JXB Advance Access originally published online on January 10, 2005
Journal of Experimental Botany 2005 56(412):597-603; doi:10.1093/jxb/eri050
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RESEARCH PAPER |
Characterization of three homologous basic leucine zipper transcription factors (bZIP) of the ABI5 family during Arabidopsis thaliana embryo maturation

Institut des Sciences du Végétal, UPR 2355 CNRS, 1. avenue de la terrasse, 91198 Gif-sur-Yvette cedex, France
* Present address and to whom correspondence should be sent: John Innes Centre, Cell and Developmental Biology Department, Colney Lane, Norwich NR4 7UH, UK. Fax: +44 (0)1603 450 025. E-mail: sandra.bensmihen{at}bbsrc.ac.uk
Received 24 June 2004; Accepted 4 October 2004
| Abstract |
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The Arabidopsis thaliana genome contains approximately 80 genes encoding basic leucine zipper transcription factors, divided into 11 groups. Abscisic Acid-Insensitive 5 (ABI5) is one of the 13 members of group A and is involved in ABA signalling during seed maturation, and germination. Seven other members of this group are expressed during seed maturation, but only one of them (Enhanced Em Level, EEL) has been functionally characterized during this developmental phase. Since EEL and two other group A genes, AtbZIP67 and AREB3 (ABA-Responsive Element Binding protein 3), display similar mRNA temporal expression in whole siliques, it is suspected that they might share some overlapping functions. To address this question, the proteins' tissular and subcellular localization in transgenic Arabidopsis were precisely characterized, using translational fusions with a green fluorescent protein (GFP) expressed under the corresponding bZIP promoter. It was found that the three fusion proteins were expressed with a largely overlapping pattern and constitutively localized in the nuclei. An RNA interference approach (RNAi) was then used to knock out the expression of all three genes simultaneously. Endogenous EEL, AREB3, and AtbZIP67 transcripts could be specifically reduced, but no visible defects could be observed during seed maturation.
Key words: ABI5, bZIP transcription factors, multigene family, RNA interference, seed maturation
| Introduction |
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Many transcription factors encoded by the Arabidopsis genome belong to multigene families (Riechmann et al., 2000
| Materials and methods |
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Plant transformation and growth
ProbZIP::GFP-bZIP and RNAi constructs were introduced into the Columbia 0 (Col0) accession by Agrobacterium transformation using the floral dip method (Clough and Bent, 1998
ProbZIP::GFP-bZIP transformants were selected by spraying young seedlings with Basta herbicide (glufosinate, 60 mg l1). RNAi T1 seeds were selected on germination medium (as described in Bensmihen et al., 2002
) containing 1% sucrose, 50 µg l1 kanamycin (Sigma) and 400 mg l1 of the antibiotics amoxicilline/clavulanic acid (1 g 100 mg1) (Augmentin, SmithKline Beecham Laboratories).
DNA constructs
Vectors:
ProbZIP::GFP-bZIP constructs were built in the pSBright vector. This new binary vector was constructed by assembling a SpeI/XbaI/HindIII multiple cloning site upstream of a smRS-GFP gene (Davis and Vierstra, 1998
) and a GatewayTM Reading Frame A (RfA) cassette (Invitrogen). ABI5, EEL, AREB3, and AtbZIP67 cDNA (as described in Bensmihen et al., 2002
) were first cloned in the pDONR201 vector (Invitrogen), prior to their recombination in pSBright following the manufacturer's instructions. The PSBright map is available online at http://www.isv.cnrs-gif.fr/jg/alligator/othervectors.html.
BZIP promoters:
1760 bp upstream of the ABI5 ATG were amplified with the 5'-TTACTAGTAGTTTTTTGGCTATTAGAAACACTTGATA-3' (ABI5for) and 5'-TTAAAGCTTTACCATTTAACAACTGCATCATATACACAA-3'(ABI5rev) primers from the F2H17 BAC (ABRC, Ohio State University, Columbus) and introduced in pSBright using the SpeI and HindIII polylinker sites.
2080 bp upstream of the EEL ATG were amplified with the 5'-ATTACTAGTCCATGCACGTAATTCCTCTTAAGAT-3' (EEL for) and 5'-TTTAAGCTTACCCATATATGTAGCCTTTACACAGA-3' (EELrev) primers from the T3K9 BAC (ABRC, Ohio State University, Columbus) and introduced in pSBright using the SpeI and HindIII polylinker sites.
1830 bp upstream of the AREB3 ATG were amplified with the 5'-TTAACTAGTTCAACGACACAGCTGAAGAATGAT-3' (AREBfor) and the 5'-TAAAAGCTTATCCATAGGCTTTTGTAGCGGACAA-3' (AREBrev) primers from the T8M6 BAC (ABRC, Ohio State University, Columbus) and introduced in pSBright using the SpeI and HindIII polylinker sites.
1900 bp upstream of the AtbZIP67 ATG were amplified with the 5'-TTACTAGTAAACTTGAAATTGTCTTGTTTGGCCTCCTA-3' (bZIP67for) and 5'-AAACTAGTCGACATCGTTTGGTAGACCTATAAATCTTGAA-3' (bZIP67rev) primers from the F14L2 BAC (ABRC, Ohio State University, Columbus) and introduced in pSBright using the SpeI polylinker site.
Each promoter amplification was performed twice independently using the Taq Hifi DNA polymerase (Invitrogen). Both amplification products were subsequently used for in planta transformation and characterization.
RNAi construct:
140 bp of EEL, AREB3, and AtbZIP67 specific probes (as described in Bensmihen et al., 2002
) were amplified respectively with: 5'-ATTTCTAGATTGTCTCGAGCTACTCCTTCTTAATCT-3' (EELifor) and 5'-ATAAACCTGCAGCTAATAGAACCCATATATGTAGC-3' (EELirev); 5'-TTCTCATGCATGAAAAGTCTGTACCTCGCAA-3' (AREBifor) and 5'-AAAGGATCCAATCGAAGGAAATGGCA-3' (AREBirev); 5'-TGAAGATCTCTAGCGAACTTGTGGACAACCGTTGAA-3' (bZIP67ifor) and 5'-AAAATTAAGCTTTCAAGGTACCCCTCGTCGACCGTTTTCT-3' (bZIP67irev) primers. The three fragments were then digested with PstI (EEL), NsiI, and BamHI (AREB3), and BglII (AtbZIP67) respectively, ligated and re-amplified with EELifor and bZIP67irev, leading to the EEL-AREB3-AtbZIP67 fragment. This fragment was then introduced as an inverted-repeated sequence in pHannibal (Wesley et al., 2001
) using the XhoI/KpnI and XbaI/HindIII cloning sites, respectively (EELifor introduces XbaI and XhoI restriction sites, bZIP67irev introduces HindIII and KpnI sites). This RNAi fragment was then transferred in pART27 using the NotI cloning site.
RNA handling
RT-PCR: Total RNA was extracted from seeds using a phenolchloroform protocol (Parcy et al., 1994
). Total RNA was then cleaned using the Clean Up protocol from the RNeasy kit (Qiagen). Reverse transcription was performed with the SuperscriptII enzyme (GibcoBRL), following the manufacturer's instructions.
One µg of total RNA was then used for the PCR reactions. Primers used were as follow: 5'-AATGGTGTCTCAGTCTTCTTTGATGG-3' (AREBforRT) and 5'-TTTAGAGATCAGAAAGGAGCCGAG-3' (AREBrevRT) for AREB3; 5'-TCTGGAAAACCACTAGGAAGCAT-3' (FP1079) and 5'-AAGAAGAGTCTTTAGGATCAGAGAG3' (EELrevRT) for EEL; 5'-TTATAACCCCGAGTTTGGAGTTG3' (67forRT) and 5'-AATTCCAACTCCAGTTCCACAG-3' (67revRT) for AtbZIP67; 5'-GTTTAGAGTGGACAACTCGGGTTCC-3' (FP1086) and 5'- GGGGAAGGAAAAGAGTAGTGG-3' (FP1089) for ABI5; 5'-ATGCCCCAGGACATCGTGATTTCAT-3' (EF1RT1) and 5'-TTGGCGGCACCCTTAGCTGGATCA3' (EF1RT2) for EF1
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Each amplification was performed with an annealing temperature of 56 °C and 25 amplification cycles.
Microscopy techniques
Staging of the individual siliques was done by tagging individual flowers on the day of pollination. Embryos were taken out of the seed coat by gently squashing seeds in a water drop between a glass slide and a cover slip. A TCS SP2 confocal microscope from Leica was used. GFP was excited with the 488 nm line of the Argon laser (3438% of power at approximately 4/10 gain). Chlorophyll excitation was reinforced using the 633 nm line of a Helium/Neon laser (30% of power). The objective used was a HCX PL Apo CS 40X, NA 1.25. The images were scanned on a 1530 µm width with 1 µm increment in Z. The images are averaging projections of the Z-series, provided by the Leica LCS software.
| Results |
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Construction of pSBright vector to express translational GFP fusions in planta
A versatile binary vector was built first to allow expression of translational fusion between any protein and a soluble version of GFP (Davis and Vierstra, 1998
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Localization of GFP-tagged bZIP during embryo maturation
The pSBright vector, as well as the feasibility of this approach in embryos using a ProABI5::GFP-ABI5 construct were tested first. The ABI5 expression pattern and subcellular location had been characterized (Brocard et al., 2002
These experiments established the functionality of the pSBright vector and demonstrated that it can be used to analyse protein expression in embryos. This vector was then used for similar constructs using the EEL, AREB3, and AtbZIP67 promoters and cDNAs.
EEL, AREB3, and AtbZIP67 genes have been characterized previously (Choi et al., 2000
; Bensmihen et al., 2002
) and are known to be expressed in maturing embryos (Bensmihen et al., 2002
). However, no information about the protein localization in the embryo has been presented.
The fluorescence of the GFP-bZIP fusions was observed in maturing embryos for all ProbZIP::GFP-bZIP constructs. None of the three constructs generated fluorescence in the embryos before 7 DAP (data not shown). GFP-AtbZIP67 fluorescence was first detected in the cotyledons and axis of 8 DAP embryos (Fig. 2I), whereas GFP-AREB3 and GFP-EEL fluorescence appeared 1 d later, in the whole embryo for AREB3 (Fig. 2E), but only in the cotyledons for EEL (Fig. 2A). From 10 DAP to 13 DAP, fluorescence was then detected for the three GFP-bZIP throughout the embryo, in both cotyledons and axis (Fig. 2B, C, F, G, J, K). At 13 DAP, GFP-EEL and GFP-AREB3 fluorescence persisted in the whole embryo (data not shown) whereas GFP-AtbZIP67 fluorescence was restricted to cotyledons (Fig. 2L). Finally, at 14 DAP, only GFP-AREB3 fluorescence remained detectable (Fig. 2H), whereas GFP-EEL was no longer visible (Fig. 2D). No GFP-bZIP fluorescence was detected in dry seeds. Throughout their expression window, fluorescence was specifically detected in the nuclei, indicating that all three proteins were constitutively nuclear.
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These results show that all three proteins are expressed during seed maturation with slightly different but overlapping expression patterns, suggesting they may perform overlapping functions. For this reason, an attempt was made to silence the expression of all three genes simultaneously, using an RNA interference approach.
Specific endogenous bZIP gene extinction using a triple RNA interference (RNAi) approach
An attempt to silence the three EEL, AREB3, and AtbZIP67 genes was made by assembling three 140 bp DNA fragments amplified from specific regions of EEL, AREB3, and AtbZIP67 genes. The resulting concatemer was introduced as an inverted-repeated fragment in the pHannibal vector, as shown on Fig. 3a, to generate an RNAi construct as described by Wesley et al. (2001)
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Twenty-two independent RNAi lines were generated. To select those displaying the most efficient silencing, each of them was crossed to the ProAREB3::GFP-AREB3 line described above. The RNAi construct is supposed to trigger the degradation of the endogenous transcript as well as any chimeric transcript containing the targeted sequence (Voinnet et al., 1998
To test whether the silencing could also be observed at the mRNA level, the expression of EEL, AREB3, and AtbZIP67 was monitored by RT-PCR in the #10.3, #17.3, and #13 T3 homozygous RNAi lines. As shown in Fig. 4, the level of EEL, AREB3, and AtbZIP67 transcripts seemed poorly affected in the siliques of the #13 RNAi line, while it was significantly decreased in the #10.3 line (Fig. 4). All three transcripts appeared similarly reduced in the #10.3 line, whereas the ABI5 transcript level was not affected (Fig. 4). It is thus possible to trigger a specific reduction of the expression of three bZIP homologous genes by an RNAi approach using a single transgene.
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No macroscopic defects could be observed in the seeds of the #10.3 line. The ABA sensitivity of the T3 RNAi homozygous lines #10.3 and #17.3 is similar to the Col0 wild-type. These RNAi lines do not seem to be either hypersensitive or insensitive to ABA. Moreover, the above-mentioned germination tests were performed on seeds after a few weeks of drying (typically between 36 weeks) and the germination rate was always similar to the wild type, indicating that desiccation tolerance was not drastically affected as in the abi3 severe alleles.
To get an insight of the molecular targets of these RNAi lines, the expression of the AtEm1 gene was assayed using semi-quantitative RT-PCR on total RNA extracted from 14 DAP #10.3 and #17.3 T3 RNAi seeds and no significant difference could be detected compared with the wild-type seeds (not shown). In addition to this, RNAi T3 homozygous lines #10.3 and #17.3 were crossed to the AtEm1::GUS reporter line and no ectopic or precocious GUS staining (assayed at 10 and 12 DAP, not shown) could be detected in the F1 progeny of the cross, showing that there is no dominant effect on the regulation of AtEm1.
By contrast with the the eel mutant, there is no earlier or stronger AtEm1 expression in the RNAi seeds. This difference can be either due to residual expression of the EEL transcript or antagonistic effect of the AtbZIP67 and AREB3 expression loss. However, a more extended molecular characterization would need to be performed to assay other possible molecular targets.
| Discussion |
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GFP-bZIP pattern in planta
This work demonstrates the feasibility of the detection of GFP-tagged bZIP proteins from the ABI5 family in embryos during seed maturation. GFP fusions can thus be detected even during the latest stages of seed maturation, despite the fragility of the tissues and the background fluorescence caused by the storage products. As shown with the ABI5 fusion, GFP-tagged proteins can be detected in the nuclei of cotyledons and axis tissues from maturing embryos. The temporal and subcellular localization of the GFP-ABI5 protein is in accordance with data using an ABI5GUS fusion (Lopez-Molina et al., 2002
The temporal expression pattern observed for the GFP-bZIP proteins is compatible with whole siliques mRNA levels (Bensmihen et al., 2002
). The expression pattern of GFP-EEL is also compatible with its function in AtEm genes repression during the desiccation phase (Bensmihen et al., 2002
). However, the proteins' localization should be confirmed by in situ immunolocalization with specific antibodies.
It was observed that GFP-EEL, GFP-AREB3, and GFP-AtbZIP67 are constitutively localized in the nuclei of the embryo during maturation. Lopez-Molina and co-workers have already described a nuclear localization for an ABI5-GUS protein in dry seeds (Lopez-Molina et al., 2002
). This study shows that other bZIP of the ABI5 family are constitutively located in the nucleus during embryo maturation, with no evidence for developmentally-related relocalization. Nuclear location is frequent for bZIP transcription factors, as the basic domain has been shown to act as a nuclear localization signal (van der Krol and Chua, 1991
). However, some bZIP are retained in the cytoplasm (Igarashi et al., 2001
) and can be targeted to the nucleus in response to external signals such as light (Kircher et al., 1999
).
EEL, AREB3, and AtbZIP67 display a large overlapping localization pattern in the embryo during the maturation phase. As these bZIP were shown to form heterodimers in vitro (Kim et al., 2002
), they are likely to interact in vivo and perform some of their functions as heterodimers. The possibility of combinatorial action increases the range of possible functions for this set of bZIP. Because of their sequence similarity and overlapping expression patterns EEL, AREB3, and AtbZIP67 proteins may also have partially overlapping functions.
RNAi approach
Using a single RNAi transgene was successful in obtaining a significant reduction in the expression of the three genes. The efficiency of the silencing seems similar on the three targeted genes, since lines such as #10.3 seem to affect the EEL, AREB3, and AtbZIP67 endogenous transcripts in the same manner. This effect is also highly specific since the ABI5 transcript is not affected in these RNAi lines, whereas ABI5 is strongly homologous to EEL, AREB3, and especially AtbZIP67 (Bensmihen et al., 2002
). This study demonstrates that it is possible to reduce the expression of the three homologous genes in a specific manner using a single transgene. Approaches using transgenes expressing sense chimeric constructs have already been described in tomato and tobacco to reduce the expression of two or three unrelated genes at the same time (Seymour et al., 1993
; Abbott et al., 2002
). Silencing of two independent genes, using the pHellsgate 8 vector to trigger intron-spliced hairpin RNA (ihpRNA) expression in Arabidopsis, has also been reported (Helliwell et al., 2002
). But in each case, an average of 300 bp to 1000 bp of every targeted sequence has been used for the silencing construct and no homologous genes were targeted. This is the first time that the use of a single transgene with such short fragments has been shown to trigger multiple and specific gene silencing for homologous genes. As mentioned by others (Abbott et al., 2002
; Helliwell et al., 2002
), this strategy is faster than combining independent single gene silencing constructs or T-DNA insertion mutants.
Even if the loss of the three bZIP expression is not complete, it might be sufficient to trigger alteration in the regulation of specific target genes expressed during seed maturation. Indeed, studies using RNAi approaches have shown that a range of severity in phenotypes could arise in different lines (Chuang and Meyerowitz, 2000
), depending on the efficiency of the silencing. It is therefore possible that an intermediate silencing could still provide an intermediate phenotype in the RNAi progeny. It cannot be excluded that defects in seed maturation (such as loss of seed viability) have prevented the isolation of lines with a stronger silencing effect.
As the efficiency of the silencing is related to the number of double-stranded RNA expressed (Fire et al., 1998
), the approach could be improved by using a strong seed-specific promoter to drive the expression of the RNAi construct. Alternatively, greater silencing efficiency could be achieved by increasing the length of the fragments used for the RNAi constructs, as longer fragments would provide more probes to initiate the RNAi degradation process (Waterhouse and Helliwell, 2003
).
Since the level of each of these three bZIP transcripts is significantly reduced in some of these RNAi lines, although the expression level of AtEm1 did not seem to be affected, it will be interesting to look for other misregulated target genes of the LEA and seed storage proteins classes. This approach would give important information on the putative functions of bZIP transcription factors of the ABI5 family in the regulation of seed maturation in Arabidopsis thaliana.
| Acknowledgements |
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We thank C Talbot, O Catrice, S Brown, and the microscopy platform of the IFR87 in Gif-sur-Yvette (supported by the Conseil de l'Essonne) for help and access to the confocal microscope, P Waterhouse for providing the pHannibal and pART27 vectors and C Giglione for providing sequenced construct of the smRS-GFP. The pDONR201-bZIP cDNAs were cloned as part of the REGIA project by G Lambert, F Parcy, and S Bensmihen. This work was supported by the Centre National de la Recherche Scientifique and partially by the European REGIA project (grant No. QLG2-CT1999-00876). Sandra Bensmihen was supported by a grant from the French Education and Research Ministry.
| Footnotes |
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Present address: Laboratoire DRDC/PCV, UMR CEA-CNRS 5168-INRA 1200-UJF, CEA, 17 rue des Martyrs, bât. C2, 38054 Grenoble Cedex 9, France. Abbreviations: ABA, abscisic acid; bp, base pair; ABI5, ABA-Insensitive 5; bZIP, basic leucine zipper; DAP, days after pollination; EEL, Enhanced Em Level; LEA, late embryogenesis abundant genes; RNAi, RNA interference.
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