Intronic regulatory elements determine the divergent expression patterns of AGAMOUS-LIKE6 subfamily members in Arabidopsis

Authors

  • Stephen E. Schauer,

    1. Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
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  • Philipp M. Schlüter,

    1. Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
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  • Ramarmurthy Baskar,

    1. Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
    2. Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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    • Present address: Department of Biotechnology, Indian Institute of Technology-Madras, Chennai-600 036, India.

  • Jacqueline Gheyselinck,

    1. Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
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    • Present address: Département de Biologie Moléculaire Végétale, Bâtiment Biophore, Université de Lausanne, CH-1015 Lausanne, Switzerland.

  • Arturo Bolaños,

    1. Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
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  • Mark D. Curtis,

    1. Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
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  • Ueli Grossniklaus

    Corresponding author
    1. Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
    2. Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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*(fax +41 44 634 8204; e-mail grossnik@botinst.uzh.ch).

Summary

The screening of enhancer detector lines in Arabidopsis thaliana has identified genes that are specifically expressed in the sporophytic tissue of the ovule. One such gene is the MADS-domain transcription factor AGAMOUS-LIKE6 (AGL6), which is expressed asymmetrically in the endothelial layer of the ovule, adjacent to the developing haploid female gametophyte. Transcription of AGL6 is regulated at multiple stages of development by enhancer and silencer elements located in both the upstream regulatory region and the large first intron. These include a bipartite enhancer, which requires elements in both the upstream regulatory region and the first intron, active in the endothelium. Transcription of the AGL13 locus, which encodes the other member of the AGL6 subfamily in Arabidopsis, is also regulated by elements located in the upstream regulatory region and in the first intron. There is, however, no overlapping expression of AGL6 and AGL13 except in the chalaza of the developing ovule, as was shown using a dual gene reporter system. Phylogenetic shadowing of the first intron of AGL6 and AGL13 homologs from other Brassicaceae identified four regions of conservation that probably contain the binding sites of transcriptional regulators, three of which are conserved outside Brassicaceae. Further phylogenetic analysis using the protein-encoding domains of AGL6 and AGL13 revealed that the MADS DNA-binding domain shows considerable divergence. Together, these results suggest that AGL6 and AGL13 show signs of subfunctionalization, with divergent expression patterns, regulatory sequences and possibly functions.

Introduction

Despite the sequencing of the Arabidopsis thaliana genome, the role of most of the identified genes has yet to be uncovered (The Arabidopsis Genome Initiative 2000). This is especially true for genes with late functions in reproductive development, due to both developmental epistasis (the use of a gene at multiple stages of development) and genetic redundancy (compensation of a loss-of-function mutation by the activity of another gene). One way to circumvent these effects is to screen enhancer detector (or enhancer trap, ET) and gene trap (GT) lines for specific late spatiotemporal expression patterns (Bellen et al., 1989; Grossniklaus et al., 1989; Klimyuk et al., 1995; Sundaresan et al., 1995; Bellen, 1999).

Enhancer detection in particular is a powerful tool for understanding genetic regulation. Enhancers are positive transcriptional regulatory elements that increase the transcription rate of target genes, and whose genomic position is not constrained: enhancers can be found upstream or downstream of the transcribed region of the gene – or in intronic regions – and their function is independent of orientation (reviewed in Kleinjan and van Heyningen, 2005). Silencers are similar to enhancers, but they are bound by transcriptional repressors rather than activators. Enhancer detector constructs contain a reporter gene [usually the uidA gene of Escherichia coli, which encodes a β-glucuronidase (GUS; Jefferson, 1989)] under the control of a minimal promoter [usually from the cauliflower mosaic virus 35S RNA promoter (min35S; Benfey and Chua, 1990)]. In the system established by Sundaresan et al. (1995), used in this study, the min35S:GUS reporter was engineered inside a modified maize Dissociator transposable element (Ds). When this Ds element is integrated into the genome, any adjacent enhancer/silencer element can regulate the transcription of the min35S:GUS gene present on Ds. While a large number of enhancer detector lines have been isolated, the nature and position of the enhancer in – or relative to – the gene has rarely been investigated (Yang et al., 2005).

While studies have illuminated the role of enhancer and silencer elements inside intronic regions of plant genes (Reddy and Reddy, 2004; Kim et al., 2006; Searle et al., 2006), the first Arabidopsis gene shown to have regulatory elements inside an intron was the MADS-domain transcription factor AGAMOUS (AG; Sieburth and Meyerowitz, 1997), and enhancer and silencer elements appear to be critical for AG evolution (Causier et al., 2005, 2008). Although most introns in Arabidopsis are between 70 and 120 bp in length, all MIKCc-type MADS-domain genes – with the exception of APETALA3 and AGAMOUS-LIKE15 (AGL15, Heck et al., 1995; Jack et al., 1992) – contain at least one intron that is larger than 500 bp. Sieburth and Meyerowitz (1997) showed that spatiotemporal regulatory elements contained in the large, second intron of AG were necessary for both gene activation and repression. Consistent with this finding, the MADS-domain transcription factor genes FLOWERING LOCUS C (or AGL25) and SEEDSTICK (or AGL11) also have important regulatory elements inside their large first intron (Sheldon et al., 2002; Kooiker et al., 2005). The roles of large introns in the regulation of other AGLs have not been thoroughly examined. Specifically, it is unknown to what extent the regulatory elements inside the large introns of AGLs are sufficient to control their spatiotemporal gene expression (i.e. act as independent enhancers or silencers), or if they require additional upstream regulatory elements for activity (as bipartite enhancers or silencers).

In this paper we report the isolation of enhancer detector line ET447, which is inserted inside AGL6 (At2g45650). AGL6 is a member of the poorly investigated AGL6 subfamily of MADS-domain proteins, with unknown function (Becker and Theißen, 2003). Like other AGLs, AGL6 has a K-domain (necessary for protein-protein interactions, Fan et al., 1997) and an intervening domain (I-domain) between the K and MADS DNA-binding domains (Ma et al., 1991). The Arabidopsis genome also contains the additional AGL6 subfamily member AGL13 (At3g61120), which is located on a genomic block that arose from a genome duplication event 35–85 million years ago (Ma; Blanc et al., 2003; Bowers et al., 2003). To date, no mutant phenotype for either gene has been identified in Arabidopsis (Ma et al., 1991; Rounsley et al., 1995). Importantly, only the first of the seven introns in AGL6 and AGL13 is longer than 120 bp, implying that the large, first intron of AGL6 and/or AGL13 could contain regulatory elements necessary for proper spatiotemporal expression.

The role of changes in spatiotemporal expression in the evolution of duplicated genes has been much researched (reviewed in Li et al., 2005; Rijpkema et al., 2007). The duplication–degeneration–complementation (DDC) model of Force et al. (1999) predicts three outcomes of duplicated genes: nonfunctionalization, neofunctionalization, and subfunctionalization. In nonfunctionalization, null mutations occur in one paralog, ultimately generating a non-expressed pseudogene. In neofunctionalization, one of the paralogs mutates to gain a novel function (perhaps due to changes in regulatory elements), and is established by positive selection. In subfunctionalization, there is a reciprocal loss of some regulatory elements from each paralog by ‘degenerative mutations’ (Force et al., 1999), such that the paralogs’ combined expression pattern replicates the ancestral expression pattern. While some gene pairs (for example pax6a and pax6b in vertebrates; Kleinjan et al., 2008) are consistent with the DDC model, the hoxb5a and hoxb5b gene pair from teleosts suggests a more complicated story: there was no evidence for a simple reciprocal loss of regulatory elements and the interactions between regulatory elements was deemed critical (Jarinova et al., 2008). While subfunctionalization has been invoked to explain many of the duplicated MADS-domain genes (Rijpkema et al., 2007), verification of the reciprocal loss of regulatory elements, which is critical for the DDC model, is lacking in plants. Here, we show that AGL6 and AGL13 are regulated through complex interactions of enhancer and silencer elements located in both the 5′-upstream regions and the large first introns of these genes. Phylogenetic analyses suggest that AGL6 and AGL13 are undergoing subfunctionalization, probably involving the attenuation of enhancer elements.

Results

The expression of AGL6 is controlled by elements both upstream and inside the first intron

The reporter activity of ET447, a line uncovered in a screen for ovule-specific expression patterns, is initiated in the presumptive endothelial layer while the female gametophyte is at the two-nuclear stage, before the morphological formation of the endothelial layer (Schneitz et al., 1995; de Folter et al., 2006) (Figure 1). Reporter activity was detected throughout the endothelial layer until fertilization, after which it became restricted to the endothelium at the chalazal end of the seed (Figure S1 in Supporting Information). By the heart stage of embryo development (Meinke and Sussex, 1979), ET447 reporter activity was no longer detected.

Figure 1.

 Expression patterns of AGL6 and AGL13 require regulatory elements located inside their first introns.
(a) Diagram of a mature ovule. The female gametophyte is shown in green, surrounded by the endothelium (shown in red) and chalaza (in purple). The other two cell layers of the inner integument are shown in pink, while the cell layers of to the outer integument are shown in orange. The vasculature is shown in blue, and the funiculus in yellow.
(b–d) In situ RNA hybridization showing the localization of AGL6 in the endothelium (b) and AGL13 in the chalaza (c) and the anther tapetum (d).
(e–x) Promoter:GUS fusions. AGL6ΔAUG:GUS expression in stage 11 flowers (e), four-nuclear stage of female gametophyte development (f), mature ovules (g) and developing seeds at globular stage of embryogenesis (h). AGL6UP:GUS expression in stage 11 flowers (i), four-nuclear stage of female gametophyte development (j), mature ovules (k) and developing seeds at the two-cell stage of embryogenesis (l). AGL13ΔAUG:GUS expression in stage 11 flowers (m), integument initiation stage of ovule development (n), mature ovules (o) and developing seeds at the two-cell stage of embryogenesis (p). AGL13UP:GUS expression in stage 11 flowers (q), integument initiation stage of ovule development (r), mature ovules (s), and developing seeds at the two-cell stage of embryogenesis (t). AGL6I1 + I2as:min35S:GUS expression in stage 11 flowers (u), and mature ovules (v). AGL13I1as:min35S:GUS expression in stage 11 flowers (w), and mature ovules (x). All bars represent 50 μm; ch, chalaza; en, endothelial layer; ta, tapetum.

The Ds insertion in ET447 is 14 bp upstream of the 5′ splice donor site of exon 1 of AGL6, which encodes the MADS DNA-binding domain. Not only does the Ds insertion introduce two in-frame stop codons, but also AGL6 mRNA was not detected by reverse transcriptase (RT)-PCR in homozygous plants (data not shown). ET8885, an additional ET line with an insertion inside intron 1 of AGL6 (267 bp downstream of the 5′ splice donor site of exon 1), reproduced the expression pattern of ET447 (Figure S1). Both expression patterns are consistent with the in situ RNA hybridization data for AGL6 (Figure 1b).

To identify the location of the enhancer identified by both ET447 and ET8885, a series of promoter:GUS constructs were made that contained: (i) the upstream sequence in combination with the first intron, (ii) the upstream sequence alone, and (iii) the first intron upstream of min35S (Figures 2, S2 and Appendix S1). The AGL6ΔAUG:GUS lines (which contain the upstream region in combination with the first intron but lack the translational initiation site of AGL6) replicated the expression pattern of ET447 and ET8885, implying that the endothelium-specific enhancer is contained in this genomic region (Figures 1f–h and S1m). In order to investigate the synergistic effects of upstream and intronic elements, the AGL6ΔAUG sequence was divided into upstream (AGL6UP) and intronic regions (AGL6I1 + 12). In plants containing AGL6UP:GUS, reporter activity was not detected early in ovule development (Figure 1j). In mature ovules, reporter activity was restricted to the chalazal region, and did not expand into the endothelial cell layer (Figure 1k), although this chalaza-specific expression was not maintained later during seed development (Figure 1l). This suggests that the endothelium-specific enhancer element is located in the first intron. However, plant lines containing the AGL6I1 + I2s:min35S:GUS or AGL6I1 + I2as:min35S:GUS constructs, which have the intron upstream of a minimal promoter in either sense or antisense orientation, showed no reporter activity throughout ovule development (Figure 1v). Taken together, this analysis suggests a bipartite endothelium-specific enhancer at the AGL6 locus that requires the activity of regulatory elements that are located upstream of the translational initiation site as well as inside the first intron (Figure 2).

Figure 2.

 Summary of the regulatory elements of the AGL6 subfamily members in Arabidopsis.
A summary of the enhancer and silencer elements demonstrated in Figures 1, S1 and S3 relative to their position in either the upstream or the intronic regions of AGL6 (a) and AGL13 (b). The exact position of the elements is unknown. Green arrows indicate positive interactions between elements, while red bars indicate attenuation. Elements with similar expression patterns in AGL6 (a) and AGL13 (b) are indicated in orange boxes.

Additionally, reporter activity was detected for both AGL6I1 + I2s:min35S:GUS and AGL6I1 + I2as:min35S:GUS constructs in the tapetum, starting in stage 8 flowers (Smyth et al., 1990) and ending before stage 12 (Figure 1u), indicating the presence of a tapetum-specific enhancer inside intron 1 of AGL6. However, tapetal expression was not seen in ET447, ET8885, AGL6ΔAUG:GUS or AGL6UP:GUS lines. Instead, reporter activity was detected in the basal parts of all the floral organs during these floral stages, ultimately restricted to the abscission zone (Figure 1e,i).

Finally, examination of 12-day-old seedlings identified a silencer activity located inside the first intron. No reporter activity was detected for either ET447 or ET8885 lines at this stage. Weak reporter activity, however, was detected in the vasculature of the cotyledons of AGL6ΔAUG:GUS lines (Figure S3b). This expression domain expanded to the vasculature of the developing leaves in the AGL6UP:GUS lines (Figure S3g), but no expression was detected in the AGL6I1 + I2s:min35S:GUS or AGL6I1 + I2as:min35S:GUS lines, indicating that there is a leaf vasculature-specific silencer present inside the first intron that prevents expression in seedlings.

A different set of upstream and intronic regulatory elements controls the expression of AGL13

To address whether a similar complex set of intronic elements are found in the other AGL6 subfamily member, the regulatory regions of AGL13 were examined. Although it was not isolated in the initial screen, the enhancer detector line ET5830, with the Ds element inserted inside intron 1 of AGL13 (189 bp upstream of the 3′ splice acceptor site of exon 2), was examined. While the insertion does not disrupt the coding sequence, no AGL13 mRNA was detected by RT-PCR in homozygous plants (data not shown). In contrast to ET447 and ET8885, no ET5830 reporter gene activity was observed throughout ovule or seed development (Figure S1). Consistent with the in situ hybridization pattern of AGL13 (Figure 1d), ET5830 showed reporter gene activity in the tapetum, in a spatiotemporal expression pattern that overlapped with the intron-encoded tapetum-specific enhancer activity of AGL6. To narrow down the location of the tapetum-specific enhancer identified by ET5830, a series of promoter:GUS constructs were made, similar to those described above (Figure S2). The AGL13ΔAUG:GUS construct replicated the expression pattern of ET5830 in the tapetum (Figure 1m), suggesting that the enhancer is located in this genomic region. AGL13UP:GUS lines, however, failed to show the broad tapetum-specific expression pattern (Figure 1q), while both AGL13I1s:min35S:GUS and AGL13I1as:min35S:GUS constructs reproduced the expression pattern of ET5830 (Figure 1w).

The AGL13 promoter:GUS constructs, however, showed some marked differences from the expression pattern observed in the enhancer detector line. Unlike ET5830, AGL13ΔAUG:GUS was expressed in the developing ovule, consistent with the observed in situ RNA hybridization pattern of AGL13 (Figure 1c; Rounsley et al., 1995). Reporter activity was detected early in the chalaza, directly adjacent to the megaspore mother cell (Figure 1n), and continued there throughout the rest of ovule development (Figure 1o); it was subsequently detected at the chalazal end of the developing seed coat (Figure 1p). In plants containing AGL13UP:GUS, which lacks the first intron, the reporter activity showed the same pattern of expression as AGL13ΔAUG:GUS, although the level of expression was higher at all stages of development (Figure 1n–p). This suggests the presence of a silencer element inside the first intron. Consistent with this hypothesis, plant lines containing either the AGL13I1s:min35S:GUS or the AGL13I1as:min35S:GUS construct showed no reporter activity throughout ovule development (Figure 1x), similar to the ET5830 enhancer detector line.

As the regulatory elements located in the first intron of AGL6 were also active in 12-day-old seedlings, the expression patterns in seedling development were examined. Similar to ET447 and ET8885, no expression was detected in the AGL13 enhancer detector line ET5830. For the AGL13ΔAUG:GUS reporter line, however, reporter activity was detected in the vasculature underlying the developing shoot apical meristem (Figure S3i). Reporter activity was also detected in the root vasculature of AGL13UP:GUS seedlings (Figure S3p), suggesting the presence of a root-specific silencer element inside the first intron of AGL13 (Figure 2).

Expression of AGL6 and AGL13 overlaps in the chalaza

To investigate the overlap in expression of AGL6 and AGL13 in the developing ovule, plant lines expressing the plant codon-optimized version of the Clostridium perfringens neuraminidase nanH (or NAN; Kirby and Kavanagh, 2002) reporter gene under the control of the AGL13 regulatory elements (AGL13ΔAUG:NAN) were crossed to AGL6ΔAUG:GUS. AGL13ΔAUG:NAN reporter activity initiated early in the chalaza, before any AGL6ΔAUG:GUS activity was detected (Figure 3a). However, around the two-nuclear stage, AGL6ΔAUG:GUS activity initiated in the presumptive endothelial layer and the chalaza, which also showed AGL13ΔAUG:NAN activity (Figure 3b). Throughout the later stages of ovulogenesis, AGL13ΔAUG:NAN activity was restricted to the chalaza, while AGL6ΔAUG:GUS activity was detected in both the chalaza and the endothelium (Figure 3c,d).

Figure 3.

 Overlapping expression of the AGL6 and AGL13 promoters in the chalaza of the developing ovule.
AGL13ΔAUG:NAN activity is detected as an indigo blue precipitate, AGL6ΔAUG:GUS activity is detected as a magenta precipitate, and overlapping expression is detected as a purple precipitate. AGL13ΔAUG:NAN activity is first detected in the chalaza at around megasporogenesis (a). At around the four-nuclear stage of female gametophyte development (b), AGL6ΔAUG:GUS starts to be expressed in the presumptive endothelial layer and AGL6ΔAUG:GUS and AGL13ΔAUG:NAN activity overlap in the chalaza. This overlapping expression in the chalaza continues throughout the rest of ovule development (c, d). All bars represent 50 μm; ch, chalaza; en, endothelial layer.

Identification of conserved regions of homology inside
the first intron

As subfunctionalization predicts the reciprocal loss of regulatory elements between paralogs, the first introns of AGL6 and AGL13 were investigated to identify paralog-specific putative binding sites for transcription factors. AthaMap and TRANSFAC® Patch scans of the intron, however, revealed a large number of putative transcription factor-binding sites, hindering the identification of the important factors (Matys et al., 2006; Galuschka et al., 2007). To reduce the number of putative sites, phylogenetic shadowing, which utilizes sequence information from homologous genes of related species (e.g. Hong et al., 2003), was used to identify regions conserved between several A. thaliana relatives. The first intron sequences were aligned for the AGL6 and AGL13 homologs from A. thaliana, Arabidopsis halleri, Arabidopsis lyrata, Boechera gunnisoniana, Boechera stricta and, for AGL6, Brassica oleracea var. botrytis (where an AGL13 homolog was not amplified). Subsequent analysis identified several conserved areas, which could be loosely grouped into four regions containing several conserved predicted transcription factor-binding sites (Figures 4a and S4–S6 and Table S1).

Figure 4.

 Regions of conservation inside the first intron of AGL6 and AGL13.
(a) A 20-nucleotide sliding window analysis of the aligned sequences showing the average pairwise mismatch for the first intron of AGL6 (top) and AGL13 (bottom). The black line on the graph represents an analysis where a gap in the sequence was treated as a mismatch, while the light gray line represents an analysis where gaps were not considered. The x-axis indicates the position of the sliding window along the aligned first intron sequence. The conserved areas (as defined from the total of phylogenetic shadowing analyses) are identified by a black line beneath the graph, while the four (loosely defined) regions of homology are identified as dark gray lines. The lower 99% confidence bounds for mismatch values with and without gaps, respectively, were 0.151 and 0.267 for AGL6, and 0.122 and 0.332 for AGL13. The insertion sites of ET8885 (top) and ET5830 (bottom) are indicated with arrows.
(b) A sliding window dot-plot (window size = 20; allowing eight mismatches per window; step size = 1) comparing the first introns of AGL6 and AGL13 of Arabidopsis thaliana. Light gray areas and, where overlapping, white boxes indicate the conserved areas of AGL6 and AGL13 identified by phylogenetic shadowing, while conserved sliding windows are represented by black dots, with stretches of similarity identified as black diagonal lines.
(c) The distribution of diagonals (i.e. matching sliding windows) identified by dot-plot analysis of intron 1 of AGL6 and AGL13. The black bars correspond to the null distribution of diagonals (as derived from randomly resampled input sequences), the dark gray bars correspond to the distribution of diagonals of the areas of the introns that are not conserved in both AGL6 and AGL13, and the light gray bars correspond to the distribution of diagonals of the areas defined by conservation in both AGL6 and AGL13. The probability of a distribution different from the null distribution (Kolmogorov–Smirnov test) is indicated.

To assess if these areas of homology were conserved between AGL6 and AGL13, dot-plot analysis was performed, which revealed no obvious sequence similarity between intron 1 of AGL6 and AGL13 of A. thaliana (Figure 4b). On a dot-plot, a diagonal line indicates a stretch of similar nucleotide sequence. To examine if the conserved intronic regions identified in AGL6 match those identified in AGL13, we looked at the diagonal density, which is a scaled representation of the number of diagonals of a given size class among a pair of sequences. Regions of sequence similarity would be expected to have higher diagonal densities with potentially longer diagonals, while regions with dissimilar sequences would be indistinguishable from the null distribution for diagonal densities (derived from randomly resampled input sequences). The non-conserved regions of intron 1 of AGL6 and AGL13 were not statistically different from the null distribution, consistent with overall sequence divergence. When comparing the conserved areas, an excess of small regions of sequence similarity (short diagonals) was observed (Figure 4c). With the exception of a putative intron-mediated enhancement site (IME; Rose et al., 2008), however, none of the predicted transcription factor-binding sites inside the conserved areas was present in both AGL6 and AGL13. Similar dot-plot analysis of the first intron of PMADS34 (the Populus trichocarpa AGL6 subfamily member) and VvMADS3 (the Vitis vinifera AGL6 subfamily member) revealed that both sequences had significant similarity to parts of Region B of AGL6, parts of Region D of AGL6 and parts of Region B of AGL13 (Figures 5 and S7). While the aforementioned parts of AGL6 Region D do not correspond to any predicted transcription factor-binding sites, the identified parts of Regions B of AGL6 and AGL13 contain binding sites for a different predicted homeodomain transcription factor, ZmHox2a (Table S1).

Figure 5.

 Regions of sequence similarity inside the first intron between Populus PMADS34 and Arabidopsis AGL6 subfamily members.
(a) A sliding window dot-plot (window size = 20; allowing eight mismatches per window; step size = 1) comparing the first intron of PMADS34 of Populus trichocarpa and the first introns of AGL6 (top) and AGL13 (bottom) of Arabidopsis thaliana. White areas indicate the conserved areas of AGL6 and AGL13 identified by phylogenetic shadowing, while matching sliding windows are represented by black dots, with stretches of similarity identified as black diagonal lines.
(b, c) The distribution of diagonals identified by dot-plot analysis of intron 1 of Populus PMADS34 and either Arabidopsis AGL6 (b) or AGL13 (c). The black bars correspond to the null distribution of diagonals, the dark gray bars correspond to the distribution diagonals of the non-conserved regions of the A. thaliana introns, and the light gray and white bars correspond to the distribution of matching sliding windows of the conserved B and C regions, respectively. Probabilities for a distribution different from the null distribution (Kolmogorov–Smirnov test) are indicated.

Divergence in different domains of AGL6 subfamily
members

AGL6 and AGL13 are located on duplicated genomic blocks that arose during the most recent genome duplication event that occurred 35–85 Ma in the common ancestor of Brassicaceae (Blanc et al., 2003; Bowers et al., 2003). This is consistent with a phylogenetic analysis of AGL6 and AGL13 coding sequences, in which the Brassicaceae AGL13 homologs formed a sister group to the Brassicaceae AGL6 homologs, but were nested within the greater AGL6 subfamily of MADS-domain genes (Figures 6 and S8). When specific domains of the genes were used, the combined I- and K-domains gave similar trees to when using the full-length (or MADS + I + K) sequences. However, the MADS-domains of the AGL13 homologs showed higher divergence from the rest of the AGL6 subfamily members, as indicated by a longer branch leading to the AGL13 homologs (Figures 6 and S9). The longer branch length (that is, more substitutions) suggested that AGL13 might have been less constrained in its MADS-domain sequence than AGL6.

Figure 6.

 Bayesian inference phylogenetic analyses of domains of AGL6 subfamily members.
Bayesian inference analysis using (a) the nucleotide sequence of the MADS + I + K domains, (b) the regions encoding the I + K domains and (c) the region encoding the MADS-domain. While the trees in (a) and (b) are similar, the trees using the MADS-domain deviate, with longer branch lengths leading to the AGL13 homologs, suggesting that their MADS-domains are less constrained than those of AGL6. Branch support values (Bayesian posterior probabilities) <1.00 are shown above the branches (support of 1.00 is not indicated). Light gray boxes indicate AGL6 homologs of Brassicaceae, while dark gray boxes indicate AGL13 homologs of Brassicaceae. The white boxes indicate related MADS-domain proteins from Arabidopsis thaliana. In the insets, the average Ka/Ks values are presented with the standard deviation (P-values from a Welsh’s t-test), and ω-values indicating the strength of positive selection (in the free-ratio branch model M1; Table S4) on three branches of each tree are shown.

Additionally, the average of the ratios of non-synonymous substitutions (Ka, altering the amino acid sequence) to synonymous substitutions (Ks, preserving the amino acid sequence) from the Brassicaceae AGL6 subfamily members were compared for the MADS + I + K, the I + K, and the MADS-domains (Figure 6). All average Ka/Ks ratios were <1.0, which is consistent with purifying selection, and all average Ka/Ks ratios were lower in AGL6 than in AGL13. Except for the I + K domain, all Ka/Ks ratios were significantly different between AGL6 and AGL13 for the homologous domains. For AGL6 there was a significant difference between I + K and MADS-domains (< 0.001), whereas for AGL13 there was no significant difference (= 0.29).

There is evidence for past positive selection using a dN/dS-based maximum likelihood ω-estimate, which also uses the ratio of non-synonymous to synonymous substitutions (Figure 6 and Table S4). Branch-specific models that allow for positive selection for the branch prior to genome duplication (ωa), or leading either to AGL6b) or AGL13c) Brassicaceae homologs, are significantly better than the null model (Table S4), with the sole exception of ωb for the MADS domain of Brassicaceae AGL6 homologs. This confirms the Ka/Ks-based analyses but also suggests that selection may already have been acting on the ancestral Brassicaceae AGL6 homolog prior to the genome duplication event that gave rise to the AGL6 and AGL13 paralogs.

Putative ancestral expression pattern of AGL6

To distinguish between subfunctionalization and neofunctionalization in the DDC model, the ancestral expression pattern of AGL6 needs to be established (Figure 7). Gymnosperm AGL6 homologs are expressed in both male and female reproductive tissues, although expression is initiated earlier and in a broader spatial pattern than for AGL6 and AGL13 in Arabidopsis (Mouradov et al., 1998; Shindo et al., 1999; Carlsbecker et al., 2004). A similar pattern occurs in angiosperms, with AGL6 homologs expressed in both male and female reproductive tissues, although male tissue-specific expression is not detected in some species. Either male-specific expression evolved de novo at least three times for the AGL6 subfamily or it was present ancestrally and then lost. Of the two, it seems most plausible that the ancestral expression pattern for the AGL6 subfamily was in both the male and female reproductive tissues.

Figure 7.

 Expression pattern of AGL6 subfamily members.
A summary of the expression patterns of AGL6 subfamily plotted on phylogeny (Table S5), with the predicted ancestral states indicated. The expression in female reproductive tissues is indicated on the tree. The expression patterns are annotated as: V, vascular; I, inflorescence; P, perianth; ♂, male reproductive organ; ♀, female reproductive organ.

Discussion

Complex regulatory interaction uncovered by enhancer detection screening

The intronic regions of AGL6 and AGL13 are necessary for their proper spatiotemporal expression, and contain both enhancer and silencer elements (Figure 2). Moreover, the interactions between upstream and intronic elements are critical. While some of the interactions are relatively simple, such as the bipartite endothelial enhancer of AGL6 that requires both upstream and intronic elements, other interactions can be more complex. For example, the intron-located tapetum enhancer of AGL6 is completely attenuated by a silencer element located in the upstream region of AGL6. Additionally, both AGL6 and AGL13 have intron-localized elements that can modify the activity of the upstream-localized chalazal enhancer, although in different ways: in AGL6 the intronic element maintains expression; while in AGL13 the intronic element attenuates expression. The complexity of these regulatory interactions might explain why it has been difficult to recapitulate some of the enhancer detector expression patterns with promoter:GUS constructs containing only upstream regulatory sequences (R. Basker and U. Grossniklaus, University of Zürich, Switzerland, unpublished data).

While both the in situ RNA localization of AGL6 and AGL6ΔAUG:GUS lines largely recapitulated the reporter gene expression of ET447 and ET8885, the reporter gene expression of ET5830 was very different from both the in situ RNA localization of AGL13 and AGL13ΔAUG:GUS. For example, both AGL13 RNA and promoter:GUS reporter activity was detected in the chalaza during ovulogenesis, while no reporter activity was detected in the ovules of line ET5830. These results are not surprising, as enhancer detector lines in Drosophila do not always reproduce all the expression pattern elements of a given detected gene (Bellen et al., 1989), although this phenomenon has not yet been reported in plants.

The subfunctionalization of the AGL6 subfamily
in Brassicaceae

In general, AGL6 and AGL13 do not appear to have overlapping expression domains, suggesting the reciprocal loss of regulatory elements, which is consistent with subfunctionalization (Figures 2 and S10). While it is unclear how this ultimately affects the transcriptional regulatory functions of AGL6 and AGL13, change in the expression profiles of the paralogs is a critical (and sufficient; Force et al., 1999) step in subfunctionalization. The only place where AGL6 and AGL13 are co-expressed in the plant is the developing chalaza, suggesting that the spatiotemporal expression patterns of AGL6 and AGL13 have diverged. This suggests that the ancestral expression pattern changed during subfunctionalization in Arabidopsis: AGL13 retained expression in the tapetum and had reduced expression in the ovule, while AGL6 lost expression in the tapetum and retained expression in the ovule. Consistent with these observations, comparison of steady-state mRNA levels by microarray analysis as well as phylogenetic footprinting of the upstream regions also suggests subfunctionalization of the AGL6 subfamily (de Bodt et al., 2006; Duarte et al., 2006). However, the mechanism for subfunctionalization does not appear to occur by the loss of regulatory elements but by attenuation due to the activity of cis-acting silencer elements, suppressing AGL6 expression in the tapetum and partially suppressing AGL13 expression in the chalaza. While this phenomenon appears to have occurred in only a minority of elements, it would provide an additional explanation for the reappearance of ‘lost’ regulatory elements over evolution (Locascio et al., 2002), due to the gain, and then loss, of attenuating silencer elements. The gain of an attenuating silencer element should be a more infrequent event than the loss of an element by mutation, which might explain why the process of subfunctionalization can take longer than predicted (compare Force et al., 1999; Jarinova et al., 2008). Interestingly, the expression of AGL6 subfamily members in male reproductive tissues may be an example in a plant of ‘lost’ regulatory elements: while AGL6 subfamily members are expressed in male reproductive tissues in the ‘ancestral’ gymnosperm, this expression domain was lost in the ‘ancestral’ angiosperm, only to reappear in eudicotyledons.

Phylogenetic shadowing revealed that the first intron of both AGL6 and AGL13 contained four regions of conservation possibly related to expression differences, although these regions were not conserved between AGL6 and AGL13, under the assumption that the expression patterns of AGL6 and AGL13 orthologs are conserved in Brassicaceae. As most AGL6 homologs have similar expression patterns (Figure 7), this assumption seems valid. While the lack of obvious sequence similarity among the first introns is consistent with subfunctionalization, it contrasts with the presence of regulatory elements, such as the tapetum enhancer, that appear to be conserved. It is possible that the regions around the attenuated tapetum-specific enhancer in AGL6, for example, could have diverged sufficiently from the tapetum-specific enhancer in AGL13 that it is not identified in this analysis, yet retained its functional activity. Comparison with AGL6 subfamily members outside of Brassicaceae, however, indicated sequence similarity to two regions of the intron of AGL6 and one region of the intron of AGL13. This suggests that there has been a reciprocal loss of regulatory elements from intron 1 after gene duplication, consistent with subfunctionalization.

Diversification of the Brassicaceae AGL6 subfamily

Comparison of the average Ka/Ks ratios for the Brassicaceae AGL6 subfamily members indicated that both AGL6 and AGL13 are undergoing purifying selection, although the strength of selection was higher for AGL6 than for AGL13. Interestingly, the largest difference between AGL6 and AGL13 was observed when the average Ka/Ks ratios for the MADS-domain were compared. The MADS-domain of AGL6 is under strong purifying selection, while selection on the MADS-domain of AGL13 is relaxed. This is consistent with the ω analysis for this domain, with ωb′ (for the branch leading to AGL6) consistent with purifying selection, which is not seen for ωc (for the branch leading to AGL13). Whether this is reflected in different DNA-binding properties between AGL6 and AGL13 is unknown. Additionally, the high ωa-value for the branch leading to the duplication implies that the MADS-domain was under positive selection prior to duplication. After the duplication event, evidence of positive selection is observed on the I + K domains in simple models (with either ωb or ωc variable and all other ω-values constant), although this is not observed in more complex models (with both ωb and ωc variable; Table S4). While the evolutionary forces driving the diversification of the Brassicaceae AGL6 subfamily are complex, the lack of unambiguous evidence of positive selection post-duplication, which has been postulated as necessary for neofunctionalization (Force et al., 1999), would argue against neofunctionalization.

Several lines of evidence support the hypothesis that the duplicated genes AGL6 and AGL13 are undergoing (or have undergone) subfunctionalization. However, like the hoxb5a and hoxb5b gene pair (Jarinova et al., 2008), it appears that the situation is more complex than predicted by the DDC model, probably involving the attenuation of enhancer elements. Further research into the activity and nature of the regulatory elements driving the expression of other gene pairs in plants is necessary to establish whether this complexity is the rule rather than the exception.

Experimental procedures

In situ hybridization

In situ hybridization was performed as published in Golden et al. (2002) with probes described in Appendix S1. Briefly, due to the high sequence similarity between AGL6 and AGL13, as well as very low transcript levels, sections were hybridized with a pooled set of probes consisting of small (∼90 bp) regions of non-conservation 3′ of the K-domain and a slightly larger (∼200 bp) region of the 3′-untranslated region (UTR).

Promoter–reporter gene constructs

To investigate both promoter and enhancer activities, a series of T-DNA vectors containing the GUS and/or NAN reporter gene(s) were made using new GATEWAY® (Invitrogen, http://www.invitrogen.com/) compatible vectors that have the 5′NOPALINE SYNTHASE promoter of Agrobacterium tumefaciens (Shaw et al., 1984) driving a plant-selectable maker (hygromycin phosphotransferase for GUS vectors, and phosphinotricin acetyl transferase for NAN vectors; see Appendix S1 for more details). These were used to generate a series of GUS reporter constructs of the AGL6 regulatory regions. The first construct (AGL6ΔAUG:GUS) contained 3.0 kb of genomic sequence upstream of the translational start site fused with 0.6 kb intron 1 containing both the 5′ splice donor site of exon 1 and the 3′ splice acceptor site of exon 2. This construct lacks 157 bp of exon 1, removing AUG start codons from exon 1 that are both in and out of the reading frame, preventing the expression of a truncated AGL protein (containing only the MADS DNA-binding domain). The second construct (AGL6UP:GUS) contains only the 3.0 kb of upstream genomic sequence. To detect the presence of enhancer elements that can work independently of upstream elements, a 0.8 kb fragment containing the first intron, second exon, and second intron was placed upstream of a min35S promoter driving the GUS reporter gene. As enhancer elements lack directionality, this fragment was cloned in both a sense and antisense orientation (AGL6I1 + I2s:min35S:GUS and AGL6I1 + I2as:min35S:GUS). The first construct (AGL13ΔAUG:GUS) contained 1.4 kb upstream and 0.7 kb of intron 1. Similar to AGL6ΔAUG:GUS, this construct lacks 177 bp of exon 1, removing AUG start codons that are both in and out of the reading frame. The second construct (AGL13UP:GUS) contains only the 1.4 kb of upstream genomic sequence. As with AGL6, a 0.7 kb fragment containing the first intron of AGL13 was placed upstream of a min35S driving the GUS reporter gene. Again, this fragment was cloned in both a sense and antisense orientation (AGL13I1s:min35S:GUS and AGL13I1as:min35S:GUS). The promoter:NAN construct (AGL13ΔAUG:NAN) contains the same promoter construct as AGL13ΔAUG:GUS upstream of NAN. Construction of these vectors is detailed in Appendix S1. All T-DNA vectors were transformed into A. tumefaciens strain GV3101, and introduced into both Arabidopsis Landsberg erecta and Columbia accessions by floral dipping (Clough and Bent, 1998). Positive transformants were selected either on hygromycin (T-DNAs containing the GUS reporter) or Basta (T-DNAs containing the NAN reporter). An average of 13 independent primary transformants were examined for each transgenic line (a minimum of six), and no obvious differences were observed in the expression patterns between independent primary transformants.

GUS staining

For GUS staining, tissue was dissected (when necessary), immersed in GUS buffer [2.9 mm Na2HPO4, 2.1 mm NaH2PO4, 1 mm EDTA, 0.1% Triton X-100, 1 mm potassium hexacyanoferrate (II), 1 mm potassium hexacyanoferrate (III), 50 μg/μl chloramphenicol, 1 mm 5-bromo-4-chloro-3-indoxyl-β-D-glucuronic acid (X-Gluc; Biosynth, http://www.biosynth.com/)], vacuum infiltrated and incubated at 37°C for several hours, washed with 1× PBS (140 mm NaCl, 2.7 mm KCl, 10.1 mm Na2HPO4, 1.8 mm KH2PO4), and cleared for over an hour in clearing solution (1× PBS, 20%dl-lactic acid, 20% glycerol). This procedure was the same for the co-localization experiments, although using a slightly different staining buffer [2.9 mm Na2HPO4, 2.1 mm NaH2PO4, 1 mm EDTA, 0.1% Triton X-100, 2.5 mm potassium hexacyanoferrate (II), 2.5 mm potassium hexacyanoferrate (III), 50 μg/μl chloramphenicol, 1 mm 5-bromo-6-chloro-3-indoxyl-β-D-glucuronic acid (X-GlucM, GUS substrate; Glycosynth, http://www.glycosynth.co.uk/), 0.5 mm 5-bromo-4-chloro-3-indolyl α-d-N-acetylneuraminic acid (X-NeuNAc, NAN substrate; Biosynth)].

Phylogenetic shadowing and reconstructions

For identification of conserved regions, the nucleotide sequence of the first introns of the AGL6 and AGL13 homologs from various Brassicaceae (primer sequences are described in Table S2) were aligned separately using ClustalX (Thompson et al., 1997; http://www.clustal.org/) and adjusted manually in BioEdit 7 (Hall, 1999; http://www.mbio.ncsu.edu/BioEdit/bioedit.html/; Figures S3 and S4). Analyses were performed using sequence mismatch and, to account for the potential effects of phylogeny on each analysis, maximum parsimony (MP) and maximum likelihood (ML). Average pairwise sequence mismatch was calculated for sliding windows of 20 nucleotides in length along the intron sequence alignment with a step size of one. This was done either excluding or including nucleotide/gap character comparisons for mismatch calculation, using a program written for this purpose. The MP and ML analyses were conducted in PAUP* 4.0b10 (Swofford, 2002; http://paup.csit.fsu.edu/), where ML analyses used the model of nucleotide evolution selected by Modeltest 3.06 (Posada and Crandall, 1998; http://darwin.uvigo.es/software/modeltest.html/) under the Akaike information criterion (AIC; TrN + I model in every case). First, a phylogeny was reconstructed for the first intron. Then, tree scores (tree length for MP, – ln likelihood for ML) for this phylogeny were calculated given the data from each 20-nucleotide-long window. A null distribution for expected mismatch values and tree scores was obtained by conducting the same analyses on 1000 independent 20-nucleotide windows taken from the randomly resampled (bootstrapped) input sequence. The null distribution was used for calculation of mean, standard deviation and 99% confidence interval on mismatch values and tree scores in Microsoft Excel 2007. AGL6 and AGL13 tree scores and mismatch were plotted along the sequence. Sequence windows consistently scoring less than the lower 99% confidence boundary in all analyses (and <15% gap characters) were considered to be conserved. Alignments and all software written for these analyses are freely available from http://botserv1.uzh.ch/home/grossnik/software/AGL/AGL_index.html.

Comparison of AGL6 and AGL13 intron sequences with those of the more distantly related PMADS34 and VvMADS3 was done by dot-plot analysis because reliable sequence alignments were not possible. Dot-plot analysis was performed with a window size of 20, allowing eight mismatches, and a step size of one. Consecutive stretches of matching windows, represented by diagonals in the dot-plot, were counted for the entire dot-plot and separately for areas that were considered conserved for AGL6 or AGL13. For every diagonal length class the sum of diagonals (or diagonal fractions) in a given area was then scaled by this area to give a diagonal density. Null distributions were derived from randomly resampled input sequences (keeping their relative length proportions) and a minimum of 500 000 diagonals. Statistical difference among expected and observed distributions of diagonal length classes was assessed by Kolmogorov–Smirnov (KS) tests using R 2.7.2 (R Development Core Team, 2008; http://www.r-project.org/).

Phylogenetic analyses were performed both on amino acid and coding nucleotide sequences (Table S3). Initial sequence alignments were produced using ClustalX (Thompson et al., 1997), and the nucleotide sequence alignment adjusted manually in BioEdit 7 (Hall, 1999), using the amino acid alignment as a guide (Figure S8). Amino acid sequences were subjected to a MP analysis in PAUP* 4.0b10 (Swofford, 2002) using a heuristic search with tree bisection–reconnection swapping and 10 random sequence addition replications, with the MulTrees option and a MaxTrees limit of one million in effect. Bootstrap analyses with 1000 pseudo-replications each were conducted using heuristic searches with the same settings as above, except that the number of sequence-addition replicates was lowered to three. For analysis of the MADS-domain only, it was necessary to perform the analysis without sequence addition replication and with a lower MaxTrees limit of 5000 enforced. Bayesian inference (BI) was used for analyses based on nucleotide sequences, using MrBayes 3.1.2 (Ronquist and Huelsenbeck, 2003; http://www.mrbayes.csit.fsu.edu/) and models of nucleotide evolution selected by MrModeltest 2.3 (Nylander, 2004; http://www.abc.se/~nylander/) under the AIC (GTR + I + Γ for both MADS and I + K domains). For each BI analysis, Markov chain Monte Carlo (MCMC) runs (four chains each) were performed, sampling one tree every 1000th generation, for 10 million generations, after which the chains seemed to have converged, as judged by inspection of interchain distances and the apparent stationarity of log-likelihood scores. In every analysis, the first 500 of the trees retained were discarded as a ‘burn-in’. Both MP and BI were performed on MADS and I + K domains separately. In addition, the entire amino acid sequence was analyzed using MP and the MADS + I + K nucleotide sequence with BI. The C-domain was not analyzed due to high sequence divergence.

Ka/Ks ratios for AGL6 subfamily members from Brassicaceae were calculated using DnaSP version 4.50 (Rozas et al., 2003; http://www.ub.edu/dnasp/). Mean and variance were calculated for AGL6 and AGL13 homologs and significance tested using a Welsh’s t-test. Maximum likelihood-based codon substitution analyses were performed using the codeml program of PAML 4.1 (Yang, 2007; http://abacus.gene.ucl.ac.uk/software/paml.html/), with site, branch and branch-site models using trees from Figure 6. Likelihood ratio tests were calculated as twice the difference in log likelihood for different models and compared against a χ2-distrubution with degrees of freedom as the difference in free model parameters. Ancestral expression patterns were reconstructed by parsimony in Mesquite 2.6 (Maddison and Maddison, 2009; http://mesquiteproject.org/mesquite/mesquite.html/), using the phylogeny from Figure 6(a) and coding expression as a ‘standard’ character.

Acknowledgements

This work was supported by the University of Zürich, a NSF International Research Fellowship to SES (INT-0301399); a Schrödinger Fellowship from the Austrian Science Fund (FWF) to PMS (J2678-B16); grants from the Swiss National Science Foundation to MDC (3100A0-100281) and UG (31-112489/1); and a grant from the USDA to UG (98-35304-6412). Seeds for ET8885 and ET5830 were obtained from the Cold Spring Harbor Laboratory Collection. We would like to thank Tony Kavanagh for the pUC19-NAN vector, Juan-Miguel Escobar-Restrepo and Anja Schmidt for plant material/DNA, Kentaro Shimizu and Takashi Tsuchimatsu for comments and suggestions on phylogenetic analyses, and Berit Rosc-Schlüter and Monica Grobei for comments on the manuscript.

Accession numbers for the sequence data: GQ117273, GQ117274, GQ117275, GQ117276, GQ117277, GQ117278, GQ117279, GQ-117280.

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