The RING-Finger E3 Ubiquitin Ligase COP1 SUPPRESSOR1 Negatively Regulates COP1 Abundance in Maintaining COP1 Homeostasis in Dark-Grown Arabidopsis Seedlings

CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) functions as an E3 ubiquitin ligase in both plants and animals. In dark-grown Arabidopsis thaliana seedlings, COP1 targets photomorphogenesis-promoting factors for degradation to repress photomorphogenesis. Little is known, however, about how COP1 itself is regulated. Here, we identify COP1 SUPPRESSOR1 (CSU1), a RING-finger E3 ubiquitin ligase, as a regulator of COP1. Genetic evidence demonstrates that csu1 mutations suppress cop1-6 phenotypes completely in the dark. Furthermore, CSU1 colocalizes with COP1 in nuclear speckles and negatively regulates COP1 protein accumulation in darkness. CSU1 can ubiquitinate COP1 in vitro and is essential for COP1 ubiquitination in vivo. Therefore, we conclude that CSU1 plays a major role in maintaining COP1 homeostasis by targeting COP1 for ubiquitination and degradation in dark-grown seedlings.

PHYTOCHROME INTERACTING FACTOR1 Enhances the E3 Ligase Activity of CONSTITUTIVE PHOTOMORPHOGENIC1 to Synergistically Repress Photomorphogenesis in Arabidopsis

CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) is a RING/WD40 repeat-containing ubiquitin E3 ligase that is conserved from plants to humans. COP1 forms complexes with SUPPRESSOR OF PHYTOCHROME A (SPA) proteins, and these complexes degrade positively acting transcription factors in the dark to repress photomorphogenesis. Phytochrome-interacting basic helix-loop-helix transcription factors (PIFs) also repress photomorphogenesis in the dark. In response to light, the phytochrome family of sensory photoreceptors simultaneously inactivates COP1-SPA complexes and induces the rapid degradation of PIFs to promote photomorphogenesis. However, the functional relationship between PIFs and COP1-SPA complexes is still unknown. Here, we present genetic evidence that the pif and cop1/spa Arabidopsis thaliana mutants synergistically promote photomorphogenesis in the dark. LONG HYPOCOTYL5 (HY5) is stabilized in the cop1 pif1, spa123 pif1, and pif double, triple, and quadruple mutants in the dark. Moreover, the hy5 mutant suppresses the constitutive photomorphogenic phenotypes of the pifq mutant in the dark. PIF1 forms complexes with COP1, HY5, and SPA1 and enhances the substrate recruitment and autoubiquitylation and transubiquitylation activities of COP1. These data uncover a novel function of PIFs as the potential cofactors of COP1 and provide a genetic and biochemical model of how PIFs and COP1-SPA complexes synergistically repress photomorphogenesis in the dark.

Photoactivated UVR8-COP1 module determines photomorphogenic UV-B signaling output in Arabidopsis

In Arabidopsis, ultraviolet (UV)-B-induced photomorphogenesis is initiated by a unique photoreceptor UV RESISTANCE LOCUS 8 (UVR8) which utilizes its tryptophan residues as internal chromophore to sense UV-B. As a result of UV-B light perception, the UVR8 homodimer shaped by its arginine residues undergoes a conformational switch of monomerization. Then UVR8 associates with the CONSTITUTIVELY PHOTOMORPHOGENIC 1-SUPPRESSOR OF PHYA (COP1-SPA) core complex(es) that is released from the CULLIN 4-DAMAGED DNA BINDING PROTEIN 1 (CUL4-DDB1) E3 apparatus. This association, in turn, causes COP1 to convert from a repressor to a promoter of photomorphogenesis. It is not fully understood, however, regarding the biological significance of light-absorbing and dimer-stabilizing residues for UVR8 activity in photomorphogenic UV-B signaling. Here, we take advantage of transgenic UVR8 variants to demonstrate that two light-absorbing tryptophans, W233 and W285, and two dimer-stabilizing arginines, R286 and R338, play pivotal roles in UV-B-induced photomorphogenesis. Mutation of each residue results in alterations in UV-B light perception, UVR8 monomerization and UVR8-COP1 association in response to photomorphogenic UV-B. We also identify and functionally characterize two constitutively active UVR8 variants, UVR8^W285A and UVR8^R338A, whose photobiological activities are enhanced by the repression of CUL4, a negative regulator in this pathway. Based on our molecular and biochemical evidence, we propose that the UVR8-COP1 affinity in plants critically determines the photomorphogenic UV-B signal transduction coupling with UVR8-mediated UV-B light perception.

Higher plants are able to sense and interpret diverse light signals to modulate their growth. In response to long-wavelength and low-intensity ultraviolet-B (UV-B) light, plants establish photomorphogenic development and stress acclimation. UV RESISTANCE LOCUS 8 (UVR8) is a unique UV-B photoreceptor that triggers photomorphogenesis in Arabidopsis thaliana. However, the signaling process following UV-B light perception by plants is not fully understood. In this study, by generating transgenic UVR8 variants in Arabidopsis, we have extensively analyzed the biological significance of key residues in UVR8 for UV-B-induced photomorphogenesis. Furthermore, by engineering and characterizing two constitutively active UVR8 variants, we have provided the biochemical insight that the in vivo association between UVR8 and CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) critically determines the photomorphogenic UV-B signaling output.

A high-density SNP genotyping array for rice biology and molecular breeding

A high-density single nucleotide polymorphism (SNP) array is critically important for geneticists and molecular breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high-density and high-quality rice SNP arrays. Here we report the development of a high-density rice SNP array and its utility. SNP probes were designed by screening more than 10 000 000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. The array contained 51 478 evenly distributed markers, 68% of which were within genic regions. Several hundred rice plants with parent/F1 relationships were used to generate a high-quality cluster file for accurate SNP calling. Application tests showed that this array had high genotyping accuracy, and could be used for different objectives. For example, a core collection of elite rice varieties was clustered with fine resolution. Genome-wide association studies (GWAS) analysis correctly identified a characterized QTL. Further, this array was successfully used for variety verification and trait introgression. As an accurate high-throughput genotyping tool, RiceSNP50 will play an important role in both functional genomics studies and molecular breeding.

Genomic features and regulatory roles of intermediate-sized non-coding RNAs in Arabidopsis

Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biological processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs (im-ncRNAs) (50~300 nt) have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half (58%) are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5'-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited significantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epigenetic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.

Convergence of Light and ABA signaling on the ABI5 promoter

Light is one of the most important environmental cues regulating multiple aspects of plant growth and development, and abscisic acid (ABA) is a plant hormone that plays important roles during many phases of the plant life cycle and in plants' responses to various environmental stresses. How plants integrate the external light signal with endogenous ABA pathway for better adaptation and survival remains poorly understood. Here, we show that BBX21 (also known as SALT TOLERANCE HOMOLOG 2), a B-box (BBX) protein previously shown to positively regulate seedling photomorphogenesis, is also involved in ABA signaling. Our genetic data show that BBX21 may act upstream of several ABA INSENSITIVE (ABI) genes and ELONGATED HYPOCOTYL 5 (HY5) in ABA control of seed germination. Previous studies showed that HY5 acts as a direct activator of ABI5 expression, and that BBX21 interacts with HY5. We further demonstrate that BBX21 negatively regulates ABI5 expression by interfering with HY5 binding to the ABI5 promoter. In addition, ABI5 was shown to directly activate its own expression, whereas BBX21 negatively regulates this activity by directly interacting with ABI5. Together, our study indicates that BBX21 coordinates with HY5 and ABI5 on the ABI5 promoter and that these transcriptional regulators work in concert to integrate light and ABA signaling in Arabidopsis thaliana.

Many factors such as light, phytohormone abscisic acid (ABA), etc., regulate multiple developmental processes throughout the plants' life cycle. Light promotes seed germination and ABA maintains seed dormancy. However, little is known about how light and ABA signaling pathways interact with each other. It was previously reported that Arabidopsis HY5, a well-known bZIP transcription factor involved in promoting seedling photomorphogenesis, is involved in ABA signaling by directly activating ABI5 expression. Here, we report that the B-box protein BBX21 negatively regulates ABI5 expression by interfering with HY5 binding to the ABI5 promoter. Interestingly, ABI5 was shown to directly bind to its own promoter and activate its expression, whereas BBX21 also negatively regulates this activity by interacting with ABI5. Together, our study shows that light and ABA signaling pathways converge on the ABI5 promoter, on which BBX21 acts as a negative regulator of ABI5 expression.

ABD1 is an Arabidopsis DCAF substrate receptor for CUL4-DDB1-based E3 ligases that acts as a negative regulator of abscisic acid signaling

Members of the DDB1-CUL4-associated factors (DCAFs) family directly bind to DAMAGED DNA BINDING PROTEIN1 (DDB1) and function as the substrate receptors in CULLIN4-based E3 (CUL4) ubiquitin ligases, which regulate the selective ubiquitination of proteins. Here, we describe a DCAF protein, ABD1 (for ABA-hypersensitive DCAF1), that negatively regulates abscisic acid (ABA) signaling in Arabidopsis thaliana. ABD1 interacts with DDB1 in vitro and in vivo, indicating that it likely functions as a CUL4 E3 ligase substrate receptor. ABD1 expression is induced by ABA, and mutations in ABD1 result in ABA- and NaCl-hypersensitive phenotypes. Loss of ABD1 leads to hyperinduction of ABA-responsive genes and higher accumulation of the ABA-responsive transcription factor ABA INSENSITIVE5 (ABI5), hypersensitivity to ABA during seed germination and seedling growth, enhanced stomatal closure, reduced water loss, and, ultimately, increased drought tolerance. ABD1 directly interacts with ABI5 in yeast two-hybrid assays and associates with ABI5 in vivo by coimmunoprecipitation, and the interaction was found in the nucleus by bimolecular fluorescence complementation. Furthermore, loss of ABD1 results in a retardation of ABI5 degradation by the 26S proteasome. Taken together, these data suggest that the DCAF-CUL4 E3 ubiquitin ligase assembled with ABD1 is a negative regulator of ABA responses by directly binding to and affecting the stability of ABI5 in the nucleus.

Targeted degradation of abscisic acid receptors is mediated by the ubiquitin ligase substrate adaptor DDA1 in Arabidopsis

CULLIN4-RING E3 ubiquitin ligases (CRL4s) regulate key developmental and stress responses in eukaryotes. Studies in both animals and plants have led to the identification of many CRL4 targets as well as specific regulatory mechanisms that modulate their function. The latter involve COP10-DET1-DDB1 (CDD)-related complexes, which have been proposed to facilitate target recognition by CRL4, although the molecular basis for this activity remains largely unknown. Here, we provide evidence that Arabidopsis thaliana DET1-, DDB1-ASSOCIATED1 (DDA1), as part of the CDD complex, provides substrate specificity for CRL4 by interacting with ubiquitination targets. Thus, we show that DDA1 binds to the abscisic acid (ABA) receptor PYL8, as well as PYL4 and PYL9, in vivo and facilitates its proteasomal degradation. Accordingly, we found that DDA1 negatively regulates ABA-mediated developmental responses, including inhibition of seed germination, seedling establishment, and root growth. All other CDD components displayed a similar regulatory function, although they did not directly interact with PYL8. Interestingly, DDA1-mediated destabilization of PYL8 is counteracted by ABA, which protects PYL8 by limiting its polyubiquitination. Altogether, our data establish a function for DDA1 as a substrate receptor for CRL4-CDD complexes and uncover a mechanism for the desensitization of ABA signaling based on the regulation of ABA receptor stability.

Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing

A new time- and cost-effective strategy was developed for medium-density SNP genotyping of rice biparental populations, using GoldenGate assays based on parental resequencing. Since the advent of molecular markers, crop researchers and breeders have dedicated huge amounts of effort to detecting quantitative trait loci (QTL) in biparental populations for genetic analysis and marker-assisted selection (MAS). In this study, we developed a new time- and cost-effective strategy for genotyping a population of progeny from a rice cross using medium-density single nucleotide polymorphisms (SNPs). Using this strategy, 728,362 "high quality" SNPs were identified by resequencing Teqing and Lemont, the parents of the population. We selected 384 informative SNPs that were evenly distributed across the genome for genotyping the biparental population using the Illumina GoldenGate assay. 335 (87.2 %) validated SNPs were used for further genetic analyses. After removing segregation distortion markers, 321 SNPs were used for linkage map construction and QTL mapping. This strategy generated SNP markers distributed more evenly across the genome than previous SSR assays. Taking the GW5 gene that controls grain shape as an example, our strategy provided higher accuracy (0.8 Mb) and significance (LOD 5.5 and 10.1) in QTL mapping than SSR analysis. Our study thus provides a rapid and efficient strategy for genetic studies and QTL mapping using SNP genotyping assays.

Ethylene promotes hypocotyl growth and HY5 degradation by enhancing the movement of COP1 to the nucleus in the light

In the dark, etiolated seedlings display a long hypocotyl, the growth of which is rapidly inhibited when the seedlings are exposed to light. In contrast, the phytohormone ethylene prevents hypocotyl elongation in the dark but enhances its growth in the light. However, the mechanism by which light and ethylene signalling oppositely affect this process at the protein level is unclear. Here, we report that ethylene enhances the movement of CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1) to the nucleus where it mediates the degradation of LONG HYPOCOTYL 5 (HY5), contributing to hypocotyl growth in the light. Our results indicate that HY5 is required for ethylene-promoted hypocotyl growth in the light, but not in the dark. Using genetic and biochemical analyses, we found that HY5 functions downstream of ETHYLENE INSENSITIVE 3 (EIN3) for ethylene-promoted hypocotyl growth. Furthermore, the upstream regulation of HY5 stability by ethylene is COP1-dependent, and COP1 is genetically located downstream of EIN3, indicating that the COP1-HY5 complex integrates light and ethylene signalling downstream of EIN3. Importantly, the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC) enriched the nuclear localisation of COP1; however, this effect was dependent on EIN3 only in the presence of light, strongly suggesting that ethylene promotes the effects of light on the movement of COP1 from the cytoplasm to the nucleus. Thus, our investigation demonstrates that the COP1-HY5 complex is a novel integrator that plays an essential role in ethylene-promoted hypocotyl growth in the light.

It is well known that light suppresses hypocotyl growth in seedlings, while the phytohormone ethylene and its precursor 1-aminocyclopropane-1-carboxylate (ACC) enhance hypocotyl growth in the light. However, the mechanism by which light and ethylene oppositely affect this process at the protein level is unclear. Here, we demonstrate that ethylene enhances the movement of CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1) to the nucleus where it promotes the degradation of LONG HYPOCOTYL 5 (HY5) in the light, contributing to hypocotyl growth. Our data indicate that HY5 is required for ethylene-promoted hypocotyl growth in the light, but not in the dark. Using genetic and biochemical analyses, we found that HY5 functions downstream of ETHYLENE INSENSITIVE 3 (EIN3) during ethylene-promoted hypocotyl growth. Further, the regulation of HY5 stability by ethylene is COP1-dependent, and COP1 is genetically located downstream of EIN3, indicating that the COP1-HY5 complex integrates light and ethylene signalling downstream of EIN3. Importantly, ACC enriched the nuclear localisation of COP1 in an EIN3-dependent manner in the presence of light, suggesting that ethylene rescued the effects of light on the movement of COP1 from the cytoplasm to the nucleus. Thus, our investigation shows that the COP1-HY5 complex is a novel integrator that plays an essential role in ethylene-promoted hypocotyl growth in the light.

Organization of protein complexes under photomorphogenic UV-B in Arabidopsis

Low-fluence and long-wavelength UV-B (UV-B) light promotes photomorphogenic development in Arabidopsis. CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) is a positive regulator in this pathway while it is a negative regulator of the traditional photomorphogenesis triggered by far-red and visible light. We have recently reported the mechanism by which the switch of COP1 function is accomplished in distinct light contexts. In response to photomorphogenic UV-B, the photoactivated UV RESISTANCE LOCUS 8 (UVR8) associates with the COP1- SUPRESSOR OF PHYA (SPA) core complexes, resulting in the physical and functional disassociation of COP1-SPA from the CULLIN4-DAMAGED DNA BINDING PROTEIN 1 (CUL4-DDB1) E3 scaffold. These UV-B dependent UVR8-COP1-SPA complexes promote the stability and activity of ELONGATED HYPOCOTYL 5 (HY5), and eventually cause COP1 to switch from repressing to promoting photomorphogenesis. In addition, it is possible that CUL4-DDB1 might simultaneously recruit alternative DDB1 BINDING WD40 (DWD) proteins to repress this UV-B-specific signaling. Further investigation is required, however, to verify this hypothesis. Overall, the coordinated organization of various protein complexes facilitates an efficient and balanced UV-B signaling.

HFR1 sequesters PIF1 to govern the transcriptional network underlying light-initiated seed germination in Arabidopsis

Seed germination is the first step for seed plants to initiate a new life cycle. Light plays a predominant role in promoting seed germination, where the initial phase is mediated by photoreceptor phytochrome B (phyB). Previous studies showed that phytochrome-interacting factor1 (PIF1) represses seed germination downstream of phyB. Here, we identify a positive regulator of phyB-dependent seed germination, long hypocotyl in far-red1 (HFR1). HFR1 blocks PIF1 transcriptional activity by forming a heterodimer with PIF1 that prevents PIF1 from binding to DNA. Our whole-genomic analysis shows that HFR1 and PIF1 oppositely mediate the light-regulated transcriptome in imbibed seeds. Through the HFR1-PIF1 module, light regulates expression of numerous genes involved in cell wall loosening, cell division, and hormone pathways to initiate seed germination. The functionally antagonistic HFR1-PIF1 pair constructs a fail-safe mechanism for fine-tuning seed germination during low-level illumination, ensuring a rapid response to favorable environmental changes. This study identifies the HFR1-PIF1 pair as a central module directing the whole genomic transcriptional network to rapidly initiate light-induced seed germination.

COP9 signalosome subunit Csn8 is involved in maintaining proper duration of the G1 phase

The COP9 signalosome (CSN) is a conserved protein complex known to be involved in developmental processes of eukaryotic organisms. Genetic disruption of a CSN gene causes arrest during early embryonic development in mice. The Csn8 subunit is the smallest and the least conserved subunit, being absent from the CSN complex of several fungal species. Nevertheless, Csn8 is an integral component of the CSN complex in higher eukaryotes, where it is essential for life. By characterizing the mouse embryonic fibroblasts (MEFs) that express Csn8 at a low level, we found that Csn8 plays an important role in maintaining the proper duration of the G1 phase of the cell cycle. A decreased level of Csn8, either in Csn8 hypomorphic MEFs or following siRNA-mediated knockdown in HeLa cells, accelerated cell growth rate. Csn8 hypomorphic MEFs exhibited a shortened G1 duration and affected expression of G1 regulators. In contrast to Csn8, down-regulation of Csn5 impaired cell proliferation. Csn5 proteins were found both as a component of the CSN complex and outside of CSN (Csn5-f), and the amount of Csn5-f relative to CSN was increased in the Csn8 hypomorphic cells. We conclude that CSN harbors both positive and negative regulators of the cell cycle and therefore is poised to influence the fate of a cell at the crossroad of cell division, differentiation, and senescence.

Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids

Background

Recent genome-wide studies suggested that in addition to genetic variations, epigenetic variations may also be associated with differential gene expression and growth vigor in plant hybrids. Maize is an ideal model system for the study of epigenetic variations in hybrids given the significant heterotic performance, the well-known complexity of the genome, and the rich history in epigenetic studies. However, integrated comparative transcriptomic and epigenomic analyses in different organs of maize hybrids remain largely unexplored.

Results

Here, we generated integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different organs and genotypes. We observed that whereas histone modifications vary both between organs and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between organs. Histone modifications were associated with transcriptomic divergence between organs and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements, and for different transposable elements in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species.

Conclusions

These results suggest that despite variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different organs of maize hybrids.

A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa

Accumulating evidence suggests that non-coding RNAs (ncRNAs) are both widespread and functionally important in many eukaryotic organisms. In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5' and 3' termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs (snoRNAs) were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20-30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGO1b in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions.

Development of genomics-based genotyping platforms and their applications in rice breeding

Breeding by design has been an aspiration of researchers in the plant sciences for a decade. With the rapid development of genomics-based genotyping platforms and available of hundreds of functional genes/alleles in related to important traits, however, it may now be possible to turn this enduring ambition into a practical reality. Rice has a relatively simple genome comparing to other crops, and its genome composition and genetic behavior have been extensively investigated. Recently, rice has been taken as a model crop to perform breeding by design. The essential process of breeding by design is to integrate functional genes/alleles in an ideal genetic background, which requires high throughput genotyping platforms to screen for expected genotypes. With large amount of genome resequencing data and high-throughput genotyping technologies available, quite a number of genomics-based genotyping platforms have been developed. These platforms are widely used in genetic mapping, integration of target traits via marker-assisted backcrossing (MABC), pyramiding, recurrent selection (MARS) or genomic selection (GS). Here, we summarize and discuss recent exciting development of rice genomics-based genotyping platforms and their applications in molecular breeding.

Global identification of miRNAs and targets in Populus euphratica under salt stress

Populus euphratica, a typical hydro-halophyte, is ideal for studying salt stress responses in woody plants. MicroRNAs (miRNAs) are endogenous non-coding small RNAs that fulfilled an important post-transcriptional regulatory function. MiRNA may regulate tolerance to salt stress but this has not been widely studied in P. euphratica. In this investigation, the small RNAome, degradome and transcriptome were studied in salt stress treated P. euphratica by deep sequencing. Two hundred and eleven conserved miRNAs between Populus trichocarpa and P. euphratica have been found. In addition, 162 new miRNAs, belonging to 93 families, were identified in P. euphratica. Degradome sequencing experimentally verified 112 targets that belonged to 51 identified miRNAs, few of which were known previously in P. euphratica. Transcriptome profiling showed that expression of 15 miRNA-target pairs displayed reverse changing pattern under salt stress. Together, these results indicate that, in P. euphratica under salt stress, a large number of new miRNAs could be discovered, and both known and new miRNA were functionally cleaving to their target mRNA. Expression of miRNA and target were correspondingly induced by salt stress but that it was a complex process in P. euphratica.

Arabidopsis CSN5B interacts with VTC1 and modulates ascorbic acid synthesis

Light regulates ascorbic acid (AsA) synthesis, which increases in the light, presumably reflecting a need for antioxidants to detoxify reactive molecules produced during photosynthesis. Here, we examine this regulation in Arabidopsis thaliana and find that alterations in the protein levels of the AsA biosynthetic enzyme GDP-Man pyrophosphorylase (VTC1) are associated with changes in AsA contents in light and darkness. To find regulatory factors involved in AsA synthesis, we identified VTC1-interacting proteins by yeast two-hybrid screening of a cDNA library from etiolated seedlings. This screen identified the photomorphogenic factor COP9 signalosome subunit 5B (CSN5B), which interacted with the N terminus of VTC1 in yeast and plants. Gel filtration profiling showed that VTC1-CSN5B also associated with the COP9 signalosome complex, and this interaction promotes ubiquitination-dependent VTC1 degradation through the 26S proteasome pathway. Consistent with this, csn5b mutants showed very high AsA levels in both light and darkness. Also, a double mutant of csn5b with the partial loss-of-function mutant vtc1-1 contained AsA levels between those of vtc1-1 and csn5b, showing that CSN5B modulates AsA synthesis by affecting VTC1. In addition, the csn5b mutant showed higher tolerance to salt, indicating that CSN5B regulation of AsA synthesis affects the response to salt stress. Together, our data reveal a regulatory role of CSN5B in light-dark regulation of AsA synthesis.

The PP6 phosphatase regulates ABI5 phosphorylation and abscisic acid signaling in Arabidopsis

The basic Leucine zipper transcription factor ABSCISIC ACID INSENSITIVE5 (ABI5) is a key regulator of abscisic acid (ABA)-mediated seed germination and postgermination seedling growth. While a family of SUCROSE NONFERMENTING1-related protein kinase2s (SnRK2s) is responsible for ABA-induced phosphorylation and stabilization of ABI5, the phosphatase(s) responsible for dephosphorylating ABI5 is still unknown. Here, we demonstrate that mutations in FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of Ser/Thr PROTEIN PHOSPHATASE6 (PP6), cause an ABA hypersensitive phenotype in Arabidopsis thaliana, including ABA-mediated inhibition of seed germination and seedling growth. Conversely, overexpression of FyPP causes reduced sensitivity to ABA. The ABA hypersensitive phenotype of FyPP loss-of-function mutants is ABI5 dependent, and the amount of phosphorylated and total ABI5 proteins inversely correlates with the levels of FyPP proteins. Moreover, FyPP proteins physically interact with ABI5 in vitro and in vivo, and the strength of the interaction depends on the ABI5 phosphorylation status. In vitro phosphorylation assays show that FyPP proteins directly dephosphorylate ABI5. Furthermore, genetic and biochemical assays show that FyPP proteins act antagonistically with SnRK2 kinases to regulate ABI5 phosphorylation and ABA responses. Thus, Arabidopsis PP6 phosphatase regulates ABA signaling through dephosphorylation and destabilization of ABI5.

Ubiquitin-specific protease16 modulates salt tolerance in Arabidopsis by regulating Na(+)/H(+) antiport activity and serine hydroxymethyltransferase stability

Protein ubiquitination is a reversible process catalyzed by ubiquitin ligases and ubiquitin-specific proteases (UBPs). We report the identification and characterization of UBP16 in Arabidopsis thaliana. UBP16 is a functional ubiquitin-specific protease and its enzyme activity is required for salt tolerance. Plants lacking UBP16 were hypersensitive to salt stress and accumulated more sodium and less potassium. UBP16 positively regulated plasma membrane Na(+)/H(+) antiport activity. Through yeast two-hybrid screening, we identified a putative target of UBP16, SERINE HYDROXYMETHYLTRANSFERASE1 (SHM1), which has previously been reported to be involved in photorespiration and salt tolerance in Arabidopsis. We found that SHM1 is degraded in a 26S proteasome-dependent process, and UBP16 stabilizes SHM1 by removing the conjugated ubiquitin. Ser hydroxymethyltransferase activity is lower in the ubp16 mutant than in the wild type but higher than in the shm1 mutant. During salt stress, UBP16 and SHM1 function in preventing cell death and reducing reactive oxygen species accumulation, activities that are correlated with increasing Na(+)/H(+) antiport activity. Overexpression of SHM1 in the ubp16 mutant partially rescues its salt-sensitive phenotype. Taken together, our results suggest that UBP16 is involved in salt tolerance in Arabidopsis by modulating sodium transport activity and repressing cell death at least partially through modulating SMH1stability and activity.

Arabidopsis FHY3 and HY5 positively mediate induction of COP1 transcription in response to photomorphogenic UV-B light

As sessile organisms, higher plants have evolved the capacity to sense and interpret diverse light signals to modulate their development. In Arabidopsis thaliana, low-intensity and long-wavelength UV-B light is perceived as an informational signal to mediate UV-B-induced photomorphogenesis. Here, we report that the multifunctional E3 ubiquitin ligase, CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1), a known key player in UV-B photomorphogenic responses, is also a UV-B-inducible gene. Two transcription factors, FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and ELONGATED HYPOCOTYL5 (HY5), directly bind to distinct regulatory elements within the COP1 promoter, which are essential for the induction of the COP1 gene mediated by photomorphogenic UV-B signaling. Absence of FHY3 results in impaired UV-B-induced hypocotyl growth and reduced tolerance against damaging UV-B. Thus, FHY3 positively regulates UV-B-induced photomorphogenesis by directly activating COP1 transcription, while HY5 promotes COP1 expression via a positive feedback loop. Furthermore, FHY3 and HY5 physically interact with each other, and this interaction is diminished by UV-B. Together, our findings reveal that COP1 gene expression in response to photomorphogenic UV-B is controlled by a combinatorial regulation of FHY3 and HY5, and this UV-B-specific working mode of FHY3 and HY5 is distinct from that in far-red light and circadian conditions.

The photomorphogenic repressors COP1 and DET1: 20 years later

COP1 and DET1 are among the first repressors of photomorphogenesis to be identified, more than 20 years ago. Discovery of these repressors as conserved regulators of the ubiquitin-proteasome system has established protein degradation as a central theme in light signal transduction. COP1 is a RING E3 ubiquitin ligase that targets key regulators for degradation, and DET1 complexes with COP10 and DDB1, which is proposed to aid in COP1-mediated degradation. Recent studies have strengthened the role of COP1 as a major signaling center. DET1 is also emerging as a chromatin regulator in repressing gene expression. Here, we review current understanding on COP1 and DET1, with a focus on their role as part of two distinct, multimeric CUL4-based E3 ligases.

Basic leucine zipper transcription factor OsbZIP16 positively regulates drought resistance in rice

Abiotic stress has been shown to limit the growth, development, and productivity of crops. Here, we characterized the function of a rice bZIP transcription factor OsbZIP16 in drought stress. Expression of OsbZIP16 was dramatically induced under drought conditions. Transient expression and transactivation assays demonstrated that OsbZIP16 was localized in the nucleus and had transactivation activity. At both the seedling and tillering stages, transgenic rice plants overexpressing OsbZIP16 exhibited significantly improved drought resistance, which was positively correlated with the observed expression levels of OsbZIP16. Representative downstream drought-inducible genes were observed to have significantly higher expression levels in transgenic rice plants than in the wild type plants under drought conditions. OsbZIP16 was shown to be induced by exogenous ABA treatment, while overexpression of OsbZIP16 was observed to make transgenic plants more sensitive to ABA than wild type plants were. Transcriptome analysis identified a number of differentially expressed genes between wild type plants and plants overexpressing OsbZIP16, many of which are involved in stress response according to their gene ontologies. Overall, our findings suggest that OsbZIP16 positively regulates drought resistance in rice.

OsELF3-1, an ortholog of Arabidopsis early flowering 3, regulates rice circadian rhythm and photoperiodic flowering

Arabidopsis thaliana early flowering 3 (ELF3) as a zeitnehmer (time taker) is responsible for generation of circadian rhythm and regulation of photoperiodic flowering. There are two orthologs (OsELF3-1 and OsELF3-2) of ELF3 in rice (Oryza sativa), but their roles have not yet been fully identified. Here, we performed a functional characterization of OsELF3-1 and revealed it plays a more predominant role than OsELF3-2 in rice heading. Our results suggest OsELF3-1 can affect rice circadian systems via positive regulation of OsLHY expression and negative regulation of OsPRR1, OsPRR37, OsPRR73 and OsPRR95 expression. In addition, OsELF3-1 is involved in blue light signaling by activating early heading date 1 (Ehd1) expression to promote rice flowering under short-day (SD) conditions. Moreover, OsELF3-1 suppresses a flowering repressor grain number, plant height and heading date 7 (Ghd7) to indirectly accelerate flowering under long-day (LD) conditions. Taken together, our results indicate OsELF3-1 is essential for circadian regulation and photoperiodic flowering in rice.

IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis

Small RNA-directed DNA methylation (RdDM) is an important epigenetic pathway in Arabidopsis that controls the expression of multiple genes and several developmental processes. RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3) are necessary factors in 24-nt small interfering RNA (siRNA) biogenesis, which is part of the RdDM pathway. Here, we found that Increase in BONSAI Methylation 1 (IBM1), a conserved JmjC family histone demethylase, is directly associated with RDR2 and DCL3 chromatin. The mutation of IBM1 induced the hypermethylation of H3K9 and DNA non-CG sites within RDR2 and DCL3, which repressed their expression. A genome-wide analysis suggested that the reduction in RDR2 and DCL3 expression affected siRNA biogenesis in a locus-specific manner and disrupted RdDM-directed gene repression. Together, our results suggest that IBM1 regulates gene expression through two distinct pathways: direct association to protect genes from silencing by preventing the coupling of histone and DNA methylation, and indirect silencing of gene expression through RdDM-directed repression.

A PP6-type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis

The directional transport of the phytohormone auxin depends on the phosphorylation status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins, the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain elusive. Here, we demonstrate that mutations simultaneously disrupting the function of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN proteins, correlating with a basal-to-apical shift in subcellular PIN localization. The changes in PIN polarity result in increased root basipetal auxin transport and severe defects, including shorter roots, fewer lateral roots, defective columella cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins (RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3) physically interact to form a novel PP6-type heterotrimeric holoenzyme complex. We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins and that for SAL the strength of the interaction depends on the PIN phosphorylation status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically with PID to direct auxin transport polarity and plant development by directly regulating PIN phosphorylation.

Phosphorylation of FAR-RED ELONGATED HYPOCOTYL1 is a key mechanism defining signaling dynamics of phytochrome A under red and far-red light in Arabidopsis

Emerging plants have to adapt to a high ratio of far-red light (FR)/red light (R) light in the canopy before they reach the R-enriched direct sunlight. Phytochrome A (phyA) is the single dominant photoreceptor in young Arabidopsis thaliana seedlings that initiates photomorphogenesis in response to a FR-enriched environment and transduces increasing R signals to early responsive genes. To date, how phyA differentially transmits FR and R signals to downstream genes remains obscure. Here, we present a phyA pathway in which FAR-RED ELONGATED HYPOCOTYL1 (FHY1), an essential partner of phyA, directly guides phyA to target gene promoters and coactivates transcription. Furthermore, we identified two phosphorylation sites on FHY1, Ser-39 and Thr-61, whose phosphorylation by phyA under R inhibits phyA signaling at each step of its pathway. Deregulation of FHY1 phosphorylation renders seedlings colorblind to FR and R. Finally, we show that the weaker phyA response resulting from FHY1 phosphorylation ensures the seedling deetiolation process in response to a R-enriched light condition. Collectively, our results reveal FHY1 phosphorylation as a key mechanism for FR/R spectrum-specific responses in plants and an essential event for plant adaption to changing light conditions in nature.

Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids

Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single-base-pair resolution the DNA methylomes of Arabidopsis thaliana Landsberg erecta and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs, implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to methylome remodeling were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes circadian clock associated1 and late elongated hypocotyl. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA enhancer1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in heterosis.

Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.)

Single nucleotide polymorphisms (SNPs) are the most abundant DNA markers in plant genomes. In this study, based on 54,465 SNPs between the genomes of two Indica varieties, Minghui 63 (MH63) and Zhenshan 97 (ZS97) and additional 20,705 SNPs between the MH63 and Nipponbare genomes, we identified and confirmed 1,633 well-distributed SNPs by PCR and Sanger sequencing. From these, a set of 372 SNPs were further selected to analyze the patterns of genetic diversity in 300 representative rice inbred lines from 22 rice growing countries worldwide. Using this set of SNPs, we were able to uncover the well-known Indica-Japonica subspecific differentiation and geographic differentiations within Indica and Japonica. Furthermore, our SNP results revealed some common and contrasting patterns of the haplotype diversity along different rice chromosomes in the Indica and Japonica accessions, which suggest different evolutionary forces possibly acting in specific regions of the rice genome during domestication and evolution of rice. Our results demonstrated that this set of SNPs can be used as anchor SNPs for large scale genotyping in rice molecular breeding research involving Indica-Japonica and Indica-Indica crosses.

TSA1 interacts with CSN1/CSN and may be functionally involved in Arabidopsis seedling development in darkness

The COP9 signalosome (CSN) is a multiprotein complex which participates in diverse cellular and developmental processes. CSN1, one of the subunits of CSN, is essential for assembly of the multiprotein complex via PCI (proteasome, COP9 signalosome and initiation factor 3) domain in the C-terminal half of CSN1. However, the role of the N-terminal domain (NTD) of CSN1, which is critical for the function of CSN, is not completely understood. Using a yeast two-hybrid (Y2H) screen, we found that the NTD of CSN1 interacts with TSK-associating protein 1 (TSA1), a reported Ca(2+)-binding protein. The interaction between CSN1 and TSA1 was confirmed by co-immunoprecipitation in Arabidopsis. tsa1 mutants exhibited a short hypocotyl phenotype in darkness but were similar to wild-type Arabidopsis under white light, which suggested that TSA1 might regulate Arabidopsis hypocotyl development in the dark. Furthermore, the expression of TSA1 was significantly lower in a csn1 null mutant (fus6), while CSN1 expression did not change in a tsa1 mutant with weak TSA1 expression. Together, these findings suggest a functional relationship between TSA1 and CSN1 in seedling development.

Phytochrome signaling mechanisms

Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.

Analysis of trehalose-6-phosphate synthase (TPS) gene family suggests the formation of TPS complexes in rice

Trehalose-6-phosphate (T6P), an intermediate in the trehalose biosynthesis pathway, is emerging as an important regulator of plant metabolism and development. T6P levels are potentially modulated by a group of trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) homologues. In this study, we have isolated 11 TPS genes encoding proteins with both TPS and TPP domains, from rice. Functional complement assays performed in yeast tps1 and tps2 mutants, revealed that only OsTPS1 encodes an active TPS enzyme and no OsTPS protein possesses TPP activity. By using a yeast two-hybrid analysis, a complicated interaction network occurred among OsTPS proteins, and the TPS domain might be essential for this interaction to occur. The interaction between OsTPS1 and OsTPS8 in vivo was confirmed by bimolecular fluorescence complementation and coimmunoprecipitation assays. Furthermore, our gel filtration assay showed that there may exist two forms of OsTPS1 (OsTPS1a and OsTPS1b) with different elution profiles in rice. OsTPS1b was particularly cofractionated with OsTPS5 and OsTPS8 in the 360 kDa complex, while OsTPS1a was predominantly incorporated into the complexes larger than 360 kDa. Collectively, these results suggest that OsTPS family members may form trehalose-6-phosphate synthase complexes and therefore potentially modify T6P levels to regulate plant development.

Plant ubiquitin-proteasome pathway and its role in gibberellin signaling

The ubiquitin-proteasome system (UPS) in plants, like in other eukaryotes, targets numerous intracellular regulators and thus modulates almost every aspect of growth and development. The well-known and best-characterized outcome of ubiquitination is mediating target protein degradation via the 26S proteasome, which represents the major selective protein degradation pathway conserved among eukaryotes. In this review, we will discuss the molecular composition, regulation and function of plant UPS, with a major focus on how DELLA protein degradation acts as a key in gibberellin signal transduction and its implication in the regulation of plant growth.

Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development

FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1), two transposase-derived transcription factors, are key components in phytochrome A signaling and the circadian clock. Here, we use chromatin immunoprecipitation-based sequencing (ChIP-seq) to identify 1559 and 1009 FHY3 direct target genes in darkness (D) and far-red (FR) light conditions, respectively, in the Arabidopsis thaliana genome. FHY3 preferentially binds to promoters through the FHY3/FAR1 binding motif (CACGCGC). Interestingly, FHY3 also binds to two motifs in the 178-bp Arabidopsis centromeric repeats. Comparison between the ChIP-seq and microarray data indicates that FHY3 quickly regulates the expression of 197 and 86 genes in D and FR, respectively. FHY3 also coregulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE5 and ELONGATED HYPOCOTYL5. Moreover, we uncover a role for FHY3 in controlling chloroplast development by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5, whose product is a structural component of the latter stages of chloroplast division in Arabidopsis. Taken together, our data suggest that FHY3 regulates multiple facets of plant development, thus providing insights into its functions beyond light and circadian pathways.

Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis

The circadian clock controls many metabolic, developmental and physiological processes in a time-of-day-specific manner in both plants and animals. The photoreceptors involved in the perception of light and entrainment of the circadian clock have been well characterized in plants. However, how light signals are transduced from the photoreceptors to the central circadian oscillator, and how the rhythmic expression pattern of a clock gene is generated and maintained by diurnal light signals remain unclear. Here, we show that in Arabidopsis thaliana, FHY3, FAR1 and HY5, three positive regulators of the phytochrome A signalling pathway, directly bind to the promoter of ELF4, a proposed component of the central oscillator, and activate its expression during the day, whereas the circadian-controlled CCA1 and LHY proteins directly suppress ELF4 expression periodically at dawn through physical interactions with these transcription-promoting factors. Our findings provide evidence that a set of light- and circadian-regulated transcription factors act directly and coordinately at the ELF4 promoter to regulate its cyclic expression, and establish a potential molecular link connecting the environmental light-dark cycle to the central oscillator.

Geminiviruses subvert ubiquitination by altering CSN-mediated derubylation of SCF E3 ligase complexes and inhibit jasmonate signaling in Arabidopsis thaliana

Viruses must create a suitable cell environment and elude defense mechanisms, which likely involves interactions with host proteins and subsequent interference with or usurpation of cellular machinery. Here, we describe a novel strategy used by plant DNA viruses (Geminiviruses) to redirect ubiquitination by interfering with the activity of the CSN (COP9 signalosome) complex. We show that geminiviral C2 protein interacts with CSN5, and its expression in transgenic plants compromises CSN activity on CUL1. Several responses regulated by the CUL1-based SCF ubiquitin E3 ligases (including responses to jasmonates, auxins, gibberellins, ethylene, and abscisic acid) are altered in these plants. Impairment of SCF function is confirmed by stabilization of yellow fluorescent protein-GAI, a substrate of the SCF(SLY1). Transcriptomic analysis of these transgenic plants highlights the response to jasmonates as the main SCF-dependent process affected by C2. Exogenous jasmonate treatment of Arabidopsis thaliana plants disrupts geminivirus infection, suggesting that the suppression of the jasmonate response might be crucial for infection. Our findings suggest that C2 affects the activity of SCFs, most likely through interference with the CSN. As SCFs are key regulators of many cellular processes, the capability of viruses to selectively interfere with or hijack the activity of these complexes might define a novel and powerful strategy in viral infections.

DWA3, an Arabidopsis DWD protein, acts as a negative regulator in ABA signal transduction

DWD (DDB1 binding WD40) proteins have been reported as substrate receptors for cullin-RING ubiquitin ligase 4 complexes (CRL4), a family of E3 ligases. Abscisic acid (ABA) plays an important role in plant responses to abiotic stresses, such as drought and salinity. Upon screening T-DNA mutants of DWD genes for ABA responses we obtained several candidates that exhibited ABA-hypersensitivity, and one was named DWA3 (DWD hypersensitive to ABA 3). DWA3 interacted with DDB1, which has been proposed to be an adaptor protein of the CUL4 E3 ligase complex, in yeast two-hybrid assays. Also, association between DWA3 and the DDB1-CUL4 machinery was detected in vivo by co-immunoprecipitation assays, indicating that DWA3 may function as a substrate receptor for CRL4. ABA-inducible transcription factors (ABI5 and AtMYC2) and their downstream genes were hyper-induced by ABA in dwa3. Taken together, we suggest that DWA3 is a negative regulator of ABA responses and may be involved in protein degradation mediated by CRL4.

The epigenome and plant development

The epigenomic regulation of chromatin structure and genome stability is essential for the interpretation of genetic information and ultimately the determination of phenotype. High-resolution maps of plant epigenomes have been obtained through a combination of chromatin technologies and genomic tiling microarrays and through high-throughput sequencing-based approaches. The transcriptomic activity of a plant at a certain stage of development is controlled by genome-wide combinatorial interactions of epigenetic modifications. Tissue- or environment-specific epigenomes are established during plant development. Epigenomic reprogramming triggered by the activation and movement of small RNAs is important for plant gametogenesis. Genome-wide loss of DNA methylation in the endosperm and the accompanying endosperm-specific gene expression during seed development provide a genomic insight into epigenetic regulation of gene imprinting in plants. Global changes of histone modifications during plant responses to different light environments play an important regulatory role in a sophisticated light-regulated transcriptional network. Epigenomic natural variation that developed during evolution is important for phenotypic diversity and can potentially contribute to the molecular mechanisms of complex biological phenomena such as heterosis in plants.

Phytochrome signaling mechanisms

Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.

Arabidopsis transcription factor ELONGATED HYPOCOTYL5 plays a role in the feedback regulation of phytochrome A signaling

Phytochrome A (phyA) is the primary photoreceptor responsible for perceiving and mediating various responses to far-red light in Arabidopsis thaliana. FAR-RED ELONGATED HYPOCOTYL1 (FHY1) and its homolog FHY1-LIKE (FHL) are two small plant-specific proteins essential for light-regulated phyA nuclear accumulation and subsequent phyA signaling processes. FHY3 and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1) are two transposase-derived transcription factors that directly activate FHY1/FHL transcription and thus mediate subsequent phyA nuclear accumulation and responses. Here, we report that ELONGATED HYPOCOTYL5 (HY5), a well-characterized bZIP transcription factor involved in promoting photomorphogenesis, directly binds ACGT-containing elements a few base pairs away from the FHY3/FAR1 binding sites in the FHY1/FHL promoters. We demonstrate that HY5 physically interacts with FHY3/FAR1 through their respective DNA binding domains and negatively regulates FHY3/FAR1-activated FHY1/FHL expression under far-red light. Together, our data show that HY5 plays a role in negative feedback regulation of phyA signaling by attenuating FHY3/FAR1-activated FHY1/FHL expression, providing a mechanism for fine-tuning phyA signaling homeostasis.

Expression analysis of miRNAs and highly-expressed small RNAs in two rice subspecies and their reciprocal hybrids

Heterosis, or hybrid vigor, is the phenomenon whereby progeny of two inbred lines exhibit superior agronomic performance compared with either parent. We analyzed the expression of miRNAs and highly expressed small RNAs (defined according to Solexa sequencing results) in two rice (Oryza sativa) subspecies (japonica cv. Nipponbare and indica cv. 93-11) and their reciprocal hybrids using microarrays. We found that of all the 1141 small RNAs tested, 140 (12%, 140 of 1141) and 157 (13%, 157 of 1141) were identified being significantly differentially expressed in two reciprocal hybrids, respectively. All possible modes of action, including additive, high- and low- parent, above high- and below low-parent modes were exhibited. Both F1 hybrids showed non-additive expression patterns, with downregulation predominating. Interestingly, 15 miRNAs displayed stark opposite expression trends relative to mid-parent in reciprocal hybrids. Computational prediction of targets of differentially expressed miRNAs showed that they participated in multifaceted developmental pathways, and were not distinguishable from the targets of non-differentially expressed miRNAs. Together, our findings reveal that small RNAs play roles in heterosis and add a new layer in the understanding and exploitation of molecular mechanisms of heterosis.

Plant hormone signaling lightens up: integrators of light and hormones

Light is an important environmental signal that regulates diverse growth and developmental processes in plants. In these light-regulated processes, multiple hormonal pathways are often modulated by light to mediate the developmental changes. Conversely, hormone levels in plants also serve as endogenous cues in influencing light responsiveness. Although interactions between light and hormone signaling pathways have long been observed, recent studies have advanced our understanding by identifying signaling integrators that connect the pathways. These integrators, namely PHYTOCHROME-INTERACTING FACTOR 3 (PIF3), PIF4, PIF3-LIKE 5 (PIL5)/PIF1 and LONG HYPOCOTYL 5 (HY5), are key light signaling components and they link light signals to the signaling of phytohormones, such as gibberellin (GA), abscisic acid (ABA), auxin and cytokinin, in regulating seedling photomorphogenesis and seed germination. This review focuses on these integrators in illustrating how light and hormone interact.

The chloroplast genome exists in multimeric forms

Chloroplast DNA conformation was analyzed by pulse-field gel electrophoresis. We found that spinach leaf chloroplast DNA molecules exist in at least four distinct forms with the apparent molecular weights of monomer, dimer, trimer, and tetramer. Two-dimensional gel analysis of DNA after UV nicking and in the presence of ethidium bromide indicates that they are not isomers that differ in superhelical density. DNA gyrase decatenation analysis demonstrates that the majority of the DNA molecules are oligomers rather than catenanes. The relative amounts of monomer, dimer, trimer, and tetramer forms, quantitated by molecular hybridization, are 1, 1/3, 1/9, and 1/27, respectively, and do not change during leaf maturation. The possible mechanisms of chloroplast DNA oligomer formation are discussed.

DWA1 and DWA2, two Arabidopsis DWD protein components of CUL4-based E3 ligases, act together as negative regulators in ABA signal transduction

To elucidate potential roles of CUL4-DDB1-DWD (for Cullin 4-Damaged DNA Binding1-DDB1 binding WD40) E3 ligases in abscisic acid (ABA) signaling, we examined ABA sensitivities of T-DNA mutants of a number of Arabidopsis thaliana DWD genes, which encode substrate receptors for CUL4 E3 ligases. Mutants in two DWD genes, DWA1 and DWA2 (DWD hypersensitive to ABA1 and 2), had ABA-hypersensitive phenotypes. Both proteins interacted with DDB1 in yeast two-hybrid assays and associated with DDB1 and CUL4 in vivo, implying they could form CUL4-based complexes. Several ABA-responsive genes were hyperinduced in both mutants, and the ABA-responsive transcription factors ABA INSENSITIVE 5 (ABI5) and MYC2 accumulated to high levels in the mutants after ABA treatment. Moreover, ABI5 interacted with DWA1 and DWA2 in vivo. Cell-free degradation assays showed ABI5 was degraded more slowly in dwa1 and dwa2 than in wild-type cell extracts. Therefore, DWA1 and/or DWA2 may be the substrate receptors for a CUL4 E3 ligase that targets ABI5 for degradation. Our data indicate that DWA1 and DWA2 can directly interact with each other, and their double mutants exhibited enhanced ABA and NaCl hypersensitivities, implying they can act together. This report thus describes a previously unknown heterodimeric cooperation between two independent substrate receptors for CUL4-based E3 ligases.

The Arabidopsis chaperone J3 regulates the plasma membrane H+-ATPase through interaction with the PKS5 kinase

The plasma membrane H(+)-ATPase (PM H(+)-ATPase) plays an important role in the regulation of ion and metabolite transport and is involved in physiological processes that include cell growth, intracellular pH, and stomatal regulation. PM H(+)-ATPase activity is controlled by many factors, including hormones, calcium, light, and environmental stresses like increased soil salinity. We have previously shown that the Arabidopsis thaliana Salt Overly Sensitive2-Like Protein Kinase5 (PKS5) negatively regulates the PM H(+)-ATPase. Here, we report that a chaperone, J3 (DnaJ homolog 3; heat shock protein 40-like), activates PM H(+)-ATPase activity by physically interacting with and repressing PKS5 kinase activity. Plants lacking J3 are hypersensitive to salt at high external pH and exhibit decreased PM H(+)-ATPase activity. J3 functions upstream of PKS5 as double mutants generated using j3-1 and several pks5 mutant alleles with altered kinase activity have levels of PM H(+)-ATPase activity and responses to salt at alkaline pH similar to their corresponding pks5 mutant. Taken together, our results demonstrate that regulation of PM H(+)-ATPase activity by J3 takes place via inactivation of the PKS5 kinase.

Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression

Lysine residue 9 of histone H3 can either be acetylated or mono-, di-, or tri-methylated. These epigenetic states have a diverse impact on regulating gene transcriptional activity and chromatin organization. H3K9ac is invariably correlated with transcriptional activation, whereas H3K9me2 has been reported to be mainly located in constitutive heterochromatin in Arabidopsis. Here, we present epigenetic landscapes for histone H3 lysine 9 acetylation (H3K9ac) and dimethylation (H3K9me2) in Arabidopsis seedlings. The results show that H3K9ac targeted 5,206 non-transposable element (non-TE) genes and 321 transposable elements (TEs), whereas H3K9me2 targeted 2,281 TEs and 1,112 non-TE genes. H3K9ac was biased towards the 5' end of genes and peaked at the ATG position, while H3K9me2 tended to span the entire gene body. H3K9ac correlated with high gene expression, while H3K9me2 correlated with low expression. Analyses of H3K9ac and H3K9me2 with the available datasets of H3K27me3 and DNA methylation revealed a correlation between the occurrence of multiple epigenetic modifications and gene expression. Genes with H3K9ac alone were actively transcribed, while genes that were also modified by either H3K27me3 or DNA methylation showed a lower expression level, suggesting that a combination of repressive marks weakened the positive regulatory effect of H3K9ac. Furthermore, we observed a significant increase of the H3K9ac modification level of selected target genes in hda19 (histone deacetylase 19) mutant seedlings, which indicated that HDA19 plays an important role in regulating the level of H3K9ac and thereby influencing the transcriptional activity in young seedlings.

Rapid and reliable detection of 11 food-borne pathogens using thin-film biosensor chips

Traditional methods for identifying food-borne pathogens are time-consuming and laborious, so it is necessary to develop innovative methods for the rapid identification of food-borne pathogens. Here, we report the development of silicon-based optical thin-film biosensor chips for sensitive detection of 11 food-borne pathogens. Briefly, aldehyde-labeled probes were arrayed and covalently attached to a hydrazine-derivatized chip surface, and then, biotinylated polymerase chain reaction (PCR) amplicons were hybridized with the probes. After washing and brief incubation with an antibiotin immunoglobulin G-horseradish peroxidase conjugate and a precipitable horseradish peroxidase substrate, biotinylated chains bound to the probes were visualized as a color change on the chip surface (gold to blue/purple). Highly sensitive and accurate examination of PCR fragment targets can be completed within 30 min. This assay is extremely robust, sensitive, specific, and economical and can be adapted to different throughputs. Thus, a rapid, sensitive, and reliable technique for detecting 11 food-borne pathogens was successfully developed.

Arabidopsis CULLIN4-damaged DNA binding protein 1 interacts with CONSTITUTIVELY PHOTOMORPHOGENIC1-SUPPRESSOR OF PHYA complexes to regulate photomorphogenesis and flowering time

CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) possesses E3 ligase activity and promotes degradation of key factors involved in the light regulation of plant development. The finding that CULLIN4 (CUL4)-Damaged DNA Binding Protein1 (DDB1) interacts with DDB1 binding WD40 (DWD) proteins to act as E3 ligases implied that CUL4-DDB1 may associate with COP1-SUPPRESSOR OF PHYA (SPA) protein complexes, since COP1 and SPAs are DWD proteins. Here, we demonstrate that CUL4-DDB1 physically associates with COP1-SPA complexes in vitro and in vivo, likely via direct interaction of DDB1 with COP1 and SPAs. The interactions between DDB1 and COP1, SPA1, and SPA3 were disrupted by mutations in the WDXR motifs of MBP-COP1, His-SPA1, and His-SPA3. CUL4 cosuppression mutants enhanced weak cop1 photomorphogenesis and flowered early under short days. Early flowering of short day-grown cul4 mutants correlated with increased FLOWERING LOCUS T transcript levels, whereas CONSTANS transcript levels were not altered. De-etiolated1 and COP1 can bind DDB1 and may work with CUL4-DDB1 in distinct complexes, but they mediate photomorphogenesis in concert. Thus, a series of CUL4-DDB1-COP1-SPA E3 ligase complexes may mediate the repression of photomorphogenesis and, possibly, of flowering time.