Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
2018 | 40 | 01 |
Tytuł artykułu

Coding single nucleotide polymorphisms and SmCPS1 and SmKSL1 subcellular localization are associated with tanshinone biosynthesis in Salvia miltiorrhiza Bunge roots

Warianty tytułu
Języki publikacji
Tanshinone is one of the major medicinal components of the roots of Salvia miltiorrhiza Bunge, and SmCPS1 and SmKSL1 are key enzymes in the tanshinone biosynthesis pathway. To increase our understanding of the coding single nucleotide polymorphisms (cSNPs) involved in tanshinone biosynthesis, seven S. miltiorrhiza landraces were examined. Our results revealed that the tanshinone content was significantly different among the seven landraces. In total, 48 cSNPs in SmCPS1 and 47 cSNPs in SmKSL1 were identified, and of these, 38 and 42 cSNPs, respectively, were associated with tanshinone content. The highest A/G and C/T base substitution rates were in SmCPS1 and SmKSL1, respectively. SmKSL1 expression was significantly, positively correlated with tanshinone IIA and tanshinone I contents, and SmCPS1 expression was significantly associated with tanshinone IIA content. Interestingly, subcellular SmCPS1 and SmKSL1 expression was enriched in the plastids. Therefore, cSNPs of SmCPS1 and SmKSL1 are involved in tanshinone biosynthesis in the plastids, where SmCPS1 and SmKSL1 enzymes catalyze tanshinone production in this species.
Słowa kluczowe
Opis fizyczny
Article 6 [11p.], fig.,ref.
  • College of Life Science, Northwest A and F University, Yangling 712100, China
  • College of Life Science, Northwest A and F University, Yangling 712100, China
  • Shanxi University of Technology, Shanxi, China
  • College of Life Science, Northwest A and F University, Yangling 712100, China
  • College of Life Science, Northwest A and F University, Yangling 712100, China
  • College of Life Science, Zhejiang Sci-Tech University, Hangzhou, China
  • Tasly R and D Institute, Tasly Holding Group Co., Ltd., Tianjin, China
  • Tasly R and D Institute, Tasly Holding Group Co., Ltd., Tianjin, China
  • Tasly R and D Institute, Tasly Holding Group Co., Ltd., Tianjin, China
  • Arai-Kichise Y, Shiwa Y, Nagasaki H, Ebana K, Yoshikawa H, Yano M, Wakasa K (2011) Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing. Plant Cell Physiol 52(2):274–282
  • Berger J, Suzuki T, Senti KA, Stubbs J, Schaffner G, Dickson BJ (2001) Genetic mapping with SNP markers in Drosophila. Nat Genet 29(4):475–481
  • Blair MW, Cortés AJ, Penmetsa RV, Farmer A, Carrasquilla-Garcia N, Cook DR (2013) A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.). Theor Appl Genet theoretische Und Angewandte Genetik 126(2):535–548
  • Bradbury PJ (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19):2633–2635
  • Chasman D, Adams RM (2001) Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation. J Mol Biol 307(2):683–706
  • Chen X, Liao B, Song J, Pang X, Han J, Chen S (2013) A fast SNP identification and analysis of intraspecific variation in the medicinal Panax species based on DNA barcoding. Gene 530(1):39–43
  • Cui G, Duan L, Jin B, Qian J, Xue Z, Shen G, Snyder JH, Song J, Chen S, Huang L (2015) Functional divergence of diterpene syntheses in the medicinal plant Salvia miltiorrhiza. Plant Physiol 169(3):1607–1618
  • Di T, Wang ZM (2007) Advances in methods for SNP detection. J Shanghai Jiaotong Univ 25(2):405–418
  • Frascaroli E, Schrag TA, Melchinger AE (2013) Genetic diversity analysis of elite European maize (Zea mays L.) inbred lines using AFLP, SSR, and SNP markers reveals ascertainment bias for a subset of SNPs. Theor Appl Genet 126(1):133–141
  • Ganal MW, Altmann T, Röder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12(12):211–217
  • Gao W, Cui GH, Kong JQ, Cheng K, Wang W, Yuan Y, Huang LQ (2008) Optimizing expression and purification of recombinant Salvia miltiorrhiza copalyl diphosphate synthase protein in E. coli and preparation of rabbit antiserum against SmCPS. Acta Pharm Sin 43(7):766–772
  • Gao W, Hu TY, Guo J, Lv DM, Dai ZB, Zhou YJ, Huang LQ (2015) Research progress of synthetic biology for tanshinones. China J Chin Mater Med 40(13):2486–2491
  • Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, Tam A, Wang S, Friedmann M, Birol I, Jones SJ, Cronk QC, Douglas CJ (2011) SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour 11(Suppl. 1):81–92
  • Hao C, Hua Y, Dan Z, Gai J, Yu D (2010) Polymorphisms of soybean isoflavone synthase and flavanone 3-hydroxylase genes are associated with soybean mosaic virus resistance. Mol Breed 25(1):13–24
  • Huang JA, Huang YH, Luo JW, Jia-Xian LI, Gong ZH, Liu ZH (2007) Identification of single nucleotide polymorphisms (SNPs) in polyphenol oxidase gene in tea plant (Camellia sinensis). J Hunan Agric Univ 33(4):454–458
  • Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genom 11(5):1–8
  • Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM (2007) A “silent” polymorphism in the MDR1 gene changes substrate specificity. Science 315(5811):525–528
  • Kwok PY, Duan S (2003) SNP discovery by direct DNA sequencing. Methods Mol Biol 212(212):71–84
  • Lee SJ, Kim WY, Kim H, Shon JH, Lee SS, Shin JG (2009) Identification of new CYP2C19 variants exhibiting decreased enzyme activity in the metabolism of S-mephenytoin and omeprazole. Drug Metab Dispos 37(11):2262–2269
  • Li SF, Guo H (2014) RNA-Seq based analysis on cSNP and gene expression level. J Shanghai Jiaotong Univ 34(2):129–133
  • Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J (2009a) SNP detection for massively parallel whole-genome resequencing. Genome Res 19(6):545–552
  • Li YG, Long S, Mei L, Hu Z-B, Wang ZT (2009b) Advancement in analysis of Salviae miltiorrhizae Radix et Rhizoma (Danshen). J Chromatogr A 1216(11):1941–1953
  • Li QDP, Lu WQ, Zhang L, Chen WS (2015) Bioinformatics analysis of copalyl diphosphate synthase in Salviae miltiorrhizae Radix et Rhizoma. Chin Tradit Herbal Drugs 46(6):887–894
  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(− Delta Delta C(T)) Method. Methods 25(4):402–408
  • Lu S (1991) Botany. China Higher Education Press, Beijing
  • Lundberg E, Fagerberg L, Klevebring D, Matic I, Geiger T, Cox J, Älgenäs C, Lundeberg J, Mann M, Uhlen M (2010) Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol 6:450.
  • Mascher M, Wu S, Amand PS, Stein N, Poland J (2013) Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 8(10):76925.
  • Nagaraj N, Wisniewski JR, Geiger T, Cox J, Kircher M, Kelso J, Pääbo S, Mann M (2011) Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 7(1):548.
  • Nelson B, Cai X, Nebenfuhr A (2007) A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. Plant J 51(6):1126–1136
  • Nelson JC, Wang S, Wu Y, Li X, Antony G, White FF, Yu J (2011) Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum. BMC Genom 12(1):352.
  • Nielsen R (2000) Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154(2):931–942
  • Ning K, Fermin D, Nesvizhskii AI (2012) Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. J Proteome Res 11(4):2261–2271
  • Novaes E, Drost DR, Farmerie WG, Pappas GJ, Grattapaglia D, Sederoff RR, Kirst M (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genom 9(1):312.
  • Ossowski S, Schneeberger K, Clark R, Lanz C, Warthmann N, Weigel D (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18(12):2024–2033
  • Peng L, Ru M, Wang B, Wang Y, Li B, Yu J, Liang Z (2014) Genetic diversity assessment of a germplasm collection of Salvia miltiorrhiza Bunge. based on morphology, ISSR and SRAP markers. Biochem Syst Ecol 55(2):156–159
  • Przeworski M, Hudson RR, Di RA (2000) Adjusting the focus on human variation. Trends Genet 16(7):296–302
  • Song QX, Zhang XY, Bu Y, Zhou GH, Feng F (2008) Identification of SNP on ITS and 5.8s gene of Panax ginseng and P. quin-quefolium by ALM-ASA. J China Pharm Univ 39(3):274–278
  • Stickney HL, Schmutz J, Woods IG, Holtzer CC, Dickson MC, Kelly PD, Myers RM, Talbot WS (2002) Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Res 12(12):1929–1934
  • Sun TP, Kamiya Y (1994) The Arabidopsis GA1 locus encodes the cyclase ent-kaurene synthetase A of gibberellin biosynthesis. Plant Cell 6(10):1509–1518
  • Tang W, Wu T, Jian Y, Sun J, Yue J, Yu J, Tang J, Chen G, Wang C, Wan J (2016) SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice. BMC Plant Biol 16(1):1–11
  • Thumma BR, Nolan MF, Evans R, Moran GF (2005) Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp. Genetics 171(3):1257–1265
  • Toyomasu T, Usui M, Sugawara C, Kanno Y, Sakai A, Takahashi H, Nakazono M, Kuroda M, Miyamoto K, Yu M (2015) Transcripts of two ent-copalyl diphosphate synthase genes differentially localize in rice plants according to their distinct biological roles. J Exp Bot 66(1):369–376
  • Vitalis R, Dawson K, Boursot P (2001) Interpretation of variation across marker loci as evidence of selection. Genetics 158(4):1811–1823
  • Wang L (2011) Mining and application of molecular markers from EST Database And Transcriptome Sequencing In Tea Plant (Camellia sinensis). Doctor Dissertation, Hang zhou, Chinese Academy of Agricultural Science.$9A4hF_YAuvQ5obgVAqNKPCYcEjKensW4ggI8Fm4gTkoUKaID8j8gFw!!&v=MTQzNThSOGVYMUx1eFlTN0RoMVQzcVRyV00xRnJDVVJMMmVaK1JxRkNublc3ckpWRjI2SDdLOUZ0Zk1wcEViUEk=
  • Wang WY, Barratt BJ, Clayton DG, Todd JA (2005) Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet 6(2):109–118
  • Wang Q, Weizhen LI, Yongyun Zhang (2010) Adevace in single nucleotide polymorphism and its application. Sichuan Anim Vet Sci 8:31–33
  • Wicks SR, Yeh RT, Gish WR, Waterston RH, Plasterk RH (2001) Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat Genet 28(2):160–164
  • Wu X, Ren C, Joshi T, Vuong T, Dong X, Nguyen HT (2010) SNP discovery by high-throughput sequencing in soybean. BMC Genom 11(1, article 469):1–10
  • Xiong G, Guo H, Wang K, Hu H, Wang D, Xu X, Guan X, Yang K, Bai Y (2010) Polymorphisms of decoy receptor 3 are associated with risk of esophageal squamous cell carcinoma in Chinese Han. Tumor Biol 31(5):443–449
  • Xu H, Song J, Luo H, Zhang Y, Li Q, Zhu Y, Xu J, Li Y, Song C, Wang B (2016) Analysis of the genome sequence of the medicinal plant Salvia miltiorrhiza. Mol Plant 9(6):949–952
  • Yang D, Ma P, Liang X, Wei Z, Liang Z, Liu Y, Liu F (2012) PEG and ABA trigger methyl jasmonate accumulation to induce the MEP pathway and increase tanshinone production in Salvia miltiorrhiza hairy roots. Physiol Plant 146(2):173–183
  • Zhao GR, Yang F, Yuan YJ, Gao XM, Zhang JP (2013) Progress in detection methods of single nucleotide polymorphisms. Prog Mod Biomed 27(1):123–129
  • Zhou XG, Ren LF, Li YT, Meng Z, Yu YD, Yu J (2010) The next-generation sequencing technology: A technology review and future perspective. Sci China Life Sci 53(1):44–57
  • Zhou CY, Jin JQ, Yao MZ (2011) Progress on purine alkaloids metabolism in tea and other plants. J Tea Sci 31(2):87–94
  • Zhou YJ, Gao W, Rong Q, Jin G, Chu H, Liu W, Yang W, Zhu Z, Li G, Zhu G (2012) Modular pathway engineering of diterpenoid synthases and the mevalonic acid pathway for miltiradiene production. J Am Chem Soc 134(6):3234–3241
Typ dokumentu
Identyfikator YADDA
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.