The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth

OsHUB1 and OsHUB2 interact with SPIN6 and form homo- and hetero-dimers in rice

Ubiquitin-mediated protein degradation is involved in various cellular processes including plant-microbe interactions and defense responses. Although there are many E3 ubiquitin ligases in rice, the functions of their targets in defense responses are unclear. We recently found that SPIN6 (SPL11-interacting Protein 6) is a Rho GTPase-activating protein and acts as the target of the E3 ligase SPL11, a negative regulator of plant cell death and innate immunity. Our results showed that SPIN6 serves as a link between the SPL11-mediated ubiquitination pathway and the OsRac1-associated defense system. Here, we show that SPIN6 interacts with OsHUB1 and OsHUB2, the homologous proteins of Arabidopsis RING finger E3 ligases HUB1 and HUB2. OsHub1 and OsHub2 are down-regulated in the Spin6 RNAi plants and during the compatible interaction between rice and Magnaporthe oryzae. OsHub1 and OsHub2 are induced by hormone treatments. Like HUB1 and HUB2 in Arabidopsis, OsHUB1 and OsHUB2 in rice form homo- and hetero-dimers. Our results suggest that OsHUB1 and OsHUB2 may be associated with the SPIN6/OsRac1 pathway in rice immunity.

Transcript elongation factors: shaping transcriptomes after transcript initiation

Elongation is a dynamic and highly regulated step of eukaryotic gene transcription. A variety of transcript elongation factors (TEFs), including modulators of RNA polymerase II (RNAPII) activity, histone chaperones, and histone modifiers, have been characterized from plants. These factors control the efficiency of transcript elongation of subsets of genes in the chromatin context and thus contribute to tuning gene expression programs. We review here how genetic and biochemical analyses, primarily in Arabidopsis thaliana, have advanced our understanding of how TEFs adjust plant gene transcription. These studies have revealed that TEFs regulate plant growth and development by modulating diverse processes including hormone signaling, circadian clock, pathogen defense, responses to light, and developmental transitions.

Chromatin meets the cell cycle

The cell cycle is one of the most comprehensively studied biological processes, due primarily to its significance in growth and development, and its deregulation in many human disorders. Studies using a diverse set of model organisms, including yeast, worms, flies, frogs, mammals, and plants, have greatly expanded our knowledge of the cell cycle and have contributed to the universally accepted view of how the basic cell cycle machinery is regulated. In addition to the oscillating activity of various cyclin-dependent kinase (CDK)-cyclin complexes, a plethora of proteins affecting various aspects of chromatin dynamics has been shown to be essential for cell proliferation during plant development. Furthermore, it was reported recently that core cell cycle regulators control gene expression by modifying histone patterns. This review focuses on the intimate relationship between the cell cycle and chromatin. It describes the dynamics and functions of chromatin structures throughout cell cycle progression and discusses the role of heterochromatin as a barrier against re-replication and endoreduplication. It also proposes that core plant cell cycle regulators control gene expression in a manner similar to that described in mammals. At present, our challenge in plants is to define the complete set of effectors and actors that coordinate cell cycle progression and chromatin structure and to understand better the functional interplay between these two processes.

The impact of chromatin dynamics on plant light responses and circadian clock function

Research on the functional properties of nucleosome structure and composition dynamics has revealed that chromatin-level regulation is an essential component of light signalling and clock function in plants, two processes that rely extensively on transcriptional controls. In particular, several types of histone post-translational modifications and chromatin-bound factors act sequentially or in combination to establish transcriptional patterns and to fine-tune the transcript abundance of a large repertoire of light-responsive genes and clock components. Cytogenetic approaches have also identified light-induced higher-order chromatin changes that dynamically organize the condensation of chromosomal domains into sub-nuclear foci containing silenced repeat elements. In this review, we report recently identified molecular actors that establish chromatin state dynamics in response to light signals such as photoperiod, intensity, and spectral quality. We also highlight the chromatin-dependent mechanisms that contribute to the 24-h circadian gene expression and its impact on plant physiology and development. The commonalities and contrasts of light- and clock-associated chromatin-based mechanisms are discussed, with particular emphasis on their impact on the selective regulation and rapid modulation of responsive genes.

Monoubiquitination of histone 2B at the disease resistance gene locus regulates its expression and impacts immune responses in Arabidopsis

Disease resistance (R) genes are key components in plant immunity. Here, we show that Arabidopsis (Arabidopsis thaliana) E3 ubiquitin ligase genes HISTONE MONOUBIQUITINATION1 (HUB1) and HUB2 regulate the expression of R genes SUPPRESSOR OF npr1-1, CONSTITUTIVE1 (SNC1) and RESISTANCE TO PERONOSPORA PARASITICA4. An increase of SNC1 expression induces constitutive immune responses in the bonzai1 (bon1) mutant, and the loss of HUB1 or HUB2 function reduces SNC1 up-regulation and suppresses the bon1 autoimmune phenotypes. HUB1 and HUB2 mediate histone 2B (H2B) monoubiquitination directly at the SNC1 R gene locus to regulate its expression. In addition, SNC1 and HUB1 transcripts are moderately up-regulated by pathogen infection, and H2B monoubiquitination at SNC1 is enhanced by pathogen infection. Together, this study indicates that H2B monoubiquitination at the R gene locus regulates its expression and that this histone modification at the R gene locus has an impact on immune responses in plants.

Histone H2B monoubiquitination is involved in regulating the dynamics of microtubules during the defense response to Verticillium dahliae toxins in Arabidopsis

Histone H2B monoubiquitination (H2Bub) is being recognized as a regulatory mechanism that controls a range of cellular processes in plants, but the molecular mechanisms of H2Bub that are involved in responses to biotic stress are largely unknown. In this study, we used wild-type and H2Bub loss-of-function mutations of Arabidopsis (Arabidopsis thaliana) to elucidate which of its mechanisms are involved in the regulation of the plant's defense response to Verticillium dahliae (Vd) toxins. We demonstrate that the depolymerization of the cortical microtubules (MTs) was different in the wild type and the mutants in the response to Vd toxins. The loss-of-function alleles of HISTONE MONOUBIQUITINATION1 and HISTONE MONOUBIQUITINATION2 mutations present a weaker depolymerization of the MTs, and protein tyrosine phosphorylation plays a critical role in the regulation of the dynamics of MTs. Moreover, H2Bub is a positive regulator of the gene expression of protein tyrosine phosphatases. These findings provide direct evidence for H2Bub as an important modification with regulatory roles in the defense against Vd toxins and demonstrate that H2Bub is involved in modulating the dynamics of MTs, likely through the protein tyrosine phosphatase-mediated signaling pathway.

Dynamic regulation and function of histone monoubiquitination in plants

Polyubiquitin chain deposition on a target protein frequently leads to proteasome-mediated degradation whereas monoubiquitination modifies target protein property and function independent of proteolysis. Histone monoubiquitination occurs in chromatin and is in nowadays recognized as one critical type of epigenetic marks in eukaryotes. While H2A monoubiquitination (H2Aub1) is generally associated with transcription repression mediated by the Polycomb pathway, H2Bub1 is involved in transcription activation. H2Aub1 and H2Bub1 levels are dynamically regulated via deposition and removal by specific enzymes. We review knows and unknowns of dynamic regulation of H2Aub1 and H2Bub1 deposition and removal in plants and highlight the underlying crucial functions in gene transcription, cell proliferation/differentiation, and plant growth and development. We also discuss crosstalks existing between H2Aub1 or H2Bub1 and different histone methylations for an ample mechanistic understanding.

Looking at plant cell cycle from the chromatin window

The cell cycle is defined by a series of complex events, finely coordinated through hormonal, developmental and environmental signals, which occur in a unidirectional manner and end up in producing two daughter cells. Accumulating evidence reveals that chromatin is not a static entity throughout the cell cycle. In fact, there are many changes that include nucleosome remodeling, histone modifications, deposition and exchange, among others. Interestingly, it is possible to correlate the occurrence of several of these chromatin-related events with specific processes necessary for cell cycle progression, e.g., licensing of DNA replication origins, the E2F-dependent transcriptional wave in G1, the activation of replication origins in S-phase, the G2-specific transcription of genes required for mitosis or the chromatin packaging occurring in mitosis. Therefore, an emerging view is that chromatin dynamics must be considered as an intrinsic part of cell cycle regulation. In this article, we review the main features of several key chromatin events that occur at defined times throughout the cell cycle and discuss whether they are actually controlling the transit through specific cell cycle stages.

Understanding the molecular defence responses of host during chickpea-Fusarium interplay: where do we stand?

Fusarium oxysporum is known to cause vascular wilt and root rot of many important plants. Although extensive studies have been reported for the model plant Arabidopsis thaliana (L.) Heynh., the question of whether those experimental interpretations are extendable to other crop species requires experimentation. Chickpea is the most important crop legume of Indian subcontinent and ranks third in the world list of important legumes. However, productivity of this crop is severely curtailed by vascular wilt caused by Fusarium oxysporum f. sp. ciceri. Based on earlier reports, the present review discusses about the external manifestations of the disease, in planta fungal progression and establishment, and the molecular responses of chickpea that occur during Fusarium oxysporum f. sp. ciceri Race 1(Foc1) interaction. Foc1, known to enter the roots through the breaches of tap root, colonise the xylem vessels and block upward translocation of essential solutes causing wilt in compatible hosts. In contrast, pathogen invasion is readily perceived by the resistant host, which activates defence signalling cascades that are directed towards protecting its primary metabolism from the harmful consequences of pathogenic mayhem. Hence, understanding the dynamic complexities of chickpea-Foc1 interplay is prerequisite to providing sustainable solutions in wilt management programs.

The Arabidopsis CAP-D proteins are required for correct chromatin organisation, growth and fertility

In plants as in other eukaryotes, the structural maintenance of chromosome (SMC) protein complexes cohesin, condensin and SMC5/6 are essential for sister chromatid cohesion, chromosome condensation, DNA repair and recombination. The presence of paralogous genes for various components of the different SMC complexes suggests the diversification of their biological functions during the evolution of higher plants. In Arabidopsis thaliana, we identified two candidate genes (Cap-D2 and Cap-D3) which may express conserved proteins presumably associated with condensin. In silico analyses using public databases suggest that both genes are controlled by factors acting in a cell cycle-dependent manner. Cap-D2 is essential because homozygous T-DNA insertion mutants were not viable. The heterozygous mutant showed wild-type growth habit but reduced fertility. For Cap-D3, we selected two homozygous mutants expressing truncated transcripts which are obviously not fully functional. Both mutants show reduced pollen fertility and seed set (one of them also reduced plant vigour), a lower chromatin density and frequent (peri)centromere association in interphase nuclei. Sister chromatid cohesion was impaired compared to wild-type in the cap-D3 mutants but not in the heterozygous cap-D2 mutant. At superresolution (Structured Illumination Microscopy), we found no alteration of chromatin substructure for both cap-D mutants. Chromosome-associated polypeptide (CAP)-D3 and the cohesin subunit SMC3 form similar but positionally non-overlapping reticulate structures in 2C-16C nuclei, suggesting their importance for interphase chromatin architecture in differentiated nuclei. Thus, we presume that CAP-D proteins are required for fertility, growth, chromatin organisation, sister chromatid cohesion and in a process preventing the association of centromeric repeats.

The function of Rad6 gene in Hevea brasiliensis extends beyond DNA repair

The Rad6 gene of Saccharomyces cerevisiae encodes an ubiquitin-conjugating enzyme (E2) which is required for DNA repair, damage-induced mutagenesis, sporulation, etc. In this study, one Rad6 homolog, designated HbRad6, was cloned in rubber tree (Hevea brasiliensis). The putative protein sequence of HbRad6 contains 152 amino acids, a conserved UBC domain, and a conserved active-site cysteine in the UBC domain, which is required for E2 enzymes catalytic activity. HbRad6 shared high similarity with Rad6 from other species. It shared the highest similarity with rice OsRad6 and Arabidopsis thaliana AtUBC2 with 96.05% identical residues, and 63.16% sequence identity with yeast Rad6 (excluding the acidic tail). Comparing expression among different Hevea tissues demonstrated that HbRad6 was ubiquitously expressed in all tissues, but it revealed a preferential expression in the latex. Furthermore, HbRad6 expression was markedly induced by DNA-damaging agent H2O2, the latex stimulator ethephon (ET), and methyl jasmonate (MeJA), while NaCl and wounding treatments had relatively minor effect upon its expression. Genetic complementation experiment revealed that HbRad6 had minor effects on the complementation of the UV sensitivity of yeast rad6 null mutant, indicating that the Hevea Rad6 protein may partially suppress the UV sensitivity of the yeast rad6 mutant. These results suggested that HbRad6 was a multifunction gene involved in DNA damage repair, hormones and stress responses in rubber tree.

Leaf development

Leaves are the most important organs for plants. Without leaves, plants cannot capture light energy or synthesize organic compounds via photosynthesis. Without leaves, plants would be unable perceive diverse environmental conditions, particularly those relating to light quality/quantity. Without leaves, plants would not be able to flower because all floral organs are modified leaves. Arabidopsis thaliana is a good model system for analyzing mechanisms of eudicotyledonous, simple-leaf development. The first section of this review provides a brief history of studies on development in Arabidopsis leaves. This history largely coincides with a general history of advancement in understanding of the genetic mechanisms operating during simple-leaf development in angiosperms. In the second section, I outline events in Arabidopsis leaf development, with emphasis on genetic controls. Current knowledge of six important components in these developmental events is summarized in detail, followed by concluding remarks and perspectives.

How do 'housekeeping' genes control organogenesis?--Unexpected new findings on the role of housekeeping genes in cell and organ differentiation

In recent years, an increasing number of mutations in what would appear to be 'housekeeping genes' have been identified as having unexpectedly specific defects in multicellular organogenesis. This is also the case for organogenesis in seed plants. Although it is not surprising that loss-of-function mutations in 'housekeeping' genes result in lethality or growth retardation, it is surprising when (1) the mutant phenotype results from the loss of function of a 'housekeeping' gene and (2) the mutant phenotype is specific. In this review, by defining housekeeping genes as those encoding proteins that work in basic metabolic and cellular functions, we discuss unexpected links between housekeeping genes and specific developmental processes. In a surprising number of cases housekeeping genes coding for enzymes or proteins with functions in basic cellular processes such as transcription, post-transcriptional modification, and translation affect plant development.

Is HUB1 a hub for plant fitness?

Recently, we have identified circadian clock genes as targets of Histone Monoubiquitination1 (HUB1) in Arabidopsis from a transcriptome comparison between the hub1-1 mutant and HUB1 overexpression lines. HUB1 affected the amplitudes of the circadian clock gene expression profiles in the hub1-1 mutant that coincided with reduced monoubiquitination of histone H2B at their coding regions. Here we showed that parameters for plant fitness are altered in HUB1 mutant and overexpression lines, suggesting that the histone H2B monoubiquitination status affects plant fitness.

Interactome-wide prediction of protein-protein binding sites reveals effects of protein sequence variation in Arabidopsis thaliana

The specificity of protein-protein interactions is encoded in those parts of the sequence that compose the binding interface. Therefore, understanding how changes in protein sequence influence interaction specificity, and possibly the phenotype, requires knowing the location of binding sites in those sequences. However, large-scale detection of protein interfaces remains a challenge. Here, we present a sequence- and interactome-based approach to mine interaction motifs from the recently published Arabidopsis thaliana interactome. The resultant proteome-wide predictions are available via www.ab.wur.nl/sliderbio and set the stage for further investigations of protein-protein binding sites. To assess our method, we first show that, by using a priori information calculated from protein sequences, such as evolutionary conservation and residue surface accessibility, we improve the performance of interface prediction compared to using only interactome data. Next, we present evidence for the functional importance of the predicted sites, which are under stronger selective pressure than the rest of protein sequence. We also observe a tendency for compensatory mutations in the binding sites of interacting proteins. Subsequently, we interrogated the interactome data to formulate testable hypotheses for the molecular mechanisms underlying effects of protein sequence mutations. Examples include proteins relevant for various developmental processes. Finally, we observed, by analysing pairs of paralogs, a correlation between functional divergence and sequence divergence in interaction sites. This analysis suggests that large-scale prediction of binding sites can cast light on evolutionary processes that shape protein-protein interaction networks.

Histone H2B monoubiquitination is required to reach maximal transcript levels of circadian clock genes in Arabidopsis

Previously, we identified HISTONE MONOUBIQUITINATION1 (HUB1) as an unconventional ubiquitin E3 ligase that is not involved in protein degradation but in the histone H2B modification that is implicated in transcriptional activation in plants. HUB1-mediated regulation of gene expression played a role in periodic and inducible processes such as the cell cycle, dormancy, flowering time and defense responses. Here, we determined the effects of the hub1-1 mutation on expression of a set of diurnally induced circadian clock genes identified from a comparative microarray analysis between the hub1-1 mutant and an HUB1 over-expression line. The hub1-1 mutation reduced the amplitudes of a number of induced clock gene expression peaks, as well as the HUB1-mediated histone H2BUb and H3K4Me3 marks associated with the coding regions, suggesting a role for HUB1 in facilitating transcriptional elongation in plants. Furthermore, double mutants between hub1-1 and elongata (elo) showed an embryo-lethal phenotype, indicating a synergistic genetic interaction. The double mutant embryos arrested at the torpedo stage, implying that together histone ubiquitination and acetylation marks are essential to activate expression of target genes in multiple pathways.

Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis

Profiling of DNA and histone modifications has recently allowed the establishment of reference epigenomes from several model organisms. This identified a major chromatin state for active genes that contains monoubiquitinated H2B (H2Bub), a mark linked to transcription elongation. However, assessment of dynamic chromatin changes during the reprogramming of gene expression in response to extrinsic or developmental signals has been more difficult. Here we used the major developmental switch that Arabidopsis thaliana plants undergo upon their initial perception of light, known as photomorphogenesis, as a paradigm to assess spatial and temporal dynamics of monoubiquitinated H2B (H2Bub) and its impact on transcriptional responses. The process involves rapid and extensive transcriptional reprogramming and represents a developmental window well suited to studying cell division–independent chromatin changes. Genome-wide H2Bub distribution was determined together with transcriptome profiles at three time points during early photomorphogenesis. This revealed de novo marking of 177 genes upon the first hour of illumination, illustrating the dynamic nature of H2Bub enrichment in a genomic context. Gene upregulation was associated with H2Bub enrichment, while H2Bub levels generally remained stable during gene downregulation. We further report that H2Bub influences the modulation of gene expression, as both gene up- and downregulation were globally weaker in hub1 mutant plants that lack H2Bub. H2Bub-dependent regulation notably impacted genes with fast and transient light induction, and several circadian clock components whose mRNA levels are tightly regulated by sharp oscillations. Based on these findings, we propose that H2B monoubiquitination is part of a transcription-coupled, chromatin-based mechanism to rapidly modulate gene expression.

In eukaryotes, chromatin-based mechanisms overlay with DNA sequence information to determine the transcriptional output of the genome. Evaluating the role of chromatin state variations in the regulation of gene expression is therefore key to understanding their contribution to development. Several transcriptional coactivators contribute to the selective regulation of cellular pathways by coordinating histone H2B monoubiquitination (H2Bub) with other histone modifications. Although H2Bub is present on a large number of genes, its loss was shown to affect RNA levels for only a small subset of genes, and therefore its influence on gene expression is not well understood. Here we assessed the impact of H2Bub on expression changes during a rapid developmental transition that initiates upon exposure of plants to light. This revealed that H2Bub marking is highly dynamic in a genomic context. Furthermore, a large repertoire of light-responsive genes was impaired for rapid up- or downregulation, indicating that H2Bub is important for attaining appropriate expression levels. Regulatory factors and circadian clock components are well represented within the set of genes impacted by H2Bub dynamics for rapid changes in RNA levels, indicating that some genes whose mRNAs need tight and rapid control are particularly sensitive to chromatin-based mechanisms linked to H2Bub deposition.

Whole organ, venation and epidermal cell morphological variations are correlated in the leaves of Arabidopsis mutants

Despite the large number of genes known to affect leaf shape or size, we still have a relatively poor understanding of how leaf morphology is established. For example, little is known about how cell division and cell expansion are controlled and coordinated within a growing leaf to eventually develop into a laminar organ of a definite size. To obtain a global perspective of the cellular basis of variations in leaf morphology at the organ, tissue and cell levels, we studied a collection of 111 non-allelic mutants with abnormally shaped and/or sized leaves, which broadly represent the mutational variations in Arabidopsis thaliana leaf morphology not associated with lethality. We used image-processing techniques on these mutants to quantify morphological parameters running the gamut from the palisade mesophyll and epidermal cells to the venation, whole leaf and rosette levels. We found positive correlations between epidermal cell size and leaf area, which is consistent with long-standing Avery's hypothesis that the epidermis drives leaf growth. In addition, venation parameters were positively correlated with leaf area, suggesting that leaf growth and vein patterning share some genetic controls. Positional cloning of the genes affected by the studied mutations will eventually establish functional links between genotypes, molecular functions, cellular parameters and leaf phenotypes.

The RPT2 subunit of the 26S proteasome directs complex assembly, histone dynamics, and gametophyte and sporophyte development in Arabidopsis

The regulatory particle (RP) of the 26S proteasome contains a heterohexameric ring of AAA-ATPases (RPT1-6) that unfolds and inserts substrates into the core protease (CP) for degradation. Through genetic analysis of the Arabidopsis thaliana gene pair encoding RPT2, we show that this subunit plays a critical role in 26S proteasome assembly, histone dynamics, and plant development. rpt2a rpt2b double null mutants are blocked in both male and female gamete transmission, demonstrating that the subunit is essential. Whereas rpt2b mutants are phenotypically normal, rpt2a mutants display a range of defects, including impaired leaf, root, trichome, and pollen development, delayed flowering, stem fasciation, hypersensitivity to mitomycin C and amino acid analogs, hyposensitivity to the proteasome inhibitor MG132, and decreased 26S complex stability. The rpt2a phenotype can be rescued by both RPT2a and RPT2b, indicative of functional redundancy, but not by RPT2a mutants altered in ATP binding/hydrolysis or missing the C-terminal hydrophobic sequence that docks the RPT ring onto the CP. Many rpt2a phenotypes are shared with mutants lacking the chromatin assembly factor complex CAF1. Like caf1 mutants, plants missing RPT2a or reduced in other RP subunits contain less histones, thus implicating RPT2 specifically, and the 26S proteasome generally, in plant nucleosome assembly.

Flickin' the ubiquitin switch: the role of H2B ubiquitylation in development

The reversible ubiquitylation of histone H2B has long been implicated in transcriptional activation and gene silencing. However, many questions regarding its regulation and effects on chromatin structure remain unanswered. In addition, while several studies have uncovered an involvement of this modification in the control of certain developmental processes, a more general understanding of its requirement is lacking. Herein, we present a broad overview of the pathways known to be regulated by H2B ubiquitylation, while drawing parallels between findings in disparate organisms, in order to facilitate continued delineation of its spatiotemporal role in development. Finally, we integrate the findings of recent studies into how H2B ubiquitylation affects chromatin, and cast an eye over emerging areas for future research.

Transcriptome analysis of chestnut (Castanea sativa) tree buds suggests a putative role for epigenetic control of bud dormancy

BACKGROUND AND AIMS

Recent papers indicated that epigenetic control is involved in transitions in bud dormancy, purportedly controlling gene expression. The present study aimed to identify genes that are differentially expressed in dormant and non-dormant Castanea sativa buds.

METHODS

Two suppression subtractive hybridization cDNA libraries were constructed to characterize the transcriptomes of dormant apical buds of C. sativa, and buds in which dormancy was released.

KEY RESULTS

A total of 512 expressed sequence tags (ESTs) were generated in a forward and reverse subtractive hybridization experiment. Classification of these ESTs into functional groups demonstrated that dormant buds were predominantly characterized by genes associated with stress response, while non-dormant buds were characterized by genes associated with energy, protein synthesis and cellular components for development and growth. ESTs for a few genes involved in different forms of epigenetic modification were found in both libraries, suggesting a role for epigenetic control in bud dormancy different from that in growth. Genes encoding histone mono-ubiquitinase HUB2 and histone acetyltransferase GCN5L were associated with dormancy, while a gene encoding histone H3 kinase AUR3 was associated with growth. Real-time RT-PCR with a selection of genes involved in epigenetic modification and stress tolerance confirmed the expression of the majority of investigated genes in various stages of bud development, revealing a cyclical expression pattern concurring with the growth seasons for most genes. However, senescing leaves also showed an increased expression of several of the genes associated with dormancy, implying pleiotropy. Furthermore, a comparison between these subtraction cDNA libraries and the poplar bud dormancy transcriptome and arabidopsis transcriptomes for seed dormancy and non-dormancy indicated a common basis for dormancy in all three systems.

CONCLUSIONS

Bud dormancy and non-dormancy in C. sativa were characterized by distinct sets of genes and are likely to be under different epigenetic control.

Transcriptome analysis of chestnut (Castanea sativa) tree buds suggests a putative role for epigenetic control of bud dormancy

BACKGROUND AND AIMS

Recent papers indicated that epigenetic control is involved in transitions in bud dormancy, purportedly controlling gene expression. The present study aimed to identify genes that are differentially expressed in dormant and non-dormant Castanea sativa buds.

METHODS

Two suppression subtractive hybridization cDNA libraries were constructed to characterize the transcriptomes of dormant apical buds of C. sativa, and buds in which dormancy was released.

KEY RESULTS

A total of 512 expressed sequence tags (ESTs) were generated in a forward and reverse subtractive hybridization experiment. Classification of these ESTs into functional groups demonstrated that dormant buds were predominantly characterized by genes associated with stress response, while non-dormant buds were characterized by genes associated with energy, protein synthesis and cellular components for development and growth. ESTs for a few genes involved in different forms of epigenetic modification were found in both libraries, suggesting a role for epigenetic control in bud dormancy different from that in growth. Genes encoding histone mono-ubiquitinase HUB2 and histone acetyltransferase GCN5L were associated with dormancy, while a gene encoding histone H3 kinase AUR3 was associated with growth. Real-time RT-PCR with a selection of genes involved in epigenetic modification and stress tolerance confirmed the expression of the majority of investigated genes in various stages of bud development, revealing a cyclical expression pattern concurring with the growth seasons for most genes. However, senescing leaves also showed an increased expression of several of the genes associated with dormancy, implying pleiotropy. Furthermore, a comparison between these subtraction cDNA libraries and the poplar bud dormancy transcriptome and arabidopsis transcriptomes for seed dormancy and non-dormancy indicated a common basis for dormancy in all three systems.

CONCLUSIONS

Bud dormancy and non-dormancy in C. sativa were characterized by distinct sets of genes and are likely to be under different epigenetic control.

Histone modifications in transcriptional activation during plant development

In eukaryotic cell nuclei, chromatin states dictated by different combinations of post-translational modifications of histones, such as acetylation, methylation and monoubiquitination of lysine residues, are part of the multitude of epigenomes involved in the fine-tuning of all genetic functions and in particular transcription. During the past decade, an increasing number of 'writers', 'readers' and 'erasers' of histone modifications have been identified. Characterization of these factors in Arabidopsis has unraveled their pivotal roles in the regulation of essential processes, such as floral transition, cell differentiation, gametogenesis, and plant response/adaptation to environmental stresses. In this review we focus on histone modification marks associated with transcriptional activation to highlight current knowledge on Arabidopsis 'writers', 'readers' and 'erasers' of histone modifications and to discuss recent findings on molecular mechanisms of integration of histone modifications with the RNA polymerase II transcriptional machinery during transcription of the flowering repressor gene FLC.

Expression of aspartyl protease and C3HC4-type RING zinc finger genes are responsive to ascorbic acid in Arabidopsis thaliana

Ascorbate (AsA) is a redox buffer and enzyme cofactor with various proposed functions in stress responses and growth. The aim was to identify genes whose transcript levels respond to changes in leaf AsA. The AsA-deficient Arabidopsis mutant vtc2-1 was incubated with the AsA precursor L-galactono-1,4-lactone (L-GalL) to increase leaf AsA concentration. Differentially expressed genes screened by DNA microarray were further characterized for AsA responsiveness in wild-type plants. The analysis of 14 candidates by real-time PCR identified an aspartyl protease gene (ASP, At1g66180) and a C3HC4-type RING zinc finger gene (AtATL15, At1g22500) whose transcripts were rapidly responsive to increases in AsA pool size caused by L-GalL and AsA supplementation and light. Transgenic Arabidopsis plants expressing an AtATL15 promoter::luciferase reporter confirmed that the promoter is L-GalL, AsA, and light responsive. The expression patterns of ASP and AtATL15 suggest they have roles in growth regulation. The promoter of AtATL15 is responsive to AsA status and will provide a tool to investigate the functions of AsA in plants further.

A chromatin perspective of plant cell cycle progression

The finely regulated series of events that span from the birth of a cell to the production of two new born cells encompass the cell cycle. Cell cycle progression occurs in a unidirectional manner and requires passing through a number of stages in response to cellular, developmental and environmental cues. In addition to these signaling cascades, transcriptional regulation plays a major role and acts coordinately with genome duplication during S-phase and chromosome segregation during mitosis. In this context, chromatin is revealing as a highly dynamic and major player in cell cycle regulation not only owing to the changes that occur as a consequence of cell cycle progression but also because some specific chromatin modifications are crucial to move across the cell cycle. These are particularly relevant for controlling transcriptional activation and repression as well as initiation of DNA replication and chromosome compaction. As a consequence the epigenetic landscape of a proliferating cell is very complex throughout the cell cycle. These aspects of chromatin dynamics together with the impact of epigenetic modifications on cell proliferation will be discussed in this article. This article is part of a Special Issue entitled: Epigenetic Control of cellular and developmental processes in plants.

SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis by stimulating S-phase progression of the cell cycle

SHORT-ROOT (SHR) and SCARECROW (SCR) are required for stem cell maintenance in the Arabidopsis (Arabidopsis thaliana) root meristem, ensuring its indeterminate growth. Mutation of SHR and SCR genes results in disorganization of the quiescent center and loss of stem cell activity, resulting in the cessation of root growth. This paper reports on the role of SHR and SCR in the development of leaves, which, in contrast to the root, have a determinate growth pattern and lack a persistent stem cell niche. Our results demonstrate that inhibition of leaf growth in shr and scr mutants is not a secondary effect of the compromised root development but is caused by an effect on cell division in the leaves: a reduced cell division rate and early exit of the proliferation phase. Consistent with the observed cell division phenotype, the expression of SHR and SCR genes in leaves is closely associated with cell division activity in most cell types. The increased cell cycle duration is due to a prolonged S-phase duration, which is mediated by up-regulation of cell cycle inhibitors known to restrain the activity of the transcription factor, E2Fa. Therefore, we conclude that, in contrast to their specific roles in cortex/endodermis differentiation and stem cell maintenance in the root, SHR and SCR primarily function as general regulators of cell proliferation in leaves.

Identification and functional analysis of the MOC1 interacting protein 1

Rice tillering is one of the most important agronomic traits that determine grain yields. Our previous study has demonstrated that the MONOCULM1 (MOC1) gene is a key component that controls the formation of rice tiller buds. To further elucidate the molecular mechanism of MOC1 involved in the regulation of rice tillering, we performed a yeast-two-hybrid screening to identify MOC1 interacting proteins (MIPs). Here we reported that MIP1 interacted with MOC1 both in vitro and in vivo. The overexpression of MIP1 resulted in enhanced tillering and reduced plant height. In-depth characterization of the context of MIP1 and MOC1 would further our understanding of molecular regulatory mechanisms of rice tillering.

The role of the transcript elongation factors FACT and HUB1 in leaf growth and the induction of flowering

In the cell nucleus, the packaging of the DNA into chromatin represses transcription by restricting the access of transcriptional regulators to their binding sites and inhibiting the progression of RNA polymerases during transcript elongation. To efficiently transcribe genes in the context of chromatin, eukaryotes have a variety of transcript elongation factors promoting transcription in vivo. The facilitates chromatin transcription (FACT) complex consisting of the SSRP1 and SPT16 proteins, is a histone chaperone that assists transcription by destabilising nucleosomes in the path of RNA polymerases. In a recent study, we report that Arabidopsis FACT is critically involved in different aspects of development including leaf growth and the transition to flowering. Moreover, FACT was found to interact genetically with HUB1 that mono-ubiquitinates histone H2B. Depending on the underlying process that is regulated by the two complexes, there appear to be different levels of interaction.

Impact of nucleosome dynamics and histone modifications on cell proliferation during Arabidopsis development

Eukaryotic chromatin is a highly structured macromolecular complex of which DNA is wrapped around a histone-containing core. DNA can be methylated at specific C residues and each histone molecule can be covalently modified at a large variety of amino acids in both their tail and core domains. Furthermore, nucleosomes are not static entities and both their position and histone composition can also vary. As a consequence, chromatin behaves as a highly dynamic cellular component with a large combinatorial complexity beyond DNA sequence that conforms the epigenetic landscape. This has key consequences on various developmental processes such as root and flower development, gametophyte and embryo formation and response to the environment, among others. Recent evidence indicate that posttranslational modifications of histones also affect cell cycle progression and processes depending on a correct balance of proliferating cell populations, which in the context of a developing organisms includes cell cycle, stem cell dynamics and the exit from the cell cycle to endoreplication and cell differentiation. The impact of epigenetic modifications on these processes will be reviewed here.

The RON1/FRY1/SAL1 gene is required for leaf morphogenesis and venation patterning in Arabidopsis

To identify genes involved in vascular patterning in Arabidopsis (Arabidopsis thaliana), we screened for abnormal venation patterns in a large collection of leaf shape mutants isolated in our laboratory. The rotunda1-1 (ron1-1) mutant, initially isolated because of its rounded leaves, exhibited an open venation pattern, which resulted from an increased number of free-ending veins. We positionally cloned the RON1 gene and found it to be identical to FRY1/SAL1, which encodes an enzyme with inositol polyphosphate 1-phosphatase and 3' (2'),5'-bisphosphate nucleotidase activities and has not, to our knowledge, previously been related to venation patterning. The ron1-1 mutant and mutants affected in auxin homeostasis share perturbations in venation patterning, lateral root formation, root hair length, shoot branching, and apical dominance. These similarities prompted us to monitor the auxin response using a DR5-GUS auxin-responsive reporter transgene, the expression levels of which were increased in roots and reduced in leaves in the ron1-1 background. To gain insight into the function of RON1/FRY1/SAL1 during vascular development, we generated double mutants for genes involved in vein patterning and found that ron1 synergistically interacts with auxin resistant1 and hemivenata-1 but not with cotyledon vascular pattern1 (cvp1) and cvp2. These results suggest a role for inositol metabolism in the regulation of auxin responses. Microarray analysis of gene expression revealed that several hundred genes are misexpressed in ron1-1, which may explain the pleiotropic phenotype of this mutant. Metabolomic profiling of the ron1-1 mutant revealed changes in the levels of 38 metabolites, including myoinositol and indole-3-acetonitrile, a precursor of auxin.

The Arabidopsis SMO2, a homologue of yeast TRM112, modulates progression of cell division during organ growth

Cell proliferation is integrated into developmental progression in multicellular organisms, including plants, and the regulation of cell division is of pivotal importance for plant growth and development. Here, we report the identification of an Arabidopsis SMALL ORGAN 2 (SMO2) gene that functions in regulation of the progression of cell division during organ growth. The smo2 knockout mutant displays reduced size of aerial organs and shortened roots, due to the decreased number of cells in these organs. Further analyses reveal that disruption of SMO2 does not alter the developmental timing but reduces the rate of cell production during leaf and root growth. Moreover, smo2 plants exhibit a constitutive activation of cell cycle-related genes and over-accumulation of cells expressing CYCB1;1:beta-glucuronidase (CYCB1;1:GUS) during organogenesis, suggesting that smo2 has a defect in G(2)-M phase progression in the cell cycle. SMO2 encodes a functional homologue of yeast TRM112, a plurifunctional component involved in a few cellular events, including tRNA and protein methylation. In addition, the mutation of SMO2 does not appear to affect endoreduplication in Arabidopsis leaf cells. Taken together we postulate that Arabidopsis SMO2 is a conserved yeast TRM112 homologue and SMO2-mediated cellular events are required for proper progression of cell division in plant growth and development.

The transcript elongation factor FACT affects Arabidopsis vegetative and reproductive development and genetically interacts with HUB1/2

The facilitates chromatin transcription (FACT) complex, consisting of the SSRP1 and SPT16 proteins, is a histone chaperone that assists the progression of transcribing RNA polymerase on chromatin templates by destabilizing nucleosomes. Here, we examined plants that harbour mutations in the genes encoding the subunits of Arabidopsis FACT. These experiments revealed that (i) SSRP1 is critical for plant viability, and (ii) plants with reduced amounts of SSRP1 and SPT16 display various defects in vegetative and reproductive development. Thus, mutant plants display an increased number of leaves and inflorescences, show early bolting, have abnormal flower and leaf architecture, and their seed production is severely affected. The early flowering of the mutant plants is associated with reduced expression of the floral repressor FLC in ssrp1 and spt16 plants. Compared to control plants, reduced amounts of FACT in mutant plants are detected at the FLC locus as well as at the locations of housekeeping genes (whose expression is not affected in the mutants), suggesting that expression of FLC is particularly sensitive to reduced FACT activity. Analysis of double mutants that are affected in the expression of both FACT subunits and factors catalysing the mono-ubiquitination of histone H2B (HUB1/2) demonstrates that they genetically interact to regulate various developmental processes (i.e. branching, leaf venation pattern, silique development) but independently regulate the growth of leaves and the induction of flowering.

Plant Elongator regulates auxin-related genes during RNA polymerase II transcription elongation

In eukaryotes, transcription of protein-encoding genes is strongly regulated by posttranslational modifications of histones that affect the accessibility of the DNA by RNA polymerase II (RNAPII). The Elongator complex was originally identified in yeast as a histone acetyltransferase (HAT) complex that activates RNAPII-mediated transcription. In Arabidopsis thaliana, the Elongator mutants elo1, elo2, and elo3 with decreased leaf and primary root growth due to reduced cell proliferation identified homologs of components of the yeast Elongator complex, Elp4, Elp1, and Elp3, respectively. Here we show that the Elongator complex was purified from plant cell cultures as a six-component complex. The role of plant Elongator in transcription elongation was supported by colocalization of the HAT enzyme, ELO3, with euchromatin and the phosphorylated form of RNAPII, and reduced histone H3 lysine 14 acetylation at the coding region of the SHORT HYPOCOTYL 2 auxin repressor and the LAX2 auxin influx carrier gene with reduced expression levels in the elo3 mutant. Additional auxin-related genes were down-regulated in the transcriptome of elo mutants but not targeted by the Elongator HAT activity showing specificity in target gene selection. Biological relevance was apparent by auxin-related phenotypes and marker gene analysis. Ethylene and jasmonic acid signaling and abiotic stress responses were up-regulated in the elo transcriptome and might contribute to the pleiotropic elo phenotype. Thus, although the structure of Elongator and its substrate are conserved, target gene selection has diverged, showing that auxin signaling and influx are under chromatin control.

Plant Elongator regulates auxin-related genes during RNA polymerase II transcription elongation

In eukaryotes, transcription of protein-encoding genes is strongly regulated by posttranslational modifications of histones that affect the accessibility of the DNA by RNA polymerase II (RNAPII). The Elongator complex was originally identified in yeast as a histone acetyltransferase (HAT) complex that activates RNAPII-mediated transcription. In Arabidopsis thaliana, the Elongator mutants elo1, elo2, and elo3 with decreased leaf and primary root growth due to reduced cell proliferation identified homologs of components of the yeast Elongator complex, Elp4, Elp1, and Elp3, respectively. Here we show that the Elongator complex was purified from plant cell cultures as a six-component complex. The role of plant Elongator in transcription elongation was supported by colocalization of the HAT enzyme, ELO3, with euchromatin and the phosphorylated form of RNAPII, and reduced histone H3 lysine 14 acetylation at the coding region of the SHORT HYPOCOTYL 2 auxin repressor and the LAX2 auxin influx carrier gene with reduced expression levels in the elo3 mutant. Additional auxin-related genes were down-regulated in the transcriptome of elo mutants but not targeted by the Elongator HAT activity showing specificity in target gene selection. Biological relevance was apparent by auxin-related phenotypes and marker gene analysis. Ethylene and jasmonic acid signaling and abiotic stress responses were up-regulated in the elo transcriptome and might contribute to the pleiotropic elo phenotype. Thus, although the structure of Elongator and its substrate are conserved, target gene selection has diverged, showing that auxin signaling and influx are under chromatin control.

The ang3 mutation identified the ribosomal protein gene RPL5B with a role in cell expansion during organ growth

The role of translation in the regulation of higher plant growth and development is not well understood. Mutational analysis is a powerful tool to identify and study the function of genes related to a biological process, such as growth. Here we analyzed functionally the angusta3 (ang3) narrow leaf mutant. The AG3 gene was cloned by fine mapping combined with candidate gene sequencing and it corresponded to the ribosomal protein gene RPL5B. Based on amino acid sequence homology, promoter DNA sequence homology and in silico gene expression analysis, RPL5B was found to be putatively functionally redundant with RPL5A. The morphological analysis of ang3 mutants showed that the leaf lamina area was significantly reduced from the third rosette leaf on, mainly because of decreased width. Cellular analysis of the abaxial epidermal cell layer of the third leaf indicated that the cell number in the mutant was similar to that of the wild type, but the cell size was significantly reduced. We postulate that the reduced cell expansion in the epidermis contributes to the narrow shape of ang3 leaves. Growth was also significantly impaired in hypocotyls and primary roots, hinting at a general role for RPL5B in organ growth, unrelated to dorsiventral axis formation. Comparison of the transcriptome of the shoot apices of the mutant and the wild type revealed a limited number of differentially expressed genes, such as MYB23 and MYB5, of which the lower expression in the ang3 mutant correlated with reduced trichome density. Our data suggest that translation is an important level of control of growth and development in plants.

Ectopic expression of PtaRHE1, encoding a poplar RING-H2 protein with E3 ligase activity, alters plant development and induces defence-related responses

RING (really interesting new gene)-H2 domain-containing proteins are widely represented in plants and play important roles in the regulation of many developmental processes as well as in plant-environment interactions. In the present report, experiments were performed to unravel the role of the poplar gene PtaRHE1, coding for a RING-H2 protein. In vitro ubiquitination assays indicate a functional E3 ligase activity for PtaRHE1 with the specific E2 ubiquitin-conjugating enzyme UbcH5a. The overexpression of PtaRHE1 in tobacco resulted in a pleiotropic phenotype characterized by a curling of the leaves, the formation of necrotic lesions on leaf blades, growth retardation, and a delay in floral transition. The plant gene expression response to PtaRHE1 overexpression provided evidence for the up-regulation of defence- and/or programmed cell death-related genes. Moreover, genes coding for WRKY transcription factors as well as for mitogen-activated protein kinases, such as wound-induced protein kinase (WIPK), were also found to be induced in the transgenic lines as compared with the wild type. In addition, histochemical beta-glucuronidase staining showed that the PtaRHE1 promoter is induced by plant pathogens and by elicitors such as salicylic acid and cellulase. Taken together, these results suggest that the E3 ligase PtaRHE1 plays a role in the ubiquitination-mediated regulation of defence response, possibly by acting upstream of WIPK and/or in the activation of WRKY factors.

Ectopic over-expression of BhHsf1, a heat shock factor from the resurrection plant Boea hygrometrica, leads to increased thermotolerance and retarded growth in transgenic Arabidopsis and tobacco

Plant heat shock transcription factors (Hsfs) are commonly found to be involved in various stress responses. Several Hsfs displayed dwarf phenotype while conferred stress tolerance when over-expressed. However, the underlying mechanisms were not fully understood. Here we report the cloning and characterization of an Hsf (BhHsf1) from the resurrection plant Boea hygrometrica. Drought, heat and wound can induce BhHsf1 expression. The over-expression of BhHsf1 conferred growth retardation and stress tolerance in both Arabidopsis and tobacco. Evidence was presented to show that the growth retardation of aerial organs in the transgenic plants was resulted from the reduction of cell proliferation. Gene expression profiling using microarray hybridization and pathway analysis showed that Hsps and stress-associated genes were induced whereas the genes related to DNA replication and mitotic cell cycle were down-regulated in BhHsf1 over-expression Arabidopsis, which was in consistence with the observation of the impaired nuclear endoreduplication. Taking together, our results suggest that BhHsf1 may play dual roles in mediating the processes in heat stress tolerance and growth retardation via regulation of target genes related to stress protection and mitotic cell cycle.

Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

Background

Analyses of gene expression data from microarray experiments has become a central tool for identifying co-regulated, functional gene modules. A crucial aspect of such analysis is the integration of data from different experiments and different laboratories. How to weigh the contribution of different experiments is an important point influencing the final outcomes. We have developed a novel method for this integration, and applied it to genome-wide data from multiple Arabidopsis microarray experiments performed under a variety of experimental conditions. The goal of this study is to identify functional globally co-regulated gene modules in the Arabidopsis genome.

Results

Following the analysis of 21,000 Arabidopsis genes in 43 datasets and about 2 × 10⁸ gene pairs, we identified a globally co-expressed gene network. We found clusters of globally co-expressed Arabidopsis genes that are enriched for known Gene Ontology annotations. Two types of modules were identified in the regulatory network that differed in their sensitivity to the node-scoring parameter; we further showed these two pertain to general and specialized modules. Some of these modules were further investigated using the Genevestigator compendium of microarray experiments. Analyses of smaller subsets of data lead to the identification of condition-specific modules.

Conclusion

Our method for identification of gene clusters allows the integration of diverse microarray experiments from many sources. The analysis reveals that part of the Arabidopsis transcriptome is globally co-expressed, and can be further divided into known as well as novel functional gene modules. Our methodology is general enough to apply to any set of microarray experiments, using any scoring function.

The histone deacetylase OsHDAC1 epigenetically regulates the OsNAC6 gene that controls seedling root growth in rice

We have previously isolated a rice gene encoding a histone deacetylase, OsHDAC1, and observed that its transgenic overexpression increases seedling root growth. To identify the transcriptional repression events that occur as a result of OsHDAC1 overexpression (OsHDAC1(OE)), a global profiling of root-expressed genes was performed on OsHDAC1(OE) or HDAC inhibitor-treated non-transgenic (NT) roots, in comparison with untreated NT roots. We selected 39 genes that are induced and repressed in HDAC inhibitor-treated NT and OsHDAC1(OE) roots, compared with NT roots, respectively. Interestingly, OsNAC6, a member of the NAM-ATAF-CUC (NAC) family, was identified as a key component of the OsHDAC1 regulon, and was found to be epigenetically repressed by OsHDAC1 overexpression. The root phenotype of OsNAC6 knock-out seedlings was observed to be similar to that of the OsHDAC1(OE) seedlings. Conversely, the root phenotype of the OsNAC6 overexpressors was similar to that of the OsHDAC1 knock-out seedlings. These observations indicate that OsHDAC1 negatively regulates the OsNAC6 gene that primarily mediates the alteration in the root growth of the OsHDAC1(OE) seedlings. Chromatin immunoprecipitation assays of the OsNAC6 promoter region using antibodies specific to acetylated histones H3 and H4 revealed that OsHDAC1 epigenetically represses the expression of OsNAC6 by deacetylating K9, K14 and K18 on H3 and K5, K12 and K16 on H4.

Nonredundant requirement for multiple histone modifications for the early anaphase release of the mitotic exit regulator Cdc14 from nucleolar chromatin

In Saccharomyces cerevisiae, the conserved phosphatase Cdc14 is required for the exit from mitosis. It is anchored on nucleolar chromatin by the Cfi1/Net1 protein until early anaphase, at which time it is released into the nucleoplasm. Two poorly understood, redundant pathways promote Cdc14 release, the FEAR (Cdc fourteen early release) network and the MEN (mitotic exit network). Through the analysis of genetic interactions, we report here a novel requirement for the ubiquitination of histone H2B by the Bre1 ubiquitin ligase in the cell cycle–dependent release of Cdc14 from nucleolar chromatin when the MEN is inactivated. This function for H2B ubiquitination is mediated by its activation of histone H3 methylation on lysines 4 and 79 (meH3K4 and meH3K79) but, surprisingly, is not dependent on the histone deacetylase (HDAC) Sir2, which associates with Cdc14 on nucleolar chromatin as part of the RENT complex. We also observed a defect in Cdc14 release in cells lacking H3 lysine 36 methylation (meH3K36) and in cells lacking an HDAC recruited by this modification. These histone modifications represent previously unappreciated factors required for the accessibility to and/or action on nucleolar chromatin of FEAR network components. The nonredundant role for these modifications in this context contrasts with the notion of a highly combinatorial code by which histone marks act to control biological processes.

During proliferation, eukaryotic cells segregate their replicated genome to generate two identical progeny through a highly regulated process called mitosis. Inaccuracy in this process results in cell inviability or aneuploidy. In the S. cerevisiae cell cycle, the exit from the mitotic state is triggered by the release of the phosphatase Cdc14 during the anaphase stage of mitosis from nucleolar chromatin, where it is sequestered and kept inactive. The role of chromatin, if any, in the regulation of Cdc14 sequestration and/or release is unexplored. Using genetic analysis, we have discovered that multiple evolutionarily conserved histone modifications are required for the early anaphase release of Cdc14. These include monoubiquitination of histone H2B as well as two methylations of histone H3 on lysines 4 and 79 that require H2B monoubiquitination to occur efficiently. In addition, methylation of H3 on lysine 36 and a histone deacetylase recruited by this modification are also required. We suggest that these histone modifications are required on nucleolar chromatin for the accessibility and/or action of factors involved in the early anaphase release of Cdc14. The nonredundant requirement for multiple chromatin modifications stands in contrast to the popular notion of a highly combinatorial “histone code” for the action of histone modifications.

Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis

Protein ubiquitylation is a central regulatory mechanism that controls numerous processes in plants, including hormone signaling, developmental progression, responses to biotic and abiotic challenges, protein trafficking and chromatin structure. Despite data implicating thousands of plant proteins as targets, so far only a few have been conclusively shown to be ubiquitylated in planta. Here we describe a method to isolate ubiquitin-protein conjugates from Arabidopsis that exploits a stable transgenic line expressing a synthetic poly-UBQ gene encoding ubiquitin (Ub) monomers N-terminally tagged with hexahistidine. Following sequential enrichment by Ub-affinity and nickel chelate-affinity chromatography, the ubiquitylated proteins were trypsinized, separated by two-dimensional liquid chromatography, and analyzed by mass spectrometry. Our list of 54 non-redundant targets, expressed by as many as 90 possible isoforms, included those predicted by genetic studies to be ubiquitylated in plants (EIN3 and JAZ6) or shown to be ubiquitylated in other eukaryotes (ribosomal subunits, elongation factor 1alpha, histone H1, HSP70 and CDC48), as well as candidates whose control by the Ub/26S proteasome system is not yet appreciated. Ub attachment site(s) were resolved for a subset of these proteins, but surprisingly little sequence consensus was detected, implying that specific residues surrounding the modified lysine are not important determinants for ubiquitylation. We also identified six of the seven available lysine residues on Ub itself as Ub attachment sites, together with evidence for a branched mixed-linkage chain, suggesting that the topologies of Ub chains can be highly complex in plants. Taken together, our method provides a widely applicable strategy to define ubiquitylation in any tissue of intact plants exposed to a wide range of conditions.

Control of the transition to flowering by chromatin modifications

The timing of floral transition is critical to reproductive success in angiosperms and is genetically controlled by a network of flowering genes. In Arabidopsis, expression of certain flowering genes is regulated by various chromatin modifications, among which are two central regulators of flowering, namely FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT). Recent studies have revealed that a number of chromatin-modifying components are involved in activation or repression of FLC expression. Activation of FLC expression is associated with various 'active' chromatin modifications including acetylation of core histone tails, histone H3 lysine-4 (H3K4) methylation, H2B monoubiquitination, H3 lysine-36 (H3K36) di- and tri-methylation and deposition of the histone variant H2A.Z, whereas various 'repressive' histone modifications are associated with FLC repression, including histone deacetylation, H3K4 demethylation, histone H3 lysine-9 (H3K9) and H3 lysine-27 (H3K27) methylation, and histone arginine methylation. In addition, recent studies have revealed that Polycomb group gene-mediated transcriptional-silencing mechanism not only represses FLC expression, but also directly represses FT expression. Regulation of FLC expression provides a paradigm for control of the expression of other developmental genes in plants through chromatin mechanisms.

The ubiquitin-26S proteasome system at the nexus of plant biology

Plants, like other eukaryotes, rely on proteolysis to control the abundance of key regulatory proteins and enzymes. Strikingly, genome-wide studies have revealed that the ubiquitin-26S proteasome system (UPS) in particular is an exceedingly large and complex route for protein removal, occupying nearly 6% of the Arabidopsis thaliana proteome. But why is the UPS so pervasive in plants? Data accumulated over the past few years now show that it targets numerous intracellular regulators that have central roles in hormone signalling, the regulation of chromatin structure and transcription, tailoring morphogenesis, responses to environmental challenges, self recognition and battling pathogens.

Preferential up-regulation of G2/M phase-specific genes by overexpression of the hyperactive form of NtmybA2 lacking its negative regulation domain in tobacco BY-2 cells

Many G2/M phase-specific genes in plants contain mitosis-specific activator (MSA) elements, which act as G2/M phase-specific enhancers and bind with R1R2R3-Myb transcription factors. Here, we examined the genome-wide effects of NtmybA2 overexpression, one of the R1R2R3-Myb transcription factors in tobacco (Nicotiana tabacum). We used a custom-made 16-K cDNA microarray for comparative transcriptome analysis of transgenic tobacco BY-2 cell lines that overexpress NtmybA2 or its truncated hyperactive form. The microarray was also used to determine the transcript profile during the cell cycle in synchronized cultures of BY-2 cells. Combined microarray data from transgenic lines and synchronized cells revealed that overexpression of the truncated hyperactive form of NtmybA2, but not its full-length form, preferentially up-regulated many G2/M phase-specific genes in BY-2 cells. We determined promoter sequences of several such up-regulated genes and showed that all contain MSA-like motifs in the proximal regions of their promoters. One of the up-regulated genes, NtE2C, encoding for cyclin-specific ubiquitin carrier proteins, contained a single functional MSA-like motif, which specifically controlled the expression of a reporter gene in the G2/M phase in BY-2 cells. Furthermore, a genomic footprint experiment showed that the MSA element in the NtE2C promoter interacted with nuclear proteins in vivo. Therefore, we propose that the transcription of many G2/M phase-specific genes in tobacco is positively regulated by NtmybA2, in most cases through direct binding to the MSA elements.

A homolog of human ski-interacting protein in rice positively regulates cell viability and stress tolerance

Abiotic stresses are major limiting factors for growth, development, and productivity of crop plants. Here, we report on OsSKIPa, a rice homolog of human Ski-interacting protein (SKIP) that can complement the lethal defect of the knockout mutant of SKIP homolog in yeast and positively modulate cell viability and stress tolerance of rice. Suppression of OsSKIPa in rice resulted in growth arrest and reduced cell viability. The expression OsSKIPa is induced by various abiotic stresses and phytohormone treatments. Transgenic rice overexpressing OsSKIPa exhibited significantly improved growth performance in the medium containing stress agents (abscisic acid, salt, or mannitol) and drought resistance at both the seedling and reproductive stages. The OsSKIPa-overexpressing rice showed significantly increased reactive oxygen species-scavenging ability and transcript levels of many stress-related genes, including SNAC1 and rice homologs of CBF2, PP2C, and RD22, under drought stress conditions. More than 30 OsSKIPa-interacting proteins were identified, but most of these proteins have no matches with the reported SKIP-interacting proteins in animals and yeast. Together, these data suggest that OsSKIPa has evolved a specific function in positive modulation of stress resistance through transcriptional regulation of diverse stress-related genes in rice.