1
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Rolli S, Langridge CA, Sontag EM. Clearing the JUNQ: the molecular machinery for sequestration, localization, and degradation of the JUNQ compartment. Front Mol Biosci 2024; 11:1427542. [PMID: 39234568 PMCID: PMC11372896 DOI: 10.3389/fmolb.2024.1427542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/25/2024] [Indexed: 09/06/2024] Open
Abstract
Cellular protein homeostasis (proteostasis) plays an essential role in regulating the folding, sequestration, and turnover of misfolded proteins via a network of chaperones and clearance factors. Previous work has shown that misfolded proteins are spatially sequestered into membrane-less compartments in the cell as part of the proteostasis process. Soluble misfolded proteins in the cytoplasm are trafficked into the juxtanuclear quality control compartment (JUNQ), and nuclear proteins are sequestered into the intranuclear quality control compartment (INQ). However, the mechanisms that control the formation, localization, and degradation of these compartments are unknown. Previously, we showed that the JUNQ migrates to the nuclear membrane adjacent to the INQ at nucleus-vacuole junctions (NVJ), and the INQ moves through the NVJ into the vacuole for clearance in an ESCRT-mediated process. Here we have investigated what mechanisms are involved in the formation, migration, and clearance of the JUNQ. We find Hsp70s Ssa1 and Ssa2 are required for JUNQ localization to the NVJ and degradation of cytoplasmic misfolded proteins. We also confirm that sequestrases Btn2 and Hsp42 sort misfolded proteins to the JUNQ or IPOD, respectively. Interestingly, proteins required for piecemeal microautophagy of the nucleus (PMN) (i.e., Nvj1, Vac8, Atg1, and Atg8) drive the formation and clearance of the JUNQ. This suggests that the JUNQ migrates to the NVJ to be cleared via microautophagy.
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Affiliation(s)
- Sarah Rolli
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Chloe A Langridge
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Emily M Sontag
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
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2
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Levin M. Self-Improvising Memory: A Perspective on Memories as Agential, Dynamically Reinterpreting Cognitive Glue. ENTROPY (BASEL, SWITZERLAND) 2024; 26:481. [PMID: 38920491 PMCID: PMC11203334 DOI: 10.3390/e26060481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024]
Abstract
Many studies on memory emphasize the material substrate and mechanisms by which data can be stored and reliably read out. Here, I focus on complementary aspects: the need for agents to dynamically reinterpret and modify memories to suit their ever-changing selves and environment. Using examples from developmental biology, evolution, and synthetic bioengineering, in addition to neuroscience, I propose that a perspective on memory as preserving salience, not fidelity, is applicable to many phenomena on scales from cells to societies. Continuous commitment to creative, adaptive confabulation, from the molecular to the behavioral levels, is the answer to the persistence paradox as it applies to individuals and whole lineages. I also speculate that a substrate-independent, processual view of life and mind suggests that memories, as patterns in the excitable medium of cognitive systems, could be seen as active agents in the sense-making process. I explore a view of life as a diverse set of embodied perspectives-nested agents who interpret each other's and their own past messages and actions as best as they can (polycomputation). This synthesis suggests unifying symmetries across scales and disciplines, which is of relevance to research programs in Diverse Intelligence and the engineering of novel embodied minds.
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Affiliation(s)
- Michael Levin
- Department of Biology, Allen Discovery Center, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155-4243, USA
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3
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Zhao P, Wang C, Sun S, Wang X, Balch WE. Tracing genetic diversity captures the molecular basis of misfolding disease. Nat Commun 2024; 15:3333. [PMID: 38637533 PMCID: PMC11026414 DOI: 10.1038/s41467-024-47520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Genetic variation in human populations can result in the misfolding and aggregation of proteins, giving rise to systemic and neurodegenerative diseases that require management by proteostasis. Here, we define the role of GRP94, the endoplasmic reticulum Hsp90 chaperone paralog, in managing alpha-1-antitrypsin deficiency on a residue-by-residue basis using Gaussian process regression-based machine learning to profile the spatial covariance relationships that dictate protein folding arising from sequence variants in the population. Covariance analysis suggests a role for the ATPase activity of GRP94 in controlling the N- to C-terminal cooperative folding of alpha-1-antitrypsin responsible for the correction of liver aggregation and lung-disease phenotypes of alpha-1-antitrypsin deficiency. Gaussian process-based spatial covariance profiling provides a standard model built on covariant principles to evaluate the role of proteostasis components in guiding information flow from genome to proteome in response to genetic variation, potentially allowing us to intervene in the onset and progression of complex multi-system human diseases.
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Affiliation(s)
- Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- Department of Nutrition and Food Hygiene, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Collaborative Innovation Center for Cancer Personalized Medicine, and Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Xi Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
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4
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Dorrity MW, Saunders LM, Duran M, Srivatsan SR, Barkan E, Jackson DL, Sattler SM, Ewing B, Queitsch C, Shendure J, Raible DW, Kimelman D, Trapnell C. Proteostasis governs differential temperature sensitivity across embryonic cell types. Cell 2023; 186:5015-5027.e12. [PMID: 37949057 PMCID: PMC11178971 DOI: 10.1016/j.cell.2023.10.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/29/2023] [Accepted: 10/11/2023] [Indexed: 11/12/2023]
Abstract
Embryonic development is remarkably robust, but temperature stress can degrade its ability to generate animals with invariant anatomy. Phenotypes associated with environmental stress suggest that some cell types are more sensitive to stress than others, but the basis of this sensitivity is unknown. Here, we characterize hundreds of individual zebrafish embryos under temperature stress using whole-animal single-cell RNA sequencing (RNA-seq) to identify cell types and molecular programs driving phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in developmental timing. The notochord is particularly sensitive to temperature, which we map to a specialized cell type: sheath cells. These cells accumulate misfolded protein at elevated temperature, leading to a cascading structural failure of the notochord and anatomic defects. Our study demonstrates that whole-animal single-cell RNA-seq can identify mechanisms for developmental robustness and pinpoint cell types that constitute key failure points.
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Affiliation(s)
- Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Lauren M Saunders
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Eliza Barkan
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Dana L Jackson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sydney M Sattler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Brent Ewing
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David W Raible
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - David Kimelman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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5
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Paukštytė J, López Cabezas RM, Feng Y, Tong K, Schnyder D, Elomaa E, Gregorova P, Doudin M, Särkkä M, Sarameri J, Lippi A, Vihinen H, Juutila J, Nieminen A, Törönen P, Holm L, Jokitalo E, Krisko A, Huiskonen J, Sarin LP, Hietakangas V, Picotti P, Barral Y, Saarikangas J. Global analysis of aging-related protein structural changes uncovers enzyme-polymerization-based control of longevity. Mol Cell 2023; 83:3360-3376.e11. [PMID: 37699397 DOI: 10.1016/j.molcel.2023.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/18/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023]
Abstract
Aging is associated with progressive phenotypic changes. Virtually all cellular phenotypes are produced by proteins, and their structural alterations can lead to age-related diseases. However, we still lack comprehensive knowledge of proteins undergoing structural-functional changes during cellular aging and their contributions to age-related phenotypes. Here, we conducted proteome-wide analysis of early age-related protein structural changes in budding yeast using limited proteolysis-mass spectrometry (LiP-MS). The results, compiled in online ProtAge catalog, unraveled age-related functional changes in regulators of translation, protein folding, and amino acid metabolism. Mechanistically, we found that folded glutamate synthase Glt1 polymerizes into supramolecular self-assemblies during aging, causing breakdown of cellular amino acid homeostasis. Inhibiting Glt1 polymerization by mutating the polymerization interface restored amino acid levels in aged cells, attenuated mitochondrial dysfunction, and led to lifespan extension. Altogether, this comprehensive map of protein structural changes enables identifying mechanisms of age-related phenotypes and offers opportunities for their reversal.
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Affiliation(s)
- Jurgita Paukštytė
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Rosa María López Cabezas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Yuehan Feng
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Kai Tong
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Ellinoora Elomaa
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Pavlina Gregorova
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Matteo Doudin
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Meeri Särkkä
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Jesse Sarameri
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Alice Lippi
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helena Vihinen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Juhana Juutila
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Anni Nieminen
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Petri Törönen
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Liisa Holm
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Anita Krisko
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Juha Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - L Peter Sarin
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
| | - Ville Hietakangas
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Paola Picotti
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Juha Saarikangas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland.
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6
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Hung PH, Liao CW, Ko FH, Tsai HK, Leu JY. Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains. iScience 2023; 26:106635. [PMID: 37138775 PMCID: PMC10149407 DOI: 10.1016/j.isci.2023.106635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 02/21/2023] [Accepted: 04/05/2023] [Indexed: 05/05/2023] Open
Abstract
Enhanced phenotypic diversity increases a population's likelihood of surviving catastrophic conditions. Hsp90, an essential molecular chaperone and a central network hub in eukaryotes, has been observed to suppress or enhance the effects of genetic variation on phenotypic diversity in response to environmental cues. Because many Hsp90-interacting genes are involved in signaling transduction pathways and transcriptional regulation, we tested how common Hsp90-dependent differential gene expression is in natural populations. Many genes exhibited Hsp90-dependent strain-specific differential expression in five diverse yeast strains. We further identified transcription factors (TFs) potentially contributing to variable expression. We found that on Hsp90 inhibition or environmental stress, activities or abundances of Hsp90-dependent TFs varied among strains, resulting in differential strain-specific expression of their target genes, which consequently led to phenotypic diversity. We provide evidence that individual strains can readily display specific Hsp90-dependent gene expression, suggesting that the evolutionary impacts of Hsp90 are widespread in nature.
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Affiliation(s)
- Po-Hsiang Hung
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chia-Wei Liao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Fu-Hsuan Ko
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Huai-Kuang Tsai
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
- Corresponding author
| | - Jun-Yi Leu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
- Corresponding author
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7
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Titus-McQuillan JE, Nanni AV, McIntyre LM, Rogers RL. Estimating transcriptome complexities across eukaryotes. BMC Genomics 2023; 24:254. [PMID: 37170194 PMCID: PMC10173493 DOI: 10.1186/s12864-023-09326-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/20/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable lack of correspondence" between genome size and complexity, there needs to be a way to quantify complexity across organisms. In this study, we use a set of complexity metrics that allow for evaluating changes in complexity using TranD. RESULTS We ascertain if complexity is increasing or decreasing across transcriptomes and at what structural level, as complexity varies. In this study, we define three metrics - TpG, EpT, and EpG- to quantify the transcriptome's complexity that encapsulates the dynamics of alternative splicing. Here we compare complexity metrics across 1) whole genome annotations, 2) a filtered subset of orthologs, and 3) novel genes to elucidate the impacts of orthologs and novel genes in transcript model analysis. Effective Exon Number (EEN) issued to compare the distribution of exon sizes within transcripts against random expectations of uniform exon placement. EEN accounts for differences in exon size, which is important because novel gene differences in complexity for orthologs and whole-transcriptome analyses are biased towards low-complexity genes with few exons and few alternative transcripts. CONCLUSIONS With our metric analyses, we are able to quantify changes in complexity across diverse lineages with greater precision and accuracy than previous cross-species comparisons under ortholog conditioning. These analyses represent a step toward whole-transcriptome analysis in the emerging field of non-model evolutionary genomics, with key insights for evolutionary inference of complexity changes on deep timescales across the tree of life. We suggest a means to quantify biases generated in ortholog calling and correct complexity analysis for lineage-specific effects. With these metrics, we directly assay the quantitative properties of newly formed lineage-specific genes as they lower complexity.
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Affiliation(s)
- James E Titus-McQuillan
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
| | - Adalena V Nanni
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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8
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Deng S. The origin of genetic and metabolic systems: Evolutionary structuralinsights. Heliyon 2023; 9:e14466. [PMID: 36967965 PMCID: PMC10036676 DOI: 10.1016/j.heliyon.2023.e14466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.
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Affiliation(s)
- Shaojie Deng
- Chongqing (Fengjie) Municipal Bureau of Planning and Natural Resources, China
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9
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Lemus T, Mason GA, Bubb KL, Alexandre CM, Queitsch C, Cuperus JT. AGO1 and HSP90 buffer different genetic variants in Arabidopsis thaliana. Genetics 2023; 223:iyac163. [PMID: 36303325 PMCID: PMC9910400 DOI: 10.1093/genetics/iyac163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/18/2022] [Indexed: 11/14/2022] Open
Abstract
Argonaute 1 (AGO1), the principal protein component of microRNA-mediated regulation, plays a key role in plant growth and development. AGO1 physically interacts with the chaperone HSP90, which buffers cryptic genetic variation in plants and animals. We sought to determine whether genetic perturbation of AGO1 in Arabidopsis thaliana would also reveal cryptic genetic variation, and if so, whether AGO1-dependent loci overlap with those dependent on HSP90. To address these questions, we introgressed a hypomorphic mutant allele of AGO1 into a set of mapping lines derived from the commonly used Arabidopsis strains Col-0 and Ler. Although we identified several cases in which AGO1 buffered genetic variation, none of the AGO1-dependent loci overlapped with those buffered by HSP90 for the traits assayed. We focused on 1 buffered locus where AGO1 perturbation uncoupled the traits days to flowering and rosette leaf number, which are otherwise closely correlated. Using a bulk segregant approach, we identified a nonfunctional Ler hua2 mutant allele as the causal AGO1-buffered polymorphism. Introduction of a nonfunctional hua2 allele into a Col-0 ago1 mutant background recapitulated the Ler-dependent ago1 phenotype, implying that coupling of these traits involves different molecular players in these closely related strains. Taken together, our findings demonstrate that even though AGO1 and HSP90 buffer genetic variation in the same traits, these robustness regulators interact epistatically with different genetic loci, suggesting that higher-order epistasis is uncommon. Plain Language Summary Argonaute 1 (AGO1), a key player in plant development, interacts with the chaperone HSP90, which buffers environmental and genetic variation. We found that AGO1 buffers environmental and genetic variation in the same traits; however, AGO1-dependent and HSP90-dependent loci do not overlap. Detailed analysis of a buffered locus found that a nonfunctional HUA2 allele decouples days to flowering and rosette leaf number in an AGO1-dependent manner, suggesting that the AGO1-dependent buffering acts at the network level.
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Affiliation(s)
- Tzitziki Lemus
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Grace Alex Mason
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | | | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
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10
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Lee U, Mortola EN, Kim EJ, Long M. Evolution and maintenance of phenotypic plasticity. Biosystems 2022; 222:104791. [DOI: 10.1016/j.biosystems.2022.104791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/20/2022] [Accepted: 10/03/2022] [Indexed: 11/02/2022]
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11
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Mother–Fetus Immune Cross-Talk Coordinates “Extrinsic”/“Intrinsic” Embryo Gene Expression Noise and Growth Stability. Int J Mol Sci 2022; 23:ijms232012467. [PMID: 36293324 PMCID: PMC9604428 DOI: 10.3390/ijms232012467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/15/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Developmental instability (DI) is thought to be inversely related to a capacity of an organism to buffer its development against random genetic and environmental perturbations. DI is represented by a trait’s inter- and intra-individual variabilities. The inter-individual variability (inversely referred to as canalization) indicates the capability of organisms to reproduce a trait from individual to individual. The intra-individual variability reflects an organism’s capability to stabilize a trait internally under the same conditions, and, for symmetric traits, it is expressed as fluctuating asymmetry (FA). When representing a trait as a random variable conditioned on environmental fluctuations, it is clear that, in statistical terms, the DI partitions into “extrinsic” (canalization) and “intrinsic” (FA) components of a trait’s variance/noise. We established a simple statistical framework to dissect both parts of a symmetric trait variance/noise using a PCA (principal component analysis) projection of the left/right measurements on eigenvectors followed by GAMLSS (generalized additive models for location scale and shape) modeling of eigenvalues. The first eigenvalue represents “extrinsic” and the second—“intrinsic” DI components. We applied this framework to investigate the impact of mother–fetus major histocompatibility complex (MHC)-mediated immune cross-talk on gene expression noise and developmental stability. We showed that “intrinsic” gene noise for the entire transcriptional landscape could be estimated from a small subset of randomly selected genes. Using a diagnostic set of genes, we found that allogeneic MHC combinations tended to decrease “extrinsic” and “intrinsic” gene noise in C57BL/6J embryos developing in the surrogate NOD-SCID and BALB/c mothers. The “intrinsic” gene noise was negatively correlated with growth (embryonic mass) and the levels of placental growth factor (PLGF), but not vascular endothelial growth factor (VEGF). However, it was positively associated with phenotypic growth instability and noise in PLGF. In mammals, the mother–fetus MHC interaction plays a significant role in development, contributing to the fitness of the offspring. Our results demonstrate that a positive impact of distant MHC combinations on embryonic growth could be mediated by the reduction of “intrinsic” gene noise followed by the developmental stabilization of growth.
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12
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Scheffer H, Coate JE, Ho EKH, Schaack S. Thermal stress and mutation accumulation increase heat shock protein expression in Daphnia. Evol Ecol 2022; 36:829-844. [PMID: 36193163 PMCID: PMC9522699 DOI: 10.1007/s10682-022-10209-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/25/2022] [Indexed: 11/28/2022]
Abstract
Understanding the short- and long-term consequences of climate change is a major challenge in biology. For aquatic organisms, temperature changes and drought can lead to thermal stress and habitat loss, both of which can ultimately lead to higher mutation rates. Here, we examine the effect of high temperature and mutation accumulation on gene expression at two loci from the heat shock protein (HSP) gene family, HSP60 and HSP90. HSPs have been posited to serve as 'mutational capacitors' given their role as molecular chaperones involved in protein folding and degradation, thus buffering against a wide range of cellular stress and destabilization. We assayed changes in HSP expression across 5 genotypes of Daphnia magna, a sentinel species in ecology and environmental biology, with and without acute exposure to thermal stress and accumulated mutations. Across genotypes, HSP expression increased ~ 6× in response to heat and ~ 4× with mutation accumulation, individually. Both factors simultaneously (lineages with high mutation loads exposed to high heat) increased gene expression ~ 23×-much more than that predicted by an additive model. Our results corroborate suggestions that HSPs can buffer against not only the effects of heat, but also mutations-a combination of factors both likely to increase in a warming world. Supplementary Information The online version contains supplementary material available at 10.1007/s10682-022-10209-1.
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Affiliation(s)
- Henry Scheffer
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
| | - Jeremy E. Coate
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
| | - Eddie K. H. Ho
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
| | - Sarah Schaack
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
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13
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Hasan A, Rizvi SF, Parveen S, Mir SS. Molecular chaperones in DNA repair mechanisms: Role in genomic instability and proteostasis in cancer. Life Sci 2022; 306:120852. [DOI: 10.1016/j.lfs.2022.120852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/14/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023]
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14
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Marongiu F, DeGregori J. The sculpting of somatic mutational landscapes by evolutionary forces and their impacts on aging-related disease. Mol Oncol 2022; 16:3238-3258. [PMID: 35726685 PMCID: PMC9490148 DOI: 10.1002/1878-0261.13275] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/29/2022] [Accepted: 05/19/2022] [Indexed: 12/19/2022] Open
Abstract
Aging represents the major risk factor for the development of cancer and many other diseases. Recent findings show that normal tissues become riddled with expanded clones that are frequently driven by cancer‐associated mutations in an aging‐dependent fashion. Additional studies show how aged tissue microenvironments promote the initiation and progression of malignancies, while young healthy tissues actively suppress the outgrowth of malignant clones. Here, we discuss conserved mechanisms that eliminate poorly functioning or potentially malignant cells from our tissues to maintain organismal health and fitness. Natural selection acts to preserve tissue function and prevent disease to maximize reproductive success but these mechanisms wane as reproduction becomes less likely. The ensuing age‐dependent tissue decline can impact the shape and direction of clonal somatic evolution, with lifestyle and exposures influencing its pace and intensity. We also consider how aging‐ and exposure‐dependent clonal expansions of “oncogenic” mutations might both increase cancer risk late in life and contribute to tissue decline and non‐malignant disease. Still, we can marvel at the ability of our bodies to avoid cancers and other diseases despite the accumulation of billions of cells with cancer‐associated mutations.
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Affiliation(s)
- Fabio Marongiu
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Biomedical Sciences, Section of Pathology, University of Cagliari, Italy
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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15
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Melanker O, Goloubinoff P, Schreiber G. In vitro evolution of uracil glycosylase towards DnaKJ and GroEL binding evolves different misfolded states. J Mol Biol 2022; 434:167627. [PMID: 35597550 DOI: 10.1016/j.jmb.2022.167627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022]
Abstract
Natural evolution is driven by random mutations that improve fitness. In vitro evolution mimics this process, however, on a short time-scale and is driven by the given bait. Here, we used directed in vitro evolution of a random mutant library of Uracil glycosylase (eUNG) displayed on yeast surface to select for binding to chaperones GroEL, DnaK+DnaJ+ATP (DnaKJ) or E.coli cell extract (CE), using binding to the eUNG inhibitor Ugi as probe for native fold. The CE selected population was further divided to Ugi binders (+U) or non-binders (-U). The aim here was to evaluate the sequence space and physical state of the evolved protein binding the different baits. We found that GroEL, DnaKJ and CE-U select and enrich for mutations causing eUNG to misfold, with the three being enriched in mutations in buried and conserved positions, with a tendency to increase positive charge. Still, each selection had its own trajectory, with GroEL and CE-U selecting mutants highly sensitive to protease cleavage while DnaKJ selected partially structured misfolded species with a tendency to refold, making them less sensitive to proteases. More general, our results show that GroEL has a higher tendency to purge promiscuous misfolded protein mutants from the system, while DnaKJ binds misfolding-prone mutant species that are, upon chaperone release, more likely to natively refold. CE-U shares some of the properties of GroEL- and DnaKJ-selected populations, while harboring also unique properties that can be explained by the presence of additional chaperones in CE, such as Trigger factor, HtpG and ClpB.
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Affiliation(s)
- Oran Melanker
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Lausanne University, 1015 Lausanne, Switzerland
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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16
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Schell R, Hale JJ, Mullis MN, Matsui T, Foree R, Ehrenreich IM. Genetic basis of a spontaneous mutation’s expressivity. Genetics 2022; 220:6515283. [PMID: 35078232 PMCID: PMC8893249 DOI: 10.1093/genetics/iyac013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/19/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Genetic background often influences the phenotypic consequences of mutations, resulting in variable expressivity. How standing genetic variants collectively cause this phenomenon is not fully understood. Here, we comprehensively identify loci in a budding yeast cross that impact the growth of individuals carrying a spontaneous missense mutation in the nuclear-encoded mitochondrial ribosomal gene MRP20. Initial results suggested that a single large effect locus influences the mutation’s expressivity, with one allele causing inviability in mutants. However, further experiments revealed this simplicity was an illusion. In fact, many additional loci shape the mutation’s expressivity, collectively leading to a wide spectrum of mutational responses. These results exemplify how complex combinations of alleles can produce a diversity of qualitative and quantitative responses to the same mutation.
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Affiliation(s)
- Rachel Schell
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Joseph J Hale
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Martin N Mullis
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Takeshi Matsui
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ryan Foree
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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17
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Arhar T, Shkedi A, Nadel CM, Gestwicki JE. The interactions of molecular chaperones with client proteins: why are they so weak? J Biol Chem 2021; 297:101282. [PMID: 34624315 PMCID: PMC8567204 DOI: 10.1016/j.jbc.2021.101282] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/30/2022] Open
Abstract
The major classes of molecular chaperones have highly variable sequences, sizes, and shapes, yet they all bind to unfolded proteins, limit their aggregation, and assist in their folding. Despite the central importance of this process to protein homeostasis, it has not been clear exactly how chaperones guide this process or whether the diverse families of chaperones use similar mechanisms. For the first time, recent advances in NMR spectroscopy have enabled detailed studies of how unfolded, "client" proteins interact with both ATP-dependent and ATP-independent classes of chaperones. Here, we review examples from four distinct chaperones, Spy, Trigger Factor, DnaK, and HscA-HscB, highlighting the similarities and differences between their mechanisms. One striking similarity is that the chaperones all bind weakly to their clients, such that the chaperone-client interactions are readily outcompeted by stronger, intra- and intermolecular contacts in the folded state. Thus, the relatively weak affinity of these interactions seems to provide directionality to the folding process. However, there are also key differences, especially in the details of how the chaperones release clients and how ATP cycling impacts that process. For example, Spy releases clients in a largely folded state, while clients seem to be unfolded upon release from Trigger Factor or DnaK. Together, these studies are beginning to uncover the similarities and differences in how chaperones use weak interactions to guide protein folding.
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Affiliation(s)
- Taylor Arhar
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Arielle Shkedi
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Cory M Nadel
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA.
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18
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Samakovli D, Tichá T, Vavrdová T, Závorková N, Pecinka A, Ovečka M, Šamaj J. HEAT SHOCK PROTEIN 90 proteins and YODA regulate main body axis formation during early embryogenesis. PLANT PHYSIOLOGY 2021; 186:1526-1544. [PMID: 33856486 PMCID: PMC8260137 DOI: 10.1093/plphys/kiab171] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/01/2021] [Indexed: 05/23/2023]
Abstract
The YODA (YDA) kinase pathway is intimately associated with the control of Arabidopsis (Arabidopsis thaliana) embryo development, but little is known regarding its regulators. Using genetic analysis, HEAT SHOCK PROTEIN 90 (HSP90) proteins emerge as potent regulators of YDA in the process of embryo development and patterning. This study is focused on the characterization and quantification of early embryonal traits of single and double hsp90 and yda mutants. HSP90s genetic interactions with YDA affected the downstream signaling pathway to control the development of both basal and apical cell lineage of embryo. Our results demonstrate that the spatiotemporal expression of WUSCHEL-RELATED HOMEOBOX 8 (WOX8) and WOX2 is changed when function of HSP90s or YDA is impaired, suggesting their essential role in the cell fate determination and possible link to auxin signaling during early embryo development. Hence, HSP90s together with YDA signaling cascade affect transcriptional networks shaping the early embryo development.
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Affiliation(s)
- Despina Samakovli
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
| | - Tereza Tichá
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
| | - Tereza Vavrdová
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
| | - Natálie Závorková
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
| | - Ales Pecinka
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc 779 00, Czech Republic
| | - Miroslav Ovečka
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
| | - Jozef Šamaj
- Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc 783 71, Czech Republic
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19
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Chakafana G, Spracklen TF, Kamuli S, Zininga T, Shonhai A, Ntusi NAB, Sliwa K. Heat Shock Proteins: Potential Modulators and Candidate Biomarkers of Peripartum Cardiomyopathy. Front Cardiovasc Med 2021; 8:633013. [PMID: 34222357 PMCID: PMC8241919 DOI: 10.3389/fcvm.2021.633013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/06/2021] [Indexed: 12/31/2022] Open
Abstract
Peripartum cardiomyopathy (PPCM) is a potentially life-threatening condition in which heart failure and systolic dysfunction occur late in pregnancy or within months following delivery. To date, no reliable biomarkers or therapeutic interventions for the condition exist, thus necessitating an urgent need for identification of novel PPCM drug targets and candidate biomarkers. Leads for novel treatments and biomarkers are therefore being investigated worldwide. Pregnancy is generally accompanied by dramatic hemodynamic changes, including a reduced afterload and a 50% increase in cardiac output. These increased cardiac stresses during pregnancy potentially impair protein folding processes within the cardiac tissue. The accumulation of misfolded proteins results in increased toxicity and cardiac insults that trigger heart failure. Under stress conditions, molecular chaperones such as heat shock proteins (Hsps) play crucial roles in maintaining cellular proteostasis. Here, we critically assess the potential role of Hsps in PPCM. We further predict specific associations between the Hsp types Hsp70, Hsp90 and small Hsps with several proteins implicated in PPCM pathophysiology. Furthermore, we explore the possibility of select Hsps as novel candidate PPCM biomarkers and drug targets. A better understanding of how these Hsps modulate PPCM pathogenesis holds promise in improving treatment, prognosis and management of the condition, and possibly other forms of acute heart failure.
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Affiliation(s)
- Graham Chakafana
- Department of Medicine, Faculty of Health Sciences, Cape Heart Institute, University of Cape Town, Cape Town, South Africa.,Division of Cardiology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Timothy F Spracklen
- Department of Medicine, Faculty of Health Sciences, Cape Heart Institute, University of Cape Town, Cape Town, South Africa.,Division of Cardiology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Stephen Kamuli
- Department of Medicine, Faculty of Health Sciences, Cape Heart Institute, University of Cape Town, Cape Town, South Africa.,Division of Cardiology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tawanda Zininga
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Addmore Shonhai
- Department of Biochemistry, University of Venda, Thohoyandou, South Africa
| | - Ntobeko A B Ntusi
- Department of Medicine, Faculty of Health Sciences, Cape Heart Institute, University of Cape Town, Cape Town, South Africa.,Division of Cardiology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Cape Universities Body Imaging Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Karen Sliwa
- Department of Medicine, Faculty of Health Sciences, Cape Heart Institute, University of Cape Town, Cape Town, South Africa.,Division of Cardiology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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20
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Abstract
Neurodegenerative diseases and other protein-misfolding disorders represent a longstanding biomedical challenge, and effective therapies remain largely elusive. This failure is due, in part, to the recalcitrant and diverse nature of misfolded protein conformers. Recent work has uncovered that many aggregation-prone proteins can also undergo liquid-liquid phase separation, a process by which macromolecules self-associate to form dense condensates with liquid properties that are compositionally distinct from the bulk cellular milieu. Efforts to combat diseases caused by toxic protein states focus on exploiting or enhancing the proteostasis machinery to prevent and reverse pathological protein conformations. Here, we discuss recent advances in elucidating and engineering therapeutic agents to combat the diverse aberrant protein states that underlie protein-misfolding disorders.
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Affiliation(s)
- Charlotte M. Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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21
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Lee Y, Puumala E, Robbins N, Cowen LE. Antifungal Drug Resistance: Molecular Mechanisms in Candida albicans and Beyond. Chem Rev 2021; 121:3390-3411. [PMID: 32441527 PMCID: PMC8519031 DOI: 10.1021/acs.chemrev.0c00199] [Citation(s) in RCA: 335] [Impact Index Per Article: 111.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fungal infections are a major contributor to infectious disease-related deaths across the globe. Candida species are among the most common causes of invasive mycotic disease, with Candida albicans reigning as the leading cause of invasive candidiasis. Given that fungi are eukaryotes like their human host, the number of unique molecular targets that can be exploited for antifungal development remains limited. Currently, there are only three major classes of drugs approved for the treatment of invasive mycoses, and the efficacy of these agents is compromised by the development of drug resistance in pathogen populations. Notably, the emergence of additional drug-resistant species, such as Candida auris and Candida glabrata, further threatens the limited armamentarium of antifungals available to treat these serious infections. Here, we describe our current arsenal of antifungals and elaborate on the resistance mechanisms Candida species possess that render them recalcitrant to therapeutic intervention. Finally, we highlight some of the most promising therapeutic strategies that may help combat antifungal resistance, including combination therapy, targeting fungal-virulence traits, and modulating host immunity. Overall, a thorough understanding of the mechanistic principles governing antifungal drug resistance is fundamental for the development of novel therapeutics to combat current and emerging fungal threats.
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Affiliation(s)
- Yunjin Lee
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Emily Puumala
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
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22
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Gan Y, Bai N, Li X, Gao S, Wang R. A study of the binding between radicicol and four proteins by means of spectroscopy and molecular docking. JOURNAL OF CHEMICAL RESEARCH 2021. [DOI: 10.1177/1747519821993068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The interactions between radicicol and four proteins (catalase, trypsin, pepsin, and human serum protein) are investigated by spectroscopic techniques and molecular docking. A static quenching process is confirmed. The binding constant value between radicicol and human serum protein is the largest among the four proteins. Results reveal changes in the micro-environment of the protein by the addition of radicicol. It is found that radicicol shows an inhibitory effect on the activity of proteins (catalase, trypsin, and pepsin). Molecular docking results are consistent with the thermodynamic experimental results. This work provides clues to the elucidation of the mechanisms of the interactions between radicicol and proteins.
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Affiliation(s)
- Ya Gan
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, P.R. China
| | - Ning Bai
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, P.R. China
| | - Xitong Li
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, P.R. China
| | - Shuiting Gao
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, P.R. China
| | - Ruiyong Wang
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, P.R. China
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23
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Baumgartner ME, Dinan MP, Langton PF, Kucinski I, Piddini E. Proteotoxic stress is a driver of the loser status and cell competition. Nat Cell Biol 2021; 23:136-146. [PMID: 33495633 PMCID: PMC7116823 DOI: 10.1038/s41556-020-00627-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/17/2020] [Indexed: 01/29/2023]
Abstract
Cell competition allows winner cells to eliminate less fit loser cells in tissues. In Minute cell competition, cells with a heterozygous mutation in ribosome genes, such as RpS3+/- cells, are eliminated by wild-type cells. How cells are primed as losers is partially understood and it has been proposed that reduced translation underpins the loser status of ribosome mutant, or Minute, cells. Here, using Drosophila, we show that reduced translation does not cause cell competition. Instead, we identify proteotoxic stress as the underlying cause of the loser status for Minute competition and competition induced by mahjong, an unrelated loser gene. RpS3+/- cells exhibit reduced autophagic and proteasomal flux, accumulate protein aggregates and can be rescued from competition by improving their proteostasis. Conversely, inducing proteotoxic stress is sufficient to turn otherwise wild-type cells into losers. Thus, we propose that tissues may preserve their health through a proteostasis-based mechanism of cell competition and cell selection.
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Affiliation(s)
| | - Michael P Dinan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Zoology Department, University of Cambridge, Cambridge, UK
- University of Cambridge, Cambridge, UK
| | - Paul F Langton
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Iwo Kucinski
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Zoology Department, University of Cambridge, Cambridge, UK
- Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Eugenia Piddini
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
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24
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Gualtieri CT. Genomic Variation, Evolvability, and the Paradox of Mental Illness. Front Psychiatry 2021; 11:593233. [PMID: 33551865 PMCID: PMC7859268 DOI: 10.3389/fpsyt.2020.593233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
Twentieth-century genetics was hard put to explain the irregular behavior of neuropsychiatric disorders. Autism and schizophrenia defy a principle of natural selection; they are highly heritable but associated with low reproductive success. Nevertheless, they persist. The genetic origins of such conditions are confounded by the problem of variable expression, that is, when a given genetic aberration can lead to any one of several distinct disorders. Also, autism and schizophrenia occur on a spectrum of severity, from mild and subclinical cases to the overt and disabling. Such irregularities reflect the problem of missing heritability; although hundreds of genes may be associated with autism or schizophrenia, together they account for only a small proportion of cases. Techniques for higher resolution, genomewide analysis have begun to illuminate the irregular and unpredictable behavior of the human genome. Thus, the origins of neuropsychiatric disorders in particular and complex disease in general have been illuminated. The human genome is characterized by a high degree of structural and behavioral variability: DNA content variation, epistasis, stochasticity in gene expression, and epigenetic changes. These elements have grown more complex as evolution scaled the phylogenetic tree. They are especially pertinent to brain development and function. Genomic variability is a window on the origins of complex disease, neuropsychiatric disorders, and neurodevelopmental disorders in particular. Genomic variability, as it happens, is also the fuel of evolvability. The genomic events that presided over the evolution of the primate and hominid lineages are over-represented in patients with autism and schizophrenia, as well as intellectual disability and epilepsy. That the special qualities of the human genome that drove evolution might, in some way, contribute to neuropsychiatric disorders is a matter of no little interest.
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25
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Goldstein I, Ehrenreich IM. The complex role of genetic background in shaping the effects of spontaneous and induced mutations. Yeast 2020; 38:187-196. [PMID: 33125810 PMCID: PMC7984271 DOI: 10.1002/yea.3530] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/09/2020] [Accepted: 10/24/2020] [Indexed: 12/27/2022] Open
Abstract
Spontaneous and induced mutations frequently show different phenotypic effects across genetically distinct individuals. It is generally appreciated that these background effects mainly result from genetic interactions between the mutations and segregating loci. However, the architectures and molecular bases of these genetic interactions are not well understood. Recent work in a number of model organisms has tried to advance knowledge of background effects both by using large‐scale screens to find mutations that exhibit this phenomenon and by identifying the specific loci that are involved. Here, we review this body of research, emphasizing in particular the insights it provides into both the prevalence of background effects across different mutations and the mechanisms that cause these background effects. A large fraction of mutations show different effects in distinct individuals. These background effects are mainly caused by epistasis with segregating loci. Mapping studies show a diversity of genetic architectures can be involved. Genetically complex changes in gene expression are often, but not always, causative.
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Affiliation(s)
- Ilan Goldstein
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089-2910, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089-2910, USA
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26
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Yan P, Ren J, Zhang W, Qu J, Liu GH. Protein quality control of cell stemness. CELL REGENERATION (LONDON, ENGLAND) 2020; 9:22. [PMID: 33179756 PMCID: PMC7658286 DOI: 10.1186/s13619-020-00064-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
Protein quality control (PQC) systems play essential roles in the recognition, refolding and clearance of aberrant proteins, thus ensuring cellular protein homeostasis, or proteostasis. Especially, continued proliferation and differentiation of stem cells require a high rate of translation; therefore, accurate PQC systems are essential to maintain stem cell function. Growing evidence suggested crucial roles of PQC systems in regulating the stemness and differentiation of stem cells. This review focuses on current knowledge regarding the components of the proteostasis network in stem cells, and the importance of proteostasis in maintaining stem cell identity and regenerative functions. A complete understanding of this process might uncover potential applications in aging intervention and aging-related diseases.
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Affiliation(s)
- Pengze Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Ren
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Center for Bioinformation, Beijing, 100101, China
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weiqi Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- China National Center for Bioinformation, Beijing, 100101, China.
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing Qu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Brain Disorders, Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
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27
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Oamen HP, Lau Y, Caudron F. Prion-like proteins as epigenetic devices of stress adaptation. Exp Cell Res 2020; 396:112262. [DOI: 10.1016/j.yexcr.2020.112262] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/26/2020] [Accepted: 08/30/2020] [Indexed: 01/03/2023]
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28
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Samakovli D, Tichá T, Šamaj J. HSP90 chaperones regulate stomatal differentiation under normal and heat stress conditions. PLANT SIGNALING & BEHAVIOR 2020; 15:1789817. [PMID: 32669038 PMCID: PMC8550182 DOI: 10.1080/15592324.2020.1789817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 05/30/2023]
Abstract
Stomatal development is tightly connected with the overall plant growth, while changes in environmental conditions, like elevated temperature, affect negatively stomatal formation. Stomatal ontogenesis follows a well-defined series of cell developmental transitions in the cotyledon and leaf epidermis that finally lead to the production of mature stomata. YODA signaling cascade regulates stomatal development mainly through the phosphorylation and inactivation of SPEECHLESS (SPCH) transcription factor, while HSP90 chaperones have a central role in the regulation of YODA cascade. Here, we report that acute heat stress affects negatively stomatal differentiation, leads to high phosphorylation levels of MPK3 and MPK6, and alters the expression of SPCH and MUTE transcription factors. Genetic depletion of HSP90 leads to decreased stomatal differentiation rates. Thus, HSP90 chaperones safeguard the completion of distinct stomatal differentiation steps depending on these two transcription factors under normal and heat stress conditions.
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Affiliation(s)
- Despina Samakovli
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Tereza Tichá
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
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29
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Distinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis. Nat Commun 2020; 11:2926. [PMID: 32522991 PMCID: PMC7286901 DOI: 10.1038/s41467-020-16804-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/27/2020] [Indexed: 12/29/2022] Open
Abstract
Metabolic changes alter the cellular milieu; can this also change intracellular protein folding? Since proteostasis can modulate mutational buffering, if change in metabolism has the ability to change protein folding, arguably, it should also alter mutational buffering. Here we find that altered cellular metabolic states in E. coli buffer distinct mutations on model proteins. Buffered-mutants have folding problems in vivo and are differently chaperoned in different metabolic states. Notably, this assistance is dependent upon the metabolites and not on the increase in canonical chaperone machineries. Being able to reconstitute the folding assistance afforded by metabolites in vitro, we propose that changes in metabolite concentrations have the potential to alter protein folding capacity. Collectively, we unravel that the metabolite pools are bona fide members of proteostasis and aid in mutational buffering. Given the plasticity in cellular metabolism, we posit that metabolic alterations may play an important role in cellular proteostasis. Changes in osmotic homeostasis alter metabolites and therefore chemical milieu of the cells. Here, the authors show that altering metabolites in E. coli also change the cellular capacity for buffering mutations that impair protein folding and influences proteostasis irrespective of molecular chaperones
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30
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Kelly JW. Pharmacologic Approaches for Adapting Proteostasis in the Secretory Pathway to Ameliorate Protein Conformational Diseases. Cold Spring Harb Perspect Biol 2020; 12:a034108. [PMID: 31088828 PMCID: PMC7197434 DOI: 10.1101/cshperspect.a034108] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Maintenance of the proteome, ensuring the proper locations, proper conformations, appropriate concentrations, etc., is essential to preserve the health of an organism in the face of environmental insults, infectious diseases, and the challenges associated with aging. Maintaining the proteome is even more difficult in the background of inherited mutations that render a given protein and others handled by the same proteostasis machinery misfolding prone and/or aggregation prone. Maintenance of the proteome or maintaining proteostasis requires the orchestration of protein synthesis, folding, trafficking, and degradation by way of highly conserved, interacting, and competitive proteostasis pathways. Each subcellular compartment has a unique proteostasis network compromising common and specialized proteostasis maintenance pathways. Stress-responsive signaling pathways detect the misfolding and/or aggregation of proteins in specific subcellular compartments using stress sensors and respond by generating an active transcription factor. Subsequent transcriptional programs up-regulate proteostasis network capacity (i.e., ability to fold and degrade proteins in that compartment). Stress-responsive signaling pathways can also be linked by way of signaling cascades to nontranscriptional means to reestablish proteostasis (e.g., by translational attenuation). Proteostasis is also strongly influenced by the inherent kinetics and thermodynamics of the folding, misfolding, and aggregation of individual proteins, and these sequence-based attributes in combination with proteostasis network capacity together influence proteostasis. In this review, we will focus on the growing body of evidence that proteostasis deficits leading to human pathology can be reversed by pharmacologic adaptation of proteostasis network capacity through stress-responsive signaling pathway activation. The power of this approach will be exemplified by focusing on the ATF6 arm of the unfolded protein response stress responsive-signaling pathway that regulates proteostasis network capacity of the secretory pathway.
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Affiliation(s)
- Jeffery W Kelly
- Departments of Chemistry and Molecular Medicine; and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
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31
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Samakovli D, Tichá T, Vavrdová T, Ovečka M, Luptovčiak I, Zapletalová V, Kuchařová A, Křenek P, Krasylenko Y, Margaritopoulou T, Roka L, Milioni D, Komis G, Hatzopoulos P, Šamaj J. YODA-HSP90 Module Regulates Phosphorylation-Dependent Inactivation of SPEECHLESS to Control Stomatal Development under Acute Heat Stress in Arabidopsis. MOLECULAR PLANT 2020; 13:612-633. [PMID: 31935463 DOI: 10.1016/j.molp.2020.01.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/23/2019] [Accepted: 01/07/2020] [Indexed: 05/24/2023]
Abstract
Stomatal ontogenesis, patterning, and function are hallmarks of environmental plant adaptation, especially to conditions limiting plant growth, such as elevated temperatures and reduced water availability. The specification and distribution of a stomatal cell lineage and its terminal differentiation into guard cells require a master regulatory protein phosphorylation cascade involving the YODA mitogen-activated protein kinase kinase kinase. YODA signaling results in the activation of MITOGEN-ACTIVATED PROTEIN KINASEs (MPK3 and MPK6), which regulate transcription factors, including SPEECHLESS (SPCH). Here, we report that acute heat stress affects the phosphorylation and deactivation of SPCH and modulates stomatal density. By using complementary molecular, genetic, biochemical, and cell biology approaches, we provide solid evidence that HEAT SHOCK PROTEINS 90 (HSP90s) play a crucial role in transducing heat-stress response through the YODA cascade. Genetic studies revealed that YODA and HSP90.1 are epistatic, and they likely function linearly in the same developmental pathway regulating stomata formation. HSP90s interact with YODA, affect its cellular polarization, and modulate the phosphorylation of downstream targets, such as MPK6 and SPCH, under both normal and heat-stress conditions. Thus, HSP90-mediated specification and differentiation of the stomatal cell lineage couples stomatal development to environmental cues, providing an adaptive heat stress response mechanism in plants.
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Affiliation(s)
- Despina Samakovli
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic.
| | - Tereza Tichá
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic
| | - Tereza Vavrdová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic
| | - Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic
| | - Ivan Luptovčiak
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic
| | - Veronika Zapletalová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic
| | - Anna Kuchařová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic
| | - Pavel Křenek
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic
| | - Yuliya Krasylenko
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic
| | - Theoni Margaritopoulou
- Molecular Biology Laboratory, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Loukia Roka
- Molecular Biology Laboratory, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Dimitra Milioni
- Molecular Biology Laboratory, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic
| | - Polydefkis Hatzopoulos
- Molecular Biology Laboratory, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc 783 71, Czech Republic
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32
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Flynn JM, Rossouw A, Cote-Hammarlof P, Fragata I, Mavor D, Hollins C, Bank C, Bolon DN. Comprehensive fitness maps of Hsp90 show widespread environmental dependence. eLife 2020; 9:53810. [PMID: 32129763 PMCID: PMC7069724 DOI: 10.7554/elife.53810] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/03/2020] [Indexed: 12/29/2022] Open
Abstract
Gene-environment interactions have long been theorized to influence molecular evolution. However, the environmental dependence of most mutations remains unknown. Using deep mutational scanning, we engineered yeast with all 44,604 single codon changes encoding 14,160 amino acid variants in Hsp90 and quantified growth effects under standard conditions and under five stress conditions. To our knowledge, these are the largest determined comprehensive fitness maps of point mutants. The growth of many variants differed between conditions, indicating that environment can have a large impact on Hsp90 evolution. Multiple variants provided growth advantages under individual conditions; however, these variants tended to exhibit growth defects in other environments. The diversity of Hsp90 sequences observed in extant eukaryotes preferentially contains variants that supported robust growth under all tested conditions. Rather than favoring substitutions in individual conditions, the long-term selective pressure on Hsp90 may have been that of fluctuating environments, leading to robustness under a variety of conditions.
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Affiliation(s)
- Julia M Flynn
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ammeret Rossouw
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Pamela Cote-Hammarlof
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Inês Fragata
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - David Mavor
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Carl Hollins
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Claudia Bank
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Daniel Na Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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33
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Alvarez-Ponce D, Aguilar-Rodríguez J, Fares MA. Molecular Chaperones Accelerate the Evolution of Their Protein Clients in Yeast. Genome Biol Evol 2020; 11:2360-2375. [PMID: 31297528 PMCID: PMC6735891 DOI: 10.1093/gbe/evz147] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2019] [Indexed: 12/23/2022] Open
Abstract
Protein stability is a major constraint on protein evolution. Molecular chaperones, also known as heat-shock proteins, can relax this constraint and promote protein evolution by diminishing the deleterious effect of mutations on protein stability and folding. This effect, however, has only been stablished for a few chaperones. Here, we use a comprehensive chaperone–protein interaction network to study the effect of all yeast chaperones on the evolution of their protein substrates, that is, their clients. In particular, we analyze how yeast chaperones affect the evolutionary rates of their clients at two very different evolutionary time scales. We first study the effect of chaperone-mediated folding on protein evolution over the evolutionary divergence of Saccharomyces cerevisiae and S. paradoxus. We then test whether yeast chaperones have left a similar signature on the patterns of standing genetic variation found in modern wild and domesticated strains of S. cerevisiae. We find that genes encoding chaperone clients have diverged faster than genes encoding non-client proteins when controlling for their number of protein–protein interactions. We also find that genes encoding client proteins have accumulated more intraspecific genetic diversity than those encoding non-client proteins. In a number of multivariate analyses, controlling by other well-known factors that affect protein evolution, we find that chaperone dependence explains the largest fraction of the observed variance in the rate of evolution at both evolutionary time scales. Chaperones affecting rates of protein evolution mostly belong to two major chaperone families: Hsp70s and Hsp90s. Our analyses show that protein chaperones, by virtue of their ability to buffer destabilizing mutations and their role in modulating protein genotype–phenotype maps, have a considerable accelerating effect on protein evolution.
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Affiliation(s)
- David Alvarez-Ponce
- Biology Department, University of Nevada, Reno.,Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
| | - José Aguilar-Rodríguez
- Department of Biology, Stanford University, CA.,Department of Chemical and Systems Biology, Stanford University School of Medicine, CA
| | - Mario A Fares
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain.,Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Ireland
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34
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Wang C, Scott SM, Sun S, Zhao P, Hutt DM, Shao H, Gestwicki JE, Balch WE. Individualized management of genetic diversity in Niemann-Pick C1 through modulation of the Hsp70 chaperone system. Hum Mol Genet 2020; 29:1-19. [PMID: 31509197 PMCID: PMC7001602 DOI: 10.1093/hmg/ddz215] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/05/2019] [Accepted: 09/02/2019] [Indexed: 12/21/2022] Open
Abstract
Genetic diversity provides a rich repository for understanding the role of proteostasis in the management of the protein fold in human biology. Failure in proteostasis can trigger multiple disease states, affecting both human health and lifespan. Niemann-Pick C1 (NPC1) disease is a rare genetic disorder triggered by mutations in NPC1, a multi-spanning transmembrane protein that is trafficked through the exocytic pathway to late endosomes (LE) and lysosomes (Ly) (LE/Ly) to globally manage cholesterol homeostasis. Defects triggered by >300 NPC1 variants found in the human population inhibit export of NPC1 protein from the endoplasmic reticulum (ER) and/or function in downstream LE/Ly, leading to cholesterol accumulation and onset of neurodegeneration in childhood. We now show that the allosteric inhibitor JG98, that targets the cytosolic Hsp70 chaperone/co-chaperone complex, can significantly improve the trafficking and post-ER protein level of diverse NPC1 variants. Using a new approach to model genetic diversity in human disease, referred to as variation spatial profiling, we show quantitatively how JG98 alters the Hsp70 chaperone/co-chaperone system to adjust the spatial covariance (SCV) tolerance and set-points on an amino acid residue-by-residue basis in NPC1 to differentially regulate variant trafficking, stability, and cholesterol homeostasis, results consistent with the role of BCL2-associated athanogene family co-chaperones in managing the folding status of NPC1 variants. We propose that targeting the cytosolic Hsp70 system by allosteric regulation of its chaperone/co-chaperone based client relationships can be used to adjust the SCV tolerance of proteostasis buffering capacity to provide an approach to mitigate systemic and neurological disease in the NPC1 population.
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Affiliation(s)
- Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Samantha M Scott
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Darren M Hutt
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Hao Shao
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158, USA
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, CA 92037, USA
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35
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Alasady MJ, Mendillo ML. The Multifaceted Role of HSF1 in Tumorigenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1243:69-85. [PMID: 32297212 DOI: 10.1007/978-3-030-40204-4_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Heat Shock Factor 1 (HSF1), the master transcriptional regulator of the heat shock response (HSR), was first cloned more than 30 years ago. Most early research interrogating the role that HSF1 plays in biology focused on its cytoprotective functions, as a factor that promotes the survival of organisms by protecting against the proteotoxicity associated with neurodegeneration and other pathological conditions. However, recent studies have revealed a deleterious role of HSF1, as a factor that is co-opted by cancer cells to promote their own survival to the detriment of the organism. In cancer, HSF1 operates in a multifaceted manner to promote oncogenic transformation, proliferation, metastatic dissemination, and anti-cancer drug resistance. Here we review our current understanding of HSF1 activation and function in malignant progression and discuss the potential for HSF1 inhibition as a novel anticancer strategy. Collectively, this ever-growing body of work points to a prominent role of HSF1 in nearly every aspect of carcinogenesis.
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Affiliation(s)
- Milad J Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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36
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Jaeger AM, Stopfer L, Lee S, Gaglia G, Sandel D, Santagata S, Lin NU, Trepel JB, White F, Jacks T, Lindquist S, Whitesell L. Rebalancing Protein Homeostasis Enhances Tumor Antigen Presentation. Clin Cancer Res 2019; 25:6392-6405. [PMID: 31213460 DOI: 10.1158/1078-0432.ccr-19-0596] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/18/2019] [Accepted: 06/14/2019] [Indexed: 12/30/2022]
Abstract
PURPOSE Despite the accumulation of extensive genomic alterations, many cancers fail to be recognized as "foreign" and escape destruction by the host immune system. Immunotherapies designed to address this problem by directly stimulating immune effector cells have led to some remarkable clinical outcomes, but unfortunately, most cancers fail to respond, prompting the need to identify additional immunomodulatory treatment options.Experimental Design: We elucidated the effect of a novel treatment paradigm using sustained, low-dose HSP90 inhibition in vitro and in syngeneic mouse models using genetic and pharmacologic tools. Profiling of treatment-associated tumor cell antigens was performed using immunoprecipitation followed by peptide mass spectrometry. RESULTS We show that sustained, low-level inhibition of HSP90 both amplifies and diversifies the antigenic repertoire presented by tumor cells on MHC-I molecules through an IFNγ-independent mechanism. In stark contrast, we find that acute, high-dose exposure to HSP90 inhibitors, the only approach studied in the clinic to date, is broadly immunosuppressive in cell culture and in patients with cancer. In mice, chronic non-heat shock-inducing HSP90 inhibition slowed progression of colon cancer implants, but only in syngeneic animals with intact immune function. Addition of a single dose of nonspecific immune adjuvant to the regimen dramatically increased efficacy, curing a subset of mice receiving combination therapy. CONCLUSIONS These highly translatable observations support reconsideration of the most effective strategy for targeting HSP90 to treat cancers and suggest a practical approach to repurposing current orally bioavailable HSP90 inhibitors as a new immunotherapeutic strategy.See related commentary by Srivastava and Callahan, p. 6277.
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Affiliation(s)
- Alex M Jaeger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology Cambridge, Massachusetts.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - Lauren Stopfer
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology Cambridge, Massachusetts.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Sunmin Lee
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, Maryland
| | - Giorgio Gaglia
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Demi Sandel
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology Cambridge, Massachusetts
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts.,Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Nancy U Lin
- Department of Oncologic Pathology, Harvard Medical School, Massachusetts.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Jane B Trepel
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, Maryland
| | - Forest White
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology Cambridge, Massachusetts.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology Cambridge, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Luke Whitesell
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts.
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37
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Echeverria PC, Bhattacharya K, Joshi A, Wang T, Picard D. The sensitivity to Hsp90 inhibitors of both normal and oncogenically transformed cells is determined by the equilibrium between cellular quiescence and activity. PLoS One 2019; 14:e0208287. [PMID: 30726209 PMCID: PMC6364869 DOI: 10.1371/journal.pone.0208287] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/11/2019] [Indexed: 12/11/2022] Open
Abstract
The molecular chaperone Hsp90 is an essential and highly abundant central node in the interactome of eukaryotic cells. Many of its large number of client proteins are relevant to cancer. A hallmark of Hsp90-dependent proteins is that their accumulation is compromised by Hsp90 inhibitors. Combined with the anecdotal observation that cancer cells may be more sensitive to Hsp90 inhibitors, this has led to clinical trials aiming to develop Hsp90 inhibitors as anti-cancer agents. However, the sensitivity to Hsp90 inhibitors has not been studied in rigorously matched normal versus cancer cells, and despite the discovery of important regulators of Hsp90 activity and inhibitor sensitivity, it has remained unclear, why cancer cells might be more sensitive. To revisit this issue more systematically, we have generated an isogenic pair of normal and oncogenically transformed NIH-3T3 cell lines. Our proteomic analysis of the impact of three chemically different Hsp90 inhibitors shows that these affect a substantial portion of the oncogenic program and that indeed, transformed cells are hypersensitive. Targeting the oncogenic signaling pathway reverses the hypersensitivity, and so do inhibitors of DNA replication, cell growth, translation and energy metabolism. Conversely, stimulating normal cells with growth factors or challenging their proteostasis by overexpressing an aggregation-prone sensitizes them to Hsp90 inhibitors. Thus, the differential sensitivity to Hsp90 inhibitors may not stem from any particular intrinsic difference between normal and cancer cells, but rather from a shift in the balance between cellular quiescence and activity.
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Affiliation(s)
- Pablo C. Echeverria
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Genève, Switzerland
| | - Kaushik Bhattacharya
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Genève, Switzerland
| | - Abhinav Joshi
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Genève, Switzerland
| | - Tai Wang
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Genève, Switzerland
| | - Didier Picard
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Genève, Switzerland
- * E-mail:
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38
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Abstract
The regulatory processes in cells are typically organized into complex genetic networks. However, it is still unclear how this network structure modulates the evolution of cellular regulation. One would expect that mutations in central and highly connected modules of a network (so-called hubs) would often result in a breakdown and therefore be an evolutionary dead end. However, a new study by Koubkova-Yu and colleagues finds that in some circumstances, altering a hub can offer a quick evolutionary advantage. Specifically, changes in a hub can induce significant phenotypic changes that allow organisms to move away from a local fitness peak, whereas the fitness defects caused by the perturbed hub can be mitigated by mutations in its interaction partners. Together, the results demonstrate how network architecture shapes and facilitates evolutionary adaptation. Genes are organized into complex interaction networks, but it is unclear how network architecture affects evolution. This Primer explores a new study which uses experimental evolution to show how alterations in a gene central to a network affect evolutionary processes.
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Affiliation(s)
- Jana Helsen
- CMPG Laboratory of Genetics and Genomics, Departement Microbiële en Moleculaire Systemen (M2S), KU Leuven, Leuven, Belgium
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Predictive Genetics and Multicellular Systems, Departement Microbiële en Moleculaire Systemen (M2S), KU Leuven, Leuven, Belgium
| | - Jens Frickel
- CMPG Laboratory of Genetics and Genomics, Departement Microbiële en Moleculaire Systemen (M2S), KU Leuven, Leuven, Belgium
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Rob Jelier
- CMPG Laboratory of Predictive Genetics and Multicellular Systems, Departement Microbiële en Moleculaire Systemen (M2S), KU Leuven, Leuven, Belgium
| | - Kevin J. Verstrepen
- CMPG Laboratory of Genetics and Genomics, Departement Microbiële en Moleculaire Systemen (M2S), KU Leuven, Leuven, Belgium
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- * E-mail:
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Clausen L, Abildgaard AB, Gersing SK, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Protein stability and degradation in health and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:61-83. [PMID: 30635086 DOI: 10.1016/bs.apcsb.2018.09.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The cellular proteome performs highly varied functions to sustain life. Since most of these functions require proteins to fold properly, they can be impaired by mutations that affect protein structure, leading to diseases such as Alzheimer's disease, cystic fibrosis, and Lynch syndrome. The cell has evolved an intricate protein quality control (PQC) system that includes degradation pathways and a multitude of molecular chaperones and co-chaperones, all working together to catalyze the refolding or removal of aberrant proteins. Thus, the PQC system limits the harmful consequences of dysfunctional proteins, including those arising from disease-causing mutations. This complex system is still not fully understood. In particular the structural and sequence motifs that, when exposed, trigger degradation of misfolded proteins are currently under investigation. Moreover, several attempts are being made to activate or inhibit parts of the PQC system as a treatment for diseases. Here, we briefly review the present knowledge on the PQC system and list current strategies that are employed to exploit the system in disease treatment.
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Affiliation(s)
- Lene Clausen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Amanda B Abildgaard
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sarah K Gersing
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Koubkova-Yu TCT, Chao JC, Leu JY. Heterologous Hsp90 promotes phenotypic diversity through network evolution. PLoS Biol 2018; 16:e2006450. [PMID: 30439936 PMCID: PMC6264905 DOI: 10.1371/journal.pbio.2006450] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 11/29/2018] [Accepted: 10/30/2018] [Indexed: 12/24/2022] Open
Abstract
Biological processes in living cells are often carried out by gene networks in which signals and reactions are integrated through network hubs. Despite their functional importance, it remains unclear to what extent network hubs are evolvable and how alterations impact long-term evolution. We investigated these issues using heat shock protein 90 (Hsp90), a central hub of proteostasis networks. When native Hsp90 in Saccharomyces cerevisiae cells was replaced by the ortholog from hypersaline-tolerant Yarrowia lipolytica that diverged from S. cerevisiae about 270 million years ago, the cells exhibited improved growth in hypersaline environments but compromised growth in others, indicating functional divergence in Hsp90 between the two yeasts. Laboratory evolution shows that evolved Y. lipolytica-HSP90–carrying S. cerevisiae cells exhibit a wider range of phenotypic variation than cells carrying native Hsp90. Identified beneficial mutations are involved in multiple pathways and are often pleiotropic. Our results show that cells adapt to a heterologous Hsp90 by modifying different subnetworks, facilitating the evolution of phenotypic diversity inaccessible to wild-type cells. Biological processes in living cells are often carried out by gene networks. Hubs are highly connected network components important for integrating signal inputs and generating responsive functional outputs. Heat shock protein 90 (Hsp90), a versatile hub in the protein homeostasis network, is a molecular chaperone essential for cell viability in all tested eukaryotic cells. In yeast, about a quarter of the expressed proteins are profoundly influenced when Hsp90 activity is reduced. Despite its pivotal role, we found that the function of Hsp90 has diverged between two yeast species, Yarrowia lipolytica and Saccharomyces cerevisiae, which split about 270 million years ago. To understand the impacts and adaptive strategies in cells with an altered network hub, we conducted laboratory evolution experiments using a S. cerevisiae strain in which native Hsp90 is replaced by its counterpart in Y. lipolytica. We observed different fitness gain or loss under various stress conditions in individual evolved clones, suggesting that cells adapted via different evolutionary paths. Genome sequencing and mutation reconstitution experiments show that beneficial mutations occurred in multiple Hsp90-related pathways that interact with each other. Our results show that a perturbed network allows cells to evolve a broader range of phenotypic diversity unavailable to wild-type cells.
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Affiliation(s)
- Tracy Chih-Ting Koubkova-Yu
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Jung-Chi Chao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
- * E-mail:
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41
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Harrison PT, Huang PH. Exploiting vulnerabilities in cancer signalling networks to combat targeted therapy resistance. Essays Biochem 2018; 62:583-593. [PMID: 30072489 PMCID: PMC6204552 DOI: 10.1042/ebc20180016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 12/13/2022]
Abstract
Drug resistance remains one of the greatest challenges facing precision oncology today. Despite the vast array of resistance mechanisms that cancer cells employ to subvert the effects of targeted therapy, a deep understanding of cancer signalling networks has led to the development of novel strategies to tackle resistance both in the first-line and salvage therapy settings. In this review, we provide a brief overview of the major classes of resistance mechanisms to targeted therapy, including signalling reprogramming and tumour evolution; our discussion also focuses on the use of different forms of polytherapies (such as inhibitor combinations, multi-target kinase inhibitors and HSP90 inhibitors) as a means of combating resistance. The promise and challenges facing each of these polytherapies are elaborated with a perspective on how to effectively deploy such therapies in patients. We highlight efforts to harness computational approaches to predict effective polytherapies and the emerging view that exceptional responders may hold the key to better understanding drug resistance. This review underscores the importance of polytherapies as an effective means of targeting resistance signalling networks and achieving durable clinical responses in the era of personalised cancer medicine.
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Affiliation(s)
- Peter T Harrison
- Division of Molecular Pathology, The Institute of Cancer Research, London, U.K
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, U.K.
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42
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Li C, Clark LVT, Zhang R, Porebski BT, McCoey JM, Borg NA, Webb GI, Kass I, Buckle M, Song J, Woolfson A, Buckle AM. Structural Capacitance in Protein Evolution and Human Diseases. J Mol Biol 2018; 430:3200-3217. [PMID: 30111491 DOI: 10.1016/j.jmb.2018.06.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/18/2018] [Accepted: 06/29/2018] [Indexed: 10/28/2022]
Abstract
Canonical mechanisms of protein evolution include the duplication and diversification of pre-existing folds through genetic alterations that include point mutations, insertions, deletions, and copy number amplifications, as well as post-translational modifications that modify processes such as folding efficiency and cellular localization. Following a survey of the human mutation database, we have identified an additional mechanism that we term "structural capacitance," which results in the de novo generation of microstructure in previously disordered regions. We suggest that the potential for structural capacitance confers select proteins with the capacity to evolve over rapid timescales, facilitating saltatory evolution as opposed to gradualistic canonical Darwinian mechanisms. Our results implicate the elements of protein microstructure generated by this distinct mechanism in the pathogenesis of a wide variety of human diseases. The benefits of rapidly furnishing the potential for evolutionary change conferred by structural capacitance are consequently counterbalanced by this accompanying risk. The phenomenon of structural capacitance has implications ranging from the ancestral diversification of protein folds to the engineering of synthetic proteins with enhanced evolvability.
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Affiliation(s)
- Chen Li
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Liah V T Clark
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rory Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Benjamin T Porebski
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Julia M McCoey
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Natalie A Borg
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Geoffrey I Webb
- Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia
| | - Itamar Kass
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Amai Proteins, Prof. A. D. Bergman 2B, Suite 212, Rehovot 7670504, Israel
| | - Malcolm Buckle
- LBPA, ENS Cachan, CNRS, Université Paris-Saclay, F-94235 Cachan, France
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | | | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
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43
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Abstract
In this Opinion article, we aim to address how cells adapt to stress and the repercussions chronic stress has on cellular function. We consider acute and chronic stress-induced changes at the cellular level, with a focus on a regulator of cellular stress, the chaperome, which is a protein assembly that encompasses molecular chaperones, co-chaperones and other co-factors. We discuss how the chaperome takes on distinct functions under conditions of stress that are executed in ways that differ from the one-on-one cyclic, dynamic functions exhibited by distinct molecular chaperones. We argue that through the formation of multimeric stable chaperome complexes, a state of chaperome hyperconnectivity, or networking, is gained. The role of these chaperome networks is to act as multimolecular scaffolds, a particularly important function in cancer, where they increase the efficacy and functional diversity of several cellular processes. We predict that these concepts will change how we develop and implement drugs targeting the chaperome to treat cancer.
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Affiliation(s)
- Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tai Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thaís L S Araujo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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44
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Abstract
From bacteria to humans, ancient stress responses enable organisms to contend with damage to both the genome and the proteome. These pathways have long been viewed as fundamentally separate responses. Yet recent discoveries from multiple fields have revealed surprising links between the two. Many DNA-damaging agents also target proteins, and mutagenesis induced by DNA damage produces variant proteins that are prone to misfolding, degradation, and aggregation. Likewise, recent studies have observed pervasive engagement of a p53-mediated response, and other factors linked to maintenance of genomic integrity, in response to misfolded protein stress. Perhaps most remarkably, protein aggregation and self-assembly has now been observed in multiple proteins that regulate the DNA damage response. The importance of these connections is highlighted by disease models of both cancer and neurodegeneration, in which compromised DNA repair machinery leads to profound defects in protein quality control, and vice versa.
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45
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Preferences in a trait decision determined by transcription factor variants. Proc Natl Acad Sci U S A 2018; 115:E7997-E8006. [PMID: 30068600 DOI: 10.1073/pnas.1805882115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Few mechanisms are known that explain how transcription factors can adjust phenotypic outputs to accommodate differing environments. In Saccharomyces cerevisiae, the decision to mate or invade relies on environmental cues that converge on a shared transcription factor, Ste12. Specificity toward invasion occurs via Ste12 binding cooperatively with the cofactor Tec1. Here, we determine the range of phenotypic outputs (mating vs. invasion) of thousands of DNA-binding domain variants in Ste12 to understand how preference for invasion may arise. We find that single amino acid changes in the DNA-binding domain can shift the preference of yeast toward either mating or invasion. These mutations define two distinct regions of this domain, suggesting alternative modes of DNA binding for each trait. We characterize the DNA-binding specificity of wild-type Ste12 to identify a strong preference for spacing and orientation of both homodimeric and heterodimeric sites. Ste12 mutants that promote hyperinvasion in a Tec1-independent manner fail to bind cooperative sites with Tec1 and bind to unusual dimeric Ste12 sites composed of one near-perfect and one highly degenerate site. We propose a model in which Ste12 alone may have evolved to activate invasion genes, which could explain how preference for invasion arose in the many fungal pathogens that lack Tec1.
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46
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Neckers L, Blagg B, Haystead T, Trepel JB, Whitesell L, Picard D. Methods to validate Hsp90 inhibitor specificity, to identify off-target effects, and to rethink approaches for further clinical development. Cell Stress Chaperones 2018; 23:467-482. [PMID: 29392504 PMCID: PMC6045531 DOI: 10.1007/s12192-018-0877-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/12/2022] Open
Abstract
The molecular chaperone Hsp90 is one component of a highly complex and interactive cellular proteostasis network (PN) that participates in protein folding, directs misfolded and damaged proteins for destruction, and participates in regulating cellular transcriptional responses to environmental stress, thus promoting cell and organismal survival. Over the last 20 years, it has become clear that various disease states, including cancer, neurodegeneration, metabolic disorders, and infection by diverse microbes, impact the PN. Among PN components, Hsp90 was among the first to be pharmacologically targeted with small molecules. While the number of Hsp90 inhibitors described in the literature has dramatically increased since the first such small molecule was described in 1994, it has become increasingly apparent that not all of these agents have been sufficiently validated for specificity, mechanism of action, and lack of off-target effects. Given the less than expected activity of Hsp90 inhibitors in cancer-related human clinical trials, a re-evaluation of potentially confounding off-target effects, as well as confidence in target specificity and mechanism of action, is warranted. In this commentary, we provide feasible approaches to achieve these goals and we discuss additional considerations to improve the clinical efficacy of Hsp90 inhibitors in treating cancer and other diseases.
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Affiliation(s)
- Len Neckers
- Urologic Oncology Branch, National Cancer Institute, Bethesda, MD, 20892, USA.
| | - Brian Blagg
- Warren Family Research Center for Drug Discovery and Development, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Timothy Haystead
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, 27710, USA
| | - Jane B Trepel
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Luke Whitesell
- Whitehead Institute, Cambridge, MA, 02142, USA
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Didier Picard
- Département de Biologie Cellulaire, Université de Genève, 1211, Geneva 4, Switzerland.
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47
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Zabinsky RA, Mason GA, Queitsch C, Jarosz DF. It's not magic - Hsp90 and its effects on genetic and epigenetic variation. Semin Cell Dev Biol 2018; 88:21-35. [PMID: 29807130 DOI: 10.1016/j.semcdb.2018.05.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 04/15/2018] [Accepted: 05/15/2018] [Indexed: 10/14/2022]
Abstract
Canalization, or phenotypic robustness in the face of environmental and genetic perturbation, is an emergent property of living systems. Although this phenomenon has long been recognized, its molecular underpinnings have remained enigmatic until recently. Here, we review the contributions of the molecular chaperone Hsp90, a protein that facilitates the folding of many key regulators of growth and development, to canalization of phenotype - and de-canalization in times of stress - drawing on studies in eukaryotes as diverse as baker's yeast, mouse ear cress, and blind Mexican cavefish. Hsp90 is a hub of hubs that interacts with many so-called 'client proteins,' which affect virtually every aspect of cell signaling and physiology. As Hsp90 facilitates client folding and stability, it can epistatically suppress or enable the expression of genetic variants in its clients and other proteins that acquire client status through mutation. Hsp90's vast interaction network explains the breadth of its phenotypic reach, including Hsp90-dependent de novo mutations and epigenetic effects on gene regulation. Intrinsic links between environmental stress and Hsp90 function thus endow living systems with phenotypic plasticity in fluctuating environments. As environmental perturbations alter Hsp90 function, they also alter Hsp90's interaction with its client proteins, thereby re-wiring networks that determine the genotype-to-phenotype map. Ensuing de-canalization of phenotype creates phenotypic diversity that is not simply stochastic, but often has an underlying genetic basis. Thus, extreme phenotypes can be selected, and assimilated so that they no longer require environmental stress to manifest. In addition to acting on standing genetic variation, Hsp90 perturbation has also been linked to increased frequency of de novo variation and several epigenetic phenomena, all with the potential to generate heritable phenotypic change. Here, we aim to clarify and discuss the multiple means by which Hsp90 can affect phenotype and possibly evolutionary change, and identify their underlying common feature: at its core, Hsp90 interacts epistatically through its chaperone function with many other genes and their gene products. Its influence on phenotypic diversification is thus not magic but rather a fundamental property of genetics.
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Affiliation(s)
- Rebecca A Zabinsky
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford, CA, United States
| | | | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, United States.
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford, CA, United States; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, United States.
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48
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Taipale M. Disruption of protein function by pathogenic mutations: common and uncommon mechanisms 1. Biochem Cell Biol 2018; 97:46-57. [PMID: 29693415 DOI: 10.1139/bcb-2018-0007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mutations in protein-coding regions underlie almost all Mendelian disorders, drive tumorigenesis, and contribute to susceptibility to common diseases. Despite the great diversity of diseases that are caused by coding mutations, the cellular processes that affect, and are affected by, pathogenic variants at the molecular level are fundamentally conserved. Experimental and computational approaches have revealed that a substantial fraction of disease mutations are not simple loss-of-function alleles. Rather, these pathogenic variants disrupt protein function in more subtle ways by tuning protein folding pathways, altering subcellular trafficking, interrupting signaling cascades, and rewiring highly connected interaction networks. Focusing mainly on Mendelian disorders, this review discusses the common mechanisms by which deleterious mutations disrupt protein function and how these disruptions can be exploited in the development of novel therapies.
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Affiliation(s)
- Mikko Taipale
- a Donnelly Centre, Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.,b Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, ON M5S 1M1, Canada
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49
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Bunney TD, Inglis AJ, Sanfelice D, Farrell B, Kerr CJ, Thompson GS, Masson GR, Thiyagarajan N, Svergun DI, Williams RL, Breeze AL, Katan M. Disease Variants of FGFR3 Reveal Molecular Basis for the Recognition and Additional Roles for Cdc37 in Hsp90 Chaperone System. Structure 2018; 26:446-458.e8. [PMID: 29478821 PMCID: PMC5846801 DOI: 10.1016/j.str.2018.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/06/2017] [Accepted: 01/26/2018] [Indexed: 11/21/2022]
Abstract
Receptor tyrosine kinase FGFR3 is involved in many signaling networks and is frequently mutated in developmental disorders and cancer. The Hsp90/Cdc37 chaperone system is essential for function of normal and neoplastic cells. Here we uncover the mechanistic inter-relationships between these proteins by combining approaches including NMR, HDX-MS, and SAXS. We show that several disease-linked mutations convert FGFR3 to a stronger client, where the determinant underpinning client strength involves an allosteric network through the N-lobe and at the lobe interface. We determine the architecture of the client kinase/Cdc37 complex and demonstrate, together with site-specific information, that binding of Cdc37 to unrelated kinases induces a common, extensive conformational remodeling of the kinase N-lobe, beyond localized changes and interactions within the binary complex. As further shown for FGFR3, this processing by Cdc37 deactivates the kinase and presents it, in a specific orientation established in the complex, for direct recognition by Hsp90.
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Affiliation(s)
- Tom D Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK.
| | - Alison J Inglis
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Domenico Sanfelice
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Brendan Farrell
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, Leeds LS2 9JT, UK
| | - Christopher J Kerr
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, DESY, Hamburg, Germany
| | - Gary S Thompson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, Leeds LS2 9JT, UK
| | - Glenn R Masson
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Nethaji Thiyagarajan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, DESY, Hamburg, Germany
| | - Roger L Williams
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, Leeds LS2 9JT, UK.
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK.
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50
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Yadav A, Dhole K, Sinha H. Differential Regulation of Cryptic Genetic Variation Shapes the Genetic Interactome Underlying Complex Traits. Genome Biol Evol 2018; 8:3559-3573. [PMID: 28172852 PMCID: PMC5381507 DOI: 10.1093/gbe/evw258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2016] [Indexed: 12/21/2022] Open
Abstract
Cryptic genetic variation (CGV) refers to genetic variants whose effects are buffered in most conditions but manifest phenotypically upon specific genetic and environmental perturbations. Despite having a central role in adaptation, contribution of CGV to regulation of quantitative traits is unclear. Instead, a relatively simplistic architecture of additive genetic loci is known to regulate phenotypic variation in most traits. In this paper, we investigate the regulation of CGV and its implication on the genetic architecture of quantitative traits at a genome-wide level. We use a previously published dataset of biparental recombinant population of Saccharomyces cerevisiae phenotyped in 34 diverse environments to perform single locus, two-locus, and covariance mapping. We identify loci that have independent additive effects as well as those which regulate the phenotypic manifestation of other genetic variants (variance QTL). We find that whereas additive genetic variance is predominant, a higher order genetic interaction network regulates variation in certain environments. Despite containing pleiotropic loci, with effects across environments, these genetic networks are highly environment specific. CGV is buffered under most allelic combinations of these networks and perturbed only in rare combinations resulting in high phenotypic variance. The presence of such environment specific genetic networks is the underlying cause of abundant gene–environment interactions. We demonstrate that overlaying identified molecular networks on such genetic networks can identify potential candidate genes and underlying mechanisms regulating phenotypic variation. Such an integrated approach applied to human disease datasets has the potential to improve the ability to predict disease predisposition and identify specific therapeutic targets.
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Affiliation(s)
- Anupama Yadav
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Kaustubh Dhole
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Himanshu Sinha
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.,Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.,Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, India
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