Brassinosteroid Regulates Cell Elongation by Modulating Gibberellin Metabolism in Rice

Brassinosteroid (BR) and gibberellin (GA) are two predominant hormones regulating plant cell elongation. A defect in either of these leads to reduced plant growth and dwarfism. However, their relationship remains unknown in rice (Oryza sativa). Here, we demonstrated that BR regulates cell elongation by modulating GA metabolism in rice. Under physiological conditions, BR promotes GA accumulation by regulating the expression of GA metabolic genes to stimulate cell elongation. BR greatly induces the expression of D18/GA3ox-2, one of the GA biosynthetic genes, leading to increased GA₁ levels, the bioactive GA in rice seedlings. Consequently, both d18 and loss-of-function GA-signaling mutants have decreased BR sensitivity. When excessive active BR is applied, the hormone mostly induces GA inactivation through upregulation of the GA inactivation gene GA2ox-3 and also represses BR biosynthesis, resulting in decreased hormone levels and growth inhibition. As a feedback mechanism, GA extensively inhibits BR biosynthesis and the BR response. GA treatment decreases the enlarged leaf angles in plants with enhanced BR biosynthesis or signaling. Our results revealed a previously unknown mechanism underlying BR and GA crosstalk depending on tissues and hormone levels, which greatly advances our understanding of hormone actions in crop plants and appears much different from that in Arabidopsis thaliana.     

Endomembrane Trafficking Protein SEC24A Regulates Cell Size Patterning in Arabidopsis

Size is a critical property of a cell, but how it is determined is still not well understood. The sepal epidermis of Arabidopsis (Arabidopsis thaliana) contains cells with a diversity of sizes ranging from giant cells to small cells. Giant cells have undergone endoreduplication, a specialized cell cycle in which cells replicate their DNA but fail to divide, becoming polyploid and enlarged. Through forward genetics, we have identified a new mutant with ectopic giant cells covering the sepal epidermis. Surprisingly, the mutated gene, SEC24A, encodes a coat protein complex II vesicle coat subunit involved in endoplasmic reticulum-to-Golgi trafficking in the early secretory pathway. We show that the ectopic giant cells of sec24a-2 are highly endoreduplicated and that their formation requires the activity of giant cell pathway genes LOSS OF GIANT CELLS FROM ORGANS, DEFECTIVE KERNEL1, and Arabidopsis CRINKLY4. In contrast to other trafficking mutants, cytokinesis appears to occur normally in sec24a-2. Our study reveals an unexpected yet specific role of SEC24A in endoreduplication and cell size patterning in the Arabidopsis sepal.Size is a fundamental characteristic of a cell, but how cell size is determined is still not well understood in most living organisms (Marshall et al., 2012). Cells of different types typically have characteristic sizes, indicating that size is carefully regulated to fit cell functions during differentiation. At the simplest level, cell size is determined by growth and division. Although many factors regulating these two processes have been studied, how they are comprehensively regulated to achieve specific size outcomes remains unclear.The sepal of Arabidopsis (Arabidopsis thaliana) is an excellent model to study the regulation of cell size because it exhibits a characteristic pattern of giant cells interspersed in between small cells. The giant cells are large cells that span about one-fifth the length of the sepal (approximately 360 μm), while the smallest cells only reach to about 10 μm (Roeder et al., 2010). Previously, we have shown that variability in cell division times is sufficient to produce the cell size pattern (Roeder et al., 2010). The giant cells stop dividing and enter endoreduplication, a specialized cell cycle in which the cell replicates its DNA but skips mitosis to continue growing (Edgar and Orr-Weaver, 2001; Sugimoto-Shirasu and Roberts, 2003; Inzé and De Veylder, 2006; Breuer et al., 2010). Alongside the giant cells, the smaller cells continue dividing mitotically. Giant cells and small cells are different cell types, as they can be distinguished by the expression pattern of two independent enhancers. Furthermore, mutant screens have shown that genes involved in epidermal specification and cell cycle regulation are crucial for sepal cell size patterning. DEFECTIVE KERNEL1 (DEK1), Arabidopsis thaliana MERISTEM LAYER1 (ATML1), Arabidopsis CRINKLY4 (ACR4), and HOMEODOMAIN GLABROUS11 first establish the identity of giant cells, and then the cyclin dependent kinase inhibitor LOSS OF GIANT CELLS FROM ORGANS (LGO) influences the probability with which cells enter endoreduplication. Endoreduplication can further suppress the identity of small cells through an unknown mechanism (Roeder et al., 2010, 2012). The number of giant cells influences the curvature of the sepal, which is important for protecting the flower (Roeder et al., 2012). Therefore, cell size patterning ensures the protective role of sepals at the physiological level.The secretory pathway in eukaryotes is crucial for cells to maintain membrane homeostasis and protein localization. Proteins destined for the cell surface are first translated on the rough endoplasmic reticulum (ER) and then incorporated into coat protein complex II (COPII) vesicles that bud from ER membranes on the way to the Golgi apparatus. COPII machinery is highly conserved in eukaryotes, and each COPII component acts sequentially on the surface of the ER (Bickford et al., 2004; Marti et al., 2010; Zanetti et al., 2012). Vesicle coat assembly is initiated by SEC12, an ER membrane-anchored guanine nucleotide exchange factor (Barlowe and Schekman, 1993). SEC12 exchanges GDP with GTP on the small GTPase Secretion-associated RAS-related protein1 (SAR1), which increases the membrane affinity of SAR1. The ER membrane-bound SAR1 subsequently brings the SEC23/SEC24 subunits to form the prebudding complex, and eventually SEC13/SEC31 are recruited to increase rigidity of the COPII vesicle coat (Nakano and Muramatsu, 1989; Barlowe et al., 1994; Shaywitz et al., 1997; Aridor et al., 1998; Kuehn et al., 1998; Stagg et al., 2006; Copic et al., 2012). For COPII vesicles to fuse with the target membrane, superfamily N-ethylmaleimide-sensitive factor adaptor protein receptors (SNAREs) must be incorporated by SEC24 (Mossessova et al., 2003; Lipka et al., 2007; Mancias and Goldberg, 2008). In addition to its role in SNARE packaging, SEC24 also binds and loads secretory cargo proteins (Miller et al., 2003). Both the cargo and SNARE specificities are determined by the correspondence between the SEC24 isoform and the various ER export signals of cargoes and SNAREs (Barlowe., 2003; Miller et al., 2003; Mossessova et al., 2003; Mancias and Goldberg, 2008). The Arabidopsis genome encodes four SEC24 isoforms, SEC24A to SEC24D; how they differentially regulate trafficking is unknown (Bassham et al., 2008). Likewise, SEC24-cargo/SNARE interactions remain elusive in plants.Secretion defects in plants often lead to cell division defects due to the unique mechanisms of plants cytokinesis (Sylvester, 2000; Jürgens, 2005). In many eukaryotes other than plants, cytokinesis is accomplished by contraction of the cleavage furrow at the division plane. By contrast, cytokinesis in plants requires de novo secretion of vesicles to the division plane, after formation of the phragmoplast as the scaffold for delivery. Homotypic vesicle fusion sets up the early cell plate, which then expands laterally by fusing with other arriving vesicles (Balasubramanian et al., 2004; Jürgens, 2005; Reichardt et al., 2007). Hence, disruption of secretion in plants can often result in cytokinesis defects. For instance, a mutation in the SNARE KNOLLE leads to enlarged embryo cells with multiple nuclei (Lukowitz et al., 1996).Another common phenotype observed in secretion-deficient plants is abnormal auxin responses. The phytohormone auxin acts as a prominent signal in Arabidopsis development, and auxin influx/efflux carriers are essential in directing auxin transport and creating local maxima in an auxin gradient (Reinhardt et al., 2003; Heisler et al., 2005; Jönsson et al., 2006; Smith et al., 2006; Vanneste and Friml, 2009). To maintain appropriate auxin gradients, the subcellular localization of auxin carriers must be delicately regulated. Thus, auxin responses are highly sensitive to trafficking perturbations in plants (Geldner et al., 2003; Grunewald and Friml, 2010).Here, we have identified a new mutant with ectopic giant cells. Through positional cloning, we determined that the mutation occurs in the SEC24A gene, which encodes the cargo-binding subunit of the COPII vesicle complex. In addition to altered cell size, this unique sec24a-2 allele shows pleiotropic defects, including dwarfism, which have not been reported previously for other SEC24A alleles (Faso et al., 2009; Nakano et al., 2009; Conger et al., 2011). Although the mutant is developmentally aberrant, both cytokinesis and auxin response appear normal in sec24a-2, unlike other transport mutants. Instead, we find SEC24A regulates cell size specifically via the giant cell development pathway. Thus, our data reveal an unexpected role of SEC24A in endoreduplication and cell size patterning in the Arabidopsis sepal.     

Stimulation of Cell Elongation by Tetraploidy in Hypocotyls of Dark-Grown Arabidopsis Seedlings

Plant size is largely determined by the size of individual cells. A number of studies showed a link between ploidy and cell size in land plants, but this link remains controversial. In this study, post-germination growth, which occurs entirely by cell elongation, was examined in diploid and autotetraploid hypocotyls of Arabidopsis thaliana (L.) Heynh. Final hypocotyl length was longer in tetraploid plants than in diploid plants, particularly when seedlings were grown in the dark. The longer hypocotyl in the tetraploid seedlings developed as a result of enhanced cell elongation rather than by an increase in cell number. DNA microarray analysis showed that genes involved in the transport of cuticle precursors were downregulated in a defined region of the tetraploid hypocotyl when compared to the diploid hypocotyl. Cuticle permeability, as assessed by toluidine-blue staining, and cuticular structure, as visualized by electron microscopy, were altered in tetraploid plants. Taken together, these data indicate that promotion of cell elongation is responsible for ploidy-dependent size determination in the Arabidopsis hypocotyl, and that this process is directly or indirectly related to cuticular function.     

Profilin-Dependent Nucleation and Assembly of Actin Filaments Controls Cell Elongation in Arabidopsis

Actin filaments in plant cells are incredibly dynamic; they undergo incessant remodeling and assembly or disassembly within seconds. These dynamic events are choreographed by a plethora of actin-binding proteins, but the exact mechanisms are poorly understood. Here, we dissect the contribution of Arabidopsis (Arabidopsis thaliana) PROFILIN1 (PRF1), a conserved actin monomer-binding protein, to actin organization and single filament dynamics during axial cell expansion of living epidermal cells. We found that reduced PRF1 levels enhanced cell and organ growth. Surprisingly, we observed that the overall frequency of nucleation events in prf1 mutants was dramatically decreased and that a subpopulation of actin filaments that assemble at high rates was reduced. To test whether profilin cooperates with plant formin proteins to execute actin nucleation and rapid filament elongation in cells, we used a pharmacological approach. Here, we used Small Molecule Inhibitor of Formin FH2 (SMIFH2), after validating its mode of action on a plant formin in vitro, and observed a reduced nucleation frequency of actin filaments in live cells. Treatment of wild-type epidermal cells with SMIFH2 mimicked the phenotype of prf1 mutants, and the nucleation frequency in prf1-2 mutant was completely insensitive to these treatments. Our data provide compelling evidence that PRF1 coordinates the stochastic dynamic properties of actin filaments by modulating formin-mediated actin nucleation and assembly during plant cell expansion.The actin cytoskeleton provides tracks for the deposition of cell wall materials and plays important roles during many cellular processes, such as cell expansion and morphogenesis, vesicle trafficking, and the response to biotic and abiotic signals (Baskin, 2005; Smith and Oppenheimer, 2005; Szymanski and Cosgrove, 2009; Ehrhardt and Bezanilla, 2013; Rounds and Bezanilla, 2013). Plant cells respond to diverse internal and external stimuli by regulating the turnover and rearrangement of actin cytoskeleton networks in the cytoplasm (Staiger, 2000; Pleskot et al., 2013). How these actin rearrangements sense the cellular environment and what accessory proteins modulate specific aspects of remodeling remain an area of active investigation (Henty-Ridilla et al., 2013; Li et al., 2014a, 2015).Using high spatial and temporal resolution imaging afforded by variable-angle epifluorescence microscopy (VAEM; Konopka and Bednarek, 2008), we quantified the behavior of actin filaments in Arabidopsis (Arabidopsis thaliana) hypocotyl epidermal cells (Staiger et al., 2009). There are two types of actin filament arrays in the cortical cytoplasm of epidermal cells: bundles and single filaments. Generally, actin bundles are stable with higher pixel intensity values, whereas individual actin filaments are fainter, more ephemeral, and constantly undergo rapid assembly and disassembly through a mechanism that has been defined as “stochastic dynamics” (Staiger et al., 2009; Henty et al., 2011; Li et al., 2012, 2015). Elongating actin filaments in the cortical cytoskeleton originate from three distinct locations: the ends of preexisting actin filaments, the side of filaments or bundles, and de novo in the cytoplasm. Plant actin filaments elongate at rates of 1.6 to 3.4 μm/s, which is the fastest assembly reported in eukaryotic cells. Distinct from the mechanism of treadmilling and fast depolymerization in vitro, however, the disassembly of single actin filaments occurs predominately through prolific severing activity (Staiger et al., 2009; Smertenko et al., 2010; Henty et al., 2011). A commonly held view is that the dynamic actin network in plant cells is regulated by the activities of conserved and novel actin-binding proteins (ABPs). Through reverse-genetic approaches and state-of-the-art imaging modalities, we and others have demonstrated that several key ABPs are involved in the regulation of stochastic actin dynamic properties in a wide variety of plants and cell types (Thomas, 2012; Henty-Ridilla et al., 2013; Li et al., 2014a, 2015). Through these efforts, the field has developed a working model for the molecular mechanisms that underpin actin organization and dynamics in plant cells (Li et al., 2015).Profilin is a small (12–15 kD), conserved actin-monomer binding protein present in all eukaryotic cells (dos Remedios et al., 2003). Profilin binds to actin by forming a 1:1 complex with globular (G-)actin, suppresses spontaneous actin nucleation, and inhibits monomer addition at filament pointed ends (Blanchoin et al., 2014). The consequences of profilin activity on actin filament turnover differ based on cellular conditions and the presence of other ABPs. In vitro studies show that the profilin-actin complex associates with the barbed ends of filaments and promotes actin polymerization by lowering the critical concentration and increasing nucleotide exchange on G-actin (Pollard and Cooper, 1984; Pantaloni and Carlier, 1993). When barbed ends are occupied by capping protein, profilin acts as an actin-monomer sequestering protein. These opposing effects of profilin might be a regulatory mechanism for profilin modulation of actin dynamics in cells. In addition to actin, profilin interacts with Pro-rich proteins, as well as polyphosphoinositide lipids in vitro (Machesky et al., 1994). Formin is an ABP that mediates both actin nucleation and processive elongation using the pool of profilin-actin complexes (Blanchoin et al., 2010). The primary sequence of formin includes a Pro-rich domain, named Formin Homology1 (FH1). Evidence from fission and budding yeast shows that profilin can increase filament elongation rates by binding to the FH1 domain (Kovar et al., 2003; Moseley and Goode, 2005; Kovar, 2006). The FH1 domain of Arabidopsis FORMIN1 (AtFH1) is also reported to modulate actin nucleation and polymerization in vitro (Michelot et al., 2005). Recently, two groups reported that profilin functions as a gatekeeper during the construction of different actin networks generated by formin or ARP2/3 complex in yeast and mammalian cells (Rotty et al., 2015; Suarez et al., 2015). These studies highlight the importance of profilin regulation in coordinating the different actin arrays present in the same cytoplasm of eukaryotic cells. However, direct evidence for how profilin facilitates formin-mediated actin nucleation or barbed end elongation in cells remains to be established.Genomic sequencing and isolation of PROFILIN (PRF) cDNAs from plants reveal that profilin is encoded by a multigene family. For example, moss (Physcomitrella patens) has three isovariants (Vidali et al., 2007) and maize (Zea mays) has five (Staiger et al., 1993; Kovar et al., 2001). In Arabidopsis, at least five PRF genes have been identified (Christensen et al., 1996; Huang et al., 1996; Kandasamy et al., 2002). Studies in maize show that the biochemical properties of profilin isoforms differ in vitro (Kovar et al., 2000). Moreover, the localization of profilin isoforms reveals organ-specific expression patterns. Detection of protein levels in vivo with isovariant-specific profilin antibodies demonstrate that Arabidopsis PRF1, PRF2, and PRF3 are constitutively expressed in vegetative tissues, whereas PRF4 and PRF5 are expressed mainly in flower and pollen tissues (Christensen et al., 1996; Huang et al., 1996; Ma et al., 2005).Several genetic studies on the functions of profilin in plants have been conducted. Reduction of profilin levels in P. patens results in the inhibition of tip growth, disorganization of F-actin, and formation of actin patches (Vidali et al., 2007). Moreover, it was shown that the interaction between profilin and actin or Pro-rich ligands is critical for tip growth in moss. Arabidopsis PRF1 has been demonstrated to be involved in cell elongation, cell shape maintenance, and control of flowering time through overexpression and antisense PRF1 transgenic plants, and further, the reduction of PRF1 inhibits the growth of hypocotyls (Ramachandran et al., 2000). However, investigation of a prf1-1 mutant, which contains a T-DNA insertion in the promoter region of the PRF1 gene, indicates that cell expansion of seedlings is promoted and that protein levels of PRF1 are regulated by light (McKinney et al., 2001). Recently, Müssar et al. (2015) reported a new Arabidopsis T-DNA insertion allele, prf1-4, that shows an obvious dwarf seedling phenotype. To date, however, there has not been a critical examination of the impact of the loss of profilin on the organization and dynamics of bona-fide single actin filaments in vivo.Here, we use a combination of genetics and live-cell imaging to investigate the role of PRF1 in the control of actin dynamics and its effect on axial cell expansion. We observed a significant decrease in the overall filament nucleation frequency in prf1 mutants, which is opposite to expectations if profilin suppresses spontaneous nucleation. Through a pharmacological approach, we found that nucleation frequency in wild-type cells treated with a formin inhibitor, SMIFH2, phenocopied prf1 mutants. We also analyzed the dynamic turnover of individual filaments in prf1 mutants and observed a significant decrease in the rate of actin filament elongation and maximum length of actin filaments. Specifically, we found that PRF1 favors the growth of a subpopulation of actin filaments that elongate at rates greater than 2 μm/s and similar results were obtained in cells after SMIFH2 treatment. Our results provide compelling evidence that Arabidopsis PRF1 contributes to stochastic actin dynamics by modulating formin-mediated actin nucleation and filament elongation during axial cell expansion.     

An-1 Encodes a Basic Helix-Loop-Helix Protein That Regulates Awn Development,Grain Size,and Grain Number in Rice

Long awns are important for seed dispersal in wild rice (Oryza rufipogon), but are absent in cultivated rice (Oryza sativa). The genetic mechanism involved in loss-of-awn in cultivated rice remains unknown. We report here the molecular cloning of a major quantitative trait locus, An-1, which regulates long awn formation in O. rufipogon. An-1 encodes a basic helix-loop-helix protein, which regulates cell division. The nearly-isogenic line (NIL-An-1) carrying a wild allele An-1 in the genetic background of the awnless indica Guangluai4 produces long awns and longer grains, but significantly fewer grains per panicle compared with Guangluai4. Transgenic studies confirmed that An-1 positively regulates awn elongation, but negatively regulates grain number per panicle. Genetic variations in the An-1 locus were found to be associated with awn loss in cultivated rice. Population genetic analysis of wild and cultivated rice showed a significant reduction in nucleotide diversity of the An-1 locus in rice cultivars, suggesting that the An-1 locus was a major target for artificial selection. Thus, we propose that awn loss was favored and strongly selected by humans, as genetic variations at the An-1 locus that cause awn loss would increase grain numbers and subsequently improve grain yield in cultivated rice.     

Phylogenetic Analysis of Zebrafish Basic Helix-Loop-Helix Transcription Factors

The basic helix-loop-helix (bHLH) proteins play important regulatory roles in eukaryotic developmental processes including neurogenesis, myogenesis, hematopoiesis, sex determination, and gut development. Zebrafish is a good model organism for developmental biology. In this study, we identified 139 bHLH genes encoded in the zebrafish genome. Phylogenetic analyses revealed that zebrafish has 58, 29, 21, 5, 19, and 5 bHLH members in groups A, B, C, D, E, and F, respectively, while 2 members were classified as “orphan.” A comparison between zebrafish and human bHLH repertoires suggested that both organisms have a certain number of specific bHLH members. Eight zebrafish bHLH genes were found to have multiple coding regions in the genome. Two of these, Bmal1 and MITF, are good anchor genes for identification of fish-specific whole-genome duplication events in comparison with mouse and chicken genomes. The present study provides useful information for future studies on gene family evolution and vertebrate development. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The NANA Gene Regulates Division and Elongation of Stem Cells in Arabidopsis thaliana (L.) Heynh.

The dominant nana (na) mutation mapped to the top arm of Arabidopsis thalianachromosome 1 blocks cell proliferation in apical meristem (AM) of the inflorescence at its early development and suppresses the subsequent elongation by internode cells. Thenamutation reduces the sensitivity of cells of the inflorescence to gibberellin (GA) and paclobutrazole (PBZ) and prevents dormant and immature seeds from restoring the germinating ability in response to exogenous GA. On the other hand, exogenous GA and PBZ affects the onset of flowering, hypocotyl length, and leaf color; i.e., thena mutant displays an alteration of only several, rather than all, GA-dependent processes. Based on the results obtained, the product of the NA gene was assumed to play a role in the negative regulation of GA signaling and to act later than the products of the known GAI and SPY genes.