Abstract
Three members of Brassica napus TRANSPARENT TESTA 2 (BnTT2) gene family encoding potential R2R3-MYB regulatory proteins of proanthocyanidin biosynthesis were isolated. BnTT2-1, BnTT2-2, and BnTT2-3 are 1102 bp with two introns, and have a 938-bp full-length cDNA with a 260 amino acid open reading frame. They share 98.2–99.3% nucleotide and 96.5–98.5% amino acid identities to each other, and are orthologous to Arabidopsis thaliana TT2 (AtTT2) with 74.1–74.8% nucleotide and 71.1–71.8% amino acid identities. An mRNA type of BnTT2-2 was found to contain unspliced intron 2 and encode a premature protein. They all have an alternative polyadenylation site. BnTT2-1 and BnTT2-3 also have an alternative transcription initiation site. Aligned with AtTT2, their 5′ untranslated regions (UTRs) are astonishingly conserved, and two conserved regions were also found in their 3′ UTRs. Oligonucleotide deletion leads to double-start codons of them. Resembling AtTT2, BnTT2 proteins are nuclear-located R2R3-MYB proteins containing predicted DNA-binding sites, bHLH interaction residues, and transcription activation domains. Southern blot indicated that there might be three BnTT2 members in B. napus, lower than triplication-based prediction. Semiquantitative reverse transcription–polymerase chain reaction (RT–PCR) revealed that the expression of BnTT2-2 is mostly like AtTT2 with intensive expression in young seeds, but it is also expressed in root in which AtTT2 has no expression. BnTT2-1 shows lower tissue specificity and transcription levels, whereas BnTT2-3 is the lowest. Comparative cloning and RT–PCR indicated that seed color near-isogenic lines L1 and L2 have equivalent BnTT2 genes, and the yellow seed color in L2 might be caused by locus/loci other than BnTT2. Our results lay the basis for further investigating the regulatory mechanism of BnTT2 genes in flavonoid pathway and for transgenic creation of novel yellow-seeded B. napus stocks.
Similar content being viewed by others
Abbreviations
- aa:
-
amino acid
- AtTT2/TT2 :
-
Arabidopsis thaliana TRANSPARENT TESTA 2
- BnTT2 :
-
Brassica napus TRANSPARENT TESTA 2
- bp:
-
base pair
- cDNA:
-
complementary DNA
- DAF:
-
day after flowering
- DIG:
-
digoxygenin
- pI:
-
isoelectric point
- Mw:
-
molecular weight
- NCBI:
-
National Center of Biotechnology Institute
- ORF:
-
open reading frame
- PA:
-
proanthocyanidin
- PCR:
-
polymerase chain reaction
- RACE:
-
rapid amplification of cDNA ends
- RT:
-
reverse transcription
- UTR:
-
untranslated region
References
Abraham V, Bhatia CR (1986) Development of strains with yellow seedcoat in Indian mustard (Brassica juncea Czern. & Coss.). Plant Breed 97:86–88
Heneen WK, Brismar K (2001) Maternal and embryonal control of seed colour by different Brassica alboglabra chromosomes. Plant Breed 120:325–329
Bartel B, Matsuda SPT (2003) Seeing red. Science 299:352–353
Debeaujon I, Nesi N, Perez P, Devic M, Grandjean O, Caboche M, Lepiniec L (2003) Proanthocyanidin-accumulating cells in Arabidopsis testa: regulation of differentiation and role in seed development. Plant Cell 15:2514–2531
Shirley BW, Kubasek WL, Storz G, Bruggemann E, Koorneef M, Ausubel FM, Goodman HM (1995) Analysis of Arabidopsis mutants deficient in flavonoid biosynthesis. Plant J 8:659–671
Nesi N, Jond C, Debeaujon I, Caboche M, Lepiniec L (2001) The Arabidopsis TT2 gene encodes an R2R3 MYB domain protein that acts as a key determinant for proanthocyanidin accumulation in developing seed. Plant Cell 13:2099–2114
Pourcel L, Routaboul JM, Kerhoas L, Caboche M, Lepiniec L, Debeaujon I (2005) TRANSPARENT TESTA10 encodes a laccase-like enzyme involved in oxidative polymerization of flavonoids in Arabidopsis seed coat. Plant Cell 17:2966–2980
Debeaujon I, Peeters AJ, Leon-Kloosterziel KM, Koornneef M (2001) The TRANSPARENT TESTA12 gene of Arabidopsis encodes a multidrug secondary transporter-like protein required for flavonoid sequestration in vacuoles of the seed coat endothelium. Plant Cell 13:853–871
Kitamura S, Shikazono N, Tanaka A (2004) TRANSPARENT TESTA19 is involved in the accumulation of both anthocyanins and proanthocyanidins in Arabidopsis. Plant J 37:104–114
Nesi N, Debeaujon I, Jond C, Stewart AJ, Jenkins GI, Caboche M, Lepiniec L (2002) The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain protein and is required for proper development and pigmentation of the seed coat. Plant Cell 14:2463–2479
Nesi N, Debeaujon I, Jond C, Pelletier G, Caboche M, Lepiniec L (2000) The TT8 gene encodes a basic helix-loop-helix domain protein required for expression of DFR and BAN genes in Arabidopsis siliques. Plant Cell 12:1863–1878
Walker AR, Davison PA, Bolognesi-Winfield AC, James CM, Srinivasan N, Blundell TL, Esch JJ, Marks MD, Gray JC (1999) The TRANSPARENT TESTA GLABRA1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes a WD40 repeat protein. Plant Cell 11:1337–1349
Johnson CS, Kolevski B, Smyth DR (2002) TRANSPARENT TESTA GLABRA2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. Plant Cell 14:1359–1375
Sagasser M, Lu G-H, Hahlbrock K, Weisshaar B (2002) A. thaliana TRANSPARENT TESTA1 is involved in seed coat development and defines the WIP subfamily of plant zinc finger proteins. Genes Dev 16:138–149
Mehrtens F, Kranz H, Bednarek P, Weisshaar B (2005) The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis. Plant Physiol 138:1083–1096
Jaakola L, Pirttilä AM, Halonen M, Hohtola A (2001) Isolation of high quality RNA from bilberry (Vaccinium myrtillus L.) fruit. Mol Biotechnol 19:201–203
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Reptr 1:19–21
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York
Gilmartin GM (2005) Eukaryotic mRNA 3' processing: a common means to different ends. Genes Dev 19:2517–2521
Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783–795
Hofmann K, Stoffel W (1993) TMbase - A database of membrane spanning proteins segments. Biol Chem Hoppe Seyler 374:166
Marchler-Bauer A, Bryant SH (2004) CD-Search: protein domain annotations on the fly. Nucleic Acids Res 32:W327–W331
Stracke R, Werber M, Weisshaar B (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol 4:447–456
Heine GF, Hernandez MJ, Grotewold E (2004) Two cysteines in plant R2R3 MYB domains participate in REDOX-dependent DNA binding. J Biol Chem 279:37878–37885
Grotewold E, Sainz MB, Tagliani L, Hernandez JM, Bowen B, Chandler VL (2000) Identification of the residues in the Myb domain of maize C1 that specify the interaction with the bHLH cofactor R. Proc Natl Acad Sci USA 97:13579–13584
Zimmermann IM, Heim MA, Weisshaar B, Uhrig JF (2004) Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins. Plant J 40:22–34
Geourjon C, Deléage G (1995) SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 11:681–684
Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis 18:2714–2723
Lukens L, Quijada P, Udall J, Pires JC, Schranz ME, Osborn TC (2004) Genome redundancy and plasticity within ancient and recent Brassica crop species. Biol J Linnean Soc 82:665–674
Cavell A, Lydiate D, Parkin I, Dean C, Trick M (1998) Collinearity between a 30-centimorgan segment in Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome. Genome 41:62–69
Lysak MA, Koch MA, Pecinka A, Schubert I (2005) Chromosome triplication found across the tribe Brassiceae. Genome Res 15:516–525
Schmidt R, Acarkan A, Boivin K (2001) Comparative structural genomics in the Brassicaceae family. Plant Physiol Biochem 39:253–262
Parkin IAP, Sharpe AG, Lydiate DJ (2003) Patterns of genome duplication within the Brassica napus genome. Genome 46:291–303
Lim YP, Plaha P, Choi SR, Uhm T, Hong CP, Bang JW, Hur YK (2006) Toward unraveling the structure of Brassica rapa genome. Physiol Plant 126:585–591
Sonnhammer EL, Koonin EV (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet 18:619–620
Chen F, Mackey AJ, Stoeckert CJ Jr, Roos DS (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 34:D363–D368
Modrek B, Lee C (2002) A genomic view of alternative splicing. Nat Genet 30:13–19
Liu L, White MJ, MacRae TH (1999) Transcription factors and their genes in higher plants: Functional domains, evolution and regulation. Eur J Biochem 262:247–257
Locatelli F, Bracale M, Magaraggia F, Faoro F, Manzocchi LA, Coraggio I (2000) The product of the rice myb7 unspliced mRNA dimerizes with the maize leucine zipper Opaque2 and stimulates its activity in a transient expression assay. J Biol Chem 275:17619–17625
Gautvik KM, Alestrom P, Oyen TB, Gabrielsen OS (2005) Production of human parathyroid hormone from microorganisms. US Patent 6,962,796
Sharma SB, Dixon RA (2005) Metabolic engineering of proanthocyanidins by ectopic expression of transcription factors in Arabidopsis thaliana. Plant J 44:62–75
Kranz HD, Denekamp M, Greco R, Jin H, Leyva A, Meissner RC, Petroni K, Urzainqui A, Bevan M, Martin C, Smeekens S, Tonelli C, Paz-Ares J, Weisshaar B (1998) Towards functional characterisation of the members of the R2R3-MYB gene family from Arabidopsis thaliana. Plant J 16:263–276
Jin H, Martin C (1999) Multifunctionality and diversity within the plant MYB-gene family. Plant Mol Biol 41:577–585
Lee MM, Schiefelbein J (2001) Developmentally distinct MYB genes encode functionally equivalent proteins in Arabidopsis. Development 128:1539–1546
Acknowledgments
This research was supported by the Major Program of Chongqing Municipal Natural Science Foundation (No. 8446) and the Major Program of National Natural Science Foundation (No. 30330400).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Wei, YL., Li, JN., Lu, J. et al. Molecular cloning of Brassica napus TRANSPARENT TESTA 2 gene family encoding potential MYB regulatory proteins of proanthocyanidin biosynthesis. Mol Biol Rep 34, 105–120 (2007). https://doi.org/10.1007/s11033-006-9024-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11033-006-9024-8