101
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Wawrzynow B, Zylicz A, Zylicz M. Chaperoning the guardian of the genome. The two-faced role of molecular chaperones in p53 tumor suppressor action. Biochim Biophys Acta Rev Cancer 2018; 1869:161-174. [DOI: 10.1016/j.bbcan.2017.12.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 12/17/2022]
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102
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She R, Jarosz DF. Mapping Causal Variants with Single-Nucleotide Resolution Reveals Biochemical Drivers of Phenotypic Change. Cell 2018; 172:478-490.e15. [PMID: 29373829 PMCID: PMC5788306 DOI: 10.1016/j.cell.2017.12.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 10/21/2017] [Accepted: 12/06/2017] [Indexed: 12/13/2022]
Abstract
Understanding the sequence determinants that give rise to diversity among individuals and species is the central challenge of genetics. However, despite ever greater numbers of sequenced genomes, most genome-wide association studies cannot distinguish causal variants from linked passenger mutations spanning many genes. We report that this inherent challenge can be overcome in model organisms. By pushing the advantages of inbred crossing to its practical limit in Saccharomyces cerevisiae, we improved the statistical resolution of linkage analysis to single nucleotides. This "super-resolution" approach allowed us to map 370 causal variants across 26 quantitative traits. Missense, synonymous, and cis-regulatory mutations collectively gave rise to phenotypic diversity, providing mechanistic insight into the basis of evolutionary divergence. Our data also systematically unmasked complex genetic architectures, revealing that multiple closely linked driver mutations frequently act on the same quantitative trait. Single-nucleotide mapping thus complements traditional deletion and overexpression screening paradigms and opens new frontiers in quantitative genetics.
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Affiliation(s)
- Richard She
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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103
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Gene expression regulation by heat-shock proteins: the cardinal roles of HSF1 and Hsp90. Biochem Soc Trans 2017; 46:51-65. [PMID: 29273620 DOI: 10.1042/bst20170335] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/21/2017] [Accepted: 10/27/2017] [Indexed: 12/31/2022]
Abstract
The ability to permit gene expression is managed by a set of relatively well known regulatory mechanisms. Nonetheless, this property can also be acquired during a life span as a consequence of environmental stimuli. Interestingly, some acquired information can be passed to the next generation of individuals without modifying gene information, but instead by the manner in which cells read and process such information. Molecular chaperones are classically related to the proper preservation of protein folding and anti-aggregation properties, but one of them, heat-shock protein 90 (Hsp90), is a refined sensor of protein function facilitating the biological activity of properly folded client proteins that already have a preserved tertiary structure. Interestingly, Hsp90 can also function as a critical switch able to regulate biological responses due to its association with key client proteins such as histone deacetylases or DNA methylases. Thus, a growing amount of evidence has connected the action of Hsp90 to post-translational modifications of soluble nuclear factors, DNA, and histones, which epigenetically affect gene expression upon the onset of an unfriendly environment. This response is commanded by the activation of the transcription factor heat-shock factor 1 (HSF1). Even though numerous stresses of diverse nature are known to trigger the stress response by activation of HSF1, it is still unknown whether there are different types of molecular sensors for each type of stimulus. In the present review, we will discuss various aspects of the regulatory action of HSF1 and Hsp90 on transcriptional regulation, and how this regulation may affect genetic assimilation mechanisms and the health of individuals.
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104
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Gunter HM, Schneider RF, Karner I, Sturmbauer C, Meyer A. Molecular investigation of genetic assimilation during the rapid adaptive radiations of East African cichlid fishes. Mol Ecol 2017; 26:6634-6653. [PMID: 29098748 DOI: 10.1111/mec.14405] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 08/06/2017] [Accepted: 08/24/2017] [Indexed: 12/19/2022]
Abstract
Adaptive radiations are characterized by adaptive diversification intertwined with rapid speciation within a lineage resulting in many ecologically specialized, phenotypically diverse species. It has been proposed that adaptive radiations can originate from ancestral lineages with pronounced phenotypic plasticity in adaptive traits, facilitating ecologically driven phenotypic diversification that is ultimately fixed through genetic assimilation of gene regulatory regions. This study aimed to investigate how phenotypic plasticity is reflected in gene expression patterns in the trophic apparatus of several lineages of East African cichlid fishes, and whether the observed patterns support genetic assimilation. This investigation used a split brood experimental design to compare adaptive plasticity in species from within and outside of adaptive radiations. The plastic response was induced in the crushing pharyngeal jaws through feeding individuals either a hard or soft diet. We find that nonradiating, basal lineages show higher levels of adaptive morphological plasticity than the derived, radiated lineages, suggesting that these differences have become partially genetically fixed during the formation of the adaptive radiations. Two candidate genes that may have undergone genetic assimilation, gif and alas1, were identified, in addition to alterations in the wiring of LPJ patterning networks. Taken together, our results suggest that genetic assimilation may have dampened the inducibility of plasticity related genes during the adaptive radiations of East African cichlids, flattening the reaction norms and canalizing their feeding phenotypes, driving adaptation to progressively more narrow ecological niches.
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Affiliation(s)
- Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,Zukunftskolleg, University of Konstanz, Konstanz, Germany
| | - Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
| | | | | | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany.,Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, USA
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105
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Negative Epistasis in Experimental RNA Fitness Landscapes. J Mol Evol 2017; 85:159-168. [PMID: 29127445 DOI: 10.1007/s00239-017-9817-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/28/2017] [Indexed: 10/18/2022]
Abstract
Mutations and their effects on fitness are a fundamental component of evolution. The effects of some mutations change in the presence of other mutations, and this is referred to as epistasis. Epistasis can occur between mutations in different genes or within the same gene. A systematic study of epistasis requires the analysis of numerous mutations and their combinations, which has recently become feasible with advancements in DNA synthesis and sequencing. Here we review the mutational effects and epistatic interactions within RNA molecules revealed by several recent high-throughput mutational studies involving two ribozymes studied in vitro, as well as a tRNA and a snoRNA studied in yeast. The data allow an analysis of the distribution of fitness effects of individual mutations as well as combinations of two or more mutations. Two different approaches to measuring epistasis in the data both reveal a predominance of negative epistasis, such that higher combinations of two or more mutations are typically lower in fitness than expected from the effect of each individual mutation. These data are in contrast to past studies of epistasis that used computationally predicted secondary structures of RNA that revealed a predominance of positive epistasis. The RNA data reviewed here are more similar to that found from mutational experiments on individual protein enzymes, suggesting that a common thermodynamic framework may explain negative epistasis between mutations within macromolecules.
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106
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Maraia RJ, Mattijssen S, Cruz-Gallardo I, Conte MR. The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1430. [PMID: 28782243 PMCID: PMC5647580 DOI: 10.1002/wrna.1430] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/02/2023]
Abstract
La was first identified as a polypeptide component of ribonucleic protein complexes targeted by antibodies in autoimmune patients and is now known to be a eukaryote cell-ubiquitous protein. Structure and function studies have shown that La binds to a common terminal motif, UUU-3'-OH, of nascent RNA polymerase III (RNAP III) transcripts and protects them from exonucleolytic decay. For precursor-tRNAs, the most diverse and abundant of these transcripts, La also functions as an RNA chaperone that helps to prevent their misfolding. Related to this, we review evidence that suggests that La and its link to RNAP III were significant in the great expansions of the tRNAomes that occurred in eukaryotes. Four families of La-related proteins (LARPs) emerged during eukaryotic evolution with specialized functions. We provide an overview of the high-resolution structural biology of La and LARPs. LARP7 family members most closely resemble La but function with a single RNAP III nuclear transcript, 7SK, or telomerase RNA. A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA. New structures of LARP domains, some complexed with RNA, provide novel insights into the functional versatility of these proteins. We also consider LARPs in relation to ancestral La protein and potential retention of links to specific RNA-related pathways. One such link may be tRNA surveillance and codon usage by LARP-associated mRNAs. WIREs RNA 2017, 8:e1430. doi: 10.1002/wrna.1430 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
- Commissioned Corps, U.S. Public Health Service, Rockville, MD USA
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Isabel Cruz-Gallardo
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
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107
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There Is an Inclusion for That: Material Properties of Protein Granules Provide a Platform for Building Diverse Cellular Functions. Trends Biochem Sci 2017; 42:765-776. [DOI: 10.1016/j.tibs.2017.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/26/2017] [Accepted: 08/03/2017] [Indexed: 12/30/2022]
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108
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Lawag AA, Napper JM, Hunter CA, Bacon NA, Deskins S, El-Hamdani M, Govender SL, Koc EC, Sollars VE. HSP90 Inhibition and Cellular Stress Elicits Phenotypic Plasticity in Hematopoietic Differentiation. Cell Reprogram 2017; 19:311-323. [PMID: 28910138 PMCID: PMC5650721 DOI: 10.1089/cell.2017.0001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cancer cells exist in a state of Darwinian selection using mechanisms that produce changes in gene expression through genetic and epigenetic alteration to facilitate their survival. Cellular plasticity, or the ability to alter cellular phenotype, can assist in survival of premalignant cells as they progress to full malignancy by providing another mechanism of adaptation. The connection between cellular stress and the progression of cancer has been established, although the details of the mechanisms have yet to be fully elucidated. The molecular chaperone HSP90 is often upregulated in cancers as they progress, presumably to allow cancer cells to deal with misfolded proteins and cellular stress associated with transformation. The objective of this work is to test the hypothesis that inhibition of HSP90 results in increased cell plasticity in mammalian systems that can confer a greater adaptability to selective pressures. The approach used is a murine in vitro model system of hematopoietic differentiation that utilizes a murine hematopoietic stem cell line, erythroid myeloid lymphoid (EML) clone 1, during their maturation from stem cells to granulocytic progenitors. During the differentiation protocol, 80%-90% of the cells die when placed in medium where the major growth factor is granulocyte-macrophage-colony stimulating factor. Using this selection point model, EML cells exhibit increases in cellular plasticity when they are better able to adapt to this medium and survive. Increases in cellular plasticity were found to occur upon exposure to geldanamycin to inhibit HSP90, when subjected to various forms of cellular stress, or inhibition of histone acetylation. Furthermore, we provide evidence that the cellular plasticity associated with inhibition of HSP90 in this model involves epigenetic mechanisms and is dependent upon high levels of stem cell factor signaling. This work provides evidence for a role of HSP90 and cellular stress in inducing phenotypic plasticity in mammalian systems that has new implications for cellular stress in progression and evolution of cancer.
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Affiliation(s)
- Abdalla A Lawag
- 1 Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University , Huntington, West Virginia
| | - Jennifer M Napper
- 2 Department of Natural Sciences, Shawnee State University , Portsmouth, Ohio
| | - Caroline A Hunter
- 1 Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University , Huntington, West Virginia
| | - Nickolas A Bacon
- 1 Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University , Huntington, West Virginia
| | - Seth Deskins
- 1 Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University , Huntington, West Virginia
| | - Manaf El-Hamdani
- 1 Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University , Huntington, West Virginia
| | - Sarah-Leigh Govender
- 1 Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University , Huntington, West Virginia
| | - Emine C Koc
- 1 Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University , Huntington, West Virginia
| | - Vincent E Sollars
- 1 Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University , Huntington, West Virginia
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109
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Auboeuf D. Genome evolution is driven by gene expression-generated biophysical constraints through RNA-directed genetic variation: A hypothesis. Bioessays 2017; 39. [DOI: 10.1002/bies.201700069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210; Laboratory of Biology and Modelling of the Cell; Site Jacques Monod; Lyon France
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110
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Kasinathan B, Ahmad K, Malik HS. Waddington Redux: De Novo Mutations Underlie the Genetic Assimilation of Stress-Induced Phenocopies in Drosophila melanogaster. Genetics 2017; 207:49-51. [PMID: 28874454 PMCID: PMC5586384 DOI: 10.1534/genetics.117.205039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 07/11/2017] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bhavatharini Kasinathan
- Medical Scientist Training Program, University of Washington School of Medicine, Seattle, Washington 98195
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington 98195
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Harmit S Malik
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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111
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Jerison ER, Kryazhimskiy S, Mitchell JK, Bloom JS, Kruglyak L, Desai MM. Genetic variation in adaptability and pleiotropy in budding yeast. eLife 2017; 6:27167. [PMID: 28826486 PMCID: PMC5580887 DOI: 10.7554/elife.27167] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/14/2017] [Indexed: 12/25/2022] Open
Abstract
Evolution can favor organisms that are more adaptable, provided that genetic variation in adaptability exists. Here, we quantify this variation among 230 offspring of a cross between diverged yeast strains. We measure the adaptability of each offspring genotype, defined as its average rate of adaptation in a specific environmental condition, and analyze the heritability, predictability, and genetic basis of this trait. We find that initial genotype strongly affects adaptability and can alter the genetic basis of future evolution. Initial genotype also affects the pleiotropic consequences of adaptation for fitness in a different environment. This genetic variation in adaptability and pleiotropy is largely determined by initial fitness, according to a rule of declining adaptability with increasing initial fitness, but several individual QTLs also have a significant idiosyncratic role. Our results demonstrate that both adaptability and pleiotropy are complex traits, with extensive heritable differences arising from naturally occurring variation.
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Affiliation(s)
- Elizabeth R Jerison
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.,Department of Physics, Harvard University, Cambridge, United States.,FAS Center for Systems Biology, Harvard University, Cambridge, United States
| | - Sergey Kryazhimskiy
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, San Diego, United States
| | | | - Joshua S Bloom
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.,Department of Physics, Harvard University, Cambridge, United States.,FAS Center for Systems Biology, Harvard University, Cambridge, United States
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112
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Tong J, Tan S, Nikolovska-Coleska Z, Yu J, Zou F, Zhang L. FBW7-Dependent Mcl-1 Degradation Mediates the Anticancer Effect of Hsp90 Inhibitors. Mol Cancer Ther 2017; 16:1979-1988. [PMID: 28619760 DOI: 10.1158/1535-7163.mct-17-0032] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/19/2017] [Accepted: 06/05/2017] [Indexed: 12/12/2022]
Abstract
Heat shock protein 90 (Hsp90) is widely overexpressed in cancer cells and necessary for maintenance of malignant phenotypes. Hsp90 inhibition induces tumor cell death through degradation of its client oncoproteins and has shown promises in preclinical studies. However, the mechanism by which Hsp90 inhibitors kill tumor cells is not well-understood. Biomarkers associated with differential sensitivity and resistance to Hsp90 inhibitors remain to be identified. In this study, we found that colorectal cancer cells containing inactivating mutations of FBW7, a tumor suppressor and E3 ubiquitin ligase, are intrinsically insensitive to Hsp90 inhibitors. The insensitive colorectal cancer cells lack degradation of Mcl-1, a prosurvival Bcl-2 family protein. Hsp90 inhibition promotes GSK3β-dependent phosphorylation of Mcl-1, which subsequently binds to FBW7 and undergoes ubiquitination and proteasomal degradation. Specifically blocking Mcl-1 phosphorylation by genetic knock-in abrogates its degradation and renders in vitro and in vivo resistance to Hsp90 inhibitors, which can be overcame by Mcl-1-selective small-molecule inhibitors. Collectively, our findings demonstrate a key role of GSK3β/FBW7-dependent Mcl-1 degradation in killing of colorectal cancer cells by Hsp90 inhibitors and suggest FBW7 mutational status as a biomarker for Hsp90-targeted therapy. Mol Cancer Ther; 16(9); 1979-88. ©2017 AACR.
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Affiliation(s)
- Jingshan Tong
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Shuai Tan
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,College of Life Sciences, Sichuan University, Chengdu, Sichuan, PR China
| | | | - Jian Yu
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Fangdong Zou
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, PR China.
| | - Lin Zhang
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania. .,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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113
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Watanabe E, Mano S, Hara-Nishimura I, Nishimura M, Yamada K. HSP90 stabilizes auxin receptor TIR1 and ensures plasticity of auxin responses. PLANT SIGNALING & BEHAVIOR 2017; 12:e1311439. [PMID: 28532230 PMCID: PMC5501234 DOI: 10.1080/15592324.2017.1311439] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 03/13/2017] [Accepted: 03/20/2017] [Indexed: 05/29/2023]
Abstract
Heat shock protein 90 (HSP90) is a highly conserved molecular chaperone that facilitates the maturation of target proteins. Here, we report that the auxin receptor TIR1 is a target of cytosolic HSP90 and that HSP90 and TIR1 form a complex. Inhibition of HSP90 compromised the nuclear localization of TIR1, and abrogated plant responses to the hormone auxin. Our findings suggest that HSP90 positively regulates auxin receptor function. We also propose that HSP90 buffers or hides phenotypic variations in animals and plants by masking mutations in some of its target proteins. Support for this proposal comes from the tir1-1 mutant of Arabidopsis, which showed a root growth defect that was only seen after inhibition of HSP90. We have developed a model in which cytosolic HSP90 works like a capacitor for auxin-related phenotypic variation via regulation of the auxin receptor in response to environmentally and genetically induced perturbations.
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Affiliation(s)
- Etsuko Watanabe
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Shoji Mano
- Department of Evolutionary Biology and Biodiversity, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Ikuko Hara-Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Kenji Yamada
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
- Malopolska Center of Biotechnology, Jagiellonian University, Krakow, Poland
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114
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Abstract
The heat shock protein 90 (HSP90) chaperone machinery is a key regulator of proteostasis under both physiological and stress conditions in eukaryotic cells. As HSP90 has several hundred protein substrates (or 'clients'), it is involved in many cellular processes beyond protein folding, which include DNA repair, development, the immune response and neurodegenerative disease. A large number of co-chaperones interact with HSP90 and regulate the ATPase-associated conformational changes of the HSP90 dimer that occur during the processing of clients. Recent progress has allowed the interactions of clients with HSP90 and its co-chaperones to be defined. Owing to the importance of HSP90 in the regulation of many cellular proteins, it has become a promising drug target for the treatment of several diseases, which include cancer and diseases associated with protein misfolding.
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Affiliation(s)
- Florian H Schopf
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching, Germany
| | - Maximilian M Biebl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching, Germany
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115
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Vineis P, Chatziioannou A, Cunliffe VT, Flanagan JM, Hanson M, Kirsch-Volders M, Kyrtopoulos S. Epigenetic memory in response to environmental stressors. FASEB J 2017; 31:2241-2251. [PMID: 28280003 DOI: 10.1096/fj.201601059rr] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/21/2017] [Indexed: 12/22/2022]
Abstract
Exposure to environmental stressors, toxicants, and nutrient deficiencies can affect DNA in several ways. Some exposures cause damage and alter the structure of DNA, but there is increasing evidence that the same or other environmental exposures, including those that occur during fetal development in utero, can cause epigenetic effects that modulate DNA function and gene expression. Some epigenetic changes to DNA that affect gene transcription are at least partially reversible (i.e., they can be enzymatically reversed after cessation of exposure to environmental agents), but some epigenetic modifications seem to persist, even for decades. To explain the effects of early life experiences (such as famine and exposures to other stressors) on the long-term persistence of specific patterns of epigenetic modifications, such as DNA methylation, we propose an analogy with immune memory. We propose that an epigenetic memory can be established and maintained in self-renewing stem cell compartments. We suggest that the observations on early life effects on adult diseases and the persistence of methylation changes in smokers support our hypothesis, for which a mechanistic basis, however, needs to be further clarified. We outline a new model based on methylation changes. Although these changes seem to be mainly adaptive, they are also implicated in the pathogenesis and onset of diseases, depending on individual genotypic background and types of subsequent exposures. Elucidating the relationships between the adaptive and maladaptive consequences of the epigenetic modifications that result from complex environmental exposures is a major challenge for current and future research in epigenetics.-Vineis, P., Chatziioannou, A., Cunliffe, V. T., Flanagan, J. M., Hanson, M., Kirsch-Volders, M., Kyrtopoulos, S. Epigenetic memory in response to environmental stressors.
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Affiliation(s)
- Paolo Vineis
- Medical Research Council-Public Health England Center for Environment and Health, Imperial College London, London, United Kingdom;
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Vincent T Cunliffe
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - James M Flanagan
- Epigenetics Unit, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Mark Hanson
- Institute of Developmental Sciences, University Hospital Southampton, University of Southampton, United Kingdom
| | | | - Soterios Kyrtopoulos
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
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116
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Shorter J. Susan Lee Lindquist (1949–2016). Trends Biochem Sci 2017. [DOI: 10.1016/j.tibs.2016.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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117
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Hummel B, Hansen EC, Yoveva A, Aprile-Garcia F, Hussong R, Sawarkar R. The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses. Nat Struct Mol Biol 2017; 24:234-242. [PMID: 28134929 DOI: 10.1038/nsmb.3368] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/22/2016] [Indexed: 12/17/2022]
Abstract
Understanding how genotypes are linked to phenotypes is important in biomedical and evolutionary studies. The chaperone heat-shock protein 90 (HSP90) buffers genetic variation by stabilizing proteins with variant sequences, thereby uncoupling phenotypes from genotypes. Here we report an unexpected role of HSP90 in buffering cis-regulatory variation affecting gene expression. By using the tripartite-motif-containing 28 (TRIM28; also known as KAP1)-mediated epigenetic pathway, HSP90 represses the regulatory influence of endogenous retroviruses (ERVs) on neighboring genes that are critical for mouse development. Our data based on natural variations in the mouse genome show that genes respond to HSP90 inhibition in a manner dependent on their genomic location with regard to strain-specific ERV-insertion sites. The evolutionary-capacitor function of HSP90 may thus have facilitated the exaptation of ERVs as key modifiers of gene expression and morphological diversification. Our findings add a new regulatory layer through which HSP90 uncouples phenotypic outcomes from individual genotypes.
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Affiliation(s)
- Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Erik C Hansen
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Aneliya Yoveva
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Fernando Aprile-Garcia
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Rebecca Hussong
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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118
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Karras GI, Yi S, Sahni N, Fischer M, Xie J, Vidal M, D'Andrea AD, Whitesell L, Lindquist S. HSP90 Shapes the Consequences of Human Genetic Variation. Cell 2017; 168:856-866.e12. [PMID: 28215707 DOI: 10.1016/j.cell.2017.01.023] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/09/2016] [Accepted: 01/19/2017] [Indexed: 11/26/2022]
Abstract
HSP90 acts as a protein-folding buffer that shapes the manifestations of genetic variation in model organisms. Whether HSP90 influences the consequences of mutations in humans, potentially modifying the clinical course of genetic diseases, remains unknown. By mining data for >1,500 disease-causing mutants, we found a strong correlation between reduced phenotypic severity and a dominant (HSP90 ≥ HSP70) increase in mutant engagement by HSP90. Examining the cancer predisposition syndrome Fanconi anemia in depth revealed that mutant FANCA proteins engaged predominantly by HSP70 had severely compromised function. In contrast, the function of less severe mutants was preserved by a dominant increase in HSP90 binding. Reducing HSP90's buffering capacity with inhibitors or febrile temperatures destabilized HSP90-buffered mutants, exacerbating FA-related chemosensitivities. Strikingly, a compensatory FANCA somatic mutation from an "experiment of nature" in monozygotic twins both prevented anemia and reduced HSP90 binding. These findings provide one plausible mechanism for the variable expressivity and environmental sensitivity of genetic diseases.
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Affiliation(s)
- Georgios I Karras
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Song Yi
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nidhi Sahni
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Máté Fischer
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Jenny Xie
- Center for DNA Damage and Repair and Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alan D D'Andrea
- Center for DNA Damage and Repair and Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Luke Whitesell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, MA 02139, USA
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119
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Abstract
The science universe is dimmer after one of our brightest stars, Susan Lee Lindquist, was taken by cancer on October 27, 2016. Sue was an innovative, creative, out-of-the-box scientific thinker. She had unique biological intuition—an instinct for both the way things worked and the right questions to ask to uncover new research insights. Her wide-ranging career began with the study of protein folding and molecular chaperones, and she went on to show that protein folding can have profound and unexpected biological effects on such diverse processes as cancer, evolution, and neurodegenerative disease. As Sue's laboratory manager, I would like to offer a ground-floor perspective on what made her an exceptional scientist, mentor, and leader. She created a harmonious, collegial environment where collaborative synergy fueled meaningful progress that will impact science for decades to come.
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Affiliation(s)
- Brooke J Bevis
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
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120
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Thouvenot P, Fourrière L, Dardillac E, Ben Yamin B, Lescure A, Lejour V, Heiligenstein X, Boulé JB, Romao M, Raposo-Benedetti G, Lopez BS, Nicolas A, Millot GA. Yeast cells reveal the misfolding and the cellular mislocalization of the human BRCA1 protein. J Cell Sci 2016; 129:4366-4378. [PMID: 27802165 DOI: 10.1242/jcs.192880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 10/12/2016] [Indexed: 01/01/2023] Open
Abstract
Understanding the effect of an ever-growing number of human variants detected by genome sequencing is a medical challenge. The yeast Saccharomyces cerevisiae model has held attention for its capacity to monitor the functional impact of missense mutations found in human genes, including the BRCA1 breast and ovarian cancer susceptibility gene. When expressed in yeast, the wild-type full-length BRCA1 protein forms a single nuclear aggregate and induces a growth inhibition. Both events are modified by pathogenic mutations of BRCA1. However, the biological processes behind these events in yeast remain to be determined. Here, we show that the BRCA1 nuclear aggregation and the growth inhibition are sensitive to misfolding effects induced by missense mutations. Moreover, misfolding mutations impair the nuclear targeting of BRCA1 in yeast cells and in a human cell line. In conclusion, we establish a connection between misfolding and nuclear transport impairment, and we illustrate that yeast is a suitable model to decipher the effect of misfolding mutations.
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Affiliation(s)
- Pierre Thouvenot
- Institut Curie, PSL Research University, CNRS, UMR3244, 26 rue d'Ulm, Paris F-75005, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris F-75005, France
| | - Lou Fourrière
- Institut Curie, PSL Research University, CNRS, UMR3244, 26 rue d'Ulm, Paris F-75005, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris F-75005, France
| | - Elodie Dardillac
- CNRS UMR 8200, Institut de Cancerologie Gustave-Roussy, Université Paris-Saclay, 114 Rue Edouard Vaillant, Villejuif 94805, France
| | - Barbara Ben Yamin
- Institut Curie, PSL Research University, CNRS, UMR3244, 26 rue d'Ulm, Paris F-75005, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris F-75005, France
| | - Aurianne Lescure
- Institut Curie, PSL Research University, CNRS, UMR3244, 26 rue d'Ulm, Paris F-75005, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris F-75005, France
| | - Vincent Lejour
- Institut Curie, PSL Research University, CNRS, UMR3244, 26 rue d'Ulm, Paris F-75005, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris F-75005, France
| | - Xavier Heiligenstein
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris F-75005, France.,Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, Paris F-75005, France
| | - Jean-Baptiste Boulé
- Institut Curie, PSL Research University, CNRS, UMR3244, 26 rue d'Ulm, Paris F-75005, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris F-75005, France
| | - Maryse Romao
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris F-75005, France.,Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, Paris F-75005, France
| | - Graça Raposo-Benedetti
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris F-75005, France.,Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, Paris F-75005, France
| | - Bernard S Lopez
- CNRS UMR 8200, Institut de Cancerologie Gustave-Roussy, Université Paris-Saclay, 114 Rue Edouard Vaillant, Villejuif 94805, France
| | - Alain Nicolas
- Institut Curie, PSL Research University, CNRS, UMR3244, 26 rue d'Ulm, Paris F-75005, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris F-75005, France
| | - Gaël A Millot
- Institut Curie, PSL Research University, CNRS, UMR3244, 26 rue d'Ulm, Paris F-75005, France .,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, Paris F-75005, France
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121
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Ryan CP, Brownlie JC, Whyard S. Hsp90 and Physiological Stress Are Linked to Autonomous Transposon Mobility and Heritable Genetic Change in Nematodes. Genome Biol Evol 2016; 8:3794-3805. [PMID: 28082599 PMCID: PMC5521727 DOI: 10.1093/gbe/evw284] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2016] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) have been recognized as potentially powerful drivers of genomic evolutionary change, but factors affecting their mobility and regulation remain poorly understood. Chaperones such as Hsp90 buffer environmental perturbations by regulating protein conformation, but are also part of the PIWI-interacting RNA pathway, which regulates genomic instability arising from mobile TEs in the germline. Stress-induced mutagenesis from TE movement could thus arise from functional trade-offs in the dual roles of Hsp90. We examined the functional constraints of Hsp90 and its role as a regulator of TE mobility by exposing nematodes (Caenorhabditis elegans and Caenorhabditis briggsae) to environmental stress, with and without RNAi-induced silencing of Hsp90. TE excision frequency increased with environmental stress intensity at multiple loci in several strains of each species. These effects were compounded by RNAi-induced knockdown of Hsp90. Mutation frequencies at the unc-22 marker gene in the offspring of animals exposed to environmental stress and Hsp90 RNAi mirrored excision frequency in response to these treatments. Our results support a role for Hsp90 in the suppression of TE mobility, and demonstrate that that the Hsp90 regulatory pathway can be overwhelmed with moderate environmental stress. By compromising genomic stability in germline cells, environmentally induced mutations arising from TE mobility and insertion can have permanent and heritable effects on both the phenotype and the genotype of subsequent generations.
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Affiliation(s)
- Calen P. Ryan
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Anthropology, Northwestern University, Evanston, IL
| | - Jeremy C. Brownlie
- School of Biomolecular and Physical Sciences, Griffith University, Brisbane, Queensland, Australia
| | - Steve Whyard
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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122
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Takahashi KH. Little effect of HSP90 inhibition on the quantitative wing traits variation in Drosophila melanogaster. Genetica 2016; 145:9-18. [PMID: 27909948 DOI: 10.1007/s10709-016-9940-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/21/2016] [Indexed: 11/29/2022]
Abstract
Drosophila wings have been a model system to study the effect of HSP90 on quantitative trait variation. The effect of HSP90 inhibition on environmental buffering of wing morphology varies among studies while the genetic buffering effect of it was examined in only one study and was not detected. Variable results so far might show that the genetic background influences the environmental and genetic buffering effect of HSP90. In the previous studies, the number of the genetic backgrounds used is limited. To examine the effect of HSP90 inhibition with a larger number of genetic backgrounds than the previous studies, 20 wild-type strains of Drosophila melanogaster were used in this study. Here I investigated the effect of HSP90 inhibition on the environmental buffering of wing shape and size by assessing within-individual and among-individual variations, and as a result, I found little or very weak effects on environmental and genetic buffering. The current results suggest that the role of HSP90 as a global regulator of environmental and genetic buffering is limited at least in quantitative traits.
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Affiliation(s)
- Kazuo H Takahashi
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama-si, Okayama-ken, 700-8530, Japan.
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123
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Abstract
Disruption of certain genes alters the heritable phenotypic variation among individuals. Research on the chaperone Hsp90 has played a central role in determining the genetic basis of this phenomenon, which may be important to evolution and disease. Key studies have shown that Hsp90 perturbation modifies the effects of many genetic variants throughout the genome. These modifications collectively transform the genotype–phenotype map, often resulting in a net increase or decrease in heritable phenotypic variation. Here, we summarize some of the foundational work on Hsp90 that led to these insights, discuss a framework for interpreting this research that is centered upon the standard genetics concept of epistasis, and propose major questions that future studies in this area should address.
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Affiliation(s)
- Rachel Schell
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Martin Mullis
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Ian M. Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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124
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Watanabe E, Mano S, Nomoto M, Tada Y, Hara-Nishimura I, Nishimura M, Yamada K. HSP90 Stabilizes Auxin-Responsive Phenotypes by Masking a Mutation in the Auxin Receptor TIR1. PLANT & CELL PHYSIOLOGY 2016; 57:2245-2254. [PMID: 27816945 DOI: 10.1093/pcp/pcw170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/30/2016] [Indexed: 05/10/2023]
Abstract
Heat shock protein 90 (HSP90) is a molecular chaperone that is required for the function of various substrate proteins, also known as client proteins. It is proposed that HSP90 buffers or hides phenotypic variations in animals and plants by masking mutations in some of its client proteins. However, none of the client proteins with cryptic mutations has been identified to date. Here, we identify the first client protein example by which HSP90 buffers a mutation: the auxin receptor transport inhibitor response 1 (TIR1). TIR1 interacts with HSP90 in the nucleus. An HSP90-specific inhibitor abolished the nuclear localization of TIR1 and the auxin-induced degradation of a TIR1-substrate, indicating that TIR1 is an HSP90 client protein. Plants with a null mutation in the TIR1 gene had a defect in auxin response, whereas plants with a point mutation in the TIR1 gene responded to auxin treatment in young seedlings, but a cryptic defect in its auxin response was exposed with HSP90 inhibitor treatment. These results demonstrate that HSP90 masks a point mutation in the auxin receptor TIR1 and thereby buffers auxin-responsive phenotypes.
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Affiliation(s)
- Etsuko Watanabe
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585 Japan
- Present address: Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, 020-8550 Japan
| | - Shoji Mano
- Department of Evolutionary Biology and Biodiversity, National Institute for Basic Biology, Okazaki, 444-8585 Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585 Japan
| | - Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602 Japan
| | - Yasuomi Tada
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602 Japan
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan
| | - Ikuko Hara-Nishimura
- Department of Botany; Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
- Present address: Faculty of Science and Engineering, Konan University, Kobe, 658-0073 Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585 Japan
| | - Kenji Yamada
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585 Japan
- Department of Botany; Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
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125
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Horváth B, Kalinka AT. Effects of larval crowding on quantitative variation for development time and viability in Drosophila melanogaster. Ecol Evol 2016; 6:8460-8473. [PMID: 28031798 PMCID: PMC5167028 DOI: 10.1002/ece3.2552] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/15/2016] [Accepted: 09/22/2016] [Indexed: 11/06/2022] Open
Abstract
Competition between individuals belonging to the same species is a universal feature of natural populations and is the process underpinning organismal adaptation. Despite its importance, still comparatively little is known about the genetic variation responsible for competitive traits. Here, we measured the phenotypic variation and quantitative genetics parameters for two fitness-related traits-egg-to-adult viability and development time-across a panel of Drosophila strains under varying larval densities. Both traits exhibited substantial genetic variation at all larval densities, as well as significant genotype-by-environment interactions (GEIs). GEI was attributable to changes in the rank order of reaction norms for both traits, and additionally to differences in the between-line variance for development time. The coefficient of genetic variation increased under stress conditions for development time, while it was higher at both high and low densities for viability. While development time also correlated negatively with fitness at high larval densities-meaning that fast developers have high fitness-there was no correlation with fitness at low density. This result suggests that GEI may be a common feature of fitness-related genetic variation and, further, that trait values under noncompetitive conditions could be poor indicators of individual fitness. The latter point could have significant implications for animal and plant breeding programs, as well as for conservation genetics.
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Affiliation(s)
- Barbara Horváth
- Institut für Populationsgenetik Veterinärmedizinische Universität Wien A-1210 Vienna Austria; Vienna Graduate School of Population Genetics, Veterinärmedizinische Universität Wien A-1210, Vienna Austria
| | - Alex T Kalinka
- Institut für Populationsgenetik Veterinärmedizinische Universität Wien A-1210 Vienna Austria
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126
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Geiler-Samerotte KA, Zhu YO, Goulet BE, Hall DW, Siegal ML. Selection Transforms the Landscape of Genetic Variation Interacting with Hsp90. PLoS Biol 2016; 14:e2000465. [PMID: 27768682 PMCID: PMC5074785 DOI: 10.1371/journal.pbio.2000465] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/26/2016] [Indexed: 11/18/2022] Open
Abstract
The protein-folding chaperone Hsp90 has been proposed to buffer the phenotypic effects of mutations. The potential for Hsp90 and other putative buffers to increase robustness to mutation has had major impact on disease models, quantitative genetics, and evolutionary theory. But Hsp90 sometimes contradicts expectations for a buffer by potentiating rapid phenotypic changes that would otherwise not occur. Here, we quantify Hsp90’s ability to buffer or potentiate (i.e., diminish or enhance) the effects of genetic variation on single-cell morphological features in budding yeast. We corroborate reports that Hsp90 tends to buffer the effects of standing genetic variation in natural populations. However, we demonstrate that Hsp90 tends to have the opposite effect on genetic variation that has experienced reduced selection pressure. Specifically, Hsp90 tends to enhance, rather than diminish, the effects of spontaneous mutations and recombinations. This result implies that Hsp90 does not make phenotypes more robust to the effects of genetic perturbation. Instead, natural selection preferentially allows buffered alleles to persist and thereby creates the false impression that Hsp90 confers greater robustness. Most biologists appreciate that natural selection filters new mutations (e.g., by eliminating deleterious ones), such that genetic variation in nature is biased. The idea that selection also skews the types of genetic interactions that exist in nature is less appreciated. For example, studies spanning diverse species have shown that the protein Hsp90, which helps other proteins to fold properly, tends to diminish the observable effects of genetic variation. This observation has led to the assumption that Hsp90 also buffers the effects of new mutations. This untested assumption has served as a rationale for cancer-treatment strategies and shaped our understanding of variation in complex traits. We measured the effects of new mutations on the shapes and sizes of individual yeast cells and found that Hsp90 does not tend to buffer these effects. Instead, Hsp90 interacts with new mutations in diverse ways, sometimes buffering, but more often enhancing mutational effects on cell shape and size. We conclude that selection preferentially allows buffered mutations to persist in natural populations. This result alters common perceptions about why cryptic (i.e., buffered) genetic variation exists and casts doubt on cancer-treatment strategies aiming to target presumed buffers of mutational effects.
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Affiliation(s)
- Kerry A Geiler-Samerotte
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America.,Department of Biology, Stanford University, Stanford, California, United States of America
| | - Yuan O Zhu
- Department of Biology, Stanford University, Stanford, California, United States of America.,Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Benjamin E Goulet
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - David W Hall
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Mark L Siegal
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
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127
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Abstract
ABSTRACT
Invasive fungal infections are becoming an increasingly important cause of human mortality and morbidity, particularly for immunocompromised populations. The fungal pathogens
Candida albicans
,
Cryptococcus neoformans
, and
Aspergillus fumigatus
collectively contribute to over 1 million human deaths annually. Hence, the importance of safe and effective antifungal therapeutics for the practice of modern medicine has never been greater. Given that fungi are eukaryotes like their human host, the number of unique molecular targets that can be exploited for drug development remains limited. Only three classes of molecules are currently approved for the treatment of invasive mycoses. The efficacy of these agents is compromised by host toxicity, fungistatic activity, or the emergence of drug resistance in pathogen populations. Here we describe our current arsenal of antifungals and highlight current strategies that are being employed to improve the therapeutic safety and efficacy of these drugs. We discuss state-of-the-art approaches to discover novel chemical matter with antifungal activity and highlight some of the most promising new targets for antifungal drug development. We feature the benefits of combination therapy as a strategy to expand our current repertoire of antifungals and discuss the antifungal combinations that have shown the greatest potential for clinical development. Despite the paucity of new classes of antifungals that have come to market in recent years, it is clear that by leveraging innovative approaches to drug discovery and cultivating collaborations between academia and industry, there is great potential to bolster the antifungal armamentarium.
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128
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Yuan W, Flowers JM, Sahraie DJ, Purugganan MD. Cryptic Genetic Variation for Arabidopsis thaliana Seed Germination Speed in a Novel Salt Stress Environment. G3 (BETHESDA, MD.) 2016; 6:3129-3138. [PMID: 27543295 PMCID: PMC5068935 DOI: 10.1534/g3.116.033944] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/29/2016] [Indexed: 11/18/2022]
Abstract
The expansion of species ranges frequently necessitates responses to novel environments. In plants, the ability of seeds to disperse to marginal areas relies in part to its ability to germinate under stressful conditions. Here we examine the genetic architecture of Arabidopsis thaliana germination speed under a novel, saline environment, using an Extreme QTL (X-QTL) mapping platform we previously developed. We find that early germination in normal and salt conditions both rely on a QTL on the distal arm of chromosome 4, but we also find unique QTL on chromosomes 1, 2, 4, and 5 that are specific to salt stress environments. Moreover, different QTLs are responsible for early vs. late germination, suggesting a temporal component to the expression of life history under these stress conditions. Our results indicate that cryptic genetic variation exists for responses to a novel abiotic stress, which may suggest a role of such variation in adaptation to new climactic conditions or growth environments.
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Affiliation(s)
- Wei Yuan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003
| | - Jonathan M Flowers
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003 Center for Genomics and Systems Biology, New York University Abu Dhabi Research Institute, New York University Abu Dhabi, United Arab Emirates
| | - Dustin J Sahraie
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003
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129
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Xia S, Wang Z, Zhang H, Hu K, Zhang Z, Qin M, Dun X, Yi B, Wen J, Ma C, Shen J, Fu T, Tu J. Altered Transcription and Neofunctionalization of Duplicated Genes Rescue the Harmful Effects of a Chimeric Gene in Brassica napus. THE PLANT CELL 2016; 28:2060-2078. [PMID: 27559024 PMCID: PMC5059798 DOI: 10.1105/tpc.16.00281] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/19/2016] [Accepted: 08/24/2016] [Indexed: 05/04/2023]
Abstract
Chimeric genes contribute to the evolution of diverse functions in plants and animals. However, new chimeric genes also increase the risk of developmental defects. Here, we show that the chimeric gene Brassica napus male sterile 4 (Bnams4b ) is responsible for genic male sterility in the widely used canola line 7365A (Bnams3 ms3ms4bms4b ). Bnams4b originated via exon shuffling ∼4.6 million years ago. It causes defects in the normal functions of plastids and induces aborted anther formation and/or albino leaves and buds. Evidence of the age of the mutation, its tissue expression pattern, and its sublocalization indicated that it coevolved with BnaC9.Tic40 (BnaMs3). In Arabidopsis thaliana, Bnams4b results in complete male sterility that can be rescued by BnaC9.Tic40, suggesting that BnaC9.Tic40 might restore fertility through effects on protein level. Another suppressor gene, Bnams4a , rescues sterility by reducing the level of transcription of Bnams4b Our results suggest that Brassica plants have coevolved altered transcription patterns and neofunctionalization of duplicated genes that can block developmental defects resulting from detrimental chimeric genes.
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Affiliation(s)
- Shengqian Xia
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhixin Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiyan Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiqiang Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Maomao Qin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoling Dun
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
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Intratumor Heterogeneity in Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 882:169-89. [PMID: 26987535 DOI: 10.1007/978-3-319-22909-6_7] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Intratumor heterogeneity is the main obstacle to effective cancer treatment and personalized medicine. Both genetic and epigenetic sources of intratumor heterogeneity are well recognized and several technologies have been developed for their characterization. With the technological advances in recent years, investigators are now elucidating intratumor heterogeneity at the single cell level and in situ. However, translating the accumulated knowledge about intratumor heterogeneity to clinical practice has been slow. We are certain that better understanding of the composition and evolution of tumors during disease progression and treatment will improve cancer diagnosis and the design of therapies. Here we review some of the most important considerations related to intratumor heterogeneity. We discuss both genetic and epigenetic sources of intratumor heterogeneity and review experimental approaches that are commonly used to quantify it. We also discuss the impact of intratumor heterogeneity on cancer diagnosis and treatment and share our perspectives on the future of this field.
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131
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Rein T. FK506 binding protein 51 integrates pathways of adaptation: FKBP51 shapes the reactivity to environmental change. Bioessays 2016; 38:894-902. [PMID: 27374865 DOI: 10.1002/bies.201600050] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This review portraits FK506 binding protein (FKBP) 51 as "reactivity protein" and collates recent publications to develop the concept of FKBP51 as contributor to different levels of adaptation. Adaptation is a fundamental process that enables unicellular and multicellular organisms to adjust their molecular circuits and structural conditions in reaction to environmental changes threatening their homeostasis. FKBP51 is known as chaperone and co-chaperone of heat shock protein (HSP) 90, thus involved in processes ensuring correct protein folding in response to proteotoxic stress. In mammals, FKBP51 both shapes the stress response and is calibrated by the stress levels through an ultrashort molecular feedback loop. More recently, it has been linked to several intracellular pathways related to the reactivity to drug exposure and stress. Through its role in autophagy and DNA methylation in particular it influences adaptive pathways, possibly also in a transgenerational fashion. Also see the video abstract here.
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Affiliation(s)
- Theo Rein
- Department of Translational Science in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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132
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Agarwal G, Garg V, Kudapa H, Doddamani D, Pazhamala LT, Khan AW, Thudi M, Lee SH, Varshney RK. Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1563-77. [PMID: 26800652 PMCID: PMC5066796 DOI: 10.1111/pbi.12520] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/03/2015] [Accepted: 11/22/2015] [Indexed: 05/19/2023]
Abstract
APETALA2/ethylene response factor (AP2/ERF) and heat-shock protein 90 (HSP90) are two significant classes of transcription factor and molecular chaperone proteins which are known to be implicated under abiotic and biotic stresses. Comprehensive survey identified a total of 147 AP2/ERF genes in chickpea, 176 in pigeonpea, 131 in Medicago, 179 in common bean and 140 in Lotus, whereas the number of HSP90 genes ranged from 5 to 7 in five legumes. Sequence alignment and phylogenetic analyses distinguished AP2, ERF, DREB, RAV and soloist proteins, while HSP90 proteins segregated on the basis of their cellular localization. Deeper insights into the gene structure allowed ERF proteins to be classified into AP2s based on DNA-binding domains, intron arrangements and phylogenetic grouping. RNA-seq and quantitative real-time PCR (qRT-PCR) analyses in heat-stressed chickpea as well as Fusarium wilt (FW)- and sterility mosaic disease (SMD)-stressed pigeonpea provided insights into the modus operandi of AP2/ERF and HSP90 genes. This study identified potential candidate genes in response to heat stress in chickpea while for FW and SMD stresses in pigeonpea. For instance, two DREB genes (Ca_02170 and Ca_16631) and three HSP90 genes (Ca_23016, Ca_09743 and Ca_25602) in chickpea can be targeted as potential candidate genes. Similarly, in pigeonpea, a HSP90 gene, C.cajan_27949, was highly responsive to SMD in the resistant genotype ICPL 20096, can be recommended for further functional validation. Also, two DREB genes, C.cajan_41905 and C.cajan_41951, were identified as leads for further investigation in response to FW stress in pigeonpea.
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Affiliation(s)
- Gaurav Agarwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Dadakhalandar Doddamani
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Lekha T Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Suk-Ha Lee
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- School of Plant Biology, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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133
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Marciano DC, Lua RC, Herman C, Lichtarge O. Cooperativity of Negative Autoregulation Confers Increased Mutational Robustness. PHYSICAL REVIEW LETTERS 2016; 116:258104. [PMID: 27391757 PMCID: PMC5152588 DOI: 10.1103/physrevlett.116.258104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 05/05/2023]
Abstract
Negative autoregulation is universally found across organisms. In the bacterium Escherichia coli, transcription factors often repress their own expression to form a negative feedback network motif that enables robustness to changes in biochemical parameters. Here we present a simple phenomenological model of a negative feedback transcription factor repressing both itself and another target gene. The strength of the negative feedback is characterized by three parameters: the cooperativity in self-repression, the maximal expression rate of the transcription factor, and the apparent dissociation constant of the transcription factor binding to its own promoter. Analysis of the model shows that the target gene levels are robust to mutations in the transcription factor, and that the robustness improves as the degree of cooperativity in self-repression increases. The prediction is tested in the LexA transcriptional network of E. coli by altering cooperativity in self-repression and promoter strength. Indeed, we find robustness is correlated with the former. Considering the proposed importance of gene regulation in speciation, parameters governing a transcription factor's robustness to mutation may have significant influence on a cell or organism's capacity to evolve.
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Affiliation(s)
- David C. Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Rhonald C. Lua
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Corresponding author.
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134
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Taylor MB, Phan J, Lee JT, McCadden M, Ehrenreich IM. Diverse genetic architectures lead to the same cryptic phenotype in a yeast cross. Nat Commun 2016; 7:11669. [PMID: 27248513 PMCID: PMC4895441 DOI: 10.1038/ncomms11669] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 04/18/2016] [Indexed: 01/09/2023] Open
Abstract
Cryptic genetic variants that do not typically influence traits can interact epistatically with each other and mutations to cause unexpected phenotypes. To improve understanding of the genetic architectures and molecular mechanisms that underlie these interactions, we comprehensively dissected the genetic bases of 17 independent instances of the same cryptic colony phenotype in a yeast cross. In eight cases, the phenotype resulted from a genetic interaction between a de novo mutation and one or more cryptic variants. The number and identities of detected cryptic variants depended on the mutated gene. In the nine remaining cases, the phenotype arose without a de novo mutation due to two different classes of higher-order genetic interactions that only involve cryptic variants. Our results may be relevant to other species and disease, as most of the mutations and cryptic variants identified in our study reside in components of a partially conserved and oncogenic signalling pathway. Cryptic genetic variants may not individually show discernible phenotypic effects, but collectively, these polymorphisms can lead to unexpected, genetically complex traits that might be relevant to evolution and disease. Here, the authors use large yeast populations to comprehensively dissect the genetic bases of 17 independent occurrences of a phenotype that arises due to combinations of epistatically interacting cryptic variants.
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Affiliation(s)
- Matthew B Taylor
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Joann Phan
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Jonathan T Lee
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Madelyn McCadden
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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135
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Khalili V, Shokri H, Md Akim A, Khosravi AR. Differential Gene Expression of Heat Shock Protein 90 (Hsp90) of Candida albicans obtained from Malaysian and Iranian Patients. Malays J Med Sci 2016; 23:64-71. [PMID: 27418871 PMCID: PMC4934720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/27/2016] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND Candida albicans (C. albicans) has several virulence factors, in particular heat shock protein 90 (Hsp90), which is expressed by Hsp90 gene. The purposes of this study were to assess the expression of Hsp90 gene in clinical and control isolates of C. albicans obtained from different geographical regions (Malaysia and Iran), different temperatures (25°C, 37°C and 42°C) and mice with candidiasis. METHODS C. albicans isolates were cultured onto sabouraud dextrose agar (SDA). The assessment of the expression of Hsp90 gene was performed using real time-polymerase chain reaction (RT-PCR). RESULTS The results showed a significant increase in the expression of C. albicans Hsp90 gene under high thermal shock (42°C) when compared to other temperatures tested (P-value = 0.001). The mean differences in the expression of Hsp90 gene at 37°C were 0.20 (95% confidence interval (CI) 0.13-0.29) between Malaysian and Iranian controls (P-value = 0.040) and 0.47 (95% CI 0.27-0.60) between Malaysian and Iranian patients (P-value = 0.040). CONCLUSION The results demonstrated that the expression of C. albicans Hsp90 gene varied between Malaysian and Iranian subjects, representing the efficacy of geographical and thermal conditions on virulence gene expression.
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Affiliation(s)
- Vajihe Khalili
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Hojjatollah Shokri
- Department of Pathobiology, Faculty of Veterinary Medicine, Amol University of Special Modern Technologies, 24th Aftab, Imam Khomeini Street 46168- 49767, Amol, Iran
| | - Abdah Md Akim
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Ali Reza Khosravi
- Mycology Research Center, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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136
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Clare DK, Saibil HR. ATP-driven molecular chaperone machines. Biopolymers 2016; 99:846-59. [PMID: 23877967 PMCID: PMC3814418 DOI: 10.1002/bip.22361] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/08/2013] [Indexed: 01/17/2023]
Abstract
This review is focused on the mechanisms by which ATP binding and hydrolysis drive chaperone machines assisting protein folding and unfolding. A survey of the key, general chaperone systems Hsp70 and Hsp90, and the unfoldase Hsp100 is followed by a focus on the Hsp60 chaperonin machine which is understood in most detail. Cryo-electron microscopy analysis of the E. coli Hsp60 GroEL reveals intermediate conformations in the ATPase cycle and in substrate folding. These structures suggest a mechanism by which GroEL can forcefully unfold and then encapsulate substrates for subsequent folding in isolation from all other binding surfaces.
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Affiliation(s)
- Daniel K Clare
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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137
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Ehrenreich IM, Pfennig DW. Genetic assimilation: a review of its potential proximate causes and evolutionary consequences. ANNALS OF BOTANY 2016; 117:769-79. [PMID: 26359425 PMCID: PMC4845796 DOI: 10.1093/aob/mcv130] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/07/2015] [Accepted: 06/29/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Most, if not all, organisms possess the ability to alter their phenotype in direct response to changes in their environment, a phenomenon known as phenotypic plasticity. Selection can break this environmental sensitivity, however, and cause a formerly environmentally induced trait to evolve to become fixed through a process called genetic assimilation. Essentially, genetic assimilation can be viewed as the evolution of environmental robustness in what was formerly an environmentally sensitive trait. Because genetic assimilation has long been suggested to play a key role in the origins of phenotypic novelty and possibly even new species, identifying and characterizing the proximate mechanisms that underlie genetic assimilation may advance our basic understanding of how novel traits and species evolve. SCOPE This review begins by discussing how the evolution of phenotypic plasticity, followed by genetic assimilation, might promote the origins of new traits and possibly fuel speciation and adaptive radiation. The evidence implicating genetic assimilation in evolutionary innovation and diversification is then briefly considered. Next, the potential causes of phenotypic plasticity generally and genetic assimilation specifically are examined at the genetic, molecular and physiological levels and approaches that can improve our understanding of these mechanisms are described. The review concludes by outlining major challenges for future work. CONCLUSIONS Identifying and characterizing the proximate mechanisms involved in phenotypic plasticity and genetic assimilation promises to help advance our basic understanding of evolutionary innovation and diversification.
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Affiliation(s)
- Ian M Ehrenreich
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA and
| | - David W Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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138
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Lachowiec J, Queitsch C, Kliebenstein DJ. Molecular mechanisms governing differential robustness of development and environmental responses in plants. ANNALS OF BOTANY 2016; 117:795-809. [PMID: 26473020 PMCID: PMC4845800 DOI: 10.1093/aob/mcv151] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/08/2015] [Accepted: 08/25/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Robustness to genetic and environmental perturbation is a salient feature of multicellular organisms. Loss of developmental robustness can lead to severe phenotypic defects and fitness loss. However, perfect robustness, i.e. no variation at all, is evolutionarily unfit as organisms must be able to change phenotype to properly respond to changing environments and biotic challenges. Plasticity is the ability to adjust phenotypes predictably in response to specific environmental stimuli, which can be considered a transient shift allowing an organism to move from one robust phenotypic state to another. Plants, as sessile organisms that undergo continuous development, are particularly dependent on an exquisite fine-tuning of the processes that balance robustness and plasticity to maximize fitness. SCOPE AND CONCLUSIONS This paper reviews recently identified mechanisms, both systems-level and molecular, that modulate robustness, and discusses their implications for the optimization of plant fitness. Robustness in living systems arises from the structure of genetic networks, the specific molecular functions of the underlying genes, and their interactions. This very same network responsible for the robustness of specific developmental states also has to be built such that it enables plastic yet robust shifts in response to environmental changes. In plants, the interactions and functions of signal transduction pathways activated by phytohormones and the tendency for plants to tolerate whole-genome duplications, tandem gene duplication and hybridization are emerging as major regulators of robustness in development. Despite their obvious implications for plant evolution and plant breeding, the mechanistic underpinnings by which plants modulate precise levels of robustness, plasticity and evolvability in networks controlling different phenotypes are under-studied.
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Affiliation(s)
- Jennifer Lachowiec
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48197, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, WA 98155, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA and DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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139
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Finka A, Mattoo RUH, Goloubinoff P. Experimental Milestones in the Discovery of Molecular Chaperones as Polypeptide Unfolding Enzymes. Annu Rev Biochem 2016; 85:715-42. [PMID: 27050154 DOI: 10.1146/annurev-biochem-060815-014124] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular chaperones control the cellular folding, assembly, unfolding, disassembly, translocation, activation, inactivation, disaggregation, and degradation of proteins. In 1989, groundbreaking experiments demonstrated that a purified chaperone can bind and prevent the aggregation of artificially unfolded polypeptides and use ATP to dissociate and convert them into native proteins. A decade later, other chaperones were shown to use ATP hydrolysis to unfold and solubilize stable protein aggregates, leading to their native refolding. Presently, the main conserved chaperone families Hsp70, Hsp104, Hsp90, Hsp60, and small heat-shock proteins (sHsps) apparently act as unfolding nanomachines capable of converting functional alternatively folded or toxic misfolded polypeptides into harmless protease-degradable or biologically active native proteins. Being unfoldases, the chaperones can proofread three-dimensional protein structures and thus control protein quality in the cell. Understanding the mechanisms of the cellular unfoldases is central to the design of new therapies against aging, degenerative protein conformational diseases, and specific cancers.
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Affiliation(s)
- Andrija Finka
- Laboratory of Biophysical Statistics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Rayees U H Mattoo
- Department of Structural Biology, Stanford University, Stanford, California 94305;
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland;
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140
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Akbarzadeh A, Leder EH. Acclimation of killifish to thermal extremes of hot spring: Transcription of gonadal and liver heat shock genes. Comp Biochem Physiol A Mol Integr Physiol 2016; 191:89-97. [DOI: 10.1016/j.cbpa.2015.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 10/01/2015] [Accepted: 10/07/2015] [Indexed: 11/26/2022]
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141
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Abstract
Cancer cells have the unusual capacity to limit the cost of the mutation load that they harbor and simultaneously harness its evolutionary potential. This property fuels drug resistance, a key failure mode in oncogene-directed therapy. However, the factors that regulate this capacity might also provide an Achilles' heel that could be exploited therapeutically. Recently, insight has come from a seemingly distant field: protein folding. It is now clear that protein homeostasis broadly supports malignancy and fuels the rapid evolution of drug resistance. Among protein homeostatic mechanisms that influence cancer biology, the essential ATP-driven molecular chaperone heat-shock protein 90 (Hsp90) is especially important. Hsp90 catalyzes folding of many proteins that regulate growth and development. These "client" kinases, transcription factors, and ubiquitin ligases often play critical roles in human disease, especially cancer. Studies in a wide range of systems-from single-celled organisms to human tumor samples-suggest that Hsp90 can broadly reshape the map between genotype and phenotype, acting as a "capacitor" and "potentiator" of genetic variation. Indeed, it has likely done so to such a degree that it has left an impress on diverse genome sequences. Hsp90 can constitute as much as 5% of total protein in transformed cells and increased levels of heat-shock activation correlate with poor prognosis in breast cancer. These findings and others have motivated a flurry of interest in Hsp90 inhibitors as cancer therapeutics, which have met with rather limited success as single agents, but may eventually prove invaluable in limiting the emergence of resistance to other chemotherapeutics, both genotoxic and molecularly targeted. Here, we provide an overview of Hsp90 function, review its relationship to genetic variation and the evolution of new traits, and discuss the importance of these findings for cancer biology and future efforts to drug this pathway.
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Affiliation(s)
- Daniel Jarosz
- Chemical & Systems Biology, Stanford University School of Medicine, Stanford, California, USA; Developmental Biology, Stanford University School of Medicine, Stanford, California, USA.
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142
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Gassen NC, Fries GR, Zannas AS, Hartmann J, Zschocke J, Hafner K, Carrillo-Roa T, Steinbacher J, Preißinger SN, Hoeijmakers L, Knop M, Weber F, Kloiber S, Lucae S, Chrousos GP, Carell T, Ising M, Binder EB, Schmidt MV, Rüegg J, Rein T. Chaperoning epigenetics: FKBP51 decreases the activity of DNMT1 and mediates epigenetic effects of the antidepressant paroxetine. Sci Signal 2015; 8:ra119. [DOI: 10.1126/scisignal.aac7695] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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143
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Takahashi KH. Novel genetic capacitors and potentiators for the natural genetic variation of sensory bristles and their trait specificity in Drosophila melanogaster. Mol Ecol 2015; 24:5561-72. [PMID: 26441383 DOI: 10.1111/mec.13407] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 11/30/2022]
Abstract
Cryptic genetic variation (CGV) is defined as the genetic variation that has little effect on phenotypic variation under a normal condition, but contributes to heritable variation under environmental or genetic perturbations. Genetic buffering systems that suppress the expression of CGV and store it in a population are called genetic capacitors, and the opposite systems are called genetic potentiators. One of the best-known candidates for a genetic capacitor and potentiator is the molecular chaperone protein, HSP90, and one of its characteristics is that it affects the genetic variation in various morphological traits. However, it remains unclear whether the wide-ranging effects of HSP90 on a broad range of traits are a general feature of genetic capacitors and potentiators. In the current study, I searched for novel genetic capacitors and potentiators for quantitative bristle traits of Drosophila melanogaster and then investigated the trait specificity of their genetic buffering effect. Three bristle traits of D. melanogaster were used as the target traits, and the genomic regions with genetic buffering effects were screened using the 61 genomic deficiencies examined previously for genetic buffering effects in wing shape. As a result, four and six deficiencies with significant effects on increasing and decreasing the broad-sense heritability of the bristle traits were identified, respectively. Of the 18 deficiencies with significant effects detected in the current study and/or by the previous study, 14 showed trait-specific effects, and four affected the genetic buffering of both bristle traits and wing shape. This suggests that most genetic capacitors and potentiators exert trait-specific effects, but that general capacitors and potentiators with effects on multiple traits also exist.
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Affiliation(s)
- Kazuo H Takahashi
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama-si, Okayama-ken, 700-8530, Japan
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144
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Roh SH, Kasembeli M, Bakthavatsalam D, Chiu W, Tweardy DJ. Contribution of the Type II Chaperonin, TRiC/CCT, to Oncogenesis. Int J Mol Sci 2015; 16:26706-20. [PMID: 26561808 PMCID: PMC4661834 DOI: 10.3390/ijms161125975] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 02/07/2023] Open
Abstract
The folding of newly synthesized proteins and the maintenance of pre-existing proteins are essential in sustaining a living cell. A network of molecular chaperones tightly guides the folding, intracellular localization, and proteolytic turnover of proteins. Many of the key regulators of cell growth and differentiation have been identified as clients of molecular chaperones, which implies that chaperones are potential mediators of oncogenesis. In this review, we briefly provide an overview of the role of chaperones, including HSP70 and HSP90, in cancer. We further summarize and highlight the emerging the role of chaperonin TRiC (T-complex protein-1 ring complex, also known as CCT) in the development and progression of cancer mediated through its critical interactions with oncogenic clients that modulate growth deregulation, apoptosis, and genome instability in cancer cells. Elucidation of how TRiC modulates the folding and function of oncogenic clients will provide strategies for developing novel cancer therapies.
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Affiliation(s)
- Soung-Hun Roh
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Moses Kasembeli
- Division of Internal Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | | | - Wah Chiu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - David J Tweardy
- Division of Internal Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Transcriptional Derepression Uncovers Cryptic Higher-Order Genetic Interactions. PLoS Genet 2015; 11:e1005606. [PMID: 26484664 PMCID: PMC4618523 DOI: 10.1371/journal.pgen.1005606] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/24/2015] [Indexed: 12/11/2022] Open
Abstract
Disruption of certain genes can reveal cryptic genetic variants that do not typically show phenotypic effects. Because this phenomenon, which is referred to as ‘phenotypic capacitance’, is a potential source of trait variation and disease risk, it is important to understand how it arises at the genetic and molecular levels. Here, we use a cryptic colony morphology trait that segregates in a yeast cross to explore the mechanisms underlying phenotypic capacitance. We find that the colony trait is expressed when a mutation in IRA2, a negative regulator of the Ras pathway, co-occurs with specific combinations of cryptic variants in six genes. Four of these genes encode transcription factors that act downstream of the Ras pathway, indicating that the phenotype involves genetically complex changes in the transcriptional regulation of Ras targets. We provide evidence that the IRA2 mutation reveals the phenotypic effects of the cryptic variants by disrupting the transcriptional silencing of one or more genes that contribute to the trait. Supporting this role for the IRA2 mutation, deletion of SFL1, a repressor that acts downstream of the Ras pathway, also reveals the phenotype, largely due to the same cryptic variants that were detected in the IRA2 mutant cross. Our results illustrate how higher-order genetic interactions among mutations and cryptic variants can result in phenotypic capacitance in specific genetic backgrounds, and suggests these interactions might reflect genetically complex changes in gene expression that are usually suppressed by negative regulation. Some genetic polymorphisms have phenotypic effects that are masked under most conditions, but can be revealed by mutations or environmental change. The genetic and molecular mechanisms that suppress and uncover these cryptic genetic variants are important to understand. Here, we show that a single mutation in a yeast cross causes a major phenotypic change through its genetic interactions with two specific combinations of cryptic variants in six genes. This result suggests that in some cases cryptic variants themselves play roles in revealing their own phenotypic effects through their genetic interactions with each other and the mutations that reveal them. We also demonstrate that most of the genes harboring cryptic variation in our system are transcription factors, a finding that supports an important role for perturbation of gene regulatory networks in the uncovering of cryptic variation. As a final part of our study, we interrogate how a mutation exposes combinations of cryptic variants and obtain evidence that it does so by disrupting the silencing of one or more genes that must be expressed for the cryptic variants to exert their effects. To prove this point, we delete the transcriptional repressor that mediates this silencing and demonstrate that this deletion reveals a similar set of cryptic variants to the ones that were discovered in the initial mutant background. These findings advance our understanding of the genetic and molecular mechanisms that reveal cryptic variation.
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146
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De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries. Nat Commun 2015; 6:8351. [PMID: 26387459 PMCID: PMC4595759 DOI: 10.1038/ncomms9351] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 08/12/2015] [Indexed: 12/13/2022] Open
Abstract
Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants. This paper described a new and efficient method for de novo assembly of multiple DNA sequence information from mutagenized clone libraries. Using codon-barcoded libraries and calling the method JigsawSeq, the authors overcome limitations of short-read sequencing assembly from next-generation sequencing.
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147
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Sattin S, Tao J, Vettoretti G, Moroni E, Pennati M, Lopergolo A, Morelli L, Bugatti A, Zuehlke A, Moses M, Prince T, Kijima T, Beebe K, Rusnati M, Neckers L, Zaffaroni N, Agard DA, Bernardi A, Colombo G. Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands. Chemistry 2015; 21:13598-608. [PMID: 26286886 PMCID: PMC5921052 DOI: 10.1002/chem.201502211] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 12/25/2022]
Abstract
Hsp90 is a molecular chaperone of pivotal importance for multiple cell pathways. ATP-regulated internal dynamics are critical for its function and current pharmacological approaches block the chaperone with ATP-competitive inhibitors. Herein, a general approach to perturb Hsp90 through design of new allosteric ligands aimed at modulating its functional dynamics is proposed. Based on the characterization of a first set of 2-phenylbenzofurans showing stimulatory effects on Hsp90 ATPase and conformational dynamics, new ligands were developed that activate Hsp90 by targeting an allosteric site, located 65 Å from the active site. Specifically, analysis of protein responses to first-generation activators was exploited to guide the design of novel derivatives with improved ability to stimulate ATP hydrolysis. The molecules' effects on Hsp90 enzymatic, conformational, co-chaperone and client-binding properties were characterized through biochemical, biophysical and cellular approaches. These designed probes act as allosteric activators of the chaperone and affect the viability of cancer cell lines for which proper functioning of Hsp90 is necessary.
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Affiliation(s)
- Sara Sattin
- Dipartimento di Chimica, Università degli Studi di Milano via Golgi, 19, 20133, Milan (Italy)
| | - Jiahui Tao
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, 600 16th Street, San Francisco, 94158 (USA)
| | - Gerolamo Vettoretti
- Istituto di Chimica del Riconoscimento Molecolare, CNR via Mario Bianco, 9, 20131, Milan (Italy)
| | - Elisabetta Moroni
- Istituto di Chimica del Riconoscimento Molecolare, CNR via Mario Bianco, 9, 20131, Milan (Italy)
| | - Marzia Pennati
- Dept. Experimental Oncology and Molecular Medicine, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori via Amadeo, 42, 20133 Milano (Italy)
| | - Alessia Lopergolo
- Dept. Experimental Oncology and Molecular Medicine, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori via Amadeo, 42, 20133 Milano (Italy)
| | - Laura Morelli
- Dipartimento di Chimica, Università degli Studi di Milano via Golgi, 19, 20133, Milan (Italy)
| | - Antonella Bugatti
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia (Italy)
| | - Abbey Zuehlke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Mike Moses
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Thomas Prince
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Toshiki Kijima
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Kristin Beebe
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Marco Rusnati
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia (Italy)
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Nadia Zaffaroni
- Dept. Experimental Oncology and Molecular Medicine, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori via Amadeo, 42, 20133 Milano (Italy)
| | - David A Agard
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, 600 16th Street, San Francisco, 94158 (USA)
| | - Anna Bernardi
- Dipartimento di Chimica, Università degli Studi di Milano via Golgi, 19, 20133, Milan (Italy)
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR via Mario Bianco, 9, 20131, Milan (Italy).
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148
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Haase M, Fitze G. HSP90AB1: Helping the good and the bad. Gene 2015; 575:171-86. [PMID: 26358502 DOI: 10.1016/j.gene.2015.08.063] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/30/2015] [Accepted: 08/27/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Michael Haase
- Department of Pediatric Surgery, University Hospital Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany.
| | - Guido Fitze
- Department of Pediatric Surgery, University Hospital Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
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149
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Ishida K, Miyauchi K, Kimura Y, Mito M, Okada S, Suzuki T, Nakagawa S. Regulation of gene expression via retrotransposon insertions and the noncoding RNA 4.5S RNAH. Genes Cells 2015; 20:887-901. [PMID: 26333314 DOI: 10.1111/gtc.12280] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 07/22/2015] [Indexed: 12/15/2022]
Abstract
Short interspersed elements (SINEs) comprise a significant portion of mammalian genomes and regulate gene expression through a variety of mechanisms. Here, we show that Myodonta clade-specific 4.5S RNAH (4.5SH), an abundant nuclear noncoding RNA that is highly homologous to the retrotransposon SINE B1, controls the expression of reporter gene that contains the antisense insertion of SINE B1 via nuclear retention. The depletion of endogenous 4.5SH with antisense oligonucleotides neutralizes the nuclear retention and changes the subcellular distribution of the reporter transcripts containing the antisense SINE B1 insertion. Importantly, endogenous transcripts with antisense SINE B1 were increased in the cytoplasm after knockdown of 4.5SH, leading to a decrease in cellular growth. We propose a tentative hypothesis that the amplification of the 4.5SH cluster in specific rodent species might delineate their evolutionary direction via the regulation of genes containing the antisense insertion of SINE B1.
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Affiliation(s)
- Kentaro Ishida
- RNA Biology Laboratory, RIKEN Advanced Research Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yuko Kimura
- RNA Biology Laboratory, RIKEN Advanced Research Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mari Mito
- RNA Biology Laboratory, RIKEN Advanced Research Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shunpei Okada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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150
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Vermulst M, Denney AS, Lang MJ, Hung CW, Moore S, Moseley MA, Mosely AM, Thompson JW, Thompson WJ, Madden V, Gauer J, Wolfe KJ, Summers DW, Schleit J, Sutphin GL, Haroon S, Holczbauer A, Caine J, Jorgenson J, Cyr D, Kaeberlein M, Strathern JN, Duncan MC, Erie DA. Transcription errors induce proteotoxic stress and shorten cellular lifespan. Nat Commun 2015; 6:8065. [PMID: 26304740 DOI: 10.1038/ncomms9065] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/14/2015] [Indexed: 11/09/2022] Open
Abstract
Transcription errors occur in all living cells; however, it is unknown how these errors affect cellular health. To answer this question, we monitor yeast cells that are genetically engineered to display error-prone transcription. We discover that these cells suffer from a profound loss in proteostasis, which sensitizes them to the expression of genes that are associated with protein-folding diseases in humans; thus, transcription errors represent a new molecular mechanism by which cells can acquire disease phenotypes. We further find that the error rate of transcription increases as cells age, suggesting that transcription errors affect proteostasis particularly in aging cells. Accordingly, transcription errors accelerate the aggregation of a peptide that is implicated in Alzheimer's disease, and shorten the lifespan of cells. These experiments reveal a previously unappreciated role for transcriptional fidelity in cellular health and aging.
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Affiliation(s)
- Marc Vermulst
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Ashley S Denney
- School of Medicine, University of Colorado, Denver, Colorado 80217, USA
| | - Michael J Lang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Chao-Wei Hung
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Stephanie Moore
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - M Arthur Moseley
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - Arthur M Mosely
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - J Will Thompson
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - William J Thompson
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - Victoria Madden
- Microscopy Services Laboratory, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jacob Gauer
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Katie J Wolfe
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Daniel W Summers
- Department of Developmental Biology, and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Jennifer Schleit
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - George L Sutphin
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Suraiya Haroon
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Agnes Holczbauer
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Joanne Caine
- CSIRO, Department of Materials Science and Engineering, Parkville 3052, Australia
| | - James Jorgenson
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Douglas Cyr
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Jeffrey N Strathern
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Chemistry, Curriculum in Applied Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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