The ubiquitin system affects agronomic plant traits

Abstract

In a single vascular plant species, the ubiquitin system consists of thousands of different proteins involved in attaching ubiquitin to substrates, recognizing or processing ubiquitinated proteins, or constituting or regulating the 26S proteasome. The ubiquitin system affects plant health, reproduction, and responses to the environment, processes that impact important agronomic traits. Here we summarize three agronomic traits influenced by ubiquitination: induction of flowering, seed size, and pathogen responses. Specifically, we review how the ubiquitin system affects expression of genes or abundance of proteins important for determining when a plant flowers (focusing on FLOWERING LOCUS C, FRIGIDA, and CONSTANS), highlight some recent studies on how seed size is affected by the ubiquitin system, and discuss how the ubiquitin system affects proteins involved in pathogen or effector recognition with details of recent studies on FLAGELLIN SENSING 2 and SUPPRESSOR OF NPR CONSTITUTIVE 1, respectively, as examples. Finally, we discuss the effects of pathogen-derived proteins on plant host ubiquitin system proteins. Further understanding of the molecular basis of the above processes could identify possible genes for modification or selection for crop improvement.

Keywords: E3 ligase; E3 ubiquitin ligase; deubiquitylation (deubiquitination); disease resistance; flowering; pathogen response; plant; plant biochemistry; plant defense; plant physiology; protein degradation; protein modification; protein stability; seed; ubiquitin; ubiquitin-conjugating enzyme (E2 enzyme).

Figure 1.

The ubiquitin system. A–C, summary of components of the ubiquitin system involved in attaching ubiquitin (Ub) to substrate proteins (the writers) (A), binding to and targeting the ubiquitinated substrate to a new biological fate (the readers) (B), and removing ubiquitin, either through deubiquitination by DUBs independent of degradation or coordinated with degradation of the substrate by the proteasome (the erasers) (C). Terms are from Komander and Rape (2). The diagram in A depicts ubiquitination of a substrate protein by E1, E2, and E3 enzymes. Diagrams in B depict two examples of ubiquitin-binding proteins (represented in green): a ubiquitin-dependent histone methyltransferase (top) and the involvement of a ubiquitin-binding protein in endocytosis (bottom). Histones and DNA represented by gray balls and rope, respectively. Me, methylation. Diagrams in C depict histone deubiquitination by a ubiquitin-specific protease (top) and proteasomal removal of ubiquitins from a proteolytic substrate (bottom).

Figure 2.

The ubiquitin system affects induction of flowering by regulating FLC and FT expression and CO protein degradation. A, the RING-type E3 ligases HUB1 and HUB2 act with the ubiquitin (Ub)-conjugating enzymes UBC1 and UBC2 to monoubiquitinate histone H2B on chromatin. H2B ubiquitination might promote activity of methyltransferases such as ATX1 and ATXR7, which interact with FLOWERING LOCUS C (FLC) chromatin and add methylation (Me) marks on histone H3. FLC is a negative regulator of flowering through repressing FLOWERING LOCUS T (FT) expression, a positive regulator of flowering. Deubiquitination by the ubiquitin-specific protease UBP26 is necessary for appropriate FLC expression. B, the CUL4-DDB1^MSI4 E3 ligase complex associates with polycomb repressive complex 2 (PRC2), containing the methyltransferase CURLY LEAF (CLF), and reduces mRNA of FLC and FT. CUL4-dependent ligases may affect expression of other genes, including CONSTANS (CO) (see “Multiple E3 ligases regulate CONSTANS protein abundance”). C, FRIGIDA acts as a scaffold in a large complex that promotes FLC expression. After exposure to cold temperatures, a CUL3 E3 ligase complex promotes degradation of FRIGIDA protein. D, the E3 ligase COP1 associates with SPA proteins to promote CONSTANS (CO) protein degradation in the dark. E, the blue light receptor CRY2 interacts with SPA and COP1 and inhibits CO degradation by competing with COP1 substrates. In addition, CO protein is stabilized by the F-box protein FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1). FKF1 is an adapter protein in an SCF E3 ligase complex and acts as a blue light receptor. F, the E3 ligase HOS1 promotes degradation of CO protein in a red light–dependent manner.

Figure 3.

The ubiquitin system affects seed size. Some of the pathways through which the ubiquitin system regulates seed size in Arabidopsis and several crop species. A, in Arabidopsis, the E3 ligase UPL3 negatively regulates seed size and lipid content. It targets the LEC2 protein for degradation. Similarly, in B. napus, UPL3 negatively regulates seed size and targets the LEC2 protein for degradation. B, top, recent studies in Arabidopsis showed that the ubiquitin-specific proteases UBP12 and UBP13 deubiquitinate the ubiquitin receptors DA1, DAR1, and DAR2, reducing their peptidase activity, and that the histone deubiquitinase OTU1 likely decreases expression of DA1 and the E3 ligase DA2. Wheat DA1 restricts cell proliferation and interacts with the E3 ligase GW2, which is orthologous to Arabidopsis DA2. A recent study found that the ubiquitin-specific protease OsUBP15 promotes large grain size in rice and interacts with rice DA1. Bottom, the effect of ubquitination/deubiquitination on DA1/DAR1/DAR2 activity is depicted. C, in the legume M. truncatula, SLB1 is a component of an E3 ligase complex that was recently shown to modulate the stability of the transcription factor BS1. Also shown are orthologous proteins in Arabidopsis. The F-box protein SAP is an SLB1 ortholog, and the PPD transcription factors are BS1 orthologs.

Figure 4.

The ubiquitin system regulates the FLS2 receptor complex. A, in the absence of the FLS2 ligand, BIK1 interacts with both BAK1 and FLS2. BAK1 stably interacts with PUB12 and PUB13 in the absence of ligand but has reduced activity prior to autophosphorylation, and BAK1 is not a target of PUB25/26. PUB25 and PUB26 target underphosphorylated (inactive) BIK1, and this results in its degradation. B, FLS2 extracellular binding to a peptide derived from bacterial flagellin, mimicked in laboratory studies by a conserved 22-amino acid region called flg22, facilitates FLS2 interaction with BAK1 and PUB12/13 and results in multiple phosphorylation events. PUB12/13 activity increases after phosphorylation by BAK1, and PUB12/13 ubiquitinate FLS2, leading to its endocytosis and degradation. Phosphorylation of PUB25 and PUB26 increases their activity, resulting in increased ubiquitination and degradation of inactive BIK1. Phosphorylated (active) BIK1 is monoubiquitinated by RHA3A and RHA3B, resulting in BIK1 endocytosis. C, two examples of how pathogen effectors mimic or interfere with the host ubiquitin system. The tomato pathogen P. syringae pv. tomato DC3000 injects an effector, the E3 ligase AvrPtoB, into the plant cell to suppress the plant defense of programmed cell death. AvrPtoB substrates include FLS2, the related PRR EFR, the exocyst subunit EXO70B1, and the Fen kinase. The pathogen P. infestans produces the effector AVR3a, which suppresses cell death defense responses by affecting activity of the endogenous E3 ligase CMPG1.