SEUSS and LEUNIG regulate cell proliferation, vascular development and organ polarity in Arabidopsis petals

The adaptor protein ECAP, the corepressor LEUNIG, and the transcription factor BEH3 interact and regulate microsporocyte generation in Arabidopsis

Histospecification and morphogenesis of anthers during development in Arabidopsis (Arabidopsis thaliana) are well understood. However, the regulatory mechanism of microsporocyte generation at the pre-meiotic stage remains unclear, especially how archesporial cells are specified and differentiate into 2 cell lineages with distinct developmental fates. SPOROCYTELESS (SPL) is a key reproductive gene that is activated during early anther development and remains active. In this study, we demonstrated that the EAR motif-containing adaptor protein (ECAP) interacts with the Gro/Tup1 family corepressor LEUNIG (LUG) and the BES1/BZR1 HOMOLOG3 (BEH3) transcription factor to form a transcription activator complex, epigenetically regulating SPL transcription. SPL participates in microsporocyte generation by modulating the specification of archesporial cells and the archesporial cell-derived differentiation of somatic and reproductive cell layers. This study illustrates the regulation of SPL expression by the ECAP-LUG-BEH3 complex, which is essential for the generation of microsporocytes. Moreover, our findings identified ECAP as a key transcription regulator that can combine with different partners to regulate gene expression in distinct ways, thereby facilitating diverse processes in various aspects of plant development.

Liquid-liquid phase separation in plants: Advances and perspectives from model species to crops

Membraneless biomolecular condensates play important roles in both normal biological activities and responses to environmental stimuli in living organisms. Liquid‒liquid phase separation (LLPS) is an organizational mechanism that has emerged in recent years to explain the formation of biomolecular condensates. In the past decade, advances in LLPS research have contributed to breakthroughs in disease fields. By contrast, although LLPS research in plants has progressed over the past 5 years, it has been concentrated on the model plant Arabidopsis, which has limited relevance to agricultural production. In this review, we provide an overview of recently reported advances in LLPS in plants, with a particular focus on photomorphogenesis, flowering, and abiotic and biotic stress responses. We propose that many potential LLPS proteins also exist in crops and may affect crop growth, development, and stress resistance. This possibility presents a great challenge as well as an opportunity for rigorous scientific research on the biological functions and applications of LLPS in crops.

JcSEUSS1 negatively regulates reproductive organ development in perennial woody Jatropha curcas

MAIN CONCLUSION

Overexpression of JcSEUSS1 resulted in late flowering, reduced flower number, wrinkled kernels, and decreased seed yield in Jatopha curcas, while downregulation of JcSEUSS1 increased flower number and seed production. The seed oil of Jatropha curcas is suitable as an ideal alternative for diesel fuel, yet the seed yield of Jatropha is restricted by its small number of female flowers and low seed setting rate. Therefore, it is crucial to identify genes that regulate flowering and seed set, and hence improve seed yield. In this study, overexpression of JcSEUSS1 resulted in late flowering, fewer flowers and fruits, and smaller fruits and seeds, causing reduced seed production and oil content. In contrast, the downregulation of JcSEUSS1 by RNA interference (RNAi) technology caused an increase in the flower number and seed yield. However, the flowering time, seed number per fruit, seed weight, and size exhibited no obvious changes in JcSEUSS1-RNAi plants. Moreover, the fatty acid composition also changed in JcSEUSS1 overexpression and RNAi plants, the percentage of unsaturated fatty acids (FAs) was increased in overexpression plants, and the saturated FAs were increased in RNAi plants. These results indicate that JcSEUSS1 played a negative role in regulating reproductive growth and worked redundantly with other genes in the regulation of flowering time, seed number per fruit, seed weight, and size.

Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants

Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.

Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in the maintenance and expression of embryogenic competence in sugarcane callus

Plant embryogenic cell culture allows mass propagation and genetic manipulation, but the mechanisms that determine the fate of these totipotent cells in somatic embryos have not yet been elucidated. Here, we performed label-free quantitative proteomics and phosphoproteomics analyses to determine signaling events related to sugarcane somatic embryo differentiation, especially those related to protein phosphorylation. Embryogenic calli were compared at multiplication (EC0, dedifferentiated cells) and after 14 days of maturation (EC14, onset of embryo differentiation). Metabolic pathway analysis showed enriched lysine degradation and starch/sucrose metabolism proteins during multiplication, whereas the differentiation of somatic embryos was found to involve the enrichment of energy metabolism, including the TCA cycle and oxidative phosphorylation. Multiplication-related phosphoproteins were associated with transcriptional regulation, including SNF1 kinase homolog 10 (KIN10), SEUSS (SEU), and LEUNIG_HOMOLOG (LUH). The regulation of multiple light harvesting complex photosystem II proteins and phytochrome interacting factor 3-LIKE 5 were predicted to promote bioenergetic metabolism and carbon fixation during the maturation stage. A motif analysis revealed 15 phosphorylation motifs. The [D-pS/T-x-D] motif was overrepresented during somatic embryo differentiation. A protein-protein network analysis predicted interactions among SNF1-related protein kinase 2 (SnRK2), abscisic acid-responsive element-binding factor 2 (ABF2), and KIN10, which indicated the role of these proteins in embryogenic competence. The predicted interactions between TOPLESS (TPL) and histone deacetylase 19 (HD19) may be involved in posttranslational protein regulation during somatic embryo differentiation. These results reveal the protein regulation dynamics of somatic embryogenesis and new players in somatic embryo differentiation, including their predicted phosphorylation motifs and phosphosites.

Characterization of Genomic Variation from Lotus (Nelumbo Adans.) Mutants with Wide and Narrow Tepals

Compared with rose, chrysanthemum, and water lily, the absence of short-wide and long-narrow tepals of ornamental lotus (Nelumbo Adans.) limits the commercial value of flowers. In this study, the genomes of two groups of lotus mutants with wide-short and narrow-long tepals were resequenced to uncover the genomic variation and candidate genes associated with tepal shape. In group NL (short for N. lutea, containing two mutants and one control of N. lutea), 716,656 single nucleotide polymorphisms (SNPs) and 221,688 insertion-deletion mutations (Indels) were obtained, while 639,953 SNPs and 134,6118 Indels were obtained in group WSH (short for ‘Weishan Hong’, containing one mutant and two controls of N. nucifera ‘Weishan Hong’). Only a small proportion of these SNPs and Indels was mapped to exonic regions of genome: 1.92% and 0.47%, respectively, in the NL group, and 1.66% and 0.48%, respectively, in the WSH group. Gene Ontology (GO) analysis showed that out of 4890 (NL group) and 1272 (WSH group) annotated variant genes, 125 and 62 genes were enriched (Q < 0.05), respectively. Additionally, in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 104 genes (NL group) and 35 genes (WSH group) were selected (p < 0.05). Finally, there were 306 candidate genes that were sieved to determine the development of tepal shape in lotus plants. It will be an essential reference for future identification of tepal-shaped control genes in lotus plants. This is the first comprehensive report of genomic variation controlling tepal shape in lotus, and the mutants in this study are promising materials for breeding novel lotus cultivars with special tepals.

YABBY Genes in the Development and Evolution of Land Plants

Mounting evidence from genomic and transcriptomic studies suggests that most genetic networks regulating the morphogenesis of land plant sporophytes were co-opted and modified from those already present in streptophyte algae and gametophytes of bryophytes sensu lato. However, thus far, no candidate genes have been identified that could be responsible for "planation", a conversion from a three-dimensional to a two-dimensional growth pattern. According to the telome theory, "planation" was required for the genesis of the leaf blade in the course of leaf evolution. The key transcription factors responsible for leaf blade development in angiosperms are YABBY proteins, which until recently were thought to be unique for seed plants. Yet, identification of a YABBY homologue in a green alga and the recent findings of YABBY homologues in lycophytes and hornworts suggest that YABBY proteins were already present in the last common ancestor of land plants. Thus, these transcriptional factors could have been involved in "planation", which fosters our understanding of the origin of leaves. Here, we summarise the current data on functions of YABBY proteins in the vegetative and reproductive development of diverse angiosperms and gymnosperms as well as in the development of lycophytes. Furthermore, we discuss a putative role of YABBY proteins in the genesis of multicellular shoot apical meristems and in the evolution of leaves in early divergent terrestrial plants.

The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

BACKGROUND

Organ shape and size covariation (allometry) factors are essential concepts for the study of evolution and development. Although ample research has been conducted on organ shape and size, little research has considered the correlated variation of these two traits and quantitatively measured the variation in a common framework. The genetic basis of allometry variation in a single organ or among different organs is also relatively unknown.

RESULTS

A principal component analysis (PCA) of organ landmarks and outlines was conducted and used to quantitatively capture shape and size variation in leaves and petals of multiparent advanced generation intercross (MAGIC) populations of Arabidopsis thaliana. The PCA indicated that size variation was a major component of allometry variation and revealed negatively correlated changes in leaf and petal size. After quantitative trait loci (QTL) mapping, five QTLs for the fourth leaf, 11 QTLs for the seventh leaf, and 12 QTLs for petal size and shape were identified. These QTLs were not identical to those previously identified, with the exception of the ER locus. The allometry model was also used to measure the leaf and petal allometry covariation to investigate the evolution and genetic coordination between homologous organs. In total, 12 QTLs were identified in association with the fourth leaf and petal allometry covariation, and eight QTLs were identified to be associated with the seventh leaf and petal allometry covariation. In these QTL confidence regions, there were important genes associated with cell proliferation and expansion with alleles unique to the maximal effects accession. In addition, the QTLs associated with life-history traits, such as days to bolting, stem length, and rosette leaf number, which were highly coordinated with climate change and local adaption, were QTL mapped and showed an overlap with leaf and petal allometry, which explained the genetic basis for their correlation.

CONCLUSIONS

This study explored the genetic basis for leaf and petal allometry and their interaction, which may provide important information for investigating the correlated variation and evolution of organ shape and size in Arabidopsis.

Investigation of genes associated with petal variations between diploid and autotetraploid in Chinese cabbage (Brassica rapa L. ssp. pekinensis) by RNA-seq and sRNA-seq

Polyploidy promotes morphological, physiological, and reproductive diversity in plants. The imminent effect of chromosome doubling in plants is the enlargement of organs such as flowers and fruits, which increases the commercial value of crops. Flowering plays a vital role in the growth and development of angiosperms. Here, we prepared an isolated microspore culture of 'FT', a doubled haploid (DH) line of Chinese cabbage (Brassica rapa L. ssp. pekinensis), and obtained diploid and autotetraploid plants with the same genetic background. Compared with diploids, the autotetraploids were characterized by large floral organs, dark petals, delayed flowering, and reduced fertility. The indole-3-acetic acid (IAA) and jasmonic acid (JA) levels in autotetraploid petals were significantly higher and the abscisic acid (ABA) level was significantly lower than those in the diploid petals. The lutein level in autotetraploid petals was nearly two times higher than that in the diploid petals. A comparative transcriptome analysis revealed 14,412 differentially expressed genes (DEGs) between the diploids and autotetraploids, and they were enriched in 117 Gene Ontology terms and 110 Kyoto Encyclopedia of Genes and Genomes pathways. We detected 231 DEGs related to phytohormone signal transduction and 29 DEGs involved in carotenoid biosynthesis. An miRNA-target mRNA analysis showed that 32 DEGs regulated by 16 DEMs were associated with flowering timing (BraA03000336, BraA09004319, and BraA09000515), petal development (BraA05002408, BraA01004006, BraA09004069, and BraA04000966), flower opening (BraA07000350), and pollen development (BraA01000720, BraA09005727, and BraA01000253). This study provides information to help elucidate the molecular mechanisms underlying phenotypic variations induced by autopolyploidy in Chinese cabbage.

Love on wings, a Dof family protein regulates floral vasculature in Vigna radiata

BACKGROUND

The interaction among plants and their pollinators has been a major factor which enriched floral traits known as pollination syndromes and promoted the diversification of flowering plants. One of the bee-pollination syndromes in Faboideae with keel blossoms is the formation of a landing platform by wing and keel petals. However, the molecular mechanisms of elaborating a keel blossom remain unclear.

RESULTS

By performing large scale mutagenesis, we isolated and characterized a mutant in Vigna radiata, love on wings (low), which shows developmental defects in petal asymmetry and vasculature, leading to a failure in landing platform formation. We cloned the locus through map-based cloning together with RNA-sequencing (RNA-seq) analysis. We found that LOW encoded a nucleus-localized Dof-like protein and was expressed in the flower provascular and vascular tissues. A single copy of LOW was detected in legumes, in contrast with other taxa where there seems to be at least 2 copies. Thirty one Dof proteins have been identified from the V. radiata's genome, which can be further divided into four Major Cluster of Orthologous Groups (MCOGs). We also showed that ectopic expression of LOW in Arabidopsis driven by its native promoter caused changes in petal vasculature pattern.

CONCLUSIONS

To summarize, our study isolated a legume Dof-like factor LOW from V. radiata, which affects vasculature development in this species and this change can, in turn, impact petal development and overall morphology of keel blossom.

Control of leaf blade outgrowth and floral organ development by LEUNIG, ANGUSTIFOLIA3 and WOX transcriptional regulators

Plant lateral organ development is a complex process involving both transcriptional activation and repression mechanisms. The WOX transcriptional repressor WOX1/STF, the LEUNIG (LUG) transcriptional corepressor and the ANGUSTIFOLIA3 (AN3) transcriptional coactivator play important roles in leaf blade outgrowth and flower development, but how these factors coordinate their activities remains unclear. Here we report physical and genetic interactions among these key regulators of leaf and flower development. We developed a novel in planta transcriptional activation/repression assay and suggest that LUG could function as a transcriptional coactivator during leaf blade development. MtLUG physically interacts with MtAN3, and this interaction appears to be required for leaf and flower development. A single amino acid substitution at position 61 in the SNH domain of MtAN3 protein abolishes its interaction with MtLUG, and its transactivation activity and biological function. Mutations in lug and an3 enhanced each other's mutant phenotypes. Both the lug and the an3 mutations enhanced the wox1 prs leaf and flower phenotypes in Arabidopsis. Our findings together suggest that transcriptional repression and activation mediated by the WOX, LUG and AN3 regulators function in concert to promote leaf and flower development, providing novel mechanistic insights into the complex regulation of plant lateral organ development.

Regulation of meristem maintenance and organ identity during rice reproductive development

Grasses have evolved complex inflorescences, where the primary unit is the specialized short branch called a spikelet. Detailed studies of the cumulative action of the genetic regulators that direct the progressive change in axillary meristem identity and their terminal differentiation are crucial to understanding the complexities of the inflorescence and the development of a determinate floret. Grass florets also pose interesting questions concerning the morphologies and functions of organs as compared to other monocots and eudicots. In this review, we summarize our current knowledge of the regulation of the transitions that occur in grass inflorescence meristems, and of the specification of floret meristems and their determinate development. We primarily use rice as a model, with appropriate comparisons to other crop models and to the extensively studied eudicot Arabidopsis. The role of MADS-domain transcription factors in floral organ patterning is well documented in many eudicots and in grasses. However, there is evidence to suggest that some of these rice floral regulators have evolved distinctive functions and that other grass species-specific factors and regulatory pathways occur - for example the LOFSEP 'E' class genes OsMADS1 and OsMAD34, and ramosa genes. A better understanding of these systems and the epigenetic regulators and hormone signaling pathways that interact with them will provide new insights into the rice inflorescence meristem and the differentiation of its floret organs, and should indicate genetic tools that can be used to control yield-related traits in both rice and other cereal crops.

Genome Sequence of Jaltomata Addresses Rapid Reproductive Trait Evolution and Enhances Comparative Genomics in the Hyper-Diverse Solanaceae

Within the economically important plant family Solanaceae, Jaltomata is a rapidly evolving genus that has extensive diversity in flower size and shape, as well as fruit and nectar color, among its ∼80 species. Here, we report the whole-genome sequencing, assembly, and annotation, of one representative species (Jaltomata sinuosa) from this genus. Combining PacBio long reads (25×) and Illumina short reads (148×) achieved an assembly of ∼1.45 Gb, spanning ∼96% of the estimated genome. Ninety-six percent of curated single-copy orthologs in plants were detected in the assembly, supporting a high level of completeness of the genome. Similar to other Solanaceous species, repetitive elements made up a large fraction (∼80%) of the genome, with the most recently active element, Gypsy, expanding across the genome in the last 1–2 Myr. Computational gene prediction, in conjunction with a merged transcriptome data set from 11 tissues, identified 34,725 protein-coding genes. Comparative phylogenetic analyses with six other sequenced Solanaceae species determined that Jaltomata is most likely sister to Solanum, although a large fraction of gene trees supported a conflicting bipartition consistent with substantial introgression between Jaltomata and Capsicum after these species split. We also identified gene family dynamics specific to Jaltomata, including expansion of gene families potentially involved in novel reproductive trait development, and loss of gene families that accompanied the loss of self-incompatibility. This high-quality genome will facilitate studies of phenotypic diversification in this rapidly radiating group and provide a new point of comparison for broader analyses of genomic evolution across the Solanaceae.

Genome-wide identification, phylogeny analysis, expression profiling, and determination of protein-protein interactions of the LEUNIG gene family members in tomato

Members of the LEUNIG gene family have recently emerged as key players in gene repression, affecting several developmental mechanisms in plants, especially flower development. LEUNIG proteins function via recruiting adaptor SEUSS proteins. Nevertheless, no systematic studies on the LEUNIG and SEUSS gene families have been undertaken in tomato (Solanum lycopersicum, a fleshy fruit-bearing model plant, belonging to the Solanaceae family). Here, we present the results of a genome-wide analysis of tomato LEUNIG and SEUSS genes. In our study, we identified three SlLUG and four SlSEU genes. All three SlLUG full-length proteins contained the LEUNIG canonical domains (LUFS and two WD40 repeats), and the four full-length SlSEU genes contained the Lim-binding domain. All the members of the SlLUG and SlSEU family proteins were localized to the nucleus. All the SlSEU and SlLUG genes were detected in the tomato tissues tested. Expression analysis showed that the SlLUGs and SlSEUs exhibited tissue-specific expression, and that they responded to exogenous plant hormone and stress treatment. Protein-protein interaction analysis showed that only SlLUGs, but not SlSEUs, interacted with SlYABBY. Only a weak interaction between SlLUG1 and SlSEU3 was observed among all the SlLUG and SlSEU proteins. Taken together, these findings may help elucidate the roles played by SlLUG and SlSEU family members in plant growth and development.

The YABBY Genes of Leaf and Leaf-Like Organ Polarity in Leafless Plant Monotropa hypopitys

Monotropa hypopitys is a mycoheterotrophic, nonphotosynthetic plant acquiring nutrients from the roots of autotrophic trees through mycorrhizal symbiosis, and, similar to other extant plants, forming asymmetrical lateral organs during development. The members of the YABBY family of transcription factors are important players in the establishment of leaf and leaf-like organ polarity in plants. This is the first report on the identification of YABBY genes in a mycoheterotrophic plant devoid of aboveground vegetative organs. Seven M. hypopitys YABBY members were identified and classified into four clades. By structural analysis of putative encoded proteins, we confirmed the presence of YABBY-defining conserved domains and identified novel clade-specific motifs. Transcriptomic and qRT-PCR analyses of different tissues revealed MhyYABBY transcriptional patterns, which were similar to those of orthologous YABBY genes from other angiosperms. These data should contribute to the understanding of the role of the YABBY genes in the regulation of developmental and physiological processes in achlorophyllous leafless plants.

Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis

Genetic studies have shown essential functions of O-linked N-acetylglucosamine (O-GlcNAc) modification in plants. However, the proteins and sites subject to this posttranslational modification are largely unknown. Here, we report a large-scale proteomic identification of O-GlcNAc-modified proteins and sites in the model plant Arabidopsis thaliana Using lectin weak affinity chromatography to enrich modified peptides, followed by mass spectrometry, we identified 971 O-GlcNAc-modified peptides belonging to 262 proteins. The modified proteins are involved in cellular regulatory processes, including transcription, translation, epigenetic gene regulation, and signal transduction. Many proteins have functions in developmental and physiological processes specific to plants, such as hormone responses and flower development. Mass spectrometric analysis of phosphopeptides from the same samples showed that a large number of peptides could be modified by either O-GlcNAcylation or phosphorylation, but cooccurrence of the two modifications in the same peptide molecule was rare. Our study generates a snapshot of the O-GlcNAc modification landscape in plants, indicating functions in many cellular regulation pathways and providing a powerful resource for further dissecting these functions at the molecular level.

An Evolutionary Framework for Carpel Developmental Control Genes

Carpels are the female reproductive organs of flowering plants (angiosperms), enclose the ovules, and develop into fruits. The presence of carpels unites angiosperms, and they are suggested to be the most important autapomorphy of the angiosperms, e.g., they prevent inbreeding and allow efficient seed dispersal. Many transcriptional regulators and coregulators essential for carpel development are encoded by diverse gene families and well characterized in Arabidopsis thaliana. Among these regulators are AGAMOUS (AG), ETTIN (ETT), LEUNIG (LUG), SEUSS (SEU), SHORT INTERNODE/STYLISH (SHI/STY), and SEPALLATA1, 2, 3, 4 (SEP1, 2, 3, 4). However, the timing of the origin and their subsequent molecular evolution of these carpel developmental regulators are largely unknown. Here, we have sampled homologs of these carpel developmental regulators from the sequenced genomes of a wide taxonomic sampling of the land plants, such as Physcomitrella patens, Selaginella moellendorfii, Picea abies, and several angiosperms. Careful phylogenetic analyses were carried out that provide a phylogenetic background for the different gene families and provide minimal estimates for the ages of these developmental regulators. Our analyses and published work show that LUG-, SEU-, and SHI/STY-like genes were already present in the Most Recent Common Ancestor (MRCA) of all land plants, AG- and SEP-like genes were present in the MRCA of seed plants and their origin may coincide with the ξ Whole Genome Duplication. Our work shows that the carpel development regulatory network was, in part, recruited from preexisting network components that were present in the MRCA of angiosperms and modified to regulate gynoecium development.

Seed abscission and fruit dehiscence required for seed dispersal rely on similar genetic networks

Seed dispersal is an essential trait that enables colonization of new favorable habitats, ensuring species survival. In plants with dehiscent fruits, such as Arabidopsis, seed dispersal depends on two processes: the separation of the fruit valves that protect the seeds (fruit dehiscence) and the detachment of the seeds from the funiculus connecting them to the mother plant (seed abscission). The key factors required to establish a proper lignin pattern for fruit dehiscence are SHATTERPROOF 1 and 2 (SHP1 and SHP2). Here, we demonstrate that the SHP-related gene SEEDSTICK (STK) is a key factor required to establish the proper lignin pattern in the seed abscission zone but in an opposite way. We show that STK acts as a repressor of lignin deposition in the seed abscission zone through the direct repression of HECATE3, whereas the SHP proteins promote lignin deposition in the valve margins by activating INDEHISCENT. The interaction of STK with the SEUSS co-repressor determines the difference in the way STK and SHP proteins control the lignification patterns. Despite this difference in the molecular control of lignification during seed abscission and fruit dehiscence, we show that the genetic networks regulating these two developmental pathways are highly conserved.

Identification of the Arabidopsis RAM/MOR signalling network: adding new regulatory players in plant stem cell maintenance and cell polarization

BACKGROUND AND AIMS

The RAM/MOR signalling network of eukaryotes is a conserved regulatory module involved in co-ordination of stem cell maintenance, cell differentiation and polarity establishment. To date, no such signalling network has been identified in plants.

METHODS

Genes encoding the bona fide core components of the RAM/MOR pathway were identified in Arabidopsis thaliana (arabidopsis) by sequence similarity searches conducted with the known components from other species. The transcriptional network(s) of the arabidopsis RAM/MOR signalling pathway were identified by running in-depth in silico analyses for genes co-regulated with the core components. In situ hybridization was used to confirm tissue-specific expression of selected RAM/MOR genes.

KEY RESULTS

Co-expression data suggested that the arabidopsis RAM/MOR pathway may include genes involved in floral transition, by co-operating with chromatin remodelling and mRNA processing/post-transcriptional gene silencing factors, and genes involved in the regulation of pollen tube polar growth. The RAM/MOR pathway may act upstream of the ROP1 machinery, affecting pollen tube polar growth, based on the co-expression of its components with ROP-GEFs. In silico tissue-specific co-expression data and in situ hybridization experiments suggest that different components of the arabidopsis RAM/MOR are expressed in the shoot apical meristem and inflorescence meristem and may be involved in the fine-tuning of stem cell maintenance and cell differentiation.

CONCLUSIONS

The arabidopsis RAM/MOR pathway may be part of the signalling cascade that converges in pollen tube polarized growth and in fine-tuning stem cell maintenance, differentiation and organ polarity.

Extensive Transcriptome Changes During Natural Onset and Release of Vegetative Bud Dormancy in Populus

To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trees growing under natural conditions. Of 44,441 Populus gene models analyzed using NimbleGen microarrays, we found that 1,362 (3.1%) were differentially expressed among the three dormancy states, and 429 (1.0%) were differentially expressed during only one of the two dormancy transitions (FDR p-value < 0.05). Of all differentially expressed genes, 69% were down-regulated from paradormancy to endodormancy, which was expected given the lower metabolic activity associated with endodormancy. Dormancy transitions were accompanied by changes in genes associated with DNA methylation (via RNA-directed DNA methylation) and histone modifications (via Polycomb Repressive Complex 2), confirming and extending knowledge of chromatin modifications as major features of dormancy transitions. Among the chromatin-associated genes, two genes similar to SPT (SUPPRESSOR OF TY) were strongly up-regulated during endodormancy. Transcription factor genes and gene sets that were atypically up-regulated during endodormancy include a gene that seems to encode a trihelix transcription factor and genes associated with proteins involved in responses to ethylene, cold, and other abiotic stresses. These latter transcription factors include ETHYLENE INSENSITIVE 3 (EIN3), ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN (EBP), ETHYLENE RESPONSE FACTOR (ERF), ZINC FINGER PROTEIN 10 (ZAT10), ZAT12, and WRKY DNA-binding domain proteins. Analyses of phytohormone-associated genes suggest important changes in responses to ethylene, auxin, and brassinosteroids occur during endodormancy. We found weaker evidence for changes in genes associated with salicylic acid and jasmonic acid, and little evidence for important changes in genes associated with gibberellins, abscisic acid, and cytokinin. We identified 315 upstream sequence motifs associated with eight patterns of gene expression, including novel motifs and motifs associated with the circadian clock and responses to photoperiod, cold, dehydration, and ABA. Analogies between flowering and endodormancy suggest important roles for genes similar to SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL), DORMANCY ASSOCIATED MADS-BOX (DAM), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1).

Scanning electron microscopy analysis of floral development

Scanning Electron Microscopy (SEM) allows the morphological characterization of the surface features of floral and inflorescence structures in a manner that retains the topography or three-dimensional appearance of the structure. Even at relatively low magnification levels it is possible to characterize early developmental stages. Using medium to high power magnification at later stages of development, cell surface morphology can be visualized allowing the identification of specific epidermal cell types. The analysis of the altered developmental progressions of mutant plants can provide insight into the developmental processes that are disrupted in that mutant background.

Regulation of floral patterning and organ identity by Arabidopsis ERECTA-family receptor kinase genes

Due to the lack of cell migration, plant organogenesis relies on coordinated cell proliferation, cell growth, and differentiation. A flower possesses a complex structure, with sepals and petals constituting the perianth, and stamens and pistils where male and female gametophytes differentiate. While advances have been made in our understanding of gene regulatory networks controlling flower development, relatively little is known of how cell-cell coordination influences floral organ specification. The Arabidopsis ERECTA (ER)-family receptor kinases, ER, ER-LIKE1 (ERL1), and ERL2, regulate inflorescence architecture, organ shape, and epidermal stomatal patterning. Here it is reported that ER-family genes together regulate floral meristem organization and floral organ identity. The stem cell marker CLAVATA3 exhibits misplaced expression in the floral meristems of the er erl1 erl2 mutant. Strikingly, homeotic conversion of sepals to carpels was observed in er erl1 erl2 flowers. Consistently, ectopic expression of AGAMOUS, which determines carpel identity, was detected in er erl1 erl2 flower primordia. Among the known downstream components of ER-family receptor kinases in stomatal patterning, YODA (YDA) is also required for proper floral patterning. YDA and the ER-family show complex, synergistic genetic interactions: er erl1 erl2 yda quadruple mutant plants become extremely small, callus-like masses. While a constitutively active YDA fully rescues stomatal clustering in er erl1 erl2, it only partially rescues er erl1 erl2 flower defects. The study suggests that ER-family signalling is crucial for ensuring proper expression domains of floral meristem and floral organ identity determinants, and further implies the existence of a non-canonical downstream pathway.

TOPLESS co-repressor interactions and their evolutionary conservation in plants

Large-scale protein-protein interaction studies recently demonstrated that the Arabidopsis TPL/TPR family of transcriptional co-repressors is involved in a broad range of developmental processes. TPL/TPRs predominantly interact with transcription factors that contain repression domain (RD) sequences. Interestingly, RDs reported in the literature are quite diverse in sequence, yet TPL/TPRs interact with proteins containing all of the known motifs. These data lead us to conclude that the TPL/TPRs act as general repressors of gene transcription in plants. To investigate this further, we examined interactions between TPL/TPR proteins encoded by the moss Physcomitrella patens genome and components of the auxin signaling pathway. As in Arabidopsis, moss TPL proteins interact with AUX/IAA and ARF proteins, suggesting that they act in both forms of ARF-mediated transcriptional repression. These data suggest that the involvement of TPL in auxin signaling has been conserved across evolution, since mosses and angiosperms diverged approximately 450 million years ago.

The Arabidopsis transcription factor LUH/MUM1 is required for extrusion of seed coat mucilage

During differentiation, the Arabidopsis (Arabidopsis thaliana) seed coat epidermal cells secrete mucilage composed primarily of rhamnogalacturonan I that is extruded from the seed coat upon imbibition. The mucilage of the mucilage modified1 (mum1) mutant contains rhamnogalacturonan I that is more highly branched and lacks the ability to be extruded when exposed to water. Our cloning of the MUM1 gene shows that it encodes a putative transcription factor, LEUNIG_HOMOLOG (LUH). Cellular localization and transcriptional assay results suggest that LUH/MUM1 is a nucleus-localized transcriptional activator. LUH/MUM1 is expressed in all the tissues examined, including the seed coat. Quantitative reverse transcription-polymerase chain reaction data suggest that LUH/MUM1 is expressed throughout seed coat development, reaching peak expression late in differentiation. LUH1/MUM1 expression in plants homozygous for mutations in several genes encoding regulators of seed coat mucilage was unchanged. Thus, LUH/MUM1 expression appears to be independent of other transcription factors known to regulate aspects of seed coat mucilage biology. The expression in the luh/mum1 mutant of three genes encoding enzymes needed for mucilage extrusion, MUM2, SUBSILIN PROTEASE1.7, and β-XYLOSIDASE1, was reduced relative to that of the wild type. Overexpression of MUM2 could partially rescue the mum1 phenotype. These data suggest that LUH/MUM1 is a positive regulator of all three genes.

Polar auxin transport together with aintegumenta and revoluta coordinate early Arabidopsis gynoecium development

In flowering plants the gynoecium is the female reproductive structure and the site of oogenesis, fertilization, and maturation of the embryo and the seed. Proper development of the gynoecium requires that the early gynoecial primordium be partitioned into distinct spatial domains with divergent fates. Regulated transport of the phytohormone auxin previously has been shown to play a role in the patterning of spatial domains along the apical-basal axis of the gynoecium. Here we establish a role for auxin transport in patterning along the medio-lateral axis of the gynoecial ovary. We demonstrate that auxin transport is required for the development of the medial ovary domain that contains the carpel margin meristem, a vital female reproductive structure. Disruptions in auxin transport enhance the medial domain defects observed in aintegumenta and revoluta mutant genotypes. Aintegumenta and revoluta are likely to function in parallel and partially overlapping pathways required for medial domain development. Our data indicate that different ovary domains are differentially sensitive to the reduction of polar auxin transport and the loss of aintegumenta and revoluta activity. We suggest that an auxin-mediated positional cue is important for the differential specification of the medial and lateral ovary domains.

Flower development

Flowers are the most complex structures of plants. Studies of Arabidopsis thaliana, which has typical eudicot flowers, have been fundamental in advancing the structural and molecular understanding of flower development. The main processes and stages of Arabidopsis flower development are summarized to provide a framework in which to interpret the detailed molecular genetic studies of genes assigned functions during flower development and is extended to recent genomics studies uncovering the key regulatory modules involved. Computational models have been used to study the concerted action and dynamics of the gene regulatory module that underlies patterning of the Arabidopsis inflorescence meristem and specification of the primordial cell types during early stages of flower development. This includes the gene combinations that specify sepal, petal, stamen and carpel identity, and genes that interact with them. As a dynamic gene regulatory network this module has been shown to converge to stable multigenic profiles that depend upon the overall network topology and are thus robust, which can explain the canalization of flower organ determination and the overall conservation of the basic flower plan among eudicots. Comparative and evolutionary approaches derived from Arabidopsis studies pave the way to studying the molecular basis of diverse floral morphologies.

The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling

The Arabidopsis thaliana MADS box transcription factors APETALA3 (AP3) and PISTILLATA (PI) heterodimerize and are required to specify petal identity, yet many details of how this regulatory process is effected are unclear. We have identified three related genes, BHLH136/BANQUO1 (BNQ1), BHLH134/BANQUO2 (BNQ2), and BHLH161/BANQUO3 (BNQ3), as being directly and negatively regulated by AP3 and PI in petals. BNQ1, BNQ2, and BNQ3 encode products belonging to a family of atypical non-DNA binding basic helix-loop-helix (bHLH) proteins that heterodimerize with and negatively regulate bHLH transcription factors. We show that bnq3 mutants have pale-green sepals and carpels and decreased chlorophyll levels, suggesting that BNQ3 has a role in regulating light responses. The ap3 bnq3 double mutant displays pale second-whorl organs, supporting the hypothesis that BNQ3 is downstream of AP3. Consistent with a role in light response, we show that the BNQ gene products regulate the function of HFR1 (for LONG HYPOCOTYL IN FAR-RED1), which encodes a bHLH protein that regulates photomorphogenesis through modulating phytochrome and cryptochrome signaling. The BNQ genes also are required for appropriate regulation of flowering time. Our results suggest that petal identity is specified in part through downregulation of BNQ-dependent photomorphogenic and developmental signaling pathways.

The SPOROCYTELESS/NOZZLE gene is involved in controlling stamen identity in Arabidopsis

The stamen, which consists of an anther and a filament, is the male reproductive organ in a flower. The specification of stamen identity in Arabidopsis (Arabidopsis thaliana) is controlled by a combination of the B genes APETALA3 (AP3) and PISTILLATA, the C gene AGAMOUS (AG), and the E genes SEPALLATA1 (SEP1) to SEP4. The "floral organ-building" gene SPOROCYTELESS/NOZZLE (SPL/NZZ) plays a central role in regulating anther cell differentiation. However, much less is known about how "floral organ identity" and floral organ-building genes interact to control floral organ development. In this study, we report that ectopic expression of SPL/NZZ not only affects flower development in the wild-type background but also leads to the transformation of petal-like organs into stamen-like organs in flowers of ap2-1, a weak ap2 mutant allele. Moreover, our loss-of-function analysis indicates that the spl/nzz mutant enhances the phenotype of the ag weak allele ag-4. Furthermore, ectopic expression and overexpression of SPL/NZZ altered expression of AG, SEP3, and AP2 in rosette leaves and flowers, while ectopic expression of SPL/NZZ resulted in ectopic expression of AG and SEP3 in the outer whorls of flowers. Our results indicate that the SPL/NZZ gene is engaged in controlling stamen identity via interacting with genes required for stamen identity in Arabidopsis.

YABBYs and the transcriptional corepressors LEUNIG and LEUNIG_HOMOLOG maintain leaf polarity and meristem activity in Arabidopsis

In Arabidopsis thaliana, FILAMENTOUS FLOWER (FIL) and YABBY3 (YAB3) encode YABBY domain proteins that regulate abaxial patterning, growth of lateral organs, and inflorescence phyllotaxy. In this study, we show that YABs physically interact with components of a transcriptional repressor complex that include LEUNIG (LUG), LEUNIG_HOMOLOG (LUH), the LUG-associated coregulator SEUSS, and related SEUSS-LIKE proteins. Consistent with the formation of a LUG-YAB complex, we find that lug mutants enhance the polarity and growth defects of fil yab3 mutant leaves and that this enhancement is due to a loss of LUG activity from the abaxial domain. We performed a more extensive genetic analysis, which included the characterization of yab triple and quadruple mutants, lug luh/+ (heterozygous only for luh) mutants, and plants expressing artificial microRNAs targeting LUG or LUH. These analyses showed that the LUG-YAB complex also promotes adaxial cell identity in leaves as well as embryonic shoot apical meristem (SAM) initiation and postembryonic SAM maintenance. Based on the likely formation of the LUG-YAB complex in the abaxial domain of cotyledons and leaves, we propose that this complex has numerous non-cell-autonomous functions during plant development.

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.

The Arabidopsis petal: a model for plant organogenesis

Organogenesis entails the regulation of cell division, cell expansion, cell and tissue type differentiation, and patterning of the organ as a whole. Petals are ideally suited to dissecting these processes. Petals are dispensable for growth and reproduction, enabling varied manipulations to be carried out with ease. In Arabidopsis, petals have a simple laminar structure with a small number of cell types, facilitating the analysis of organogenesis. This review summarizes recent studies that have illuminated some of the complex interplay between the genetic pathways controlling petal specification, growth and differentiation in Arabidopsis. These advances, coupled with the advantages of using petals as a model experimental system, provide an excellent platform to investigate the underlying mechanisms driving plant organogenesis.

LEUNIG_HOMOLOG and LEUNIG perform partially redundant functions during Arabidopsis embryo and floral development

Transcription corepressors play important roles in animal and plant development. In Arabidopsis (Arabidopsis thaliana), LEUNIG (LUG) and LEUNIG_HOMOLOG (LUH) encode two highly homologous proteins that are similar to the animal and fungal Gro/Tup1-type corepressors. LUG was previously shown to form a putative corepressor complex with another protein, SEUSS (SEU), and to repress the transcription of AGAMOUS in floral organ identity specification. However, the function of LUH is completely unknown. Here, we show that single luh loss-of-function mutants develop normal flowers, but lug; luh double mutants are embryo lethal, uncovering a previously unknown function of LUG and LUH in embryonic development. In addition, luh/+ enhances the floral phenotype of lug, revealing a minor role of LUH in flower development. Functional diversification between LUH and LUG is evidenced by the inability of 35S::LUH overexpression to rescue lug mutants and by the opposite expression trends of LUG and LUH in response to biotic and abiotic stresses. The luh-1 mutation does not enhance the defect of seu in flower development, but LUH could directly interact with SEU in yeast. We propose a model that explains the complex relationships among LUH, LUG, and SEU. As most eukaryotes have undergone at least one round of whole-genome duplication during evolution, gene duplication and functional diversification are important issues to consider in uncovering gene function. Our study provides important insights into the complexity in the relationship between two highly homologous paralogous genes.

Groucho/Tup1 family co-repressors in plant development

Transcription repression is emerging as a key regulatory mechanism underlying cell fate specification and body patterning in both animals and plants. In animals and fungi, the Groucho (Gro)/Tup1 family co-repressors generate the repressed chromatin state in genetic loci that control major developmental decisions ranging from dorsal-ventral patterning to eye development. In higher plants, information about the Gro/Tup1 co-repressors is beginning to emerge. Several recent publications have revealed both conserved and unique structural and mechanistic features of plant Gro/Tup1 co-repressors, including LEUNIG (LUG), TOPLESS (TPL) and WUSCHEL-INTERACTING PROTEINS (WSIPs). These co-repressors regulate key developmental processes in floral organ identity specification, embryo apical-basal fate determination, and stem cell maintenance at the shoot apex.

SEUSS and AINTEGUMENTA mediate patterning and ovule initiation during gynoecium medial domain development

The Arabidopsis (Arabidopsis thaliana) gynoecium, the female floral reproductive structure, requires the action of genes that specify positional identities during its development to generate an organ competent for seed development and dispersal. Early in gynoecial development, patterning events divide the primordium into distinct domains that will give rise to specific tissues and organs. The medial domain of the gynoecium gives rise to the ovules, and several other structures critical for reproductive competence. Here we report a synergistic genetic interaction between seuss and aintegumenta mutants resulting in a complete loss of ovule initiation and a reduction of the structures derived from the medial domain. We show that patterning events are disrupted early in the development of the seuss aintegumenta gynoecia and we identify PHABULOSA (PHB), REVOLUTA, and CRABS CLAW (CRC) as potential downstream targets of SEUSS (SEU) and AINTEGUMENTA (ANT) regulation. Our genetic data suggest that SEU additionally functions in pathways that are partially redundant and parallel to PHB, CRC, and ANT. Thus, SEU and ANT are part of a complex and robust molecular system that coordinates patterning cues and cellular proliferation along the three positional axes of the developing gynoecium.

The transcription corepressor LEUNIG interacts with the histone deacetylase HDA19 and mediator components MED14 (SWP) and CDK8 (HEN3) to repress transcription

Transcription corepressors are general regulators controlling the expression of genes involved in multiple signaling pathways and developmental programs. Repression is mediated through mechanisms including the stabilization of a repressive chromatin structure over control regions and regulation of Mediator function inhibiting RNA polymerase II activity. Using whole-genome arrays we show that the Arabidopsis thaliana corepressor LEUNIG, a member of the GroTLE transcription corepressor family, regulates the expression of multiple targets in vivo. LEUNIG has a role in the regulation of genes involved in a number of different physiological processes including disease resistance, DNA damage response, and cell signaling. We demonstrate that repression of in vivo LEUNIG targets is achieved through histone deacetylase (HDAC)-dependent and -independent mechanisms. HDAC-dependent mechanisms involve direct interaction with HDA19, a class 1 HDAC, whereas an HDAC-independent repression activity involves interactions with the putative Arabidopsis Mediator components AtMED14/SWP and AtCDK8/HEN3. We suggest that changes in chromatin structure coupled with regulation of Mediator function are likely to be utilized by LEUNIG in the repression of gene transcription.

Divergent regulatory OsMADS2 functions control size, shape and differentiation of the highly derived rice floret second-whorl organ

Functional diversification of duplicated genes can contribute to the emergence of new organ morphologies. Model eudicot plants like Arabidopsis thaliana and Antirrhinum majus have a single PI/GLO gene that together with AP3/DEF regulate petal and stamen formation. Lodicules of grass flowers are morphologically distinct reduced organs occupying the position of petals in other flowers. They serve a distinct function in partial and transient flower opening to allow stamen emergence and cross-pollination. Grasses have duplicated PI/GLO-like genes and in rice (Oryza sativa) one these genes, OsMADS2, controls lodicule formation without affecting stamen development. In this study, we investigate the mechanistic roles played by OsMADS2. We ascribe a function for OsMADS2 in controlling cell division and differentiation along the proximal-distal axis. OsMADS2 is required to trigger parenchymatous and lodicule-specific vascular development while maintaining a small organ size. Our data implicate the developmentally late spatially restricted accumulation of OsMADS2 transcripts in the differentiating lodicule to control growth of these regions. The global architecture of transcripts regulated by OsMADS2 gives insights into the regulation of cell division and vascular differentiation that together can form this highly modified grass organ with important functions in floret opening and stamen emergence independent of the paralogous gene OsMADS4.

AINTEGUMENTA contributes to organ polarity and regulates growth of lateral organs in combination with YABBY genes

Lateral organs in flowering plants display polarity along their adaxial-abaxial axis with distinct cell types forming at different positions along this axis. Members of three classes of transcription factors in Arabidopsis (Arabidopsis thaliana; the Class III homeodomain/leucine zipper [HD-ZIP] proteins, KANADI proteins, and YABBY proteins) are expressed in either the adaxial or abaxial domain of organ primordia where they confer these respective identities. Little is known about the factors that act upstream of these polarity-determining genes to regulate their expression. We have investigated the relationship between AINTEGUMENTA (ANT), a gene that promotes initiation and growth of lateral organ primordia, and polarity genes. Although ant single mutants do not display any obvious defects in organ polarity, loss of ANT activity in combination with mutations in one or more YABBY genes results in polarity defects greater than those observed in the yabby mutants alone. Our results suggest that ANT acts in combination with the YABBY gene FILAMENTOUS FLOWER (FIL) to promote organ polarity by up-regulating the expression of the adaxial-specifying HD-ZIP gene PHABULOSA. Furthermore, we show that ANT acts with FIL to up-regulate expression of the floral homeotic gene APETALA3. Our work defines new roles for ANT in the development of lateral organs.