Reversible ubiquitylation in plant biology

Post-translational modification by ubiquitin plays a critical regulatory function in nearly all aspects of plant biology (Vierstra, 2009). Diverse conjugation enzymes attach monoubiquitin or polyubiquitin, with eight different linkages, as distinct signals to the regulatory and mechanistic components of various cellular processes. This ebook updates the functions, targets, and mechanisms of the conjugation components involved in the monoubiquitination of histones H2A and H2B and the polyubiquitination of all linkage types. Additionally, the roles and mechanisms of E3 ligases in biotic and abiotic stress responses and self-incompatibility (SI) and the regulation of cullin-based ligases (CRLs) by neddylation/deneddylation are updated. Finally, the functional roles of deubiquitination enzymes (DUBs) are reviewed together with a report on the biochemical and phylogenetic analyses of Arabidopsis OTU DUBs that support their functional differences. The topology of the polyubiquitin chain produced by the ubiquitin E3 ligase determines the fate of the conjugated substrate. Here, Walsh and Sadanandom review the functional roles of different ubiquitin linkages in Arabidopsis (Walsh and Sadanandom, 2014). The conjugation components involved in the assembly of the K11-, K48-, and K63-linkages are conserved in plants. The K48-linked polyubiquitination targets regulatory factors for proteasomal degradation and is involved in diverse plant functions. The K63 linkage-forming RING E3s, RGLG1/2, are involved in auxin signaling, where they regulate auxin levels by affecting endocytic turnover of the auxin efflux transporter PIN2. In addition, plants overexpressing the K63-linkage-specific E2, UBC13, or harboring rglg1/rglg2 double mutations exhibit bifurcated root hairs, showing an iron deficiency response. Two other reports also detail the importance of the K63 linkage in PIN2 turnover and iron deficiency response (Pan and Schmidt, 2014; Tomanov et al., 2014). While the Bachmair’s group extends his discussion on K63linkage in effector-triggered immunity, the second paper proposes that UBC13 and RGLGs are competed by DNA replication/repair under iron deficient conditions. Histone H2A and H2B monoubiquitination represents distinct epigenetic marks that repress or activate transcription. Feng and Shen discuss the Arabidopsis E2s, E3s, and DUBs responsible for H2B monoubiquitination, which is crucial for the transcriptional activation of key regulators controlling flowering, seed dormancy, clock, photomorphogenesis, and pathogen defense (Feng and Shen, 2014). The mechanisms underlying the targeting of H2B monoubiquitination enzymes and transcriptional activation are updated. Conversely, H2A monoubiquitination, mediated by the polycomb repressive complex PRC1, is a repressive chromatin mark that is important for stem apical meristem maintenance, embryonic cell fate determinacy, and seed germination. The maintenance of gene repression also requires another polycomb complex PRC2, which is responsible for the Lys 27 methylation of histone H3 (H3K27me2/3). Interestingly, findings that challenge the paradigm of PRC2 and PRC1 sequential recruitment are discussed. Duplan and Rivas update the functional roles of ubiquitin ligases in plant immune signaling (Duplan and Rivas, 2014). Ubiquitin E3 ligases are involved in pathogen perception, where they modulate pathogen-associated molecular pattern receptors at the plasma membrane or intracellular nucleotide-binding leucine-rich repeat-type receptors. These E3s are also involved in signaling responses downstream of pathogen perception through targeting and modulating vesicle trafficking components or transcription factors. Duplan and Rivas also discuss microbial effectors that target host E3s or act as E3s to counteract plant resistance. In parallel, Stone updates the functional roles of E3s in plant responses to abiotic stresses (Stone, 2014). Here E3s are involved in the suppression of stress response activators under non-stress conditions and the inactivation of response suppressors under stress. The roles of E3s in attenuating stress response signaling after stress relief are also discussed. Interestingly, this report outlines how multiple E3s and their targets are involved in the production and signaling of the stress-related hormone abscisic acid (ABA). Additionally, these reviews discuss the importance of the plant U-box armadillo repeat ligases (PUBARMs) in biotic and abiotic stress responses. Several PUB-ARMs target the plasma membrane or intracellular trafficking components. Moreover, Vogelmann et al. report that the Arabidopsis PUB-ARMs, SAUL1 (SENESCENCE-ASSOCIATED UBIQUITIN LIGASE 1) and its paralogs are plasma membrane (PM)-localized via their C-terminal ARM repeats (Vogelmann et al., 2014). PMlocalization is conserved for SAUL1-type PUB-ARM orthologs in land plants, suggesting functional importance; however, their membrane targets have not yet been identified. E3s are also involved in two major plant SI systems: S receptor kinase (SRK)-based and S-RNase-based. ARC1, a PUB-ARM E3, is critical for SRK-based SI in Brassicaceae plants. Indriolo and Goring provide updates on the conserved role of SRK-ARC1