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Crapart CC, Scott ZC, Konno T, Sharma A, Parutto P, Bailey DMD, Westrate LM, Avezov E, Koslover EF. Luminal transport through intact endoplasmic reticulum limits the magnitude of localized Ca 2+ signals. Proc Natl Acad Sci U S A 2024; 121:e2312172121. [PMID: 38502705 PMCID: PMC10990089 DOI: 10.1073/pnas.2312172121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 02/09/2024] [Indexed: 03/21/2024] Open
Abstract
The endoplasmic reticulum (ER) forms an interconnected network of tubules stretching throughout the cell. Understanding how ER functionality relies on its structural organization is crucial for elucidating cellular vulnerability to ER perturbations, which have been implicated in several neuronal pathologies. One of the key functions of the ER is enabling Ca[Formula: see text] signaling by storing large quantities of this ion and releasing it into the cytoplasm in a spatiotemporally controlled manner. Through a combination of physical modeling and live-cell imaging, we demonstrate that alterations in ER shape significantly impact its ability to support efficient local Ca[Formula: see text] releases, due to hindered transport of luminal content within the ER. Our model reveals that rapid Ca[Formula: see text] release necessitates mobile luminal buffer proteins with moderate binding strength, moving through a well-connected network of ER tubules. These findings provide insight into the functional advantages of normal ER architecture, emphasizing its importance as a kinetically efficient intracellular Ca[Formula: see text] delivery system.
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Affiliation(s)
- Cécile C. Crapart
- UK Dementia Research Institute at the University of Cambridge, CambridgeCB2 0AH, United Kingdom
- Department of Clinical Neurosciences, School of Clinical Medicine, The University of Cambridge, CambridgeCB2 0AH, United Kingdom
| | | | - Tasuku Konno
- UK Dementia Research Institute at the University of Cambridge, CambridgeCB2 0AH, United Kingdom
- Department of Clinical Neurosciences, School of Clinical Medicine, The University of Cambridge, CambridgeCB2 0AH, United Kingdom
| | - Aman Sharma
- Department of Physics, University of California, San Diego, La Jolla, CA92130
| | - Pierre Parutto
- UK Dementia Research Institute at the University of Cambridge, CambridgeCB2 0AH, United Kingdom
- Department of Clinical Neurosciences, School of Clinical Medicine, The University of Cambridge, CambridgeCB2 0AH, United Kingdom
| | - David M. D. Bailey
- UK Dementia Research Institute at the University of Cambridge, CambridgeCB2 0AH, United Kingdom
- Department of Clinical Neurosciences, School of Clinical Medicine, The University of Cambridge, CambridgeCB2 0AH, United Kingdom
| | - Laura M. Westrate
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI49546
| | - Edward Avezov
- UK Dementia Research Institute at the University of Cambridge, CambridgeCB2 0AH, United Kingdom
- Department of Clinical Neurosciences, School of Clinical Medicine, The University of Cambridge, CambridgeCB2 0AH, United Kingdom
| | - Elena F. Koslover
- Department of Physics, University of California, San Diego, La Jolla, CA92130
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Eble H, Joswig M, Lamberti L, Ludington WB. Master regulators of biological systems in higher dimensions. Proc Natl Acad Sci U S A 2023; 120:e2300634120. [PMID: 38096409 PMCID: PMC10743376 DOI: 10.1073/pnas.2300634120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/23/2023] [Indexed: 12/18/2023] Open
Abstract
A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present, generating higher-order interactions. The important regulators of higher-order interactions are unstudied. To address this, we applied a high-dimensional geometry approach that quantifies epistasis in a fitness landscape to ask how individual genes and species influence the interactions in the rest of the biological network. We then generated and also reanalyzed 5-dimensional datasets (two genetic, two microbiome). We identified key genes (e.g., the rbs locus and pykF) and species (e.g., Lactobacilli) that control the interactions of many other genes and species. These higher-order master regulators can induce or suppress evolutionary and ecological diversification by controlling the topography of the fitness landscape. Thus, we provide a method and mathematical justification for exploration of biological networks in higher dimensions.
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Affiliation(s)
- Holger Eble
- Chair of Discrete Mathematics/Geometry, Technical University Berlin, Berlin10623, Germany
| | - Michael Joswig
- Chair of Discrete Mathematics/Geometry, Technical University Berlin, Berlin10623, Germany
- Max Planck Institute for Mathematics in the Sciences, Leipzig04103, Germany
| | - Lisa Lamberti
- Department of Biosystems Science and Engineering, Federal Institute of Technology (ETH Zürich), Basel4058, Switzerland
- Swiss Institute of Bioinformatics, Basel4058, Switzerland
| | - William B. Ludington
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD21218
- Department of Biology, Johns Hopkins University, Baltimore, MD21218
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Ma S, Kotar A, Hall I, Grote S, Rouskin S, Keane SC. Structure of pre-miR-31 reveals an active role in Dicer-TRBP complex processing. Proc Natl Acad Sci U S A 2023; 120:e2300527120. [PMID: 37725636 PMCID: PMC10523476 DOI: 10.1073/pnas.2300527120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/01/2023] [Indexed: 09/21/2023] Open
Abstract
As an essential posttranscriptional regulator of gene expression, microRNA (miRNA) levels must be strictly maintained. The biogenesis of many miRNAs is mediated by trans-acting protein partners through a variety of mechanisms, including remodeling of the RNA structure. miR-31 functions as an oncogene in numerous cancers, and interestingly, its biogenesis is not known to be regulated by protein-binding partners. Therefore, the intrinsic structural properties of the precursor element of miR-31 (pre-miR-31) can provide a mechanism by which its biogenesis is regulated. We determined the solution structure of pre-miR-31 to investigate the role of distinct structural elements in regulating processing by the Dicer-TRBP complex. We found that the presence or absence of mismatches within the helical stem does not strongly influence Dicer-TRBP processing of the pre-miRNAs. However, both the apical loop size and structure at the Dicing site are key elements for discrimination by the Dicer-TRBP complex. Interestingly, our NMR-derived structure reveals the presence of a triplet of base pairs that link the Dicer cleavage site and the apical loop. Mutational analysis in this region suggests that the stability of the junction region strongly influences processing by the Dicer-TRBP complex. Our results enrich our understanding of the active role that RNA structure plays in regulating miRNA biogenesis, which has direct implications for the control of gene expression.
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Affiliation(s)
- Sicong Ma
- Biophysics Program, University of Michigan, Ann Arbor, MI48109
| | - Anita Kotar
- Biophysics Program, University of Michigan, Ann Arbor, MI48109
| | - Ian Hall
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Scott Grote
- Department of Microbiology, Harvard Medical School,Boston, MA02115
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School,Boston, MA02115
| | - Sarah C. Keane
- Biophysics Program, University of Michigan, Ann Arbor, MI48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
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Djutanta F, Brown PT, Nainggolan B, Coullomb A, Radhakrishnan S, Sentosa J, Yurke B, Hariadi RF, Shepherd DP. Decoding the hydrodynamic properties of microscale helical propellers from Brownian fluctuations. Proc Natl Acad Sci U S A 2023; 120:e2220033120. [PMID: 37235635 PMCID: PMC10235983 DOI: 10.1073/pnas.2220033120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
The complex motility of bacteria, ranging from single-swimmer behaviors such as chemotaxis to collective dynamics, including biofilm formation and active matter phenomena, is driven by their microscale propellers. Despite extensive study of swimming flagellated bacteria, the hydrodynamic properties of their helical-shaped propellers have never been directly measured. The primary challenges to directly studying microscale propellers are 1) their small size and fast, correlated motion, 2) the necessity of controlling fluid flow at the microscale, and 3) isolating the influence of a single propeller from a propeller bundle. To solve the outstanding problem of characterizing the hydrodynamic properties of these propellers, we adopt a dual statistical viewpoint that connects to the hydrodynamics through the fluctuation-dissipation theorem (FDT). We regard the propellers as colloidal particles and characterize their Brownian fluctuations, described by 21 diffusion coefficients for translation, rotation, and correlated translation-rotation in a static fluid. To perform this measurement, we applied recent advances in high-resolution oblique plane microscopy to generate high-speed volumetric movies of fluorophore-labeled, freely diffusing Escherichia coli flagella. Analyzing these movies with a bespoke helical single-particle tracking algorithm, we extracted trajectories, calculated the full set of diffusion coefficients, and inferred the average propulsion matrix using a generalized Einstein relation. Our results provide a direct measurement of a microhelix's propulsion matrix and validate proposals that the flagella are highly inefficient propellers, with a maximum propulsion efficiency of less than 3%. Our approach opens broad avenues for studying the motility of particles in complex environments where direct hydrodynamic approaches are not feasible.
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Affiliation(s)
- Franky Djutanta
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ85287
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ85287
| | - Peter T. Brown
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ85287
| | - Bonfilio Nainggolan
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ85287
| | - Alexis Coullomb
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ85287
| | - Sritharini Radhakrishnan
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ85287
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ85287
| | - Jason Sentosa
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ85287
| | - Bernard Yurke
- Micron School of Materials Science and Electrical and Computer Engineering Department, Boise State University, Boise, ID83725
| | - Rizal F. Hariadi
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ85287
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ85287
| | - Douglas P. Shepherd
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ85287
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