1
|
Rendleman J, Cheng Z, Maity S, Kastelic N, Munschauer M, Allgoewer K, Teo G, Zhang YBM, Lei A, Parker B, Landthaler M, Freeberg L, Kuersten S, Choi H, Vogel C. New insights into the cellular temporal response to proteostatic stress. eLife 2018; 7:39054. [PMID: 30272558 PMCID: PMC6185107 DOI: 10.7554/elife.39054] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
Maintaining a healthy proteome involves all layers of gene expression regulation. By quantifying temporal changes of the transcriptome, translatome, proteome, and RNA-protein interactome in cervical cancer cells, we systematically characterize the molecular landscape in response to proteostatic challenges. We identify shared and specific responses to misfolded proteins and to oxidative stress, two conditions that are tightly linked. We reveal new aspects of the unfolded protein response, including many genes that escape global translation shutdown. A subset of these genes supports rerouting of energy production in the mitochondria. We also find that many genes change at multiple levels, in either the same or opposing directions, and at different time points. We highlight a variety of putative regulatory pathways, including the stress-dependent alternative splicing of aminoacyl-tRNA synthetases, and protein-RNA binding within the 3’ untranslated region of molecular chaperones. These results illustrate the potential of this information-rich resource.
Collapse
Affiliation(s)
- Justin Rendleman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Zhe Cheng
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Shuvadeep Maity
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Nicolai Kastelic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mathias Munschauer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Kristina Allgoewer
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Guoshou Teo
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Yun Bin Matteo Zhang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Amy Lei
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Brian Parker
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Integrative Research Institute for the Life Sciences, Institute of Biology, Humboldt University, Berlin, Germany
| | | | | | - Hyungwon Choi
- National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| |
Collapse
|