strength past storytelling. Thus, the KA/Ks ratio of 0.93
would not, by itself, compel any particular interpretation.


Its implications are greater given the relatively low KA/Ks
ratios of other branches of the tree. But the addition of
crystallographic information, itself not compelling,
makes a combination that is more compelling.

Further, this hypothesis generation itself generates discov-
eries that might lead to their own hypotheses. An analysis
of the evolutionary branches separating pigs and humans
suggests an additional episode of adaptive change. The
branch leading to the ancestor of human aromatase
(branch 3) has a remarkably high KA/Ks ratio (13 non-syn-
onymous and no synonymous changes; Figure 5). This is
a KA/Ks ratio greater than unity, and does (pending evalu-
ation of its statistical significance) compel the inference of
an episode of adaptive change. Intriguingly, these changes
are also clustered in the same regions of the structure as
those changing along branch 1 leading to the stem fetal/
placental enzyme, near the substrate and co-reductant
binding sites. This implies that the substrate/product spe-
cificity of the ancestral aromatase protein was not like that
of either the human or the pig placental forms, but rather
reflects features that arose convergently in these two spe-
cies [58].

Notably, four of the sites (positions 47, 153, 219, 269)
that undergo replacement during the emergence of pig
placental aromatase from the last common ancestor are
the same as four that arose in the emergence of the human
aromatase from its last common ancestor. Of these, the
amino acid replacements are identical at two sites (Thr ->
Met at site 153; His -> Arg at site 269). The probability
associated with randomly observing this pattern is
extremely low (0.000021) [59]. An additional site is dis-
placed by a single position in the sequence alignment
(259/260). We hypothesize that these represent an exam-
ple of adaptive parallel evolution.

It is important to point out that even an analysis this
broad is likely to cover only a small part of a complicated
reproductive endocrinology that must be associated with
larger litter sizes. For example, the exact nature of the
products produced by individual aromatases remains
controversial, and may be different in laboratory studies
depending on the conditions where they are studied
[50,60-62]. This is especially the case with the 19-nortes-
tosterone derivatives in Figure 1.

Further, an elegant recent study by Corbin et al. [23] iden-
tified 1 P-hydroxytestosterone as a novel product pro-
duced by recombinant pig ovarian aromatase that is
absent from the products produced by the porcine placen-
tal paralog, or by either human or bovine aromatase. This
testosterone derivative binds to an androgen receptor,
consistent with physiological activity. This was unknown
before just this year, suggesting that more endocrine nov-


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elties remain to be discovered. Any of these may be rele-
vant to a test of this system. For example, these hypotheses
make predictions about the product specificities of the
two peccary aromatases reported here.

In fact, some data suggest that uterine exposure to andro-
gens severely decreases litter size and embryonic survival
during the time of maternal recognition of pregnancy
[63]. This is consistent with the hypothesis of Corbin et al.
[50] that the evolution of the placental paralog is associ-
ated with increased efficiency of testosterone aromatiza-
tion. This is also consistent with the current data, and the
argument presented here.

It goes without saying that still more factors might be
associated with an increase in litter size from one-two
(presumed in Diacodexis, see Figure 4) to 12 or more in
domestic swine. Most trivially, this increase might be
associated with an increase in ovulation rate, and/or an
adjustment in the structures and binding specificities of
estrogen receptors [64].

Nevertheless, the first aromatase duplication, shared by
pigs and peccaries, appears to have happened in the late
Eocene (recognizing the error associated with these
dates), around 35 Ma (Figure 4). This was a time of great
global change, with dramatic cooling in the higher lati-
tudes. More archaic kinds of mammals (e.g., some earlier
families of perissodactyls and artiodactyls) became
extinct, while many modem families (including the Sui-
dae and Tayassuidae) became established at this time
[65]. Suoids differed from other contemporaneous ungu-
lates in their commitment to omnivory, even though a
few forms, such as the modem warthog Phacochoerus
aethiopicus, are more specialized herbivores. Perhaps the
ability to bear a slightly larger litter than other artiodactyls
was advantageous to them in this time of global ecological
transition. However, it should be noted that larger litters
usually mean altricial (i.e., relatively underdeveloped)
young, a reproductive strategy apparently not available to
larger, cursorial (running-adapted) ungulates, which give
birth to precocial (i.e., well developed) young that are
fully locomotory at birth [66].

The second aromatase duplication, with the ensuing
capacity to produce multiple young, probably occurred
within the family Suidae, some time during the
Oligocene. The molecular data suggest dates of divergence
between porcine fetal and placental aromatases as
between 27-38 Ma, and the earliest known suid is of early
Oligocene age [67], around 33 Ma (Figure 4). Large litters
may have characterized the entire suid family. While the
extant subfamily Suinae is primarily a Plio-Pleistocene
radiation, during the Oligocene to Pliocene suids were
exceedingly diverse taxonomically (with six other sub-


families known) as well as individually abundant as fos-
sils [32,33,67]. In contrast, the predominantly North
American tayassuids were never as diverse. It is possible
that this tremendous Old-World diversity of suids, which
continues to this day, is related to their capacity for the
production of large litters.

This type of speculation opens questions. For example,
the babirusa (an Indonesian pig) is reported to have aver-
age litters of one-two individuals [68,69]. While it is pos-
sible that litters contain three-four individuals, the
occurrence is low [70]. If the common ancestor of babi-
rusa with the African/Eurasian Suinae had a larger litter,
then the babirusa must be hypothesized to represent a
reversion to the more primitive condition. At present,
however, relatively little is known of either the molecular
biology or the natural history of babirusa. The date of
divergence from modern swine is placed between 12-26
million years [71,72], while our TREx analysis using cyto-
chrome b places this data at ca. 18 Ma (data not shown).
Clearly, further study is warranted.

Conclusions
The aromatase family offers an example where a combina-
tion of phylogenetic analysis, molecular evolutionary
analysis, and chemical analysis set within the context of
the paleontological and geological records, and supported
by contemporary bioinformatics and molecular modeling
tools, permits a higher order level of hypothesis genera-
tion concerning the function of proteins. Rather than sim-
ply an Enzyme Commission number (E.C. 1.14.14.1 for
aromatase), a description of catalytic activity (the enzyme
oxidizes testosterone), or a description of the regulatory
pattern (the protein expressed between day 10 and 13),
this type of analysis can generate a truly functional
hypothesis: that the embryonic enzyme oxidizes testoster-
one as a way of managing the larger litter sizes that
emerged in the Suoidea during a time of dramatic plane-
tary cooling (ca. 35 Ma).

Such hypotheses set a higher bar, and a more useful stand-
ard, for the field of systems biology. Evolutionary theory
holds that the only mechanism for obtaining functional
behavior in a biological system is natural selection. Selec-
tion, based on a frequently poorly defined concept of "fit-
ness", is determined by a context that not only includes
the cell and tissue, but also the organism, the ecosystem,
and a changing planet [73]. One cannot expect a collec-
tion of expression data with a mathematical model, by
themselves, to provide this type of functional information
unless it is set in the organismic, ecosystem, and planetary
context. The historical view, of the type outlined here,
becomes a critical tool for constructing this setting (Sup-
plementary Figure [see Additional File 1]).



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Humans have evidently exploited the molecular biology
of larger litters to select for pigs that have truly large litters
(as many as 14) following their domestication. Evidence
for ancient domestication of pigs comes, inter alia, from a
study of Indo-European languages. Proto-Indo-European
(PIE) language had words for "pig" (PIE su-, compared
with Tocharian B suwo, Latin sus, Greek us, Sanskrit sukara,
Church Slavic svinija, Old High German swin, and English
sow; also compare PIE porko-, with Latin porcus, Church
Slavic prase, Old High German farah, etc. [74]), indicating
that the pig has been under human domestication for at
least 6000 years, enough time to have suffered a signifi-
cant impact on its genotype through husbandry. We are
unable, at this time, to exploit complete genome
sequences of pigs or other closely related taxa to discuss
the impact of domestication on aromatase, steroid recep-
tors, amphiregulins, or other proteins that appear to be
associated with uterine capacity and large litter sizes in the
domesticated pig [75]. With the anticipated complete
genome sequences of representatives of various mammal
orders, including artiodactyls, it should be possible to
extend this planetary biology approach.

Methods
Calculations were done under the RedHat Linux 6.3 oper-
ating system on an Intel-Pentium III instrument using
Blackdown's Java-SDK 1.1.8. PAML calculations were
done on an IBM PC using the Unix operating system.
Sequence analyses were aided by the DARWIN bioinfor-
matics package [76]. The DARWIN package can be
obtained by mailing a request to cbrg@inf.ethz.ch.

Initially, pairwise alignments were constructed for the aro-
matase protein sequences available in the database. An
evolutionary distance in PAM units was calculated for
each pair by applying the PamEstimator-package from
DARWIN using an empirical log-odds matrix. From this, a
preliminary evolutionary tree was built for the mamma-
lian sequences, with branch lengths along internal nodes
calculated to minimize a least-squares distance. The
sequences of the ancestral genes and proteins at branch
points in the tree were then reconstructed. From there,
mutations (including fractional mutations) at both the
DNA level and protein level were assigned to individual
branches in the tree using the method of Fitch [77].

The evolutionary history of the aromatase family was then
analyzed using the transition redundant exchange (TREx)
metric based on an analysis of two-fold redundant codon
systems [24,78]. These were obtained for each pairwise
comparison of aligned aromatase genes. The number (n)
of two-fold redundant amino acids (Cys, Asp, Glu, Phe,
His, Lys, Asn, Gln, and Tyr) that are conserved in the
aligned pairs was determined. The number of those
amino acids that are encoded by the same codon (c) was


determined, and the fraction (f2 = c/n) of the codons that
are the same were then tabulated (Supplementary Table
[see Additional File 2]). The TREx distances were calcu-
lated from f2 values using the expression kt = -ln((f2-Equil)/
(1-Equil)), where Equil is the f, value expected after a large
number of nucleotide substitutions have occurred at the
synonymous sites [24].

The DNA sequences for aromatase were phylogenetically
analyzed using a maximum likelihood framework in
PAUP 4.0* (beta 10) [791, with the following parameters:
alpha value representing the gamma distribution (2.1),
the transition-transversion ratio (1.6), proportion of
invariable sites (0.24), and empirical base frequencies.
The resulting topology of the tree mirrors those based on
other molecular studies [80].

For inter-taxon analyses, families in the MasterCatalog
(EraGen Biosciences, Madison WI) were identified that
contained at least one representative protein from both of
the taxa of interest. For these families, all inter-taxa pairs
of genes were extracted, together with the pairwise protein
sequence alignment. A pairwise alignment of the DNA
sequences was then generated to follow the protein
sequence alignment. If a family contained more than one
sequence of a species belonging to one of the taxa ana-
lyzed, then those sequences were checked to determine
whether they were duplicate entries into the database. If
this was the case, only one of the duplicate sequences was
retained in the analysis. A histogram of inter-taxa pairs
was constructed, and the f, value characteristic of
orthologs determined [24]. This was used to calibrate the
TREx clock using the divergence of pigs and oxen, and pigs
and humans.

Codon biases were obtained from the CUTG (Codon
Usage Tabulated from GenBank) made available by the
Kazusa DNA Research Institute Foundation, Japan [81].

Pairwise TREx distances were used to generate lengths for
the branches connecting the swine paralogs using the
minimum evolution criterion in PAUP. This preliminary
analysis was followed by a maximum likelihood analysis
for the complete dataset using the PAML program [82].
This includes the assignment of KA/Ks values to individual
branches. Tests of parallel evolution were conducted using
Converge [59], implementing the YIT model.

Secondary structural data based on homology modeling
for aromatases were generated using the DARWIN bioin-
formatics package, and in agreement with previous stud-
ies [83,84]. Renderings of the three dimensional structure
of the proteins were obtained using a beta version of the
HyperProtein package (HyperCube, Gainesville FL, USA
32601).


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Authors' contributions
EAG performed the evolutionary, statistical and structural
analyses, and prepared the manuscript. LGG cloned genes
as part of his Masters work, and called the evolutionary
problem to the attention of SAB. TL provided computa-
tional infrastructure. RCMS and FAS initiated the work
with suid reproductive endocrinology, and supervised
LGG. DRS and DAL did the initial bioinformatics analysis.
CMJ provided paleontological expertise, constructed the
cladogram, and helped prepare the manuscript. SAB has
developed planetary biological analysis as a paradigm for
generating hypotheses about the biological function of
proteins, and prepared the manuscript.


Additional material


Additional File 1
Illustration of planetary biology. This figure illustrates the concepts of
planetary biology as they relate to combining genomic, paleontological,
chemical and ecological records to understand the history of the biosphere.
Click here for file
[http://www.biomedcentral.com/content/supplementary/1741-
7007-2-19-Si.jpeg]

Additional File 2
An analysis ofsilent nucleotide substitutions in vertebrate aromatases. The
first five columns from the left indicate the index number of sequence 1
compared with sequence 2, the fraction of sites at conserved two-fold
redundant coding systems that are identical (f2), the number of such sites
that are conserved (c2), and the number of such sites overall (n2). The
remaining columns report analogous data: for silent sites in codon systems
where a change at the third nucleotide is silent only if the change is a pyri-
midine-pyrimidine transition (f2y, c2y, n2y); in silent sites where a
change at the third nucleotide is silent only if the change is a purine-
purine transition (f2r, c2r, n2r); for the silent sites at three-fold redun-
dant codon systems (f3, c3, n3); and for the silent sites at four-fold redun-
dant codon systems (f4, c4, n4).
Click here for file
[http://www.biomedcentral.com/content/supplementary/1741-
7007-2-19-S2.pdf]


Acknowledgements
We thank three anonymous reviewers for their invaluable comments. We
also thank Alaric Falcon, Andres A. Kowalski and Ge Zhao for their assist-
ance. This work was supported in part by N.I.H. grants GM 54075 and GM
067439-01 (S.A.B.), N.I.H. grant HD 21961 (R.C.M.S., F.A.S.) and USDA-
NRICGP grant 98-35205-6739 (F.A.S., R.C.M.S.).

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