The tumor suppressor p53, well known to shield cells from DNA damage, may also protect against malformed proteins, according to a paper in the April 2 PLoS Biology. First author Goran Periz and colleagues at Johns Hopkins University in Baltimore discovered this new proteostasis mechanism in a screen for mutations that protect round worms from toxic protein aggregates. The authors have not yet fleshed out details of the system, but it appears to operate in fruit flies and people as well.
Periz and senior author Jiou Wang were searching for genes involved in protein quality control. For their initial screen, they chose Caenorhabditis elegans expressing a mutant version of the amyotrophic lateral sclerosis gene superoxide dismutase 1 (SOD1). They treated the animals with the mutagen ethyl methanesulfonate to create random mutations. Nematodes toting mSOD1 can barely move, allowing Periz to screen for wriggly worms likely to have mutations that partially saved them from this toxicity.
Strain M1 was quite squirmy. The Wang lab quantifies this by placing a worm in a droplet of liquid medium and counting its “thrashings,” or full-body twists. Control worms with wild-type SOD1 thrash about 60 times per minute and those with mutant SOD1 about five times. M1 pulled off approximately 45. When Periz sequenced M1’s genome, he found not one but two mutations. One was a truncation to a ubiquitin ligase called ubiquitin fusion degradation 2 (ufd-2). The other was a substitution, glutamine for arginine, in a conserved residue of the demethylase known as suppressor of presenilin 5 (spr-5). Spr-5 got its name because mutations in the gene suppress an egg-laying phenotype due to mutations in a worm presenilin (Elmer et al., 2002).
Wait—presenilin? The fact that presenilins are involved in Alzheimer’s is likely coincidental to his work, Periz said. By themselves, the mutations in ufd-2 or spr-5 made only a subtle functional difference, enabling five to10 thrashes per minute, but together they restored motility to the mSOD1 mutants. They also diminished protein levels of mutant SOD1 in the animals’ neurons (see image above). Periz and Wang christened the pair SUNS, for “spr-5- and ufd-2-dependent neurodegeneration suppressor.”
Was SUNS good only for nematodes and mutant SOD1, or more generally? Periz tested other proteins that form toxic inclusions. In worm neurons, mutant SUNS diminished the amount of aggregated TDP-43 and a peptide harboring an expanded polyglutamine repeat. Next, Periz tested SUNS in Drosophila expressing mutant TDP-43 or FUS. These ALS-linked mutations cause neurodegeneration in the fly eye, but knocking down the Drosophila homologs of ufd-2 and spr-5 rescued the eye.
The human homologs of ufd-2 and spr-5 are ubiquitination factor E4B (UBE4B) and lysine-specific demethylase 1A (LSD1), respectively. In human embryonic kidney cell HEK293T cultures expressing mutant SOD1, or mutant TDP-43, knocking down both UBE4B and LSD1 via RNA interference lessened the amount of mutant protein present by 90 percent. “We now know it is not just C. elegans; this whole pathway operates elsewhere, too,” Periz concluded.
In analyzing the transcriptome of the HEK293T cells lacking UBE4B and LSD1, Periz was struck to see a pattern of gene expression similar to that induced by the transcription factor p53. In fact, LSD1 was already known to demethylate p53, deactivating it (Huang et al., 2007). Moreover, UBE4B is required for the ubiquitination and degradation of p53 (Wu and Leng, 2011). Together, these data suggested to Periz that p53 mediates the effects of the SUNS mutations. Supporting this idea, he found that p53 was activated in the SUNS cultures.
“We think p53 is emerging as a potential regulator of both genotoxic and proteotoxic stress,” Periz concluded. It seems to be part of a proteostasis pathway, in addition to known protein-repair processes such as the heat shock response. However, Ralph Nixon of the Nathan Kline Institute in Orangeburg, New York, wondered if Periz’s new pathway might overlap with the unfolded protein response (UPR) mechanism. It might be a previously unrecognized branch of the UPR, rather than a totally new pathway, he speculated.
Periz is now investigating whether cells stressed by aggregating proteins upregulate p53, and what other molecules might participate in the cascade leading from UBE4B and LSD1 to p53 activation and degradation of misfolded proteins. Brian Kraemer of the University of Washington in Seattle, who was not involved in the study, added that he would be interested to know which of p53’s many target genes participate in protein degradation. “We may see more to come on this particular pathway and its importance in neurodegenerative disease,” Kraemer predicted. There have been hints that p53 might be linked to Alzheimer’s and related diseases (see Jun 2006 news; Feb 2013 news; Jul 2005 news).
Periz suggested that p53 could protect cells from toxic proteins, and plans to test p53-activating drugs in mouse models. In addition, scientists are investigating p53 gene therapy to treat cancer, since p53 promotes DNA repair (Chen et al., 2014).
“The study does bring to light a target that seems to be ‘druggable,’” commented David Borchelt of the University of Florida in Gainesville, who trained Wang but was not involved in the current research. “The question is whether p53 is too scary of a drug target to be brought to bear for disease,” he added. Besides suppressing tumors, p53 also promotes apoptosis in cells overloaded with DNA damage.
Periz G, Lu J, Zhang T, Kankel MW, Jablonski AM, Kalb R, McCampbell A, Wang J. Regulation of Protein Quality Control by UBE4B and LSD1 through P53-Mediated Transcription. PLoS Biol. 2015 Apr;13(4):e1002114. Epub 2015 Apr 2. [PubMed].
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