Evolution of class B floral homeotic proteins: obligate heterodimerization originated from homodimerization

Tradeoff between speed and robustness in primordium initiation mediated by auxin-CUC1 interaction

Robustness is the reproducible development of a phenotype despite stochastic noise. It often involves tradeoffs with other performance metrics, but the mechanisms underlying such tradeoffs were largely unknown. An Arabidopsis flower robustly develops four sepals from four precisely positioned auxin maxima. The development related myb-like 1 (drmy1) mutant generates noise in auxin signaling that disrupts robustness in sepal initiation. Here, we find that increased expression of CUP-SHAPED COTYLEDON1 (CUC1), a boundary specification transcription factor, in drmy1 underlies this loss of robustness. CUC1 surrounds and amplifies stochastic auxin noise in drmy1 to form variably positioned auxin maxima and sepal primordia. Removing CUC1 from drmy1 provides time for noisy auxin signaling to resolve into four precisely positioned auxin maxima, restoring robust sepal initiation. However, removing CUC1 decreases the intensity of auxin maxima and slows down sepal initiation. Thus, CUC1 increases morphogenesis speed but impairs robustness against auxin noise. Further, using a computational model, we find that the observed phenotype can be explained by the effect of CUC1 in repolarizing PIN FORMED1 (PIN1), a polar auxin transporter. Lastly, our model predicts that reducing global growth rate improves developmental robustness, which we validate experimentally. Thus, our study illustrates a tradeoff between speed and robustness during development.

Tradeoff Between Speed and Robustness in Primordium Initiation Mediated by Auxin-CUC1 Interaction

Robustness is the reproducible development of a phenotype despite stochastic noise. It often involves tradeoffs with other performance metrics, but the mechanisms underlying such tradeoffs were largely unknown. An Arabidopsis flower robustly develops four sepals from four precisely positioned auxin maxima. The development related myb-like 1 (drmy1) mutant generates noise in auxin signaling that disrupts robustness in sepal initiation. Here, we found that increased expression of CUP-SHAPED COTYLEDON1 (CUC1), a boundary specification transcription factor, in drmy1 underlies this loss of robustness. CUC1 surrounds and amplifies stochastic auxin noise in drmy1 to form variably positioned auxin maxima and sepal primordia. Removing CUC1 from drmy1 provides time for noisy auxin signaling to resolve into four precisely positioned auxin maxima, restoring robust sepal initiation. However, removing CUC1 decreases auxin maxima intensity and slows down sepal initiation. Thus, CUC1 increases morphogenesis speed but impairs robustness against auxin noise. Further, using a computational model, we found that the observed phenotype can be explained by the effect of CUC1 in repolarizing PIN FORMED1 (PIN1), a polar auxin transporter. Lastly, our model predicts that reducing global growth rate improves developmental robustness, which we validated experimentally. Thus, our study illustrates a tradeoff between speed and robustness during development.

HvSL1 and HvMADS16 promote stamen identity to restrict multiple ovary formation in barley

Correct floral development is the result of a sophisticated balance of molecular cues. Floral mutants provide insight into the main genetic determinants that integrate these cues, as well as providing opportunities to assess functional variation across species. In this study, we characterize the barley (Hordeum vulgare) multiovary mutants mov2.g and mov1, and propose causative gene sequences: a C2H2 zinc-finger gene HvSL1 and a B-class gene HvMADS16, respectively. In the absence of HvSL1, florets lack stamens but exhibit functional supernumerary carpels, resulting in multiple grains per floret. Deletion of HvMADS16 in mov1 causes homeotic conversion of lodicules and stamens into bract-like organs and carpels that contain non-functional ovules. Based on developmental, genetic, and molecular data, we propose a model by which stamen specification in barley is defined by HvSL1 acting upstream of HvMADS16. The present work identifies strong conservation of stamen formation pathways with other cereals, but also reveals intriguing species-specific differences. The findings lay the foundation for a better understanding of floral architecture in Triticeae, a key target for crop improvement.

One pattern analysis (OPA) for the quantitative determination of protein interactions in plant cells

BACKGROUND

A commonly used approach to study the interaction of two proteins of interest (POIs) in vivo is measuring Förster Resonance Energy Transfer (FRET). This requires the expression of the two POIs fused to two fluorescent proteins that function as a FRET pair. A precise way to record FRET is Fluorescence Lifetime IMaging (FLIM) which generates quantitative data that, in principle, can be used to resolve both complex structure and protein affinities. However, this potential resolution is often lost in many experimental approaches. Here we introduce a novel tool for FLIM data analysis of multiexponential decaying donor fluorophores, one pattern analysis (OPA), which allows to obtain information about protein affinity and complex arrangement by extracting the relative amplitude of the FRET component and the FRET transfer efficiency from other FRET parameters.

RESULTS

As a proof of concept for OPA, we used FLIM-FRET, or FLIM-FRET in combination with BiFC to reassess the dimerization and tetramerization properties of known interacting MADS-domain transcription factors in Nicotiana benthamiana leaf cells and Arabidopsis thaliana flowers. Using the OPA tool and by extracting protein BINDING efficiencies from FRET parameters to dissect MADS-domain protein interactions in vivo in transient N. benthamiana experiments, we could show that MADS-domain proteins display similar proximities within dimeric or tetrameric complexes but bind with variable affinities. By combining FLIM with BiFC, we were able to identify SEPALLATA3 as a mediator for tetramerization between the other MADS-domain factors. OPA also revealed that in vivo expression from native promoters at low levels in Arabidopsis flower meristems, makes in situ complex formation of MADS-domain proteins barely detectable.

CONCLUSIONS

We conclude that MADS-domain protein interactions are transient in situ and may involve additional, so far unknown interaction mediators. We conclude that OPA can be used to separate protein binding from information about proximity and orientation of the interacting proteins in their complexes. Visualization of individual protein interactions within the underlying interaction networks in the native environment is still restrained if expression levels are low and will require continuous improvements in fluorophore labelling, instrumentation set-ups and analysis tools.

Cracking the Floral Quartet Code: How Do Multimers of MIKCC-Type MADS-Domain Transcription Factors Recognize Their Target Genes?

MADS-domain transcription factors (MTFs) are involved in the control of many important processes in eukaryotes. They are defined by the presence of a unique and highly conserved DNA-binding domain, the MADS domain. MTFs bind to double-stranded DNA as dimers and recognize specific sequences termed CArG boxes (such as 5'-CC(A/T)₆GG-3') and similar sequences that occur hundreds of thousands of times in a typical flowering plant genome. The number of MTF-encoding genes increased by around two orders of magnitude during land plant evolution, resulting in roughly 100 genes in flowering plant genomes. This raises the question as to how dozens of different but highly similar MTFs accurately recognize the cis-regulatory elements of diverse target genes when the core binding sequence (CArG box) occurs at such a high frequency. Besides the usual processes, such as the base and shape readout of individual DNA sequences by dimers of MTFs, an important sublineage of MTFs in plants, termed MIKC^C-type MTFs (M^C-MTFs), has evolved an additional mechanism to increase the accurate recognition of target genes: the formation of heterotetramers of closely related proteins that bind to two CArG boxes on the same DNA strand involving DNA looping. M^C-MTFs control important developmental processes in flowering plants, ranging from root and shoot to flower, fruit and seed development. The way in which M^C-MTFs bind to DNA and select their target genes is hence not only of high biological interest, but also of great agronomic and economic importance. In this article, we review the interplay of the different mechanisms of target gene recognition, from the ordinary (base readout) via the extravagant (shape readout) to the idiosyncratic (recognition of the distance and orientation of two CArG boxes by heterotetramers of M^C-MTFs). A special focus of our review is on the structural prerequisites of M^C-MTFs that enable the specific recognition of target genes.

Evolutionary divergence of motifs in B-class MADS-box proteins of seed plants

Background

MADS-box transcription factors function as homo- or heterodimers and regulate many aspects of plant development; moreover, MADS-box genes have undergone extensive duplication and divergence. For example, the morphological diversity of floral organs is closely related to the functional divergence of the MADS-box gene family. B-class genes (such as Arabidopsis thaliana APETALA3 [AP3] and PISTILLATA [PI]) belong to a subgroup of MADS-box genes. Here, we collected 97 MADS-box B protein sequences from 21 seed plant species and examined their motifs to better understand the functional evolution of B proteins.

Results

We used the MEME tool to identify conserved sequence motifs in these B proteins; unique motif arrangements and sequences were identified in these B proteins. The keratin-like domains of Malus domestica and Populus trichocarpa B proteins differed from those in other angiosperms, suggesting that a novel regulatory network might have evolved in these species. The MADS domains of Nelumbo nucifera, Glycine max, and Amborella trichopoda B-proteins contained motif 9; in contrast, those of other plants contained motif 1. Protein modelling analyses revealed that MADS domains with motif 9 may lack amino acid sites required for DNA-binding. These results suggested that the three species might share an alternative mechanism controlling floral development.

Conclusions

Amborella trichopoda has B proteins with either motif 1 or motif 9 MADS domains, suggesting that these two types of MADS domains evolved from the ancestral domain into two groups, those with motif 9 (N. nucifera and G. max), and those with motif 1. Moreover, our results suggest that the homodimer/heterodimer intermediate transition structure first appeared in A. trichopoda. Therefore, our systematic analysis of the motifs in B proteins sheds light on the evolution of these important transcription factors.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40709-021-00144-7.

Transcriptome-wide analysis of MADS-box family genes involved in aluminum and fluoride assimilation in Camellia sinensis

MADS-box transcription factors (TFs) are involved in a variety of processes in flowering plants ranging from root growth to flower and fruit development. However, studies of the tolerance-related functions of MADS-box genes are very limited, and to date no such studies have been conducted on Camellia sinensis. To gain insight into the functions of genes of this family and to elucidate the role they may play in tissue development and Al and F response, we identified 45 MADS-box genes through transcriptomic analysis of C. sinensis. Phylogenetic analysis of these CsMADS-box genes, along with their homologues in Arabidopsis thaliana, enabled us to classify them into distinct groups, including: M-type (Mα), MIKC* and MIKC^c (which contains the SOC1, AGL12, AGL32, SEP, ANR1, SVP, and FLC subgroups). Conserved motif analysis of the CsMADS-box proteins revealed diverse motif compositions indicating a complex evolutionary relationship. Finally, we examined the expression patterns of CsMADS-box genes in various tissues and under different Al and F concentration treatments. Our qPCR results showed that these CsMADS-box genes were involved in Al and F accumulation and root growth in C. sinensis. These findings lay the foundation for future research on the function of CsMADS-box genes and their role in response to Al and F accumulation in root tissues.

PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificity

BACKGROUND

Floral organs are specified by MADS-domain transcription factors that act in a combinatorial manner, as summarized in the (A)BCE model. However, this evolutionarily conserved model is in contrast to a remarkable amount of morphological diversity in flowers. One of the mechanisms suggested to contribute to this diversity is duplication of floral MADS-domain transcription factors. Although gene duplication is often followed by loss of one of the copies, sometimes both copies are retained. If both copies are retained they will initially be redundant, providing freedom for one of the paralogs to change function. Here, we examine the evolutionary fate and functional consequences of a transposition event at the base of the Brassicales that resulted in the duplication of the floral regulator PISTILLATA (PI), using Tarenaya hassleriana (Cleomaceae) as a model system.

RESULTS

The transposition of a genomic region containing a PI gene led to two paralogs which are located at different positions in the genome. The original PI copy is syntenic in position with most angiosperms, whereas the transposed copy is syntenic with the PI genes in Brassicaceae. The two PI paralogs of T. hassleriana have very similar expression patterns. However, they may have diverged in function, as only one of these PI proteins was able to act heterologously in the first whorl of A. thaliana flowers. We also observed differences in protein complex formation between the two paralogs, and the two paralogs exhibit subtle differences in DNA-binding specificity. Sequence analysis indicates that most of the protein sequence divergence between the two T. hassleriana paralogs emerged in a common ancestor of the Cleomaceae and the Brassicaceae.

CONCLUSIONS

We found that the PI paralogs in T. hassleriana have similar expression patterns, but may have diverged at the level of protein function. Data suggest that most protein sequence divergence occurred rapidly, prior to the origin of the Brassicaceae and Cleomaceae. It is tempting to speculate that the interaction specificities of the Brassicaceae-specific PI proteins are different compared to the PI found in other angiosperms. This could lead to PI regulating partly different genes in the Brassicaceae, and ultimately might result in change floral in morphology.

Isolation and Functional Analysis of PISTILLATA Homolog From Magnolia wufengensis

PISTILLATA (PI) homologs are crucial regulators of flower development in angiosperms. In this study, we isolated the MAwuPI homolog from Magnolia wufengensis, a basal angiosperm belonging to the Magnoliaceae. Molecular phylogenetic analysis suggested that MAwuPI was grouped into the PI/GLO lineages of B-class MADS-box gene with the distinctive PI motif. Further expression profiling analysis showed that MAwuPI was expressed in tepals and stamens but not in juvenile leaves and carpels, similar to the spatial expression pattern of AtPI in Arabidopsis. Interestingly, MAwuPI had higher expression level in inner-tepals than in outer-tepals, whereas the M. wufengensis flower is homochlamydeous. Moreover, ectopic expression of MAwuPI in Arabidopsis pi-1 mutant emerged filament-like structures but had no obvious petals, suggesting a partial phenotypic recovery of pi-1 mutant. The features of MAwuPI in the expression pattern and gene function improved our acknowledgment of B-class genes in M. wufengensis, and contributed to the clarification of M. wufengensis evolution status and relations with other sibling species in molecular perspective.

Overexpression of Lilium formosanumMADS-box (LFMADS) Causing Floral Defects While Promoting Flowering in Arabidopsis thaliana, Whereas Only Affecting Floral Transition Time in Nicotiana tabacum

The Formosa lily (Lilium formosanum) is one of the most common horticultural species in Taiwan. To explore gene regulation involved in this species, we used transcriptome analysis to generate PH-FB (mixed floral buds) and PH-LF (mature leaves) datasets. Combination of the PH-FB and PH-LF constructed a de novo assembly of the ALL dataset, including 18,041 contigs and 23,807 unigenes by Nr, GO, COG, and KEGG databases. The differential gene expression (DGE) analysis revealed 9937 genes were upregulated while 10,383 genes were downregulated in the developing floral buds compared to mature leaves. Seven putative genes (LFMADS1 to 7) encoding floral organ identity proteins were selected for further analysis. LFMADS1-6 genes were specifically expressed in the floral organ, while LFMADS7 in the floral buds and mature leaves. Phylogenetic analysis revealed that LFMADS1-3 is classified into B-class, LFMADS4 into C-class, LFMADS5 into D-class, and LFMADS6-7 into E-class, respectively. LFMADS-GFP fusion proteins appeared to localize in the nucleus, supporting their roles as transcription factors (TFs). Overexpression of the LFMADS2, LFMADS4, and LFMADS6 genes in Arabidopsis resulted in early flowering and floral defect, however, only early flowering in transgenic tobacco was observed. Highly expressed floral integrator genes, including AtFT, AtLFY, and AtFUL in transgenic Arabidopsis and NtFUL and NtSOC1 in transgenic tobacco, resulted in early flowering phenotype through qRT-PCR analysis. Yeast two-hybrid analysis suggested that LFMADSs may form higher order complexes with the B-, C-, D, and/or E-class proteins to determine the floral organ identity. Furthermore, E-class LFMADS proteins may function as a glue to mediate and strengthen the protein-protein interactions. Therefore, our de novo datasets would provide information for investigating other differentially expressed candidate transcripts. In addition, functional conservation of LFMADSs appears to be vital in floral transition and floral organ identity.

Changing MADS-Box Transcription Factor Protein-Protein Interactions as a Mechanism for Generating Floral Morphological Diversity

Flowers display fantastic morphological diversity. Despite extreme variability in form, floral organ identity is specified by a core set of deeply conserved proteins-the floral MADS-box transcription factors. This indicates that while core gene function has been maintained, MADS-box transcription factors have evolved to regulate different downstream genes. Thus, the evolution of gene regulation downstream of the MADS-box transcription factors is likely central to the evolution of floral form. Gene regulation is determined by the combination of transcriptional regulators present at a particular cis-regulatory element at a particular time. Therefore, the interactions between transcription factors can be of profound importance in determining patterns of gene regulation. Here, after a short primer on flowers and floral morphology, I discuss the centrality of protein-protein interactions to MADS-box transcription factor function, and review the evidence that the evolution of MADS-box protein-protein interactions is a key driver in the evolution of gene regulation downstream of the MADS-box genes.

Dissecting the role of MADS-box genes in monocot floral development and diversity

Many monocot plants have high social and economic value. These include grasses such as rice (Oryza sativa), wheat (Triticum aestivum), and barley (Hordeum vulgare), which produce soft commodities for many food and beverage industries, and ornamental flowers such ase lily (Lilium longiflorum) and orchid (Oncidium Gower Ramsey), which represent an important component of international flower markets. There is constant pressure to improve the development and diversity of these species, with a significant emphasis on flower development, and this is particularly relevant considering the impact of changing environments on reproduction and thus yield. MADS-box proteins are a family of transcription factors that contain a conserved 60 amino acid MADS-box motif. In plants, attention has been devoted to characterization of this family due to their roles in inflorescence and flower development, which holds promise for the modification of floral architecture for plant breeding. This has been explored in diverse angiosperms, but particularly the dicot model Arabidopsis thaliana. The focus of this review is on the less well characterized roles of the MADS-box proteins in monocot flower development and how changes in MADS-box proteins throughout evolution may have contributed to creating a diverse range of flowers. Examining these changes within the monocots can identify the importance of certain genes and pinpoint those which might be useful in future crop improvement and breeding strategies.

Role of floral organ identity genes in the development of unisexual flowers of Quercus suber L

Monoecious species provide an excellent system to study the specific determinants that underlie male and female flower development. Quercus suber is a monoecious species with unisexual flowers at inception. Despite the overall importance of this and other tree species with a similar reproductive habit, little is known regarding the mechanisms involved in the development of their male and female flowers. Here, we have characterised members of the ABCDE MADS-box gene family of Q. suber. The temporal expression of these genes was found to be sex-biased. The B-class genes, in particular, are predominantly, or exclusively (in the case of QsPISTILLATA), expressed in the male flowers. Functional analysis in Arabidopsis suggests that the B-class genes have their function conserved. The identification of sex-biased gene expression plus the identification of unusual protein-protein interactions suggest that the floral organ identity of Q. suber may be under control of specific changes in the dynamics of the ABCDE model. This study constitutes a major step towards the characterisation of the mechanisms involved in reproductive organ identity in a monoecious tree with a potential contribution towards the knowledge of conserved developmental mechanisms in other species with a similar sex habit.

Duplication and Whorl-Specific Down-Regulation of the Obligate AP3-PI Heterodimer Genes Explain the Origin of Paeonia lactiflora Plants with Spontaneous Corolla Mutation

Herbaceous peony (Paeonia lactiflora) is a globally important ornamental plant. Spontaneous floral mutations occur frequently during cultivation, and are selected as a way to release new cultivars, but the underlying evolutionary developmental genetics remain largely elusive. Here, we investigated a collection of spontaneous corolla mutational plants (SCMPs) whose other floral organs were virtually unaffected. Unlike the corolla in normal plants (NPs) that withered soon after fertilization, the transformed corolla (petals) in SCMPs was greenish and persistent similar to the calyx (sepals). Epidermal cellular morphology of the SCMP corolla was also similar to that of calyx cells, further suggesting a sepaloid corolla in SCMPs. Ten floral MADS-box genes from these Paeonia plants were comparatively characterized with respect to sequence and expression. Codogenic sequence variation of these MADS-box genes was not linked to corolla changes in SCMPs. However, we found that both APETALA3 (AP3) and PISTILLATA (PI) lineages of B-class MADS-box genes were duplicated, and subsequent selective expression alterations of these genes were closely associated with the origin of SCMPs. AP3-PI obligate heterodimerization, essential for organ identity of corolla and stamens, was robustly detected. However, selective down-regulation of these duplicated genes might result in a reduction of this obligate heterodimer concentration in a corolla-specific manner, leading to the sepaloid corolla in SCMPs, thus representing a new sepaloid corolla model taking advantage of gene duplication. Our work suggests that modifying floral MADS-box genes could facilitate the breeding of novel cultivars with distinct floral morphology in ornamental plants, and also provides new insights into the functional evolution of the MADS-box genes in plants.

Transcriptomic Analysis of Differentially Expressed Genes during Flower Organ Development in Genetic Male Sterile and Male Fertile Tagetes erecta by Digital Gene-Expression Profiling

Tagetes erecta is an important commercial plant of Asteraceae family. The male sterile (MS) and male fertile (MF) two-type lines of T. erecta have been utilized in F1 hybrid production for many years, but no report has been made to identify the genes that specify its male sterility that is caused by homeotic conversion of floral organs. In this study, transcriptome assembly and digital gene expression profiling were performed to generate expression profiles of MS and MF plants. A cDNA library was generated from an equal mixture of RNA isolated from MS and MF flower buds (1 mm and 4 mm in diameter). Totally, 87,473,431 clean tags were obtained and assembled into 128,937 transcripts among which 65,857 unigenes were identified with an average length of 1,188 bp. About 52% of unigenes (34,176) were annotated in Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KO (KEGG Ortholog database) and/or GO. Taking the above transcriptome as reference, 125 differentially expressed genes were detected in both developmental stages of MS and MF flower buds. MADS-box genes were presumed to be highly related to male sterility in T. erecta based on histological and cytological observations. Twelve MADS-box genes showed significantly different expression levels in flower buds 4 mm in diameter, whereas only one gene expressed significantly different in flower buds 1 mm in diameter between MS and MF plants. This is the first transcriptome analysis in T. erecta and will provide a valuable resource for future genomic studies, especially in flower organ development and/or differentiation.

Flower development: the evolutionary history and functions of the AGL6 subfamily MADS-box genes

AGL6 is an ancient subfamily of MADS-box genes found in both gymnosperms and angiosperms. Its functions remained elusive despite the fact that the MADS-box genes and the ABC model have been studied for >20 years. Nevertheless, recent discoveries in petunia, rice, and maize support its involvement in the 'E' function of floral development, very similar to the closely related AGL2 (SEPALLATA) subfamily which has been well characterized. The known functions of AGL6 span from ancient conserved roles to new functions acquired in specific plant families. The AGL6 genes are involved in floral meristem regulation, in floral organs, and ovule (integument) and seed development, and have possible roles in both male and female germline and gametophyte development. In grasses, they are also important for the development of the first whorl of the flower, whereas in Arabidopsis they may play additional roles before floral meristem formation. This review covers these recent insights and some other aspects that are not yet fully elucidated, which deserve more studies in the future.

Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein-Protein Interactions

Protein–protein interactions (PPIs) have widely acknowledged roles in the regulation of development, but few studies have addressed the timing and mechanism of shifting PPIs over evolutionary history. The B-class MADS-box transcription factors, PISTILLATA (PI) and APETALA3 (AP3) are key regulators of floral development. PI-like (PI^L) and AP3-like (AP3^L) proteins from a number of plants, including Arabidopsis thaliana (Arabidopsis) and the grass Zea mays (maize), bind DNA as obligate heterodimers. However, a PI^L protein from the grass relative Joinvillea can bind DNA as a homodimer. To ascertain whether Joinvillea PI^L homodimerization is an anomaly or indicative of broader trends, we characterized PI^L dimerization across the Poales and uncovered unexpected evolutionary lability. Both obligate B-class heterodimerization and PI^L homodimerization have evolved multiple times in the order, by distinct molecular mechanisms. For example, obligate B-class heterodimerization in maize evolved very recently from PI^L homodimerization. A single amino acid change, fixed during domestication, is sufficient to toggle one maize PI^L protein between homodimerization and obligate heterodimerization. We detected a signature of positive selection acting on residues preferentially clustered in predicted sites of contact between MADS-box monomers and dimers, and in motifs that mediate MADS PPI specificity in Arabidopsis. Changing one positively selected residue can alter PI^L dimerization activity. Furthermore, ectopic expression of a Joinvillea PI^L homodimer in Arabidopsis can homeotically transform sepals into petals. Our results provide a window into the evolutionary remodeling of PPIs, and show that novel interactions have the potential to alter plant form in a context-dependent manner.

Paralogue Interference Affects the Dynamics after Gene Duplication

Proteins tend to form homomeric complexes of identical subunits, which act as functional units. By definition, the subunits are encoded from a single genetic locus. When such a gene is duplicated, the gene products are suggested initially to cross-interact when coexpressed, thus resulting in the phenomenon of paralogue interference. In this opinion article, we explore how paralogue interference can shape the fate of a duplicated gene. One important outcome is a prolonged time window in which both copies remain under selection increasing the chance to accumulate mutations and to develop new properties. Thereby, paralogue interference can mediate the coevolution of duplicates and here we illustrate the potential of this phenomenon in light of recent new studies.

The C-Terminal Sequence and PI motif of the Orchid (Oncidium Gower Ramsey) PISTILLATA (PI) Ortholog Determine its Ability to Bind AP3 Orthologs and Enter the Nucleus to Regulate Downstream Genes Controlling Petal and Stamen Formation

This study focused on the investigation of the effects of the PI motif and C-terminus of the Oncidium Gower Ramsey MADS box gene 8 (OMADS8), a PISTILLATA (PI) ortholog, on floral organ formation. 35S::OMADS8 completely rescued and 35S::OMADS8-PI (with the PI motif deleted) partially rescued petal/stamen formation, whereas these deficiencies were not rescued by 35S::OMADS8-C (C-terminal 29 amino acids deleted) in pi-1 mutants. OMADS8 could interact with Arabidopsis APETALA3 (AP3) and enter the nucleus. The nuclear entry efficiency was reduced for OMADS8-PI/AP3 and OMADS8-C/AP3. OMADS8 could also interact with OMADS5/OMADS9 (the Oncidium AP3 ortholog) and enter the nucleus with an efficiency only slightly affected by the deletion of the C-terminal sequence or PI motif. However, the stability of the OMADS8/OMADS5 and OMADS8/OMADS9 complexes was significantly reduced by deletion of the C-terminal sequence or PI motif. Further analysis indicated that the expression of genes downstream of AP3/PI (BNQ1/BNQ2/GNC/At4g30270) was compensated by 35S::OMADS8 and 35S::OMADS8-PI to a level similar to wild-type plants but was not affected by 35S::OMADS8-C in the pi-1 mutants. A similar FRET (fluorescence resonance energy transfer) efficiency was observed for Arabidopsis AGAMOUS (AG) and the Oncidium AG ortholog OMADS4 for OMADS8, OMADS8-PI and OMADS8-C. These results indicated that the OMADS8 PI motif and C-terminus were valuable for the interaction of OMADS8 with the AP3 orthologs to form higher order heterotetrameric complexes that regulated petal/stamen formation in both Oncidium orchids and transgenic Arabidopsis. However, the C-terminal sequence and PI motif were dispensable for the interaction of OMADS8 with the AG orthologs.

Genome-wide identification and characterization of MADS-box family genes related to organ development and stress resistance in Brassica rapa

BACKGROUND

MADS-box transcription factors (TFs) are important in floral organ specification as well as several other aspects of plant growth and development. Studies on stress resistance-related functions of MADS-box genes are very limited and no such functional studies in Brassica rapa have been reported. To gain insight into this gene family and to elucidate their roles in organ development and stress resistance, we performed genome-wide identification, characterization and expression analysis of MADS-box genes in B. rapa.

RESULTS

Whole-genome survey of B. rapa revealed 167 MADS-box genes, which were categorized into type I (Mα, Mβ and Mγ) and type II (MIKC(c) and MIKC*) based on phylogeny, protein motif structure and exon-intron organization. Expression analysis of 89 MIKC(c) and 11 MIKC* genes was then carried out. In addition to those with floral and vegetative tissue expression, we identified MADS-box genes with constitutive expression patterns at different stages of flower development. More importantly, from a low temperature-treated whole-genome microarray data set, 19 BrMADS genes were found to show variable transcript abundance in two contrasting inbred lines of B. rapa. Among these, 13 BrMADS genes were further validated and their differential expression was monitored in response to cold stress in the same two lines via qPCR expression analysis. Additionally, the set of 19 BrMADS genes was analyzed under drought and salt stress, and 8 and 6 genes were found to be induced by drought and salt, respectively.

CONCLUSION

The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of MADS-box genes in stress resistance in addition to their growth and developmental functions, which ultimately provides the basis for functional characterization and exploitation of the candidate genes for genetic engineering of B. rapa.

Distinct subfunctionalization and neofunctionalization of the B-class MADS-box genes in Physalis floridana

This work suggested that in Physalis PFGLO1-PFDEF primarily determined corolla and androecium identity, and acquired a novel role in gynoecia functionality, while PFGLO2-PFTM6 functioned in pollen maturation only. The B-class MADS-box genes play a crucial role in determining the organ identity of the corolla and androecium. Two GLOBOSA-like (GLO-like) PFGLO1 and PFGLO2 and two DEFICIENS-like (DEF-like) PFDEF and PFTM6 genes were present in Physalis floridana. However, the double-layered-lantern1 (doll1) mutant is the result of a single recessive mutation in PFGLO1, hinting a distinct divergent pattern of B-class genes. In this work, we utilized the tobacco rattle virus (TRV)-mediated gene silencing approach to further verify this assumption in P. floridana. Silencing of PFGLO1 or/and PFDEF demonstrated their primary role in determining corolla and androecium identity. However, specific PFGLO2 or/and PFTM6 silencing did not affect any organ identity but showed a reduction in mature pollen. These results suggested that both PFGLO2 and PFTM6 had lost their role in organ identity determination but functioned in pollen maturation. Evaluation of fruit setting in reciprocal crosses suggested that both PFGLO1 and PFDEF might have acquired an essential and novel role in the functionality of gynoecia. Such a divergence of the duplicated GLO-DEF heterodimer genes in floral development is different from the existing observations within Solanaceae. Therefore, our research sheds new light on the functional evolution of the duplicated B-class MADS-box genes in angiosperms.

Flower Development and Perianth Identity Candidate Genes in the Basal Angiosperm Aristolochia fimbriata (Piperales: Aristolochiaceae)

Aristolochia fimbriata (Aristolochiaceae: Piperales) exhibits highly synorganized flowers with a single convoluted structure forming a petaloid perianth that surrounds the gynostemium, putatively formed by the congenital fusion between stamens and the upper portion of the carpels. Here we present the flower development and morphology of A. fimbriata, together with the expression of the key regulatory genes that participate in flower development, particularly those likely controlling perianth identity. A. fimbriata is a member of the magnoliids, and thus gene expression detected for all ABCE MADS-box genes in this taxon, can also help to elucidate patterns of gene expression prior the independent duplications of these genes in eudicots and monocots. Using both floral development and anatomy in combination with the isolation of MADS-box gene homologs, gene phylogenetic analyses and expression studies (both by reverse transcription PCR and in situ hybridization), we present hypotheses on floral organ identity genes involved in the formation of this bizarre flower. We found that most MADS-box genes were expressed in vegetative and reproductive tissues with the exception of AfimSEP2, AfimAGL6, and AfimSTK transcripts that are only found in flowers and capsules but are not detected in leaves. Two genes show ubiquitous expression; AfimFUL that is found in all floral organs at all developmental stages as well as in leaves and capsules, and AfimAG that has low expression in leaves and is found in all floral organs at all stages with a considerable reduction of expression in the limb of anthetic flowers. Our results indicate that expression of AfimFUL is indicative of pleiotropic roles and not of a perianth identity specific function. On the other hand, expression of B-class genes, AfimAP3 and AfimPI, suggests their conserved role in stamen identity and corroborates that the perianth is sepal and not petal-derived. Our data also postulates an AGL6 ortholog as a candidate gene for sepal identity in the Aristolochiaceae and provides testable hypothesis for a modified ABCE model in synorganized magnoliid flowers.

CsPI from the perianthless early-diverging Chloranthus spicatus show function on petal development in Arabidopsis thaliana

BACKGROUND

In the floral ABC model, B-class genes comprised of DEFICIENS (DEF)/APETALA3 (AP3) and GLOBOSA (GLO)/PISTILLATA (PI) had been proposed to involve in second and third whorl floral organ development. However, less is known about the function of B-class genes from early-diverging angiosperms. Chloranthaceae is one of the early-diverging angiosperm families. In this study, we characterized the role of the PI-like gene CsPI cloned from Chloranthus spicatus which have the simplest perianthless bisexual flowers.

RESULTS

The expression profile analysis reveals high levels of CsPI mRNA in stamens in Chloranthus spicatus, with weak distribution in leaves and other floral organs. Nevertheless, CsPI rescued both stamen and petal development in Arabidopsis thaliana pi-1 mutants and caused partially conversion of sepals into petaloid organs in wild-type Arabidopsis thaliana plants. Yeast two-hybrid analysis showed that CsPI can form not only homodimers but also heterodimers with proteins encoded by Arabidopsis thaliana and Chloranthus spicatus AP3-like genes.

CONCLUSIONS

These results suggested that CsPI has an ancestral function on stamen development and that CsPI has capability to specify petal development in Arabidopsis thaliana. The finding indicates that the activity of the encoded PI-like proteins is highly conserved between the early-diverging Chloranthus and Arabidopsis. Moreover, our results appear to suggest that B-function genes may not play a role in perianth development in Chloranthus spicatus.

DEF- and GLO-like proteins may have lost most of their interaction partners during angiosperm evolution

BACKGROUND AND AIMS

DEFICIENS (DEF)- and GLOBOSA (GLO)-like proteins constitute two sister clades of floral homeotic transcription factors that were already present in the most recent common ancestor (MRCA) of extant angiosperms. Together they specify the identity of petals and stamens in flowering plants. In core eudicots, DEF- and GLO-like proteins are functional in the cell only as heterodimers with each other. There is evidence that this obligate heterodimerization contributed to the canalization of the flower structure of core eudicots during evolution. It remains unknown as to whether this strict heterodimerization is an ancient feature that can be traced back to the MRCA of extant flowering plants or if it evolved later during the evolution of the crown group angiosperms.

METHODS

The interactions of DEF- and GLO-like proteins of the early-diverging angiosperms Amborella trichopoda and Nuphar advena and of the magnoliid Liriodendron tulipifera were analysed by employing yeast two-hybrid analysis and electrophoretic mobility shift assay (EMSA). Character-state reconstruction, including data from other species as well, was used to infer the ancestral interaction patterns of DEF- and GLO-like proteins.

KEY RESULTS

The yeast two-hybrid and EMSA data suggest that DEF- and GLO-like proteins from early-diverging angiosperms both homo- and heterodimerize. Character-state reconstruction suggests that the ability to form heterodimeric complexes already existed in the MRCA of extant angiosperms and that this property remained highly conserved throughout angiosperm evolution. Homodimerization of DEF- and GLO-like proteins also existed in the MRCA of all extant angiosperms. DEF-like protein homodimerization was probably lost very early in angiosperm evolution and was not present in the MRCA of eudicots and monocots. GLO-like protein homodimerization might have been lost later during evolution, but very probably was not present in the MRCA of eudicots.

CONCLUSIONS

The flexibility of DEF- and GLO-like protein interactions in early-diverging angiosperms may be one reason for the highly diverse flower morphologies observed in these species. The results strengthen the hypothesis that a reduction in the number of interaction partners of DEF- and GLO-like proteins, with DEF-GLO heterodimers remaining the only DNA-binding dimers in core eudicots, contributed to developmental robustness, canalization of flower development and the diversification of angiosperms.

Lily breeding by using molecular tools and transformation systems

In our review, we highlighted the progresses made in molecular breeding of lily's flowering, including the ABCDE models, the gene cloning, the establishment of regeneration system, the gene transformation methods, the transgene technology application in lily. Meanwhile, questions that were met at present in molecular breeding in flowering of lily were underlined, and we provide viable solutions. Although many researches on lily literature had been published in the world, in our review, we provided a valuable and unique resource and spring-board from which to understand or further study the molecular breeding in flowering of lily.

Slow co-evolution of the MAGO and Y14 protein families is required for the maintenance of their obligate heterodimerization mode

The exon junction complex (EJC) plays important roles in RNA metabolisms and the development of eukaryotic organisms. MAGO (short form of MAGO NASHI) and Y14 (also Tsunagi or RBM8) are the EJC core components. Their biological roles have been well investigated in various species, but the evolutionary patterns of the two gene families and their protein-protein interactions are poorly known. Genome-wide survey suggested that the MAGO and Y14 two gene families originated in eukaryotic organisms with the maintenance of a low copy. We found that the two protein families evolved slowly; however, the MAGO family under stringent purifying selection evolved more slowly than the Y14 family that was under relative relaxed purifying selection. MAGO and Y14 were obliged to form heterodimer in a eukaryotic organism, and this obligate mode was plesiomorphic. Lack of binding of MAGO to Y14 as functional barrier was observed only among distantly species, suggesting that a slow co-evolution of the two protein families. Inter-protein co-evolutionary signal was further quantified in analyses of the Tol-MirroTree and co-evolution analysis using protein sequences. About 20% of the 41 significantly correlated mutation groups (involving 97 residues) predicted between the two families was clade-specific. Moreover, around half of the predicted co-evolved groups and nearly all clade-specific residues fell into the minimal interaction domains of the two protein families. The mutagenesis effects of the clade-specific residues strengthened that the co-evolution is required for obligate MAGO-Y14 heterodimerization mode. In turn, the obliged heterodimerization in an organism serves as a strong functional constraint for the co-evolution of the MAGO and Y14 families. Such a co-evolution allows maintaining the interaction between the proteins through large evolutionary time scales. Our work shed a light on functional evolution of the EJC genes in eukaryotes, and facilitates to understand the co-evolutionary processes among protein families.

Flower diversity and angiosperm diversification

The flower itself, which comprises most of the evolutionary innovations of flowering plants, bears special significance for understanding the origin and diversification of angiosperms. The sudden origin of angiosperms in the fossil record poses unanswered questions on both the origins of flowering plants and their rapid spread and diversification. Central to these questions is the role that the flower, and floral diversity, played. Recent clarifications of angiosperm phylogeny provide the foundation for investigating evolutionary transitions in floral features and the underlying genetic mechanisms of stasis and change. The general features of floral diversity can best be addressed by considering key patterns of variation: an undifferentiated versus a differentiated perianth; elaboration of perianth organs in size and color; merosity of the flower; and phyllotaxy of floral organs. Various models of gene expression now explain the regulation of floral organization and floral organ identity; the best understood are the ABC(E) model and its modifications, but other gene systems are important in specific clades and require further study. Furthermore, the propensity for gene and genome duplications in angiosperms provides abundant raw material for novel floral features--emphasizing the importance of understanding the conservation and diversification of gene lineages and functions in studies of macroevolution.

Analysis of the APETALA3- and PISTILLATA-like genes in Hedyosmum orientale (Chloranthaceae) provides insight into the evolution of the floral homeotic B-function in angiosperms

BACKGROUND AND AIMS

According to the floral ABC model, B-function genes appear to play a key role in the origin and diversification of the perianth during the evolution of angiosperms. The basal angiosperm Hedyosmum orientale (Chloranthaceae) has unisexual inflorescences associated with a seemingly primitive reproductive morphology and a reduced perianth structure in female flowers. The aim of this study was to investigate the nature of the perianth and the evolutionary state of the B-function programme in this species.

METHODS

A series of experiments were conducted to characterize B-gene homologues isolated from H. orientale, including scanning electron microscopy to observe the development of floral organs, phylogenetic analysis to reconstruct gene evolutionary history, reverse transcription-PCR, quantitative real-time PCR and in situ hybridization to identify gene expression patterns, the yeast two-hybrid assay to explore protein dimerization affinities, and transgenic analyses in Arabidopsis thaliana to determine activities of the encoded proteins.

KEY RESULTS

The expression of HoAP3 genes was restricted to stamens, whereas HoPI genes were broadly expressed in all floral organs. HoAP3 was able to partially restore the stamen but not petal identity in Arabidopsis ap3-3 mutants. In contrast, HoPI could rescue aspects of both stamen and petal development in Arabidopsis pi-1 mutants. When the complete C-terminal sequence of HoPI was deleted, however, no or weak transgenic phenotypes were observed and homodimerization capability was completely abolished.

CONCLUSIONS

The results suggest that Hedyosmum AP3-like genes have an ancestral function in specifying male reproductive organs, and that the activity of the encoded PI-like proteins is highly conserved between Hedyosmum and Arabidopsis. Moreover, there is evidence that the C-terminal region is important for the function of HoPI. Our findings indicate that the development of the proposed perianth in Hedyosmum does not rely on the B homeotic function.

Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity

Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism's phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection's source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; altered protein-protein interactions; altered domain content; altered activity as an activator or repressor; altered protein stability; and hypomorphic and hypermorphic alleles. There was also variability in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution.

The corona of the daffodil Narcissus bulbocodium shares stamen-like identity and is distinct from the orthodox floral whorls

The structural homology of the daffodil corona has remained a source of debate throughout the history of botany. Over the years it has been separately referred to as a modified petal stipule, stamen and tepal. Here we provide insights from anatomy and molecular studies to clarify the early developmental stages and position of corona initiation in Narcissus bulbocodium. We demonstrate that the corona initiates as six separate anlagen from hypanthial tissue between the stamens and perianth. Scanning electron microscope images and serial sections demonstrate that corona initiation occurs late in development, after the other floral whorls are fully developed. To define more precisely the identity of the floral structures, daffodil orthologues of the ABC floral organ identity genes were isolated and expression patterns were examined in perianth, stamens, carpel, hypanthial tube and corona tissue. Coupled with in situ hybridisation experiments, these analyses showed that the expression pattern of the C-class gene NbAGAMOUS in the corona is more similar to that of the stamens than that of the tepals. In combination, our results demonstrate that the corona of the daffodil N. bulbocodium exhibits stamen-like identity, develops independently from the orthodox floral whorls and is best interpreted as a late elaboration of the region between the petals and stamens associated with epigyny and the hypanthium.

Developmental genetics of the perianthless flowers and bracts of a paleoherb species, Saururus chinensis

Saururus chinensis is a core member of Saururaceae, a perianthless (lacking petals or sepals) family. Due to its basal phylogenetic position and unusual floral composition, study of this plant family is important for understanding the origin and evolution of perianthless flowers and petaloid bracts among angiosperm species. To isolate genes involved in S. chinensis flower development, subtracted floral cDNA libraries were constructed by using suppression subtractive hybridization (SSH) on transcripts isolated from developing inflorescences and seedling leaves. The subtracted cDNA libraries contained a total of 1,141 ESTs and were used to create cDNA microarrays to analyze transcript profiles of developing inflorescence tissues. Subsequently, qRT-PCR analyses of eight MADS-box transcription factors and in situ hybridizations of two B-class MADS-box transcription factors were performed to verify and extend the cDNA microarray results. Finally, putative phylogenetic relationships within the B-class MADS-box gene family were determined using the discovered S. chinensis B-class genes to compare K-domain sequences with B genes from other basal angiosperms. Two hundred seventy-seven of the 1,141 genes were found to be expressed differentially between S. chinensis inflorescence tissues and seedling leaves, 176 of which were grouped into at least one functional category, including transcription (14.75%), energy (12.59%), metabolism (9.12%), protein-related function (8.99%), and cellular transport (5.76%). qRT-PCR and in situ hybridization of selected MADS-box genes supported our microarray data. Phylogenetic analysis indicated that a total of six B-class MADS-box genes were isolated from S. chinensis. The differential regulation of S. chinensis B-class MADS-box transcription factors likely plays a role during the development of subtending bracts and perianthless flowers. This study contributes to our understanding of inflorescence development in Saururus, and represents an initial step toward understanding the formation of petaloid bracts in this species.

Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies

Members of the MADS-box transcription factor family play essential roles in almost every developmental process in plants. Many MADS-box genes have conserved functions across the flowering plants, but some have acquired novel functions in specific species during evolution. The analyses of MADS-domain protein interactions and target genes have provided new insights into their molecular functions. Here, we review recent findings on MADS-box gene functions in Arabidopsis and discuss the evolutionary history and functional diversification of this gene family in plants. We also discuss possible mechanisms of action of MADS-domain proteins based on their interactions with chromatin-associated factors and other transcriptional regulators.

Quantitative levels of Deficiens and Globosa during late petal development show a complex transcriptional network topology of B function

The transcriptional network topology of B function in Antirrhinum, required for petal and stamen development, is thought to rely on initial activation of transcription of DEFICIENS (DEF) and GLOBOSA (GLO), followed by a positive autoregulatory loop maintaining gene expression levels. Here, we show that the mutant compacta (co), whose vegetative growth and petal size are affected, plays a role in B function. Late events in petal morphogenesis such as development of conical cell area and scent emissions were reduced in co and def (nicotianoides) (def (nic) ), and absent in co def (nic) double mutants, suggesting a role for CO in petal identity. Expression of DEF was down-regulated in co but surprisingly GLO was not affected. We investigated the levels of DEF and GLO at late stages of petal development in the co, def (nic) and glo-1 mutants, and established a reliable transformation protocol that yielded RNAi-DEF lines. We show that the threshold levels of DEF or GLO required to obtain petal tissue are approximately 11% of wild-type. The relationship between DEF and GLO transcripts is not equal or constant and changes during development. Furthermore, down-regulation of DEF or GLO does not cause parallel down-regulation of the partner. Our results demonstrate that, at late stages of petal development, the B function transcriptional network topology is not based on positive autoregulation, and has additional components of transcriptional maintenance. Our results suggest changes in network topology that may allow changes in protein complexes that would explain the fact that not all petal traits appear early in development.

Evolution of the YABBY gene family with emphasis on the basal eudicot Eschscholzia californica (Papaveraceae)

YABBY genes are seed plant-specific transcriptional regulators that are involved in diverse aspects of leaf, shoot and flower development. A series of duplications gave rise to five gene groups found throughout flowering plants. In Arabidopsis and other species, expression of two gene groups, CRABS CLAW and INNER NO OUTER, is restricted to floral organs. In contrast, members of the FILAMENTOUS FLOWER, YABBY2 and YABBY5 gene groups are also expressed in leaves and have been termed 'vegetative YABBYs'. How the five paralogue groups evolved and how their expression and function diversified have remained largely unresolved, precluding a reconstruction of the natural history of this gene family. Here, we report new genes from Eschscholzia californica (Ranunculales, Papaveraceae) that we use together with currently available database sequences in a comprehensive phylogenetic re-evaluation of the YABBY gene family. Multilayered Bayesian analysis covering seed plants allowed us to locate Eschscholzia YABBY sequences within the gene family phylogeny. We established that vegetative YABBYs do not form a monophyletic clade, and that CRABS CLAW and FILAMENTOUS FLOWER arose from a common ancestor gene. INNER NO OUTER genes are sister to that ancestral gene. We identified several conserved motifs outside of known amino acid domains that define all five angiosperm YABBY gene clades. Further, we inferred the evolution of gene expression and provide evidence for release of purifying constraint in certain branches of the gene family tree. Finally, we report expression patterns for five Eschscholzia YABBY genes consistent with functional conservation between early-diverged and core eudicots.

Transference of function shapes organ identity in the dove tree inflorescence

• An important evolutionary mechanism shaping the biodiversity of flowering plants is the transfer of function from one plant organ to another. To investigate whether and how transference of function is associated with the remodeling of the floral organ identity program we studied Davidia involucrata, a species with conspicuous, petaloid bracts subtending a contracted inflorescence with reduced flowers. • A detailed ontogeny enabled the interpretation of expression patterns of B-, C- and E-class homeotic MADS-box genes using qRT-PCR and in situ hybridization techniques. We investigated protein-protein interactions using yeast two-hybrid assays. • Although loss of organs does not appear to have affected organ identity in the retained organs of the reduced flowers of D. involucrata, the bracts express the B-class TM6 (Tomato MADS box gene 6) and GLOBOSA homologs, but not DEFICIENS, and the C-class AGAMOUS homolog, representing a subset of genes also involved in stamen identity. • Our results may illustrate how petal identity can be partially transferred outside the flower by expressing a subset of stamen identity genes. This adds to the molecular mechanisms explaining the diversity of plant reproductive morphology.

Functional analysis reveals the possible role of the C-terminal sequences and PI motif in the function of lily (Lilium longiflorum) PISTILLATA (PI) orthologues

Two lily (Lilium longiflorum) PISTILLATA (PI) genes, Lily MADS Box Gene 8 and 9 (LMADS8/9), were characterized. LMADS9 lacked 29 C-terminal amino acids including the PI motif that was present in LMADS8. Both LMADS8/9 mRNAs were prevalent in the first and second whorl tepals during all stages of development and were expressed in the stamen only in young flower buds. LMADS8/9 could both form homodimers, but the ability of LMADS8 homodimers to bind to CArG1 was relatively stronger than that of LMADS9 homodimers. 35S:LMADS8 completely, and 35S:LMADS9 only partially, rescued the second whorl petal formation and partially converted the first whorl sepal into a petal-like structure in Arabidopsis pi-1 mutants. Ectopic expression of LMADS8-C (with deletion of the 29 amino acids of the C-terminal sequence) or LMADS8-PI (with only the PI motif deleted) only partially rescued petal formation in pi mutants, which was similar to what was observed in 35S:LMADS9/pi plants. In contrast, 35:LMADS9+L8C (with the addition of the 29 amino acids of the LMADS8 C-terminal sequence) or 35S:LMADS9+L8PI (with the addition of the LMADS8 PI motif) demonstrated an increased ability to rescue petal formation in pi mutants, which was similar to what was observed in 35S:LMADS8/pi plants. Furthermore, ectopic expression of LMADS8-M (with the MADS domain truncated) generated more severe dominant negative phenotypes than those seen in 35S:LMADS9-M flowers. These results revealed that the 29 amino acids including the PI motif in the C-terminal region of the lily PI orthologue are valuable for its function in regulating perianth organ formation.

Functional analysis of the two Brassica AP3 genes involved in apetalous and stamen carpelloid phenotypes

The Arabidopsis homeotic genes APETALA3 (AP3) and PISTILLATA (PI) are B genes which encode MADS-box transcription factors and specify petal and stamen identities. In the current study, the stamen carpelloid (SC) mutants, HGMS and AMS, of B. rapa and B. napus were investigated and two types of AP3 genes, B.AP3.a and B.AP3.b, were functional characterized. B.AP3.a and B.AP3.b share high similarity in amino acid sequences except for 8 residues difference located at the C-terminus. Loss of this 8 residues in B.AP3.b led to the change of PI-derived motifs. Meanwhile, B.AP3.a specified petal and stamen development, whereas B.AP3.b only specified stamen development. In B. rapa, the mutations of both genes generated the SC mutant HGMS. In B. napus that contained two B.AP3.a and two B.AP3.b, loss of the two B.AP3.a functions was the key reason for the apetalous mutation, however, the loss-of-function in all four AP3 was related to the SC mutant AMS. We inferred that the 8 residues or the PI-derived motif in AP3 gene probably relates to petal formation.

Robustness and evolvability in the B-system of flower development

BACKGROUND

Gene duplication has often been invoked as a key mechanism responsible for evolution of new morphologies. The floral homeotic B-group gene family has undergone a number of gene duplication events, and yet the functions of these genes appear to be largely conserved. However, detailed comparative analysis has indicated that such duplicate genes have considerable cryptic variability in their functions. In the Solanaceae, two duplicate B-group gene lineages have been retained in three subfamilies. Comparisons of orthologous genes across members of the Solanaceae have demonstrated that the combined function of all four B-gene members is to establish petal and stamen identity, but that this function was partitioned differently in each species. These observations emphasize both the robustness and the evolvability of the B-system.

SCOPE

We provide an overview of how the B-function genes can robustly specify petal and stamen identity and at the same time evolve through changes in protein-protein interaction, gene expression patterns, copy number variation or alterations in the downstream genes they control. By using mathematical models we explore regulatory differences between species and how these impose constraints on downstream gene regulation.

CONCLUSIONS

Evolvability of the B-genes can be understood through the multiple ways in which the B-system can be robust. Quantitative approaches should allow for the incorporation of more biological realism in the representations of these regulatory systems and this should contribute to understanding the constraints under which different B-systems can function and evolve. This, in turn, can provide a better understanding of the ways in which B-genes have contributed to flower diversity.

Transcriptome and metabolite profiling show that APETALA2a is a major regulator of tomato fruit ripening

Fruit ripening in tomato (Solanum lycopersicum) requires the coordination of both developmental cues as well as the plant hormone ethylene. Although the role of ethylene in mediating climacteric ripening has been established, knowledge regarding the developmental regulators that modulate the involvement of ethylene in tomato fruit ripening is still lacking. Here, we show that the tomato APETALA2a (AP2a) transcription factor regulates fruit ripening via regulation of ethylene biosynthesis and signaling. RNA interference (RNAi)-mediated repression of AP2a resulted in alterations in fruit shape, orange ripe fruits, and altered carotenoid accumulation. Microarray expression analyses of the ripe AP2 RNAi fruits showed altered expression of genes involved in various metabolic pathways, such as the phenylpropanoid and carotenoid pathways, as well as in hormone synthesis and perception. Genes involved in chromoplast differentiation and other ripening-associated processes were also differentially expressed, but softening and ethylene biosynthesis occurred in the transgenic plants. Ripening regulators RIPENING-INHIBITOR, NON-RIPENING, and COLORLESS NON-RIPENING (CNR) function upstream of AP2a and positively regulate its expression. In the pericarp of AP2 RNAi fruits, mRNA levels of CNR were elevated, indicating that AP2a and CNR are part of a negative feedback loop in the regulation of ripening. Moreover, we demonstrated that CNR binds to the promoter of AP2a in vitro.

Ectopic expression of TrPI, a Taihangia rupestris (Rosaceae) PI ortholog, causes modifications of vegetative architecture in Arabidopsis

In eudicotyledonous model plants, the B-function genes encode a pair of partner MADS-domain proteins, APETALA3 (AP3) and PISTILLATA (PI) in Arabidopsis and DEFICIENS (DEF) and GLOBOSA (GLO) in Antirrhinum. These proteins, which must form heterodimers to function, are required to specify petal and stamen identity during flower development. Here, we report cloning and characterization of TrPI (Taihangia rupestris PISTILLATA), a PI/GLO-like gene from the core eudicot species Taihangia rupestris (Rosaceae). DNA gel blot analysis showed that TrPI is a single copy gene in the T. rupestris genome. Quantitative RT-PCR and in situ hybridization analyses revealed that TrPI is transcribed in both the vegetative and reproductive organs at different levels. Ectopic expression of TrPI in Arabidopsis caused severe modifications in vegetative plant architecture, including rosette leaves and cauline leaves arranged in a non-spiral phyllotaxy, and a flattened primary inflorescence stem that produced two or three offshoots at the base, middle or top. Moreover, we show that the TrPI gene is capable of rescuing pi-1 mutant phenotypes. Yeast two-hybrid assays showed that TrPI forms homodimers. Taken together, these results show that TrPI might function in regulating plant architecture in addition to its function as a floral organ identity gene in T. rupestris, suggesting that the TrPI protein has biochemical features that distinguish it from the well-studied orthologs, PI and GLO.

B-function expression in the flower center underlies the homeotic phenotype of Lacandonia schismatica (Triuridaceae)

Spontaneous homeotic transformations have been described in natural populations of both plants and animals, but little is known about the molecular-genetic mechanisms underlying these processes in plants. In the ABC model of floral organ identity in Arabidopsis thaliana, the B- and C-functions are necessary for stamen morphogenesis, and C alone is required for carpel identity. We provide ABC model-based molecular-genetic evidence that explains the unique inside-out homeotic floral organ arrangement of the monocotyledonous mycoheterotroph species Lacandonia schismatica (Triuridaceae) from Mexico. Whereas a quarter million flowering plant species bear central carpels surrounded by stamens, L. schismatica stamens occur in the center of the flower and are surrounded by carpels. The simplest explanation for this is that the B-function is displaced toward the flower center. Our analyses of the spatio-temporal pattern of B- and C-function gene expression are consistent with this hypothesis. The hypothesis is further supported by conservation between the B-function genes of L. schismatica and Arabidopsis, as the former are able to rescue stamens in Arabidopsis transgenic complementation lines, and Ls-AP3 and Ls-PI are able to interact with each other and with the corresponding Arabidopsis B-function proteins in yeast. Thus, relatively simple molecular modifications may underlie important morphological shifts in natural populations of extant plant taxa.

Molecular interactions of orthologues of floral homeotic proteins from the gymnosperm Gnetum gnemon provide a clue to the evolutionary origin of 'floral quartets'

Several lines of evidence suggest that the identity of floral organs in angiosperms is specified by multimeric transcription factor complexes composed of MADS-domain proteins. These bind to specific cis-regulatory elements ('CArG-boxes') of their target genes involving DNA-loop formation, thus constituting 'floral quartets'. Gymnosperms, angiosperms' closest relatives, contain orthologues of floral homeotic genes, but when and how the interactions constituting floral quartets were established during evolution has remained unknown. We have comprehensively studied the dimerization and DNA-binding of several classes of MADS-domain proteins from the gymnosperm Gnetum gnemon. Determination of protein-protein and protein-DNA interactions by yeast two-hybrid, in vitro pull-down and electrophoretic mobility shift assays revealed complex patterns of homo- and heterodimerization among orthologues of floral homeotic class B, class C and class E proteins and B(sister) proteins. Using DNase I footprint assays we demonstrate that both orthologues of class B with C proteins, and orthologues of class C proteins alone, but not orthologues of class B proteins alone can loop DNA in floral quartet-like complexes. This is in contrast to class B and class C proteins from angiosperms, which require other factors such as class E floral homeotic proteins to 'glue' them together in multimeric complexes. Our findings suggest that the evolutionary origin of floral quartet formation is based on the interaction of different DNA-bound homodimers, does not depend on class E proteins, and predates the origin of angiosperms.

MIKC* MADS-box proteins: conserved regulators of the gametophytic generation of land plants

Land plants (embryophytes) are characterized by an alternation of two generations, the haploid gametophyte and the diploid sporophyte. The development of the small and simple male gametophyte of the flowering plant Arabidopsis (Arabidopsis thaliana) critically depends on the action of five MIKC* group MCM1-AGAMOUS-DEFICIENS-SRF-box (MADS-box) proteins. In this study, these MIKC* MADS-box genes were isolated from land plants with relatively large and complex gametophyte bodies, namely the bryophytes. We found that although the gene family expanded in the mosses Sphagnum subsecundum, Physcomitrella patens, and Funaria hygrometrica, only a single homologue, Marchantia polymorpha MADS-box gene 1 (MpMADS1), has been retained in the liverwort M. polymorpha. Liverworts are the earliest diverging land plants, and so a comparison of MpMADS1 with its angiosperm homologues addresses the molecular evolution of an embryophyte-specific transcription factor over the widest phylogenetic distance. MpMADS1 was found to form a homodimeric DNA-binding complex, which is in contrast to the Arabidopsis proteins that are functional only as heterodimeric complexes. The M. polymorpha homodimer, nevertheless, recognizes the same DNA sequences as its angiosperm counterparts and can functionally replace endogenous MIKC* complexes to a significant extent when heterologously expressed in Arabidopsis pollen. The 11 MIKC* homologues from the moss F. hygrometrica are highly and almost exclusively expressed in the gametophytic generation. Taken together, these findings suggest that MIKC* MADS-box proteins have largely preserved molecular roles in the gametophytic generation of land plants.

Extended expression of B-class MADS-box genes in the paleoherb Asarum caudigerum

Asarum caudigerum (Aristolochiaceae) is a paleoherb species that is important for research in origin and evolution of angiosperm flowers due to its basal position in the angiosperm phylogeny. In this study, a subtracted floral cDNA library from floral buds of A. caudigerum was constructed and cDNA arrays by suppression subtractive hybridization were generated. cDNAs of floral buds at different stages before flower opening and of leaves at the seedling stage were used. The macroarray analyses of expression profiles of isolated floral genes showed that 157 genes out of the 612 unique ESTs tested revealed higher transcript abundance in the floral buds and uppermost leaves. Among them, 78 genes were determined to be differentially expressed in the perianth, 62 in the stamens, and 100 genes in the carpels. Quantitative real-time PCR of selected genes validated the macroarray results. Remarkably, APETALA3 (AP3) B-class genes isolated from A. caudigerum were upregulated in the perianth, stamens and carpels, implying that the expression domain of B-class genes in this basal angiosperm was broader than those in their eudicot counterparts.

Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses

BACKGROUND

Positive selection is recognized as the prevalence of nonsynonymous over synonymous substitutions in a gene. Models of the functional evolution of duplicated genes consider neofunctionalization as key to the retention of paralogues. For instance, duplicate transcription factors are specifically retained in plant and animal genomes and both positive selection and transcriptional divergence appear to have played a role in their diversification. However, the relative impact of these two factors has not been systematically evaluated. Class B MADS-box genes, comprising DEF-like and GLO-like genes, encode developmental transcription factors essential for establishment of perianth and male organ identity in the flowers of angiosperms. Here, we contrast the role of positive selection and the known divergence in expression patterns of genes encoding class B-like MADS-box transcription factors from monocots, with emphasis on the family Orchidaceae and the order Poales. Although in the monocots these two groups are highly diverse and have a strongly canalized floral morphology, there is no information on the role of positive selection in the evolution of their distinctive flower morphologies. Published research shows that in Poales, class B-like genes are expressed in stamens and in lodicules, the perianth organs whose identity might also be specified by class B-like genes, like the identity of the inner tepals of their lily-like relatives. In orchids, however, the number and pattern of expression of class B-like genes have greatly diverged.

RESULTS

The DEF-like genes from Orchidaceae form four well-supported, ancient clades of orthologues. In contrast, orchid GLO-like genes form a single clade of ancient orthologues and recent paralogues. DEF-like genes from orchid clade 2 (OMADS3-like genes) are under less stringent purifying selection than the other orchid DEF-like and GLO-like genes. In comparison with orchids, purifying selection was less stringent in DEF-like and GLO-like genes from Poales. Most importantly, positive selection took place before the major organ reduction and losses in the floral axis that eventually yielded the zygomorphic grass floret.

CONCLUSION

In DEF-like genes of Poales, positive selection on the region mediating interactions with other proteins or DNA could have triggered the evolution of the regulatory mechanisms behind the development of grass-specific reproductive structures. Orchidaceae show a different trend, where gene duplication and transcriptional divergence appear to have played a major role in the canalization and modularization of perianth development.

SEPALLATA3: the 'glue' for MADS box transcription factor complex formation

A yeast 3-hybrid screen in Arabidopsis reveals MADS box protein complexes: SEP3 is shown to mediate complex formation and floral timing.

Background

Plant MADS box proteins play important roles in a plethora of developmental processes. In order to regulate specific sets of target genes, MADS box proteins dimerize and are thought to assemble into multimeric complexes. In this study a large-scale yeast three-hybrid screen is utilized to provide insight into the higher-order complex formation capacity of the Arabidopsis MADS box family. SEPALLATA3 (SEP3) has been shown to mediate complex formation and, therefore, special attention is paid to this factor in this study.

Results

In total, 106 multimeric complexes were identified; in more than half of these at least one SEP protein was present. Besides the known complexes involved in determining floral organ identity, various complexes consisting of combinations of proteins known to play a role in floral organ identity specification, and flowering time determination were discovered. The capacity to form this latter type of complex suggests that homeotic factors play essential roles in down-regulation of the MADS box genes involved in floral timing in the flower via negative auto-regulatory loops. Furthermore, various novel complexes were identified that may be important for the direct regulation of the floral transition process. A subsequent detailed analysis of the APETALA3, PISTILLATA, and SEP3 proteins in living plant cells suggests the formation of a multimeric complex in vivo.

Conclusions

Overall, these results provide strong indications that higher-order complex formation is a general and essential molecular mechanism for plant MADS box protein functioning and attribute a pivotal role to the SEP3 'glue' protein in mediating multimerization.

Developmental robustness by obligate interaction of class B floral homeotic genes and proteins

DEF-like and GLO-like class B floral homeotic genes encode closely related MADS-domain transcription factors that act as developmental switches involved in specifying the identity of petals and stamens during flower development. Class B gene function requires transcriptional upregulation by an autoregulatory loop that depends on obligate heterodimerization of DEF-like and GLO-like proteins. Because switch-like behavior of gene expression can be displayed by single genes already, the functional relevance of this complex circuitry has remained enigmatic. On the basis of a stochastic in silico model of class B gene and protein interactions, we suggest that obligate heterodimerization of class B floral homeotic proteins is not simply the result of neutral drift but enhanced the robustness of cell-fate organ identity decisions in the presence of stochastic noise. This finding strongly corroborates the view that the appearance of this regulatory mechanism during angiosperm phylogeny led to a canalization of flower development and evolution.

Evolution of petal identity

Petals appear in many angiosperm taxa, yet when and how these attractive organs originated remains unclear. Phylogenetic reconstructions based on morphological data suggest that petals have evolved multiple times during the radiation of the angiosperms. Based on the diversity of petal morphologies, it is likely that the developmental programmes specifying petal identity are distinct in different lineages. On the other hand, molecular genetic analyses have suggested that the specification of petal identity in different lineages utilizes similar genetic pathways. Together, these observations indicate that the evolution of petals has relied on the repeated recruitment of a suite of interacting developmental control genes, albeit in different ways in different lineages. These observations suggest that this gene regulatory network represents a 'deep homology' in plant evolution. A major challenge is to understand how this ancestral developmental pathway has been redeployed in different angiosperm lineages, and how changes in the workings of this pathway have led to the myriad shapes, colours, and sizes of petals.