Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway

Kleindt CK, Stracke R, Mehrtens F, Weisshaar B (2010)
BMC Research Notes 3(1): 255.

Download
OA
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Volltext vorhanden für diesen Nachweis
Abstract / Bemerkung
Background: The coordinated activity of different flavonoid biosynthesis genes in Arabidopsis thaliana results in tissue-specific accumulation of flavonols, anthocyanins and proanthocyanidins (PAs). These compounds possess diverse functions in plants including light-attenuation and oxidative stress protection. Flavonoids accumulate in a stimulus- and/or development-dependent manner in specific parts of the plant. PAs accumulate in the seed coat (testa). Findings: We describe the biological material and the preparation of total RNA for the AtGenExpress developmental silique and seed series. AtGenExpress ATH1 GeneChip expression data from the different stages were reanalyzed and verified using quantitative real time PCR (qPCR). We observed organ-specific transcript accumulation of specific flavonoid biosynthetic genes consistent with previously published data and our PA compound accumulation data. In addition, we investigated the regulation of PA accumulation in developing A. thaliana seeds by correlating gene expression patterns of specific flavonoid biosynthesis genes with different seed embryonic developmental stages and organs and present two useful marker genes for isolated valve and replum organs, as well as one seed-specific marker. Conclusions: Potential caveats of array-based expression data are discussed based on comparisons with qPCR data. Results from ATH1 microarray and qPCR experiments revealed a shift in gene activity from general flavonoid biosynthesis at early stages of seed development to PA synthesis at late (mature) stages of embryogenesis. The examined PA accumulation-associated genes, including biosynthetic and regulatory genes, were found to be exclusively expressed in immature seeds. Accumulation of PAs initiates at the early heart stage of silique and seed development. Our findings provide new insights for further studies targeting the PA pathway in seeds.
Erscheinungsjahr
Zeitschriftentitel
BMC Research Notes
Band
3
Zeitschriftennummer
1
Artikelnummer
255
ISSN
PUB-ID

Zitieren

Kleindt CK, Stracke R, Mehrtens F, Weisshaar B. Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes. 2010;3(1): 255.
Kleindt, C. K., Stracke, R., Mehrtens, F., & Weisshaar, B. (2010). Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes, 3(1), 255. doi:10.1186/1756-0500-3-255
Kleindt, C. K., Stracke, R., Mehrtens, F., and Weisshaar, B. (2010). Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes 3:255.
Kleindt, C.K., et al., 2010. Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes, 3(1): 255.
C.K. Kleindt, et al., “Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway”, BMC Research Notes, vol. 3, 2010, : 255.
Kleindt, C.K., Stracke, R., Mehrtens, F., Weisshaar, B.: Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes. 3, : 255 (2010).
Kleindt, Christiane Katja, Stracke, Ralf, Mehrtens, Frank, and Weisshaar, Bernd. “Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway”. BMC Research Notes 3.1 (2010): 255.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2016-02-11T10:32:15Z

16 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Time-Course Transcriptome Analysis of Arabidopsis Siliques Discloses Genes Essential for Fruit Development and Maturation.
Mizzotti C, Rotasperti L, Moretto M, Tadini L, Resentini F, Galliani BM, Galbiati M, Engelen K, Pesaresi P, Masiero S., Plant Physiol 178(3), 2018
PMID: 30275057
ASN1-encoded asparagine synthetase in floral organs contributes to nitrogen filling in Arabidopsis seeds.
Gaufichon L, Marmagne A, Belcram K, Yoneyama T, Sakakibara Y, Hase T, Grandjean O, Clément G, Citerne S, Boutet-Mercey S, Masclaux-Daubresse C, Chardon F, Soulay F, Xu X, Trassaert M, Shakiebaei M, Najihi A, Suzuki A., Plant J 91(3), 2017
PMID: 28390103
Proanthocyanidin accumulation and transcriptional responses in the seed coat of cranberry beans (Phaseolus vulgaris L.) with different susceptibility to postharvest darkening.
Freixas Coutin JA, Munholland S, Silva A, Subedi S, Lukens L, Crosby WL, Pauls KP, Bozzo GG., BMC Plant Biol 17(1), 2017
PMID: 28545577
A landscape of hairy and twisted: hunting for new trichome mutants in the Saskatoon Arabidopsis T-DNA population.
Taheri A, Gao P, Yu M, Cui D, Regan S, Parkin I, Gruber M., Plant Biol (Stuttg) 17(2), 2015
PMID: 25348773
Seed production temperature regulation of primary dormancy occurs through control of seed coat phenylpropanoid metabolism.
MacGregor DR, Kendall SL, Florance H, Fedi F, Moore K, Paszkiewicz K, Smirnoff N, Penfield S., New Phytol 205(2), 2015
PMID: 25412428
TRANSPARENT TESTA2 regulates embryonic fatty acid biosynthesis by targeting FUSCA3 during the early developmental stage of Arabidopsis seeds.
Wang Z, Chen M, Chen T, Xuan L, Li Z, Du X, Zhou L, Zhang G, Jiang L., Plant J 77(5), 2014
PMID: 24397827
Functional analysis of Arabidopsis CYP714A1 and CYP714A2 reveals that they are distinct gibberellin modification enzymes.
Nomura T, Magome H, Hanada A, Takeda-Kamiya N, Mander LN, Kamiya Y, Yamaguchi S., Plant Cell Physiol 54(11), 2013
PMID: 24009336
Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon.
Mönke G, Seifert M, Keilwagen J, Mohr M, Grosse I, Hähnel U, Junker A, Weisshaar B, Conrad U, Bäumlein H, Altschmied L., Nucleic Acids Res 40(17), 2012
PMID: 22730287

69 References

Daten bereitgestellt von Europe PubMed Central.

Flower color variation: a model for the experimental study of evolution.
Clegg MT, Durbin ML., Proc. Natl. Acad. Sci. U.S.A. 97(13), 2000
PMID: 10860965
Genetics and biochemistry of seed flavonoids.
Lepiniec L, Debeaujon I, Routaboul JM, Baudry A, Pourcel L, Nesi N, Caboche M., Annu Rev Plant Biol 57(), 2006
PMID: 16669768
Arabidopsis Flavonoid Mutants Are Hypersensitive to UV-B Irradiation.
Li J, Ou-Lee TM, Raba R, Amundson RG, Last RL., Plant Cell 5(2), 1993
PMID: 12271060
The genetics and biochemistry of floral pigments.
Grotewold E., Annu Rev Plant Biol 57(), 2006
PMID: 16669781

AUTHOR UNKNOWN, 1988
The BANYULS gene encodes a DFR-like protein and is a marker of early seed coat development.
Devic M, Guilleminot J, Debeaujon I, Bechtold N, Bensaude E, Koornneef M, Pelletier G, Delseny M., Plant J. 19(4), 1999
PMID: 10504561
Development and function of the angiosperm female gametophyte.
Drews GN, Yadegari R., Annu. Rev. Genet. 36(), 2002
PMID: 12429688

AUTHOR UNKNOWN, 1994
Ovule and embryo development, apomixis and fertilization.
Chaudhury AM, Craig S, Dennis E, Peacock W., Curr. Opin. Plant Biol. 1(1), 1998
PMID: 10066555
Transcriptional programs of early reproductive stages in Arabidopsis.
Hennig L, Gruissem W, Grossniklaus U, Kohler C., Plant Physiol. 135(3), 2004
PMID: 15247381
Transcript profiling of transcription factor genes during silique development in Arabidopsis.
de Folter S, Busscher J, Colombo L, Losa A, Angenent GC., Plant Mol. Biol. 56(3), 2004
PMID: 15604749
Influence of the testa on seed dormancy, germination, and longevity in Arabidopsis.
Debeaujon I, Leon-Kloosterziel KM, Koornneef M., Plant Physiol. 122(2), 2000
PMID: 10677433
Proanthocyanidin-accumulating cells in Arabidopsis testa: regulation of differentiation and role in seed development.
Debeaujon I, Nesi N, Perez P, Devic M, Grandjean O, Caboche M, Lepiniec L., Plant Cell 15(11), 2003
PMID: 14555692
Die morphologischen Mutanten des Göttinger Arabidopsis-Sortiments, einschließlich der Mutanten mit abweichender Samenfarbe
AUTHOR UNKNOWN, 1971
Mutations affecting the testa colour in Arabidopsis
AUTHOR UNKNOWN, 1990
Role of anthocyanidin reductase, encoded by BANYULS in plant flavonoid biosynthesis.
Xie DY, Sharma SB, Paiva NL, Ferreira D, Dixon RA., Science 299(5605), 2003
PMID: 12532018
The mysteries of proanthocyanidin transport and polymerization.
Zhao J, Pang Y, Dixon RA., Plant Physiol. 153(2), 2010
PMID: 20388668
The regulation of flavonoid biosynthesis
AUTHOR UNKNOWN, 2006
The TT8 gene encodes a basic helix-loop-helix domain protein required for expression of DFR and BAN genes in Arabidopsis siliques.
Nesi N, Debeaujon I, Jond C, Pelletier G, Caboche M, Lepiniec L., Plant Cell 12(10), 2000
PMID: 11041882
TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana.
Baudry A, Heim MA, Dubreucq B, Caboche M, Weisshaar B, Lepiniec L., Plant J. 39(3), 2004
PMID: 15255866
Stress-Induced Phenylpropanoid Metabolism.
Dixon RA, Paiva NL., Plant Cell 7(7), 1995
PMID: 12242399
Flavonoids as developmental regulators.
Taylor LP, Grotewold E., Curr. Opin. Plant Biol. 8(3), 2005
PMID: 15860429
A gene expression map of Arabidopsis thaliana development.
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU., Nat. Genet. 37(5), 2005
PMID: 15806101
Increased DNA microarray hybridization specificity using sscDNA targets.
Barker CS, Griffin C, Dolganov GM, Hanspers K, Yang JY, Erle DJ., BMC Genomics 6(), 2005
PMID: 15847692
Evaluation of DNA microarray results with quantitative gene expression platforms.
Canales RD, Luo Y, Willey JC, Austermiller B, Barbacioru CC, Boysen C, Hunkapiller K, Jensen RV, Knight CR, Lee KY, Ma Y, Maqsodi B, Papallo A, Peters EH, Poulter K, Ruppel PL, Samaha RR, Shi L, Yang W, Zhang L, Goodsaid FM., Nat. Biotechnol. 24(9), 2006
PMID: 16964225
A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction.
Barnett MJ, Toman CJ, Fisher RF, Long SR., Proc. Natl. Acad. Sci. U.S.A. 101(47), 2004
PMID: 15542588
The Affymetrix Medicago GeneChip array is applicable for transcript analysis of alfalfa (Medicago sativa)
Tesfaye M, Silverstein KAT, Bucciarelli B, Samac DA, Vance CP., Functional plant biology : FPB. 33(8), 2006
PMID: IND43838515
Independence and reproducibility across microarray platforms.
Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J., Nat. Methods 2(5), 2005
PMID: 15846360
An analysis of intra array repeats: the good, the bad and the non informative
AUTHOR UNKNOWN, 2006
Explaining differences in saturation levels for Affymetrix GeneChip arrays.
Skvortsov D, Abdueva D, Curtis C, Schaub B, Tavare S., Nucleic Acids Res. 35(12), 2007
PMID: 17567617
ATS1 and ATS3: two novel embryo-specific genes in Arabidopsis thaliana.
Nuccio ML, Thomas TL., Plant Mol. Biol. 39(6), 1999
PMID: 10380802
An Arabidopsis gene encoding a Ca2+-binding protein is induced by abscisic acid during dehydration.
Takahashi S, Katagiri T, Yamaguchi-Shinozaki K, Shinozaki K., Plant Cell Physiol. 41(7), 2000
PMID: 10965948
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M., Plant J. 37(6), 2004
PMID: 14996223
TRANSPARENT TESTA10 encodes a laccase-like enzyme involved in oxidative polymerization of flavonoids in Arabidopsis seed coat.
Pourcel L, Routaboul JM, Kerhoas L, Caboche M, Lepiniec L, Debeaujon I., Plant Cell 17(11), 2005
PMID: 16243908
The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain protein and is required for proper development and pigmentation of the seed coat.
Nesi N, Debeaujon I, Jond C, Stewart AJ, Jenkins GI, Caboche M, Lepiniec L., Plant Cell 14(10), 2002
PMID: 12368498
The TRANSPARENT TESTA GLABRA1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes a WD40 repeat protein.
Walker AR, Davison PA, Bolognesi-Winfield AC, James CM, Srinivasan N, Blundell TL, Esch JJ, Marks MD, Gray JC., Plant Cell 11(7), 1999
PMID: 10402433
Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor.
Tohge T, Nishiyama Y, Hirai MY, Yano M, Nakajima J, Awazuhara M, Inoue E, Takahashi H, Goodenowe DB, Kitayama M, Noji M, Yamazaki M, Saito K., Plant J. 42(2), 2005
PMID: 15807784

AUTHOR UNKNOWN, 0
Protocol for small-scale RNA isolation and transcriptional profiling of developing Arabidopsis seeds
AUTHOR UNKNOWN, 2001

AUTHOR UNKNOWN, 2001

AUTHOR UNKNOWN, 0
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Dondrup M, Albaum SP, Griebel T, Henckel K, Junemann S, Kahlke T, Kleindt CK, Kuster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Puhler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
Bioconductor: open software development for computational biology and bioinformatics.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J., Genome Biol. 5(10), 2004
PMID: 15461798
Summaries of Affymetrix GeneChip probe level data.
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP., Nucleic Acids Res. 31(4), 2003
PMID: 12582260
Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP., Biostatistics 4(2), 2003
PMID: 12925520
affy--analysis of Affymetrix GeneChip data at the probe level.
Gautier L, Cope L, Bolstad BM, Irizarry RA., Bioinformatics 20(3), 2004
PMID: 14960456
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.
Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P., Nucleic Acids Res. 31(1), 2003
PMID: 12519987
The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis.
Mehrtens F, Kranz H, Bednarek P, Weisshaar B., Plant Physiol. 138(2), 2005
PMID: 15923334
Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes.
Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P., Adv Bioinformatics 2008(), 2008
PMID: 19956698
A transcriptomic and proteomic characterization of the Arabidopsis mitochondrial protein import apparatus and its response to mitochondrial dysfunction.
Lister R, Chew O, Lee MN, Heazlewood JL, Clifton R, Parker KL, Millar AH, Whelan J., Plant Physiol. 134(2), 2004
PMID: 14730085
The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.
Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT., Clin. Chem. 55(4), 2009
PMID: 19246619

AUTHOR UNKNOWN, 0
Standardized determination of real-time PCR efficiency from a single reaction set-up.
Tichopad A, Dilger M, Schwarz G, Pfaffl MW., Nucleic Acids Res. 31(20), 2003
PMID: 14530455
Thirteen Ways to Look at the Correlation Coefficient
AUTHOR UNKNOWN, 1988
Tannin analysis of food products.
Deshpande SS, Cheryan M, Salunkhe DK., Crit Rev Food Sci Nutr 24(4), 1986
PMID: 3536314
The flavonoid biosynthetic pathway in plants: function and evolution
AUTHOR UNKNOWN, 1994
Flavonoid diversity and biosynthesis in seed of Arabidopsis thaliana.
Routaboul JM, Kerhoas L, Debeaujon I, Pourcel L, Caboche M, Einhorn J, Lepiniec L., Planta 224(1), 2006
PMID: 16395586

AUTHOR UNKNOWN, 0

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Quellen

PMID: 20929528
PubMed | Europe PMC

Suchen in

Google Scholar