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2019

Research paper highlight- Excised linear introns regulate growth in yeast

04 Mar 2019
Science Journal Club TORC1 introns yeast

Excised linear introns regulate growth in yeast.

Morgan et. al., Nature volume 565, pages606–611 (2019)

Introns are generally thought of as a waste by-product of RNA processing and molecules that are rapidly degraded soon after they are produced.They are assumed to be very short lived species- once the spliceosome joins the two exons, the spliceosome disassembles and the intron (lariat structure which looks like a lasso) is released. It is very quickly debranched by Dbr1, polyadenylated by the TRAMP complex and degraded by the nuclear exosome. Most introns don’t accumulate or seem to have any phenotype in log phase cultures in rich media.

The authors perform RNA seq in log phase vs saturated cultures, and show that some of the introns (their best examples are ECM33 and SAC6) are dramatically stablized in saturated cultures. In fact they show by RNA seq and Northern blots that the mature RNA for these is completely non-detectable in saturated cultures but the intron is really stable. They also show that the stability is intrinsic to the intron, and not dependent on the host gene, i.e, moving the intron into a completely different context (in a URA3 reporter), still phenocopies the intron stability phenotype in saturated cultures. Yet, the sequence does not show any conserved motif or RNA structural motif. They observe that the distance between the branch point and the 3’ splice site tends to be shorter for stable introns as opposed to introns that are not stable, and they nicely test that if they extend the length of this distance, the ECM33 intron is no longer stable or if they shorten the length in an otherwise non-stable intron of ACT1, the intron is now stable. They also attempt to understand how these introns are accumulating, and are only slightly successful in understanding it at all. The introns are stabilized after prolonged treatment (4h) with Rapamycin, DTT and tunicamycin but not short treatments (1h). The effect does not depend on a specific nutrient starvation but general secretory stress (not IRE1 dependent, so not UPR), nor mediated by Tor1 effectors, Sch9 or Tap42. So conclusions for these data are, not surprisingly, a bit hand-wavy.

They conclude by showing that accumulation of stable introns is advantageous to cellular fitness in stationary phase, but detrimental during rapid log phase growth. Their model is that TORC1 inhibition results in accumulation of these introns, these introns engage and titrate away the spliceosomal machinery, preventing them from too much splicing (esp ribosomal genes which are particularly enriched in introns), thus reducing the growth rate overall but allowing for better survival in limiting conditions. Overall, I think the observation of stable introns is quite striking, but it opens up so many questions that they were attempted to address in the work. For instance, what are the Tor1 effectors involved? Is the splicing machinery really getting titrated away? How are the stable introns specifically protected from degradation? And then, bringing into perspective that only 5% of yeast contain introns, as compared to roughly 95% of human genes. If this is indeed a conserved response, this should have a really important contribution to growth signaling in mammalian cells. But that will be for a later time.

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Happy New Year and check out the Ithaca Murals website

06 Jan 2019
public art murals Ithaca Links

Check out the Ithaca murals website if you haven’t visited it already. Caleb et al. have done a wonderful job putting together a murals map that you could refer to. Great idea for organizing a group mural walk/ bike ride! Ithaca murals website link

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2018

Research paper highlight- Translocon Declogger Ste24 Protects against IAPP Oligomer-Induced Proteotoxicity

14 Mar 2018
Science Journal Club protein quality control yeast

Translocon Declogger Ste24 Protects against IAPP Oligomer-Induced Proteotoxicity.

Kayatekin et. al., Cell 173, 1-12, March 2018

Islet amyloid polypeptide (IAPP) is a small peptide secreted by the pancreatic β islet cells. It is thought to regulate the function of the islet cells by inhibiting insulin secretion. It was discovered (and named) due to its tendency to aggregate into insoluble amyloid fibrils in patients with type 2 diabetes (T2D). Subsequent work showed that the cytotoxicity was contributed by smaller, intracellular oligomeric intermediates of IAPP, not the mature amyloid fibrils. Yet what aspect of cellular biology is impacted by these toxic oligomers has remained unclear.

Kayatekin and colleagues report that IAPP-induced proteotoxicity is in part contributed by the clogging of the endoplasmic reticulum (ER) translocon, and can be rescued by translocon associated transmembrane protease Ste24 in yeast or its human homolog ZMPSTE24. Ste24/ZMPSTE24 were recently discovered to directly interact with clogged translocons and cleave jammed proteins.

In order to understand IAPP toxicity, the authors took advantage of the cell death associated with the expression of an oligomeric version of the IAPP peptide in budding yeast, Saccharomyces cerevisiae. Using complementary genetic screens the authors found that functional Ste24 protease was critical for alleviating IAPP toxicity in yeast. The suppression by Ste24 was specific to IAPP and did not mitigate the toxicity caused by other aggregation prone proteins such as α-synuclein or TDP-43. Emphasizing the conservation of the declogging function, overexpression of the human homolog ZMPSTE24 in yeast lacking Ste24 could efficiently rescue IAPP toxicity. Using their yeast model for assaying declogging capability, the authors analyzed 111 ZMPSTE24 single nucleotide polymorphisms discovered in T2D patients and non-diabetic controls and found an enrichment of loss-of-function mutations among people with T2D (although somewhat mild).

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Check out Traffic Light Cook's cooking motivation

10 Feb 2018
Food Granola Links Personal

Garima Lal who writes this great blog on heathy eating and cooking practices, featured me on one of her ‘Cooking Motivation’ series! Check out the post here.

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2017

Site Launched!

03 Dec 2017
Jekyll Friday Theme Bootstrap 4 Markdown

Finally got around to putting this website together. It is powered by Jekyll using Friday theme and I can use Markdown to author my posts. It is styled almost entirely with Bootstrap 4. It actually is a lot easier than I thought it was going to be. I’ll write up my experience in more detail later with instructions and links that I found useful.

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