Showing papers by "Susan Lindquist published in 2016"

Luminidependens (LD) is an Arabidopsis protein with prion behavior

Abstract: Prion proteins provide a unique mode of biochemical memory through self-perpetuating changes in protein conformation and function. They have been studied in fungi and mammals, but not yet identified in plants. Using a computational model, we identified candidate prion domains (PrDs) in nearly 500 plant proteins. Plant flowering is of particular interest with respect to biological memory, because its regulation involves remembering and integrating previously experienced environmental conditions. We investigated the prion-forming capacity of three prion candidates involved in flowering using a yeast model, where prion attributes are well defined and readily tested. In yeast, prions heritably change protein functions by templating monomers into higher-order assemblies. For most yeast prions, the capacity to convert into a prion resides in a distinct prion domain. Thus, new prion-forming domains can be identified by functional complementation of a known prion domain. The prion-like domains (PrDs) of all three of the tested proteins formed higher-order oligomers. Uniquely, the Luminidependens PrD (LDPrD) fully replaced the prion-domain functions of a well-characterized yeast prion, Sup35. Our results suggest that prion-like conformational switches are evolutionarily conserved and might function in a wide variety of normal biological processes.

Inhibition of heat shock protein synthesis by heat-inducible antisense RNA (conditional mutation/gene-dosage analysis/feedback regulation/hsp7O promoter)

Abstract: We show that antisense RNAs transcribed from genes that are stably integrated into the genome can be used to inhibit the expression of an endogenous cellular gene. Drosophila tissue culture cells were stably transformed with a gene encoding a heat-inducible RNA complementary to the message for hsp26, one of the small heat shock proteins. These cells produced much less hsp26 after heat shock than did untransformed cells. The inhibition was highly specific: expression of the closely related heat shock proteins hsp22, hsp23, and hsp28 was unaffected. By varying the copy number of the antisense gene, the degree of inhibition was varied over a broad range. Reducing the rate of hsp26 synthesis did not appear to affect the synthesis of any other protein during either heat shock or recovery.

An inter-species protein-protein interaction network across vast evolutionary distance.

Abstract: In cellular systems, biophysical interactions between macromolecules underlie a complex web of functional interactions. How biophysical and functional networks are coordinated, whether all biophysical interactions correspond to functional interactions, and how such biophysical-versus-functional network coordination is shaped by evolutionary forces are all largely unanswered questions. Here, we investigate these questions using an "inter-interactome" approach. We systematically probed the yeast and human proteomes for interactions between proteins from these two species and functionally characterized the resulting inter-interactome network. After a billion years of evolutionary divergence, the yeast and human proteomes are still capable of forming a biophysical network with properties that resemble those of intra-species networks. Although substantially reduced relative to intra-species networks, the levels of functional overlap in the yeast-human inter-interactome network uncover significant remnants of co-functionality widely preserved in the two proteomes beyond human-yeast homologs. Our data support evolutionary selection against biophysical interactions between proteins with little or no co-functionality. Such non-functional interactions, however, represent a reservoir from which nascent functional interactions may arise.

A Fungal-Selective Cytochrome bc₁ Inhibitor Impairs Virulence and Prevents the Evolution of Drug Resistance

Abstract: To cause disease, a microbial pathogen must adapt to the challenges of its host environment. The leading fungal pathogen Candida albicans colonizes nutrient-poor bodily niches, withstands attack from the immune system, and tolerates treatment with azole antifungals, often evolving resistance. To discover agents that block these adaptive strategies, we screened 300,000 compounds for inhibition of azole tolerance in a drug-resistant Candida isolate. We identified a novel indazole derivative that converts azoles from fungistatic to fungicidal drugs by selective inhibition of mitochondrial cytochrome bc1. We synthesized 103 analogs to optimize potency (half maximal inhibitory concentration 0.4 ?M) and fungal selectivity (28-fold over human). In addition to reducing azole resistance, targeting cytochrome bc1 prevents C. albicans from adapting to the nutrient-deprived macrophage phagosome and greatly curtails its virulence in mice. Inhibiting mitochondrial respiration and restricting metabolic flexibility with this synthetically tractable chemotype provides an attractive therapeutic strategy to limit both fungal virulence and drug resistance.

An inter-species protein-protein interaction network across vast evolutionary distance

Abstract: In cellular systems, biophysical interactions between macromolecules underlie a complex web of functional interactions. How biophysical and functional networks are coordinated, whether all biophysical interactions correspond to functional interactions, and how such biophysical-versus-functional network coordination is shaped by evolutionary forces are all largely unanswered questions. Here, we investigate these questions using an "inter-interactome" approach. We systematically probed the yeast and human proteomes for interactions between proteins from these two species and functionally characterized the resulting inter-interactome network. After a billion years of evolutionary divergence, the yeast and human proteomes are still capable of forming a biophysical network with properties that resemble those of intra-species networks. Although substantially reduced relative to intra-species networks, the levels of functional overlap in the yeast-human inter-interactome network uncover significant remnants of co-functionality widely preserved in the two proteomes beyond human-yeast homologs. Our data support evolutionary selection against biophysical interactions between proteins with little or no co-functionality. Such non-functional interactions, however, represent a reservoir from which nascent functional interactions may arise.

Scarless Gene Tagging with One-Step Transformation and Two-Step Selection in Saccharomyces cerevisiae and Schizosaccharomyces pombe.

Abstract: Gene tagging with fluorescent proteins is commonly applied to investigate the localization and dynamics of proteins in their cellular environment. Ideally, a fluorescent tag is genetically inserted at the endogenous locus at the N- or C- terminus of the gene of interest without disrupting regulatory sequences including the 5’ and 3’ untranslated region (UTR) and without introducing any extraneous unwanted “scar” sequences, which may create unpredictable transcriptional or translational effects. We present a reliable, low-cost, and highly efficient method for the construction of such scarless C-terminal and N-terminal fusions with fluorescent proteins in yeast. The method relies on sequential positive and negative selection and uses an integration cassette with long flanking regions, which is assembled by two-step PCR, to increase the homologous recombination frequency. The method also enables scarless tagging of essential genes with no need for a complementing plasmid. To further ease high-throughput strain construction, we have computationally automated design of the primers, applied the primer design code to all open reading frames (ORFs) of the budding yeast Saccharomyces cerevisiae (S. cerevisiae) and the fission yeast Schizosaccharomyces pombe (S. pombe), and provide here the computed sequences. To illustrate the scarless N- and C-terminal gene tagging methods in S. cerevisiae, we tagged various genes including the E3 ubiquitin ligase RSP5, the proteasome subunit PRE1, and the eleven Rab GTPases with yeast codon-optimized mNeonGreen or mCherry; several of these represent essential genes. We also implemented the scarless C-terminal gene tagging method in the distantly related organism S. pombe using kanMX6 and HSV1tk as positive and negative selection markers, respectively, as well as ura4. The scarless gene tagging methods presented here are widely applicable to visualize and investigate the functional roles of proteins in living cells.

Methods and compositions relating to proteasome inhibitor resistance

Abstract: In some aspects, the disclosure provides methods of modulating the level of proteasome inhibitor resistance of a cell, the methods comprising manipulating the level of expression or activity of a subunit of the 19S proteasome in the cell. In some aspects, cells in which the level of a 19S subunit is modulated, e.g., reduced, are provided. In some aspects, methods of identifying agents that reduce proteasome inhibitor resistance are provided. In some aspects, methods of classifying cancers according to predicted proteasome inhibitor resistance are provided. In some aspects, methods of killing or inhibiting proliferation of cancer cells, e.g., proteasome inhibitor resistant cancer cells, are provided. In some aspects, methods of treating cancer, e.g., proteasome inhibitor resistant cancer, are provided.

Method of treating neurodegenerative disorders by rescuing alpha-synuclein toxicity

Abstract: A method for treating neurodegenerative disease in a subject in need thereof by administering to the subject an effective amount of a Nedd4 activator as described herein.

Analysis of the AAA sensor-2 ATPase domain of Hsp104 wi fluorescent probe of nucleoti

Abstract: Hsp104 from Saccharomyces cerevisiae is a hexameric protein with pc two AAA ATPase domains (N- and C-terminal nucleotide-binding 18 domains NBD1 and NBD2, respectively) per monomer. Our previous hy analysis of the Hsp104 ATP hydrolysis cycle revealed that NBD1 and arn NBD2 have very different catalytic properties, but each shows posi- fr( tive cooperativity in hydrolysis. There is also communication between m; the two domains, in that ATP hydrolysis at NBD1 depends on the ne nucleotide that is bound to NBD2. Here, we extend our understanding of the Hsp104 ATP hydrolysis cycle through mutagenesis of the AAA lit sensor-2 motif in NBD2. To do so, we took advantage of the lack of ex tryptophan residues in Hsp104 to place a single tryptophan in the m; C-terminal domain (Y819W). The Y819W substitution has no signifi- A. cant effects on folding stability of the C-terminal domain or on ATP wi hydrolysis by NBD1 or NBD2. The fluorescence of this tryptophan de changes in response to ATP and ADP binding, allowing the Kd and Hill 22 coefficient to be determined for each nucleotide. By using this Csite-specific probe of binding, we analyze the effect of mutating the to conserved arginine residue in the sensor-2 motif in Hsp104 NBD2. An pr R826M mutation causes nearly equal decreases in affinity of NBD2 for pr both ATP and ADP, indicating that at this site, the sensor-2 provides co binding energy, but does not act to sense the difference between ac these nucleotides. In addition, the rate of ATP hydrolysis at NBD1 is as decreased by the R826M mutation, providing further evidence for na interdomain communication in the Hsp104 ATP hydrolysis cycle. th