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1.  Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness 
Nature chemical biology  2014;10(3):178-180.
Bioengineering advances have made it possible to fundamentally alter the genetic codes of organisms. However, the evolutionary consequences of expanding an organism's genetic code with a non-canonical amino acid are poorly understood. Here we show that bacteriophages evolved on a host that incorporates 3-iodotyrosine at the amber stop codon acquired neutral and beneficial mutations to this new amino acid in their proteins, demonstrating that an expanded genetic code increases evolvability.
doi:10.1038/nchembio.1450
PMCID: PMC3932624  PMID: 24487692
2.  Dynamic Reorganization of Metabolic Enzymes into Intracellular Bodies 
Both focused and large-scale cell biological and biochemical studies have revealed that hundreds of metabolic enzymes across diverse organisms form large intracellular bodies. These proteinaceous bodies range in form from fibers and intracellular foci—such as those formed by enzymes of nitrogen and carbon utilization and of nucleotide biosynthesis—to high-density packings inside bacterial microcompartments and eukaryotic microbodies. Although many enzymes clearly form functional mega-assemblies, it is not yet clear for many recently discovered cases whether they represent functional entities, storage bodies, or aggregates. In this article, we survey intracellular protein bodies formed by metabolic enzymes, asking when and why such bodies form and what their formation implies for the functionality—and dysfunctionality—of the enzymes that comprise them. The panoply of intracellular protein bodies also raises interesting questions regarding their evolution and maintenance within cells. We speculate on models for how such structures form in the first place and why they may be inevitable.
doi:10.1146/annurev-cellbio-101011-155841
PMCID: PMC4089986  PMID: 23057741
self-assembly; allosteric regulation; fibers; foci; storage bodies; aggregates; metabolic efficiency
3.  Transiently Transfected Purine Biosynthetic Enzymes Form Stress Bodies 
PLoS ONE  2013;8(2):e56203.
It has been hypothesized that components of enzymatic pathways might organize into intracellular assemblies to improve their catalytic efficiency or lead to coordinate regulation. Accordingly, de novo purine biosynthesis enzymes may form a purinosome in the absence of purines, and a punctate intracellular body has been identified as the purinosome. We investigated the mechanism by which human de novo purine biosynthetic enzymes might be organized into purinosomes, especially under differing cellular conditions. Irregardless of the activity of bodies formed by endogenous enzymes, we demonstrate that intracellular bodies formed by transiently transfected, fluorescently tagged human purine biosynthesis proteins are best explained as protein aggregation.
doi:10.1371/journal.pone.0056203
PMCID: PMC3566086  PMID: 23405267
4.  Evolutionarily Repurposed Networks Reveal the Well-Known Antifungal Drug Thiabendazole to Be a Novel Vascular Disrupting Agent 
PLoS Biology  2012;10(8):e1001379.
Analysis of a genetic module repurposed between yeast and vertebrates reveals that a common antifungal medication is also a potent vascular disrupting agent.
Studies in diverse organisms have revealed a surprising depth to the evolutionary conservation of genetic modules. For example, a systematic analysis of such conserved modules has recently shown that genes in yeast that maintain cell walls have been repurposed in vertebrates to regulate vein and artery growth. We reasoned that by analyzing this particular module, we might identify small molecules targeting the yeast pathway that also act as angiogenesis inhibitors suitable for chemotherapy. This insight led to the finding that thiabendazole, an orally available antifungal drug in clinical use for 40 years, also potently inhibits angiogenesis in animal models and in human cells. Moreover, in vivo time-lapse imaging revealed that thiabendazole reversibly disassembles newly established blood vessels, marking it as vascular disrupting agent (VDA) and thus as a potential complementary therapeutic for use in combination with current anti-angiogenic therapies. Importantly, we also show that thiabendazole slows tumor growth and decreases vascular density in preclinical fibrosarcoma xenografts. Thus, an exploration of the evolutionary repurposing of gene networks has led directly to the identification of a potential new therapeutic application for an inexpensive drug that is already approved for clinical use in humans.
Author Summary
Yeast cells and vertebrate blood vessels would not seem to have much in common. However, we have discovered that during the course of evolution, a group of proteins whose function in yeast is to maintain cell walls has found an alternative use in vertebrates regulating angiogenesis. This remarkable repurposing of the proteins during evolution led us to hypothesize that, despite the different functions of the proteins in humans compared to yeast, drugs that modulated the yeast pathway might also modulate angiogenesis in humans and in animal models. One compound seemed a particularly promising candidate for this sort of approach: thiabendazole (TBZ), which has been in clinical use as a systemic antifungal and deworming treatment for 40 years. Gratifyingly, our study shows that TBZ is indeed able to act as a vascular disrupting agent and an angiogenesis inhibitor. Notably, TBZ also slowed tumor growth and decreased vascular density in human tumors grafted into mice. TBZ’s historical safety data and low cost make it an outstanding candidate for translation to clinical use as a complement to current anti-angiogenic strategies for the treatment of cancer. Our work demonstrates how model organisms from distant branches of the evolutionary tree can be exploited to arrive at a promising new drug.
doi:10.1371/journal.pbio.1001379
PMCID: PMC3423972  PMID: 22927795
5.  A Synthetic Genetic Edge Detection Program 
Cell  2009;137(7):1272-1281.
Summary
Edge detection is a signal processing algorithm common in artificial intelligence and image recognition programs. We have constructed a genetically encoded edge detection algorithm that programs an isogenic community of E.coli to sense an image of light, communicate to identify the light-dark edges, and visually present the result of the computation. The algorithm is implemented using multiple genetic circuits. An engineered light sensor enables cells to distinguish between light and dark regions. In the dark, cells produce a diffusible chemical signal that diffuses into light regions. Genetic logic gates are used so that only cells that sense light and the diffusible signal produce a positive output. A mathematical model constructed from first principles and parameterized with experimental measurements of the component circuits predicts the performance of the complete program. Quantitatively accurate models will facilitate the engineering of more complex biological behaviors and inform bottom-up studies of natural genetic regulatory networks.
doi:10.1016/j.cell.2009.04.048
PMCID: PMC2775486  PMID: 19563759
6.  Systematic Definition of Protein Constituents along the Major Polarization Axis Reveals an Adaptive Reuse of the Polarization Machinery in Pheromone-Treated Budding Yeast 
Polarizing cells extensively restructure cellular components in a spatially and temporally coupled manner along the major axis of cellular extension. Budding yeast are a useful model of polarized growth, helping to define many molecular components of this conserved process. Besides budding, yeast cells also differentiate upon treatment with pheromone from the opposite mating type, forming a mating projection (the ‘shmoo’) by directional restructuring of the cytoskeleton, localized vesicular transport and overall reorganization of the cytosol. To characterize the proteomic localization changes accompanying polarized growth, we developed and implemented a novel cell microarray-based imaging assay for measuring the spatial redistribution of a large fraction of the yeast proteome, and applied this assay to identify proteins localized along the mating projection following pheromone treatment. We further trained a machine learning algorithm to refine the cell imaging screen, identifying additional shmoo-localized proteins. In all, we identified 74 proteins that specifically localize to the mating projection, including previously uncharacterized proteins (Ycr043c, Ydr348c, Yer071c, Ymr295c, and Yor304c-a) and known polarization complexes such as the exocyst. Functional analysis of these proteins, coupled with quantitative analysis of individual organelle movements during shmoo formation, suggests a model in which the basic machinery for cell polarization is generally conserved between processes forming the bud and the shmoo, with a distinct subset of proteins used only for shmoo formation. The net effect is a defined ordering of major organelles along the polarization axis, with specific proteins implicated at the proximal growth tip.
Upon sensing mating pheromone, budding yeast cells form a mating projection (the ‘shmoo’) that serves as a model for polarized cell growth, involving cytoskeletal/cytosolic restructuring and directed vesicular transport. We developed a cell microarray-based imaging assay for measuring localization of the yeast proteome during polarized growth. We find major organelles ordered along the polarization axis, localize 74 proteins to the growth tip, and observe adaptive reuse of general polarization machinery.
doi:10.1021/pr800524g
PMCID: PMC2651748  PMID: 19053807
Proteomics; polarized growth; subcellular localization; pheromone response; yeast

Results 1-6 (6)