151
|
Zheng B, Aoi Y, Shah AP, Iwanaszko M, Das S, Rendleman EJ, Zha D, Khan N, Smith ER, Shilatifard A. Acute perturbation strategies in interrogating RNA polymerase II elongation factor function in gene expression. Genes Dev 2021; 35:273-285. [PMID: 33446572 PMCID: PMC7849361 DOI: 10.1101/gad.346106.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022]
Abstract
The regulation of gene expression catalyzed by RNA polymerase II (Pol II) requires a host of accessory factors to ensure cell growth, differentiation, and survival under environmental stress. Here, using the auxin-inducible degradation (AID) system to study transcriptional activities of the bromodomain and extraterminal domain (BET) and super elongation complex (SEC) families, we found that the CDK9-containing BRD4 complex is required for the release of Pol II from promoter-proximal pausing for most genes, while the CDK9-containing SEC is required for activated transcription in the heat shock response. By using both the proteolysis targeting chimera (PROTAC) dBET6 and the AID system, we found that dBET6 treatment results in two major effects: increased pausing due to BRD4 loss, and reduced enhancer activity attributable to BRD2 loss. In the heat shock response, while auxin-mediated depletion of the AFF4 subunit of the SEC has a more severe defect than AFF1 depletion, simultaneous depletion of AFF1 and AFF4 leads to a stronger attenuation of the heat shock response, similar to treatment with the SEC inhibitor KL-1, suggesting a possible redundancy among SEC family members. This study highlights the usefulness of orthogonal acute depletion/inhibition strategies to identify distinct and redundant biological functions among Pol II elongation factor paralogs.
Collapse
Affiliation(s)
- Bin Zheng
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Avani P Shah
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Siddhartha Das
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Emily J Rendleman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Didi Zha
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Nabiha Khan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Edwin R Smith
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| |
Collapse
|
152
|
Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression. Mol Cell 2021; 81:502-513.e4. [PMID: 33400923 DOI: 10.1016/j.molcel.2020.12.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/11/2020] [Accepted: 11/30/2020] [Indexed: 02/04/2023]
Abstract
Stress-induced readthrough transcription results in the synthesis of downstream-of-gene (DoG)-containing transcripts. The mechanisms underlying DoG formation during cellular stress remain unknown. Nascent transcription profiles during DoG induction in human cell lines using TT-TimeLapse sequencing revealed widespread transcriptional repression upon hyperosmotic stress. Yet, DoGs are produced regardless of the transcriptional level of their upstream genes. ChIP sequencing confirmed that stress-induced redistribution of RNA polymerase (Pol) II correlates with the transcriptional output of genes. Stress-induced alterations in the Pol II interactome are observed by mass spectrometry. While certain cleavage and polyadenylation factors remain Pol II associated, Integrator complex subunits dissociate from Pol II under stress leading to a genome-wide loss of Integrator on DNA. Depleting the catalytic subunit of Integrator using siRNAs induces hundreds of readthrough transcripts, whose parental genes partially overlap those of stress-induced DoGs. Our results provide insights into the mechanisms underlying DoG production and how Integrator activity influences DoG transcription.
Collapse
|
153
|
Rébé C, Ghiringhelli F, Garrido C. Can the hyperthermia-mediated heat shock factor/heat shock protein 70 pathway dampen the cytokine storm during SARS-CoV-2 infection? Br J Pharmacol 2020; 179:4910-4916. [PMID: 33314076 DOI: 10.1111/bph.15343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/05/2020] [Accepted: 12/04/2020] [Indexed: 12/25/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major global public health problem. Infection by this virus involves many pathophysiological processes, such as a "cytokine storm," that is, very aggressive inflammatory response that offers new perspectives for the management and treatment of patients. Here, we analyse relevant mechanism involved in the hyperthermia-mediated heat shock factors (HSFs)/heat shock proteins (HSP)70 pathway which may provide a possible treatment tool.
Collapse
Affiliation(s)
- Cédric Rébé
- Platform of Transfer in Cancer Biology, Centre Georges François Leclerc, INSERM LNC UMR1231, University of Bourgogne Franche-Comté, Dijon, France
| | - François Ghiringhelli
- Platform of Transfer in Cancer Biology, Centre Georges François Leclerc, INSERM LNC UMR1231, University of Bourgogne Franche-Comté, Dijon, France
| | - Carmen Garrido
- INSERM LNC UMR1231, University of Bourgogne Franche-Comté, Centre Georges François Leclerc, Dijon, France
| |
Collapse
|
154
|
Green EH, Kikis EA. Determining the effects of nanoparticulate air pollution on proteostasis in Caenorhabditis elegans. PLoS One 2020; 15:e0243419. [PMID: 33270781 PMCID: PMC7714337 DOI: 10.1371/journal.pone.0243419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/20/2020] [Indexed: 11/24/2022] Open
Abstract
The proteostasis network comprises the biochemical pathways that together maintain and regulate proper protein synthesis, transport, folding, and degradation. Many neurodegenerative diseases are characterized by a failure of the proteostasis network to sustain the health of the proteome, resulting in protein misfolding, aggregation, and, often, neurotoxicity. Although important advances have been made in recent years to identify genetic risk factors for neurodegenerative diseases, we still know relatively little about environmental risk factors such as air pollution. Exposure to nano-sized particulate air pollution, referred to herein as nanoparticulate matter (nPM), has been shown to trigger the accumulation of misfolded and oligomerized amyloid beta in mice. This suggests that the ability to maintain proteostasis is likely compromised in Alzheimer 's disease (AD) pathogenesis upon exposure to nPM. We aim to determine whether this aspect of the environment interacts with proteostasis network machinery to trigger protein misfolding. This could at least partially explain how air pollution exacerbates the symptoms of neurodegenerative diseases of aging, such as AD. We hypothesize that nPM challenges the buffering capacity of the proteostasis network by reducing the efficiency of folding for metastable proteins, thereby disrupting what has proven to be a very delicate proteostasis balance. We will test this hypothesis using C. elegans as our model system. Specifically, we will determine the impact of particulate air pollution on the aggregation and toxicity of disease-associated reporters of proteostasis and on transcriptional responses to stress.
Collapse
Affiliation(s)
- Emily H. Green
- Biology Department, The University of the South, Sewanee, TN, United States of America
| | - Elise A. Kikis
- Biology Department, The University of the South, Sewanee, TN, United States of America
- * E-mail:
| |
Collapse
|
155
|
Amelkina O, Comizzoli P. Initial response of ovarian tissue transcriptome to vitrification or microwave-assisted dehydration in the domestic cat model. BMC Genomics 2020; 21:828. [PMID: 33238878 PMCID: PMC7690003 DOI: 10.1186/s12864-020-07236-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Background Long term preservation of living ovarian tissues is a critical approach in human reproductive medicine as well as in the conservation of rare animal genotypes. Compared to single cell preservation, optimization of protocols for tissues is highly complex because of the diversity of cells responding differently to non-physiological conditions. Using the prepubertal domestic cat as a model, the objective was to study immediate effects of vitrification or microwave-assisted dehydration on the global transcriptome dynamics in the ovarian cortex. RNA sequencing was performed on ovarian tissues (n = 6 individuals) from different conditions: fresh tissue after dissection (F), vitrified/warmed tissue (V), tissue dehydrated for 5 min (D5) or 10 min (D10) followed by rehydration. Differential gene expression analysis was performed for comparison pairs V vs. F, D10 vs. F, D5 vs. F and D10 vs. D5, and networks were built based on results of functional enrichment and in silico protein-protein interactions. Results The impact of the vitrification protocol was already measurable within 20 min after warming and involved upregulation of the expression of seven mitochondrial DNA genes related to mitochondrial respiration. The analysis of D10 vs. F revealed, 30 min after rehydration, major downregulation of gene expression with enrichment of in silico interacting genes in Ras, Rap1, PI3K-Akt and MAPK signaling pathways. However, comparison of D5 vs. F showed negligible effects of the shorter dehydration protocol with two genes enriched in Ras signaling. Comparison of D10 vs. D5 showed downregulation of only seven genes. Vitrification and dehydration protocols mainly changed the expression of different genes and functional terms, but some of the differentially expressed genes formed a major in silico protein-protein interaction cluster enriched for mitochondrial respiration and Ras/MAPK signaling pathways. Conclusions Our results showed, for the first time, different effects of vitrification and microwave-assisted dehydration protocols on the global transcriptome of the ovarian cortex (using the domestic cat as a biomedical model). Acquired data and networks built on the basis of differentially expressed genes (1) can help to better understand stress responses to non-physiological stresses and (2) can be used as directions for future preservation protocol optimizations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07236-z.
Collapse
Affiliation(s)
- Olga Amelkina
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Pierre Comizzoli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA.
| |
Collapse
|
156
|
Burchfiel ET, Vihervaara A, Guertin MJ, Gomez-Pastor R, Thiele DJ. Comparative interactomes of HSF1 in stress and disease reveal a role for CTCF in HSF1-mediated gene regulation. J Biol Chem 2020; 296:100097. [PMID: 33208463 PMCID: PMC7948500 DOI: 10.1074/jbc.ra120.015452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 01/09/2023] Open
Abstract
Heat shock transcription factor 1 (HSF1) orchestrates cellular stress protection by activating or repressing gene transcription in response to protein misfolding, oncogenic cell proliferation, and other environmental stresses. HSF1 is tightly regulated via intramolecular repressive interactions, post-translational modifications, and protein-protein interactions. How these HSF1 regulatory protein interactions are altered in response to acute and chronic stress is largely unknown. To elucidate the profile of HSF1 protein interactions under normal growth and chronic and acutely stressful conditions, quantitative proteomics studies identified interacting proteins in the response to heat shock or in the presence of a poly-glutamine aggregation protein cell-based model of Huntington's disease. These studies identified distinct protein interaction partners of HSF1 as well as changes in the magnitude of shared interactions as a function of each stressful condition. Several novel HSF1-interacting proteins were identified that encompass a wide variety of cellular functions, including roles in DNA repair, mRNA processing, and regulation of RNA polymerase II. One HSF1 partner, CTCF, interacted with HSF1 in a stress-inducible manner and functions in repression of specific HSF1 target genes. Understanding how HSF1 regulates gene repression is a crucial question, given the dysregulation of HSF1 target genes in both cancer and neurodegeneration. These studies expand our understanding of HSF1-mediated gene repression and provide key insights into HSF1 regulation via protein-protein interactions.
Collapse
Affiliation(s)
- Eileen T Burchfiel
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Anniina Vihervaara
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Michael J Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Rocio Gomez-Pastor
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dennis J Thiele
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA.
| |
Collapse
|
157
|
Cheng Y, Saville L, Gollen B, Isaac C, Belay A, Mehla J, Patel K, Thakor N, Mohajerani MH, Zovoilis A. Increased processing of SINE B2 ncRNAs unveils a novel type of transcriptome deregulation in amyloid beta neuropathology. eLife 2020; 9:61265. [PMID: 33191914 PMCID: PMC7717908 DOI: 10.7554/elife.61265] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/15/2020] [Indexed: 12/18/2022] Open
Abstract
The functional importance of many non-coding RNAs (ncRNAs) generated by repetitive elements and their connection with pathologic processes remains elusive. B2 RNAs, a class of ncRNAs of the B2 family of SINE repeats, mediate through their processing the transcriptional activation of various genes in response to stress. Here, we show that this response is dysfunctional during amyloid beta toxicity and pathology in the mouse hippocampus due to increased levels of B2 RNA processing, leading to constitutively elevated B2 RNA target gene expression and high Trp53 levels. Evidence indicates that Hsf1, a master regulator of stress response, mediates B2 RNA processing in hippocampal cells and is activated during amyloid toxicity, accelerating the processing of SINE RNAs and gene hyper-activation. Our study reveals that in mouse, SINE RNAs constitute a novel pathway deregulated in amyloid beta pathology, with potential implications for similar cases in the human brain, such as Alzheimer’s disease (AD).
Collapse
Affiliation(s)
- Yubo Cheng
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Luke Saville
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Babita Gollen
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Christopher Isaac
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Abel Belay
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Jogender Mehla
- Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Kush Patel
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Majid H Mohajerani
- Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| |
Collapse
|
158
|
Gbotsyo YA, Rowarth NM, Weir LK, MacRae TH. Short-term cold stress and heat shock proteins in the crustacean Artemia franciscana. Cell Stress Chaperones 2020; 25:1083-1097. [PMID: 32794096 PMCID: PMC7591681 DOI: 10.1007/s12192-020-01147-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/02/2020] [Accepted: 07/28/2020] [Indexed: 01/09/2023] Open
Abstract
In their role as molecular chaperones, heat shock proteins (Hsps) mediate protein folding thereby mitigating cellular damage caused by physiological and environmental stress. Nauplii of the crustacean Artemia franciscana respond to heat shock by producing Hsps; however, the effects of cold shock on Hsp levels in A. franciscana have not been investigated previously. The effect of cold shock at 1 °C followed by recovery at 27 °C on the amounts of ArHsp90, Hsp70, ArHsp40, and ArHsp40-2 mRNA and their respective proteins in A. franciscana nauplii was examined by quantitative PCR (qPCR) and immunoprobing of western blots. The same Hsp mRNAs and proteins were also quantified during incubation of nauplii at their optimal growth temperature of 27 °C. qPCR analyses indicated that the abundance of ArHsp90, Hsp70, and ArHsp40 mRNA remained relatively constant during both cold shock and recovery and was not significantly different compared with levels at optimal temperature. Western blotting revealed that ArHsp90, ArHsp40, and ArHsp40-2 were generally below baseline, but at detectable levels during the 6 h of cold shock, and persisted in early recovery stages before declining. Hsp70 was the only protein that remained constant in quantity throughout cold shock and recovery. By contrast, all Hsps declined rapidly during 6 h when nauplii were incubated continuously at 27 °C optimal temperature. Generally, the amounts of ArHsp90, ArHsp40, and ArHsp40-2 were higher during cold shock/recovery than those during continuous incubation at 27 °C. Our data support the conclusion that low temperature preserves Hsp levels, making them available to assist in protein repair and recovery after cold shock.
Collapse
Affiliation(s)
- Yayra A Gbotsyo
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
| | - Nathan M Rowarth
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
| | - Laura K Weir
- Biology Department, Saint Mary's University Halifax, Halifax, N. S., B3H 3C3, Canada.
| | - Thomas H MacRae
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
| |
Collapse
|
159
|
Adjirackor NA, Harvey KE, Harvey SC. Eukaryotic response to hypothermia in relation to integrated stress responses. Cell Stress Chaperones 2020; 25:833-846. [PMID: 32676830 PMCID: PMC7591648 DOI: 10.1007/s12192-020-01135-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 12/25/2022] Open
Abstract
Eukaryotic cells respond to hypothermic stress through a series of regulatory mechanisms that preserve energy resources and prolong cell survival. These mechanisms include alterations in gene expression, attenuated global protein synthesis and changes in the lipid composition of the phospholipid bilayer. Cellular responses to hyperthermia, hypoxia, nutrient deprivation and oxidative stress have been comprehensively investigated, but studies of the cellular response to cold stress are more limited. Responses to cold stress are however of great importance both in the wild, where exposure to low and fluctuating environmental temperatures is common, and in medical and biotechnology settings where cells and tissues are frequently exposed to hypothermic stress and cryopreservation. This means that it is vitally important to understand how cells are impacted by low temperatures and by the decreases and subsequent increases in temperature associated with cold stress. Here, we review the ways in which eukaryotic cells respond to hypothermic stress and how these compare to the well-described and highly integrated stress response systems that govern the cellular response to other types of stress.
Collapse
Affiliation(s)
- Naki A Adjirackor
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, UK.
| | - Katie E Harvey
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, UK
| | - Simon C Harvey
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, UK
| |
Collapse
|
160
|
Liu Y, Li L, Qi H, Que H, Wang W, Zhang G. Regulation Between HSF1 Isoforms and HSPs Contributes to the Variation in Thermal Tolerance Between Two Oyster Congeners. Front Genet 2020; 11:581725. [PMID: 33193707 PMCID: PMC7652795 DOI: 10.3389/fgene.2020.581725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/06/2020] [Indexed: 01/09/2023] Open
Abstract
Heat shock transcription factor 1 (HSF1) plays an important role in regulating heat shock, which can activate heat shock proteins (HSPs). HSPs can protect organisms from thermal stress. Oysters in the intertidal zone can tolerate thermal stress. The Pacific oyster (Crassostrea gigas gigas) and Fujian oyster (C. gigas angulata)—allopatric subspecies with distinct thermal tolerances—make good study specimens for analyzing and comparing thermal stress regulation. We cloned and compared HSF1 isoforms, which is highly expressed under heat shock conditions in the two subspecies. The results revealed that two isoforms (HSF1a and HSF1d) respond to heat shock in both Pacific and Fujian oysters, and different heat shock conditions led to various combinations of isoforms. Subcellular localization showed that isoforms gathered in the nucleus when exposed to heat shock. The co-immunoprecipitation revealed that HSF1d can be a dimer. In addition, we selected HSPs that are expressed under the heat shock response, according to the RNA-seq and proteomic analyses. For the HSPs, we analyzed the coding part and the promoter sequences. The result showed that the domains of HSPs are conserved in two subspecies, but the promoters are significantly different. The Dual-Luciferase assay showed that the induced expression isoform HSF1d had the highest activity in C. gigas gigas, while the constitutively-expressed HSF1a was most active in C. gigas angulata. In addition, variation in the level of HSP promoters appeared to be correlated with gene expression. We argue that this gene is regulated based on the different expression levels between the two subspecies’ responses to heat shock. In summary, various stress conditions can yield different HSF1 isoforms and respond to heat shock in both oyster subspecies. Differences in how the isoforms and promoter are activated may contribute to their differential expressions. Overall, the results comparing C. gigas gigas and C. gigas angulata suggest that these isoforms have a regulatory relationship under heat shock, providing valuable information on the thermal tolerance mechanism in these commercially important oyster species.
Collapse
Affiliation(s)
- Youli Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China
- *Correspondence: Li Li,
| | - Haigang Qi
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China
| | - Huayong Que
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China
| | - Wei Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China
| |
Collapse
|
161
|
Wang Q, Hao X, Liu K, Feng B, Li S, Zhang Z, Tang L, Mahboob S, Shao C. Early response to heat stress in Chinese tongue sole (Cynoglossus semilaevis): performance of different sexes, candidate genes and networks. BMC Genomics 2020; 21:745. [PMID: 33109079 PMCID: PMC7590793 DOI: 10.1186/s12864-020-07157-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Temperature is known to affect living organisms and alter the expression of responsive genes, which affects a series of life processes, such as development, reproduction and metabolism. Several genes and gene families have been involved in high temperature responses, such as heat shock protein (hsp) family, Jumonji family and genes related to cortisol synthesis. Gonad is a vital organ related to the existence of a species. However, the comprehensive understanding of gonadal responses to environmental temperature is limited. RESULTS To explore the effects of environmental temperature on genes and gene networks in gonads, we performed acute heat treatment (48 h) on Chinese tongue sole (Cynoglossus semilaevis). Gonadal transcriptome analysis was conducted on females, pseudomales and males exposed to high (28 °C) and normal (22 °C) temperatures. A total of 1226.24 million clean reads were obtained from 18 libraries. Principal component analysis (PCA) and differentially expressed gene (DEG) analysis revealed different performance of sex responses to heat stress. There were 4565, 790 and 1117 specific genes altered their expression level in females, pseudomales and males, respectively. Of these, genes related to hsp gene family, cortisol synthesis and metabolism and epigenetic regulation were involved in early heat response. Furthermore, a total of 1048 DEGs were shared among females, pesudomales and males, which may represent the inherent difference between high and normal temperatures. Genes, such as eef1akmt3, eef1akmt4, pnmt and hsp family members, were found. CONCLUSIONS Our results depicted for the first time the gonadal gene expression under acute high temperature treatment in Chinese tongue sole. The findings may provide a clue for understanding the responses of genes and networks to environmental temperature.
Collapse
Affiliation(s)
- Qian Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Xiancai Hao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kaiqiang Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Bo Feng
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Shuo Li
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Zhihua Zhang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Lili Tang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
| |
Collapse
|
162
|
Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations. Int J Mol Sci 2020; 21:ijms21217944. [PMID: 33114694 PMCID: PMC7663484 DOI: 10.3390/ijms21217944] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 12/15/2022] Open
Abstract
Different cell isolation techniques exist for transcriptomic and proteotype profiling of brain cells. Here, we provide a systematic investigation of the influence of different cell isolation protocols on transcriptional and proteotype profiles in mouse brain tissue by taking into account single-cell transcriptomics of brain cells, proteotypes of microglia and astrocytes, and flow cytometric analysis of microglia. We show that standard enzymatic digestion of brain tissue at 37 °C induces profound and consistent alterations in the transcriptome and proteotype of neuronal and glial cells, as compared to an optimized mechanical dissociation protocol at 4 °C. These findings emphasize the risk of introducing technical biases and biological artifacts when implementing enzymatic digestion-based isolation methods for brain cell analyses.
Collapse
|
163
|
Mühlhofer M, Berchtold E, Stratil CG, Csaba G, Kunold E, Bach NC, Sieber SA, Haslbeck M, Zimmer R, Buchner J. The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins. Cell Rep 2020; 29:4593-4607.e8. [PMID: 31875563 DOI: 10.1016/j.celrep.2019.11.109] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022] Open
Abstract
Life is resilient because living systems are able to respond to elevated temperatures with an ancient gene expression program called the heat shock response (HSR). In yeast, the transcription of hundreds of genes is upregulated at stress temperatures. Besides stress protection conferred by chaperones, the function of the majority of the upregulated genes under stress has remained enigmatic. We show that those genes are required to directly counterbalance increased protein turnover at stress temperatures and to maintain the metabolism. This anaplerotic reaction together with molecular chaperones allows yeast to efficiently buffer proteotoxic stress. When the capacity of this system is exhausted at extreme temperatures, aggregation processes stop translation and growth pauses. The emerging concept is that the HSR is modular with distinct programs dependent on the severity of the stress.
Collapse
Affiliation(s)
- Moritz Mühlhofer
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Evi Berchtold
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 Munich, Germany
| | - Chris G Stratil
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Gergely Csaba
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 Munich, Germany
| | - Elena Kunold
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Nina C Bach
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Stephan A Sieber
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Martin Haslbeck
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Ralf Zimmer
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 Munich, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.
| |
Collapse
|
164
|
Gong L, Zhang Q, Pan X, Chen S, Yang L, Liu B, Yang W, Yu L, Xiao ZX, Feng XH, Wang H, Yuan ZM, Peng J, Tan WQ, Chen J. p53 Protects Cells from Death at the Heatstroke Threshold Temperature. Cell Rep 2020; 29:3693-3707.e5. [PMID: 31825845 DOI: 10.1016/j.celrep.2019.11.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/12/2019] [Accepted: 11/07/2019] [Indexed: 01/28/2023] Open
Abstract
When the core body temperature is higher than 40°C, life is threatened due to heatstroke. Tumor repressor p53 is required for heat-induced apoptosis at hyperthermia conditions (>41°C). However, its role in sub-heatstroke conditions (≤40°C) remains unclear. Here, we reveal that both zebrafish and human p53 promote survival at 40°C, the heatstroke threshold temperature, by preventing a hyperreactive heat shock response (HSR). At 40°C, both Hsf1 and Hsp90 are activated. Hsf1 upregulates the expression of Hsc70 to trigger Hsc70-mediated protein degradation, whereas Hsp90 stabilizes p53 to repress the expression of Hsf1 and Hsc70, which prevents excessive HSR to maintain cell homeostasis. Under hyperthermia conditions, ATM is activated to phosphorylate p53 at S37, which increases BAX expression to induce apoptosis. Furthermore, growth of p53-deficient tumor xenografts, but not that of their p53+/+ counterparts, was inhibited by 40°C treatment. Our findings may provide a strategy for individualized therapy for p53-deficient cancers.
Collapse
Affiliation(s)
- Lu Gong
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Qinghe Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiao Pan
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuming Chen
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lina Yang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bin Liu
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, 74 Second Zhonshan Road, Guangzhou 510080, China
| | - Weijun Yang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Luyang Yu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Xin-Hua Feng
- Life Sciences Institute and Innovation Center for Signaling Network, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou 310058, China
| | - Haihe Wang
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, 74 Second Zhonshan Road, Guangzhou 510080, China
| | - Zhi-Min Yuan
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou 310058, China
| | - Wei-Qiang Tan
- Department of Plastic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Hangzhou 310016, China.
| | - Jun Chen
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
165
|
Ray J, Kruse A, Ozer A, Kajitani T, Johnson R, MacCoss M, Heck M, Lis JT. RNA aptamer capture of macromolecular complexes for mass spectrometry analysis. Nucleic Acids Res 2020; 48:e90. [PMID: 32609809 PMCID: PMC7470977 DOI: 10.1093/nar/gkaa542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/03/2020] [Accepted: 06/27/2020] [Indexed: 12/25/2022] Open
Abstract
Specific genomic functions are dictated by macromolecular complexes (MCs) containing multiple proteins. Affinity purification of these complexes, often using antibodies, followed by mass spectrometry (MS) has revolutionized our ability to identify the composition of MCs. However, conventional immunoprecipitations suffer from contaminating antibody/serum-derived peptides that limit the sensitivity of detection for low-abundant interacting partners using MS. Here, we present AptA-MS (aptamer affinity-mass spectrometry), a robust strategy primarily using a specific, high-affinity RNA aptamer against Green Fluorescent Protein (GFP) to identify interactors of a GFP-tagged protein of interest by high-resolution MS. Utilizing this approach, we have identified the known molecular chaperones that interact with human Heat Shock Factor 1 (HSF1), and observed an increased association with several proteins upon heat shock, including translation elongation factors and histones. HSF1 is known to be regulated by multiple post-translational modifications (PTMs), and we observe both known and new sites of modifications on HSF1. We show that AptA-MS provides a dramatic target enrichment and detection sensitivity in evolutionarily diverse organisms and allows identification of PTMs without the need for modification-specific enrichments. In combination with the expanding libraries of GFP-tagged cell lines, this strategy offers a general, inexpensive, and high-resolution alternative to conventional approaches for studying MCs.
Collapse
Affiliation(s)
- Judhajeet Ray
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Angela Kruse
- Department of Plant Pathology and Plant-microbe Biology, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Takuya Kajitani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michelle Heck
- Department of Plant Pathology and Plant-microbe Biology, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center, United States Department of Agriculture Agricultural Research Service (USDA ARS), Ithaca, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| |
Collapse
|
166
|
Baker-Williams AJ, Hashmi F, Budzyński MA, Woodford MR, Gleicher S, Himanen SV, Makedon AM, Friedman D, Cortes S, Namek S, Stetler-Stevenson WG, Bratslavsky G, Bah A, Mollapour M, Sistonen L, Bourboulia D. Co-chaperones TIMP2 and AHA1 Competitively Regulate Extracellular HSP90:Client MMP2 Activity and Matrix Proteolysis. Cell Rep 2020; 28:1894-1906.e6. [PMID: 31412254 DOI: 10.1016/j.celrep.2019.07.045] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 06/01/2019] [Accepted: 07/15/2019] [Indexed: 11/26/2022] Open
Abstract
The extracellular molecular chaperone heat shock protein 90 (eHSP90) stabilizes protease client the matrix metalloproteinase 2 (MMP2), leading to tumor cell invasion. Although co-chaperones are critical modulators of intracellular HSP90:client function, how the eHSP90:MMP2 complex is regulated remains speculative. Here, we report that the tissue inhibitor of metalloproteinases-2 (TIMP2) is a stress-inducible extracellular co-chaperone that binds to eHSP90, increases eHSP90 binding to ATP, and inhibits its ATPase activity. In addition to disrupting the eHSP90:MMP2 complex and terminally inactivating MMP2, TIMP2 loads the client to eHSP90, keeping the protease in a transient inhibitory state. Secreted activating co-chaperone AHA1 displaces TIMP2 from the complex, providing a "reactivating" mechanism for MMP2. Gene knockout or blocking antibodies targeting TIMP2 and AHA1 released by HT1080 cancer cells modify their gelatinolytic activity. Our data suggest that TIMP2 and AHA1 co-chaperones function as a molecular switch that determines the inhibition and reactivation of the eHSP90 client protein MMP2.
Collapse
Affiliation(s)
- Alexander J Baker-Williams
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Fiza Hashmi
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Marek A Budzyński
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Stephanie Gleicher
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Samu V Himanen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Alan M Makedon
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Derek Friedman
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; College of Medicine, MD Program, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Stephanie Cortes
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; College of Medicine, MD Program, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Sara Namek
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | | | - Gennady Bratslavsky
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Alaji Bah
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
| |
Collapse
|
167
|
Gopal U, Pizzo SV. Cell surface GRP78 signaling: An emerging role as a transcriptional modulator in cancer. J Cell Physiol 2020; 236:2352-2363. [PMID: 32864780 DOI: 10.1002/jcp.30030] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022]
Abstract
Cancer cells acquire dysregulated gene expression to establish specific transcriptional dependencies and their underlying mechanisms that are ultimately responsible for this addictions have not been fully elucidated. Glucose-regulated protein 78 (GRP78) is a stress-inducible, multifunctional, prosurvival, endoplasmic reticulum chaperone in the heat shock protein 70 family. Expression of cell surface GRP78 (CS-GRP78) is associated with increased malignant behavior and resistance to chemotherapy and radiotherapy by endowing various cancer cells with increased proliferative ability, altered metabolism, improved survival, and augmented invasive and metastatic potential. Emerging evidence has highlighted an unusual role of CS-GRP78 in regulating transcription factors (TFs) by mediating various signaling pathways involved in malignant transformation, metabolic reprogramming, and tumor progression. During the last decade, we targeted CS-GRP78 with C38 monoclonal antibody (C38 Mab) in numerous studies, which have highlighted the epigenetic interplay between CS-GRP78 and various TFs including c-MYC, Yes-associated protein/transcriptional coactivator with PDZ-binding motif, c-Fos, and histone acetylation to potentiate subsequent modulation of tumorigenesis, invasion, and metastasis. Here, we summarize the current state of knowledge about the role of CS-GRP78 in cancer development and progression, including epigenetic regulation and sheds light on CS-GRP78 as vulnerable target for cancer therapy. Overall, this review focuses on the mechanisms of TFs that are behind the transcriptional dysregulation in cancer and lays the groundwork for rational therapeutic use of C38 Mab based on CS-GRP78 biology.
Collapse
Affiliation(s)
- Udhayakumar Gopal
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Salvatore V Pizzo
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| |
Collapse
|
168
|
Masser AE, Ciccarelli M, Andréasson C. Hsf1 on a leash - controlling the heat shock response by chaperone titration. Exp Cell Res 2020; 396:112246. [PMID: 32861670 DOI: 10.1016/j.yexcr.2020.112246] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 01/06/2023]
Abstract
Heat shock factor 1 (Hsf1) is an ancient transcription factor that monitors protein homeostasis (proteostasis) and counteracts disturbances by triggering a transcriptional programme known as the heat shock response (HSR). The HSR is transiently activated and upregulates the expression of core proteostasis genes, including chaperones. Dysregulation of Hsf1 and its target genes are associated with disease; cancer cells rely on a constitutively active Hsf1 to promote rapid growth and malignancy, whereas Hsf1 hypoactivation in neurodegenerative disorders results in formation of toxic aggregates. These central but opposing roles highlight the importance of understanding the underlying molecular mechanisms that control Hsf1 activity. According to current understanding, Hsf1 is maintained latent by chaperone interactions but proteostasis perturbations titrate chaperone availability as a result of chaperone sequestration by misfolded proteins. Liberated and activated Hsf1 triggers a negative feedback loop by inducing the expression of key chaperones. Until recently, Hsp90 has been highlighted as the central negative regulator of Hsf1 activity. In this review, we focus on recent advances regarding how the Hsp70 chaperone controls Hsf1 activity and in addition summarise several additional layers of activity control.
Collapse
Affiliation(s)
- Anna E Masser
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91, Stockholm, Sweden
| | - Michela Ciccarelli
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91, Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91, Stockholm, Sweden.
| |
Collapse
|
169
|
Nytko KJ, Thumser-Henner P, Russo G, Weyland MS, Rohrer Bley C. Role of HSP70 in response to (thermo)radiotherapy: analysis of gene expression in canine osteosarcoma cells by RNA-seq. Sci Rep 2020; 10:12779. [PMID: 32728031 PMCID: PMC7391659 DOI: 10.1038/s41598-020-69619-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/14/2020] [Indexed: 11/12/2022] Open
Abstract
Pre-treatment of tumors with hyperthermia is often used to increase the efficacy of radiotherapy. One of the main proteins induced in response to hyperthermia is heat shock protein 70 (HSP70). The aim of our study was to investigate up- and down-regulated genes in response to (thermo)radiotherapy in HSP70 proficient and deficient canine osteosarcoma cell line (Abrams), and functional role of HSP70 in the mechanism of thermoradiosensitization. Cells were transfected with negative control siRNA or siRNA targeting HSP70 and treated with hyperthermia (HT), radiotherapy (RT), and thermoradiotherapy (HTRT). RNA sequencing was used to analyze gene expression. Hyperthermia and thermoradiotherapy, but not radiotherapy alone, induced differential gene expression. We identified genes differentially expressed only in HSP70 knockdown (thus HSP70-dependent) cells in response to hyperthermia and thermoradiotherapy. Interestingly, cell proliferation but not clonogenicity and apoptosis/necrosis was affected by the HSP70 knockdown in response to thermoradiotherapy. The results suggest that HSP70 regulates expression of specific genes in response to hyperthermia and thermoradiotherapy. Further investigations into the role of specific genes regulated in a HSP70-dependent manner in response to thermoradiotherapy could pave a way into new, combinatorial treatment options for (canine) osteosarcoma and other cancer types.
Collapse
Affiliation(s)
- Katarzyna J Nytko
- Division of Radiation Oncology, Vetsuisse Faculty University of Zurich, 8057, Zurich, Switzerland. .,Center for Applied Biotechnology and Molecular Medicine, University of Zurich, 8057, Zurich, Switzerland. .,Center for Clinical Studies at the Vetsuisse Faculty of the University of Zurich, 8057, Zurich, Switzerland.
| | - Pauline Thumser-Henner
- Division of Radiation Oncology, Vetsuisse Faculty University of Zurich, 8057, Zurich, Switzerland.,Center for Applied Biotechnology and Molecular Medicine, University of Zurich, 8057, Zurich, Switzerland.,Center for Clinical Studies at the Vetsuisse Faculty of the University of Zurich, 8057, Zurich, Switzerland
| | - Giancarlo Russo
- Functional Genomics Center Zurich, ETH/University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Mathias S Weyland
- ZHAW School of Engineering, Zurich University of Applied Sciences, 8400, Winterthur, Switzerland.,BioNanomaterials Group, Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Carla Rohrer Bley
- Division of Radiation Oncology, Vetsuisse Faculty University of Zurich, 8057, Zurich, Switzerland.,Center for Applied Biotechnology and Molecular Medicine, University of Zurich, 8057, Zurich, Switzerland.,Center for Clinical Studies at the Vetsuisse Faculty of the University of Zurich, 8057, Zurich, Switzerland
| |
Collapse
|
170
|
Baru Pulp ( Dipteryx alata Vogel): Fruit from the Brazilian Savanna Protects against Oxidative Stress and Increases the Life Expectancy of Caenorhabditis elegans via SOD-3 and DAF-16. Biomolecules 2020; 10:biom10081106. [PMID: 32722431 PMCID: PMC7463619 DOI: 10.3390/biom10081106] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 12/27/2022] Open
Abstract
Fruits are sources of bioactive compounds that are responsible for several biological activities. Therefore, this study aimed to identify the chemical composition of the pulp of the Brazilian Savanna fruit Dipteryx alata; evaluate its toxic effects, influence on the life expectancy of the nematode Caenorhabditis elegans, and its antioxidant activities in vitro and in vivo; and describe the mechanisms involved. The chemical compounds identified include phenols, terpenes, fatty acid derivatives, vitamins, and a carboxylic acid. The in vitro antioxidant activity was demonstrated by radical scavenging methods. In vivo, the D. alata fruit pulp was not toxic and promoted resistance to oxidative stress in nematodes exposed to a chemical oxidizing agent. Furthermore, it promoted an increased life expectancy in wild-type nematodes and increased the expression of superoxide dismutase and the nuclear translocation of DAF-16. These results suggest that the beneficial effects identified are related to these two genes, which are involved in the regulation of metabolic activities, the control of oxidative stress, and the lifespan of C. elegans. These beneficial effects, which may be related to its chemical constituents, demonstrate its potential use as a functional and/or nutraceutical food.
Collapse
|
171
|
Nekongo EE, Ponomarenko AI, Dewal MB, Butty VL, Browne EP, Shoulders MD. HSF1 Activation Can Restrict HIV Replication. ACS Infect Dis 2020; 6:1659-1666. [PMID: 32502335 DOI: 10.1021/acsinfecdis.0c00166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Host protein folding stress responses can play important roles in RNA virus replication and evolution. Prior work suggested a complicated interplay between the cytosolic proteostasis stress response, controlled by the transcriptional master regulator heat shock factor 1 (HSF1), and human immunodeficiency virus-1 (HIV-1). We sought to uncouple HSF1 transcription factor activity from cytotoxic proteostasis stress and thereby better elucidate the proposed role(s) of HSF1 in the HIV-1 lifecycle. To achieve this objective, we used chemical genetic, stress-independent control of HSF1 activity to establish whether and how HSF1 influences HIV-1 replication. Stress-independent HSF1 induction decreased both the total quantity and infectivity of HIV-1 virions. Moreover, HIV-1 was unable to escape HSF1-mediated restriction over the course of several serial passages. These results clarify the interplay between the host's heat shock response and HIV-1 infection and motivate continued investigation of chaperones as potential antiviral therapeutic targets.
Collapse
Affiliation(s)
- Emmanuel E. Nekongo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anna I. Ponomarenko
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mahender B. Dewal
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vincent L. Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Edward P. Browne
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27516, United States
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
172
|
Heat Stress Affects H3K9me3 Level at Human Alpha Satellite DNA Repeats. Genes (Basel) 2020; 11:genes11060663. [PMID: 32570830 PMCID: PMC7348797 DOI: 10.3390/genes11060663] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022] Open
Abstract
Satellite DNAs are tandemly repeated sequences preferentially assembled into large arrays within constitutive heterochromatin and their transcription is often activated by stress conditions, particularly by heat stress. Bioinformatic analyses of sequenced genomes however reveal single repeats or short arrays of satellite DNAs dispersed in the vicinity of genes within euchromatin. Here, we analyze transcription of a major human alpha satellite DNA upon heat stress and follow the dynamics of “silent” H3K9me3 and “active” H3K4me2/3 histone marks at dispersed euchromatic and tandemly arranged heterochromatic alpha repeats. The results show H3K9me3 enrichment at alpha repeats upon heat stress, which correlates with the dynamics of alpha satellite DNA transcription activation, while no change in H3K4me2/3 level is detected. Spreading of H3K9me3 up to 1–2 kb from the insertion sites of the euchromatic alpha repeats is detected, revealing the alpha repeats as modulators of local chromatin structure. In addition, expression of genes containing alpha repeats within introns as well as of genes closest to the intergenic alpha repeats is downregulated upon heat stress. Further studies are necessary to reveal the possible contribution of H3K9me3 enriched alpha repeats, in particular those located within introns, to the silencing of their associated genes.
Collapse
|
173
|
Pincus D. Regulation of Hsf1 and the Heat Shock Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1243:41-50. [PMID: 32297210 DOI: 10.1007/978-3-030-40204-4_3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The heat shock response (HSR) is characterized by the induction of molecular chaperones following a sudden increase in temperature. In eukaryotes, the HSR comprises the set of genes controlled by the transcription factor Hsf1. The HSR is induced by defects in co-translational protein folding, ribosome biogenesis, organellar targeting of nascent proteins, and protein degradation by the ubiquitin proteasome system. Upon heat shock, these processes may be endogenous sources of polypeptide ligands that activate the HSR. Mechanistically, these ligands are thought to titrate the chaperone Hsp70 away from Hsf1, releasing Hsf1 to induce the full arsenal of cellular chaperones to restore protein homeostasis. In metazoans, this cell-autonomous feedback loop is modulated by the microenvironment and neuronal cues to enable tissue-level and organism-wide coordination.
Collapse
Affiliation(s)
- David Pincus
- Department of Molecular Genetics and Cell Biology, Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
174
|
Levine DC, Hong H, Weidemann BJ, Ramsey KM, Affinati AH, Schmidt MS, Cedernaes J, Omura C, Braun R, Lee C, Brenner C, Peek CB, Bass J. NAD + Controls Circadian Reprogramming through PER2 Nuclear Translocation to Counter Aging. Mol Cell 2020; 78:835-849.e7. [PMID: 32369735 PMCID: PMC7275919 DOI: 10.1016/j.molcel.2020.04.010] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/12/2020] [Accepted: 04/07/2020] [Indexed: 12/18/2022]
Abstract
Disrupted sleep-wake and molecular circadian rhythms are a feature of aging associated with metabolic disease and reduced levels of NAD+, yet whether changes in nucleotide metabolism control circadian behavioral and genomic rhythms remains unknown. Here, we reveal that supplementation with the NAD+ precursor nicotinamide riboside (NR) markedly reprograms metabolic and stress-response pathways that decline with aging through inhibition of the clock repressor PER2. NR enhances BMAL1 chromatin binding genome-wide through PER2K680 deacetylation, which in turn primes PER2 phosphorylation within a domain that controls nuclear transport and stability and that is mutated in human advanced sleep phase syndrome. In old mice, dampened BMAL1 chromatin binding, transcriptional oscillations, mitochondrial respiration rhythms, and late evening activity are restored by NAD+ repletion to youthful levels with NR. These results reveal effects of NAD+ on metabolism and the circadian system with aging through the spatiotemporal control of the molecular clock.
Collapse
Affiliation(s)
- Daniel C Levine
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Heekyung Hong
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Benjamin J Weidemann
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kathryn M Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alison H Affinati
- Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark S Schmidt
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Jonathan Cedernaes
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Medical Sciences, Uppsala University, Uppsala SE-75124, Sweden
| | - Chiaki Omura
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rosemary Braun
- Biostatistics Division, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA; NSF-Simons Center for Quantitative Biology at Northwestern University, Evanston, IL 60208, USA
| | - Choogon Lee
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Charles Brenner
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Clara Bien Peek
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| |
Collapse
|
175
|
Ooi CP, Benz C, Urbaniak MD. Phosphoproteomic analysis of mammalian infective Trypanosoma brucei subjected to heat shock suggests atypical mechanisms for thermotolerance. J Proteomics 2020; 219:103735. [PMID: 32198071 DOI: 10.1016/j.jprot.2020.103735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/11/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
Abstract
The symptoms of African sleeping sickness, caused by the parasite Trypanosoma brucei, can include periods of fever as high as 41 °C which triggers a heat shock response in the parasite. To capture events involved in sensing and responding to heat shock in the mammalian infective form we have conducted a SILAC-based quantitative proteomic and phosphoproteomic analysis of T. brucei cells treated at 41 °C for 1h. Our analysis identified 193 heat shock responsive phosphorylation sites with an average of 5-fold change in abundance, but only 20 heat shock responsive proteins with average of 1.5-fold change. These data indicate that protein abundance does not rapidly respond (≤1 h) to heat shock, and that the changes observed in phosphorylation site abundance are larger and more widespread. The heat shock responsive phosphorylation sites showed enrichment of RNA binding proteins with putative roles in heat shock response included P-body / stress granules and the eukaryotic translation initiation 4F complex. The ZC3H11-MKT1 complex, which stabilises mRNAs of thermotolerance proteins, appears to represent a key signal integration node in the heat shock response. SIGNIFICANCE: We report the first quantitative study of changes in protein and phosphorylation site abundance in response to heat shock in the clinically relevant form of the human parasite Trypanosoma brucei. The identification of heat shock responsive phosphorylation sites on proteins with putative roles in thermotolerance including the ZC3H11-MKT1 complex provides evidence of the role dynamic phosphorylation of RNA binding proteins in co-ordinating heat shock. Temperature changes in the host are a major physiological challenge to parasites and factors conferring tolerance to heat shock constitute overlooked virulence factors. A better understanding of these virulence factors will pave the way for the development of novel drug therapies which selectively target T. brucei.
Collapse
Affiliation(s)
- Cher P Ooi
- Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, UK.
| | - Corinna Benz
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
| | - Michael D Urbaniak
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK.
| |
Collapse
|
176
|
Puustinen MC, Sistonen L. Molecular Mechanisms of Heat Shock Factors in Cancer. Cells 2020; 9:cells9051202. [PMID: 32408596 PMCID: PMC7290425 DOI: 10.3390/cells9051202] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 12/12/2022] Open
Abstract
Malignant transformation is accompanied by alterations in the key cellular pathways that regulate development, metabolism, proliferation and motility as well as stress resilience. The members of the transcription factor family, called heat shock factors (HSFs), have been shown to play important roles in all of these biological processes, and in the past decade it has become evident that their activities are rewired during tumorigenesis. This review focuses on the expression patterns and functions of HSF1, HSF2, and HSF4 in specific cancer types, highlighting the mechanisms by which the regulatory functions of these transcription factors are modulated. Recently developed therapeutic approaches that target HSFs are also discussed.
Collapse
Affiliation(s)
- Mikael Christer Puustinen
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland;
- Turku Bioscience, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Lea Sistonen
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland;
- Turku Bioscience, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
- Correspondence: ; Tel.: +358-2215-3311
| |
Collapse
|
177
|
Negative elongation factor complex enables macrophage inflammatory responses by controlling anti-inflammatory gene expression. Nat Commun 2020; 11:2286. [PMID: 32385332 PMCID: PMC7210294 DOI: 10.1038/s41467-020-16209-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 04/21/2020] [Indexed: 01/06/2023] Open
Abstract
Studies on macrophage gene expression have historically focused on events leading to RNA polymerase II recruitment and transcription initiation, whereas the contribution of post-initiation steps to macrophage activation remains poorly understood. Here, we report that widespread promoter-proximal RNA polymerase II pausing in resting macrophages is marked by co-localization of the negative elongation factor (NELF) complex and facilitated by PU.1. Upon inflammatory stimulation, over 60% of activated transcriptome is regulated by polymerase pause-release and a transient genome-wide NELF dissociation from chromatin, unexpectedly, independent of CDK9, a presumed NELF kinase. Genetic disruption of NELF in macrophages enhanced transcription of AP-1-encoding Fos and Jun and, consequently, AP-1 targets including Il10. Augmented expression of IL-10, a critical anti-inflammatory cytokine, in turn, attenuated production of pro-inflammatory mediators and, ultimately, macrophage-mediated inflammation in vivo. Together, these findings establish a previously unappreciated role of NELF in constraining transcription of inflammation inhibitors thereby enabling inflammatory macrophage activation. Macrophage activation is integral to innate immunity and inflammation, and involves transcriptome remodeling leading to the rapid upregulation of pro- and anti-inflammatory effector genes. Here the authors show that the negative elongation factor (NELF) complex controls the transcription of anti-inflammatory genes through Pol II pause release.
Collapse
|
178
|
Chakraborty A, Edkins AL. Hop depletion reduces HSF1 levels and activity and coincides with reduced stress resilience. Biochem Biophys Res Commun 2020; 527:440-446. [PMID: 32334836 DOI: 10.1016/j.bbrc.2020.04.072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/15/2020] [Indexed: 01/09/2023]
Abstract
Heat-shock factor 1 (HSF1) regulates the transcriptional response to stress and controls expression of molecular chaperones required for cell survival. Here we report that HSF1 is regulated by the abundance of the Hsp70-Hsp90 organizing protein (Hop/STIP1). HSF1 levels were significantly reduced in Hop-depleted HEK293T cells. HSF1 transcriptional activity at the Hsp70 promoter, and binding of a biotinylated HSE oligonucleotide under both basal and heat-shock conditions were significantly reduced. Hop-depleted HEK293T cells were more sensitive to the HSF1 inhibitor KRIBB11 and showed reduced short-term proliferation, and reduced long-term survival under basal and heat-shock conditions. HSF1 nuclear localization was reduced in response to heat-shock and the nuclear staining pattern in Hop-depleted cells was punctate. Taken together, these data suggest that Hop regulates HSF1 function under both basal and stress conditions through a mechanism involving changes in levels, activity and subcellular localization, and coincides with reduced cellular fitness.
Collapse
Affiliation(s)
- Abantika Chakraborty
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Adrienne Lesley Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
| |
Collapse
|
179
|
From Snapshots to Flipbook-Resolving the Dynamics of Ribosome Biogenesis with Chemical Probes. Int J Mol Sci 2020; 21:ijms21082998. [PMID: 32340379 PMCID: PMC7215809 DOI: 10.3390/ijms21082998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 12/27/2022] Open
Abstract
The synthesis of ribosomes is one of the central and most resource demanding processes in each living cell. As ribosome biogenesis is tightly linked with the regulation of the cell cycle, perturbation of ribosome formation can trigger severe diseases, including cancer. Eukaryotic ribosome biogenesis starts in the nucleolus with pre-rRNA transcription and the initial assembly steps, continues in the nucleoplasm and is finished in the cytoplasm. From start to end, this process is highly dynamic and finished within few minutes. Despite the tremendous progress made during the last decade, the coordination of the individual maturation steps is hard to unravel by a conventional methodology. In recent years small molecular compounds were identified that specifically block either rDNA transcription or distinct steps within the maturation pathway. As these inhibitors diffuse into the cell rapidly and block their target proteins within seconds, they represent excellent tools to investigate ribosome biogenesis. Here we review how the inhibitors affect ribosome biogenesis and discuss how these effects can be interpreted by taking the complex self-regulatory mechanisms of the pathway into account. With this we want to highlight the potential of low molecular weight inhibitors to approach the dynamic nature of the ribosome biogenesis pathway.
Collapse
|
180
|
Prince TL, Lang BJ, Guerrero-Gimenez ME, Fernandez-Muñoz JM, Ackerman A, Calderwood SK. HSF1: Primary Factor in Molecular Chaperone Expression and a Major Contributor to Cancer Morbidity. Cells 2020; 9:E1046. [PMID: 32331382 PMCID: PMC7226471 DOI: 10.3390/cells9041046] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 02/07/2023] Open
Abstract
Heat shock factor 1 (HSF1) is the primary component for initiation of the powerful heat shock response (HSR) in eukaryotes. The HSR is an evolutionarily conserved mechanism for responding to proteotoxic stress and involves the rapid expression of heat shock protein (HSP) molecular chaperones that promote cell viability by facilitating proteostasis. HSF1 activity is amplified in many tumor contexts in a manner that resembles a chronic state of stress, characterized by high levels of HSP gene expression as well as HSF1-mediated non-HSP gene regulation. HSF1 and its gene targets are essential for tumorigenesis across several experimental tumor models, and facilitate metastatic and resistant properties within cancer cells. Recent studies have suggested the significant potential of HSF1 as a therapeutic target and have motivated research efforts to understand the mechanisms of HSF1 regulation and develop methods for pharmacological intervention. We review what is currently known regarding the contribution of HSF1 activity to cancer pathology, its regulation and expression across human cancers, and strategies to target HSF1 for cancer therapy.
Collapse
Affiliation(s)
- Thomas L. Prince
- Department of Molecular Functional Genomics, Geisinger Clinic, Danville, PA 17821, USA
| | - Benjamin J. Lang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Martin E. Guerrero-Gimenez
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Buenos Aires B1657, Argentina
| | - Juan Manuel Fernandez-Muñoz
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Buenos Aires B1657, Argentina
| | - Andrew Ackerman
- Department of Molecular Functional Genomics, Geisinger Clinic, Danville, PA 17821, USA
| | - Stuart K. Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
181
|
Aoi Y, Smith ER, Shah AP, Rendleman EJ, Marshall SA, Woodfin AR, Chen FX, Shiekhattar R, Shilatifard A. NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release. Mol Cell 2020; 78:261-274.e5. [PMID: 32155413 PMCID: PMC7402197 DOI: 10.1016/j.molcel.2020.02.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 12/17/2019] [Accepted: 02/18/2020] [Indexed: 02/08/2023]
Abstract
RNA polymerase II (RNA Pol II) is generally paused at promoter-proximal regions in most metazoans, and based on in vitro studies, this function has been attributed to the negative elongation factor (NELF). Here, we show that upon rapid depletion of NELF, RNA Pol II fails to be released into gene bodies, stopping instead around the +1 nucleosomal dyad-associated region. The transition to the 2nd pause region is independent of positive transcription elongation factor P-TEFb. During the heat shock response, RNA Pol II is rapidly released from pausing at heat shock-induced genes, while most genes are paused and transcriptionally downregulated. Both of these aspects of the heat shock response remain intact upon NELF loss. We find that NELF depletion results in global loss of cap-binding complex from chromatin without global reduction of nascent transcript 5' cap stability. Thus, our studies implicate NELF functioning in early elongation complexes distinct from RNA Pol II pause-release.
Collapse
Affiliation(s)
- Yuki Aoi
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Edwin R Smith
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Avani P Shah
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Emily J Rendleman
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Stacy A Marshall
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ashley R Woodfin
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Fei X Chen
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| |
Collapse
|
182
|
Choi Y, Jeong K, Shin S, Lee JW, Lee YS, Kim S, Kim SA, Jung J, Kim KP, Kim VN, Kim JS. MS1-Level Proteome Quantification Platform Allowing Maximally Increased Multiplexity for SILAC and In Vitro Chemical Labeling. Anal Chem 2020; 92:4980-4989. [PMID: 32167278 DOI: 10.1021/acs.analchem.9b05148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Quantitative proteomic platforms based on precursor intensity in mass spectrometry (MS1-level) uniquely support in vivo metabolic labeling with superior quantification accuracy but suffer from limited multiplexity (≤3-plex) and frequent missing quantities. Here we present a new MS1-level quantification platform that allows maximal multiplexing with high quantification accuracy and precision for the given labeling scheme. The platform currently comprises 6-plex in vivo SILAC or in vitro diethylation labeling with a dedicated algorithm and is also expandable to higher multiplexity (e.g., nine-plex for SILAC). For complex samples with broad dynamic ranges such as total cell lysates, our platform performs highly accurately and free of missing quantities. Furthermore, we successfully applied our method to measure protein synthesis rate under heat shock response in human cells by 6-plex pulsed SILAC experiments, demonstrating the unique biological merits of our in vivo platform to disclose translational regulations for cellular response to stress.
Collapse
Affiliation(s)
- Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Kyowon Jeong
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Sanghee Shin
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Joon Won Lee
- Department of Applied Chemistry, Kyung Hee University, Yongin 17104, Korea
| | - Young-Suk Lee
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Sangtae Kim
- Illumina, Inc., San Diego, California 92122, United States
| | - Sun Ah Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jaehun Jung
- Department of Applied Chemistry, Kyung Hee University, Yongin 17104, Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Kyung Hee University, Yongin 17104, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| |
Collapse
|
183
|
Leng X, Ivanov M, Kindgren P, Malik I, Thieffry A, Brodersen P, Sandelin A, Kaplan CD, Marquardt S. Organismal benefits of transcription speed control at gene boundaries. EMBO Rep 2020; 21:e49315. [PMID: 32103605 PMCID: PMC7132196 DOI: 10.15252/embr.201949315] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
RNA polymerase II (RNAPII) transcription is crucial for gene expression. RNAPII density peaks at gene boundaries, associating these key regions for gene expression control with limited RNAPII movement. The connections between RNAPII transcription speed and gene regulation in multicellular organisms are poorly understood. Here, we directly modulate RNAPII transcription speed by point mutations in the second largest subunit of RNAPII in Arabidopsis thaliana. A RNAPII mutation predicted to decelerate transcription is inviable, while accelerating RNAPII transcription confers phenotypes resembling auto-immunity. Nascent transcription profiling revealed that RNAPII complexes with accelerated transcription clear stalling sites at both gene ends, resulting in read-through transcription. The accelerated transcription mutant NRPB2-Y732F exhibits increased association with 5' splice site (5'SS) intermediates and enhanced splicing efficiency. Our findings highlight potential advantages of RNAPII stalling through local reduction in transcription speed to optimize gene expression for the development of multicellular organisms.
Collapse
Affiliation(s)
- Xueyuan Leng
- Department of Plant and Environmental SciencesCopenhagen Plant Science CentreUniversity of CopenhagenFrederiksbergDenmark
| | - Maxim Ivanov
- Department of Plant and Environmental SciencesCopenhagen Plant Science CentreUniversity of CopenhagenFrederiksbergDenmark
| | - Peter Kindgren
- Department of Plant and Environmental SciencesCopenhagen Plant Science CentreUniversity of CopenhagenFrederiksbergDenmark
| | - Indranil Malik
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
- Present address:
Department of NeurologyUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Axel Thieffry
- Biotech Research and Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Peter Brodersen
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Albin Sandelin
- Biotech Research and Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Craig D Kaplan
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Sebastian Marquardt
- Department of Plant and Environmental SciencesCopenhagen Plant Science CentreUniversity of CopenhagenFrederiksbergDenmark
| |
Collapse
|
184
|
Abstract
The functional health of the proteome is determined by properties of the proteostasis network (PN) that regulates protein synthesis, folding, macromolecular assembly, translocation, and degradation. In eukaryotes, the PN also integrates protein biogenesis across compartments within the cell and between tissues of metazoans for organismal health and longevity. Additionally, in metazoans, proteome stability and the functional health of proteins is optimized for development and yet declines throughout aging, accelerating the risk for misfolding, aggregation, and cellular dysfunction. Here, I describe the cell-nonautonomous regulation of organismal PN by tissue communication and cell stress-response pathways. These systems are robust from development through reproductive maturity and are genetically programmed to decline abruptly in early adulthood by repression of the heat shock response and other cell-protective stress responses, thus compromising the ability of cells and tissues to properly buffer against the cumulative stress of protein damage during aging. While the failure of multiple protein quality control processes during aging challenges cellular function and tissue health, genetic studies, and the identification of small-molecule proteostasis regulators suggests strategies that can be employed to reset the PN with potential benefit on cellular health and organismal longevity.
Collapse
Affiliation(s)
- Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208
| |
Collapse
|
185
|
Liu Y, Zhu Q, Li L, Wang W, Zhang G. Identification of HSF1 Target Genes Involved in Thermal Stress in the Pacific Oyster Crassostrea gigas by ChIP-seq. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:167-179. [PMID: 31965439 DOI: 10.1007/s10126-019-09942-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
The Pacific oyster Crassostrea gigas, a commercially important species inhabiting the intertidal zone, facing enormous temperature fluctuations. Therefore, it is important to identify candidate genes and key regulatory relationships associated with thermal tolerance, which can aid the molecular breeding of oysters. Heat shock transcription factor 1 (HSF1) plays an important role in the thermal stress resistance. However, the regulatory relationship between the expansion of heat shock protein (HSP) HSP 70 and HSF1 is not yet clear in C. gigas. In this study, we analyzed genes regulated by HSF1 in response to heat shock by chromatin immunoprecipitation followed by sequencing (ChIP-seq), determined the expression patterns of target genes by qRT-PCR, and validated the regulatory relationship between one HSP70 and HSF1. We found 916 peaks corresponding to HSF1 binding sites, and these peaks were annotated to the nearest genes. In Gene Ontology analysis, HSF1 target genes were related to signal transduction, energy production, and response to biotic stimulus. Four HSP70 genes, two HSP40 genes, and one small HSP gene exhibited binding to HSF1. One HSP70 with a binding site in the promoter region was validated to be regulated by HSF1 under heat shock. These results provide a basis for future studies aimed at determining the mechanisms underlying thermal tolerance and provide insights into gene regulation in the Pacific oyster.
Collapse
Affiliation(s)
- Youli Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Qihui Zhu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan, 316100, People's Republic of China
| | - Li Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, People's Republic of China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, People's Republic of China.
| | - Wei Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, People's Republic of China
| | - Guofan Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, People's Republic of China
| |
Collapse
|
186
|
Fant CB, Levandowski CB, Gupta K, Maas ZL, Moir J, Rubin JD, Sawyer A, Esbin MN, Rimel JK, Luyties O, Marr MT, Berger I, Dowell RD, Taatjes DJ. TFIID Enables RNA Polymerase II Promoter-Proximal Pausing. Mol Cell 2020; 78:785-793.e8. [PMID: 32229306 DOI: 10.1016/j.molcel.2020.03.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/15/2019] [Accepted: 03/05/2020] [Indexed: 02/07/2023]
Abstract
RNA polymerase II (RNAPII) transcription is governed by the pre-initiation complex (PIC), which contains TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, RNAPII, and Mediator. After initiation, RNAPII enzymes pause after transcribing less than 100 bases; precisely how RNAPII pausing is enforced and regulated remains unclear. To address specific mechanistic questions, we reconstituted human RNAPII promoter-proximal pausing in vitro, entirely with purified factors (no extracts). As expected, NELF and DSIF increased pausing, and P-TEFb promoted pause release. Unexpectedly, the PIC alone was sufficient to reconstitute pausing, suggesting RNAPII pausing is an inherent PIC function. In agreement, pausing was lost upon replacement of the TFIID complex with TATA-binding protein (TBP), and PRO-seq experiments revealed widespread disruption of RNAPII pausing upon acute depletion (t = 60 min) of TFIID subunits in human or Drosophila cells. These results establish a TFIID requirement for RNAPII pausing and suggest pause regulatory factors may function directly or indirectly through TFIID.
Collapse
Affiliation(s)
- Charli B Fant
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | | | - Kapil Gupta
- School of Biochemistry, Bristol Research Centre for Synthetic Biology, University of Bristol, Bristol, UK
| | - Zachary L Maas
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - John Moir
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Jonathan D Rubin
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Andrew Sawyer
- Department of Biology, Brandeis University, Waltham, MA, USA
| | - Meagan N Esbin
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Jenna K Rimel
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Olivia Luyties
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Michael T Marr
- Department of Biology, Brandeis University, Waltham, MA, USA
| | - Imre Berger
- School of Biochemistry, Bristol Research Centre for Synthetic Biology, University of Bristol, Bristol, UK
| | - Robin D Dowell
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA; BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
| |
Collapse
|
187
|
McKechnie AE, Wolf BO. The Physiology of Heat Tolerance in Small Endotherms. Physiology (Bethesda) 2020; 34:302-313. [PMID: 31389778 DOI: 10.1152/physiol.00011.2019] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Understanding the heat tolerances of small mammals and birds has taken on new urgency with the advent of climate change. Here, we review heat tolerance limits, pathways of evaporative heat dissipation that permit the defense of body temperature during heat exposure, and mechanisms operating at tissue, cellular, and molecular levels.
Collapse
Affiliation(s)
- Andrew E McKechnie
- South African Research Chair in Conservation Physiology, National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa.,DST-NRF Centre of Excellence at the FitzPatrick Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - Blair O Wolf
- UNM Biology Department, University of New Mexico, Albuquerque, New Mexico
| |
Collapse
|
188
|
Abstract
Protein folding in the cell is mediated by an extensive network of >1,000 chaperones, quality control factors, and trafficking mechanisms collectively termed the proteostasis network. While the components and organization of this network are generally well established, our understanding of how protein-folding problems are identified, how the network components integrate to successfully address challenges, and what types of biophysical issues each proteostasis network component is capable of addressing remains immature. We describe a chemical biology-informed framework for studying cellular proteostasis that relies on selection of interesting protein-folding problems and precise researcher control of proteostasis network composition and activities. By combining these methods with multifaceted strategies to monitor protein folding, degradation, trafficking, and aggregation in cells, researchers continue to rapidly generate new insights into cellular proteostasis.
Collapse
Affiliation(s)
- Rebecca M Sebastian
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| |
Collapse
|
189
|
McMenamin AJ, Daughenbaugh KF, Flenniken ML. The Heat Shock Response in the Western Honey Bee (Apis mellifera) is Antiviral. Viruses 2020; 12:E245. [PMID: 32098425 PMCID: PMC7077298 DOI: 10.3390/v12020245] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/22/2022] Open
Abstract
Honey bees (Apismellifera) are an agriculturally important pollinator species that live in easily managed social groups (i.e., colonies). Unfortunately, annual losses of honey bee colonies in many parts of the world have reached unsustainable levels. Multiple abiotic and biotic stressors, including viruses, are associated with individual honey bee and colony mortality. Honey bees have evolved several antiviral defense mechanisms including conserved immune pathways (e.g., Toll, Imd, JAK/STAT) and dsRNA-triggered responses including RNA interference and a non-sequence specific dsRNA-mediated response. In addition, transcriptome analyses of virus-infected honey bees implicate an antiviral role of stress response pathways, including the heat shock response. Herein, we demonstrate that the heat shock response is antiviral in honey bees. Specifically, heat-shocked honey bees (i.e., 42 °C for 4 h) had reduced levels of the model virus, Sindbis-GFP, compared with bees maintained at a constant temperature. Virus-infection and/or heat shock resulted in differential expression of six heat shock protein encoding genes and three immune genes, many of which are positively correlated. The heat shock protein encoding and immune gene transcriptional responses observed in virus-infected bees were not completely recapitulated by administration of double stranded RNA (dsRNA), a virus-associated molecular pattern, indicating that additional virus-host interactions are involved in triggering antiviral stress response pathways.
Collapse
Affiliation(s)
- Alexander J. McMenamin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (K.F.D.)
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
| | - Katie F. Daughenbaugh
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (K.F.D.)
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
| | - Michelle L. Flenniken
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (K.F.D.)
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
| |
Collapse
|
190
|
Pradhan R, Nallappa MJ, Sengupta K. Lamin A/C modulates spatial organization and function of the Hsp70 gene locus via nuclear myosin I. J Cell Sci 2020; 133:jcs236265. [PMID: 31988151 DOI: 10.1242/jcs.236265] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023] Open
Abstract
The structure-function relationship of the nucleus is tightly regulated, especially during heat shock. Typically, heat shock activates molecular chaperones that prevent protein misfolding and preserve genome integrity. However, the molecular mechanisms that regulate nuclear structure-function relationships during heat shock remain unclear. Here, we show that lamin A and C (hereafter lamin A/C; both lamin A and C are encoded by LMNA) are required for heat-shock-mediated transcriptional induction of the Hsp70 gene locus (HSPA genes). Interestingly, lamin A/C regulates redistribution of nuclear myosin I (NM1) into the nucleus upon heat shock, and depletion of either lamin A/C or NM1 abrogates heat-shock-induced repositioning of Hsp70 gene locus away from the nuclear envelope. Lamins and NM1 also regulate spatial positioning of the SC35 (also known as SRSF2) speckles - important nuclear landmarks that modulates Hsp70 gene locus expression upon heat shock. This suggests an intricate crosstalk between nuclear lamins, NM1 and SC35 organization in modulating transcriptional responses of the Hsp70 gene locus during heat shock. Taken together, this study unravels a novel role for lamin A/C in the regulation of the spatial dynamics and function of the Hsp70 gene locus upon heat shock, via the nuclear motor protein NM1.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Roopali Pradhan
- Biology, Main Building, First Floor, Room B-216, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Muhunden Jayakrishnan Nallappa
- Biology, Main Building, First Floor, Room B-216, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Kundan Sengupta
- Biology, Main Building, First Floor, Room B-216, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| |
Collapse
|
191
|
Gamboa L, Phung EV, Li H, Meyers JP, Hart AC, Miller IC, Kwong GA. Heat-Triggered Remote Control of CRISPR-dCas9 for Tunable Transcriptional Modulation. ACS Chem Biol 2020; 15:533-542. [PMID: 31904924 DOI: 10.1021/acschembio.9b01005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
CRISPR-associated proteins (Cas) are enabling powerful new approaches to control mammalian cell functions, yet the lack of spatially defined, noninvasive modalities limits their use as biological tools. Here, we integrate thermal gene switches with dCas9 complexes to confer remote control of gene activation and suppression with short pulses of heat. Using a thermal switch constructed from the heat shock protein A6 (HSPA6) locus, we show that a single heat pulse 3-5 °C above basal temperature is sufficient to trigger expression of dCas9 complexes. We demonstrate that dCas9 fused to the transcriptional activator VP64 is functional after heat activation, and, depending on the number of heat pulses, drives transcription of endogenous genes GzmB and CCL21 to levels equivalent to that achieved by a constitutive viral promoter. Across a range of input temperatures, we find that downstream protein expression of GzmB closely correlates with transcript levels (R2 = 0.99). Using dCas9 fused with the transcriptional suppressor KRAB, we show that longitudinal suppression of the reporter d2GFP depends on key thermal input parameters including pulse magnitude, number of pulses, and dose fractionation. In living mice, we extend our study using photothermal heating to spatially target implanted cells to suppress d2GFP in vivo. Our study establishes a noninvasive and targeted approach to harness Cas-based proteins for modulation of gene expression to complement current methods for remote control of cell function.
Collapse
Affiliation(s)
- Lena Gamboa
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Erick V. Phung
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Haoxin Li
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Jared P. Meyers
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Anna C. Hart
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Ian C. Miller
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Gabriel A. Kwong
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Integrated Cancer Research Center, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Georgia Immunoengineering Consortium, Emory University and Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
192
|
Dougherty SE, Maduka AO, Inada T, Silva GM. Expanding Role of Ubiquitin in Translational Control. Int J Mol Sci 2020; 21:E1151. [PMID: 32050486 PMCID: PMC7037965 DOI: 10.3390/ijms21031151] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic proteome has to be precisely regulated at multiple levels of gene expression, from transcription, translation, and degradation of RNA and protein to adjust to several cellular conditions. Particularly at the translational level, regulation is controlled by a variety of RNA binding proteins, translation and associated factors, numerous enzymes, and by post-translational modifications (PTM). Ubiquitination, a prominent PTM discovered as the signal for protein degradation, has newly emerged as a modulator of protein synthesis by controlling several processes in translation. Advances in proteomics and cryo-electron microscopy have identified ubiquitin modifications of several ribosomal proteins and provided numerous insights on how this modification affects ribosome structure and function. The variety of pathways and functions of translation controlled by ubiquitin are determined by the various enzymes involved in ubiquitin conjugation and removal, by the ubiquitin chain type used, by the target sites of ubiquitination, and by the physiologic signals triggering its accumulation. Current research is now elucidating multiple ubiquitin-mediated mechanisms of translational control, including ribosome biogenesis, ribosome degradation, ribosome-associated protein quality control (RQC), and redox control of translation by ubiquitin (RTU). This review discusses the central role of ubiquitin in modulating the dynamism of the cellular proteome and explores the molecular aspects responsible for the expanding puzzle of ubiquitin signals and functions in translation.
Collapse
Affiliation(s)
- Shannon E. Dougherty
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Austin O. Maduka
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| |
Collapse
|
193
|
DAF-16/FOXO requires Protein Phosphatase 4 to initiate transcription of stress resistance and longevity promoting genes. Nat Commun 2020; 11:138. [PMID: 31919361 PMCID: PMC6952425 DOI: 10.1038/s41467-019-13931-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 12/09/2019] [Indexed: 12/21/2022] Open
Abstract
In C. elegans, the conserved transcription factor DAF-16/FOXO is a powerful aging regulator, relaying dire conditions into expression of stress resistance and longevity promoting genes. For some of these functions, including low insulin/IGF signaling (IIS), DAF-16 depends on the protein SMK-1/SMEK, but how SMK-1 exerts this role has remained unknown. We show that SMK-1 functions as part of a specific Protein Phosphatase 4 complex (PP4SMK-1). Loss of PP4SMK-1 hinders transcriptional initiation at several DAF-16-activated genes, predominantly by impairing RNA polymerase II recruitment to their promoters. Search for the relevant substrate of PP4SMK-1 by phosphoproteomics identified the conserved transcriptional regulator SPT-5/SUPT5H, whose knockdown phenocopies the loss of PP4SMK-1. Phosphoregulation of SPT-5 is known to control transcriptional events such as elongation and termination. Here we also show that transcription initiating events are influenced by the phosphorylation status of SPT-5, particularly at DAF-16 target genes where transcriptional initiation appears rate limiting, rendering PP4SMK-1 crucial for many of DAF-16’s physiological roles. The transcription factor DAF-16/FOXO mediates a wide variety of aging-preventive responses by driving the expression of stress resistance and longevity promoting genes. Here the authors show that transcriptional initiation at many DAF-16/FOXO target genes requires the dephosphorylation of SPT-5 by Protein Phosphatase 4.
Collapse
|
194
|
Jayaraj GG, Hipp MS, Hartl FU. Functional Modules of the Proteostasis Network. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a033951. [PMID: 30833457 DOI: 10.1101/cshperspect.a033951] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cells invest in an extensive network of factors to maintain protein homeostasis (proteostasis) and prevent the accumulation of potentially toxic protein aggregates. This proteostasis network (PN) comprises the machineries for the biogenesis, folding, conformational maintenance, and degradation of proteins with molecular chaperones as central coordinators. Here, we review recent progress in understanding the modular architecture of the PN in mammalian cells and how it is modified during cell differentiation. We discuss the capacity and limitations of the PN in maintaining proteome integrity in the face of proteotoxic stresses, such as aggregate formation in neurodegenerative diseases. Finally, we outline various pharmacological interventions to ameliorate proteostasis imbalance.
Collapse
Affiliation(s)
- Gopal G Jayaraj
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Mark S Hipp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| |
Collapse
|
195
|
Workman P. Reflections and Outlook on Targeting HSP90, HSP70 and HSF1 in Cancer: A Personal Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1243:163-179. [PMID: 32297218 DOI: 10.1007/978-3-030-40204-4_11] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This personal perspective focuses on small-molecule inhibitors of proteostasis networks in cancer-specifically the discovery and development of chemical probes and drugs acting on the molecular chaperones HSP90 and HSP70, and on the HSF1 stress pathway. Emphasis is on progress made and lessons learned and a future outlook is provided. Highly potent, selective HSP90 inhibitors have proved invaluable in exploring the role of this molecular chaperone family in biology and disease pathology. Clinical activity was observed, especially in non small cell lung cancer and HER2 positive breast cancer. Optimal use of HSP90 inhibitors in oncology will likely require development of creative combination strategies. HSP70 family members have proved technically harder to drug. However, recent progress has been made towards useful chemical tool compounds and these may signpost future clinical drug candidates. The HSF1 stress pathway is strongly validated as a target for cancer therapy. HSF1 itself is a ligandless transcription factor that is extremely challenging to drug directly. HSF1 pathway inhibitors have been identified mostly by phenotypic screening, including a series of bisamides from which a clinical candidate has been identified for treatment of ovarian cancer, multiple myeloma and potentially other cancers.
Collapse
Affiliation(s)
- Paul Workman
- CRUK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
| |
Collapse
|
196
|
Garrigues JM, Tsu BV, Daugherty MD, Pasquinelli AE. Diversification of the Caenorhabditis heat shock response by Helitron transposable elements. eLife 2019; 8:51139. [PMID: 31825311 PMCID: PMC6927752 DOI: 10.7554/elife.51139] [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] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022] Open
Abstract
Heat Shock Factor 1 (HSF-1) is a key regulator of the heat shock response (HSR). Upon heat shock, HSF-1 binds well-conserved motifs, called Heat Shock Elements (HSEs), and drives expression of genes important for cellular protection during this stress. Remarkably, we found that substantial numbers of HSEs in multiple Caenorhabditis species reside within Helitrons, a type of DNA transposon. Consistent with Helitron-embedded HSEs being functional, upon heat shock they display increased HSF-1 and RNA polymerase II occupancy and up-regulation of nearby genes in C. elegans. Interestingly, we found that different genes appear to be incorporated into the HSR by species-specific Helitron insertions in C. elegans and C. briggsae and by strain-specific insertions among different wild isolates of C. elegans. Our studies uncover previously unidentified targets of HSF-1 and show that Helitron insertions are responsible for rewiring and diversifying the Caenorhabditis HSR.
Collapse
Affiliation(s)
- Jacob M Garrigues
- Division of Biology, University of California, San Diego, San Diego, United States
| | - Brian V Tsu
- Division of Biology, University of California, San Diego, San Diego, United States
| | - Matthew D Daugherty
- Division of Biology, University of California, San Diego, San Diego, United States
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, San Diego, United States
| |
Collapse
|
197
|
Bauer DLV, Tellier M, Martínez-Alonso M, Nojima T, Proudfoot NJ, Murphy S, Fodor E. Influenza Virus Mounts a Two-Pronged Attack on Host RNA Polymerase II Transcription. Cell Rep 2019; 23:2119-2129.e3. [PMID: 29768209 PMCID: PMC5972227 DOI: 10.1016/j.celrep.2018.04.047] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 04/03/2018] [Accepted: 04/11/2018] [Indexed: 12/24/2022] Open
Abstract
Influenza virus intimately associates with host RNA polymerase II (Pol II) and mRNA processing machinery. Here, we use mammalian native elongating transcript sequencing (mNET-seq) to examine Pol II behavior during viral infection. We show that influenza virus executes a two-pronged attack on host transcription. First, viral infection causes decreased Pol II gene occupancy downstream of transcription start sites. Second, virus-induced cellular stress leads to a catastrophic failure of Pol II termination at poly(A) sites, with transcription often continuing for tens of kilobases. Defective Pol II termination occurs independently of the ability of the viral NS1 protein to interfere with host mRNA processing. Instead, this termination defect is a common effect of diverse cellular stresses and underlies the production of previously reported downstream-of-gene transcripts (DoGs). Our work has implications for understanding not only host-virus interactions but also fundamental aspects of mammalian transcription. Influenza virus infection dysregulates host transcription Viral infection depletes Pol II from gene bodies downstream of the TSS Virus-induced stress leads to a catastrophic failure of Pol II termination Defective termination does not require viral NS1: host CPSF30 interaction
Collapse
Affiliation(s)
- David L V Bauer
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Mónica Martínez-Alonso
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| |
Collapse
|
198
|
Schreiner WP, Pagliuso DC, Garrigues JM, Chen JS, Aalto AP, Pasquinelli AE. Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock. Nucleic Acids Res 2019; 47:9829-9841. [PMID: 31396626 PMCID: PMC6765114 DOI: 10.1093/nar/gkz693] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023] Open
Abstract
Elevated temperatures activate a heat shock response (HSR) to protect cells from the pathological effects of protein mis-folding, cellular mis-organization, organelle dysfunction and altered membrane fluidity. This response includes activation of the conserved transcription factor heat shock factor 1 (HSF-1), which binds heat shock elements (HSEs) in the promoters of genes induced by heat shock (HS). The upregulation of protein-coding genes (PCGs), such as heat shock proteins and cytoskeletal regulators, is critical for cellular survival during elevated temperatures. While the transcriptional response of PCGs to HS has been comprehensively analyzed in a variety of organisms, the effect of this stress on the expression of non-coding RNAs (ncRNAs) has not been systematically examined. Here we show that in Caenorhabditis elegans HS induces up- and downregulation of specific ncRNAs from multiple classes, including miRNA, piRNA, lincRNA, pseudogene and repeat elements. Moreover, some ncRNA genes appear to be direct targets of the HSR, as they contain HSF-1 bound HSEs in their promoters and their expression is regulated by this factor during HS. These results demonstrate that multiple ncRNA genes respond to HS, some as direct HSF-1 targets, providing new candidates that may contribute to organismal survival during this stress.
Collapse
Affiliation(s)
- William P Schreiner
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Delaney C Pagliuso
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Jacob M Garrigues
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Jerry S Chen
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Antti P Aalto
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| |
Collapse
|
199
|
Wissink EM, Vihervaara A, Tippens ND, Lis JT. Nascent RNA analyses: tracking transcription and its regulation. Nat Rev Genet 2019; 20:705-723. [PMID: 31399713 PMCID: PMC6858503 DOI: 10.1038/s41576-019-0159-6] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2019] [Indexed: 12/19/2022]
Abstract
The programmes that direct an organism's development and maintenance are encoded in its genome. Decoding of this information begins with regulated transcription of genomic DNA into RNA. Although transcription and its control can be tracked indirectly by measuring stable RNAs, it is only by directly measuring nascent RNAs that the immediate regulatory changes in response to developmental, environmental, disease and metabolic signals are revealed. Multiple complementary methods have been developed to quantitatively track nascent transcription genome-wide at nucleotide resolution, all of which have contributed novel insights into the mechanisms of gene regulation and transcription-coupled RNA processing. Here we critically evaluate the array of strategies used for investigating nascent transcription and discuss the recent conceptual advances they have provided.
Collapse
Affiliation(s)
- Erin M Wissink
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Anniina Vihervaara
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Nathaniel D Tippens
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
200
|
Kovács D, Sigmond T, Hotzi B, Bohár B, Fazekas D, Deák V, Vellai T, Barna J. HSF1Base: A Comprehensive Database of HSF1 (Heat Shock Factor 1) Target Genes. Int J Mol Sci 2019; 20:ijms20225815. [PMID: 31752429 PMCID: PMC6888953 DOI: 10.3390/ijms20225815] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/11/2019] [Accepted: 11/15/2019] [Indexed: 12/28/2022] Open
Abstract
HSF1 (heat shock factor 1) is an evolutionarily conserved master transcriptional regulator of the heat shock response (HSR) in eukaryotic cells. In response to high temperatures, HSF1 upregulates genes encoding molecular chaperones, also called heat shock proteins, which assist the refolding or degradation of damaged intracellular proteins. Accumulating evidence reveals however that HSF1 participates in several other physiological and pathological processes such as differentiation, immune response, and multidrug resistance, as well as in ageing, neurodegenerative demise, and cancer. To address how HSF1 controls these processes one should systematically analyze its target genes. Here we present a novel database called HSF1Base (hsf1base.org) that contains a nearly comprehensive list of HSF1 target genes identified so far. The list was obtained by manually curating publications on individual HSF1 targets and analyzing relevant high throughput transcriptomic and chromatin immunoprecipitation data derived from the literature and the Yeastract database. To support the biological relevance of HSF1 targets identified by high throughput methods, we performed an enrichment analysis of (potential) HSF1 targets across different tissues/cell types and organisms. We found that general HSF1 functions (targets are expressed in all tissues/cell types) are mostly related to cellular proteostasis. Furthermore, HSF1 targets that are conserved across various animal taxa operate mostly in cellular stress pathways (e.g., autophagy), chromatin remodeling, ribosome biogenesis, and ageing. Together, these data highlight diverse roles for HSF1, expanding far beyond the HSR.
Collapse
Affiliation(s)
- Dániel Kovács
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary; (D.K.); (T.S.); (B.H.); (B.B.); (D.F.)
| | - Tímea Sigmond
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary; (D.K.); (T.S.); (B.H.); (B.B.); (D.F.)
| | - Bernadette Hotzi
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary; (D.K.); (T.S.); (B.H.); (B.B.); (D.F.)
| | - Balázs Bohár
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary; (D.K.); (T.S.); (B.H.); (B.B.); (D.F.)
- Earlham Institute, Norwich NR4 7UZ, UK
- Quadram Institute, Norwich NR4 7UA, UK
| | - Dávid Fazekas
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary; (D.K.); (T.S.); (B.H.); (B.B.); (D.F.)
- Earlham Institute, Norwich NR4 7UZ, UK
- Quadram Institute, Norwich NR4 7UA, UK
| | - Veronika Deák
- Department of Applied Biotechnology and Food Science, Laboratory of Biochemistry and Molecular Biology, University of Technology, H-1111 Budapest, Hungary;
| | - Tibor Vellai
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary; (D.K.); (T.S.); (B.H.); (B.B.); (D.F.)
- MTA-ELTE Genetics Research Group, Eötvös Loránd University, H-1117 Budapest, Hungary
- Correspondence: (T.V.); (J.B.); Tel.: +36-1-372-2500 (ext. 8684) (T.V.); +36-1-372-2500 (ext. 8349) (J.B.); Fax: +36-1-372-2641 (T.V.)
| | - János Barna
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary; (D.K.); (T.S.); (B.H.); (B.B.); (D.F.)
- MTA-ELTE Genetics Research Group, Eötvös Loránd University, H-1117 Budapest, Hungary
- Correspondence: (T.V.); (J.B.); Tel.: +36-1-372-2500 (ext. 8684) (T.V.); +36-1-372-2500 (ext. 8349) (J.B.); Fax: +36-1-372-2641 (T.V.)
| |
Collapse
|