Research Article Evolutionary Pattern and Regulation Analysis to

Hindawi Publishing Corporation
BioMed Research International
Article ID 613910
Research Article
Evolutionary Pattern and Regulation Analysis to Support Why
Diversity Functions Existed within PPAR Gene Family Members
Tianyu Zhou,1 Xiping Yan,1 Guosong Wang,1 Hehe Liu,1,2 Xiang Gan,1
Tao Zhang,1 Jiwen Wang,1 and Liang Li1
1
Key Lab of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University,
Ya’an, Sichuan 625014, China
2
College of Animal Science and Technology, Sichuan Agricultural University, Ya’an, Sichuan 625014, China
Correspondence should be addressed to Hehe Liu; [email protected]
Received 30 June 2014; Accepted 4 November 2014
Academic Editor: Ryuji Hamamoto
Copyright © Tianyu Zhou et al. This is an open access article distributed under the Creative Commons Attribution License, which
permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Peroxisome proliferators-activated receptor (PPAR) gene family members exhibit distinct patterns of distribution in tissues and
differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and
the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and
analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events.
The conserved domains of HOLI (ligand binding domain of hormone receptors) domain and ZnF C4 (C4 zinc finger in nuclear in
hormone receptors) are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible
for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity
functions. The evolutionary variants in the promoter regions and 3 UTR regions of PPARs result into differential transcription
factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions.
These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3 UTR
are essential for PPARs evolution and diversity functions acquired.
1. Introduction
Peroxisome proliferators-activated receptors (PPARs) are transcription factors belonging to the ligand-activated nuclear
receptor superfamily, which play key roles in regulating metabolism, inflammation, and immunity. In vertebrates, the gene
family of PPAR consisted of PPAR, PPAR (also called
PPARb/d or PPAR), and PPAR [1]. Recently, a considerable number of papers have reviewed their importance
in functions within various physiological and biochemistry
processes [2–5]. Their special effects and functional manners
of depending on a ligand-activated way even have attracted
some scientists to consider them as a drug target for therapy
of some metabolic disorders, such as the type 2 diabetes mellitus and atherosclerosis [6].
It has been well established that the PPARs can be divided
into five distinct functional regions, which include DBD
(DNA-binding domain), LBD (ligand-binding domain), AF1
(activation function 1), AF2 (activation function 2), and a
variable hinge region. The DBD and LBD consist of a highly
conserved DNA-binding domain and a moderately conserved ligand-binding domain, respectively. The AF1 and AF2
are two ligand-independent activation function domains. All
these regions except the variable hinge region are highly
conserved among PPAR members and are responsible for
keeping their functions [3]. Although the PPARs share high
similarities with each other in structures, they exhibit distinct
patterns of distribution in tissues and differ in functions [7].
It has been summarized that PPAR mainly is involved in
the oxidation process of hepatocytes, PPAR mainly targets
within the adipocyte proliferation, and PPAR plays essential
roles in origination and fate determination of preadipocyte.
In adult rat, it has shown that PPARs had different expression patterns [8]. Definitely, PPAR is highly expressed in
2
hepatocytes, cardiomyocytes, enterocytes, and the proximal
tubule cells of kidney, PPAR is expressed ubiquitously and
often at higher levels than PPAR and PPAR, and PPAR is
expressed predominantly in adipose tissue and the immune
tissues [4].
It is interesting to investigate why PPARs exhibit distinct
patterns of distribution in tissues and differ in functions even
if they share high similarity of regions. There may be at least
two main aspects of molecular reasons accounting for their
differences. Firstly, it could be explained by the molecular
evolutionary process, for example, the gene duplication event
and the selective patterns. PPAR gene family as one of
the nuclear hormone receptor (NHR) superfamilies evolves
together with other NHR members. It has been demonstrated
that a large number of NHR members are likely to result
from two waves of gene duplication events. The first wave
occurs before the arthropod/vertebrate divergence and has
generated the ancestors of the NHR subfamilies, for instance,
PPARs, RARs, and RXRs. The second wave of duplication
is vertebrate-specific and leads to a diversification inside the
subfamilies, with the emergence of the presently known isotypes such as PPAR, PPAR, and PPAR [3, 7]. However, it
is still unknown which one is the common ancestor gene in
PPAR members, and what the impacts of PPARs divergence
on their functions are. Secondly, the special transcriptions
factors binging in the promoter regions and the miRNAs
target at 3 UTRs of PPARs may be responsible for the distinct
patterns of distribution in tissues. Numerous reports have
established the basis for gene expression patterns in distribution by predicting and comprising the transcription factors
and miRNAs of interested genes [9].
Therefore, in this present study, we took advantage of the
availability of gene sequence data to analyze the PPAR gene
family based on a view of molecular evolutionary relationship
by deducing the possibility of evolution in PPAR gene family,
as well as by predicting and comparing their transcription
factors and miRNAs to primarily understand the reasons for
diversity functions and distinct patterns of expressions in
tissues of PPAR members. These analyses may contribute to
a comprehensive understanding for the functions of PPAR
gene family.
2. Materials and Methods
2.1. PPAR Gene Homology Sequence Collection. The Genomic
Blast function (http://blast.ncbi.nlm.nih.gov/Blast.cgi) was
used for collecting homologous sequences of PPAR gene family members in species. The parameters were set as the default
value. For the minority of the PPAR gene sequences unfound
by blast, we separated supplement in the website of Nucleotide database (http://www.ncbi.nlm.nih.gov/nuccore/) by
manually using keywords. Through blasting the homology
sequences of PPAR, PPAR, and PPAR on NCBI, we
finally obtained 63 homology sequences that belong to
31 species (Table S1 in Supplementary Material available
online at http://dx.doi.org/10.1155/2014/613910). Most of these
sequences were from mammals, and a few of them were
obtained from fish and birds. These collected sequences were
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edited and aligned by the MegAlign in DNAStar (Madison,
Wisconsin, USA).
2.2. Search for Protein Domains. The open reading frames
(ORF) of PPAR sequences in different species were predicted
using online software (http://www.ncbi.nlm.nih.gov/gorf/orfig.cgi). Next, these ORF sequences were confirmed by Pfam
(http://pfam.sanger.ac.uk/). Only if there were homology
amino acid sequences blasted, Pfam would show the ORF
sequences being correctly predicted. Furthermore, the correct amino acid sequences were entered into SMART
(http://smart.embl-heidelberg.de/) platform for a prediction
of protein structure domain.
2.3. Construction of Phylogenetic Tree. The format of each
PPAR homologous protein sequence was edited by BioEdit
software [10]. Then, the protein sequences were used for
constructing phylogenetic tree through a model of maximum
likelihood method (ML) by Mega 5.1 [11]. The topological stability of the maximum likelihood tree was evaluated by 1000
bootstrap replications. The Atlantic salmon PPAR protein
sequence (NM 001123546.1) was selected as the outgroup of
the protein phylogenetic tree.
2.4. Amino Acid Site Selection Pressure Analysis. The sequences of two conserved protein domains (ZnF C4 and HOLI
domains) were chosen and compared by BioEdit, and then
they were classified and merged. According to the analysis
of Bayesian tree phylogeny, we used the site model in PAML
software package in Codeml program [12] to analyze these
two domains.
The site model was constructed to test whether PPAR
gene is subjected to positive selection ( > 1) or negative
selection ( < 1) [13]. This model allows different sites to
have different selection pressure, while there is no difference
in different branches of the phylogenetic tree. The models
named M1a (neutral) and M2a (selection) [13, 14] in the
current study were used twice the log-likelihood difference
(2Δ) following 2 distribution of likelihood ratio test (LRT),
the difference degree of freedom for the two parameters of the
model number.
2.5. Analysis of Transcription Factors. By using Gene (http://
www.ncbi.nlm.nih.gov/gene/) of the NCBI, the location of
the PPAR gene was determined on the chromosome corresponding species. And then, we confirmed the first exon of
the PPAR gene transcription initiation site on a chromosome.
Sequence about 1000 bp was selected to use as the predicted
promoter regions from the upstream of the first exon. On the
TRANSFAC, the Alibaba (http://www.gene-regulation.com/
pub/programs/alibaba2/index.html) can estimate transcription factor binding sites (TFBS) in unknown DNA sequences.
2.6. Predictions of miRNAs in 3 UTR Region of PPAR Members. The miRNAs in 3 UTR region of PPAR members and
their regulatory sites were predicted by TargetScan release
(http://www.targetscan.org/). In the TargetScan, the 3 UTR
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3
PPAR
LCR1
72
Homo sapiens
LCR2
18aa
32
Xenopus laevis
Danio rerio
71aa
28
13aa
37
Gallus gallus
71aa
56
17aa
52
71aa
47
14aa
71aa
98
Canis lupus familiaris
71aa
98
Sus scrofa
33
Mus musculus
21
18aa
HOLI
ZnF C4
8
71aa
9
17aa
71aa
108
107
105
108
108
108
108
160aa
160aa
160aa
160aa
28aa
8
LCR2
19aa
15
ZnF C4
71aa
27
Xenopus laevis
64
Danio rerio
5
Gallus gallus
Canis lupus familiaris
19aa
22
3
Sus scrofa
24aa
25aa
71aa
72
12aa
1
7
7
1
Mus musculus
71aa
12
34aa
71aa
15
20aa
71aa
19
16aa
71aa
51
17aa
LCR1
71aa
LCR2
109
108
107
110
109
109
109
71aa
109
Xenopus laevis
33
71aa
7aa
105
Canis lupus familiaris
468aa
160aa
31 468aa
160aa
31
468aa
HOLI
160aa
160aa
160aa
160aa
160aa
160aa
160aa
31
31
31
31
31
31
31
Length
441aa
396aa
459aa
443aa
459aa
441aa
440aa
159
Sus scrofa
134
Mus musculus
105
Start
108
Length
HOLI
160aa 31 477aa
106
160aa 31 477aa
ZnF C4
107
Gallus gallus
459aa
End
Homo sapiens
Danio rerio
31
474aa
31 468aa
Start
PPAR
30
End
LCR1
1
Homo sapiens
31
468aa
160aa
Start
PPAR
Length
31
111
71aa
71aa
71aa
71aa
71aa
114
108
108
108
108
160aa
31 527aa
160aa
31 475aa
160aa 31 529aa
160aa
31 504aa
160aa 31 475aa
End
Figure 1: The protein domains of PPARs were predicted in 7 representative species. A box represents a conserved domain. The numerals
labeled in the boxes and lines represent the number of amino acid residues. The PPARs coding domain sequences were collected in 7
representative species including human, xenopus, zebrafish, chicken, dog, pig, and mouse.
region of PPAR members of human was searched for miRNAs. The search results were sorted in the miR2Disease Base
(http://www.mir2disease.org/) for predicting functions of the
predicted conservative miRNAs.
3. Results and Analysis
3.1. The Unique Homology and Conserved Domains in PPAR
Gene Family. As it was shown in Table S1, the coding regions
of all PPAR nucleotides were in average length of about
1400 bp, which encode about 466 amino acids. The average
length of nucleotides of PPAR coding domain is 1406 bp,
whereas the average length of nucleotides of PPAR is 1284 bp
which is lower than the average value of the entire PPAR
family. The nucleotide of PPAR is 1479 bp which is obviously
higher than the average value.
The protein domains were predicted corresponding to
each sequence in the coding region through SMART. The
PPAR coding domain sequences in 7 representative species
including human, xenopus, zebrafish, chicken, dog, pig, and
mouse were obtained for a further analysis (Figure 1). The
data demonstrated that all PPARs family members contained
4
the ZnF C4 and HOLI domains, which are conserved among
species. In addition to the conserved domains, low complexity 1 and low complexity 2 regions (LCRs) were in great differences among PPAR members and species. In PPAR, it was
found that LCR2 widely existed in most species, and LCR1
only existed in mice. It is also worth noticing that more
than half of the studied species contained the LCRs domains
in PPAR, except for the absence of LCR2 in xenopus.
In PPAR, the LCR2 domain was only found in zebrafish,
whereas the LCR1 domain was absent in all studied species.
3.2. The Phylogenetic Tree of PPAR Gene Family. In order to
investigate the homologous relationships among PPAR gene
family members, we constructed phylogenetic tree based on
the amino acid level. The phylogenetic tree was constructed
based on the 63 amino acid sequences from 31 species (Table
S1), and the results were shown in Figure 2. The orthologs of
PPAR members from fishes were placed at the base of the
three branches of the tree. Furthermore, the PPAR genes were
spitted into three lineages (support value = 100%). Through
the branches and distances of the phylogenetic tree, PPAR
and PPAR were clustered together. The branch of PPAR
stood alone and was closer to the outgroup than the other
two branches. PPAR might be the earliest ancestor form of
the PPAR gene family. According to the classification, it suggested that the first independent duplication event may occur
in bony fishes before separation from the birds and mammals
during the whole evolutionary process of PPAR gene family.
And after a second duplication event, the isolated types of
PPAR and PPAR may emerge as the paralogs of PPAR.
3.3. Selection Pressure of Amino Acid Residues in PPAR Gene.
To determine the selection states of each amino acid site in
conserved structure of PPARs during the evolution process,
the tools of selective pressure were used for investigating the
different selection patterns based on the conserved motifs
of ZnF C4 domain and HOLI domain, which were widely
included and conserved in PPAR gene family. In branchsite models (Table 1), we found the estimated  value ≥ 1
with the M2a model for HOLI domain and ZnF C4 domain.
It suggests that PPAR genes were under positive selection.
By the LRT test, M1a and M2a were compared with their
corresponding null models (M0), respectively. The results
suggested that M2a ( < 0.05) was more in coincidence with
the data than M1a ( > 0.05). What is more, the LRT tests of
all PPAR members were different. The HOLI domain could
be accepted by M2a, indicating a positive selection pressure
of HOLI domain during the molecular evolution process,
whereas the ZnF C4 domain was rejected.
In a 95% posterior probability, the results (Figures 3(a)
and 3(b)) showed that the positive selection sites in PPAR
HOLI domain were 118G, 137S, and 143I, in PPAR HOLI
domain 20S, 21S, 58S, and 117P, and in PPAR HOLI domain
16S and 75G, whereas in the ZnF C4 domain, there were
no positive selection sites observed in all PPAR members,
except for only one suspected amino acid residue with  value
between 0.5 and 1 observed in ZnF C4 domain of PPAR and
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PPAR, respectively. In PPAR ZnF C4 domain, there were
no positive selection sites observed either.
3.4. Prediction of Transcription Factors. The transcription
factors and their binding sites in promoter regions of PPAR
gene family were predicted in human and chicken, respectively, and the results were listed in Table S2. In chicken, 45,
44, and 39 transcription factors were predicted and targeted at
the promoter regions of PPAR, PPAR, and PPAR, respectively. In human, only a total of 31, 36, and 40 transcription
factors have been predicted at promoter regions of PPAR,
PPAR, and PPAR, respectively, which were different from
it in chicken.
Through comparing transcription factors, we found that
numerous common transcription factors existed among
PPAR members. Then they were compared pairwise among
the three PPAR members, and the results were listed in
Table 2. The PPARs shared 9 common transcription factors
which were targeted at the promoter regions, including Sp1,
CPE bind, CP1, Oct-1, GATA-1, AP-2, NF-1, GR, and
C/EBP in human, while in chicken, 11 common transcription factors were predicted and targeted at the promoter
regions of chicken PPARs, which included CREB, SRF, ICSBP,
Ftz, AP-1, Oct-1, GATA-1, AP-2, NF-1, GR, and C/EBP.
However, the binding sites for each common transcription
factor were varied among PPAR members.
Finally, we quantified the coexisting transcription factors
among PPAR members (Table 3). In human, the amount
of the identical transcription factors between PPAR and
PPAR was 18, while the amount between PPAR and PPAR
is 16. The number of identical transcription factors of PPAR
and PPAR was 12. In chicken, the group of PPAR/ and
PPAR/ shared 20 and 15 identical transcription factors,
respectively.
3.5. Prediction of miRNAs Target at the 3 UTR Region of PPAR
Members. The miRNAs in 3 UTR of PPAR members were
predicted in human. The results (Table S3) showed that, in the
3 UTR region of PPAR, a total of 23 conserved binding sites
of miRNAs were predicted in vertebrates, and 4 conserved
sites of miRNA families were predicted in mammals. In
the 3 UTR region of PPAR (Figure 4(b)) and PPAR
(Figure 4(c)), 5 and 3 conserved sites of miRNA families were
predicted in vertebrates, respectively. Notably, the miR-17 and
miR-9 were predicted in both 3 UTR regions of PPAR and
PPAR, and the miR-27abc and miR-128 were predicted in
both 3 UTR regions of PPAR and PPAR (Figure 4(a)).
The functions of these miRNAs were enriched in PUBMED online. Among the 27 miRNA families, the vast majority were closely related with cancer. For example, the miR142-3p [15], miR-19a [16], and miR-124 [17] were reported
to be involved in hepatocellular carcinoma; the miR-9 [18]
targeting to the 3 UTR region of PPAR was associated with
Hodgkin’s lymphoma. In the 3 UTR region of PPAR, the
miR-138 [19] were reported to be linked to anaplastic thyroid
carcinoma; the miR-17 [20] was related to B-cell lymphoma;
the miR-29c [21] was interrelated with chronic lymphocytic
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Orcinus orca (PPARA)-aa
Tursiops truncatus (PPARA)-aa
Sus scrofa (PPARA)-aa
Ovis aries (PPARA)-aa
69 Bos taurus (PPARA)-aa
Bubalus bubalis (PPARA)-aa
Felis catus (PPARA)-aa
Odobenus rosmarus divergens (PPARA)-aa
65
60 Canis lupus familiaris (PPARA)-aa
Mustela putorius furo (PPARA)-aa
Equus caballus (PPARA)-aa
Homo sapiens (PPARA)-aa
99 Gorilla gorilla gorilla (PPARA)-aa
Macaca mulatta (PPARA)-aa
64
Loxodonta africana (PPARA)-aa
PPAR
Ceratotherium simum simum (PPARA)-aa
64
Rattus norvegicus (PPARA)-aa
100
Mus musculus (PPARA)-aa
94
Oryctolagus cuniculus (PPARA)-aa
83
Cavia porcellus (PPARA)-aa
Octodon degus (PPARA)-aa
90
91
Gallus gallus (PPARA)-aa
97 Anser anser (PPARA)-aa
94 Anas platyrhynchos (PPARA)-aa
100
Xenopus laevis
Danio rerio (PPARA)-aa
100
Salmo salar (PPARA)-aa
100
Xenopus laevis (PPARD)-aa
Danio rerio (PPARD)-aa
Gallus gallus (PPARD)-aa
Anas platyrhynchos (PPARD)-aa
51
96
99
94
100
Rattus norvegicus (PPARD)-aa
Mus musculus (PPARD)-aa
Cavia porcellus (PPARD)-aa
Equus caballus (PPARD)-aa
Dasypus novemcinctus (PPARD)-aa
Sus scrofa (PPARD)-aa
63
99
PPAR
99
99
Bos taurus (PPARD)-aa
Canis lupus familiaris (PPARD)-aa
Oryctolagus cuniculus (PPARD)-aa
65
Homo sapiens (PPARD)-aa
Gorilla gorilla gorilla (PPARD)-aa
Pan troglodytes (PPARD)-aa
Xenopus laevis (PPARG)-aa
Gallus gallus (PPARG)-aa
Anas platyrhynchos (PPARG)-aa
85
67
99
Ficedula albicollis (PPARG)-aa
Cavia porcellus (PPARG)-aa
Octodon degus (PPARG)-aa
59
Rattus norvegicus (PPARG)-aa
95
PPAR
Bubalus bubalis (PPARG)-aa
71 Ovis aries (PPARG)-aa
91 Bos taurus (PPARG)-aa
Sus scrofa (PPARG)-aa
Mus musculus (PPARG)-aa
Felis catus (PPARG)-aa
Pan troglodytes (PPARG)-aa
Canis lupus familiaris (PPARG)-aa
56
Macaca mulatta (PPARG)-aa
Homo sapiens (PPARG)-aa
Nomascus leucogenys (PPARG)-aa
Danio rerio (PPARG)-aa
Salmo salar (PPARG)-aa
0.05
Figure 2: The phylogenetic tree based amino acid sequences. The phylogenetic tree was constructed by amino acid sequences. The sequences
information was provided in Table S1. The phylogenetic tree was constructed by the maximum likelihood method with Mega 5.1. The numbers
on nodes indicate the support values. It showed the bootstrap values were more than 50%.
6
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Table 1: Selection pressure analysis of amino acid sites in PPARs.
Model
Model 0
-HOLI
-HOLI
-HOLI
-ZnF C4
-ZnF C4
-ZnF C4
Model 1a
ln
Parameters estimates
2Δ
−4720.995579
−2960.312353
−2719.120808
−1050.374116
−1033.465323
−1276.57302
-HOLI
−4622.51301
-HOLI
−2894.97063
-HOLI
−2689.49404
-ZnF C4
−1062.29037
-ZnF C4
−1027.39487
-ZnF C4
−1276.57373
0 = 0.93383, 1 = 0.06617
0 = 0.01746, 1 = 1.00000
0 = 0.94599, 1 = 0.05401
0 = 0.02167, 1 = 1.00000
0 = 0.97407, 1 = 0.02593
0 = 0.00539, 1 = 1.00000
0 = 0.98590, 1 = 0.01410
0 = 0.00862, 1 = 1.00000
0 = 0.97625, 1 = 0.02375
0 = 0.00722, 1 = 1.00000
0 = 0.99999, 1 = 0.00001
0 = 0.00168, 1 = 1.00000
Model 2a
-HOLI
−4622.51301
-HOLI
−2894.97063
-HOLI
−2689.49404
-ZnF C4
−1044.04256
-ZnF C4
−1027.39487
-ZnF C4
−1276.57302
0 = 0.93383, 1 = 0.03245, 2 = 0.03372
0 = 0.01746, 1 = 1.00000, 2 = 1.00000
0 = 0.94599, 1 = 0.04003, 2 = 0.01398
0 = 0.02167, 1 = 1.00000, 2 = 1.00000
0 = 0.97407, 1 = 0.00429, 2 = 0.02163
0 = 0.00539, 1 = 1.00000, 2 = 1.00000
0 = 0.98590, 1 = 0.01410, 2 = 0.00000
0 = 0.00737, 1 = 1.00000, 2 = 6.14876
0 = 0.97625, 1 = 0.00871, 2 = 0.01504
0 = 0.00722, 1 = 1.00000, 2 = 1.00000
0 = 1.00000, 1 = 0.00000, 2 = 0.00000
0 = 0.00168, 1 = 1.00000, 2 = 1.00000
196.96513
130.683442
59.253532
12.66312
12.140902
0.000004
Note: selection pressure on amino acid sites of the inspection is based on the calculation of / (), where  is nonsynonymous coding sequences of each
base mutation rate (nonsynonymous substitution rate) and  is a synonymous mutation rate (synonymous substitution rate). When the  > 1, the gene is by
positive selection;  = 1, no selection pressure;  < 1, by purifying selection.
leukemia. In the 3 UTR region of PPAR, the miR-128 [22]
was associated with glioma.
4. Discussions
One new gene is mainly generated by the gene or genome
duplication event [23]. PPARs as one of the NHR superfamilies evolve together with other NHR members, and after it
has undergone twice time of gene duplication events, the
vertebrate-specific PPAR is eventually diverged into three
different isotypes [3, 7]. The phylogenetic tree of PPARs in the
present study demonstrated that PPAR gene family may have
yielded a gene duplication event, which first occurs in bony
fishes before separation from the birds and mammals during
the whole evolution process. PPAR is closer to the outgroup
than the other two branches, supporting that PPAR might
be the original ancestor gene in PPAR gene family. After
being firstly duplicated in fish, PPAR begins to divide into
two subtypes, including the PPAR and the common ancestor
of PPAR and PPAR. These findings are consistent with
the previous studies by Michalik et al., which depicted
an evolutionary process of PPARs. Moreover, PPAR and
PPAR were clustered closer than others, supporting that
they may originate from a homology ancestor gene, and their
divergence may result from another gene duplication event in
vertebrates; however, there is no sufficient evidence to support this hypothesis currently.
Following the gene duplication event in PPARs, the newly
emerging receptors would have acquired the ligand binding
capacities in an independent fashion [24]. Once such capacity
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Mean 
1.5
1.0
0.5
0.0
Mean 
Mean 
HOLI domain
1.5
1.0
0.5
0.0
1.5
1.0
0.5
0.0
118G 137S 143I
50
0
0
50
16S
0
200
117P
58S
20S 21S
150
100
PPAR
100
PPAR
150
200
75G
50
PPAR
100
Amino acid sites
150
200
(a)
Mean 
0.4
0.3
0.2
0.1
0.0
Mean 
Mean 
ZnF C4 domain
0.8
0.6
0.4
0.2
0.0
20
0
40
PPAR
60
80
PPAR
20
0
0.054
0.052
0.050
0.048
0.046
40
60
80
PPAR
0
20
40
Amino acid sites
60
80
(b)
Figure 3: Approximate posterior mean of amino acid sites. There
was a list of amino acids in each sequence of the corresponding 
value. The amino acid residue marked on the image represents the
 > 1 with probability of more than 95%.
was acquired, each receptor of PPARs may begin to further
evolve and refine its specificity for a given ligand. Each PPAR
isotype may then evolve by mutations, which lead to a more
specific range of ligands across species. These hypotheses
could be supported by the sequence variants among PPARs
across species in the present study. Our results showed that all
PPAR members contained the conserved HOLI and ZnF C4
domains, which are important for keeping the functions of
PPAR gene family. HOLI domain located in N-terminal of
the PPAR protein is also known as ligand binding domain of
hormone receptors [25]. It belongs to the LBD region that acts
in response to ligand binding, which caused a conformational
change in the receptor to induce a response, thereby acting
as a molecular switch to turn on transcriptional activity [26].
In addition, ZnF C4 domain is also called C4 zinc finger
in nuclear hormone receptors. This domain was the DBD
region, which recognizes specific sequences, connected via
a linker region to a C-terminal LBD. Both HOLI and ZnF C4
domains are highly conserved among PPAR members and are
responsible for keeping their basic functions for PPAR family
members.
In addition to the two conserved domains, PPAR family
contained low complexity regions (LCRs). LCRs located near
the left of ZnF C4 domain are in great differences among
PPAR members across species. Studies suggested that the
positions of LCRs within a sequence might be important to
both determine their binding properties and maintain biological functions [27]. There are no LCRs existing in PPAR,
suggesting that PPAR might only keep the basic function of
PPAR family. The number of LCRs in PPAR and PPAR
is similar and obviously more than PPAR, indicating differential functions of PPAR and PPAR from PPAR. The
results showed that the variants in LCRs might be involved
in the diversity functions of PPAR members and supported a
common origin of PPAR and PPAR.
Due to the reason that ZnF C4 and HOLI domain are
important for keeping roles of PPAR members, we used patterns of selection pressure to analyze the adaptive evolution
of the conserved protein sequences. The results showed that
the HOLI domain was selected under a natural pressure in the
evolutionary process, whereas the ZnF C4 domain was not.
It showed that ZnF C4 domain was more conservative than
HOLI domain in PPAR family, supporting a more important
role of PPAR zinc finger in keeping PPARs’ functions [28].
The HOLI domain in PPAR with the most amounts of
positive selection sites among PPAR members suggested that
the variations in these positive selection sites were more beneficial for PPAR phylogenetic towards diversity functions.
Studies have confirmed that these chemical properties of
amino acid residues were important to sustain normal protein
folding and keep functions [29]. For instance, sulfhydryl
groups of the peptide chain of two cysteines (cysteine,
referred to as S) form two disulfide linkages with oxidation
reaction. Whether it breaks or reshapes into a new one, it
also could adjust protein to perform certain function [30].
Therefore, it can be inferred that the nucleotide variants in
HOLI domain could be responsible for diversity functions of
PPAR members. In a 95% posterior probability, the positive
selection sites were 118G, 137S, and 143I in PPAR HOLI
domain, were 20S, 21S, 58S, and 117P in PPAR HOLI
domain, and were 16S and 75G in PPAR HOLI domain. It
is interesting to point out that the positive selection sites in
HOLI domain of PPAR and PPAR share more similarity
in locations and amino acid residues, supporting a homology
function of PPAR and PPAR.
The regulatory mechanism of gene expressions plays an
important role in tissue distribution and distinct biological
functions of genes. In eukaryotes, most genes are initiated
and transcribed by lots of specific transcription factors
targeting at their promoter regions [31]. Through predicting
the transcription factors and their binding sites in promoter
region of PPARs, we found that the transcription factors were
varied among PPAR members in human and chicken, which
may account for the specific tissue expression and distinct
functions of PPARs. Some of these predicted transcription
factors and their regulatory effects on PPARs are consistent
8
BioMed Research International
Table 2: The common transcription factors predicted in human and in chicken.
Transcription factor
Binding sites and position
Chicken ()
Human ()
Chicken ()
Oct-1
TTAT (−205)
TGCAT (−50)
TTAwTTk (−463) GCTkT (−737)
C/EBP
AP-2
NF-1
TTGA (−62)
GTTGC (−302)
ACAT (−29)
GGGG (−84)
GGCyG (−239)
GGCT (−108)
TTTTGG (−457) TGGCCA (−127) GCCAA (−140)
ATCCCA (−23)
CCCrG (−65)
TGsC (−15)
ACTC (−71)
TTGC (−192)
AGCCTG (−684) GCCTG (−136)
TGCCA (−560)
GCCAA (−383)
GR
GATA-1
TGTTCT (−137)
TTAT (−205)
ACAsA (−123)
CwGAT (−175)
ACAG (−128)
AGATA (−58)
CREB
SRF
ICSBP
GTCA (−942)
GCCwT (−385)
GGAAA (−399)
CGTCA (−941)
TTCCGG (−896)
CCCT (−39)
ACrTCA (−432)
AnATGG (−174)
GTTT (−42)
Ftz
AP-1
TAAT (−840)
TGAsT (−776)
TTAATT (−463)
TCAGC (−556)
TAAwTG (−343)
TGACTC (−69)
Sp1
CPE bind
CP1
ACAA (−185)
GsATT (−51)
AGAACA (−26)
GCAGA (−312)
GGAGGG (−12)
CrTCA (−74)
ATTGG (−125)
GrGG (−38)
TGACGT (−968)
ATTGG (−913)
Table 3: The number of identical transcription factors among
PPARs in human and in chicken.
PPAR
Human
PPAR PPAR
Human ()
Chicken
PPAR PPAR PPAR
PPAR
PPAR
—
18
18
—
12
16
—
15
15
—
20
18
PPAR
12
16
—
20
18
—
with the previous reports; for example, the transcription factors AP1 and NF-kB were proved to enhance the expression
of PPAR activity [32]. Some of these transcription factors
are also tissue specific, for example, the SP1 expressed in
adenocarcinomas of the stomach [33], CP1 highly expressed
in liver, kidney, and intestine but weakly expressed in adrenals
and in lactating mammary glands [34, 35], and NF-1 detected
in brain, peripheral nerve, lung, colon, and muscle [36], and
so forth. It can be speculated that the variants in the promoter
regions of PPAR and PPAR result into differential transcription factors binding on them that eventually influence
their expressions and tissues distributions. Additionally, there
are 18 common transcription factors between PPAR and
PPAR, whereas the PPAR shared the least amount of common transcription factors with the other two members, which
may contribute to the similarity in expression characteristics
between PPAR and PPAR.
The miRNA can combine with the target mRNA by base
pair, which leads to degradation or inhibition of the quantity
levels of the target mRNA, thereby regulating gene expressions [37]. The regulation of miRNA on gene expressions is
another path shaping gene expression patterns and biological
processes [38]. In the present study, the miRNAs and their
targets sites in 3 UTR region of PPARs were predicted, and
Chicken ()
Human ()
AATAT (−18)
AATT (−75)
AGAAC (−679)
CTTATC (−438)
TGGG (−139)
CCCC (−876)
AkTGGT (−401)
it was observed that the quantity of miRNAs was obviously
differential in PPAR members. The number of miRNAs
predicted in PPAR was significantly more than the other two
members. Moreover, it was worth noticing that most of the
miRNAs were predicted in PPAR, only a minority of them
predicted in at least two PPAR isotypes; for example, only
miRNA-128 was found in PPAR and PPAR and miRNA9 was found in PPAR and PPAR. These differences may
be correlated with the distinct functions of PPAR isotypes,
and PPAR may be regulated by miRNAs in a much more
complex way than the other two PPARs.
5. Conclusions
In the present study, the evolutionary pattern and regulation
characteristics of PPARs were analyzed. The three isotypes
of PPAR gene family may emerge from twice times of gene
duplication events. PPAR might be the original ancestor
gene in PPAR gene family. The conserved domains of HOLI
domain and ZnF C4 are essential for keeping basic roles
of PPAR gene family, and the variant domain of LCRs
may be responsible for their divergences in functions. The
positive selection sites in HOLI domain are beneficial for
PPARs to evolve towards diversity functions. The variants
in the promoter regions and 3 UTR of PPARs resulted
into differential transcription factors and miRNAs involved
in regulating PPAR members that may eventually influence
their expressions and tissue distributions.
Conflict of Interests
The authors declare that there is no conflict of interests
regarding the publication of this paper.
BioMed Research International
9
0
1
2
3
Gene

Human PPARA NM 001001928 3 UTR length: 8376
4
(k)
5
6
7
8
Conserved sites for miRNA families broadly conserved among vertebrates
miR-19ab
miR-21/590-5p
miR-33ab/33-5p
miR-181abc
miR-141/200a
miR-22/22-3p
miR-24/24ab/24-3p
miR-93/93a/105/106a/291a-3p/294/295/302abcde/372/373/428/519a/520be/520acd-3p/1378/1420ac
miR-144 miR-9/9ab
miR-17/17-5p/20ab/20b-5p/93/106ab/427/518a-3p/519d
miR-101/10
miR-124/124ab/50
miR-142-3p
miR-27abc/27a-3p
miR-144
miR-141/200a miR-10abc/
miR-124/1
let-7/98/4458/4500
miR-128/128ab
miR-219-5p/508/508-3p/4782miR-125a-5p/125b-5p/3
Conserved sites for miRNA families conserved only among mammals
miR-539/539-5p
miR-873
miR-335/335-5p
miR-202-3p
(a)
1
(k)
0
Gene
Human PPARD NM 006238 3 UTR length: 2112
2
Conserved sites for miRNA families broadly conserved among vertebrates
miR-138/138ab
miR-148ab-3p/152
miR-9/9ab
miR-29abcd
miR-17/17-5p/20ab/20b-5p/93/106ab/427/518a-3p/519d
Conserved sites for miRNA families conserved only among mammals
(b)
10
20
30
40
50
60
70
80
Gene

Human PPARG NM 015869 3 UTR length: 211
90
100
110
120
130
140
150
160
170
180
190
200
210
Conserved sites for miRNA families broadly conserved among vertebrates
miR-130ac/301ab/301b/301b-3p/454/721/4295/3666
miR-27abc/27a-3p
miR-128/128ab
Conserved sites for miRNA families conserved only among mammals
Sites with higher probability of preferential conversation
8mer
8mer
7mer-8m
7mer-8m
7mer-1A
7mer-1A
3 comp ∗
3 comp ∗
(c)
Figure 4: The miRNAs predicted and their targets sites in 3 UTR region of PPAR genes in human. (a) PPAR; (b) PPAR; (c) PPAR. The
miRNAs targets sites correspond to the 3 UTR region of PPAR genes. The lower corner is the probability of preferential conservation for
sites.
Authors’ Contribution
Tianyu Zhou and Xiping Yan contribute equally as the co-first
authors of the paper.
Multiple Crossbreeding Systems in Waterfowl (2011NZ00998).
References
Acknowledgments
This work was supported by the National Natural Science
Foundation of China (no. 31301964), Chinese Agriculture
Research Service (no. CARS-43-6), the Major Project of Sichuan Education Department (13ZA0252), and the Breeding of
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