2
|
Gomis Perez C, Dudzinski NR, Rouches M, Landajuela A, Machta B, Zenisek D, Karatekin E. Rapid propagation of membrane tension at retinal bipolar neuron presynaptic terminals. Sci Adv 2022; 8:eabl4411. [PMID: 34985955 DOI: 10.1126/sciadv.abl4411] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Many cellular activities, such as cell migration, cell division, phagocytosis, and exo-endocytosis, generate and are regulated by membrane tension gradients. Membrane tension gradients drive membrane flows, but there is controversy over how rapidly plasma membrane flow can relax tension gradients. Here, we show that membrane tension can propagate rapidly or slowly, spanning orders of magnitude in speed, depending on the cell type. In a neuronal terminal specialized for rapid synaptic vesicle turnover, membrane tension equilibrates within seconds. By contrast, membrane tension does not propagate in neuroendocrine adrenal chromaffin cells secreting catecholamines. Stimulation of exocytosis causes a rapid, global decrease in the synaptic terminal membrane tension, which recovers slowly due to endocytosis. Thus, membrane flow and tension equilibration may be adapted to distinct membrane recycling requirements.
Collapse
Affiliation(s)
- Carolina Gomis Perez
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Natasha R Dudzinski
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, USA
| | - Mason Rouches
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
| | - Ane Landajuela
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Benjamin Machta
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| | - David Zenisek
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, USA
- Kavli Institute for Neuroscience, Yale University, New Haven, CT, USA
- Department of Neuroscience, Yale University, New Haven, CT, USA
- Department of Ophthalmology and Visual Sciences, Yale University, New Haven, CT, USA
| | - Erdem Karatekin
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Université de Paris, SPPIN-Saints-Pères Paris Institute for the Neurosciences, Centre National de la Recherche Scientifique (CNRS), Paris F-75006, France
| |
Collapse
|
5
|
Danaee P, Rouches M, Wiley M, Deng D, Huang L, Hendrix D. bpRNA: large-scale automated annotation and analysis of RNA secondary structure. Nucleic Acids Res 2019; 46:5381-5394. [PMID: 29746666 PMCID: PMC6009582 DOI: 10.1093/nar/gky285] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/11/2018] [Indexed: 01/04/2023] Open
Abstract
While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here, we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, ‘bpRNA-1m’, of over 100 000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar (≥90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.
Collapse
Affiliation(s)
| | | | | | - Dezhong Deng
- School of Electrical Engineering and Computer Science
| | - Liang Huang
- School of Electrical Engineering and Computer Science
| | - David Hendrix
- School of Electrical Engineering and Computer Science.,Department of Biochemistry and Biophysics
| |
Collapse
|