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Transcriptome-based gene mining and bioinformatics analysis of p-hydroxybenzoate geranyltransferase genes in Arnebia euchroma

基于新疆紫草转录组的对羟基苯甲酸香叶基转移酶(PGT)基因的挖掘及生物信息学分析



全 文 :2016
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Vol41,No.8 April,2016

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Transcriptomebasedgeneminingandbioinformaticsanalysisof
phydroxybenzoategeranyltransferasegenesinArnebiaeuchroma
LIUTan1,LVChaogeng1,WANGSheng1,YANGWanzhen1,2,GUOLanping1
(StateKeyLaboratoryBreedingBaseofDaodiHerbs,NationalResourceCenterforChineseMateriaMedica,
ChinaAcademyofChineseMedicalSciences,Beijing100700,China;
2SchoolofTraditionalChineseMedicine,CapitalMedicalUniversity,Beijing100069,China)
[Abstract] Thephydroxybenzoategeranyltransferases(PGT)playanimportantroleinthebiosynthesispathwaysofshikoninderiva
tivesSixPGTswereobtainedfromtranscriptomedatebaseofArnebiaeuchromabyusingbioinformaticsmethodsandtheproteins'physio
chemicalpropertiestheyencodedwerepredictedTheresultofproteindomainpredictionshowedalofthesixproteinsequencescon
tainedtheconserveddomainofUbiaprenyltransferasefamilyandpossessedthemotifNDxxDxxxDforprenyldiphosphatebindinganda
GX(K/Y)STALsequenceforputativearomaticringbindingThephylogenetictreeshowedthatPGTandphydroxybenzoatepolypre
nyltransferase(PPT)belongedtotwodiferentcladesTheresultsofgeneexpressionanalysesshowedthattheexpressionlevelsinthe
redshikoninproficientlineandtheovergroundpartofAeuchromathatcouldproduceshikoninderivativeswasmuchhigherthanthe
whiteshikonindeficientlineandtheundergroundpart,whichsuggestedapositivecorelationbetweentheexpressionlevelsofPGT
genesandshikoninproductionThisstudyaimstolayafoudationforfurtherunderstandingofthefunctionandenzymaticpropertiesof
PGTandprovideabasisforthebiosynthesispathwaysandmetabolicregulationofshikoninderivatives
[Keywords] Arnebiaeuchroma;phydroxybenzoategeranyltransferasegene;bioinformaticsanalysis;RealtimePCR
doi:10.4268/cjcmm20160809
·2241·
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èáÆÇ
ßàáÆ
Arnebiaeuchroma(Royle)Johnst
»8—ƒ
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A.gutataBunge,
:B²k
[12]、
²_
[3]、
²
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[7]
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DNA
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q
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[10]。


iãé
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µk¬Ä
PGT
×ØAB

Y

T
Yazaki[11]
Ô
Singh[12]
Ö%žqªáÆ­ßàáÆ$µªTÄ
LePGT1,LePGT2,AePGT。
LÃÄÛ÷©×/m³É
‘GB

,

T
GPP,
SB

YøÄA‚M
NDxxDxxxD
»
GX(K/Y)STAL,
ùÃéÛ÷©Íf
çäHøù

žÃéÕöÄ,MäHøù
[13]。
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£

…†m×Ô?É

øø»jdçæýöUOc‘
?É×$áÆ56
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1 
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AeuchromaPGT
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ßàáÆ
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HiSeq2000
©ó

ñü°
SOAdenovo
¶âã´Mq
2´§
。LePGT1,LePGT2,AePGT
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NCBI
=¼V
(htp://wwwncbinlmnihgov/)。
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figcgi)
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·3241·
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Vol41,No.8 April,2016
Bioedit
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Table1 PrimersusedinRTPCR
ø×Ø =Éó¯
(5′3′)
18S F:TGTTGGATGTGGTGGATTGTG
R:AACGAACGAGTTGGAAAGCA
AePGT1 F:AAGAGAAACAGGGTGGTTGAG
R:CCCAATGCACACTTTCAATCTC
AePGT2 F:GCTAACACTAGCTGGCCTTATT
R:ATCTGCCGGAGATGATAGGT
AePGT3 F:TTAGTTGGCCTTATTACATTTCCTT
R:CACCGACAAAGATGATGGCTC
AePGT4 F:CGCATTGGCTGCTGATATTG
R:CGAAATCGCGGTCGAAGTA
AePGT5 F:GGCTATAGTCCATGTGCCATTA
R:AGCAGAGGAACCCAAGAAAG
AePGT6 F:GCTTCTTGGTGGGTTTGTTATC
R:CGGTGAAGATAGGTCAACTGTAA
AePGT F:GCAAGCACAGCAGAAGAAAG
R:CAATGCAACGGACCAGAAAG
  
g
:F
r/=É
;R
À/=É

3 
äÔµî
31 
ßàáÆ

Y
AePGTs
×Øě™çƹµî
q
NCBI
¾0=¼V$/oT
LePGT1,LeP
GT2,AePGT
ó ¯

ó ¯ < µ e é
18389306,
18389308,158957517),
ñµeçLÃé¹¼


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¯

ñäH
Nr,Nt,Swissprot,COG,KEGG
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aâ
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PGT
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Y)STAL
A‚M

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AePGT1,AePGT2,AePGT3,AePGT4,AePGT5,AePGT6。
ORFFinder
Ñ©+
AePGT1
w(é
1170bp;
AePGT2
w(é
741bp;AePGT3
w(é
771bp;
AePGT4
w(é
924bp;AePGT5
w(é
735bp;
·4241·
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×ÞßàáÆâã´Ä¶ä×åæçèé×âêë
(PGT)
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w(é
924bp。
-VâÄ

YßàáÆ
PGT
×؟°
GenBank
›çó¯V
,GenBank

Šé
KT991519,KT991520,KT991521,KT991522,
KT991523,KT991524。
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ßàáÆ

Y
AePGTs
×Ø/о0ƹµî
Ü°
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¦§g:¶u½.âÄ

Y
AePGTs
×ØÄ/о0ó¯‘n×uè_¹ôÑ
©

+
2)。
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=¼Vµîäý`

ä+

Y
AePGTs
‘:B
UbiA
Û÷©×âêëGde
äý`

ãGd¾0ª«Êöæ-Û÷©/mâê
T,è_HÉVmZÌ_Ä

2-r

ÐÔû˜

æߘ

ôm˜Ö_HÉÄËÉHÊ
。PROSITE
µ
î䐑[¸+

Y
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$‘:B
UbiA
Û÷
©×âêëGdy

q
2),
_yó¯$ýxï
äHq,èdÛ÷©×âêëV:BÄÛ÷©Íf
çäHJ
(N/D)DxxDxxxD。Psortb
Ñ©äøH

Y
AePGTs
‘!ø¦56ôïr
(cytoplasmicmem
brane),
UO
SignalP41Server
»
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†pµîäøH

Y
AePGTs
‘f§³mv<š

í7næ¾ÿÔµàÄ

Y
PGTs,LePGT1,LePGT2
ç­
AePGT
Äa¹

UOAæ
PGT
BeÞ®xÈÉ
(>ÄĶä×åæçØÛ÷©âêë
(phydroxy
benzoatepolyprenyltransferase,PPT)
ÄF
[14],
ïÌ
©
PGTs
Ô
PPTs
×ØÇÞÒU‘_

Ü°
TM
HMMServerv20
‘ntïäý`Ñ©

ä+
AePGT3,AePGT5,AePGT6
:B

YtïzU

AePGT1
B

YtïzU
,AePGT2
B

YtïzU

AePGT4
ôB

YtïzU

+
2 
ßàáÆ
PGT
×ØÄQ‹ËÉví
Table2 SeveralbiologicalinformationsofAePGTs
×Ø
w(
/bp
/ÐÅ
×ç=
èÒÖ

µ-!
Òm!
`=
EN
`=
ô‚¹
͑^
U>¹
/%
AePGT LePGT1 LePGT2
AePGT11875 389 903 C2036H3092N516O537S24 4781 9329 0216 60 49 47
AePGT2 995 246 946 C1302H1944N314O324S8 2494 10118 0491 72 72 73
AePGT31522 256 896 C1326H2009N323O341S9 2987 10672 0523 71 71 69
AePGT41877 307 942 C1621H2447N391O407S9 3783 10583 0447 94 91 86
AePGT5 872 244 932 C1289H1937N307O316S9 2952 11074 0674 89 87 87
AePGT61149 307 910 C1611H2463N389O409S12 3384 10997 0431 77 77 77
q
2 AePGTs
ó¯
UbiA
Û÷©×âêëGdy
Fig2 LabelofUbiAprenyltransferasefamilyinAePGTs
33 
ßàáÆ

Y
AePGTs
×Ø/о0ÄØ/ä
ýµî
“°
ExPaSySOPMA
¦§†p¶

Y
AePGTs
¾0‘nØ/äýÑ©

+
3)。
34 
Ù=‘_×µî
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NCBI
=¼V$µe/TTÔ

Y
AePGTs
U>ÄáÆ

R9Ð

gËo{

ÕÕ

||

)­

k}ÖÉ,ó¯

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÷©âêë
(phydroxybenzoatepolyprenyltransferase,
PPT)。PPT
Ô
PGT
UéïäHq,èdÛ÷©×
   +3 ßàáÆPGTØ/äýví
Table3 ThesecondarystructureinformationsofAePGTs %
×Ø αzU βL’ βâÚ fôââ
AePGT1 4087 1979 617 3316
AePGT2 3902 2805 935 2358
AePGT3 4102 2383 1133 2383
AePGT4 3616 2280 1107 2997
AePGT5 3689 2418 1393 2500
AePGT6 3876 1889 945 3290
AePGT 3725 2255 1144 2876
LePGT1 3681 2117 1238 2964
LePGT2 3595 2353 1013 3039
âêë

SÆÛÄç¶ä×åæç
(PHB)¯
éÛ
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,PPT
ÄÛ÷©×/m³
É@©Òú[,

í
PGT
ôÆÛÄç
GPP¯
éÛ÷
©×Ä/m
[13]。
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PGTs:LePGT1,LePGT2
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·5241·
2016
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41
âÓ

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Vol41,No.8 April,2016
Y
AePGTs
ÄU>¹l+
2。
Õl
,AePGT1
ÔLÃ
ÄU>¹–®

Y
AePGTs
øö±

í
AePGT4,
AePGT5
ÔLÃÄU>¹]O
。LePGT1,LePGT2,
AePGT
Ôu½.âÄ

YßàáÆ
PGTs
•¶ä
Õl
,6
Y
AePGTs
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LePGT1,LePGT2,AePGT
ó
¯¦eJ`ÄU>¹wO

f¦ó¯Ä

V‘B
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AePGT1
–
AePGT
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84aa,
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