1
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Liu Z, Gillis TG, Raman S, Cui Q. A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery. eLife 2024; 12:RP92262. [PMID: 38836839 DOI: 10.7554/elife.92262] [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] [Indexed: 06/06/2024] Open
Abstract
New experimental findings continue to challenge our understanding of protein allostery. Recent deep mutational scanning study showed that allosteric hotspots in the tetracycline repressor (TetR) and its homologous transcriptional factors are broadly distributed rather than spanning well-defined structural pathways as often assumed. Moreover, hotspot mutation-induced allostery loss was rescued by distributed additional mutations in a degenerate fashion. Here, we develop a two-domain thermodynamic model for TetR, which readily rationalizes these intriguing observations. The model accurately captures the in vivo activities of various mutants with changes in physically transparent parameters, allowing the data-based quantification of mutational effects using statistical inference. Our analysis reveals the intrinsic connection of intra- and inter-domain properties for allosteric regulation and illustrate epistatic interactions that are consistent with structural features of the protein. The insights gained from this study into the nature of two-domain allostery are expected to have broader implications for other multi-domain allosteric proteins.
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Affiliation(s)
- Zhuang Liu
- Department of Physics, Boston University, Boston, United States
| | - Thomas G Gillis
- Department of Biochemistry, University of Wisconsin, Madison, United States
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin, Madison, United States
- Department of Chemistry, University of Wisconsin, Madison, United States
- Department of Bacteriology, University of Wisconsin, Madison, United States
| | - Qiang Cui
- Department of Physics, Boston University, Boston, United States
- Department of Chemistry, Boston University, Boston, United States
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2
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Rao J, Xin R, Macdonald C, Howard MK, Estevam GO, Yee SW, Wang M, Fraser JS, Coyote-Maestas W, Pimentel H. Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage. Genome Biol 2024; 25:138. [PMID: 38789982 PMCID: PMC11127319 DOI: 10.1186/s13059-024-03279-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Deep mutational scanning (DMS) measures the effects of thousands of genetic variants in a protein simultaneously. The small sample size renders classical statistical methods ineffective. For example, p-values cannot be correctly calibrated when treating variants independently. We propose Rosace, a Bayesian framework for analyzing growth-based DMS data. Rosace leverages amino acid position information to increase power and control the false discovery rate by sharing information across parameters via shrinkage. We also developed Rosette for simulating the distributional properties of DMS. We show that Rosace is robust to the violation of model assumptions and is more powerful than existing tools.
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Affiliation(s)
- Jingyou Rao
- Department of Computer Science, UCLA, Los Angeles, CA, USA
| | - Ruiqi Xin
- Computational and Systems Biology Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - Christian Macdonald
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
| | - Matthew K Howard
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
- Tetrad Graduate Program, UCSF, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
| | - Gabriella O Estevam
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
- Tetrad Graduate Program, UCSF, San Francisco, CA, USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
| | - Mingsen Wang
- Department of Mathematics, Baruch College, CUNY, New York, NY, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
- Quantitative Biosciences Institute, UCSF, San Francisco, CA, USA
| | - Willow Coyote-Maestas
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA.
- Quantitative Biosciences Institute, UCSF, San Francisco, CA, USA.
| | - Harold Pimentel
- Department of Computer Science, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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3
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Ribeiro TDS, Lollar MJ, Sprengelmeyer QD, Huang Y, Benson DM, Orr MS, Johnson ZC, Corbett-Detig RB, Pool JE. Recombinant inbred line panels inform the genetic architecture and interactions of adaptive traits in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594228. [PMID: 38798433 PMCID: PMC11118405 DOI: 10.1101/2024.05.14.594228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The distribution of allelic effects on traits, along with their gene-by-gene and gene-by-environment interactions, contributes to the phenotypes available for selection and the trajectories of adaptive variants. Nonetheless, uncertainty persists regarding the effect sizes underlying adaptations and the importance of genetic interactions. Herein, we aimed to investigate the genetic architecture and the epistatic and environmental interactions involving loci that contribute to multiple adaptive traits using two new panels of Drosophila melanogaster recombinant inbred lines (RILs). To better fit our data, we re-implemented functions from R/qtl (Broman et al. 2003) using additive genetic models. We found 14 quantitative trait loci (QTL) underlying melanism, wing size, song pattern, and ethanol resistance. By combining our mapping results with population genetic statistics, we identified potential new genes related to these traits. None of the detected QTLs showed clear evidence of epistasis, and our power analysis indicated that we should have seen at least one significant interaction if sign epistasis or strong positive epistasis played a pervasive role in trait evolution. In contrast, we did find roles for gene-by-environment interactions involving pigmentation traits. Overall, our data suggest that the genetic architecture of adaptive traits often involves alleles of detectable effect, that strong epistasis does not always play a role in adaptation, and that environmental interactions can modulate the effect size of adaptive alleles.
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Affiliation(s)
- Tiago da Silva Ribeiro
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Matthew J. Lollar
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Yuheng Huang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Derek M. Benson
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Megan S. Orr
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zachary C. Johnson
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Russell B. Corbett-Detig
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - John E. Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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4
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Ardell S, Martsul A, Johnson MS, Kryazhimskiy S. Environment-independent distribution of mutational effects emerges from microscopic epistasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.18.567655. [PMID: 38014325 PMCID: PMC10680819 DOI: 10.1101/2023.11.18.567655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Predicting how new mutations alter phenotypes is difficult because mutational effects vary across genotypes and environments. Recently discovered global epistasis, where the fitness effects of mutations scale with the fitness of the background genotype, can improve predictions, but how the environment modulates this scaling is unknown. We measured the fitness effects of ~100 insertion mutations in 42 strains of Saccharomyces cerevisiae in six laboratory environments and found that the global-epistasis scaling is nearly invariant across environments. Instead, the environment tunes one global parameter, the background fitness at which most mutations switch sign. As a consequence, the distribution of mutational effects is predictable across genotypes and environments. Our results suggest that the effective dimensionality of genotype-to-phenotype maps across environments is surprisingly low.
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Affiliation(s)
- Sarah Ardell
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA 92093
| | - Alena Martsul
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA 92093
| | - Milo S. Johnson
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA 92093
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5
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Flynn JM, Joyce ME, Bolon DNA. Dominant negative mutations in yeast Hsp90 reveal triage decision mechanism targeting client proteins for degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573950. [PMID: 38260708 PMCID: PMC10802349 DOI: 10.1101/2024.01.02.573950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Most of the fundamental processes of cells are mediated by proteins. However, the biologically-relevant mechanism of most proteins are poorly understood. Dominant negative mutations have provided a valuable tool for investigating protein mechanisms but can be difficult to isolate because of their toxic effects. We used a mutational scanning approach to identify dominant negative mutations in yeast Hsp90. Hsp90 is a chaperone that forms dynamic complexes with many co-chaperones and client proteins. In vitro analyses have elucidated some key biochemical states and structures of Hsp90, co-chaperones, and clients; however, the biological mechanism of Hsp90 remains unclear. For example, high throughput studies have found that many E3 ubiquitin ligases bind to Hsp90, but it is unclear if these are primarily clients or acting to tag other clients for degradation. We introduced a library of all point mutations in the ATPase domain of Hsp90 into yeast and noticed that 176 were more than 10-fold depleted at the earliest point that we could analyze. There were two hot spot regions of the depleted mutations that were located at the hinges of a loop that closes over ATP. We quantified the dominant negative growth effects of mutations in the hinge regions using a library of mutations driven by an inducible promoter. We analyzed individual dominant negative mutations in detail and found that addition of the E33A mutation that prevents ATP hydrolysis by Hsp90 abrogated the dominant negative phenotype. Pull-down experiments did not reveal any stable binding partners, indicating that the dominant effects were mediated by dynamic complexes. DN Hsp90 decreased the expression level of two model Hsp90 clients, glucocorticoid receptor (GR) and v-src kinase. Using MG132, we found that GR was rapidly destabilized in a proteasome-dependent fashion. These findings provide evidence that the binding of E3 ligases to Hsp90 may serve a quality control function fundamental to eukaryotes.
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Affiliation(s)
- Julia M. Flynn
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Margot E. Joyce
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Daniel N. A. Bolon
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
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6
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Kohanovski I, Pontz M, Vande Zande P, Selmecki A, Dahan O, Pilpel Y, Yona AH, Ram Y. Aneuploidy Can Be an Evolutionary Diversion on the Path to Adaptation. Mol Biol Evol 2024; 41:msae052. [PMID: 38427813 PMCID: PMC10951435 DOI: 10.1093/molbev/msae052] [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: 11/23/2023] [Revised: 01/29/2024] [Accepted: 02/27/2024] [Indexed: 03/03/2024] Open
Abstract
Aneuploidy is common in eukaryotes, often leading to decreased fitness. However, evidence from fungi and human tumur cells suggests that specific aneuploidies can be beneficial under stressful conditions and facilitate adaptation. In a previous evolutionary experiment with yeast, populations evolving under heat stress became aneuploid, only to later revert to euploidy after beneficial mutations accumulated. It was therefore suggested that aneuploidy is a "stepping stone" on the path to adaptation. Here, we test this hypothesis. We use Bayesian inference to fit an evolutionary model with both aneuploidy and mutation to the experimental results. We then predict the genotype frequency dynamics during the experiment, demonstrating that most of the evolved euploid population likely did not descend from aneuploid cells, but rather from the euploid wild-type population. Our model shows how the beneficial mutation supply-the product of population size and beneficial mutation rate-determines the evolutionary dynamics: with low supply, much of the evolved population descends from aneuploid cells; but with high supply, beneficial mutations are generated fast enough to outcompete aneuploidy due to its inherent fitness cost. Our results suggest that despite its potential fitness benefits under stress, aneuploidy can be an evolutionary "diversion" rather than a "stepping stone": it can delay, rather than facilitate, the adaptation of the population, and cells that become aneuploid may leave less descendants compared to cells that remain diploid.
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Affiliation(s)
- Ilia Kohanovski
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- School of Computer Science, Reichman University, Herzliya, Israel
| | - Martin Pontz
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Pétra Vande Zande
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Orna Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Avihu H Yona
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yoav Ram
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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7
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Liu Z, Gillis T, Raman S, Cui Q. A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.06.552196. [PMID: 37662419 PMCID: PMC10473640 DOI: 10.1101/2023.08.06.552196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
New experimental findings continue to challenge our understanding of protein allostery. Recent deep mutational scanning study showed that allosteric hotspots in the tetracycline repressor (TetR) and its homologous transcriptional factors are broadly distributed rather than spanning well-defined structural pathways as often assumed. Moreover, hotspot mutation-induced allostery loss was rescued by distributed additional mutations in a degenerate fashion. Here, we develop a two-domain thermodynamic model for TetR, which readily rationalizes these intriguing observations. The model accurately captures the in vivo activities of various mutants with changes in physically transparent parameters, allowing the data-based quantification of mutational effects using statistical inference. Our analysis reveals the intrinsic connection of intra- and inter-domain properties for allosteric regulation and illustrate epistatic interactions that are consistent with structural features of the protein. The insights gained from this study into the nature of two-domain allostery are expected to have broader implications for other multidomain allosteric proteins.
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Affiliation(s)
- Zhuang Liu
- Department of Physics, Boston University, Boston, United States
| | - Thomas Gillis
- Department of Biochemistry, University of Wisconsin, Madison, United States
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin, Madison, United States
- Department of Chemistry, University of Wisconsin, Madison, United States
- Department of Bacteriology, University of Wisconsin, Madison, United States
| | - Qiang Cui
- Department of Physics, Boston University, Boston, United States
- Department of Chemistry, Boston University, Boston, United States
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8
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Rios EI, Hunsberger IL, Johnson JL. Insights into Hsp90 mechanism and in vivo functions learned from studies in the yeast, Saccharomyces cerevisiae. Front Mol Biosci 2024; 11:1325590. [PMID: 38389899 PMCID: PMC10881880 DOI: 10.3389/fmolb.2024.1325590] [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: 11/13/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
The molecular chaperone Hsp90 (Heat shock protein, 90 kDa) is an abundant and essential cytosolic protein required for the stability and/or folding of hundreds of client proteins. Hsp90, along with helper cochaperone proteins, assists client protein folding in an ATP-dependent pathway. The laboratory of Susan Lindquist, in collaboration with other researchers, was the first to establish the yeast Saccharomyces cerevisiae as a model organism to study the functional interaction between Hsp90 and clients. Important insights from studies in her lab were that Hsp90 is essential, and that Hsp90 functions and cochaperone interactions are highly conserved between yeast and mammalian cells. Here, we describe key mechanistic insights into the Hsp90 folding cycle that were obtained using the yeast system. We highlight the early contributions of the laboratory of Susan Lindquist and extend our analysis into the broader use of the yeast system to analyze the understanding of the conformational cycle of Hsp90 and the impact of altered Hsp90 function on the proteome.
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Affiliation(s)
- Erick I Rios
- Department of Biological Sciences and Center for Reproductive Biology, University of Idaho, Moscow, ID, United States
| | - Isabel L Hunsberger
- Department of Biological Sciences and Center for Reproductive Biology, University of Idaho, Moscow, ID, United States
| | - Jill L Johnson
- Department of Biological Sciences and Center for Reproductive Biology, University of Idaho, Moscow, ID, United States
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9
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Notin P, Kollasch AW, Ritter D, van Niekerk L, Paul S, Spinner H, Rollins N, Shaw A, Weitzman R, Frazer J, Dias M, Franceschi D, Orenbuch R, Gal Y, Marks DS. ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570727. [PMID: 38106144 PMCID: PMC10723403 DOI: 10.1101/2023.12.07.570727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease to designing novel proteins that can address our most pressing challenges in climate, agriculture and healthcare. Despite a surge in machine learning-based protein models to tackle these questions, an assessment of their respective benefits is challenging due to the use of distinct, often contrived, experimental datasets, and the variable performance of models across different protein families. Addressing these challenges requires scale. To that end we introduce ProteinGym, a large-scale and holistic set of benchmarks specifically designed for protein fitness prediction and design. It encompasses both a broad collection of over 250 standardized deep mutational scanning assays, spanning millions of mutated sequences, as well as curated clinical datasets providing high-quality expert annotations about mutation effects. We devise a robust evaluation framework that combines metrics for both fitness prediction and design, factors in known limitations of the underlying experimental methods, and covers both zero-shot and supervised settings. We report the performance of a diverse set of over 70 high-performing models from various subfields (eg., alignment-based, inverse folding) into a unified benchmark suite. We open source the corresponding codebase, datasets, MSAs, structures, model predictions and develop a user-friendly website that facilitates data access and analysis.
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Affiliation(s)
| | | | | | | | | | | | | | - Ada Shaw
- Applied Mathematics, Harvard University
| | | | | | - Mafalda Dias
- Centre for Genomic Regulation, Universitat Pompeu Fabra
| | | | | | - Yarin Gal
- Computer Science, University of Oxford
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10
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Quan N, Eguchi Y, Geiler-Samerotte K. Intra- FCY1: a novel system to identify mutations that cause protein misfolding. Front Genet 2023; 14:1198203. [PMID: 37745845 PMCID: PMC10512024 DOI: 10.3389/fgene.2023.1198203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Protein misfolding is a common intracellular occurrence. Most mutations to coding sequences increase the propensity of the encoded protein to misfold. These misfolded molecules can have devastating effects on cells. Despite the importance of protein misfolding in human disease and protein evolution, there are fundamental questions that remain unanswered, such as, which mutations cause the most misfolding? These questions are difficult to answer partially because we lack high-throughput methods to compare the destabilizing effects of different mutations. Commonly used systems to assess the stability of mutant proteins in vivo often rely upon essential proteins as sensors, but misfolded proteins can disrupt the function of the essential protein enough to kill the cell. This makes it difficult to identify and compare mutations that cause protein misfolding using these systems. Here, we present a novel in vivo system named Intra-FCY1 that we use to identify mutations that cause misfolding of a model protein [yellow fluorescent protein (YFP)] in Saccharomyces cerevisiae. The Intra-FCY1 system utilizes two complementary fragments of the yeast cytosine deaminase Fcy1, a toxic protein, into which YFP is inserted. When YFP folds, the Fcy1 fragments associate together to reconstitute their function, conferring toxicity in media containing 5-fluorocytosine and hindering growth. But mutations that make YFP misfold abrogate Fcy1 toxicity, thus strains possessing misfolded YFP variants rise to high frequency in growth competition experiments. This makes such strains easier to study. The Intra-FCY1 system cancels localization of the protein of interest, thus can be applied to study the relative stability of mutant versions of diverse cellular proteins. Here, we confirm this method can identify novel mutations that cause misfolding, highlighting the potential for Intra-FCY1 to illuminate the relationship between protein sequence and stability.
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Affiliation(s)
- N. Quan
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Y. Eguchi
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
| | - K. Geiler-Samerotte
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
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11
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Alao JP, Obaseki I, Amankwah YS, Nguyen Q, Sugoor M, Unruh E, Popoola HO, Tehver R, Kravats AN. Insight into the Nucleotide Based Modulation of the Grp94 Molecular Chaperone Using Multiscale Dynamics. J Phys Chem B 2023. [PMID: 37294929 DOI: 10.1021/acs.jpcb.3c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Grp94, an ER-localized molecular chaperone, is required for the folding and activation of many membrane and secretory proteins. Client activation by Grp94 is mediated by nucleotide and conformational changes. In this work, we aim to understand how microscopic changes from nucleotide hydrolysis can potentiate large-scale conformational changes of Grp94. We performed all-atom molecular dynamics simulations on the ATP-hydrolysis competent state of the Grp94 dimer in four different nucleotide bound states. We found that Grp94 was the most rigid when ATP was bound. ATP hydrolysis or nucleotide removal enhanced mobility of the N-terminal domain and ATP lid, resulting in suppression of interdomain communication. In an asymmetric conformation with one hydrolyzed nucleotide, we identified a more compact state, similar to experimental observations. We also identified a potential regulatory role of the flexible linker, as it formed electrostatic interactions with the Grp94 M-domain helix near the region where BiP is known to bind. These studies were complemented with normal-mode analysis of an elastic network model to investigate Grp94's large-scale conformational changes. SPM analysis identified residues that are important in signaling conformational change, many of which have known functional relevance in ATP coordination and catalysis, client binding, and BiP binding. Our findings suggest that ATP hydrolysis in Grp94 alters allosteric wiring and facilitates conformational changes.
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Affiliation(s)
- John Paul Alao
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Ikponwmosa Obaseki
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Yaa Sarfowah Amankwah
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Quinn Nguyen
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Meghana Sugoor
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Erin Unruh
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Cell, Molecular, and Structural Biology Program, Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | | | - Riina Tehver
- Department of Physics, Denison University, Granville, Ohio 43023, United States
| | - Andrea N Kravats
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Cell, Molecular, and Structural Biology Program, Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
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12
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Kinsler G, Schmidlin K, Newell D, Eder R, Apodaca S, Lam G, Petrov D, Geiler-Samerotte K. Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch. J Mol Evol 2023; 91:293-310. [PMID: 37237236 PMCID: PMC10276131 DOI: 10.1007/s00239-023-10114-3] [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: 08/30/2022] [Accepted: 04/30/2023] [Indexed: 05/28/2023]
Abstract
The phrase "survival of the fittest" has become an iconic descriptor of how natural selection works. And yet, precisely measuring fitness, even for single-celled microbial populations growing in controlled laboratory conditions, remains a challenge. While numerous methods exist to perform these measurements, including recently developed methods utilizing DNA barcodes, all methods are limited in their precision to differentiate strains with small fitness differences. In this study, we rule out some major sources of imprecision, but still find that fitness measurements vary substantially from replicate to replicate. Our data suggest that very subtle and difficult to avoid environmental differences between replicates create systematic variation across fitness measurements. We conclude by discussing how fitness measurements should be interpreted given their extreme environment dependence. This work was inspired by the scientific community who followed us and gave us tips as we live tweeted a high-replicate fitness measurement experiment at #1BigBatch.
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Affiliation(s)
| | - Kara Schmidlin
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
| | - Daphne Newell
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | - Rachel Eder
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | - Sam Apodaca
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | | | | | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA.
- School of Life Sciences, Arizona State University, Tempe, USA.
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13
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Mathy CJP, Kortemme T. Emerging maps of allosteric regulation in cellular networks. Curr Opin Struct Biol 2023; 80:102602. [PMID: 37150039 PMCID: PMC10960510 DOI: 10.1016/j.sbi.2023.102602] [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: 12/29/2022] [Revised: 03/24/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
Allosteric regulation is classically defined as action at a distance, where a perturbation outside of a protein active site affects function. While this definition has motivated many studies of allosteric mechanisms at the level of protein structure, translating these insights to the allosteric regulation of entire cellular processes - and their crosstalk - has received less attention, despite the broad importance of allostery for cellular regulation foreseen by Jacob and Monod. Here, we revisit an evolutionary model for the widespread emergence of allosteric regulation in colocalized proteins, describe supporting evidence, and discuss emerging advances in mapping allostery in cellular networks that link precise and often allosteric perturbations at the molecular level to functional changes at the pathway and systems levels.
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Affiliation(s)
- Christopher J P Mathy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, CA, 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, 94158, USA.
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, CA, 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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14
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Ghenu AH, Amado A, Gordo I, Bank C. Epistasis decreases with increasing antibiotic pressure but not temperature. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220058. [PMID: 37004727 PMCID: PMC10067269 DOI: 10.1098/rstb.2022.0058] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Predicting mutational effects is essential for the control of antibiotic resistance (ABR). Predictions are difficult when there are strong genotype-by-environment (G × E), gene-by-gene (G × G or epistatic) or gene-by-gene-by-environment (G × G × E) interactions. We quantified G × G × E effects in Escherichia coli across environmental gradients. We created intergenic fitness landscapes using gene knock-outs and single-nucleotide ABR mutations previously identified to vary in the extent of G × E effects in our environments of interest. Then, we measured competitive fitness across a complete combinatorial set of temperature and antibiotic dosage gradients. In this way, we assessed the predictability of 15 fitness landscapes across 12 different but related environments. We found G × G interactions and rugged fitness landscapes in the absence of antibiotic, but as antibiotic concentration increased, the fitness effects of ABR genotypes quickly overshadowed those of gene knock-outs, and the landscapes became smoother. Our work reiterates that some single mutants, like those conferring resistance or susceptibility to antibiotics, have consistent effects across genetic backgrounds in stressful environments. Thus, although epistasis may reduce the predictability of evolution in benign environments, evolution may be more predictable in adverse environments. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Ana-Hermina Ghenu
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal
- Division of Theoretical Ecology and Evolution, Institut für Ökologie und Evolution, Universität Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - André Amado
- Division of Theoretical Ecology and Evolution, Institut für Ökologie und Evolution, Universität Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal
| | - Claudia Bank
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal
- Division of Theoretical Ecology and Evolution, Institut für Ökologie und Evolution, Universität Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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15
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Mathy CJP, Mishra P, Flynn JM, Perica T, Mavor D, Bolon DNA, Kortemme T. A complete allosteric map of a GTPase switch in its native cellular network. Cell Syst 2023; 14:237-246.e7. [PMID: 36801015 PMCID: PMC10173951 DOI: 10.1016/j.cels.2023.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 11/08/2022] [Accepted: 01/06/2023] [Indexed: 02/19/2023]
Abstract
Allosteric regulation is central to protein function in cellular networks. A fundamental open question is whether cellular regulation of allosteric proteins occurs only at a few defined positions or at many sites distributed throughout the structure. Here, we probe the regulation of GTPases-protein switches that control signaling through regulated conformational cycling-at residue-level resolution by deep mutagenesis in the native biological network. For the GTPase Gsp1/Ran, we find that 28% of the 4,315 assayed mutations show pronounced gain-of-function responses. Twenty of the sixty positions enriched for gain-of-function mutations are outside the canonical GTPase active site switch regions. Kinetic analysis shows that these distal sites are allosterically coupled to the active site. We conclude that the GTPase switch mechanism is broadly sensitive to cellular allosteric regulation. Our systematic discovery of new regulatory sites provides a functional map to interrogate and target GTPases controlling many essential biological processes.
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Affiliation(s)
- Christopher J P Mathy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Parul Mishra
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA; School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Julia M Flynn
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Tina Perica
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David Mavor
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel N A Bolon
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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16
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Agajanian S, Alshahrani M, Bai F, Tao P, Verkhivker GM. Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. J Chem Inf Model 2023; 63:1413-1428. [PMID: 36827465 DOI: 10.1021/acs.jcim.2c01634] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Allosteric mechanisms are commonly employed regulatory tools used by proteins to orchestrate complex biochemical processes and control communications in cells. The quantitative understanding and characterization of allosteric molecular events are among major challenges in modern biology and require integration of innovative computational experimental approaches to obtain atomistic-level knowledge of the allosteric states, interactions, and dynamic conformational landscapes. The growing body of computational and experimental studies empowered by emerging artificial intelligence (AI) technologies has opened up new paradigms for exploring and learning the universe of protein allostery from first principles. In this review we analyze recent developments in high-throughput deep mutational scanning of allosteric protein functions; applications and latest adaptations of Alpha-fold structural prediction methods for studies of protein dynamics and allostery; new frontiers in integrating machine learning and enhanced sampling techniques for characterization of allostery; and recent advances in structural biology approaches for studies of allosteric systems. We also highlight recent computational and experimental studies of the SARS-CoV-2 spike (S) proteins revealing an important and often hidden role of allosteric regulation driving functional conformational changes, binding interactions with the host receptor, and mutational escape mechanisms of S proteins which are critical for viral infection. We conclude with a summary and outlook of future directions suggesting that AI-augmented biophysical and computer simulation approaches are beginning to transform studies of protein allostery toward systematic characterization of allosteric landscapes, hidden allosteric states, and mechanisms which may bring about a new revolution in molecular biology and drug discovery.
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Affiliation(s)
- Steve Agajanian
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology and Information Science and Technology, Shanghai Tech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, United States
| | - Gennady M Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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17
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Flynn J, Samant N, Schneider-Nachum G, Tenzin T, Bolon DNA. Mutational fitness landscape and drug resistance. Curr Opin Struct Biol 2023; 78:102525. [PMID: 36621152 PMCID: PMC10243218 DOI: 10.1016/j.sbi.2022.102525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 01/08/2023]
Abstract
Robust technology has been developed to systematically quantify fitness landscapes that provide valuable opportunities to improve our understanding of drug resistance and define new avenues to develop drugs with reduced resistance susceptibility. We outline the critical importance of drug resistance studies and the potential for fitness landscape approaches to contribute to this effort. We describe the major technical advancements in mutational scanning, which is the primary approach used to quantify protein fitness landscapes. There are many complex steps to consider in planning and executing mutational scanning projects including developing a selection scheme, generating mutant libraries, tracking the frequency of variants using next-generation sequencing, and processing and interpreting the data. Key experimental parameters impacting each of these steps are discussed to aid in planning fitness landscape studies. There is a strong need for improved understanding of drug resistance, and fitness landscapes provide a promising new approach.
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Affiliation(s)
- Julia Flynn
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Neha Samant
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gily Schneider-Nachum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tsepal Tenzin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Daniel N A Bolon
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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18
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Abstract
Gene-by-environment interactions play a crucial role in horizontal gene transfer by affecting how the transferred genes alter host fitness. However, how the environment modulates the fitness effect of transferred genes has not been tested systematically in an experimental study. We adapted a high-throughput technique for obtaining very precise estimates of bacterial fitness, in order to measure the fitness effects of 44 orthologs transferred from Salmonella Typhimurium to Escherichia coli in six physiologically relevant environments. We found that the fitness effects of individual genes were highly dependent on the environment, while the distributions of fitness effects across genes were not, with all tested environments resulting in distributions of same shape and spread. Furthermore, the extent to which the fitness effects of a gene varied between environments depended on the average fitness effect of that gene across all environments, with nearly neutral and nearly lethal genes having more consistent fitness effects across all environments compared to deleterious genes. Put together, our results reveal the unpredictable nature of how environmental conditions impact the fitness effects of each individual gene. At the same time, distributions of fitness effects across environments exhibit consistent features, pointing to the generalizability of factors that shape horizontal gene transfer of orthologous genes.
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Affiliation(s)
- Hande Acar Kirit
- Veterinary and Ecological Sciences, Institute of Infection, University of Liverpool, Liverpool, Merseyside, United Kingdom
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK
- Department of Anthropology, University of Oklahoma, Norman, OK
| | - Jonathan P Bollback
- Veterinary and Ecological Sciences, Institute of Infection, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Mato Lagator
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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19
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Leander M, Liu Z, Cui Q, Raman S. Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins. eLife 2022; 11:e79932. [PMID: 36226916 PMCID: PMC9662819 DOI: 10.7554/elife.79932] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/13/2022] [Indexed: 01/29/2023] Open
Abstract
A fundamental question in protein science is where allosteric hotspots - residues critical for allosteric signaling - are located, and what properties differentiate them. We carried out deep mutational scanning (DMS) of four homologous bacterial allosteric transcription factors (aTFs) to identify hotspots and built a machine learning model with this data to glean the structural and molecular properties of allosteric hotspots. We found hotspots to be distributed protein-wide rather than being restricted to 'pathways' linking allosteric and active sites as is commonly assumed. Despite structural homology, the location of hotspots was not superimposable across the aTFs. However, common signatures emerged when comparing hotspots coincident with long-range interactions, suggesting that the allosteric mechanism is conserved among the homologs despite differences in molecular details. Machine learning with our large DMS datasets revealed global structural and dynamic properties to be a strong predictor of whether a residue is a hotspot than local and physicochemical properties. Furthermore, a model trained on one protein can predict hotspots in a homolog. In summary, the overall allosteric mechanism is embedded in the structural fold of the aTF family, but the finer, molecular details are sequence-specific.
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Affiliation(s)
- Megan Leander
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Zhuang Liu
- Department of Physics, Boston UniversityBostonUnited States
| | - Qiang Cui
- Department of Physics, Boston UniversityBostonUnited States
- Department of Chemistry, Boston UniversityBostonUnited States
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
- Department of Bacteriology, University of Wisconsin-MadisonMadisonUnited States
- Department of Chemical and Biological Engineering, University of Wisconsin-MadisonMadisonUnited States
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20
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Chandra S, Gupta K, Khare S, Kohli P, Asok A, Mohan SV, Gowda H, Varadarajan R. The High Mutational Sensitivity of ccdA Antitoxin Is Linked to Codon Optimality. Mol Biol Evol 2022; 39:6693774. [PMID: 36069948 PMCID: PMC9555053 DOI: 10.1093/molbev/msac187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Deep mutational scanning studies suggest that synonymous mutations are typically silent and that most exposed, nonactive-site residues are tolerant to mutations. Here, we show that the ccdA antitoxin component of the Escherichia coli ccdAB toxin-antitoxin system is unusually sensitive to mutations when studied in the operonic context. A large fraction (∼80%) of single-codon mutations, including many synonymous mutations in the ccdA gene shows inactive phenotype, but they retain native-like binding affinity towards cognate toxin, CcdB. Therefore, the observed phenotypic effects are largely not due to alterations in protein structure/stability, consistent with a large region of CcdA being intrinsically disordered. E. coli codon preference and strength of ribosome-binding associated with translation of downstream ccdB gene are found to be major contributors of the observed ccdA mutant phenotypes. In select cases, proteomics studies reveal altered ratios of CcdA:CcdB protein levels in vivo, suggesting that the ccdA mutations likely alter relative translation efficiencies of the two genes in the operon. We extend these results by studying single-site synonymous mutations that lead to loss of function phenotypes in the relBE operon upon introduction of rarer codons. Thus, in their operonic context, genes are likely to be more sensitive to both synonymous and nonsynonymous point mutations than inferred previously.
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Affiliation(s)
| | | | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Pehu Kohli
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aparna Asok
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Harsha Gowda
- Institute of Bioinformatics, Bangalore 560100, India
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21
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Verkhivker GM. Conformational Dynamics and Mechanisms of Client Protein Integration into the Hsp90 Chaperone Controlled by Allosteric Interactions of Regulatory Switches: Perturbation-Based Network Approach for Mutational Profiling of the Hsp90 Binding and Allostery. J Phys Chem B 2022; 126:5421-5442. [PMID: 35853093 DOI: 10.1021/acs.jpcb.2c03464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the allosteric mechanisms of the Hsp90 chaperone interactions with cochaperones and client protein clientele is fundamental to dissect activation and regulation of many proteins. In this work, atomistic simulations are combined with perturbation-based approaches and dynamic network modeling for a comparative mutational profiling of the Hsp90 binding and allosteric interaction networks in the three Hsp90 maturation complexes with FKBP51 and P23 cochaperones and the glucocorticoid receptor (GR) client. The conformational dynamics signatures of the Hsp90 complexes and dynamics fluctuation analysis revealed how the intrinsic plasticity of the Hsp90 dimer can be modulated by cochaperones and client proteins to stabilize the closed dimer state required at the maturation stage of the ATPase cycle. In silico deep mutational scanning of the protein residues characterized the hot spots of protein stability and binding affinity in the Hsp90 complexes, showing that binding hot spots may often coincide with the regulatory centers that modulate dynamic allostery in the Hsp90 dimer. We introduce a perturbation-based network approach for mutational scanning of allosteric residue potentials and characterize allosteric switch clusters that control mechanism of cochaperone-dependent client recognition and remodeling by the Hsp90 chaperone. The results revealed a conserved network of allosteric switches in the Hsp90 complexes that allow cochaperones and GR protein to become integrated into the Hsp90 system by anchoring to the conformational switch points in the functional Hsp90 regions. This study suggests that the Hsp90 binding and allostery may operate under a regulatory mechanism in which activation or repression of the Hsp90 activity can be pre-encoded in the allosterically regulated Hsp90 dimer motions. By binding directly to the conformational switch centers on the Hsp90, cochaperones and interacting proteins can efficiently modulate the allosteric interactions and long-range communications required for client remodeling and activation.
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Affiliation(s)
- Gennady M Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, California 92866, United States
- Depatment of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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22
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Samant N, Nachum G, Tsepal T, Bolon DNA. Sequence dependencies and biophysical features both govern cleavage of diverse cut-sites by HIV protease. Protein Sci 2022; 31:e4366. [PMID: 35762719 DOI: 10.1002/pro.4366] [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: 03/03/2022] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 11/12/2022]
Abstract
The infectivity of HIV-1 requires its protease (PR) cleave multiple cut-sites with low sequence similarity. The diversity of cleavage sites has made it challenging to investigate the underlying sequence properties that determine binding and turnover of substrates by PR. We engineered a mutational scanning approach utilizing yeast display, flow cytometry, and deep sequencing to systematically measure the impacts of all individual amino acid changes at 12 positions in three different cut-sites (MA/CA, NC/p1, and p1/p6). The resulting fitness landscapes revealed common physical features that underlie cutting of all three cut-sites at the amino acid positions closest to the scissile bond. In contrast, positions more than two amino acids away from the scissile bond exhibited a strong dependence on the sequence background of the rest of the cut-site. We observed multiple amino acid changes in cut-sites that led to faster cleavage rates, including a preference for negative charge five and six amino acids away from the scissile bond at locations where the surface of protease is positively charged. Analysis of individual cut sites using full-length matrix-capsid proteins indicate that long-distance sequence context can contribute to cutting efficiency such that analyses of peptides or shorter engineered constructs including those in this work should be considered carefully. This work provides a framework for understanding how diverse substrates interact with HIV-1 PR and can be extended to investigate other viral PRs with similar properties.
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Affiliation(s)
- Neha Samant
- Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Gily Nachum
- Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Tenzin Tsepal
- Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Daniel N A Bolon
- Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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23
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Böndel KB, Samuels T, Craig RJ, Ness RW, Colegrave N, Keightley PD. The distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii inferred using frequency changes under experimental evolution. PLoS Genet 2022; 18:e1009840. [PMID: 35704655 PMCID: PMC9239454 DOI: 10.1371/journal.pgen.1009840] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 06/28/2022] [Accepted: 04/13/2022] [Indexed: 12/23/2022] Open
Abstract
The distribution of fitness effects (DFE) for new mutations is fundamental for many aspects of population and quantitative genetics. In this study, we have inferred the DFE in the single-celled alga Chlamydomonas reinhardtii by estimating changes in the frequencies of 254 spontaneous mutations under experimental evolution and equating the frequency changes of linked mutations with their selection coefficients. We generated seven populations of recombinant haplotypes by crossing seven independently derived mutation accumulation lines carrying an average of 36 mutations in the haploid state to a mutation-free strain of the same genotype. We then allowed the populations to evolve under natural selection in the laboratory by serial transfer in liquid culture. We observed substantial and repeatable changes in the frequencies of many groups of linked mutations, and, surprisingly, as many mutations were observed to increase as decrease in frequency. Mutation frequencies were highly repeatable among replicates, suggesting that selection was the cause of the observed allele frequency changes. We developed a Bayesian Monte Carlo Markov Chain method to infer the DFE. This computes the likelihood of the observed distribution of changes of frequency, and obtains the posterior distribution of the selective effects of individual mutations, while assuming a two-sided gamma distribution of effects. We infer that the DFE is a highly leptokurtic distribution, and that approximately equal proportions of mutations have positive and negative effects on fitness. This result is consistent with what we have observed in previous work on a different C. reinhardtii strain, and suggests that a high fraction of new spontaneously arisen mutations are advantageous in a simple laboratory environment.
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Affiliation(s)
- Katharina B. Böndel
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Toby Samuels
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rory J. Craig
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rob W. Ness
- Department of Biology, William G. Davis Building, University of Toronto, Mississauga, Canada
| | - Nick Colegrave
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter D. Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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24
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Synonymous mutations in representative yeast genes are mostly strongly non-neutral. Nature 2022; 606:725-731. [PMID: 35676473 PMCID: PMC9650438 DOI: 10.1038/s41586-022-04823-w] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/28/2022] [Indexed: 01/12/2023]
Abstract
Synonymous mutations in protein-coding genes do not alter protein sequences and are thus generally presumed to be neutral or nearly neutral1-5. Here, to experimentally verify this presumption, we constructed 8,341 yeast mutants each carrying a synonymous, nonsynonymous or nonsense mutation in one of 21 endogenous genes with diverse functions and expression levels and measured their fitness relative to the wild type in a rich medium. Three-quarters of synonymous mutations resulted in a significant reduction in fitness, and the distribution of fitness effects was overall similar-albeit nonidentical-between synonymous and nonsynonymous mutations. Both synonymous and nonsynonymous mutations frequently disturbed the level of mRNA expression of the mutated gene, and the extent of the disturbance partially predicted the fitness effect. Investigations in additional environments revealed greater across-environment fitness variations for nonsynonymous mutants than for synonymous mutants despite their similar fitness distributions in each environment, suggesting that a smaller proportion of nonsynonymous mutants than synonymous mutants are always non-deleterious in a changing environment to permit fixation, potentially explaining the common observation of substantially lower nonsynonymous than synonymous substitution rates. The strong non-neutrality of most synonymous mutations, if it holds true for other genes and in other organisms, would require re-examination of numerous biological conclusions about mutation, selection, effective population size, divergence time and disease mechanisms that rely on the assumption that synoymous mutations are neutral.
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25
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Environmental selection and epistasis in an empirical phenotype-environment-fitness landscape. Nat Ecol Evol 2022; 6:427-438. [PMID: 35210579 DOI: 10.1038/s41559-022-01675-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022]
Abstract
Fitness landscapes, mappings of genotype/phenotype to their effects on fitness, are invaluable concepts in evolutionary biochemistry. Although widely discussed, measurements of phenotype-fitness landscapes in proteins remain scarce. Here, we quantify all single mutational effects on fitness and phenotype (EC50) of VIM-2 β-lactamase across a 64-fold range of ampicillin concentrations. We then construct a phenotype-fitness landscape that takes variations in environmental selection pressure into account. We found that a simple, empirical landscape accurately models the ~39,000 mutational data points, suggesting that the evolution of VIM-2 can be predicted on the basis of the selection environment. Our landscape provides new quantitative knowledge on the evolution of the β-lactamases and proteins in general, particularly their evolutionary dynamics under subinhibitory antibiotic concentrations, as well as the mechanisms and environmental dependence of non-specific epistasis.
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26
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Exploring Mechanisms of Allosteric Regulation and Communication Switching in the Multiprotein Regulatory Complexes of the Hsp90 Chaperone with Cochaperones and Client Proteins : Atomistic Insights from Integrative Biophysical Modeling and Network Analysis of Conformational Landscapes. J Mol Biol 2022; 434:167506. [DOI: 10.1016/j.jmb.2022.167506] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/16/2022]
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27
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Peri G, Gibard C, Shults NH, Crossin K, Hayden EJ. Dynamic RNA fitness landscapes of a group I ribozyme during changes to the experimental environment. Mol Biol Evol 2022; 39:6502289. [PMID: 35020916 PMCID: PMC8890501 DOI: 10.1093/molbev/msab373] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fitness landscapes of protein and RNA molecules can be studied experimentally using high-throughput techniques to measure the functional effects of numerous combinations of mutations. The rugged topography of these molecular fitness landscapes is important for understanding and predicting natural and experimental evolution. Mutational effects are also dependent upon environmental conditions, but the effects of environmental changes on fitness landscapes remains poorly understood. Here, we investigate the changes to the fitness landscape of a catalytic RNA molecule while changing a single environmental variable that is critical for RNA structure and function. Using high-throughput sequencing of in vitro selections, we mapped a fitness landscape of the Azoarcus group I ribozyme under eight different concentrations of magnesium ions (1–48 mM MgCl2). The data revealed the magnesium dependence of 16,384 mutational neighbors, and from this, we investigated the magnesium induced changes to the topography of the fitness landscape. The results showed that increasing magnesium concentration improved the relative fitness of sequences at higher mutational distances while also reducing the ruggedness of the mutational trajectories on the landscape. As a result, as magnesium concentration was increased, simulated populations evolved toward higher fitness faster. Curve-fitting of the magnesium dependence of individual ribozymes demonstrated that deep sequencing of in vitro reactions can be used to evaluate the structural stability of thousands of sequences in parallel. Overall, the results highlight how environmental changes that stabilize structures can also alter the ruggedness of fitness landscapes and alter evolutionary processes.
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Affiliation(s)
- Gianluca Peri
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, ID, USA
| | - Clémentine Gibard
- Department of Biological Science, Boise State University, Boise, ID, USA
| | - Nicholas H Shults
- Department of Biological Science, Boise State University, Boise, ID, USA
| | - Kent Crossin
- Department of Biological Science, Boise State University, Boise, ID, USA
| | - Eric J Hayden
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, ID, USA.,Department of Biological Science, Boise State University, Boise, ID, USA
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28
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Wang RYR, Noddings CM, Kirschke E, Myasnikov AG, Johnson JL, Agard DA. Structure of Hsp90-Hsp70-Hop-GR reveals the Hsp90 client-loading mechanism. Nature 2022; 601:460-464. [PMID: 34937942 PMCID: PMC9179170 DOI: 10.1038/s41586-021-04252-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 11/16/2021] [Indexed: 01/03/2023]
Abstract
Maintaining a healthy proteome is fundamental for the survival of all organisms1. Integral to this are Hsp90 and Hsp70, molecular chaperones that together facilitate the folding, remodelling and maturation of the many 'client proteins' of Hsp902. The glucocorticoid receptor (GR) is a model client protein that is strictly dependent on Hsp90 and Hsp70 for activity3-7. Chaperoning GR involves a cycle of inactivation by Hsp70; formation of an inactive GR-Hsp90-Hsp70-Hop 'loading' complex; conversion to an active GR-Hsp90-p23 'maturation' complex; and subsequent GR release8. However, to our knowledge, a molecular understanding of this intricate chaperone cycle is lacking for any client protein. Here we report the cryo-electron microscopy structure of the GR-loading complex, in which Hsp70 loads GR onto Hsp90, uncovering the molecular basis of direct coordination by Hsp90 and Hsp70. The structure reveals two Hsp70 proteins, one of which delivers GR and the other scaffolds the Hop cochaperone. Hop interacts with all components of the complex, including GR, and poises Hsp90 for subsequent ATP hydrolysis. GR is partially unfolded and recognized through an extended binding pocket composed of Hsp90, Hsp70 and Hop, revealing the mechanism of GR loading and inactivation. Together with the GR-maturation complex structure9, we present a complete molecular mechanism of chaperone-dependent client remodelling, and establish general principles of client recognition, inhibition, transfer and activation.
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Affiliation(s)
- Ray Yu-Ruei Wang
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Chari M. Noddings
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Elaine Kirschke
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alexander G. Myasnikov
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA,Present address: Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Jill L. Johnson
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - David A. Agard
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA,Correspondence and requests for materials should be addressed to David A. Agard.
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29
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Pant A, Chittayil Krishnakumar K, Chakkalaparambil Dileep N, Yamana M, Meenakshisundaran Alamelu N, Paithankar K, Amash V, Amere Subbarao S. Hsp90 and its mitochondrial homologue TRAP-1 independently regulate hypoxia adaptations in Caenorhabditis elegans. Mitochondrion 2021; 60:101-111. [PMID: 34365052 DOI: 10.1016/j.mito.2021.08.002] [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: 06/07/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 11/30/2022]
Abstract
Mitochondrial adaptations to various environmental cues contribute to cellular and organismal adaptations across multiple model organisms. Due to increased complexity, a direct connection between mitochondrial integrity and oxygen fluctuations, and survival fitness was not demonstrated. Here, using C. elegans as a model system, we studied the role of HIF-1, Hsp90, and TRAP-1 in mitochondrial adaptations during chemical hypoxia. We show that Hsp90mt (Hsp90 mutant) but not HIF-1mt (HIF-1 mutant) affects hypoxia adaptation in nematodes. TRAP-1KD (TRAP-1 knockdown) interfered with the survival and fecundity of worms. Compared to Hsp90mt, TRAP-1KD has induced a significant decrease in mitochondrial integrity and oxygen consumption rate. The complex I inhibitor rotenone did not affect ATP levels in Hsp90mt worms. However, ATP levels were decreased in TRAP-1KD worms under similar conditions. The glucose restriction has reduced, and glucose supplementation has increased the survival rate in Hsp90mt worms. Neither glucose restriction nor glucose supplementation has significantly affected the survival of TRAP-1KD worms in response to hypoxia. However, TRAP-1 inhibition using a nanocarrier drug has dramatically reduced the survival rate in response to hypoxia. Our results suggest that Hsp90 and TRAP-1 independently regulate hypoxia adaptations and metabolic plasticity in C. elegans. Considering the emerging roles of TRAP-1 in altered energy metabolism and cellular adaptations, our findings gain importance.
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Affiliation(s)
- Aakanksha Pant
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | | | | | - Meghana Yamana
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
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30
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Shifting landscapes of human MTHFR missense-variant effects. Am J Hum Genet 2021; 108:1283-1300. [PMID: 34214447 PMCID: PMC8322931 DOI: 10.1016/j.ajhg.2021.05.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/18/2021] [Indexed: 12/20/2022] Open
Abstract
Most rare clinical missense variants cannot currently be classified as pathogenic or benign. Deficiency in human 5,10-methylenetetrahydrofolate reductase (MTHFR), the most common inherited disorder of folate metabolism, is caused primarily by rare missense variants. Further complicating variant interpretation, variant impacts often depend on environment. An important example of this phenomenon is the MTHFR variant p.Ala222Val (c.665C>T), which is carried by half of all humans and has a phenotypic impact that depends on dietary folate. Here we describe the results of 98,336 variant functional-impact assays, covering nearly all possible MTHFR amino acid substitutions in four folinate environments, each in the presence and absence of p.Ala222Val. The resulting atlas of MTHFR variant effects reveals many complex dependencies on both folinate and p.Ala222Val. MTHFR atlas scores can distinguish pathogenic from benign variants and, among individuals with severe MTHFR deficiency, correlate with age of disease onset. Providing a powerful tool for understanding structure-function relationships, the atlas suggests a role for a disordered loop in retaining cofactor at the active site and identifies variants that enable escape of inhibition by S-adenosylmethionine. Thus, a model based on eight MTHFR variant effect maps illustrates how shifting landscapes of environment- and genetic-background-dependent missense variation can inform our clinical, structural, and functional understanding of MTHFR deficiency.
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31
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Cote-Hammarlof PA, Fragata I, Flynn J, Mavor D, Zeldovich KB, Bank C, Bolon DNA. The Adaptive Potential of the Middle Domain of Yeast Hsp90. Mol Biol Evol 2021; 38:368-379. [PMID: 32871012 PMCID: PMC7826181 DOI: 10.1093/molbev/msaa211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The distribution of fitness effects (DFEs) of new mutations across different environments quantifies the potential for adaptation in a given environment and its cost in others. So far, results regarding the cost of adaptation across environments have been mixed, and most studies have sampled random mutations across different genes. Here, we quantify systematically how costs of adaptation vary along a large stretch of protein sequence by studying the distribution of fitness effects of the same ≈2,300 amino-acid changing mutations obtained from deep mutational scanning of 119 amino acids in the middle domain of the heat shock protein Hsp90 in five environments. This region is known to be important for client binding, stabilization of the Hsp90 dimer, stabilization of the N-terminal-Middle and Middle-C-terminal interdomains, and regulation of ATPase–chaperone activity. Interestingly, we find that fitness correlates well across diverse stressful environments, with the exception of one environment, diamide. Consistent with this result, we find little cost of adaptation; on average only one in seven beneficial mutations is deleterious in another environment. We identify a hotspot of beneficial mutations in a region of the protein that is located within an allosteric center. The identified protein regions that are enriched in beneficial, deleterious, and costly mutations coincide with residues that are involved in the stabilization of Hsp90 interdomains and stabilization of client-binding interfaces, or residues that are involved in ATPase–chaperone activity of Hsp90. Thus, our study yields information regarding the role and adaptive potential of a protein sequence that complements and extends known structural information.
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Affiliation(s)
| | - Inês Fragata
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Julia Flynn
- University of Massachusetts Medical School, Worcester, MA
| | - David Mavor
- University of Massachusetts Medical School, Worcester, MA
| | | | - Claudia Bank
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Institute of Ecology and Evolution, University of Bern, Switzerland
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32
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Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Mol Ecol 2021; 30:2710-2723. [PMID: 33955064 DOI: 10.1111/mec.15936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/30/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023]
Abstract
A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.
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Affiliation(s)
- Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Alexander Suh
- School of Biological Sciences - Organisms and the Environment, University of East Anglia, Norwich, UK.,Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anja M Westram
- IST Austria, Klosterneuburg, Austria.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Inês Fragata
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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33
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Routh S, Acharyya A, Dhar R. A two-step PCR assembly for construction of gene variants across large mutational distances. Biol Methods Protoc 2021; 6:bpab007. [PMID: 33928191 PMCID: PMC8062255 DOI: 10.1093/biomethods/bpab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/09/2021] [Accepted: 04/01/2021] [Indexed: 11/14/2022] Open
Abstract
Construction of empirical fitness landscapes has transformed our understanding of genotype–phenotype relationships across genes. However, most empirical fitness landscapes have been constrained to the local genotype neighbourhood of a gene primarily due to our limited ability to systematically construct genotypes that differ by a large number of mutations. Although a few methods have been proposed in the literature, these techniques are complex owing to several steps of construction or contain a large number of amplification cycles that increase chances of non-specific mutations. A few other described methods require amplification of the whole vector, thereby increasing the chances of vector backbone mutations that can have unintended consequences for study of fitness landscapes. Thus, this has substantially constrained us from traversing large mutational distances in the genotype network, thereby limiting our understanding of the interactions between multiple mutations and the role these interactions play in evolution of novel phenotypes. In the current work, we present a simple but powerful approach that allows us to systematically and accurately construct gene variants at large mutational distances. Our approach relies on building-up small fragments containing targeted mutations in the first step followed by assembly of these fragments into the complete gene fragment by polymerase chain reaction (PCR). We demonstrate the utility of our approach by constructing variants that differ by up to 11 mutations in a model gene. Our work thus provides an accurate method for construction of multi-mutant variants of genes and therefore will transform the studies of empirical fitness landscapes by enabling exploration of genotypes that are far away from a starting genotype.
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Affiliation(s)
- Shreya Routh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Anamika Acharyya
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Riddhiman Dhar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
- Correspondence address. Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India. Tel. +91-3222-304562; E-mail:
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34
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Hohrman K, Gonçalves D, Morano KA, Johnson JL. Disrupting progression of the yeast Hsp90 folding pathway at different transition points results in client-specific maturation defects. Genetics 2021; 217:iyab009. [PMID: 33789348 PMCID: PMC8045699 DOI: 10.1093/genetics/iyab009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/11/2021] [Indexed: 11/12/2022] Open
Abstract
The protein molecular chaperone Hsp90 (Heat shock protein, 90 kilodalton) plays multiple roles in the biogenesis and regulation of client proteins impacting myriad aspects of cellular physiology. Amino acid alterations located throughout Saccharomyces cerevisiae Hsp90 have been shown to result in reduced client activity and temperature-sensitive growth defects. Although some Hsp90 mutants have been shown to affect activity of particular clients more than others, the mechanistic basis of client-specific effects is unknown. We found that Hsp90 mutants that disrupt the early step of Hsp70 and Sti1 interaction, or show reduced ability to adopt the ATP-bound closed conformation characterized by Sba1 and Cpr6 interaction, similarly disrupt activity of three diverse clients, Utp21, Ssl2, and v-src. In contrast, mutants that appear to alter other steps in the folding pathway had more limited effects on client activity. Protein expression profiling provided additional evidence that mutants that alter similar steps in the folding cycle cause similar in vivo consequences. Our characterization of these mutants provides new insight into how Hsp90 and cochaperones identify and interact with diverse clients, information essential for designing pharmaceutical approaches to selectively inhibit Hsp90 function.
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Affiliation(s)
- Kaitlyn Hohrman
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Davi Gonçalves
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Kevin A Morano
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Jill L Johnson
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
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35
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Scossa F, Fernie AR. Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants? Comput Struct Biotechnol J 2021; 19:1579-1594. [PMID: 33868595 PMCID: PMC8039532 DOI: 10.1016/j.csbj.2021.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Whilst substantial research effort has been placed on understanding the interactions of plant proteins with their molecular partners, relatively few studies in plants - by contrast to work in other organisms - address how these interactions evolve. It is thought that ancestral proteins were more promiscuous than modern proteins and that specificity often evolved following gene duplication and subsequent functional refining. However, ancestral protein resurrection studies have found that some modern proteins have evolved de novo from ancestors lacking those functions. Intriguingly, the new interactions evolved as a consequence of just a few mutations and, as such, acquisition of new functions appears to be neither difficult nor rare, however, only a few of them are incorporated into biological processes before they are lost to subsequent mutations. Here, we detail the approach of ancestral sequence reconstruction (ASR), providing a primer to reconstruct the sequence of an ancestral gene. We will present case studies from a range of different eukaryotes before discussing the few instances where ancestral reconstructions have been used in plants. As ASR is used to dig into the remote evolutionary past, we will also present some alternative genetic approaches to investigate molecular evolution on shorter timescales. We argue that the study of plant secondary metabolism is particularly well suited for ancestral reconstruction studies. Indeed, its ancient evolutionary roots and highly diverse landscape provide an ideal context in which to address the focal issue around the emergence of evolutionary novelties and how this affects the chemical diversification of plant metabolism.
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Key Words
- APR, ancestral protein resurrection
- ASR, ancestral sequence reconstruction
- Ancestral sequence reconstruction
- CDS, coding sequence
- Evolution
- GR, glucocorticoid receptor
- GWAS, genome wide association study
- Genomics
- InDel, insertion/deletion
- MCMC, Markov Chain Monte Carlo
- ML, maximum likelihood
- MP, maximum parsimony
- MR, mineralcorticoid receptor
- MSA, multiple sequence alignment
- Metabolism
- NJ, neighbor-joining
- Phylogenetics
- Plants
- SFS, site frequency spectrum
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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36
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37
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Kinsler G, Geiler-Samerotte K, Petrov DA. Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation. eLife 2020; 9:e61271. [PMID: 33263280 PMCID: PMC7880691 DOI: 10.7554/elife.61271] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023] Open
Abstract
Building a genotype-phenotype-fitness map of adaptation is a central goal in evolutionary biology. It is difficult even when adaptive mutations are known because it is hard to enumerate which phenotypes make these mutations adaptive. We address this problem by first quantifying how the fitness of hundreds of adaptive yeast mutants responds to subtle environmental shifts. We then model the number of phenotypes these mutations collectively influence by decomposing these patterns of fitness variation. We find that a small number of inferred phenotypes can predict fitness of the adaptive mutations near their original glucose-limited evolution condition. Importantly, inferred phenotypes that matter little to fitness at or near the evolution condition can matter strongly in distant environments. This suggests that adaptive mutations are locally modular - affecting a small number of phenotypes that matter to fitness in the environment where they evolved - yet globally pleiotropic - affecting additional phenotypes that may reduce or improve fitness in new environments.
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Affiliation(s)
- Grant Kinsler
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Kerry Geiler-Samerotte
- Department of Biology, Stanford UniversityStanfordUnited States
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State UniversityTempeUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
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38
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Abildgaard AB, Gersing SK, Larsen-Ledet S, Nielsen SV, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome. Biomolecules 2020; 10:biom10081141. [PMID: 32759676 PMCID: PMC7463752 DOI: 10.3390/biom10081141] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 12/11/2022] Open
Abstract
Protein homeostasis (proteostasis) is essential for the cell and is maintained by a highly conserved protein quality control (PQC) system, which triages newly synthesized, mislocalized and misfolded proteins. The ubiquitin-proteasome system (UPS), molecular chaperones, and co-chaperones are vital PQC elements that work together to facilitate degradation of misfolded and toxic protein species through the 26S proteasome. However, the underlying mechanisms are complex and remain partly unclear. Here, we provide an overview of the current knowledge on the co-chaperones that directly take part in targeting and delivery of PQC substrates for degradation. While J-domain proteins (JDPs) target substrates for the heat shock protein 70 (HSP70) chaperones, nucleotide-exchange factors (NEFs) deliver HSP70-bound substrates to the proteasome. So far, three NEFs have been established in proteasomal delivery: HSP110 and the ubiquitin-like (UBL) domain proteins BAG-1 and BAG-6, the latter acting as a chaperone itself and carrying its substrates directly to the proteasome. A better understanding of the individual delivery pathways will improve our ability to regulate the triage, and thus regulate the fate of aberrant proteins involved in cell stress and disease, examples of which are given throughout the review.
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Affiliation(s)
- Amanda B. Abildgaard
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sarah K. Gersing
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sven Larsen-Ledet
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sofie V. Nielsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (S.V.N.); (A.S.)
| | - Amelie Stein
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (S.V.N.); (A.S.)
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
- Correspondence:
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39
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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: 36] [Impact Index Per Article: 9.0] [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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