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一种不经热浴从双孢蘑菇子实体中提取DNA的新方法(英文)



全 文 :ACTA EDULIS FUNGI2012.19(2):8~14
Received:April 9,2012; Accepted:April 26,2012
Supported by National Natural Science Foundation of China(No.30800774)
*Corresponding author.Tel:+86-20-85280266 E-mail:xuxuefeng@scau.edu.cn
A New Protocol for ExtractingDNA from Agaricus
bisporus Fruit Bodies without Thermal Incubation
JI Hongchao,WAN Yanjuan,MO Meihua,XU Xuefeng*
(Colege of Food Science,South China Agricultural University,Guangzhou,Guangdong 510642,China)
Abstract:A new,simple and rapid method for obtaining DNA fromAgaricus bisporus fruit bodies is described
and compared with the widely used CTAB and SDS methods in terms of yield,DNA quality and integrity,
and duration of extraction time.Total DNA quality was estimated by restriction endonuclease digestion and
by ITS,ISSR and RAPD analyses using standard protocols.Our data demonstrated that the new method
renders improved yields of total DNA of high quality and integrity,and is less time-consuming than existing
procedures.
Key words:Agaricus bisporus;DNA isolation;restriction endonuclease digestion
  Agaricus bisporus, the white button
mushroom,contains high levels of dietary fiber
and antioxidants,including vitamins C,D and
B12,folates and polyphenols,that are generaly
recognized  as  beneficial  in  preventing
cardiovascular disease and diabetes[1-3]. A.
bisporus is cultivated worldwide,and extensive
research has been undertaken on the molecular
biology of this important mushroom.This
requires a simple and effective method for
extracting genomic DNA and, although
different methods are available,and the quality
of DNA obtained is generaly satisfactory,
these procedures are time consuming and
tedious. Extended  incubation  of  fungal
material in hot water (65 ℃)[4,5] makes a
method unsuitable for analyzing large number
of samples and,furthermore,toxic chemicals
such as phenol and chloroform are required.
Loss and fragmentation of DNA can easily
occur during these stages,which is particularly
undesirable when attempting to isolate DNA
from smal amounts of starting material.
A sufficient quantity of DNA containing
low levels of protein and other impurities is
necessary for PCR amplification. When
extracting DNA from mushroom tissue (fruit
bodies,mycelium),efficient disruption of the
cel wals is important to ensure a high recovery
rate.Several methods have been employed for
disrupting cel wals including intensive shaking
with glass beads[6],grinding with a mortar and
pestle, mechanical  homogenization[7,8],
sonication,enzymic digestion,the French
press[9,10], and microwave irradiation[5,11].
Although shaking with glass beads is widely
used,it is not very effective for extracting
DNA from mushroom fruit bodies.Freezing
fruit bodies with liquid nitrogen is versatile but
leads to severe DNA fragmentation,while
enzymic  digestion  is  relatively  costly.
Moreover,isolation of DNA from fungal
mycelium by incubating at 65 ℃ in buffers
containing either 3% SDS or 2% CTAB
requires several steps,toxic chemicals,and is
time consuming.Since there are disadvantages
associated with al the available methods,we
have developed a new protocol for isolating
DNA from A.bisporus fruit bodies,and
compared it with other procedures in terms of
cost,rapidity,and the quality and quantity of
the DNA obtained.
No.2 JI Hongchao,WAN Yanjuan,MO Meihua,et al
1 Materials and Methods
1.1Fungal material
  Fresh fruit bodies of Agaricus bisporus
were purchased from Jiangnan Market,
Guangzhou,washed with sterile distiled water
and stored at-80℃.
1.2Reagents
  Extraction buffer consisted of 100mmol/L
Tris-HCl,50mmol/L Na2EDTA and 500mmol/L
NaCl,adjusted to pH 8.0.PCI[phenol∶
chloroform∶isoamyl alcohol(25∶24∶1,v/v/
v)],70%isopropanol,absolute ethanol,and
sodium acetate were from Guangzhou Jingke
Chemical and Equipment Co.Ltd,Guangzhou,
China.
1.3DNA extraction
  A.bisporus fruit body tissue(0.5g)was
mixed with liquid nitrogen and ground using a
mortar and pestle.Extraction buffer(0.7mL,
70 ℃)was added and the mixture further
homogenized during thawing. Lysate was
transferred directly to a 2mL centrifuge tube,
an equal volume of PCI was added,and the
mixture was vortexed for 2 min. After
centrifugation(12000 g,10min,room temp),
the supernatant was transferred to a fresh
centrifuge tube,and mixed gently with 1/10th
volume of 3mol/L sodium acetate.An equal
volume of isopropanol was then added and,
after mixing,the suspension was kept at
-20℃ for 30 min before centrifugation as
above.After removing the supernatant,the
DNA residue was washed twice with 70%
ethanol,dried at room temperature,dissolved
in 400μL sterile distiled water and treated with
5μL RNase(Takara,10U/μL)for 30min at
37℃.Sodium acetate(1/10th volume,3mol/L)
and two volumes of absolute ethanol were added,
the mixture was alowed to stand at-80℃for
10min,and the reprecipitated DNA was colected
by centrifugation as above.The purification step
was repeated,after which the DNA was dissolved
in 20-50μL sterile distiled water and stored at
-20℃ until further use.DNA extraction using
the CTAB and SDS methods was carried out
as reported previously by NEUHAUSER
[12]and
ERNANDEZ[13],respectively.
1.4Assessment of the extracted DNA
  The quantity and purity of the extracted DNA
were determined using spectrophotometry.A260/280
and A260/230 absorbance ratios were used to
determine the levels of protein and polyphenol/
polysaccharide contamination,respectively.DNA
integrity was determined by gel electrophoresis of
2μL samples on 1%agarose gels.
1.5Primers
Table1 Primers for RAPD,ISSR and ITS analysis
表1 RAPD、ISSR和ITS分析所用引物
Primer
引物
Sequence(5-3)
序列
U20 ACAGCCCCCA
U16 CTGCGCTGGA
M17 CCGTGACTCA
ISSR01 (CA)8GT
ISSR02 (AC)8C
ISSR03 (CA)8T
ITS4 TCCTCCGCTTATTGATATGC
ITS5 GGAAGTAAAAGTCGTAACAAGG
1.6PCR amplification
  The quality and integrity of the extracted
DNA,and its suitability for PCR amplification,
were determined using Internal Transcribed Spacer
(ITS),Random Amplified Polymorphic DNA
(RAPD)and Inter-Simple Sequence Repeat
(ISSR)primers(Table 1).
1.6.1ITS analysis
   DNA quality was assessed by PCR using
ITS[14,15]primers in reaction mixtures(50μL total
volume)consisting of 2.5UTaq DNA polymerase
(Takara),5μL(10×)PCR buffer(with Mg
2+),
4μL dNTP mixture(0.25mmol/L each),0.5μL
each of forward and reverse primers(10mmol/L)
(Table1,synthesized by Invitrogen,Guangzhou),
and 50ng DNA.Amplification conditions were:
94℃for 3min,30cycles of 40sat 94℃,40s
at 56℃,1min at 72℃,folowed by a final
extension at 72℃for 10min.

ACTA EDULIS FUNGI  Vol.19
1.6.2RAPD and ISSR analysis
  DNA quality and the presence of potential
inhibitors was also determined by PCR using
RAPD and ISSR primers in reaction mixtures
(50μL total volume)consisting of 1.25UTaq
DNA polymerase,5μL(10×)PCR buffer(with
Mg2+),4 μL dNTP mixture (0.25 mmol/L
each),0.5μL primer(10 mmol/L)(Table
1),and 10ng DNA
[16].RAPD amplification
conditions consisted of:94 ℃ for 3 min,
40cycles of 40sat 94 ℃,1 min at 50 ℃,
1min at 72℃,folowed by a final extension at
72℃for 5min.ISSR amplification conditions
consisted of 94℃for 3min,42cycles of 40s
at 94℃,40sat 45℃,2 min at 72℃,
folowed by a final extension at 72 ℃ for
10min.Aliquots (5 μL)of each reaction
mixture was analyzed on 1.2% (w/v)agarose
gels run at 3v/cm for 40min and stained with
Gold View.
1.7Digestion with restriction endonuclease
  Treatment with restriction enzymes was
used to further evaluate DNA purity,quality
and integrity.Digests (20μL total volume)
containing 1μg DNA,2μL(10×)buffer and
1μL restriction endonuclease were incubated at
37℃for 4h(EcoRI,EcoRV and KpnI)or at
30℃for 4h(HindIII).
2 Results and Discussion
2.1Effect of different isolation methods on DNA
yields and quality
   Several methods are available to isolate
DNA from the mycelia of filamentous fungi but
not al are suitable for extracting DNA from
mushroom fruit bodies. In the improved
method described,addition of extraction buffer
at 70 ℃ to the homogenate produced by
grinding the sample with liquid nitrogen
resulted in a series of thawing and freezing
phases.Cel wals in the mushroom tissue were
thereby disrupted both by the mechanical effect
of grinding and by the repeated formation of
ice crystals within the sample.Solubilising the
crude DNA in distiled H2O prior to treatment
with RNase,folowed by re-precipitation with
sodium acetate solution and absolute ethanol,
also negates the use of phenol.
Yields and quality parameters of DNA
isolated using the three procedures are
presented in Table 2and clearly demonstrate
the benefits of the new protocol.Both the SDS
and CTAB methods require samples to be
incubated in boiling water for about 1hand
include six centrifugation steps,so that the total
work-up time is approximately twice as long as
the new protocol.The additional centrifugation
steps may also result in greater DNA losses and
degradation,thereby accounting in part for the
lower yields recorded using the traditional
methods.DNA extracted with the new protocol
gave A260/280values ranging between 1.8∶1and
2∶1,when values higher than 2∶1indicate
protein contamination or DNA degradation.
A260/230values>2.0confirmed there was little
contamination of the samples with phenol or
other aromatic compounds.Elimination of the
requirements for phenol and chloroform also
make the new procedure more environmentaly
friendly and less costly.
As shown in Fig.1,when the same amount
of extracted sample was applied,DNA bands
generated using the new protocol were sharper,
brighter and more unified compared to material
isolated using the SDS and CTAB methods,
indicating lower protein and polysaccharide
contamination and minimal degradation.No
RNA bands were evident,confirming that
treatment with RNase for 30min at 37℃ was
effective in removing this material.
01
No.2 JI Hongchao,WAN Yanjuan,MO Meihua,et al
Table 2 Comparison of three DNA extraction methods
表2 三种DNA提取方法的比较
Method
方法
Incubation
time
温育
时间 (h)
No.of
centrifugations
离心次数
Duration时间(h)
No RNase
treatment
无核糖核酸酶
处理
RNase
treatment
核糖核酸酶
处理
Extracted
DNA
提取 DNA
(μg/μL)
Toxic
chemicals
有毒试剂
(mL)
A260/280 A260/230
Improved
新方法
0  3 <1  2  0.310-1.600 <1.4 1.8-2.0 2.0-2.4
SDS
十二烷基硫酸钠
1  6 >2  4.5  0.124-0.580 >2.8 1.7-1.9 1.6-2.0
CTAB
十六烷基
三甲基溴化铵
1  6 >2  4.5  0.475-0.682 >2.8 1.9-2.2 1.8-2.3
Genomic DNA(1μL)was applied to 1% (w/v)agarose gels in each
case.Lanes:M,M2000molecular weight ladder;1,SDS method;
2,Improved method;3,CTAB method
泳道M:分子量标记;泳道1:十二烷基硫酸钠方法;泳道2:新方法;
泳道3:十六烷基三甲基溴化铵方法。基因组DNA用量为1μL。
Fig.1 Electrophoretic paterns of DNA isolated from
A.bisporusfruit bodies using different extraction methods
图1 不同方法提取双孢蘑菇子实体DNA电泳图
   Preliminary experiments have indicated
that the improved DNA extraction method can,
with minor modifications,also be applied to
fruit bodies of other mushroom species.For
example,efficient DNA extraction was effected
from wild fruit bodies of Auricularia auricula-
judae when higher volumes of lysis buffer were
used to reduce the effect of endogenous
coloidal components.High quality DNA was
also obtained from fruit bodies of Tricholoma
giganteumby initialy slicing the sporophores to
reduce the amount of grinding required.
2.2PCR analysis
  As shown in Fig 2,the target PCR bands
were al of excelent quality,and there was no
discernable difference in the amplification
results using DNA obtained using the new and
the traditional methods.
ITS analysis using ITS4/ITS5primers
[17]is a
popular molecular tool for identifying wild-type
fungal strains and these primers generated a
distinct fragment approximately 750bp in size
using genomic DNA extracted from A.
bisporus using the new protocol(Fig.2A).
Similar fragments were also amplified using
genomic DNA extracted by the new method
from A.auricula-judae and other species(data
not shown).
RAPD analysis, performed with A.
bisporus genomic DNA isolated by the new
protocol using primers M17,U20and U16,
generated fragments ranging from 150bp to>
2.5kb in size(Fig.2B).
ISSR amplification has been applied to
several edible fungi including research on the
delineation of wild and cultivated homokaryotic
strains of A.bisporus[18].The ISSR technique
is more economical than other molecular
fingerprinting methods (i.e.RFLP,AFLP,
SSCP,or SSR)and was used to determine the
quality of the DNA isolated using the new
protocol(Fig.2C).Primers ISSR1,ISSR2and
ISSR3were chosen at random,and fragment
sizes ranging from 300bp to >3.0kb were
obtained.
11
ACTA EDULIS FUNGI  Vol.19
Fig.2 PCR analysis of genomic DNA
图2 新方法提取基因组DNA的不同引物扩增结果
A ITS amplification;Lanes:M,2000bp molecular weight ladder
B RAPD analysis of genomic DNA isolated by the new protocol using three random primers;Lanes:1,Primer M17;2,primer U20;
3,primer U16;M,5000bp molecular weight ladder
C ISSR analysis of genomic DNA extracted by the new protocol using three universal primers;Lanes:1,ISSR01;2,ISSR02;3,
ISSR03;M,5000bp molecular weight ladder
A ITS扩增,泳道 M:分子量标记;B不同引物RAPD分析,泳道1:引物 M17;泳道2:引物U20;泳道3:引物U16;泳道 M:分子量标记;
C不同引物ISSR分析,泳道1ISSR01;泳道2ISSR02;泳道3,ISSR03;泳道 M:分子量标记
2.3Enzymatic digestion analysis
    Digestion with restriction enzymes was
adopted to evaluate the purity,quality and
integrity of the isolated DNA.LOPEZ used
EcoRⅠ and HindⅢ to analyse mitochondrial
DNA  from  industrial  yeasts[19], while
ABOLFAZL used these two restriction enzymes
to determine the quality of genomic DNA
isolated from coniferous tissue [20]. Band
patterns produced folowing enzymatic digestion
of extracted DNA using EcoR Ⅰ,EcoR Ⅴ,
HindⅢ and KpnⅠ are shown in Fig.3.Al
four endonucleases digested the extracted
DNA, with EcoR Ⅰ and EcoR Ⅴ each
generating more than four bands(lanes 1and
2).Our data indicated that the DNA extracted
by the newly developed method was of
sufficiently high quality for restriction enzyme
analysis.
Fig.3 Electrophoretic analysis of DNA fragments
generated by treatment with endonucleases
图3 核酸内切酶酶切DNA电泳
Lanes:1-4,DNA treated with EcoRⅠ,EcoRⅤ,HindⅢand
KpnⅠ,respectively;5,untreated DNA (negative control);
M,10000bp molecular weight ladder
泳道1-4分别为:EcoRⅠ,EcoRⅤ,HindⅢ and KpnⅠ处理
DNA;5未酶切DNA(对照)
21
No.2 JI Hongchao,WAN Yanjuan,MO Meihua,et al
3 Conclusion
  In summary,we have developed a new
protocol for isolating DNA from A.bisporus
fruit bodies.Compared with other procedures
it has several advantages in terms of cost,
rapidity,lower environmental impact,and the
quality and quantity of the DNA obtained.
Acknowledgement: We thank Professor
Jiang Zide for access to laboratory equipment,
and members of the Fungal Institute of South
China Agricultural University for assistance.
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一种不经热浴从双孢蘑菇子实体中提取DNA的新方法
姬宏超,万艳娟,莫美华,徐学锋*
(华南农业大学食品学院,广东广州510642)
摘 要:介绍一种不经热浴快速从双孢蘑菇子实体中提取DNA的新方法,并与传统的CTAB和SDS法相比
较,结果显示:该方法得到的DNA完整性好,时间短,步骤少,有毒试剂用量少,在提取DNA的质量、得率、时
间及完整性等方面都优于传统的CTAB和SDS法,为食药用菌子实体DNA的提取参考。
关键词:双孢蘑菇;DNA提取;内切酶消解
[本文编辑] 王瑞霞
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