Arch. Biol. Sci., Belgrade, 59 (3), 161-167, 2007.
DOI:10.2298/ABS0703161S
MUTATIONS IN THE PAH GENE: A TOOL FOR POPULATION GENETICS STUDY
MAJA STOJILJKOVIĆ1, ANA STEVANOVIĆ1, MAJA DJORDJEVIĆ2, BRANKA PETRUČEV1, NATAŠA TOŠIĆ1,
TEODORA KARAN DJURAŠEVIĆ1, SANJA AVEIĆ1, MILENA RADMILOVIĆ1, and SONJA PAVLOVIĆ1
1 Institute
2 Dr
of Molecular Genetics and Genetic Engineering, 11000 Belgrade, Serbia
Vukan Čupić Mother and Child Healthcare Institute, 11000 Belgrade, Serbia
Abstract – Phenylketonuria (PKU), an inborn error of metabolism, is caused by mutations in the phenylalanine hydroxylase (PAH) gene. In the Serbian population, 19 different PAH mutations have been identified. We used PAH mutations
as molecular markers for population genetics study. The low homozygosity value of the PAH gene (0.10) indicates that
PKU in Serbia is heterogeneous, reflecting numerous migrations throughout Southeast Europe. The strategy for molecular diagnostics of PKU was designed accordingly. To elucidate the origin of the most common (L48S) PKU mutation
in Serbia, we performed haplotype analysis by PCR-RFLP. Our results suggest that the L48S mutation was imported into
Serbia from populations with different genetic backgrounds.
Key words: Phenylketonuria, phenylalanine hydroxylase gene mutations, homozygosity value, expected heterozygosity,
haplotype analysis
UDC 616.441-008.6 : 575.17 : 577.2
INTRODUCTION
mation of a defect in the PAH enzyme and could be a
helpful tool for phenotype prediction in a newborn infant,
for refining diagnosis, and for implementing optimal dietary therapy (K a y a a l p et al., 1997; G u l d b e r g et
al., 1998; G u t t l e r and G u l d b e r g , 2000). Also,
the correlation between mutations in the PAH gene and
responsiveness to tetrahydrobiopterin, a cofactor of the
PAH enzyme used as a specific therapeutic drug, is under
investigation (B l a u and E r l a n d s e n, 2004).
Phenylketonuria (PKU, MIM#261600) is the most common inborn error of amino acid metabolism in Caucasians (average incidence of 1/10000). It is transmitted in
an autosomal recessive pattern and is caused by deficiency of the hepatic enzyme, phenylalanine hydroxylase
(PAH, EC 1.14.16.1), which catalyzes the conversion of
phenylalanine to tyrosine. Disfunction of the PAH enzyme results in an elevated serum level of phenylalanine
and mental retardation, unless dietary intake of phenylalanine is restricted (D o n l o n et al., 2006).
In a previous study of the Serbian population, 19
different disease-causing mutations were identified, corresponding to a mutation detection rate of 97%. The most
frequent mutations, L48S (21%), R408W (18%), P281L
(9%), E390G (7%) and R261Q (6%), account for 60% of
all mutant alleles. Less frequent ones are: R158Q (4.4%),
I306V (4.4%), IVS12+1G>A (4.4%), Q20X (2.9%),
R111X (2.9%), V177L (2.9%), P225T (2.9%), R261X
(2.9%), p.S16>XfsX1 (1.5%), S231F (1.5%), R252Q
(1.5%), R297H (1.5%), IVS10-11G>A (1.5%), and
R413P (1.5%) (http://www.goldenhelix.org/serbian)
(S t o j i l j k o v i ć et al., 2006).
Deficiency of PAH is mainly caused by mutations in
the PAH gene (GenBank accession no. AF404777),
mapped to human chromosome 12q24.1. The PAH gene
contains 13 exons and 12 large introns spanning approximately 90 kb. Over 500 different mutations have been
identified in the PAH gene so far and recorded in the PAH
locus knowledgebase (http://www.pahdb.mcgill.ca)
(S c r i v e r et al., 2003).
Characterization of PAH mutations is a final confir161
162
MAJA STOJILJKOVIĆ ET AL.
The most frequent mutation in PKU patients in Serbia and Montenegro is L48S, with a relative frequency of
21%. This mutation was initially reported in Turkey
(K o n e c k i et al., 1991). It was later reported in many
European populations (Bulgaria, Romania, Czech Republic, Germany, and Belgium - 2%; Croatia and Sicily 5%, Southern Italy - 11%; Turkish patients in Germany13.3%) (Z s c h o c k e, 2003; Z s c h o c k e et al.,
2003). However, the exceptional prominence of L48S detected in Serbia suggests the influence of either a founder
effect and genetic drift or its autochthonous origin. Haplotypes of PAH are nowadays widely used to determine
the chromosomal background on which a mutation arose,
as well as its geographic pattern.
The PAH gene sequence contains a large number of
recognized polymorphisms. There are three forms of polymorphisms: i) seven biallelic restriction fragment length
polymorphisms (RFLPs: BglII, PvuIIa, PvuIIb, EcoRI,
MspI, XmnI, and EcoRV); ii) multiallelic polymorphisms
(variable number of tandem repeats, VNTR, and short
tandem repeats, STR); and iii) silent single nucleotide
polymorphisms, SNPs (e.g., Q232Q).
RFLP, VNTR and STR alleles can be combined to
generate PAH haplotypes. Although several thousands of
different polymorphic PAH haplotypes could be generated from combinations of these alleles, far fewer have actually been observed on human chromosomes. Particular
PAH haplotypes are associated with disease-causing mutations in European populations (S c r i v e r and
K a u f m a n, 2006).
In this study, we analyzed allele frequencies of PKU
mutations in Serbia in order to determine genetic variations at the PAH locus in the Serbian population. We have
also performed haplotype analyses to elucidate the origin
of the most common PKU mutation (L48S) in Serbia.
with L48S being one of two mutations, and one homozygote for L48S, were studied for polymorphism in the
PAH gene.
Calculation of Homozygosity
Homozygosity (j) at the PAH locus in the population
was determined using the equation j = Σxi2, where xi is the
frequency of the ith allele. Here each of the uncharacterized alleles is defined as having a frequency of 1/N,
where N is the total number of mutant chromosomes investigated.
This value is the theoretical frequency of patients
carrying two identical mutations. Homozygosity values
of different populations reflect their mutational heterogeneity for the particular locus (G u l d b e r g et al., 1996).
Calculation of Expected Heterozygosity for
Intron Polymorphisms
Expected heterozygosyties for individual sites were
estimated as one minus the sum of the squares of the allele frequencies (1-∑pi2). For a biallelic system, there are
only two different possibilities (K i d d et al., 2000).
Polymorphism Analysis
Venous blood (5-10 mL) was collected in 3.8% Nacitrate anticoagulant and genomic DNA was extracted using standard procedure (P o n c z et al., 1983).
Detection of EcoRI and XmnI biallelic restriction
fragment length polymorphisms was performed by polymerase chain reaction (PCR) followed by restriction enzyme digestions (PCR-RFLP).
Thirty four patients with PKU, identified through a
neonatal screening program or during genetic counseling
in Dr Vukan Čupić Mother and Child Healthcare Institute
in Belgrade, were further referred to the Institute of Molecular Genetics and Genetic Engineering in Belgrade for
DNA analysis. Detection of PAH gene mutations was
successfully performed using PCR-RFLP, DGGE, and
sequencing methods (S t o j i l j k o v i ć et al., 2006).
We performed PCR for PAH gene introns 5 and 8.
PCR conditions being the same for both EcoRI and XmnI
polymorphisms. Performance of PCR was in a 25-μl final
volume for a reaction medium containing 100 ng of primers, 200 μM dNTPs, 2.25 mM MgCl2, 50 mM KCl, 10
mM Tris-HCl (pH 8.4), and 1 U Taq Polymerase (Perkin
Elmer). Amplification of DNA was acheived by 30 cycles
at 95°C for 30 sec, 58°C for 30 sec, and 72°C for 30 sec,
preceded by an initial denaturation step (95°C for 5 min)
and followed by final elongation (72°C for 10 min). Amplified PCR products were electrophoretically analyzed
on 2% agarose gel, stained with ethidium bromide and
visualized under UV light.
Twelve unrelated patients, compound heterozygotes
Primers used for the EcoRI restriction enzyme poly-
MATERIALS AND METHODS
MUTATIONS IN THE PAH GENE
morphic site were as follows: 5’-AGAGTTTTTAGCATGAAAGGC-3’; and 5’-CTACCCACCAAAAAAAGTACA-3’. The PCR product was 458 bp long. Primers used
for the XmnI restriction enzyme polymorphic site were as
follows: 5’-CTGTACTTGTAAGATGCAGC-3’; and 5’ACTGTCCCAAGCAATCAAAG-3’. The PCR product
was 205 bp long (www.alfred.med.yale.edu).
The amplified products were digested with EcoRI or
XmnI (Biolabs, England) according to manufacturer recommendations. In the presence of an EcoRI or XmnI site,
the amplified fragment was digested into two fragments
of 412 and 45 bp or 110 and 95 bp, respectively, easily
distinguishable upon electrophoresis on 8% polyacrylamide gel. The undigested PCR product indicates the absence of an EcoRI or XmnI site. Detection of three fragments (undigested and digested PCR products) indicates
heterozygosity at the polymorphic site.
The PAH gene intron 5 DNA fragment of a patient
homozygous for the L48S mutation was sequenced for
using the ABI PRISM 310 Sequence Analyzer (Applied
Biosystems, Foster City, CA, USA).
163
ent disease-causing mutations have been identified
(S t o j i l j k o v i ć et al., 2006). This finding suggests
that PKU in Serbia is heterogeneous. Also, the number of
different mutations in relation to the number of mutant
chromosomes is, in itself, a reflection of the allelic variation. In our study, one third of mutations were found on
just one chromosome in the population, and only two mutations, L48S and R408W, were detected on more than 10
chromosomes (Fig. 1). Additionally, the three most common PAH gene mutations account for less that 50% of all
mutant alleles. Homozygosity was observed in three patients only, which gives a frequency of homoallelic PKU
genotypes of 8.82%. As expected, each of them was homozygous for one of the three most frequent mutations.
However, a more direct measure of the heterogeneity of PAH mutations was needed. The homozygosity value was therefore calculated on the basis of mutation frequencies (j= Σxi2). For the population of Serbia, the homozygosity value, j, is 0.10.
RESULTS
Heterogeneity
The Serbian population is characterized by a high
number of different mutations in the PAH gene: 19 differ-
Fig. 1. Number of different PAH mutations in relation to the number of
mutant alleles detected in the Serbian population. 1 - fraction of PAH
mutations detected on one chromosome (31%), 2 - fraction of PAH
mutations detected on two chromosomes (26%), 3 - fraction of PAH
mutations detected on three to 10 chromosomes (32%), 4 - fraction of
PAH mutations detected on more than 10 chromosomes (11%).
Fig. 2. Detection of EcoRI polymorphism by the PCR-RFLP method.
Lanes: 1, 3 - heterozygote for EcoRI polymorphic site, 2 – 100-bp
marker.
164
MAJA STOJILJKOVIĆ ET AL.
Fig. 3. Detection of XmnI polymorphism by the PCR-RFLP method.
Lanes: 1 – 100 bp marker, 2, 5 - homozygote for XmnI polymorphic site, 3, 4 - heterozygote for XmnI polymorphic site.
Polymorphism Analysis
In order to elucidate the origin of the most common
PAH mutation in Serbia (L48S), we analyzed two polymorphic sites (EcoRI and XmnI) of 12 unrelated patients,
compound heterozygotes with L48S being one of two
mutations, as well as one homozygote for L48S.
Our research strategy was based on the finding that
L48S was associated with four different haplotypes (3, 4,
16, and 28) in the populations studied so far (Table 1)
(www.pahdb.mcgill.ca). Since the difference between
these four haplotypes is in the polymorphic sites EcoRI,
XmnI, and EcoRV, our research was focused on these polymorphisms. The exact position of the EcoRV polymorphic restriction site has not yet been determined. We
therefore restricted our analysis to the XmnI and EcoRI
polymorphisms. Using this experimental approach, we
could distinguish between haplotypes 4, 16, and 28.
Our PCR-RFLP analysis of patients carrying the
L48S mutation showed that all of them were heterozygous (+/-) for the EcoRI restriction site. The homozygote
for L48S was also heterozygous for the EcoRI site (Fig.
2). Heterozygosity of the EcoRI site in this patient was
confirmed by DNA sequencing (data not shown). The expected heterozygosity for the intron 5 EcoRI site therefore is 0.5.
Digestion with XmnI revealed three homozygotes
(+/+) and nine heterozygotes (+/-). The homozygote for
L48S was also homozygous XmnI (+/+). The expected
heterozygosity for the intron 8 XmnI site is 0.46 (Fig. 3).
Based on high heterozygosity for the analyzed polymorphic sites, we can conclude that at least two different
haplotypes associated with the L48S mutation exist in the
Serbian population.
MUTATIONS IN THE PAH GENE
165
Table 1. Different PAH haplotype configurations associated with the L48S mutation. [Polymorphic restriction sites: BglII, PvuIIa, PvuIIb, EcoRI,
MspI, XmnI, and EcoRV. +) Restriction site present; -) Restriction site absent].
Haplotype
(position)
BglII
(intron 1)
PvuIIa
(intron 2)
PvuIIb
(intron 3)
EcoRI
(intron 5)
MspI
(intron 7)
XmnI
(intron 8)
EcoRV
(gene 3’
downstream)
3
4
16
28
-
+
+
+
+
-
+
+
+
-
-
+
+
+
+
+
+
DISCUSSION
In this study, mutations in the PAH locus were used
as markers for genetic variations in the Serbian population.
We analyzed a homozygosity value (j) because it indicates the extent of genetic variation at the PAH locus in
a given population. The higher homozygosity value, the
more homogeneous the population is with respect to PAH
mutations (G u l d b e r g et al., 1996).
The most homogeneous population described so far
are Yemenite Jews, in whom a single molecular defect
(deletion in the exon 3 of the PAH gene) is responsible
for all the PKU cases in the population. Accordingly, the
homozygosity value for this population is 1. Populations
of Northeast and Eastern European countries (Latvia,
Lithuania, Southern Poland) are also quite homogeneous.
For the Serbian population, j is 0.10. It is rather low, more
similar to the situation in ethnically mixed populations
(those of Germany and the United States) than to the case
of a small isolated population (Yemenite Jews). It would
be interesting to compare homogeneity of the Serbian
population with that of other populations residing on the
Balkan Peninsula. However, in the majority of Balkan
populations, less than 90% ascertainment of mutations
has been achieved. It does not give an idea of the level of
heterogeneity, since a great number of mutations have not
been characterized. The exception is Croatia, where the
homozygosity value is 0.17, indicating that PKU is moderately homogeneous (Table 2).
Heterogeneity of the PAH gene in the Serbian population reflects numerous historically documented migrations and coexistence of different populations in this part
of the Balkan Peninsula and confirms that gene flow occurred between populations.
The homozygosity value has to be considered when
a PAH gene mutation detection strategy for a particular
population is being created. Since the homozygosity value for the Serbian population is low, a diagnostic strategy has to be designed to identify a great number of mutations. We use denaturation gradient gel electrophoresis
followed by sequencing analysis of all 13 exons of the
Table 2. Homozygosity at the PAH locus in different populations. Σxi2 - homozygosity value; ∗ Σxi2calculated in this study.
Σxi2
No. of
chromosomes
Yemenite Jews
Latvia
Lithuania
Southern Poland
Romania
Croatia
Northern Ireland
Serbia
Germany
1.00
0.58∗
0.54∗
0.44
0,26∗
0.17
0.14
0.10
0.08
44
96
184
80
44
78
242
68
90
Mutation
detection
rate (%)
100
98
95
91.3
88
99.0
99.6
97.0
95.6
United States
0.06
294
94.9
Population
Reference
Avigad et al., 1990
Pronina et al., 2003
Kasnauskiene et al., 2003
Zygulska et al., 1994
Popescu et al., 1998
Zschocke et al., 2003
Zschocke et al., 1995
Stojiljković et al., 2006
Zschocke and Hoffmann.,
2003
Guldberg et al., 1996
166
MAJA STOJILJKOVIĆ ET AL.
PAH gene. The detection rate of 97% achieved in our previous study confirms that our diagnostic approach was
well designed.
with the L48S mutation in the Serbian population, despite
the fact that extended haplotype analysis was not performed.
Polymorphic haplotypes at the PAH locus are used
to study human evolution and the history of human populations. They are markers that can be used to follow migrations between different populations. In addition to
this, PAH haplotypes can also be used to determine the
origin of PAH mutations.
Our preliminary results exclude the possibility that
the L48S mutation originates from Serbia and suggest
that it was imported from populations with different genetic backgrounds.
In a previous study of PAH gene mutations, we
speculated that high frequency of the L48S mutation in
the Serbian population is possibly attributable to mixing
of South Slavic populations with autochthonous populations residing in the region, influenced by east-to-west
Neolithic migrations. However, we could not exclude additional factors, such as the founder effect and/or genetic
drift (S t o j i l j k o v i ć et al., 2006). This hypothesis
had to be tested by determining the haplotype of chromosomes affected by the L48S mutation.
A unique haplotype associated with L48S would
suggest its independent (Serbian) origin. Otherwise, the
association of L48S with different haplotypes would suggest that it was imported during migrations on the territory of Serbia.
Association of L48S with haplotypes 3, 4, 16, and
28 has been reported to date (www.pahdb.mcgill.ca). In
the majority of populations, mutation L48S is associated
with haplotype 4. Haplotype 16 was reported in Croatian
patients with PKU. Haplotype 3 was found in Turkish
and Italian patients. Haplotype 28 was found in Italy.
Since the difference beetwen haplotypes 3, 4, 16, and 28
is in polymorphic sites XmnI, EcoRI and EcoRV (Table
1), we decided to start with haplotype analysis of these
polymorphic sites. Additionally, we had to exclude analysis of EcoRV, since its exact position is not known. We
therefore were not able to discriminate between haplotypes 3 and 4. However, it has been hypothesized that
haplotypes 3 and 4 evolved from a common ancestor
(L i c h t e r - K o n e c k i et al., 1994). Accordingly,
precise data about association of L48S with haplotype 3
or 4 would not contribute to the explanation of its origin.
Our results showed that expected heterozygosities
for the intron 5 EcoRI and intron 8 XmnI polymorphic
sites were high. This finding indicates that L48S is not associated with a particular haplotype. It can therefore be
concluded that more than one haplotype is associated
Family study of all patients with the L48S mutation
will provide full and final information about haplotypes
in the Serbian population and definitely elucidate its origin.
Acknowledgments – This work was supported by the Ministry of Science and Environment Protection, Republic of Serbia (Grant
No.143051).
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МУТАЦИЈЕ У PAH ГЕНУ: ОСНОВА ЗА ПОПУЛАЦИОНО-ГЕНЕТИЧКО ИСТРАЖИВАЊЕ
МАЈА СТОЈИЉКОВИЋ1, АНА СТЕВАНОВИЋ1, МАЈА ЂОРЂЕВИЋ2, БРАНКА ПЕТРУЧЕВ1, НАТАША ТОШИЋ1, ТЕОДОРА КАРАН
ЂУРАШЕВИЋ1, САЊА АВЕИЋ1, МИЛЕНА РАДМИЛОВИЋ1, СОЊА ПАВЛОВИЋ1
1 Институт
2 Институт
за молекуларну генетику и генетичко инжењерство, 11000 Београд, Србија
за здравствену заштиту мајке и детета “Др Вукан Чупић”, 11000 Београд, Србија
Фенилкетонурија је урођена метаболичка болест проузрокована мутацијама у гену за фенилаланин хидроксилазу (PAH). У српској популацији је идентификовано 19 различитих PAH мутација. PAH мутације
коришћене су као молекуларни маркери за популационо-генетичко истраживање. Ниска вредност хомозиготности PAH гена (0,10) указује на хетерогеност
фенилкетонурије у Србији и одражава бројне мигра-
ције у региону југоисточне Европе. У складу са тим,
осмишљена је стратегија молекуларне дијагностике
фенилкетонурије за Србију. У циљу расветљавања
порекла најчешће мутације која узрокује фенилкетонурију у Србији, L48S, урађена је хаплотипска анализа PCR-RFLP методом. Наши резултати сугеришу да
је L48S мутација пореклом из више популација са
различитим генетичким карактеристикама.