1
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Tawfeeq MT, Voordeckers K, van den Berg P, Govers SK, Michiels J, Verstrepen KJ. Mutational robustness and the role of buffer genes in evolvability. EMBO J 2024; 43:2294-2307. [PMID: 38719995 PMCID: PMC11183146 DOI: 10.1038/s44318-024-00109-1] [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: 11/08/2023] [Revised: 03/19/2024] [Accepted: 04/17/2024] [Indexed: 06/19/2024] Open
Abstract
Organisms rely on mutations to fuel adaptive evolution. However, many mutations impose a negative effect on fitness. Cells may have therefore evolved mechanisms that affect the phenotypic effects of mutations, thus conferring mutational robustness. Specifically, so-called buffer genes are hypothesized to interact directly or indirectly with genetic variation and reduce its effect on fitness. Environmental or genetic perturbations can change the interaction between buffer genes and genetic variation, thereby unmasking the genetic variation's phenotypic effects and thus providing a source of variation for natural selection to act on. This review provides an overview of our understanding of mutational robustness and buffer genes, with the chaperone gene HSP90 as a key example. It discusses whether buffer genes merely affect standing variation or also interact with de novo mutations, how mutational robustness could influence evolution, and whether mutational robustness might be an evolved trait or rather a mere side-effect of complex genetic interactions.
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Affiliation(s)
- Mohammed T Tawfeeq
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Karin Voordeckers
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Pieter van den Berg
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Jan Michiels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium.
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2
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Zhao P, Wang C, Sun S, Wang X, Balch WE. Tracing genetic diversity captures the molecular basis of misfolding disease. Nat Commun 2024; 15:3333. [PMID: 38637533 PMCID: PMC11026414 DOI: 10.1038/s41467-024-47520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Genetic variation in human populations can result in the misfolding and aggregation of proteins, giving rise to systemic and neurodegenerative diseases that require management by proteostasis. Here, we define the role of GRP94, the endoplasmic reticulum Hsp90 chaperone paralog, in managing alpha-1-antitrypsin deficiency on a residue-by-residue basis using Gaussian process regression-based machine learning to profile the spatial covariance relationships that dictate protein folding arising from sequence variants in the population. Covariance analysis suggests a role for the ATPase activity of GRP94 in controlling the N- to C-terminal cooperative folding of alpha-1-antitrypsin responsible for the correction of liver aggregation and lung-disease phenotypes of alpha-1-antitrypsin deficiency. Gaussian process-based spatial covariance profiling provides a standard model built on covariant principles to evaluate the role of proteostasis components in guiding information flow from genome to proteome in response to genetic variation, potentially allowing us to intervene in the onset and progression of complex multi-system human diseases.
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Affiliation(s)
- Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- Department of Nutrition and Food Hygiene, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Collaborative Innovation Center for Cancer Personalized Medicine, and Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Xi Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
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3
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Leone S, Srivastava A, Herrero-Ruiz A, Hummel B, Tittel L, Campalastri R, Aprile-Garcia F, Tan JH, Rawat P, Andersson P, Willis AE, Sawarkar R. HSP70 binds to specific non-coding RNA and regulates human RNA polymerase III. Mol Cell 2024; 84:687-701.e7. [PMID: 38266641 DOI: 10.1016/j.molcel.2024.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 10/20/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024]
Abstract
Molecular chaperones are critical for protein homeostasis and are implicated in several human pathologies such as neurodegeneration and cancer. While the binding of chaperones to nascent and misfolded proteins has been studied in great detail, the direct interaction between chaperones and RNA has not been systematically investigated. Here, we provide the evidence for widespread interaction between chaperones and RNA in human cells. We show that the major chaperone heat shock protein 70 (HSP70) binds to non-coding RNA transcribed by RNA polymerase III (RNA Pol III) such as tRNA and 5S rRNA. Global chromatin profiling revealed that HSP70 binds genomic sites of transcription by RNA Pol III. Detailed biochemical analyses showed that HSP70 alleviates the inhibitory effect of cognate tRNA transcript on tRNA gene transcription. Thus, our study uncovers an unexpected role of HSP70-RNA interaction in the biogenesis of a specific class of non-coding RNA with wider implications in cancer therapeutics.
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Affiliation(s)
- Sergio Leone
- MRC Toxicology Unit, University of Cambridge, Cambridge CB21QR, UK.
| | | | | | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Lena Tittel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | | | | | - Jun Hao Tan
- MRC Toxicology Unit, University of Cambridge, Cambridge CB21QR, UK
| | - Prashant Rawat
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Patrik Andersson
- Safety Innovation, Clinical Pharmacology and Safety Sciences, AstraZeneca R&D, Gothenburg 43183, Sweden
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge CB21QR, UK
| | - Ritwick Sawarkar
- MRC Toxicology Unit, University of Cambridge, Cambridge CB21QR, UK; Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany.
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4
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Guo Y, Xue Z, Gong M, Jin S, Wu X, Liu W. CRISPR-TE: a web-based tool to generate single guide RNAs targeting transposable elements. Mob DNA 2024; 15:3. [PMID: 38303094 PMCID: PMC10832116 DOI: 10.1186/s13100-024-00313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/13/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND The CRISPR/Cas systems have emerged as powerful tools in genome engineering. Recent studies highlighting the crucial role of transposable elements (TEs) have stimulated research interest in manipulating these elements to understand their functions. However, designing single guide RNAs (sgRNAs) that are specific and efficient for TE manipulation is a significant challenge, given their sequence repetitiveness and high copy numbers. While various sgRNA design tools have been developed for gene editing, an optimized sgRNA designer for TE manipulation has yet to be established. RESULTS We present CRISPR-TE, a web-based application featuring an accessible graphical user interface, available at https://www.crisprte.cn/ , and currently tailored to the human and mouse genomes. CRISPR-TE identifies all potential sgRNAs for TEs and provides a comprehensive solution for efficient TE targeting at both the single copy and subfamily levels. Our analysis shows that sgRNAs targeting TEs can more effectively target evolutionarily young TEs with conserved sequences at the subfamily level. CONCLUSIONS CRISPR-TE offers a versatile framework for designing sgRNAs for TE targeting. CRISPR-TE is publicly accessible at https://www.crisprte.cn/ as an online web service and the source code of CRISPR-TE is available at https://github.com/WanluLiuLab/CRISPRTE/ .
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Affiliation(s)
- Yixin Guo
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China
| | - Ziwei Xue
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314100, China
| | - Meiting Gong
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China
| | - Siqian Jin
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China
| | - Xindi Wu
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China
| | - Wanlu Liu
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China.
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314100, China.
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5
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Wu C, Wagner ND, Moyle AB, Feng A, Sharma N, Stubbs SH, Donahue C, Davey RA, Gross ML, Leung DW, Amarasinghe GK. Disruption of Ebola NP 0VP35 Inclusion Body-like Structures reduce Viral Infection. J Mol Biol 2023; 435:168241. [PMID: 37598728 PMCID: PMC11312838 DOI: 10.1016/j.jmb.2023.168241] [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: 01/04/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 08/22/2023]
Abstract
Viral inclusion bodies (IBs) are potential sites of viral replication and assembly. How viral IBs form remains poorly defined. Here we describe a combined biophysical and cellular approach to identify the components necessary for IB formation during Ebola virus (EBOV) infection. We find that the eNP0VP35 complex containing Ebola nucleoprotein (eNP) and viral protein 35 (eVP35), the functional equivalents of nucleoprotein (N) and phosphoprotein (P) in non-segmented negative strand viruses (NNSVs), phase separates to form inclusion bodies. Phase separation of eNP0VP35 is reversible and modulated by ionic strength. The multivalency of eVP35, and not eNP, is also critical for phase separation. Furthermore, overexpression of an eVP35 peptide disrupts eNP0VP35 complex formation, leading to reduced frequency of IB formation and limited viral infection. Together, our results show that upon EBOV infection, the eNP0VP35 complex forms the minimum unit to drive IB formation and viral replication.
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Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Austin B Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Annie Feng
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Nitin Sharma
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sarah H Stubbs
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Callie Donahue
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Robert A Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
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6
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Chakrabarty P, Sen R, Sengupta S. From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution. Funct Integr Genomics 2023; 23:278. [PMID: 37610667 DOI: 10.1007/s10142-023-01206-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Transposable elements, often referred to as "jumping genes," have long been recognized as genomic parasites due to their ability to integrate and disrupt normal gene function and induce extensive genomic alterations, thereby compromising the host's fitness. To counteract this, the host has evolved a plethora of mechanisms to suppress the activity of the transposons. Recent research has unveiled the host-transposon relationships to be nuanced and complex phenomena, resulting in the coevolution of both entities. Transposition increases the mutational rate in the host genome, often triggering physiological pathways such as immune and stress responses. Current gene transfer technologies utilizing transposable elements have potential drawbacks, including off-target integration, induction of mutations, and modifications of cellular machinery, which makes an in-depth understanding of the host-transposon relationship imperative. This review highlights the dynamic interplay between the host and transposable elements, encompassing various factors and components of the cellular machinery. We provide a comprehensive discussion of the strategies employed by transposable elements for their propagation, as well as the mechanisms utilized by the host to mitigate their parasitic effects. Additionally, we present an overview of recent research identifying host proteins that act as facilitators or inhibitors of transposition. We further discuss the evolutionary outcomes resulting from the genetic interactions between the host and the transposable elements. Finally, we pose open questions in this field and suggest potential avenues for future research.
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Affiliation(s)
- Prayas Chakrabarty
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
| | - Raneet Sen
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
- Institute of Bioorganic Chemistry, Department of RNA Metabolism, Polish Academy of Sciences, Poznan, Poland
| | - Sugopa Sengupta
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India.
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7
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Hung PH, Liao CW, Ko FH, Tsai HK, Leu JY. Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains. iScience 2023; 26:106635. [PMID: 37138775 PMCID: PMC10149407 DOI: 10.1016/j.isci.2023.106635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 02/21/2023] [Accepted: 04/05/2023] [Indexed: 05/05/2023] Open
Abstract
Enhanced phenotypic diversity increases a population's likelihood of surviving catastrophic conditions. Hsp90, an essential molecular chaperone and a central network hub in eukaryotes, has been observed to suppress or enhance the effects of genetic variation on phenotypic diversity in response to environmental cues. Because many Hsp90-interacting genes are involved in signaling transduction pathways and transcriptional regulation, we tested how common Hsp90-dependent differential gene expression is in natural populations. Many genes exhibited Hsp90-dependent strain-specific differential expression in five diverse yeast strains. We further identified transcription factors (TFs) potentially contributing to variable expression. We found that on Hsp90 inhibition or environmental stress, activities or abundances of Hsp90-dependent TFs varied among strains, resulting in differential strain-specific expression of their target genes, which consequently led to phenotypic diversity. We provide evidence that individual strains can readily display specific Hsp90-dependent gene expression, suggesting that the evolutionary impacts of Hsp90 are widespread in nature.
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Affiliation(s)
- Po-Hsiang Hung
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chia-Wei Liao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Fu-Hsuan Ko
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Huai-Kuang Tsai
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
- Corresponding author
| | - Jun-Yi Leu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
- Corresponding author
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8
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van Oosten-Hawle P. Organismal Roles of Hsp90. Biomolecules 2023; 13:biom13020251. [PMID: 36830620 PMCID: PMC9952938 DOI: 10.3390/biom13020251] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Heat shock protein 90 (Hsp90) is a highly conserved molecular chaperone that assists in the maturation of many client proteins involved in cellular signal transduction. As a regulator of cellular signaling processes, it is vital for the maintenance of cellular proteostasis and adaptation to environmental stresses. Emerging research shows that Hsp90 function in an organism goes well beyond intracellular proteostasis. In metazoans, Hsp90, as an environmentally responsive chaperone, is involved in inter-tissue stress signaling responses that coordinate and safeguard cell nonautonomous proteostasis and organismal health. In this way, Hsp90 has the capacity to influence evolution and aging, and effect behavioral responses to facilitate tissue-defense systems that ensure organismal survival. In this review, I summarize the literature on the organismal roles of Hsp90 uncovered in multicellular organisms, from plants to invertebrates and mammals.
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Affiliation(s)
- Patricija van Oosten-Hawle
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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9
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Bhattacharya K, Maiti S, Zahoran S, Weidenauer L, Hany D, Wider D, Bernasconi L, Quadroni M, Collart M, Picard D. Translational reprogramming in response to accumulating stressors ensures critical threshold levels of Hsp90 for mammalian life. Nat Commun 2022; 13:6271. [PMID: 36270993 PMCID: PMC9587034 DOI: 10.1038/s41467-022-33916-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
The cytosolic molecular chaperone Hsp90 is essential for eukaryotic life. Although reduced Hsp90 levels correlate with aging, it was unknown whether eukaryotic cells and organisms can tune the basal Hsp90 levels to alleviate physiologically accumulated stress. We have investigated whether and how mice adapt to the deletion of three out of four alleles of the two genes encoding cytosolic Hsp90, with one Hsp90β allele being the only remaining one. While the vast majority of such mouse embryos die during gestation, survivors apparently manage to increase their Hsp90β protein to at least wild-type levels. Our studies reveal an internal ribosome entry site in the 5' untranslated region of the Hsp90β mRNA allowing translational reprogramming to compensate for the genetic loss of Hsp90 alleles and in response to stress. We find that the minimum amount of total Hsp90 required to support viability of mammalian cells and organisms is 50-70% of what is normally there. Those that fail to maintain a threshold level are subject to accelerated senescence, proteostatic collapse, and ultimately death. Therefore, considering that Hsp90 levels can be reduced ≥100-fold in the unicellular budding yeast, critical threshold levels of Hsp90 have markedly increased during eukaryotic evolution.
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Affiliation(s)
- Kaushik Bhattacharya
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Samarpan Maiti
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Szabolcs Zahoran
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Lorenz Weidenauer
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Dina Hany
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Diana Wider
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Lilia Bernasconi
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Martine Collart
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Didier Picard
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
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10
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Scheffer H, Coate JE, Ho EKH, Schaack S. Thermal stress and mutation accumulation increase heat shock protein expression in Daphnia. Evol Ecol 2022; 36:829-844. [PMID: 36193163 PMCID: PMC9522699 DOI: 10.1007/s10682-022-10209-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/25/2022] [Indexed: 11/28/2022]
Abstract
Understanding the short- and long-term consequences of climate change is a major challenge in biology. For aquatic organisms, temperature changes and drought can lead to thermal stress and habitat loss, both of which can ultimately lead to higher mutation rates. Here, we examine the effect of high temperature and mutation accumulation on gene expression at two loci from the heat shock protein (HSP) gene family, HSP60 and HSP90. HSPs have been posited to serve as 'mutational capacitors' given their role as molecular chaperones involved in protein folding and degradation, thus buffering against a wide range of cellular stress and destabilization. We assayed changes in HSP expression across 5 genotypes of Daphnia magna, a sentinel species in ecology and environmental biology, with and without acute exposure to thermal stress and accumulated mutations. Across genotypes, HSP expression increased ~ 6× in response to heat and ~ 4× with mutation accumulation, individually. Both factors simultaneously (lineages with high mutation loads exposed to high heat) increased gene expression ~ 23×-much more than that predicted by an additive model. Our results corroborate suggestions that HSPs can buffer against not only the effects of heat, but also mutations-a combination of factors both likely to increase in a warming world. Supplementary Information The online version contains supplementary material available at 10.1007/s10682-022-10209-1.
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Affiliation(s)
- Henry Scheffer
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
| | - Jeremy E. Coate
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
| | - Eddie K. H. Ho
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
| | - Sarah Schaack
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
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11
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Stekelenburg C, Blouin JL, Santoni F, Zaghloul N, O'Hare EA, Dusaulcy R, Maechler P, Schwitzgebel VM. Loss of Nexmif results in the expression of phenotypic variability and loss of genomic integrity. Sci Rep 2022; 12:13815. [PMID: 35970867 PMCID: PMC9378738 DOI: 10.1038/s41598-022-17845-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
We identified two NEXMIF variants in two unrelated individuals with non-autoimmune diabetes and autistic traits, and investigated the expression of Nexmif in mouse and human pancreas and its function in pancreatic beta cells in vitro and in vivo. In insulin-secreting INS-1E cells, Nexmif expression increased strongly in response to oxidative stress. CRISPR Cas9-generated Nexmif knockout mice exhibited a reduced number of proliferating beta cells in pancreatic islets. RNA sequencing of pancreatic islets showed that the downregulated genes in Nexmif mutant islets are involved in stress response and the deposition of epigenetic marks. They include H3f3b, encoding histone H3.3, which is associated with the regulation of beta-cell proliferation and maintains genomic integrity by silencing transposable elements, particularly LINE1 elements. LINE1 activity has been associated with autism and neurodevelopmental disorders in which patients share characteristics with NEXMIF patients, and can cause genomic instability and genetic variation through retrotransposition. Nexmif knockout mice exhibited various other phenotypes. Mortality and phenotypic abnormalities increased in each generation in both Nexmif mutant and non-mutant littermates. In Nexmif mutant mice, LINE1 element expression was upregulated in the pancreas, brain, and testis, possibly inducing genomic instability in Nexmif mutant mice and causing phenotypic variability in their progeny.
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Affiliation(s)
- Caroline Stekelenburg
- Pediatric Endocrine and Diabetes Unit, Division of Development and Growth, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Children's University Hospital, 6, Rue Willy Donze, 1205, Geneva, Switzerland.,Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jean-Louis Blouin
- Department of Genetic Medicine and Laboratory, University Hospitals of Geneva, 1211, Geneva, Switzerland.,Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Federico Santoni
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Norann Zaghloul
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, USA
| | - Elisabeth A O'Hare
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, USA
| | - Rodolphe Dusaulcy
- Pediatric Endocrine and Diabetes Unit, Division of Development and Growth, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Children's University Hospital, 6, Rue Willy Donze, 1205, Geneva, Switzerland.,Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pierre Maechler
- Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Cell Physiology and Metabolism, University of Geneva Medical Center, 1206, Geneva, Switzerland
| | - Valerie M Schwitzgebel
- Pediatric Endocrine and Diabetes Unit, Division of Development and Growth, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Children's University Hospital, 6, Rue Willy Donze, 1205, Geneva, Switzerland. .,Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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12
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Fueyo R, Judd J, Feschotte C, Wysocka J. Roles of transposable elements in the regulation of mammalian transcription. Nat Rev Mol Cell Biol 2022; 23:481-497. [PMID: 35228718 PMCID: PMC10470143 DOI: 10.1038/s41580-022-00457-y] [Citation(s) in RCA: 128] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
Abstract
Transposable elements (TEs) comprise about half of the mammalian genome. TEs often contain sequences capable of recruiting the host transcription machinery, which they use to express their own products and promote transposition. However, the regulatory sequences carried by TEs may affect host transcription long after the TEs have lost the ability to transpose. Recent advances in genome analysis and engineering have facilitated systematic interrogation of the regulatory activities of TEs. In this Review, we discuss diverse mechanisms by which TEs contribute to transcription regulation. Notably, TEs can donate enhancer and promoter sequences that influence the expression of host genes, modify 3D chromatin architecture and give rise to novel regulatory genes, including non-coding RNAs and transcription factors. We discuss how TEs spur regulatory evolution and facilitate the emergence of genetic novelties in mammalian physiology and development. By virtue of their repetitive and interspersed nature, TEs offer unique opportunities to dissect the effects of mutation and genomic context on the function and evolution of cis-regulatory elements. We argue that TE-centric studies hold the key to unlocking general principles of transcription regulation and evolution.
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Affiliation(s)
- Raquel Fueyo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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13
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Colonna Romano N, Fanti L. Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns. Cells 2022; 11:cells11061048. [PMID: 35326499 PMCID: PMC8947103 DOI: 10.3390/cells11061048] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs) are ubiquitous genetic elements, able to jump from one location of the genome to another, in all organisms. For this reason, on the one hand, TEs can induce deleterious mutations, causing dysfunction, disease and even lethality in individuals. On the other hand, TEs can increase genetic variability, making populations better equipped to respond adaptively to environmental change. To counteract the deleterious effects of TEs, organisms have evolved strategies to avoid their activation. However, their mobilization does occur. Usually, TEs are maintained silent through several mechanisms, but they can be reactivated during certain developmental windows. Moreover, TEs can become de-repressed because of drastic changes in the external environment. Here, we describe the ‘double life’ of TEs, being both ‘parasites’ and ‘symbionts’ of the genome. We also argue that the transposition of TEs contributes to two important evolutionary processes: the temporal dynamic of evolution and the induction of genetic variability. Finally, we discuss how the interplay between two TE-dependent phenomena, insertional mutagenesis and epigenetic plasticity, plays a role in the process of evolution.
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14
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Abstract
Organisms mount the cellular stress response whenever environmental parameters exceed the range that is conducive to maintaining homeostasis. This response is critical for survival in emergency situations because it protects macromolecular integrity and, therefore, cell/organismal function. From an evolutionary perspective, the cellular stress response counteracts severe stress by accelerating adaptation via a process called stress-induced evolution. In this Review, we summarize five key physiological mechanisms of stress-induced evolution. Namely, these are stress-induced changes in: (1) mutation rates, (2) histone post-translational modifications, (3) DNA methylation, (4) chromoanagenesis and (5) transposable element activity. Through each of these mechanisms, organisms rapidly generate heritable phenotypes that may be adaptive, maladaptive or neutral in specific contexts. Regardless of their consequences to individual fitness, these mechanisms produce phenotypic variation at the population level. Because variation fuels natural selection, the physiological mechanisms of stress-induced evolution increase the likelihood that populations can avoid extirpation and instead adapt under the stress of new environmental conditions.
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Affiliation(s)
- Elizabeth A Mojica
- Department of Animal Science, University of California, Davis, One Shields Avenue, Meyer Hall, Davis, CA 95616, USA
| | - Dietmar Kültz
- Department of Animal Science, University of California, Davis, One Shields Avenue, Meyer Hall, Davis, CA 95616, USA
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15
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Signor S, Yocum G, Bowsher J. Life stage and the environment as effectors of transposable element activity in two bee species. JOURNAL OF INSECT PHYSIOLOGY 2022; 137:104361. [PMID: 35063439 DOI: 10.1016/j.jinsphys.2022.104361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Diapause is a complex physiological phenomenon that allows insects to weather stressful environmental conditions. The regulation of diapause is accordingly complex, including signaling pathways that involve both small RNA and mRNA and affect the cell cycle, stress resistance, and developmental timing. Transposable elements, mobile genetic elements that replicate within the genome, are also thought to be stress responsive and regulated by the small RNA pathway. Therefore, we asked what the relationship was between environmental stress, diapause status, and transposable element expression in two species of agriculturally important bees, Megachile rotundata and Osmia lignaria. We characterized the TE content of the genomes of both species, then evaluated the expression of TE families during temperature stress, general environmental stress, and diapause stage. We found that the genomic TE content of the two species was very different, and M. rotundata has a larger number of annotated TEs compared to O. lignaria. We also found that both diapause stage and temperature stress had large effects on TE expression. The fold change of TE famlies tended to be larger in those expressed during diapause, however there was only a small majority that were upregulated during diapause. This suggests that stress and diapause do not break down to a simple up-regulation or down-regulation of TEs, but rather that the TE family, the genomic position of its insertions, and the exact heterochromatin formation of the organism at any given environmental state or life stage may affect overall expression of TEs.
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Affiliation(s)
- Sarah Signor
- North Dakota State University, Department of Biological Sciences, United States.
| | - George Yocum
- Bioscience Research Laboratory, U.S. Department of Agriculture/Agricultural Research Service, United States
| | - Julia Bowsher
- North Dakota State University, Department of Biological Sciences, United States
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16
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Muller H, Loiseau V, Guillier S, Cordaux R, Gilbert C. Assessing the Impact of a Viral Infection on the Expression of Transposable Elements in the Cabbage Looper Moth (Trichoplusia ni). Genome Biol Evol 2021; 13:evab231. [PMID: 34613390 PMCID: PMC8634313 DOI: 10.1093/gbe/evab231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Most studies of stress-induced transposable element (TE) expression have so far focused on abiotic sources of stress. Here, we analyzed the impact of an infection by the AcMNPV baculovirus on TE expression in a cell line (Tnms42) and midgut tissues of the cabbage looper moth (Trichoplusia ni). We find that a large fraction of TE families (576/636 in Tnms42 cells and 503/612 in midgut) is lowly expressed or not expressed at all [≤ 4 transcripts per million (TPM)] in the uninfected condition (median TPM of 0.37 in Tnms42 and 0.46 in midgut cells). In the infected condition, a total of 62 and 187 TE families were differentially expressed (DE) in midgut and Tnms42 cells, respectively, with more up- (46) than downregulated (16) TE families in the former and as many up- (91) as downregulated (96) TE families in the latter. Expression log2 fold changes of DE TE families varied from -4.95 to 9.11 in Tnms42 cells and from -4.28 to 7.66 in midgut. Large variations in expression profiles of DE TEs were observed depending on the type of cells and on time after infection. Overall, the impact of AcMNPV on TE expression in T. ni is moderate but potentially sufficient to affect TE activity and genome architecture. Interestingly, one host-derived TE integrated into AcMNPV genomes is highly expressed in infected Tnms42 cells. This result shows that virus-borne TEs can be expressed, further suggesting that they may be able to transpose and that viruses may act as vectors of horizontal transfer of TEs in insects.
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Affiliation(s)
- Héloïse Muller
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Vincent Loiseau
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Sandra Guillier
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Universite de Poitiers, CNRS, France
| | - Clément Gilbert
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
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17
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Clapes T, Polyzou A, Prater P, Sagar, Morales-Hernández A, Ferrarini MG, Kehrer N, Lefkopoulos S, Bergo V, Hummel B, Obier N, Maticzka D, Bridgeman A, Herman JS, Ilik I, Klaeylé L, Rehwinkel J, McKinney-Freeman S, Backofen R, Akhtar A, Cabezas-Wallscheid N, Sawarkar R, Rebollo R, Grün D, Trompouki E. Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration. Nat Cell Biol 2021; 23:704-717. [PMID: 34253898 PMCID: PMC8492473 DOI: 10.1038/s41556-021-00707-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
Abstract
Haematopoietic stem cells (HSCs) are normally quiescent, but have evolved mechanisms to respond to stress. Here, we evaluate haematopoietic regeneration induced by chemotherapy. We detect robust chromatin reorganization followed by increased transcription of transposable elements (TEs) during early recovery. TE transcripts bind to and activate the innate immune receptor melanoma differentiation-associated protein 5 (MDA5) that generates an inflammatory response that is necessary for HSCs to exit quiescence. HSCs that lack MDA5 exhibit an impaired inflammatory response after chemotherapy and retain their quiescence, with consequent better long-term repopulation capacity. We show that the overexpression of ERV and LINE superfamily TE copies in wild-type HSCs, but not in Mda5-/- HSCs, results in their cycling. By contrast, after knockdown of LINE1 family copies, HSCs retain their quiescence. Our results show that TE transcripts act as ligands that activate MDA5 during haematopoietic regeneration, thereby enabling HSCs to mount an inflammatory response necessary for their exit from quiescence.
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Affiliation(s)
- Thomas Clapes
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Aikaterini Polyzou
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Pia Prater
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Sagar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Medicine II, Gastroenterology, Hepatology, Endocrinology and Infectious Diseases, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | | | - Natalie Kehrer
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Stylianos Lefkopoulos
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Veronica Bergo
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Nadine Obier
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Daniel Maticzka
- Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Josip S Herman
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Würzburg Institute of Systems Immunology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Ibrahim Ilik
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Lhéanna Klaeylé
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Rolf Backofen
- Department of Computer Science, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Nina Cabezas-Wallscheid
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
- Medical Research Council (MRC), University of Cambridge, Cambridge, UK
| | - Rita Rebollo
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, Villeurbanne, France
| | - Dominic Grün
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Würzburg Institute of Systems Immunology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany.
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18
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Jit BP, Qazi S, Arya R, Srivastava A, Gupta N, Sharma A. An immune epigenetic insight to COVID-19 infection. Epigenomics 2021; 13:465-480. [PMID: 33685230 PMCID: PMC7958646 DOI: 10.2217/epi-2020-0349] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/14/2021] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 is a positive-sense RNA virus, a causal agent of ongoing COVID-19 pandemic. ACE2R methylation across three CpG sites (cg04013915, cg08559914, cg03536816) determines the host cell's entry. It regulates ACE2 expression by controlling the SIRT1 and KDM5B activity. Further, it regulates Type I and III IFN response by modulating H3K27me3 and H3K4me3 histone mark. SARS-CoV-2 protein with bromodomain and protein E mimics bromodomain histones and evades from host immune response. The 2'-O MTases mimics the host's cap1 structure and plays a vital role in immune evasion through Hsp90-mediated epigenetic process to hijack the infected cells. Although the current review highlighted the critical epigenetic events associated with SARS-CoV-2 immune evasion, the detailed mechanism is yet to be elucidated.
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Affiliation(s)
- Bimal P Jit
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sahar Qazi
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rakesh Arya
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ankit Srivastava
- Regional Institute of Ophthalmology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 220115, India
| | - Nimesh Gupta
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ashok Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
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19
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Pappalardo AM, Ferrito V, Biscotti MA, Canapa A, Capriglione T. Transposable Elements and Stress in Vertebrates: An Overview. Int J Mol Sci 2021; 22:1970. [PMID: 33671215 PMCID: PMC7922186 DOI: 10.3390/ijms22041970] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 12/17/2022] Open
Abstract
Since their identification as genomic regulatory elements, Transposable Elements (TEs) were considered, at first, molecular parasites and later as an important source of genetic diversity and regulatory innovations. In vertebrates in particular, TEs have been recognized as playing an important role in major evolutionary transitions and biodiversity. Moreover, in the last decade, a significant number of papers has been published highlighting a correlation between TE activity and exposition to environmental stresses and dietary factors. In this review we present an overview of the impact of TEs in vertebrate genomes, report the silencing mechanisms adopted by host genomes to regulate TE activity, and finally we explore the effects of environmental and dietary factor exposures on TE activity in mammals, which is the most studied group among vertebrates. The studies here reported evidence that several factors can induce changes in the epigenetic status of TEs and silencing mechanisms leading to their activation with consequent effects on the host genome. The study of TE can represent a future challenge for research for developing effective markers able to detect precocious epigenetic changes and prevent human diseases.
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Affiliation(s)
- Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences-Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences-Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Maria Assunta Biscotti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Adriana Canapa
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Teresa Capriglione
- Department of Biology, University of Naples "Federico II", Via Cinthia 21-Ed7, 80126 Naples, Italy
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20
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The aging proteostasis decline: From nematode to human. Exp Cell Res 2021; 399:112474. [PMID: 33434530 PMCID: PMC7868887 DOI: 10.1016/j.yexcr.2021.112474] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 02/08/2023]
Abstract
The aging proteostasis decline manifests in a failure of aging cells and organisms to properly respond to proteotoxic challenges. This proteostasis collapse has long been considered a hallmark of aging in nematodes, and has recently been shown to occur also in human cells upon entry to senescence, opening the way to exploring the phenomenon in the broader context of human aging. Cellular senescence is part of the normal human physiology of aging, with senescent cell accumulation as a prominent feature of aged tissues. Being highly resistant to cell death, senescent cells, as they accumulate, become pro-inflammatory and promote disease. Here we discuss the causes of human senescence proteostasis decline, in view of the current literature on nematodes, on the one hand, and senescence, on the other hand. We review two major aspects of the phenomenon: (1) the decline in transcriptional activation of stress-response pathways, and (2) impairments in proteasome function. We further outline potential underlying mechanisms of transcriptional proteostasis decline, focusing on reduced chromatin dynamics and compromised nuclear integrity. Finally, we discuss potential strategies for reinforcing proteostasis as a means to improve organismal health and address the relationship to senolytics.
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21
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Han B, Luo J, Jiang P, Li Y, Wang Q, Bai Y, Chen J, Wang J, Zhang J. Inhibition of Embryonic HSP 90 Function Promotes Variation of Cold Tolerance in Zebrafish. Front Genet 2020; 11:541944. [PMID: 33343615 PMCID: PMC7746879 DOI: 10.3389/fgene.2020.541944] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
Accumulating evidence indicates that heat shock protein 90 (HSP90) plays essential roles in modulation of phenotypic plasticity in vertebrate development, however, the roles of HSP90 in modulation of cold tolerance capacity in fish are still unclear. In the present study, we showed that transient inhibition of embryonic HSP90 function by a chemical inhibitor or low conductivity stress promoted variation of cold tolerance capacity in adult zebrafish. Further work showed that embryonic HSP90 inhibition enhanced cold tolerance in adult zebrafish could be transmitted to their offspring. RNA-seq data showed that embryonic HSP90 inhibition enhanced cold tolerance involves variation of gene expression related to proteasome, lysosome, autophagy, and ribosome. Experiments with zebrafish ZF4 cells showed that two differentially expressed genes atg9b and psmd12 were up-regulated by radicicol treatment and provided protective roles for cells under cold stress, indicating that up-regulation of autophagy and proteasome function contributes to enhanced cold tolerance. The present work sheds a light on the roles of HSP90 in regulation of phenotypic plasticity associated with thermal adaptation in fish.
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Affiliation(s)
- Bingshe Han
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Juntao Luo
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Penglei Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Yan Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Qiong Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Yajing Bai
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Jing Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Jian Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Junfang Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
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22
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Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly. Viruses 2020; 12:v12101089. [PMID: 32993145 PMCID: PMC7650545 DOI: 10.3390/v12101089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
The human genome has been under selective pressure to evolve in response to emerging pathogens and other environmental challenges. Genome evolution includes the acquisition of new genes or new isoforms of genes and changes to gene expression patterns. One source of genome innovation is from transposable elements (TEs), which carry their own promoters, enhancers and open reading frames and can act as ‘controlling elements’ for our own genes. TEs include LINE-1 elements, which can retrotranspose intracellularly and endogenous retroviruses (ERVs) that represent remnants of past retroviral germline infections. Although once pathogens, ERVs also represent an enticing source of incoming genetic material that the host can then repurpose. ERVs and other TEs have coevolved with host genes for millions of years, which has allowed them to become embedded within essential gene expression programmes. Intriguingly, these host genes are often subject to the same epigenetic control mechanisms that evolved to combat the TEs that now regulate them. Here, we illustrate the breadth of host gene regulation through TEs by focusing on examples of young (The New), ancient (The Old), and disease-causing (The Ugly) TE integrants.
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23
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Antonova A, Hummel B, Khavaran A, Redhaber DM, Aprile-Garcia F, Rawat P, Gundel K, Schneck M, Hansen EC, Mitschke J, Mittler G, Miething C, Sawarkar R. Heat-Shock Protein 90 Controls the Expression of Cell-Cycle Genes by Stabilizing Metazoan-Specific Host-Cell Factor HCFC1. Cell Rep 2020; 29:1645-1659.e9. [PMID: 31693902 DOI: 10.1016/j.celrep.2019.09.084] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/06/2019] [Accepted: 09/27/2019] [Indexed: 12/18/2022] Open
Abstract
Molecular chaperones such as heat-shock proteins (HSPs) help in protein folding. Their function in the cytosol has been well studied. Notably, chaperones are also present in the nucleus, a compartment where proteins enter after completing de novo folding in the cytosol, and this raises an important question about chaperone function in the nucleus. We performed a systematic analysis of the nuclear pool of heat-shock protein 90. Three orthogonal and independent analyses led us to the core functional interactome of HSP90. Computational and biochemical analyses identify host cell factor C1 (HCFC1) as a transcriptional regulator that depends on HSP90 for its stability. HSP90 was required to maintain the expression of HCFC1-targeted cell-cycle genes. The regulatory nexus between HSP90 and the HCFC1 module identified in this study sheds light on the relevance of chaperones in the transcription of cell-cycle genes. Our study also suggests a therapeutic avenue of combining chaperone and transcription inhibitors for cancer treatment.
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Affiliation(s)
- Aneliya Antonova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ashkan Khavaran
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Desiree M Redhaber
- German Consortium for Translational Cancer Research (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Prashant Rawat
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Kathrin Gundel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Megan Schneck
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Erik C Hansen
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Jan Mitschke
- Department of Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Cornelius Miething
- German Consortium for Translational Cancer Research (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany; MRC Toxicology Unit, University of Cambridge, Cambridge, UK.
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24
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Jakobson CM, Jarosz DF. What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit? Annu Rev Genet 2020; 54:439-464. [PMID: 32897739 DOI: 10.1146/annurev-genet-021920-102037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complexity of heredity has been appreciated for decades: Many traits are controlled not by a single genetic locus but instead by polymorphisms throughout the genome. The importance of complex traits in biology and medicine has motivated diverse approaches to understanding their detailed genetic bases. Here, we focus on recent systematic studies, many in budding yeast, which have revealed that large numbers of all kinds of molecular variation, from noncoding to synonymous variants, can make significant contributions to phenotype. Variants can affect different traits in opposing directions, and their contributions can be modified by both the environment and the epigenetic state of the cell. The integration of prospective (synthesizing and analyzing variants) and retrospective (examining standing variation) approaches promises to reveal how natural selection shapes quantitative traits. Only by comprehensively understanding nature's genetic tool kit can we predict how phenotypes arise from the complex ensembles of genetic variants in living organisms.
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Affiliation(s)
- Christopher M Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA; .,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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25
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Barrere-Cain R, Allard P. An Understudied Dimension: Why Age Needs to Be Considered When Studying Epigenetic-Environment Interactions. Epigenet Insights 2020; 13:2516865720947014. [PMID: 32864568 PMCID: PMC7430070 DOI: 10.1177/2516865720947014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/06/2020] [Indexed: 02/02/2023] Open
Abstract
We live in a complex chemical environment where there are an estimated 350 000 chemical compounds or mixtures commercially produced. A strong body of literature shows that there are time points during early development when an organism’s epigenome is particularly sensitive to chemicals in its environment. What is less understood is how gene-environment and epigenetic-environment interactions change with age. This question is bidirectional: (1) how do chemicals in the environment affect the aging process and (2) how does aging affect an organism’s response to its chemical environment? The study of gene-environment interactions with age is especially important because, in many parts of the world, older individuals are a large and rapidly growing proportion of the population and because aging is a process universal to most of the animal kingdom. Epigenetics has emerged as a crucial framework for studying aging as epigenetic pathways, often triggered by environmental stimuli, have been shown to be essential regulators of the aging process. In this perspective article, we delineate the connection between aging, epigenetics, and environmental exposures. We discuss why it is essential to consider age when researching how an organism interacts with its environment. We describe recent advances in understanding how the chemical environment affects aging and the gap in research on how age affects an organism’s response to the environment. Finally, we highlight how model organisms and network approaches can help fill this crucial gap. Taken together, systemic changes that occur in the epigenome with age indicate that adult organisms cannot be treated as a homogeneous population and that there are discrete mechanisms modulating the aging epigenome that we do not yet understand.
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Affiliation(s)
- Rio Barrere-Cain
- Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Patrick Allard
- Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
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26
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Hematopoietic regeneration under the spell of epigenetic-epitranscriptomic factors and transposable elements. Curr Opin Hematol 2020; 27:264-272. [DOI: 10.1097/moh.0000000000000585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Percharde M, Sultana T, Ramalho-Santos M. What Doesn't Kill You Makes You Stronger: Transposons as Dual Players in Chromatin Regulation and Genomic Variation. Bioessays 2020; 42:e1900232. [PMID: 32053231 DOI: 10.1002/bies.201900232] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/10/2020] [Indexed: 12/22/2022]
Abstract
Transposable elements (TEs) are sequences currently or historically mobile, and are present across all eukaryotic genomes. A growing interest in understanding the regulation and function of TEs has revealed seemingly dichotomous roles for these elements in evolution, development, and disease. On the one hand, many gene regulatory networks owe their organization to the spread of cis-elements and DNA binding sites through TE mobilization during evolution. On the other hand, the uncontrolled activity of transposons can generate mutations and contribute to disease, including cancer, while their increased expression may also trigger immune pathways that result in inflammation or senescence. Interestingly, TEs have recently been found to have novel essential functions during mammalian development. Here, the function and regulation of TEs are discussed, with a focus on LINE1 in mammals. It is proposed that LINE1 is a beneficial endogenous dual regulator of gene expression and genomic diversity during mammalian development, and that both of these functions may be detrimental if deregulated in disease contexts.
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Affiliation(s)
- Michelle Percharde
- MRC London Institute of Medical Sciences (LMS), London, W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Tania Sultana
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5T 3L9, Ontario, Canada
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5T 3L9, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Ontario, Canada
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28
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Fouché S, Badet T, Oggenfuss U, Plissonneau C, Francisco CS, Croll D. Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen. Mol Biol Evol 2020; 37:221-239. [PMID: 31553475 DOI: 10.1093/molbev/msz216] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are drivers of genome evolution and affect the expression landscape of the host genome. Stress is a major factor inducing TE activity; however, the regulatory mechanisms underlying de-repression are poorly understood. Plant pathogens are excellent models to dissect the impact of stress on TEs. The process of plant infection induces stress for the pathogen, and virulence factors (i.e., effectors) located in TE-rich regions become expressed. To dissect TE de-repression dynamics and contributions to virulence, we analyzed the TE expression landscape of four strains of the major wheat pathogen Zymoseptoria tritici. We experimentally exposed strains to nutrient starvation and host infection stress. Contrary to expectations, we show that the two distinct conditions induce the expression of different sets of TEs. In particular, the most highly expressed TEs, including miniature inverted-repeat transposable element and long terminal repeat-Gypsy element, show highly distinct de-repression across stress conditions. Both the genomic context of TEs and the genetic background stress (i.e., different strains harboring the same TEs) were major predictors of de-repression under stress. Gene expression profiles under stress varied significantly depending on the proximity to the closest TEs and genomic defenses against TEs were largely ineffective to prevent de-repression. Next, we analyzed the locus encoding the Avr3D1 effector. We show that the insertion and subsequent silencing of TEs in close proximity likely contributed to reduced expression and virulence on a specific wheat cultivar. The complexity of TE responsiveness to stress across genetic backgrounds and genomic locations demonstrates substantial intraspecific genetic variation to control TEs with consequences for virulence.
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Affiliation(s)
- Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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29
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Zohn IE. Hsp90 and complex birth defects: A plausible mechanism for the interaction of genes and environment. Neurosci Lett 2020; 716:134680. [PMID: 31821846 DOI: 10.1016/j.neulet.2019.134680] [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: 07/08/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/17/2022]
Abstract
How genes and environment interact to cause birth defects is not well understood, but key to developing new strategies to modify risk. The threshold model has been proposed to represent this complex interaction. This model stipulates that while environmental exposure or genetic mutation alone may not result in a defect, factors in combination increase phenotypic variability resulting in more individuals crossing the disease threshold where birth defects manifest. Many environmental factors that contribute to birth defects induce widespread cellular stress and misfolding of proteins. Yet, the impact of the stress response on the threshold model is not typically considered in discephering the etiology of birth defects. This mini-review will explore a potential mechanism for gene-environment interactions co-opted from studies of evolution. This model stipulates that heat shock proteins that mediate the stress response induced by environmental factors can influence the number of individuals that cross disease thresholds resulting in increased incidence of birth defects. Studies in the field of evolutionary biology have demonstrated that heat shock proteins and Hsp90 in particular provide a link between environmental stress, genotype and phenotype. Hsp90 is a highly expressed molecular chaperone that assists a wide variety of protein clients with folding and conformational changes needed for proper function. Hsp90 also chaperones client proteins with potentially deleterious amino acid changes to suppress variation caused by genetic mutations. However, upon exposure to stress, Hsp90 abandons its normal physiological clients and is diverted to assist with the misfolded protein response. This can impact the activity of signaling pathways that involve Hsp90 clients as well as unmask suppressed protein variation, essentially creating complex traits in a single step. In this capacity Hsp90 acts as an evolutionary capacitor allowing stored variation to accumulate and then become expressed in times of stress. This mechanism provides a substrate which natural selection can act upon at the population level allowing survival of the species with selective pressure. However, at the level of the individual, this mechanism can result in simultaneous expression of deleterious variants as well as reduced activity of a variety of Hsp90 chaperoned pathways, potentially shifting phenotypic variability over the disease threshold resulting in birth defects.
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Affiliation(s)
- Irene E Zohn
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC, 20010, USA.
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30
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Regulation of Molecular Chaperone GRP78 by Hepatitis B Virus: Control of Viral Replication and Cell Survival. Mol Cell Biol 2020; 40:MCB.00475-19. [PMID: 31712392 DOI: 10.1128/mcb.00475-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/01/2019] [Indexed: 12/11/2022] Open
Abstract
Chronic hepatitis B (CHB) remains a global health problem, carrying a high risk for progression into cirrhosis and liver failure. Molecular chaperones are involved in diverse pathophysiological processes including viral infection. However, the role of molecular chaperones in hepatitis B virus (HBV) infection and its underlying mechanisms remain unclear. Here, we identified GRP78 as one of the molecular chaperones most strongly induced by HBV in human hepatocytes. Gain- and loss-of-function analyses demonstrated that GRP78 exerted an inhibitory effect on HBV transcription and replication. Further study showed that GRP78 was involved in the activation of AKT/mTOR signaling in hepatocytes, which contributed to GRP78-mediated inhibition of HBV. Of note, HBV-upregulated GRP78 was found to play a crucial role in maintaining the survival of hepatocytes via facilitating a mild endoplasmic reticulum (ER) stress. Together, our findings suggest that HBV may sacrifice part of its replication for establishing a persistent infection through induction of GRP78, a master ER stress regulator. Targeting GRP78 may help develop to design novel therapeutic strategies against chronic HBV infection and the associated hepatocellular carcinoma.
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31
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Gvozdenov Z, Bendix LD, Kolhe J, Freeman BC. The Hsp90 Molecular Chaperone Regulates the Transcription Factor Network Controlling Chromatin Accessibility. J Mol Biol 2019; 431:4993-5003. [PMID: 31628945 PMCID: PMC6983977 DOI: 10.1016/j.jmb.2019.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/29/2019] [Accepted: 09/11/2019] [Indexed: 01/02/2023]
Abstract
Genomic events including gene regulation and chromatin status are controlled by transcription factors. Here we report that the Hsp90 molecular chaperone broadly regulates the transcription factor protein family. Our studies identified a biphasic use of Hsp90 in which early inactivation (15 min) of the chaperone triggered a wide reduction of DNA binding events along the genome with concurrent changes to chromatin structure. Long-term loss (6 h) of Hsp90 resulted in a decline of a divergent yet overlaying pool of transcription factors that produced a distinct chromatin pattern. Although both phases involve protein folding, the early point correlated with Hsp90 acting in a late folding step that is critical for DNA binding function, whereas prolonged Hsp90 inactivation led to a significant decrease in the steady-state transcription factor protein levels. Intriguingly, despite the broad chaperone impact on a variety of transcription factors, the operational influence of Hsp90 was at the level of chromatin with only a mild effect on gene regulation. Thus, Hsp90 selectively governs the transcription factor process overseeing local chromatin structure.
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Affiliation(s)
- Zlata Gvozdenov
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, 601 S. Goodwin Avenue, Urbana, IL 61801, USA
| | - Lindsey D Bendix
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, 601 S. Goodwin Avenue, Urbana, IL 61801, USA
| | - Janhavi Kolhe
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, 601 S. Goodwin Avenue, Urbana, IL 61801, USA
| | - Brian C Freeman
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, 601 S. Goodwin Avenue, Urbana, IL 61801, USA.
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32
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Grünert SC, Marquardt T, Lausch E, Fuchs H, Thiel C, Sutter M, Schumann A, Hannibal L, Spiekerkoetter U. Unsuccessful intravenous D-mannose treatment in PMM2-CDG. Orphanet J Rare Dis 2019; 14:231. [PMID: 31640729 PMCID: PMC6805611 DOI: 10.1186/s13023-019-1213-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/24/2019] [Indexed: 01/13/2023] Open
Abstract
Background PMM2-CDG (Phosphomannomutase 2 - Congenital disorder of glycosylation-Ia; CDG-Ia) is the most common glycosylation defect, often presenting as a severe multisystem disorder that can be fatal within the first years of life. While mannose treatment has been shown to correct glycosylation in vitro and in vivo in mice, no convincing effects have been observed in short-term treatment trials in single patients so far. Results We report on a boy with a severe PMM2-CDG who received a continuous intravenous mannose infusion over a period of 5 months during the first year of life in a dose of 0.8 g/kg/day. N-glycosylation of serum glycoproteins and mannose concentrations in serum were studied regularly. Unfortunately, no biochemical or clinical improvement was observed, and the therapy was terminated at age 9 months. Conclusion Postnatal intravenous D-mannose treatment seems to be ineffective in PMM2-CDG.
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Affiliation(s)
- Sarah C Grünert
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, Mathildenstraße 1, 79106, Freiburg, Germany.
| | - Thorsten Marquardt
- Department of General Pediatrics, University Children's Hospital Münster, Münster, Germany
| | - Ekkehart Lausch
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, Mathildenstraße 1, 79106, Freiburg, Germany
| | - Hans Fuchs
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, Mathildenstraße 1, 79106, Freiburg, Germany
| | - Christian Thiel
- Center for Child and Adolescent Medicine, Department I, University of Heidelberg, 69120, Heidelberg, Germany
| | - Martin Sutter
- Pharmacy Department, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Anke Schumann
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, Mathildenstraße 1, 79106, Freiburg, Germany
| | - Luciana Hannibal
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Ute Spiekerkoetter
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, Mathildenstraße 1, 79106, Freiburg, Germany
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33
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Deng L, Ren R, Liu Z, Song M, Li J, Wu Z, Ren X, Fu L, Li W, Zhang W, Guillen P, Izpisua Belmonte JC, Chan P, Qu J, Liu GH. Stabilizing heterochromatin by DGCR8 alleviates senescence and osteoarthritis. Nat Commun 2019; 10:3329. [PMID: 31350386 PMCID: PMC6659673 DOI: 10.1038/s41467-019-10831-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/03/2019] [Indexed: 01/01/2023] Open
Abstract
DiGeorge syndrome critical region 8 (DGCR8) is a critical component of the canonical microprocessor complex for microRNA biogenesis. However, the non-canonical functions of DGCR8 have not been studied. Here, we demonstrate that DGCR8 plays an important role in maintaining heterochromatin organization and attenuating aging. An N-terminal-truncated version of DGCR8 (DR8dex2) accelerated senescence in human mesenchymal stem cells (hMSCs) independent of its microRNA-processing activity. Further studies revealed that DGCR8 maintained heterochromatin organization by interacting with the nuclear envelope protein Lamin B1, and heterochromatin-associated proteins, KAP1 and HP1γ. Overexpression of any of these proteins, including DGCR8, reversed premature senescent phenotypes in DR8dex2 hMSCs. Finally, DGCR8 was downregulated in pathologically and naturally aged hMSCs, whereas DGCR8 overexpression alleviated hMSC aging and mouse osteoarthritis. Taken together, these analyses uncovered a novel, microRNA processing-independent role in maintaining heterochromatin organization and attenuating senescence by DGCR8, thus representing a new therapeutic target for alleviating human aging-related disorders.
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Affiliation(s)
- Liping Deng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ruotong Ren
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Moshi Song
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jingyi Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, 100053, Beijing, China
| | - Zeming Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoqing Ren
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lina Fu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wei Li
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, 100053, Beijing, China
| | - Weiqi Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, 100053, Beijing, China
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Pedro Guillen
- Clinica Cemtro. Av. del Ventisquero de la Condesa, 42, 28035, Madrid, Spain
| | | | - Piu Chan
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, 100053, Beijing, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Guang-Hui Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, 100053, Beijing, China.
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, 510632, Guangzhou, China.
- Beijing Institute for Brain Disorders, Capital Medical University, 100069, Beijing, China.
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34
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Azébi S, Batsché E, Michel F, Kornobis E, Muchardt C. Expression of endogenous retroviruses reflects increased usage of atypical enhancers in T cells. EMBO J 2019; 38:embj.2018101107. [PMID: 31068361 DOI: 10.15252/embj.2018101107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/20/2019] [Accepted: 03/28/2019] [Indexed: 01/02/2023] Open
Abstract
Several autoimmune diseases including multiple sclerosis (MS) cause increased transcription of endogenous retroviruses (HERVs) normally repressed by heterochromatin. In parallel, HERV-derived sequences were reported to drive gene expression. Here, we have examined a possible link between promoter and enhancer divergent transcription and the production of HERV transcripts. We find that HERV-derived sequences are in general counter-selected at regulatory regions, a counter-selection that is strongest in brain tissues while very moderate in stem cells. By exposing T cells to the pesticide dieldrin, we further found that a series of HERV-driven enhancers otherwise active only at stem cell stages can be reactivated by stress. This in part relies on peptidylarginine deiminase activity, possibly participating in the reawakening of silenced enhancers. Likewise, usage of HERV-driven enhancers was increased in myelin-reactive T cells from patients with MS, correlating with activation of nearby genes at several sites. Altogether, we propose that HERV-driven enhancers constitute a reservoir of auxiliary enhancers transiently induced by stress while chronically active in diseases like MS.
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Affiliation(s)
- Saliha Azébi
- Unité de Régulation Epigénétique, UMR3738, CNRS, Institut Pasteur, Paris, France.,Unit of Cytokine Signaling, Department of Immunology, Institut Pasteur, Paris, France
| | - Eric Batsché
- Unité de Régulation Epigénétique, UMR3738, CNRS, Institut Pasteur, Paris, France
| | - Frédérique Michel
- Ecole Doctorale "Complexité du Vivant" (ED515), Sorbonne Université, Paris, France
| | - Etienne Kornobis
- Unité de Régulation Epigénétique, UMR3738, CNRS, Institut Pasteur, Paris, France
| | - Christian Muchardt
- Unité de Régulation Epigénétique, UMR3738, CNRS, Institut Pasteur, Paris, France
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35
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SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells. Nat Commun 2019; 10:1335. [PMID: 30902974 PMCID: PMC6430823 DOI: 10.1038/s41467-019-09078-0] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
Endogenous retroviruses (ERVs) can confer benefits to their host but present a threat to genome integrity if not regulated correctly. Here we identify the SWI/SNF-like remodeler SMARCAD1 as a key factor in the control of ERVs in embryonic stem cells. SMARCAD1 is enriched at ERV subfamilies class I and II, particularly at active intracisternal A-type particles (IAPs), where it preserves repressive histone methylation marks. Depletion of SMARCAD1 results in de-repression of IAPs and adjacent genes. Recruitment of SMARCAD1 to ERVs is dependent on KAP1, a central component of the silencing machinery. SMARCAD1 and KAP1 occupancy at ERVs is co-dependent and requires the ATPase function of SMARCAD1. Our findings uncover a role for the enzymatic activity of SMARCAD1 in cooperating with KAP1 to silence ERVs. This reveals ATP-dependent chromatin remodeling as an integral step in retrotransposon regulation in stem cells and advances our understanding of the mechanisms driving heterochromatin establishment. Tight regulation of retrotransposons such as endogenous retroviruses (ERVs) is essential for genome and transcriptome integrity. Here, the authors show that the ATPase function of the chromatin remodeler SMARCAD1 facilitates the binding of KAP1 to ERVs and is required for their repression in embryonic stem cells.
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Hughes S, Vrinds I, de Roo J, Francke C, Shimeld SM, Woollard A, Sato A. DnaJ chaperones contribute to canalization. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2019; 331:201-212. [PMID: 30653842 DOI: 10.1002/jez.2254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 01/04/2023]
Abstract
Canalization, an intrinsic robustness of development to external (environmental) or internal (genetic) perturbations, was first proposed over half a century ago. However, whether the robustness to environmental stress (environmental canalization [EC]) and to genetic variation (genetic canalization) are underpinned by the same molecular basis remains elusive. The recent discovery of the involvement of two endoplasmic reticulum (ER)-associated DnaJ genes in developmental buffering, orthologues of which are conserved across Metazoa, indicates that the role of ER-associated DnaJ genes might be conserved across the animal kingdom. To test this, we surveyed the ER-associated DnaJ chaperones in the nematode Caenorhabditis elegans. We then quantified the phenotype, in the form of variance and mean of seam cell counts, from RNA interference knockdown of DnaJs under three different temperatures. We find that seven out of eight ER-associated DnaJs are involved in either EC or microenvironmental canalization. Moreover, we also found two DnaJ genes not specifically associated with ER (DNAJC2/dnj-11 and DNAJA2/dnj-19) were involved in canalization. Protein expression pattern showed that these DnaJs are upregulated by heat stress, yet not all of them are expressed in the seam cells. Moreover, we found that most of the buffering DnaJs also control lifespan. We therefore concluded that a number of DnaJ chaperones, not limited to those associated with the ER, are involved in canalization as a part of the complex system that underlies development.
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Affiliation(s)
- Samantha Hughes
- HAN BioCentre, HAN University of Applied Science, Isnstitute of Applied Biosciences and Chemistry, Nijmegen, The Netherlands
| | - Inge Vrinds
- HAN BioCentre, HAN University of Applied Science, Isnstitute of Applied Biosciences and Chemistry, Nijmegen, The Netherlands
| | - Joris de Roo
- HAN BioCentre, HAN University of Applied Science, Isnstitute of Applied Biosciences and Chemistry, Nijmegen, The Netherlands
| | - Christof Francke
- HAN BioCentre, HAN University of Applied Science, Isnstitute of Applied Biosciences and Chemistry, Nijmegen, The Netherlands
| | | | - Alison Woollard
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Atsuko Sato
- Department of Biology, Ochanomizu University, Tokyo, Japan
- Institute for Human Life Innovation, Ochanomizu University, Tokyo, Japan
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Dahiya V, Buchner J. Functional principles and regulation of molecular chaperones. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:1-60. [PMID: 30635079 DOI: 10.1016/bs.apcsb.2018.10.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To be able to perform their biological function, a protein needs to be correctly folded into its three dimensional structure. The protein folding process is spontaneous and does not require the input of energy. However, in the crowded cellular environment where there is high risk of inter-molecular interactions that may lead to protein molecules sticking to each other, hence forming aggregates, protein folding is assisted. Cells have evolved robust machinery called molecular chaperones to deal with the protein folding problem and to maintain proteins in their functional state. Molecular chaperones promote efficient folding of newly synthesized proteins, prevent their aggregation and ensure protein homeostasis in cells. There are different classes of molecular chaperones functioning in a complex interplay. In this review, we discuss the principal characteristics of different classes of molecular chaperones, their structure-function relationships, their mode of regulation and their involvement in human disorders.
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Affiliation(s)
- Vinay Dahiya
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany.
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Transposable element dysregulation in systemic lupus erythematosus and regulation by histone conformation and Hsp90. Clin Immunol 2018; 197:6-18. [PMID: 30149120 DOI: 10.1016/j.clim.2018.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 01/27/2023]
Abstract
Systemic lupus erythematosus (SLE) represents an autoimmune disease in which activation of the type I interferon pathway leads to dysregulation of tolerance and the generation of autoantibodies directed against nuclear constituents. The mechanisms driving the activation of the interferon pathway in SLE have been the subject of intense investigation but are still incompletely understood. Transposable elements represent an enormous source of RNA that could potentially stimulate the cell intrinsic RNA-recognition pathway, leading to upregulation of interferons. We used RNA-seq to define transposable element families and subfamilies in three cell types in SLE and found diverse effects on transposable element expression in the three cell types and even within a given family of transposable elements. When potential mechanisms were examined, we found that Hsp90 inhibition could drive increased expression of multiple type of transposable elements. Both direct inhibition and the delivery of a heat shock itself, which redirects heat shock regulators (including Hsp90) off of basal expression promoters and onto heat shock-responsive promoters, led to increased transposable element expression. This effect was amplified by the concurrent delivery of a histone deacetylase inhibitor. We conclude that transposable elements are dysregulated in SLE and there are tissue-specific effects and locus-specific effects. The magnitude of RNAs attributable to transposable elements makes their dysregulation of critical interest in SLE where transposable element RNA complexed with proteins has been shown to drive interferon expression.
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Schrader L, Schmitz J. The impact of transposable elements in adaptive evolution. Mol Ecol 2018; 28:1537-1549. [PMID: 30003608 DOI: 10.1111/mec.14794] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/06/2018] [Indexed: 12/16/2022]
Abstract
The growing knowledge about the influence of transposable elements (TEs) on (a) long-term genome and transcriptome evolution; (b) genomic, transcriptomic and epigenetic variation within populations; and (c) patterns of somatic genetic differences in individuals continues to spur the interest of evolutionary biologists in the role of TEs in adaptive evolution. As TEs can trigger a broad range of molecular variation in a population with potentially severe fitness and phenotypic consequences for individuals, different mechanisms evolved to keep TE activity in check, allowing for a dynamic interplay between the host, its TEs and the environment in evolution. Here, we review evidence for adaptive phenotypic changes associated with TEs and the basic molecular mechanisms by which the underlying genetic changes arise: (a) domestication, (b) exaptation, (c) host gene regulation, (d) TE-mediated formation of intronless gene copies-so-called retrogenes and (e) overall increased genome plasticity. Furthermore, we review and discuss how the stress-dependent incapacitation of defence mechanisms against the activity of TEs might facilitate adaptive responses to environmental challenges and how such mechanisms might be particularly relevant in species frequently facing novel environments, such as invasive, pathogenic or parasitic species.
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Affiliation(s)
- Lukas Schrader
- Institute for Evolution and Biodiversity (IEB), University of Münster, Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology, University of Münster, Münster, Germany
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Zabinsky RA, Mason GA, Queitsch C, Jarosz DF. It's not magic - Hsp90 and its effects on genetic and epigenetic variation. Semin Cell Dev Biol 2018; 88:21-35. [PMID: 29807130 DOI: 10.1016/j.semcdb.2018.05.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 04/15/2018] [Accepted: 05/15/2018] [Indexed: 10/14/2022]
Abstract
Canalization, or phenotypic robustness in the face of environmental and genetic perturbation, is an emergent property of living systems. Although this phenomenon has long been recognized, its molecular underpinnings have remained enigmatic until recently. Here, we review the contributions of the molecular chaperone Hsp90, a protein that facilitates the folding of many key regulators of growth and development, to canalization of phenotype - and de-canalization in times of stress - drawing on studies in eukaryotes as diverse as baker's yeast, mouse ear cress, and blind Mexican cavefish. Hsp90 is a hub of hubs that interacts with many so-called 'client proteins,' which affect virtually every aspect of cell signaling and physiology. As Hsp90 facilitates client folding and stability, it can epistatically suppress or enable the expression of genetic variants in its clients and other proteins that acquire client status through mutation. Hsp90's vast interaction network explains the breadth of its phenotypic reach, including Hsp90-dependent de novo mutations and epigenetic effects on gene regulation. Intrinsic links between environmental stress and Hsp90 function thus endow living systems with phenotypic plasticity in fluctuating environments. As environmental perturbations alter Hsp90 function, they also alter Hsp90's interaction with its client proteins, thereby re-wiring networks that determine the genotype-to-phenotype map. Ensuing de-canalization of phenotype creates phenotypic diversity that is not simply stochastic, but often has an underlying genetic basis. Thus, extreme phenotypes can be selected, and assimilated so that they no longer require environmental stress to manifest. In addition to acting on standing genetic variation, Hsp90 perturbation has also been linked to increased frequency of de novo variation and several epigenetic phenomena, all with the potential to generate heritable phenotypic change. Here, we aim to clarify and discuss the multiple means by which Hsp90 can affect phenotype and possibly evolutionary change, and identify their underlying common feature: at its core, Hsp90 interacts epistatically through its chaperone function with many other genes and their gene products. Its influence on phenotypic diversification is thus not magic but rather a fundamental property of genetics.
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Affiliation(s)
- Rebecca A Zabinsky
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford, CA, United States
| | | | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, United States.
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford, CA, United States; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, United States.
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Robbez-Masson L, Tie CH, Conde L, Tunbak H, Husovsky C, Tchasovnikarova IA, Timms RT, Herrero J, Lehner PJ, Rowe HM. The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes. Genome Res 2018; 28:836-845. [PMID: 29728366 PMCID: PMC5991525 DOI: 10.1101/gr.228171.117] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/23/2018] [Indexed: 11/24/2022]
Abstract
Retrotransposons encompass half of the human genome and contribute to the formation of heterochromatin, which provides nuclear structure and regulates gene expression. Here, we asked if the human silencing hub (HUSH) complex is necessary to silence retrotransposons and whether it collaborates with TRIM28 and the chromatin remodeler ATRX at specific genomic loci. We show that the HUSH complex contributes to de novo repression and DNA methylation of an SVA retrotransposon reporter. By using naïve versus primed mouse pluripotent stem cells, we reveal a critical role for the HUSH complex in naïve cells, implicating it in programming epigenetic marks in development. Although the HUSH component FAM208A binds to endogenous retroviruses (ERVs) and long interspersed element-1s (LINE-1s or L1s), it is mainly required to repress evolutionarily young L1s (mouse-specific lineages <5 million years old). TRIM28, in contrast, is necessary to repress both ERVs and young L1s. Genes co-repressed by TRIM28 and FAM208A are evolutionarily young, or exhibit tissue-specific expression, are enriched in young L1s, and display evidence for regulation through LTR promoters. Finally, we demonstrate that the HUSH complex is also required to repress L1 elements in human cells. Overall, these data indicate that the HUSH complex and TRIM28 co-repress young retrotransposons and new genes rewired by retrotransposon noncoding DNA.
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Affiliation(s)
- Luisa Robbez-Masson
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Christopher H.C. Tie
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
| | - Hale Tunbak
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Connor Husovsky
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Iva A. Tchasovnikarova
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Richard T. Timms
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
| | - Paul J. Lehner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Helen M. Rowe
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
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Panzeri I, Pospisilik JA. Epigenetic control of variation and stochasticity in metabolic disease. Mol Metab 2018; 14:26-38. [PMID: 29909200 PMCID: PMC6034039 DOI: 10.1016/j.molmet.2018.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/11/2018] [Accepted: 05/14/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The alarming rise of obesity and its associated comorbidities represents a medical burden and a major global health and economic issue. Understanding etiological mechanisms underpinning susceptibility and therapeutic response is of primary importance. Obesity, diabetes, and metabolic diseases are complex trait disorders with only partial genetic heritability, indicating important roles for environmental programing and epigenetic effects. SCOPE OF THE REVIEW We will highlight some of the reasons for the scarce predictability of metabolic diseases. We will outline how genetic variants generate phenotypic variation in disease susceptibility across populations. We will then focus on recent conclusions about epigenetic mechanisms playing a fundamental role in increasing variability and subsequently disease triggering. MAJOR CONCLUSIONS Currently, we are unable to predict or mechanistically define how "missing heritability" drives disease. Unravelling this black box of regulatory processes will allow us to move towards a truly personalized and precision medicine.
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Affiliation(s)
- Ilaria Panzeri
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - John Andrew Pospisilik
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.
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Lanciano S, Mirouze M. Transposable elements: all mobile, all different, some stress responsive, some adaptive? Curr Opin Genet Dev 2018; 49:106-114. [PMID: 29705597 DOI: 10.1016/j.gde.2018.04.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/06/2018] [Accepted: 04/11/2018] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) were first identified through the polymorphisms they induced in plants and animals. Genomic studies have later revealed that TEs were highly abundant in eukaryotic genomes. Recently, more precise single individual genomic analyses have unravelled the huge diversity of TE insertions in many plant and animal species. In most cases the stress conditions behind this diversity are not known and neither is the adaptive capacity of these natural TE-induced variants. Here, we review some of the most recent examples of TE-related impacts on gene expression at the locus or the genome level and discuss the rich diversity of the TE repertoire and its potential role in adaptive evolution.
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Affiliation(s)
- Sophie Lanciano
- IRD, DIADE, University of Perpignan, Laboratory of Plant Genome and Development, Perpignan, France
| | - Marie Mirouze
- IRD, DIADE, University of Perpignan, Laboratory of Plant Genome and Development, Perpignan, France.
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Hsp90 shapes protein and RNA evolution to balance trade-offs between protein stability and aggregation. Nat Commun 2018; 9:1781. [PMID: 29725062 PMCID: PMC5934419 DOI: 10.1038/s41467-018-04203-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/10/2018] [Indexed: 01/16/2023] Open
Abstract
Acquisition of mutations is central to evolution; however, the detrimental effects of most mutations on protein folding and stability limit protein evolvability. Molecular chaperones, which suppress aggregation and facilitate polypeptide folding, may alleviate the effects of destabilizing mutations thus promoting sequence diversification. To illuminate how chaperones can influence protein evolution, we examined the effect of reduced activity of the chaperone Hsp90 on poliovirus evolution. We find that Hsp90 offsets evolutionary trade-offs between protein stability and aggregation. Lower chaperone levels favor variants of reduced hydrophobicity and protein aggregation propensity but at a cost to protein stability. Notably, reducing Hsp90 activity also promotes clusters of codon-deoptimized synonymous mutations at inter-domain boundaries, likely to facilitate cotranslational domain folding. Our results reveal how a chaperone can shape the sequence landscape at both the protein and RNA levels to harmonize competing constraints posed by protein stability, aggregation propensity, and translation rate on successful protein biogenesis.
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Horváth V, Merenciano M, González J. Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response. Trends Genet 2017; 33:832-841. [DOI: 10.1016/j.tig.2017.08.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/02/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
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Tie CHC, Rowe HM. Epigenetic control of retrotransposons in adult tissues: implications for immune regulation. Curr Opin Virol 2017; 25:28-33. [DOI: 10.1016/j.coviro.2017.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/26/2017] [Accepted: 06/19/2017] [Indexed: 12/29/2022]
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Affiliation(s)
- Mark L Siegal
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
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