Susan Lindquist

Bio: Susan Lindquist is an academic researcher from Massachusetts Institute of Technology. The author has contributed to research in topics: Heat shock protein & Saccharomyces cerevisiae. The author has an hindex of 147, co-authored 440 publications receiving 81067 citations. Previous affiliations of Susan Lindquist include University of Illinois at Chicago & Howard Hughes Medical Institute.

A heritable switch in carbon source utilization driven by an unusual yeast prion

Abstract: The stable inheritance of biological information and phenotype across generations is a fundamental property of living systems. Prions, self-perpetuating and heritable protein conformations that cause multiple phenotypes, represent an unusual mechanism of information transfer that occurs via protein instead of nucleic acid (Wickner 1994). Prion proteins can assume at least two conformations and each conformation alters protein function, resulting in different phenotypes (Wickner et al. 2004; Shorter and Lindquist 2005). When in the self-templating or prion conformation, prion proteins acquire characteristics normally restricted to nucleic acids. The first prion protein identified, the mammalian protein PrP, can behave as a transmissible pathogen and causes a neurodegenerative disease in its prion form (PrPSc) (Prusiner 1998). Prion proteins in fungi, which are functionally unrelated to PrP and to each other, act as non-Mendelian elements of inheritance by switching to the self-perpetuating, cytoplasmically transmissible prion conformation (Wickner 1994). Four prions have been extensively characterized in fungi: [PSI+], [URE3], [Het-s], and [RNQ+]. [PSI+] (Cox 1965) is the prion form of the translation termination factor Sup35, which causes nonsense suppression (Stansfield et al. 1995; Patino et al. 1996; Paushkin et al. 1996). [URE3] (Lacroute 1971) is an altered form (Wickner 1994) of the nitrogen catabolite repressor Ure2 (Courchesne and Magasanik 1988). [RNQ+] controls the ability of a cell to acquire other prions (Derkatch et al. 2000, 2001; Sondheimer and Lindquist 2000). [Het-s], found in Podospora anserina, causes heterokaryon incompatibility with certain mating partners (Rizet 1952; Coustou et al. 1997). These four fungal prions, as well as several recently identified prions ([SWI+], [MCA], [OCT+], and [MOT+]) (Du et al. 2008; Alberti et al. 2009; Nemecek et al. 2009; Patel et al. 2009), share key genetic and physical characteristics despite their disparate functions (Chien et al. 2004; Shorter and Lindquist 2005). Their phenotypes appear spontaneously at higher frequencies than those caused by genetic mutations. They are dominant, show non-Mendelian segregation following meiosis, and are also transmissible by cytoduction (cytoplasmic transfer). Physically, they form a self-templating amyloid conformation in the [PRION+] state. Furthermore, their inheritance is linked to the activities of chaperones, proteins that mediate conformational changes in other proteins. Transient changes in chaperone levels, particularly Hsp104, are sufficient to eliminate the prions permanently from cells. This occurs because chaperones alter the prion conformations and transmission to daughter cells. Once the prion template is gone, cells are “cured” of the elements (Uptain and Lindquist 2002; Shorter and Lindquist 2005). Another unusual feature is that transient overexpression of the prion protein causes permanent inheritance of the prion phenotype. This is because the protein∷protein interactions involved in prion formation are more likely to occur at higher protein concentrations (Chernoff et al. 1993; Ter-Avanesyan et al. 1993; Wickner 1994; Serio et al. 2000; Sondheimer and Lindquist 2000; Derkatch et al. 2001; Uptain and Lindquist 2002; Shorter and Lindquist 2005). The yeast prions also share a distinctive feature with mammalian prions: a strong transmission barrier across species. Even subtle differences in amino acid sequence can reduce the ability of prion proteins from one species to convert the homolog from other species, even though the homologous protein is itself capable of forming a prion on its own (Aguzzi et al. 2007; Chen et al. 2007). The precise nature of the mammalian prion template is not known, but all of the well-characterized fungal prions, as well as the newly discovered prions and prion domains (Du et al. 2008; Alberti et al. 2009; Nemecek et al. 2009; Patel et al. 2009), are self-templating amyloid amyloids. The simple and robust character of self-templating amyloids provides a compelling framework for protein-based inheritance (Glover et al. 1997; Shorter and Lindquist 2005). Indeed, in many cases the amyloid has been shown to be the sole determinant needed for prion formation: Recombinant amyloid fibers alone are sufficient to convert [prion−] cells to [PRION+] cells (Maddelein et al. 2002; King and Diaz-Avalos 2004; Tanaka et al. 2004; Brachmann et al. 2005; Patel and Liebman 2007; Alberti et al. 2009). Amyloid structure is therefore commonly held to be a critical feature of all naturally occurring systems for protein-based inheritance. Indeed, a recent genome-wide screen for new prion domains in yeast began by examining proteins likely to be amyloidogenic (Alberti et al. 2009). Here, we took a different approach. We searched the literature for Saccharomyces. cerevisiae phenotypes with prion-like inheritance patterns. One was described many years ago in a screen for cells with an alteration in carbon source utilization (Ball et al. 1976). The basis of the screen was the extreme preference of S. cerevisiae for glucose as a carbon source. In glucose media, cells repress genes necessary to process other carbon sources such as glycerol (Santangelo 2006). Glucosamine, a nonmetabolizable glucose mimetic, induces a similar repression. Therefore, yeast cells cannot use glycerol as a carbon source if even small amounts of glucosamine are present (Hockney and Freeman 1980; Nevado and Heredia 1996). Some cells spontaneously acquire the ability to use glycerol in the presence of glucosamine, presumably due to defects in glucose repression. Some of these exhibit dominant, non-Mendelian inheritance (Ball et al. 1976). Further, the phenotype is neither carried by the mitochondrial genome nor by a plasmid (Kunz and Ball 1977). Employing a variety of methods, we show here that this factor, [GAR+] (for “resistant to glucose-associated repression,” with capital letters indicating dominance and brackets indicating its non-Mendelian character), exhibits all of the genetic characteristics of a yeast prion, and we use a broad range of biochemical and genetic methods to identify proteins that play a key role in [GAR+] inheritance.

Chaperone-dependent amyloid assembly protects cells from prion toxicity.

Abstract: Protein conformational diseases are associated with the aberrant accumulation of amyloid protein aggregates, but whether amyloid formation is cytotoxic or protective is unclear. To address this issue, we investigated a normally benign amyloid formed by the yeast prion [RNQ+]. Surprisingly, modest overexpression of Rnq1 protein was deadly, but only when preexisting Rnq1 was in the [RNQ+] prion conformation. Molecular chaperones protect against protein aggregation diseases and are generally believed to do so by solubilizing their substrates. The Hsp40 chaperone, Sis1, suppressed Rnq1 proteotoxicity, but instead of blocking Rnq1 protein aggregation, it stimulated conversion of soluble Rnq1 to [RNQ+] amyloid. Furthermore, interference with Sis1-mediated [RNQ+] amyloid formation exacerbated Rnq1 toxicity. These and other data establish that even subtle changes in the folding homeostasis of an amyloidogenic protein can create a severe proteotoxic gain-of-function phenotype and that chaperone-mediated amyloid assembly can be cytoprotective. The possible relevance of these findings to other phenomena, including prion-driven neurodegenerative diseases and heterokaryon incompatibility in fungi, is discussed.

Is the major Drosophila heat shock protein present in cells that have not been heat shocked

Abstract: When eukaryotic cells are exposed to elevated temperatures they respond by vigorously synthesizing a small group of proteins called the heat shock proteins. An essential element in defining the role of these proteins is determining whether they are unique to a stressed state or are also found in healthy, rapidly growing cells at normal temperatures. To date, there have been conflicting reports concerning the major heat-induced protein of Drosophila cells, HSP 70. We report the development of monoclonal antibodies specific for this protein. These antibodies were used to assay HSP 70 in cells incubated under different culture conditions. The protein was detectable in cells maintained at normal temperatures, but only when immunological techniques were pushed to the limits of their sensitivity. To test for the possibility that these cells contain a reservoir of protein in a cryptic antigenic state (i.e., waiting posttranslational modification for use at high temperature), we treated cells with cycloheximide or actinomycin D immediately before heat shock. HSP 70 was not detected in these cells. Finally, we tested for the presence of a reservoir of inactive messages by using a high stringency hybridization of 32P-labeled cloned gene sequences to electrophoretically separated RNAs. Although HSP 70 mRNA was detectable in rapidly growing cells, it was present at less than 1/1,000th the level achieved after induction.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

Abstract: Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.

Genome engineering using the CRISPR-Cas9 system

Abstract: Targeted nucleases are powerful tools for mediating genome alteration with high precision. The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA. Here we describe a set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells, as well as generation of modified cell lines for downstream functional studies. To minimize off-target cleavage, we further describe a double-nicking strategy using the Cas9 nickase mutant with paired guide RNAs. This protocol provides experimentally derived guidelines for the selection of target sites, evaluation of cleavage efficiency and analysis of off-target activity. Beginning with target design, gene modifications can be achieved within as little as 1-2 weeks, and modified clonal cell lines can be derived within 2-3 weeks.

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

Abstract: We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted. Here the use of SnpEff is illustrated by annotating ~356,660 candidate SNPs in ~117 Mb unique sequences, representing a substitution rate of ~1/305 nucleotides, between the Drosophila melanogaster w1118; iso-2; iso-3 strain and the reference y1; cn1 bw1 sp1 strain. We show that ~15,842 SNPs are synonymous and ~4,467 SNPs are non-synonymous (N/S ~0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in...

Principles of Neural Science

Abstract: I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or