A WUSCHEL-LIKE HOMEOBOX gene represses a YABBY gene expression required for rice leaf development

Genome-wide analysis of WOX gene family in rice, sorghum, maize, Arabidopsis and poplar

WUSCHEL-related homeobox (WOX) genes form a large gene family specifically expressed in plants. They are known to play important roles in regulating the development of plant tissues and organs by determining cell fate. Recent available whole genome sequences allow us to do more comprehensive phylogenetic analysis of the WOX genes in plants. In the present study, we identified 11 and 21 WOXs from sorghum (Sorghum bicolor) and maize (Zea mays), respectively. The 72 WOX genes from rice (Oryza sativa), sorghum, maize, Arabidopsis (Arabidopsis thaliana) and poplar (Populus trichocarpa) were grouped into three well supported clades with nine subgroups according to the amino acid sequences of their homodomains. Their phylogenetic relationship was also supported by the observation of the motifs outside the homodomain. We observed the variation of duplication events among the nine sub-groups between monocots and eudicots, for instance, more gene duplication events of WOXs within subgroup A for monocots, while, less for dicots in this subgroup. Furthermore, we observed the conserved intron/exon structural patterns of WOX genes in rice, sorghum and Arabidopsis. In addition, WUS (Wuschel)-box and EAR (the ERF-associated amphiphilic repression)-like motif were observed to be conserved among several WOX subgroups in these five plants. Comparative analysis of expression patterns of WOX genes in rice and Arabidopsis suggest that the WOX genes play conserved and various roles in plants. This work provides insights into the evolution of the WOX gene family and is useful for future research.

Linking differential domain functions of the GS3 protein to natural variation of grain size in rice

Grain yield in many cereal crops is largely determined by grain size. Here we report the genetic and molecular characterization of GS3, a major quantitative trait locus for grain size. It functions as a negative regulator of grain size and organ size. The wild-type isoform is composed of four putative domains: a plant-specific organ size regulation (OSR) domain in the N terminus, a transmembrane domain, a tumor necrosis factor receptor/nerve growth factor receptor (TNFR/NGFR) family cysteine-rich domain, and a von Willebrand factor type C (VWFC) in the C terminus. These domains function differentially in grain size regulation. The OSR domain is both necessary and sufficient for functioning as a negative regulator. The wild-type allele corresponds to medium grain. Loss of function of OSR results in long grain. The C-terminal TNFR/NGFR and VWFC domains show an inhibitory effect on the OSR function; loss-of-function mutations of these domains produced very short grain. This study linked the functional domains of the GS3 protein to natural variation of grain size in rice.

Comparative expression pattern analysis of WUSCHEL-related homeobox 2 (WOX2) and WOX8/9 in developing seeds and somatic embryos of the gymnosperm Picea abies

• In seed plants, current knowledge concerning embryonic pattern formation by polar auxin transport (PAT) and WUSCHEL-related homeobox (WOX) gene activity is primarily derived from studies on angiosperms, while less is known about these processes in gymnosperms. In view of the differences in their embryogeny, and the fact that somatic embryogenesis is used for mass propagation of conifers, a better understanding of embryo development is vital. • The expression patterns of PaWOX2 and PaWOX8/9 were followed with quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and in situ hybridization (ISH) during seed and somatic embryo development in Norway spruce (Picea abies), and in somatic embryos treated with the PAT inhibitor N-1-naphthylphthalamic acid (NPA). • Both PaWOX2 and PaWOX8/9 were highly expressed at the early growth stages of zygotic and somatic embryos, and shared a similar expression pattern over the entire embryo. At later embryo stages, high expression of PaWOX8/9 became restricted to cotyledon primordia, epidermis, procambium and root apical meristem (RAM), which became most evident in NPA-treated somatic embryos, while expression of PaWOX2 was much lower. • Our results suggest an ancestral role of WOX in seed plant embryo development, and strengthen the proposed connection between PAT, PIN-FORMED (PIN) and WOX in the regulation of embryo patterning in seed plants.

Transcriptome divergence between the hexaploid salt-marsh sister species Spartina maritima and Spartina alterniflora (Poaceae)

Invasive species are ideal model systems to investigate the evolutionary processes associated with their ecological success by comparison with closely related species. In this article, we explore transcriptome evolution following divergence between two closely related salt-marsh species, the invasive Spartina alterniflora (native to the East-American Atlantic coast, introduced in several continents) and the declining Spartina maritima (native to the Euro-African Atlantic coast). We have explored the utility of cross-species hybridization microarrays using rice (Oryza sativa) oligo-microarrays to compare leaf expression patterns between these species. Coding sequence comparisons from 10 nuclear genes (2256 bp) revealed that nucleotide divergence between Spartina and Oryza range from 8% to 14%. More than 70% of the 60-mer oligonucleotide sequences spotted on the rice microarray exhibited stable and repeatable patterns when hybridized against Spartina RNA. In total, 9353 (44.5%) genes on the array hybridized with both species S. maritima and S. alterniflora. Among these genes, 1247 genes were found to be differentially expressed between the two Spartina species, most of them (957) being up-regulated in S. alterniflora. In particular, developmental and cellular growth genes (gene ontology, biological process) were highly up-regulated in S. alterniflora and down-regulated in S. maritima, whereas genes involved in stress response were up-regulated in S. maritima. Our findings indicate the suitability of cross-species microarray hybridization between Spartina and O. sativa and reveal the extent of leaf transcriptome evolution that took place during the divergence between S. alterniflora and S. maritima. Expression patterns are consistent with the morphological differentiation and differential expansion of the two species.

Rice SUVH histone methyltransferase genes display specific functions in chromatin modification and retrotransposon repression

Histone lysine methylation plays an important role in heterochromatin formation and reprogramming of gene expression. SET-domain-containing proteins are shown to have histone lysine methyltransferase activities. A large number of SET-domain genes are identified in plant genomes. The function of most SET-domain genes is not known. In this work, we studied the 12 rice (Oryza sativa) homologs of Su(var)3-9, the histone H3 lysine 9 (H3K9) methyltransferase identified in Drosophila. Several rice SUVHs (i.e. SDG714, SDG727, and SDG710) were found to have an antagonistic function to the histone H3K9 demethylase JMJ706, as down-regulation of these genes could partially complement the jmj706 phenotype and reduced histone H3K9 methylation. Down-regulation of a rice Su(var)3-9 homolog (SUVH), namely SDG728, decreased H3K9 methylation and altered seed morphology. Overexpression of the gene increased H3K9 methylation. SDG728 and other SUVH genes were found to be involved in the repression of retrotransposons such as Tos17 and a Ty1-copia element. Analysis of histone methylation suggested that SDG728-mediated H3K9 methylation may play an important role in retrotransposon repression.

WOX4 promotes procambial development

Plant shoot organs arise from initial cells that are recruited from meristematic tissues. Previous studies have shown that members of the WUSCHEL-related HOMEOBOX (WOX) gene family function to organize various initial cell populations during plant development. The function of the WOX4 gene is previously undescribed in any plant species. Comparative analyses of WOX4 transcription and function are presented in Arabidopsis (Arabidopsis thaliana), a simple-leafed plant with collateral vasculature, and in tomato (Solanum lycopersicum), a dissected-leafed species with bicollateral venation. WOX4 is transcribed in the developing vascular bundles of root and shoot lateral organs in both Arabidopsis and tomato. RNA interference-induced down-regulation of WOX4 in Arabidopsis generated small plants whose vascular bundles accumulated undifferentiated ground tissue and exhibited severe reductions in differentiated xylem and phloem. In situ hybridization analyses of Atwox4-RNA interference plants revealed delayed and reduced expression of both the phloem developmental marker ALTERED PHLOEM1 and HOMEOBOX GENE8, a marker of the vascular procambium. Overexpression of SlWOX4 correlated with overproliferation of xylem and phloem in transgenic tomato seedlings. The cumulative data suggest that the conserved WOX4 function is to promote differentiation and/or maintenance of the vascular procambium, the initial cells of the developing vasculature.

Signaling sides adaxial-abaxial patterning in leaves

Most leaves are dorsiventrally flattened and develop clearly defined upper and lower surfaces. Light capturing is the specialization of the adaxial or upper surface and the abaxial or lower surface is specialized for gas exchange (Fig. 5.1). This division into adaxial and abaxial domains is also key for the outgrowth of the leaf blade or lamina, which occurs along the boundary between the upper and lower sides. How this polarity is set up is not clear but genetic analysis in a range of species suggests that several highly conserved interlocking pathways are involved. Positional information from the meristem is reinforced by signaling through the epidermal layer as the meristem grows away from the leaf primordium. Opposing ta-siRNA and miRNA gradients help refine distinct adaxial and abaxial sides, and mutual inhibition between the genes expressed on each side stabilizes the boundary. In this review we consider how recent work in a range of species is clarifying our understanding of these processes.

The WUS homeobox-containing (WOX) protein family

The plant-specific WOX family of homeobox proteins have key functions in plant development.

The WOX genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved DNA-binding homeodomain. The analysis of WOX gene expression and function shows that WOX family members fulfill specialized functions in key developmental processes in plants, such as embryonic patterning, stem-cell maintenance and organ formation. These functions can be related to either promotion of cell division activity and/or prevention of premature cell differentiation. The phylogenetic tree of the plant WOX proteins can be divided into three clades, termed the WUS, intermediate and ancient clade. WOX proteins of the WUS clade appear to some extent able to functionally complement other members. The specific function of individual WOX-family proteins is most probably determined by their spatiotemporal expression pattern and probably also by their interaction with other proteins, which may repress their transcriptional activity. The prototypic WOX-family member WUS has recently been shown to act as a bifunctional transcription factor, functioning as repressor in stem-cell regulation and as activator in floral patterning. Past research has mainly focused on part of the WOX protein family in some model flowering plants, such as Arabidopsis thaliana (thale cress) or Oryza sativa (rice). Future research, including so-far neglected clades and non-flowering plants, is expected to reveal how these master switches of plant differentiation and embryonic patterning evolved and how they fulfill their function.

Signals and prepatterns: new insights into organ polarity in plants

The flattening of leaves results from the interaction between upper (adaxial) and lower (abaxial) domains in the developing primordium. These domains are specified by conserved, overlapping genetic pathways involving several distinct transcription factor families and small regulatory RNAs. Polarity determinants employ a series of antagonistic interactions to produce mutually exclusive cell fates whose positioning is likely refined by signaling across the adaxial-abaxial boundary. Signaling candidates include a mobile small RNA-the first positional signal described in adaxial-abaxial polarity. Possible mechanisms to polarize the incipient primordium are discussed, including meristem-derived signaling and a model in which a polarized organogenic zone prepatterns the adaxial-abaxial axis.

Rice histone deacetylase genes display specific expression patterns and developmental functions

Histone deacetylases (HDAC) are important in plant gene expression. Here we show that the expression of rice HDAC genes is both tissue/organ-specific, and most of them are responsive to drought or salt stresses. Over-expression of several rice HDACs did not produce any visible phenotype, whereas down-regulation of a few HDAC genes affected different developmental aspects. Specifically, down-regulation of HDA703 by amiRNA reduced rice peduncle elongation and fertility, while inactivation of a closely related homolog HDA710 by RNAi affected vegetative growth. HDA704 RNAi altered plant height and flag leaf morphology. Down-regulation of HDT702 led to the production of narrowed leaves and stems. These data suggest that rice HDAC genes may have divergent developmental functions compared with closely related homologs in Arabidopsis.

The WUSCHEL-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice

In rice (Oryza sativa), the shoot-borne crown roots are the major root type and are initiated at lower stem nodes as part of normal plant development. However, the regulatory mechanism of crown root development is poorly understood. In this work, we show that a WUSCHEL-related Homeobox (WOX) gene, WOX11, is involved in the activation of crown root emergence and growth. WOX11 was found to be expressed in emerging crown roots and later in cell division regions of the root meristem. The expression could be induced by exogenous auxin or cytokinin. Loss-of-function mutation or downregulation of the gene reduced the number and the growth rate of crown roots, whereas overexpression of the gene induced precocious crown root growth and dramatically increased the root biomass by producing crown roots at the upper stem nodes and the base of florets. The expressions of auxin- and cytokinin-responsive genes were affected in WOX11 overexpression and RNA interference transgenic plants. Further analysis showed that WOX11 directly repressed RR2, a type-A cytokinin-responsive regulator gene that was found to be expressed in crown root primordia. The results suggest that WOX11 may be an integrator of auxin and cytokinin signaling that feeds into RR2 to regulate cell proliferation during crown root development.

Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice

OsbZIP23 is a member of the basic leucine zipper (bZIP) transcription factor family in rice (Oryza sativa). Expression of OsbZIP23 is strongly induced by a wide spectrum of stresses, including drought, salt, abscisic acid (ABA), and polyethylene glycol treatments, while other stress-responsive genes of this family are slightly induced only by one or two of the stresses. Transactivation assay in yeast demonstrated that OsbZIP23 functions as a transcriptional activator, and the sequences at the N terminus (amino acids 1-59) and a region close to the C terminus (amino acids 210-240) are required for the transactivation activity. Transient expression of OsbZIP23-green fluorescent protein in onion (Allium cepa) cells revealed a nuclear localization of the protein. Transgenic rice overexpressing OsbZIP23 showed significantly improved tolerance to drought and high-salinity stresses and sensitivity to ABA. On the other hand, a null mutant of this gene showed significantly decreased sensitivity to a high concentration of ABA and decreased tolerance to high-salinity and drought stress, and this phenotype can be complemented by transforming the OsbZIP23 back into the mutant. GeneChip and real-time polymerase chain reaction analyses revealed that hundreds of genes were up- or down-regulated in the rice plants overexpressing OsbZIP23. More than half of these genes have been annotated or evidenced for their diverse functions in stress response or tolerance. In addition, more than 30 genes that are possible OsbZIP23-specific target genes were identified based on the comparison of the expression profiles in the overexpressor and the mutant of OsbZIP23. Collectively, these results indicate that OsbZIP23 functions as a transcriptional regulator that can regulate the expression of a wide spectrum of stress-related genes in response to abiotic stresses through an ABA-dependent regulation pathway. We propose that OsbZIP23 is a major player of the bZIP family in rice for conferring ABA-dependent drought and salinity tolerance and has high potential usefulness in genetic improvement of stress tolerance.

ROLLED LEAF 9, encoding a GARP protein, regulates the leaf abaxial cell fate in rice

Leaves, the collective organ produced by the shoot apical meristem (SAM), are polarized along their adaxial-abaxial axis. In this study, we characterized two rice (Oryza sativa) allelic rolled-leaf mutants, rolled leaf 9-1 (rl9-1) and rl9-2, which display very similar phenotypes with completely adaxialized leaves and malformed spikelets. We cloned the RL9 gene by way of a map-based cloning strategy. Molecular studies have revealed that RL9 encodes a GARP protein, an orthologue of Arabidopsis KANADIs. RL9 is mainly expressed in roots, leaves, and flowers. The transient expression of a RL9-GFP (green fluorescent protein) fusion protein has indicated that RL9 protein is localized in the nucleus, suggesting that RL9 acts as a putative transcription factor.

[Molecular mechanism of leaf development]

Leaf plays important roles during plant development for their function of photosynthesis and transpiration. Leaf development includes initiation of leaf primordium and establishment of leaf polarity. Various studies indicate that leaf development is controlled through the interaction of transcription factors, small RNAs and auxin. This review focuses on re-cent advances in studying on leaf development and morphogenesis, and provides information on the regulation network in the process.

Functional analysis of rice HOMEOBOX4 (Oshox4) gene reveals a negative function in gibberellin responses

The homeodomain-leucine zipper (HD-Zip) putative transcription factor genes are divided into 4 families. In this work, we studied the function of a rice HD-Zip I gene, H OME O BO X4 (Oshox4). Oshox4 transcripts were detected in leaf and floral organ primordia but excluded from the shoot apical meristem and the protein was nuclear localized. Over-expression of Oshox4 in rice induced a semi-dwarf phenotype that could not be complemented by applied GA3. The over-expression plants accumulated elevated levels of bioactive GA, while the GA catabolic gene GA2ox3 was upregulated in the transgenic plants. In addition, over-expression of Oshox4 blocked GA-dependent alpha-amylase production. However, down-regulation of Oshox4 in RNAi transgenic plants induced no phenotypic alteration. Interestingly, the expression of YAB1 that is involved in the negative feedback regulation of the GA biosynthesis was upregulated in the Oshox4 over-expressing plants. One-hybrid assays showed that Oshox4 could interact with YAB1 promoter in yeast. In addition, Oshox4 expression was upregulated by GA. These data together suggest that Oshox4 may be involved in the negative regulation of GA signalling and may play a role to fine tune GA responses in rice.

pSAT RNA interference vectors: a modular series for multiple gene down-regulation in plants

RNA interference (RNAi) is a powerful tool for functional gene analysis, which has been successfully used to down-regulate the levels of specific target genes, enabling loss-of-function studies in living cells. Hairpin (hp) RNA expression cassettes are typically constructed on binary plasmids and delivered into plant cells by Agrobacterium-mediated genetic transformation. Realizing the importance of RNAi for basic plant research, various vectors have been developed for RNAi-mediated gene silencing, allowing the silencing of single target genes in plant cells. To further expand the collection of available tools for functional genomics in plant species, we constructed a set of modular vectors suitable for hpRNA expression under various constitutive promoters. Our system allows simple cloning of the target gene sequences into two distinct multicloning sites and its modular design provides a straightforward route for replacement of the expression cassette's regulatory elements. More importantly, our system was designed to facilitate the assembly of several hpRNA expression cassettes on a single plasmid, thereby enabling the simultaneous suppression of several target genes from a single vector. We tested the functionality of our new vector system by silencing overexpressed marker genes (green fluorescent protein, DsRed2, and nptII) in transgenic plants. Various combinations of hpRNA expression cassettes were assembled in binary plasmids; all showed strong down-regulation of the reporter genes in transgenic plants. Furthermore, assembly of all three hpRNA expression cassettes, combined with a fourth cassette for the expression of a selectable marker, resulted in down-regulation of all three different marker genes in transgenic plants. This vector system provides an important addition to the plant molecular biologist's toolbox, which will significantly facilitate the use of RNAi technology for analyses of multiple gene function in plant cells.

Regulatory Networks Involving YABBY Genes in Rice Shoot Development

Shoot development is regulated by specific gene expression programs depending on the interplay between transcription factors and growth hormones that function in specific domains of the meristem and lateral organs. Functional relationship between different regulators is not clearly established. In the May issue of Plant Physiology (2007) we have shown that Wuschel-like Homeobox3 and YABBY3 are coexpressed in the leaf primordia and young leaves, and that WOX3 functions as a transcriptional repressor of YAB3. Overexpression of WOX3 or downregulation of YAB3 induced ectopic expression of Knotted 1-like homeobox1 genes in leaves and consequently produced a phenotype similar to plants ectopically expressing KNOXI genes. In a parallel work published in the same issue, we have shown that another YABBY gene, YAB1, which is expressed in the same domains as YAB3 or WOX3, binds to the gibberellic acid responsive element and is involved in the feedback regulation of gibberellin biosynthesis. Our study demonstrates that rice YABBY genes are involved in two pathways to control cell division and differentiation during leaf formation and growth and establishes a rice shoot developmental regulatory hierarchy involving WOX3, YAB3, KNOX1 and gibberellin.

Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice

The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD(+)-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions. In this work, we investigated the role of OsSRT1, one of the two SIR2-related genes found in rice (Oryza sativa). We show that OsSRT1 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues. OsSRT1 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H(2)O(2) production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of OsSRT1 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that OsSRT1 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by OsSRT1. Our data together suggest that the rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth, but likely implicates different molecular mechanisms than yeast and animal homologs.

Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice

The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD(+)-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions. In this work, we investigated the role of OsSRT1, one of the two SIR2-related genes found in rice (Oryza sativa). We show that OsSRT1 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues. OsSRT1 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H(2)O(2) production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of OsSRT1 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that OsSRT1 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by OsSRT1. Our data together suggest that the rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth, but likely implicates different molecular mechanisms than yeast and animal homologs.

The rice YABBY1 gene is involved in the feedback regulation of gibberellin metabolism

Gibberellin (GA) biosynthesis is regulated by feedback control providing a mechanism for GA homeostasis in plants. However, regulatory elements involved in the feedback control are not known. In this report, we show that a rice (Oryza sativa) YABBY1 (YAB1) gene had a similar expression pattern as key rice GA biosynthetic genes GA3ox2 and GA20ox2. Overexpression of YAB1 in transgenic rice resulted in a semidwarf phenotype that could be fully rescued by applied GA. Quantification of the endogenous GA content revealed increases of GA(20) and decreases of GA(1) levels in the overexpression plants, in which the transcripts of the biosynthetic gene GA3ox2 were decreased. Cosuppression of YAB1 in transgenic plants induced expression of GA3ox2. The repression of GA3ox2 could be obtained upon treatment by dexamethasone of transgenic plants expressing a YAB1-glucocorticoid receptor fusion. Importantly, we show that YAB1 bound to a GA-responsive element within the GA3ox2 promoter. In addition, the expression of YAB1 was deregulated in GA biosynthesis and signaling mutants and could be either transiently induced by GA or repressed by a GA inhibitor. Finally, either overexpression or cosuppression of YAB1 impaired GA-mediated repression of GA3ox2. These data together suggest that YAB1 is involved in the feedback regulation of GA biosynthesis in rice.