Involvement of KDM1C histone demethylase–OTLD1 otubain-like histone deubiquitinase complexes in plant gene repression

Abstract

Covalent modifications of histones, such as acetylation, methylation and ubiquitination, are central for regulation of gene expression. Heterochromatic gene silencing, for example, is associated with hypoacetylation, methylation and demethylation, and deubiquitination of specific amino acid residues in histone molecules. Many of these changes can be effected by histone-modifying repressor complexes that include histone lysine demethylases, such as KDM1 in animals and KDM1C in plants. However, whereas KDM1-containing repressor complexes have been implicated in histone demethylation, methylation and deacetylation, whether or not they can also mediate histone deubiquitination remains unknown. We identify an Arabidopsis otubain-like deubiquitinase OTLD1 which directly interacts with the Arabidopsis KDM1C in planta, and use one target gene to exemplify that both OTLD1 and KDM1C are involved in transcriptional gene repression via histone deubiquitination and demethylation. We also show that OTLD1 binds plant chromatin and has enzymatic histone deubiquitinase activity, specific for the H2B histone. Thus, we suggest that, during gene repression, lysine demethylases can directly interact and function in a protein complex with histone deubiquitinases.otubain superfamily | repression of gene expression | bimolecular fluorescence complementation C ovalent modifications of histones are critical for eukaryotic DNA metabolism, determining structure and gene expression activity of the corresponding chromosomal region (1-5). They govern chromatin folding, which in turn determines cell fate. Proteins containing the hallmark SWIRM (Swi3p, Rsc8p, Moira) (6) and polyamine oxidase (PAO) domains, including histone lysine demethylase LSD1/KDM1 in animals (7) and LDL1/KDM1C in plants (8), are frequently found in chromatin-associated transcriptional repressor enzymatic complexes (9) and play a key role in regulation of gene expression (10) during such diverse developmental events as acquisition of neuronspecific traits in mammals (11, 12) and determination of flower timing in plants (8). One of the major effects of KDM1-containing complexes is transcriptional gene silencing through posttranslational modifications of the core histones. Silenced heterochromatic loci are distinguished by general histone hypoacetylation, methylation on lysines 9 (K9) and 27 (K27) (1, 13, 14) and demethylation on lysine 4 (K4) (7) and lysine 36 (15) of histone H3, and recently described deubiquitination of histones H2A and H2B in animals and yeast (16-19) and H2B in plants (20). Although KDM1-containing repressor complexes have been implicated in histone methylation, demethylation, and deacetylation, whether or not they can also mediate histone deubiquitination is enigmatic.Monoubiquitination of histone H2B, in both animals and plants, is typically associated with transcriptional activation, and amino acid sequences adjacent to the H2B ubiquitination sites are remarkably conserved between various eukaryotes (20). For instance, ubiquitinated H2B is enriched ar...

Sugarcane genes differentially expressed in response to Puccinia melanocephala infection: identification and transcript profiling

“…Little is known about OTU-like proteases in plants. An Arabidopsis otubain-like histone deubiquitinase involved in chromatin modification and regulation of plant gene expression has recently been described (Krichevsky et al 2011). Sugarcane perceives P. melanocephala and triggers defense An important step in plant defense response to biotic stress is pathogen perception and signal transduction.…”

Deubiquitinating Enzyme OTU5 Contributes to DNA Methylation Patterns and Is Critical for Phosphate Nutrition Signals

“…DUBs are involved in important biological processes such as proofreading ubiquitin-protein conjugates, chromatin remodeling, transcriptional regulation, cell cycle regulation, DNA repair, and signal transduction (ReyesTurcu et al, 2009). Although clear roles in cellular processes have been defined for OVARIAN TUMOR DOMAIN-CONTAINING DEUBIQUITINATING ENZYME (OTU) deubiquitinases in Drosophila melanogaster, Saccharomyces cerevisiae, and Homo sapiens (King and Storto, 1988;Steinhauer et al, 1989;Lee et al, 2000;Stanisi c et al, 2009;Nakada et al, 2010), in plants, a biological role has only been described for OTLD1, which functions as a direct interactor of the histone Lys demethylase complex KDM1C to suppress the expression of a subset of genes via deubiquitination of histone H2B (Krichevsky et al, 2011).…”

Epigenetic interplay of histone modifications and DNA methylation mediated by HDA6

“…1). More recently, OTU6 was found to directly interact with the histone lysine demethylase LDL1/ KDM1C in planta, 25 suggesting that regulatory crosstalk between histone demethylation and deubiquitination through the direct interaction between LDL1/KDM1C and OTU6. Taken together, data described above indicate that the crosstalk among different epigenetic modifications could be mediated by the interaction of various histone modification proteins and complexes.…”