Activation of gene expression by histone deubiquitinase OTLD1

ALOG/LSHs: a novel class of transcription factors that regulate plant growth and development

The ARABIDOPSIS LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 and rice G1/LIGHT-DEPENDENT SHORT HYPOCOTYLS (ALOG/LSH) group proteins are highly conserved across plant lineages from moss to higher flowering plants, suggesting their crucial role in the evolution and adaptation of land plants. The role of ALOG/LSH proteins is highly conserved in various developmental responses, such as vegetative and reproductive developmental programs. Their role in meristem identity, cotyledon development, seedling photomorphogenesis, and leaf and shoot development has been relatively well established. Moreover, several key pieces of evidence suggest their role in inflorescence architecture and flower development, including male and female reproductive organs and flower colouration. Recent research has started to explore their role in stress response. Functionally, ALOG/LSH proteins have been demonstrated to act as transcriptional regulators and are considered a newly emerging class of transcription factors in plants that regulate diverse developmental and physiological processes. This review aims to stimulate discussion about their role in plant development and as transcription factors. It also seeks to further unravel the underlying molecular mechanism by which they regulate growth and development throughout the plant lineage.

The Arabidopsis Deubiquitylase OTU5 Suppresses Flowering by Histone Modification-Mediated Activation of the Major Flowering Repressors FLC, MAF4, and MAF5

Distinct phylogeny and substrate specificities suggest that 12 Arabidopsis Ovarian Tumor domain-containing (OTU) deubiquitinases participate in conserved or plant-specific functions. The otu5-1 null mutant displayed a pleiotropic phenotype, including early flowering, mimicking that of mutants harboring defects in subunits (e.g., ARP6) of the SWR1 complex (SWR1c) involved in histone H2A.Z deposition. Transcriptome and RT-qPCR analyses suggest that downregulated FLC and MAF4-5 are responsible for the early flowering of otu5-1. qChIP analyses revealed a reduction and increase in activating and repressive histone marks, respectively, on FLC and MAF4-5 in otu5-1. Subcellular fractionation, GFP-fusion expression, and MNase treatment of chromatin showed that OTU5 is nucleus-enriched and chromatin-associated. Moreover, OTU5 was found to be associated with FLC and MAF4-5. The OTU5-associated protein complex(es) appears to be distinct from SWR1c, as the molecular weights of OTU5 complex(es) were unaltered in arp6-1 plants. Furthermore, the otu5-1 arp6-1 double mutant exhibited synergistic phenotypes, and H2A.Z levels on FLC/MAF4-5 were reduced in arp6-1 but not otu5-1. Our results support the proposition that Arabidopsis OTU5, acting independently of SWR1c, suppresses flowering by activating FLC and MAF4-5 through histone modification. Double-mutant analyses also indicate that OTU5 acts independently of the HUB1-mediated pathway, but it is partially required for FLC-mediated flowering suppression in autonomous pathway mutants and FRIGIDA-Col.

Plant deubiquitinases: from structure and activity to biological functions

This article attempts to provide comprehensive review of plant deubiquitinases, paying special attention to recent advances in their biochemical activities and biological functions. Proteins in eukaryotes are subjected to post-translational modifications, in which ubiquitination is regarded as a reversible process. Cellular deubiquitinases (DUBs) are a key component of the ubiquitin (Ub)-proteasome system responsible for cellular protein homeostasis. DUBs recycle Ub by hydrolyzing poly-Ub chains on target proteins, and maintain a balance of the cellular Ub pool. In addition, some DUBs prefer to cleave poly-Ub chains not linked through the conventional K48 residue, which often alter the substrate activity instead of its stability. In plants, all seven known DUB subfamilies have been identified, namely Ub-binding protease/Ub-specific protease (UBP/USP), Ub C-terminal hydrolase (UCH), Machado-Joseph domain-containing protease (MJD), ovarian-tumor domain-containing protease (OTU), zinc finger with UFM1-specific peptidase domain protease (ZUFSP), motif interacting with Ub-containing novel DUB family (MINDY), and JAB1/MPN/MOV34 protease (JAMM). This review focuses on recent advances in the structure, activity, and biological functions of plant DUBs, particularly in the model plant Arabidopsis.

Arabidopsis LSH10 transcription factor and OTLD1 histone deubiquitinase interact and transcriptionally regulate the same target genes

Histone ubiquitylation/deubiquitylation plays a major role in the epigenetic regulation of gene expression. In plants, OTLD1, a member of the ovarian tumor (OTU) deubiquitinase family, deubiquitylates histone 2B and represses the expression of genes involved in growth, cell expansion, and hormone signaling. OTLD1 lacks the intrinsic ability to bind DNA. How OTLD1, as well as most other known plant histone deubiquitinases, recognizes its target genes remains unknown. Here, we show that Arabidopsis transcription factor LSH10, a member of the ALOG protein family, interacts with OTLD1 in living plant cells. Loss-of-function LSH10 mutations relieve the OTLD1-promoted transcriptional repression of the target genes, resulting in their elevated expression, whereas recovery of the LSH10 function results in down-regulated transcription of the same genes. We show that LSH10 associates with the target gene chromatin as well as with DNA sequences in the promoter regions of the target genes. Furthermore, without LSH10, the degree of H2B monoubiquitylation in the target promoter chromatin increases. Hence, our data suggest that OTLD1-LSH10 acts as a co-repressor complex potentially representing a general mechanism for the specific function of plant histone deubiquitinases at their target chromatin.

Investigating Interactions Between Histone Modifying Enzymes and Transcription Factors in vivo by Fluorescence Resonance Energy Transfer

Epigenetic regulation of gene expression is commonly affected by histone modifying enzymes (HMEs) that generate heterochromatic or euchromatic histone marks for transcriptional repression or activation, respectively. HMEs are recruited to their target chromatin by transcription factors (TFs). Thus, detecting and characterizing direct interactions between HMEs and TFs are critical for understanding their function and specificity better. These studies would be more biologically relevant if performed in vivo within living tissues. Here, a protocol is described for visualizing interactions in plant leaves between a plant histone deubiquitinase and a plant transcription factor using fluorescence resonance energy transfer (FRET), which allows the detection of complexes between protein molecules that are within <10 nm from each other. Two variations of the FRET technique are presented: SE-FRET (sensitized emission) and AB-FRET (acceptor bleaching), in which the energy is transferred non-radiatively from the donor to the acceptor or emitted radiatively by the donor upon photobleaching of the acceptor. Both SE-FRET and AB-FRET approaches can be adapted easily to discover other interactions between other proteins in planta.

Reducing expression of TaOTUB1s decreases tiller number in wheat

Tiller number is an important agronomic trait that affects crop yield. The roles of OTUB1 in regulating tiller numbers in rice have been reported. However, the roles of OTUB1 in wheat remain elusive. In this study, TaOTUB1s were identified in wheat. TaOTUB1 proteins were localized in the nucleus and cytoplasm. Compared with wild-type Fielder, TaOTUB1-RNAi transgenic wheat plants had fewer tillers. Similar to OTUB1 in rice, the yeast double hybrid indicated that the TaOTUB1-A protein could interact with TaSPL17 and TaUBC13 proteins. The results of quantitative real-time polymerase chain reaction revealed that the expression levels of TaOTUB1s decreased while those of TaSPL17 significantly improved in TaOTUB1-RNAi lines. These findings suggested that TaOTUB1s influenced tiller number in wheat.

Submergence deactivates wound-induced plant defence against herbivores

Flooding is a common and critical disaster in agriculture, because it causes defects in plant growth and even crop loss. An increase in herbivore populations is often observed after floods, which leads to additional damage to the plants. Although molecular mechanisms underlying the plant responses to flooding have been identified, how plant defence systems are affected by flooding remains poorly understood. Herein, we show that submergence deactivates wound-induced defence against herbivore attack in Arabidopsis thaliana. Submergence rapidly suppressed the wound-induced expression of jasmonic acid (JA) biosynthesis genes, resulting in reduced JA accumulation. While plants exposed to hypoxia in argon gas exhibited similar reduced wound responses, the inhibitory effects were initiated after short-term submergence without signs for lack of oxygen. Instead, expression of ethylene-responsive genes was increased after short-term submergence. Blocking ethylene signalling by ein2-1 mutation partially restored suppressed expression of several wound-responsive genes by submergence. In addition, submergence rapidly removed active markers of histone modifications at a gene locus involved in JA biosynthesis. Our findings suggest that submergence inactivates defence systems of plants, which would explain the proliferation of herbivores after flooding.

Hyo-Jun Lee et al. show that submergence in Arabidopsis deactivates wound-induced defence against herbivore attack by suppressing the expression of jasmonic acid biosynthesis genes and increasing expression of ethylene-responsive genes. These results shed light on how flooding may impact plant defence systems.

Histone Deubiquitinase OTU1 Epigenetically Regulates DA1 and DA2, Which Control Arabidopsis Seed and Organ Size

Seeds are central to plant life cycle and to human nutrition, functioning as the major supplier of human population energy intake. To understand better the roles of enzymic writers and erasers of the epigenetic marks, in particular, histone ubiquitylation and the corresponding histone modifiers, involved in control of seed development, we identified the otubain-like cysteine protease OTU1 as a histone deubiquitinase involved in transcriptional repression of the DA1 and DA2 genes known to regulate seed and organ size in Arabidopsis. Loss-of-function mutants of OTU1 accumulate H2B monoubiquitylation and such euchromatic marks as H3 trimethylation and hyperacetylation in the DA1 and DA2 chromatin. These data advance our knowledge about epigenetic regulation of the DA1 and DA2 genes by recognizing OTU1 as a member of a putative repressor complex that negatively regulates their transcription.

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Histone ubiquitylation regulates transcription of DA1/DA2 that control seed/organ size

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OTU1 deubiquitinase is involved in deubiquitylation of the DA1/DA2 chromatin

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OTU1 acts as an epigenetic transcriptional repressor of the DA1/DA2 genes

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OTU1 is nucleocytoplasmic, indicating involvement in nuclear and cytoplasmic processes

Coordinate activation of a target gene by KDM1C histone demethylase and OTLD1 histone deubiquitinase in Arabidopsis

Potential functional coordination between histone deubiquitinases and histone lysine demethylases represents one of the least studied aspects of epigenetic control of transcriptional outcomes. Here, this question was addressed using Arabidopsis histone modification erasers deubiquitinase OTLD1 and demethylase KDM1C known to interact with each other in plant cells. Characterization of gain- and loss-of-function mutants of OTLD1 and KDM1C showed that both enzymes associate with the promoter chromatin of their target gene AN3 and function as coactivators of its expression. This transcriptional outcome was underlain by demethylation of the H3K9 repression mark, presumably by the KDM1C histone demethylase activity. Association of KDM1C and OTLD1 with the target chromatin was interdependent such that OTLD1 was not detected at the AN3 in the absence of KDM1C and KDM1C displayed a different and non-functional pattern of association in the absence of OTLD1. Thus, OTLD1 and KDM1C may crosstalk with each other to assemble a functional coactivator complex at the AN3 promoter chromatin and set the KDM1C specificity for the methylated H3K9 to determine the correct transcriptional outcome.

A Tangled Web: Origins of Reproductive Parasitism

While typically a flea parasite and opportunistic human pathogen, the presence of Rickettsia felis (strain LSU-Lb) in the non-blood-feeding, parthenogenetically reproducing booklouse, Liposcelis bostrychophila, provides a system to ascertain factors governing not only host transitions but also obligate reproductive parasitism (RP). Analysis of plasmid pLbAR, unique to R. felis str. LSU-Lb, revealed a toxin–antitoxin module with similar features to prophage-encoded toxin–antitoxin modules utilized by parasitic Wolbachia strains to induce another form of RP, cytoplasmic incompatibility, in their arthropod hosts. Curiously, multiple deubiquitinase and nuclease domains of the large (3,841 aa) pLbAR toxin, as well the entire antitoxin, facilitated the detection of an assortment of related proteins from diverse intracellular bacteria, including other reproductive parasites. Our description of these remarkable components of the intracellular mobilome, including their presence in certain arthropod genomes, lends insight on the evolution of RP, while invigorating research on parasite-mediated biocontrol of arthropod-borne viral and bacterial pathogens.

Plant Deubiquitinases and Their Role in the Control of Gene Expression Through Modification of Histones

Selective degradation of proteins in the cell occurs through ubiquitination, which consists of post-translational deposition of ubiquitin on proteins to target them for degradation by proteases. However, ubiquitination does not only impact on protein stability, but promotes changes in their functions. Whereas the deposition of ubiquitin has been amply studied and discussed, the antagonistic activity, deubiquitination, is just emerging and the full model and players involved in this mechanism are far from being completely understood. Nevertheless, it is the dynamic balance between ubiquitination and deubiquitination that is essential for the development and homeostasis of organisms. In this review, we present a detailed analysis of the members of the deubiquitinase (DUB) superfamily in plants and its division in different clades. We describe current knowledge in the molecular and functional characterisation of DUB proteins, focusing primarily on Arabidopsis thaliana. In addition, the striking function of the duality between ubiquitination and deubiquitination in the control of gene expression through the modification of chromatin is discussed and, using the available information of the activities of the DUB superfamily in yeast and animals as scaffold, we propose possible scenarios for the role of these proteins in plants.