Proteasomes are the main proteases responsible for cytosolic protein degradation and the production of major histocompatibility complex class I ligands. Incorporation of the interferon γ–inducible subunits low molecular weight protein (LMP)-2, LMP-7, and multicatalytic endopeptidase complex–like (MECL)-1 leads to the formation of immunoproteasomes which have been associated with more efficient class I antigen processing. Although differences in cleavage specificities of constitutive and immunoproteasomes have been observed frequently, cleavage motifs have not been described previously.We now report that cells expressing immunoproteasomes display a different peptide repertoire changing the overall cytotoxic T cell–specificity as indicated by the observation that LMP-7−/− mice react against cells of LMP-7 wild-type mice. Moreover, using the 436 amino acid protein enolase-1 as an unmodified model substrate in combination with a quantitative approach, we analyzed a large collection of peptides generated by either set of proteasomes. Inspection of the amino acids flanking proteasomal cleavage sites allowed the description of two different cleavage motifs. These motifs finally explain recent findings describing differential processing of epitopes by constitutive and immunoproteasomes and are important to the understanding of peripheral T cell tolerization/activation as well as for effective vaccine development.

Interaction between auxin and auxin-induced ethylene was suggested in previous work to up-regulate abscisic acid (ABA) biosynthesis in cleavers (Galium aparine) through stimulated cleavage of xanthophylls to xanthoxin, catalysed by 9-cis-epoxycarotenoid dioxygenase (NCED). Here, the effects of auxin on NCED gene expression were studied in relation to changes in ethylene synthesis and ABA levels. A gene from G. aparine shoot tissue was cloned based on sequence similarity to cloned NCED genes from tomato (LeNCED1), potato, Phaseolus, and Arabidopsis. When the roots of G. aparine plants were treated with 0.5 mM indole-3-acetic acid (IAA), IAA concentrations increased from 0.2 microM to 65 microM IAA in the shoot tissue after 3 h. Transient increases in GaNCED1 mRNA levels were detectable as early as 1 h after treatment and reached maximum values of 40-fold, relative to the control, after 3 h. Increases in GaNCED1 mRNA preceded increases in 1-aminocyclopropane-1-carboxylic acid and ethylene. Levels of ABA began to increase more slowly and, significantly, with a lag phase of 2 h, and reached levels 24-fold higher than those in controls after 24 h. GaNCED1 gene expression was also stimulated by auxin herbicides. The ethylene-releasing compound ethephon induced GaNCED1 transcript levels only moderately. In accordance with this, aminoethoxyvinylglycine and cobalt ions, which inhibit ethylene synthesis, only slightly affected the increase in GaNCED1 transcript levels by IAA. However, both ethylene inhibitors decreased IAA-induced ABA accumulation by up to 70%. This suggests that auxin and auxin-induced ethylene are involved in ABA accumulation. While auxin is the primary trigger for NCED gene expression, ethylene appears to enhance ABA biosynthesis, possibly by up-regulation of NCED activity post-transcriptionally.

Spinocerebellar ataxia type 3 (SCA3) is caused by an expanded polyglutamine stretch in ataxin-3. While wild-type ataxin-3 has important functions, e.g., as a deubiquitinase, downregulation of mutant ataxin-3 is likely to slow down the course of this fatal disease. We established a screening platform with human neurons of patients and controls derived from induced pluripotent stem cells to test antisense oligonucleotides (ASOs) for their effects on ataxin-3 expression. We identified an ASO that suppressed mutant and wild-type ataxin-3 levels by >90% after a singular treatment. Next, we screened pairs of ASOs designed to selectively target the mutant or the wild-type allele by taking advantage of a SNP (c.987G > C) in ATXN3 that is present in most SCA3 patients. We found ASOmut4 to reduce levels of mutant ataxin-3 by 80% after 10 days while leaving expression of wild-type ataxin-3 largely unaffected. In a long-term study we proved this effect to last for about 4 weeks after a single treatment without signs of neurotoxicity. This study provides proof of principle that allele-specific lowering of poly(Q)-expanded ataxin-3 by selective ASOs is feasible and long lasting, with sparing of wild-type ataxin-3 expression in a human cell culture model that is genetically identical to SCA3 patients.