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a marker of early seed coat development
Martine Devic, Jocelyne Guilleminot, Isabelle Debeaujon, Nicole Bechtold, Emmanuelle Bensaude, Maarten Koornneef, Georges Pelletier, Michel Delseny
To cite this version:
Martine Devic, Jocelyne Guilleminot, Isabelle Debeaujon, Nicole Bechtold, Emmanuelle Bensaude, et al.. The BANYULS gene encodes a DFR-like protein and is a marker of early seed coat development.
Plant Journal, Wiley, 1999, 19 (4), pp.387-398. �10.1046/j.1365-313X.1999.00529.x�. �hal-02699207�
The BANYULS gene encodes a DFR-like protein and is a marker of early seed coat development
Martine Devic
1,*, Jocelyne Guilleminot
1, Isabelle Debeaujon
2, Nicole Bechtold
3, Emmanuelle Bensaude
1, Maarten Koornneef
2, Georges Pelletier
3and Michel Delseny
11
Laboratoire de Physiologie et Biologie MoleÂculaire des Plantes, Universite de Perpignan, Avenue de Villeneuve, 66860 Perpignan Cedex, France,
2
Wageningen Agricultural University, Laboratory of Genetics, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands, and
3
Station de GeÂneÂtique et d'AmeÂlioration des Plantes, INRA, Route de Saint-Cyr, 78026 Versailles Cedex, France
Summary
Mutations in the BANYULS (BAN) gene lead to precocious accumulation of anthocyanins in immature seed coat in Arabidopsis. The ban ±1 allele has been isolated from a collection of T-DNA transformants and found to be tagged by the integrative molecule. The sequencing of wild-type and two independent mutant alleles con®rmed the identity of the gene. Analysis of the full-length cDNA sequence revealed an open reading frame encoding a 342 amino acid protein which shared strong similarities with DFR and other enzymes of the phenylpropanoid biosynthesis pathway. BAN expression was restricted to the endothelium of immature seeds at the pre-globular to early globular stages of development as predicted from the maternal inheritance of the phenotype, and therefore represents a marker for early differentiation and development of the seed coat. BAN is probably involved in a metabolic channelling between the production of anthocyanins and pro-anthocyanidins in the seed coat.
Introduction
Flavonoids are produced in plants by secondary metabo- lism and comprise several subclasses (Figure 1). Some of the ¯avonoids, the anthocyanidins, anthocyanins and tannins are responsible for the red, purple and brown pigmentation of ¯owers, fruits, seeds and other plant tissues and organs (Chapple et al., 1994). Since these products are not essential for the viability of the plants,
¯avonoid biosynthesis represents an excellent model
system in which to study the regulation of a complex biosynthetic pathway. Thus, the genetic control of ¯avo- noid biosynthesis has been studied in several model plants including maize, snapdragon, petunia (Holton and Cornish, 1995) and Arabidopsis (Shirley et al., 1995). Most of the genes encoding the structural enzymes have been cloned and their sequences are well conserved among plant species. However, the manner in which the plant has solved the problem of the regulation of synthesis of the
¯avonoids in different organs and tissues varies according to the plant species. Some plant species have duplicated the structural and regulatory genes leading to speci®c isoforms with distinct promoter regions for various cell types, tissues and/or organs, while other species have a single-copy gene but with a complex cell-speci®c regula- tion. For example, in Petunia, the CHS genes are present as a multigene family (Koes et al., 1989) whilst Arabidopsis has a single copy of CHS in its genome (Feinbaum and Ausubel, 1988). Most of the regulatory genes encode transcription factors that act as activators (for review, see Weisshaar and Jenkins, 1998), indicating that the regula- tion of ¯avonoid biosynthesis occurs mainly at the level of transcription. These regulatory proteins belong to the MYB, bHLH and bZIP families, and the genes encoding these transcription factors may themselves be subjected to spatial, temporal and environmental regulation (DroÈge- Laser et al., 1997; Procissi et al., 1997). Recently, regulatory genes that do not encode transcription factors have been characterized. These genes are thought to act upstream of the regulatory transcription factors. The AN 11 protein of petunia which regulates the expression of a subset of anthocyanin genes and controls the intracellular pH, possesses WD-40 repeats important for protein±protein interactions (de Vetten et al., 1997). In Arabidopsis, ¯avo- noid mutants have been named tt for transparent testa (Koornneef, 1990; Shirley et al., 1992). Some of the tt mutants encode structural genes and others are thought to be regulatory genes or tissue-speci®c enzymes (Figure 1).
Recently, we described the genetic characterization of a negative regulator of anthocyanin biosynthesis speci®c to the Arabidopsis seed coat (Albert et al., 1997). Mutation in the BANYULS (BAN) gene induces precocious accumula- tion of anthocyanins in the seed coat. A similar mutant was subsequently described as ast (for Arabidopsis spotted testa) (Tanaka et al., 1997) and based on the phenotype and map position may be an allele of ban. The cloning of BAN has revealed that BAN is not a transcription factor but most probably a structural enzyme of the ¯avonoid pathway, leucoanthocyanindin reductase (LCR). Its expression is
Received 1 March 1999; revised 9 June 1999; accepted 15 June 1999.
*For correspondence (fax +33 4 68 66 84 99; email devic@univ-perp.fr).
387
restricted to the most internal cell layer of the seed coat at early development in accordance with the maternal inheritance of the mutation.
Results
Characterization of the T-DNA insertion site in ban plants The banyuls mutant was originally isolated during a screen for the embryo-defective (emb) phenotype and has been described by Albert et al. (1997). The mutation causes a precocious pigment accumulation in the seed coat resulting in a purple colour of the immature seeds.
The initial transformant exhibited both the ban and the emb phenotype and had complex T-DNA insertions. In order to segregate the two mutations and the multiple copies of T-DNA, we identi®ed plants presenting the ban phenotype and containing a single T-DNA insert using Southern blot analysis on plants from the progeny of the cross ban 3 tt2 (Albert et al., 1997). PCR walking (Devic et al., 1997) allowed us to amplify and characterize about 500 bp of plant genomic sequences ¯anking each border of the T-DNA of the transgenic plants. The corresponding
genomic sequences of the wild-type were ampli®ed in two rounds of PCR walking using the ban-5¢ and wsban-5¢
nested primers for the 5¢ end, and the ban-3¢ and wsban-3¢
nested primers for the 3¢end. A contig of 2023 bp corresponding to the complete gene was constructed and sequenced. T-DNA integration into the BAN gene resulted in a deletion of 16 bp of plant genomic DNA.
Southern blot analysis demonstrated that BAN is present as a single copy in the Arabidopsis genome (data not shown).
Comparisons with various databases revealed simila- rities to known genes encoding the dihydro¯avonol reductase (DFR) of Rosa 3 hybrida and many other plant species and with the vestitone reductase of Medicago sativa. This information helped us to predict the exon±
intron boundaries and to design primers for the cloning of the corresponding cDNA by Marathon-based PCR (Clontech). cDNA fragments were ampli®ed from a Marathon-like library made from RNA of immature siliques using the ban-5¢ (for the 5¢ portion) and ban-3¢ (for the 3¢
portion) primers in combination with the adaptor primers.
The 5¢ extremity was ampli®ed using the ban-5¢ and banATG nested primers on the same library and by sequencing up to 10 independent clones. The complete cDNA is 1213 bp long with 45 bp of 5¢ untranslated leader sequence and a 3¢ end of 142 bp. It encodes a protein of 342 amino acids with a molecular mass of 38 kDa. Its cellular localization is predicted to be the cytoplasm (PSORT program, Nakai and Kanehisa, 1992). Alignment of the genomic and cDNA sequences showed that the BAN gene is composed of six exons and ®ve introns. The T-DNA was found to have integrated into the third intron.
Regular submissions of large genomic sequences to the databases have prompted us to perform routine searches with the BAN cDNA sequence. Recently, a near identical sequence to BAN has been found in a BAC clone assigned to chromosome I. The rare differences in nucleotides may be due to the ecotype, WS for BAN and Col for the BAC clone (Federspiel et al., 1998, unpublished). These data validate the genetic positioning of BAN (Albert et al., 1997).
BAN is located on the BAC T13M11 (AC005882).
BANYULS is a member of the NADPH-dependent oxido- reductase superfamily
The amino acid sequence of the BAN protein is very similar to NADP(H) binding oxido-reductases and can be aligned over its entire length to DFR, an enzyme of the anthocyanin biosynthesis pathway, CCR (cinnamoyl CoA reductase) and CAD (cinnamoyl alcohol dehydrogenase), enzymes of the lignin pathway, and vestitone reductase, an enzyme of the iso¯avone pathway (Figure 2). The highest scores for DFR were found with the DFR of Rosa 3 hybrida (Tanaka et al., 1995; D85102, 41% identity) and
Figure 1.
Schematic representation of the phenylpropanoid pathway that comprises the two main branches leading to the synthesis of lignins and
¯avonoids with an emphasis on the ¯avonoid pathways.
The abbreviations of the principal enzymes are written in bold with the corresponding mutation in parentheses. Abbreviations: PAL, phenylammonium lyase; C4H, cinnamate 4-hydroxylase; C4L, 4- coumarate CoA ligase; CAD, cynnamoyl alcohol dehydrogenase; CCR, cynnamyl CoA reductase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, ¯avanone 3-hydroxylase; F3¢H, ¯avonoid 3¢-hydroxylase;
DFR, dihydro¯avonol 4-reductase; FLS, ¯avonol synthase; LDOX,
leucoanthocyanidin dioxygenase; LCR, leucoanthocyanidin reductase;
tt,transparent testa;
ttg1, transparent testa glabrous 1; icx 1, increasedchalcone synthase expression 1.
Arabidopsis (Shirley et al., 1992; P51102, 40%). In terms of other enzymes, BAN showed similarity with the vestitone reductase of Medicago sativa (Guo and Paiva, 1995;
U28213, 39%), and with CCR (Pichon, unpublished data, X98083, 36%) and CAD (Goffner, Van Doorsselaere and Boudet, unpublished data, X88797, 35%) of Eucalyptus
Figure 2.
Alignment of BAN deduced amino acid sequence with related sequences.
The left part of the ®gure represents the alignment of BAN with DFR from
Rosa3hybrida(DFR-Rh) and
Arabidopsis(DFR-At), CAD from
Eucalyptus, CCRfrom maize and vestitone reductase (vest) from
Medicago sativaon all the length of the proteins. Boxed amino acids are homologues and shaded amino
acids are identical. On the right side of the ®gure, the upper panel shows the conserved NADPH binding domain including the sequences of the 3-b-
hydroxysteroid dehydrogenase (steroid) from hamster, the NADPH-dependent reductase gene of barley that inactivates HC toxin (toxin) and the UDP-
galactose 4-epimerase from yeast (epimerase). The bottom panel demonstrates the presence of a leucine zipper motif (asterisks) exclusive to the BAN
sequence.
gunnii. The motif of 13 amino acid residues common to DFRs (Figure 2, DFR-Rh and DFR-At: residues 132±144) and thought to de®ne their substrate speci®city (Beld et al., 1989) is not found in BAN and other members of the family. There is also an insertion of one amino acid residue (in BAN, G168) within the motif KNWYCYGK (Figure 2, CCR: residues 158±165), a sequence thought to be involved in the catalytic site of CCR (Lacombe et al., 1997). The positions of the ®ve introns are well conserved between BAN and DFR, although the introns have no sequence homology. Thus, the conserved gene structure of BAN, DFR and CCR (Lacombe et al., 1997) suggests a common ancestor for these proteins.
To a lesser extent, and within a portion of the protein only, BAN also shares homologies with the NADPH- dependent reductase of barley which inactivates HC toxin
(Han et al., 1997; HVU7746, 32%), the UDP-galactose 4- epimerase (Adams et al., 1988; P13226, 26%) of yeast, and the 3-b-hydroxysteroid dehydrogenase of hamster (Rogerson et al., 1995; HAHMSD3B, 19%). The NADPH binding site in BAN (15±35) is well conserved among this family of oxido-reductase proteins (Figure 2). In addition, BAN exhibits a perfect leucine zipper consensus (192±213) that is not be found in other members of the family (Figure 2).
A phylogenetic tree was constructed using the DARWIN program (Gonnet et al., 1992) and is presented in Figure 3.
The tree summarizes the theoretical evolutionary dis- tances among the different NADPH-dependent oxido- reductase superfamily members and BAN. The DFR proteins from several plant species represent a separate cluster from which BAN is excluded. We can conclude that BAN belongs to the mammalian 3b-hydroxysteroid dehy- drogenase/plant dihydro¯avonol reductase superfamily as described by Baker et al. (1990) and Baker and Blasco (1992) and that BAN does not correspond to a second DFR in Arabidopsis.
Mutations are present in different ban alleles
Allelism tests were performed between ban plants and two mutant plants, F36 and F52, from the Kranz and RoÈbbelen Arabidopsis Information Service (AIS) collection exhibiting a similar phenotype. The three mutations were found to be allelic. The complete cDNA corresponding to the BAN gene was ampli®ed by RT±PCR from RNA of immature siliques of F36 and F52 using the RT5¢ and RT3¢ primers and were sequenced. The wild-type BAN cDNA from Enkheim-1 (En-1) was also sequenced in order to distin- guish ecotype sequence variation from mutation in the gene sequence. A striking ecotype difference was the absence of the two terminal amino acids in the En-1 ecotype compared to the WS sequence. In the ban cDNA of the F36 mutant, we observed a small deletion of 14 bp that removed ®ve amino-acids (217-SFITG-221) and created a frameshift. In the ban cDNA of the F52 mutant, a base substitution of C to T introduced a stop codon at position Q307. These mutations were veri®ed by sequencing several clones derived from each mutant line. In both F36 and F52, Q at position 32 is replaced by K. Although this substitution is located within the NADPH binding domain, the residue at position 32 is apparently not conserved (Figure 2), and this variation will probably not result in a loss of function of the protein. This substitution was not found in the wild-type En-1 sequence and may also be due to the mutagen, or, most probably, the En-1 ecotype that we have used is not the same wild-type ecotype in which F36 and F52 were generated. The mutagen used for the AIS collection is unknown. The conversion C®T is consistent with ethyl methyl sulfonate (EMS) mutagenesis since EMS
Figure 3.
Phylogenetic tree of the members of the superfamily of NADPH- dependent oxido-reductase.
The sequences used to build this tree are: for BAN,
ArabidopsisAF092912; for the DFR sequences,
Rosa 3 hybridaD85102,
Forsythia intermediaY09127,
Vitis viniferaY11749,
Arabidopsis thalianaP51102,
Gerbera 3 hybridaP51105,
Perilla frutescensAB002817,
Dianthus cariophyllusP51104,
Petunia 3 hybridaX15537,
Antirrhinium majusP14721,
Lycopersicon esculentumP51107,
Hordeum vulgareP51106,
Zea maysP51108,
Ipomea purpureaU90432,
Lotus corniculatusX97576,
Callistephus chinensisP51103,
Gentiana tri¯oraD85185,
Oryza sativaY07956 and the putative DFR from
Synechocystissp. D1017972; plus the vestitone reductase from
Medicago sativaS61416, the toxin reductase from
Hordeum vulgareU77463 and
Zea maysL02540, the cinnamyl alcohol dehydrogenase (CAD) from
Eucalyptus gunniiX88797, and the cinnamoyl-CoA reductase (CCR) from
Eucalyptus gunniiX97433 and
Vigna unguiculataD83972.
The branch carrying the various UDP-galactose 4-epimerases and 3b-
hydroxysteroid dehydrogenases is not drawn to scale as shown by the
broken line.
has been shown to cause primarily base substitution of G:C to A:T. These results demonstrate that mutations in the BAN gene are responsible for the ban phenotype and that the mutation is tagged by the T-DNA insertion in the ban mutant plant. The mutation in the T-DNA tagged allele might be null, since there is no evidence of the presence of a transcript corresponding to the altered BAN gene (data not shown). In the case of F36 and F52, the mutations are probably null since they produce truncated proteins and no difference in strength of the phenotype of the three alleles was noticeable.
Expression of the BAN gene during plant development The qualitative expression of the BAN gene was studied by RT±PCR using the RT5¢ and RT3¢ primers and was compared with the expression of chalcone synthase (CHS) which is involved in the biosynthesis of ¯avo- noids. The expression of the histone H2A variant (H2A) was used as a constitutive control. CHS transcripts were ampli®ed from leaf tissues, ¯ower buds, ¯owers and young siliques samples (Figure 4). No CHS transcripts were detected during seed maturation. The faint band in last two lanes (torpedo and cotyledon) corresponds to ampli®cation from residual genomic DNA since the amplimer is of a slightly higher molecular weight due to the presence of an intron. In contrast, the BAN transcripts were detected only in ¯owers and young siliques and were absent from the other samples (Figure 4). Increasing the number of PCR cycles to 45 did not result in the detection of BAN transcripts from leaf cDNA (data not shown).
The localization and transient expression of the BAN transcript were analysed in detail by in situ hybridization during wild-type seed development (Figure 5a±d). The BAN transcripts were detected speci®cally in the endothe-
lium of the seed coat, the cell layer that precociously accumulates purple pigments in the ban mutant seeds (Figure 5a). During seed coat development, the presence of the BAN transcripts in the endothelium was transient and corresponded to pre-globular embryo stages (Figure 5a).
From the early globular stage of embryo development until desiccation, the transcripts could no longer be detected (Figure 5b±d). Since no signal was observed in the ovules prior to fertilization, we infer that the expression of the BAN gene may be triggered by fertilization (data not shown). The pro®le of the expression of the BAN gene is consistent with the observed phenotype of the ban seeds.
The temporal expression of the ¯avonoid genes is similar during wild-type and ban seed coat development and is triggered by fertilization
Most of the ¯avonoid genes are present as a single- copy gene in the Arabidopsis genome, and, in contrast to BAN, they are not endothelium-speci®c but are expressed in many tissues. Since the study of their expression during seed development has not already been described in detail, we analysed their expression by in situ hybridization. Several key genes were used as probes: the CHS gene, encoding the ®rst enzyme leading to the ¯avonoid pathway, the CHI gene, the second gene; the DFR gene, for the ®rst enzyme of the anthocyanin-speci®c pathway; the LDOX gene, for catalysis of the leucoanthocyanidins to anthocyanidins thereby producing the purple±red pigments (Figure 1).
The results of in situ hybridization with the LDOX probe are presented in Figure 5(e±h). Similar results were obtained with the three other probes (data not shown).
The transcripts for each of these four genes were detected in the endothelium soon after fertilization (Figure 5e) and persisted until the heart stage (Figure 5e±g). From the torpedo stage onwards, tran- scripts were no longer visible (Figure 5h). The expres- sion of these four genes of the ¯avonoid pathway was induced at a similar time in comparison to the induction of the BAN gene; however, in contrast to BAN, their expression differed in that gene expression persisted until the torpedo stage and was not seed coat-speci®c.
Since the ban mutation induced a precocious accu- mulation of anthocyanins in the seed coat, we also studied the expression of the ¯avonoid genes in the ban seed coat. Only the results of the LDOX gene expression are presented in Figure 5(i±l) since the four probes gave similar results. We have found that the temporal and spatial pattern of expression of CHS, CHI, DFR and LDOX genes in the ban seed coat did not differ from their normal pattern of expression in the wild-type seed coat. Using the in situ hybridization (ISH) techni- que, it is not possible to ascertain whether quantitative
Figure 4.
Study of
BANgene expression during seed development.
RT±PCR was performed with oligo(dT)-primed ®rst-strand cDNA stocks from RNA extracted from young rosette leaves, ¯ower buds, open
¯owers and siliques at different stages of development. The siliques
contained embryos at the globular stage (globular), at the torpedo stage
(torpedo) and at the green cotyledon stage (cotyledon).
Figure 5.In situ
hybridization experiments illustrating the expression of
BANand
LDOXgenes during seed coat development.
Study of the accumulation of
BANtranscripts during seed coat development (a±d). The pictures correspond to different stages of development of the seed coat monitored as the stage of embryo development. (a) Pre-globular stage embryo; (b) globular stage embryo; (c) heart stage; (d) torpedo. The endothelium is the most internal cell layer of the seed coat, speci®cally labelled by the
BANprobe in (a).
Expression of the
LDOXgene during wild-type seed coat development (e±h). (e) Pre-globular stage embryo; (f) globular stage; (g) heart stage; (h) torpedo stage. The
LDOXtranscripts are detected from the early pre-globular stage to the heart stage both in the embryo and in the ®ve cell layers of the seed coat, but with a preferential site of accumulation in the endothelium.
Expression of the
LDOXgene during seed coat development of
banseeds (i±l).
LDOXtranscripts are detected at the pre-globular stage embryo (i and j),
globular (k) and heart stage (l). The bars represent 20m
M.
differences may exist between transcript levels in the wild type and ban seed coat.
Catechins are not produced in ban seeds
A cytological comparison of ban and wild-type seeds revealed cytological differences in the endothelium. The characteristic brown granules that start to accumulate at the pre-globular stage in the wild-type endothelium (Figure 5a±h) are absent in the ban seed coat (Figure 5I±L).
These granules are not coloured in non-treated wild-type seeds. The coloration is due to treatment of the samples necessary for microscopic studies. To obtain a superior image of the structure of the seed coat, the seeds were embedded into resin used for making thin sections. The results of this study are presented in Figure 6. When stained with toluidine blue, these granules are blue and can be observed only in the endothelium of wild-type (Figure 6a) but not the ban testa (Figure 6b). This difference is clearly visible at higher magni®cation in Figure 6(c, d). In order to de®ne the nature of these products, we studied the presence or absence of these granules in the developing seed coat of various mutants. Granules were absent from the testa of tt3, tt4 and tt5, as in ban (Table 1). Therefore, the products are probably not iso¯avones or ¯avanones. Most probably, the ¯avonoids that accumulate at early embry- ogenesis are catechins, precursors of tannins.
Using barley grains, Kristensen and Aastrup (1986) have developed a vanillin test for detection of catechins.
Catechins are produced by the leucoanthocyanidin reduc- tase (LCR) from leucoanthocyanidin precusors. The cate- chins are coloured red in the endothelium cell layer in this in vivo test. Staining with vanillin con®rmed the nature of the granules in wild-type Arabidopsis seeds (Figure 6e) as catechins, precursors of tannins, and con®rmed the absence of these products in ban seeds (Figure 6f).
Similarly, no red staining appeared in immature seeds of the F36 and F52 alleles (Table 1). There is a strict correlation between the presence of the granules in the endothelium and the vanillin coloration in all the mutants tested (Table 1). Immature seeds of tt1, tt9 and tt10, as well as double mutants ban/tt were also tested with vanillin. In these double mutants, the ban phenotype is epistatic to the tt phenotype for anthocyanin accumulation. The results presented in Table 1 show that the ban/tt1 seeds synthesize both anthocyanins and catechins and can be distinguished from single-mutant ban seeds, while the other double mutants are similar to ban. In the tt1 seed coat, the cathechins are present mainly as traces at the base of the seed, surrounding the suspensor and the nucellus. A closer inspection of the wild-type seed coat (Figure 6a) shows the presence of fewer granules in the cell layer adjacent to the endothelium at the level of the suspensor (arrow). In tt1, only this second cell layer produces granules and vanillin staining. This result suggests an independent regulation of the synthesis of tannins in the different cell layers of the seed coat. In ban/
Figure 6.