1
|
Steinbach S, Molina M, Grinberg LT, Aring L, Guntermann A, Marcus K, Heinsen H, Paraizo Leite RE, May C. Don't die like me: Which proteins are responsible for the selective neuronal vulnerability within the substantia nigra? PLoS One 2024; 19:e0296730. [PMID: 39089320 DOI: 10.1371/journal.pone.0296730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 12/18/2023] [Indexed: 08/03/2024] Open
Abstract
A hallmark of Parkinson's disease is the specific degeneration of dopaminergic neurons in the substantia nigra pars compacta. Interestingly, not all of these neurons are affected to the same extent. Studies revealed that neurons located more ventrally within the substantia nigra pars compacta have a higher prevalence to degenerate than those located in the dorsal tier. The underlying reasons for this selective neuronal vulnerability are still unknown. The aim of the present study was to gain a better understanding of molecular differences between these two neuronal subpopulations that may explain the selective neuronal vulnerability within the human substantia nigra. For this purpose, the neurons from the ventral as well as dorsal tier of the substantia nigra were specifically isolated out of neuropathologically unremarkable human substantia nigra sections with laser microdissection. Following, their proteome was analyzed by data independent acquisition mass spectrometry. The samples were analysed donor-specifically and not pooled for this purpose. A total of 5,391 proteins were identified in the substantia nigra. Of these, 2,453 proteins could be quantified in 100% of the dorsal tier samples. 1,629 could be quantified in 100% of the ventral tier samples. Nine proteins were differentially regulated with a log2 value ≥0.5 and a Qvalue ≤0.05. Of these 7 were higher abundant in the dorsal tier and 2 higher in the ventral tier. These proteins are associated with the cytoskeleton, neuronal plasticity, or calcium homeostasis. With these findings a deeper understanding can be gained of the selective neuronal vulnerability within the substantia nigra and of protective mechanisms against neurodegeneration in specific neuronal subpopulations.
Collapse
Affiliation(s)
- Simone Steinbach
- Medizinisches Proteom-Center, Center of Protein Diagnostics (ProDi), Ruhr-Universität Bochum, Bochum, Germany
| | - Mariana Molina
- Physiopathology in Aging Lab/Brazilian Aging Brain Study Group-LIM22, University of São Paulo Medical School, São Paulo, Brazil
- Discipline of Pathophysiology, University of São Paulo Medical School, São Paulo, Brazil
| | - Lea T Grinberg
- Physiopathology in Aging Lab/Brazilian Aging Brain Study Group-LIM22, University of São Paulo Medical School, São Paulo, Brazil
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Luisa Aring
- Medizinisches Proteom-Center, Center of Protein Diagnostics (ProDi), Ruhr-Universität Bochum, Bochum, Germany
| | - Annika Guntermann
- Medizinisches Proteom-Center, Center of Protein Diagnostics (ProDi), Ruhr-Universität Bochum, Bochum, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Center of Protein Diagnostics (ProDi), Ruhr-Universität Bochum, Bochum, Germany
| | | | - Renata E Paraizo Leite
- Physiopathology in Aging Lab/Brazilian Aging Brain Study Group-LIM22, University of São Paulo Medical School, São Paulo, Brazil
- Discipline of Geriatrics, University of São Paulo Medical School, São Paulo, Brazil
| | - Caroline May
- Medizinisches Proteom-Center, Center of Protein Diagnostics (ProDi), Ruhr-Universität Bochum, Bochum, Germany
| |
Collapse
|
2
|
van Tartwijk FW, Kaminski CF. Protein Condensation, Cellular Organization, and Spatiotemporal Regulation of Cytoplasmic Properties. Adv Biol (Weinh) 2022; 6:e2101328. [PMID: 35796197 DOI: 10.1002/adbi.202101328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/15/2022] [Indexed: 01/28/2023]
Abstract
The cytoplasm is an aqueous, highly crowded solution of active macromolecules. Its properties influence the behavior of proteins, including their folding, motion, and interactions. In particular, proteins in the cytoplasm can interact to form phase-separated assemblies, so-called biomolecular condensates. The interplay between cytoplasmic properties and protein condensation is critical in a number of functional contexts and is the subject of this review. The authors first describe how cytoplasmic properties can affect protein behavior, in particular condensate formation, and then describe the functional implications of this interplay in three cellular contexts, which exemplify how protein self-organization can be adapted to support certain physiological phenotypes. The authors then describe the formation of RNA-protein condensates in highly polarized cells such as neurons, where condensates play a critical role in the regulation of local protein synthesis, and describe how different stressors trigger extensive reorganization of the cytoplasm, both through signaling pathways and through direct stress-induced changes in cytoplasmic properties. Finally, the authors describe changes in protein behavior and cytoplasmic properties that may occur in extremophiles, in particular organisms that have adapted to inhabit environments of extreme temperature, and discuss the implications and functional importance of these changes.
Collapse
Affiliation(s)
- Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| |
Collapse
|
3
|
S Mogre S, Brown AI, Koslover EF. Getting around the cell: physical transport in the intracellular world. Phys Biol 2020; 17:061003. [PMID: 32663814 DOI: 10.1088/1478-3975/aba5e5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We outline several key biological functions that depend on physically transporting components across the cell, including the delivery of secreted proteins, support of cell growth and repair, propagation of intracellular signals, establishment of organelle contacts, and spatial organization of metabolic gradients. We then review the three primary physical modes of transport in eukaryotic cells: diffusive motion, motor-driven transport, and advection by cytoplasmic flow. For each mechanism, we identify the main factors that determine speed and directionality. We also highlight the efficiency of each transport mode in fulfilling various key objectives of transport, such as particle mixing, directed delivery, and rapid target search. Taken together, the interplay of diffusion, molecular motors, and flows supports the intracellular transport needs that underlie a broad variety of biological phenomena.
Collapse
Affiliation(s)
- Saurabh S Mogre
- Department of Physics, University of California, San Diego, San Diego, California 92093, United States of America
| | | | | |
Collapse
|
4
|
Hitching a Ride: Mechanics of Transport Initiation through Linker-Mediated Hitchhiking. Biophys J 2020; 118:1357-1369. [PMID: 32061275 DOI: 10.1016/j.bpj.2020.01.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/16/2020] [Accepted: 01/21/2020] [Indexed: 12/14/2022] Open
Abstract
In contrast to the canonical picture of transport by direct attachment to motor proteins, recent evidence shows that a number of intracellular "cargos" navigate the cytoplasm by hitchhiking on motor-driven "carrier" organelles. We describe a quantitative model of intracellular cargo transport via hitchhiking, examining the efficiency of hitchhiking initiation as a function of geometric and mechanical parameters. We focus specifically on the parameter regime relevant to the hitchhiking motion of peroxisome organelles in fungal hyphae. Our work predicts the dependence of transport initiation rates on the distribution of cytoskeletal tracks and carrier organelles, as well as the number, length, and flexibility of the linker proteins that mediate contact between the carrier and the hitchhiking cargo. Furthermore, we demonstrate that attaching organelles to microtubules can result in a substantial enhancement of the hitchhiking initiation rate in tubular geometries such as those found in fungal hyphae. This enhancement is expected to increase the overall transport rate of hitchhiking organelles and lead to greater efficiency in organelle dispersion. Our results leverage a quantitative physical model to highlight the importance of organelle encounter dynamics in noncanonical intracellular transport.
Collapse
|
5
|
Mogre SS, Koslover EF. Multimodal transport and dispersion of organelles in narrow tubular cells. Phys Rev E 2018; 97:042402. [PMID: 29758750 DOI: 10.1103/physreve.97.042402] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 11/07/2022]
Abstract
Intracellular components explore the cytoplasm via active motor-driven transport in conjunction with passive diffusion. We model the motion of organelles in narrow tubular cells using analytical techniques and numerical simulations to study the efficiency of different transport modes in achieving various cellular objectives. Our model describes length and time scales over which each transport mode dominates organelle motion, along with various metrics to quantify exploration of intracellular space. For organelles that search for a specific target, we obtain the average capture time for given transport parameters and show that diffusion and active motion contribute to target capture in the biologically relevant regime. Because many organelles have been found to tether to microtubules when not engaged in active motion, we study the interplay between immobilization due to tethering and increased probability of active transport. We derive parameter-dependent conditions under which tethering enhances long-range transport and improves the target capture time. These results shed light on the optimization of intracellular transport machinery and provide experimentally testable predictions for the effects of transport regulation mechanisms such as tethering.
Collapse
Affiliation(s)
- Saurabh S Mogre
- Department of Physics, University of California San Diego, La Jolla, California 92093, USA
| | - Elena F Koslover
- Department of Physics, University of California San Diego, La Jolla, California 92093, USA
| |
Collapse
|
6
|
Gross P, Kumar KV, Grill SW. How Active Mechanics and Regulatory Biochemistry Combine to Form Patterns in Development. Annu Rev Biophys 2017; 46:337-356. [DOI: 10.1146/annurev-biophys-070816-033602] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Peter Gross
- BIOTEC, Technische Universität Dresden, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - K. Vijay Kumar
- International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bengaluru 560089, India
| | - Stephan W. Grill
- BIOTEC, Technische Universität Dresden, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| |
Collapse
|
7
|
Rotational friction of dipolar colloids measured by driven torsional oscillations. Sci Rep 2016; 6:34193. [PMID: 27680399 PMCID: PMC5040963 DOI: 10.1038/srep34193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/05/2016] [Indexed: 01/02/2023] Open
Abstract
Despite its prominent role in the dynamics of soft materials, rotational friction remains a quantity that is difficult to determine for many micron-sized objects. Here, we demonstrate how the Stokes coefficient of rotational friction can be obtained from the driven torsional oscillations of single particles in a highly viscous environment. The idea is that the oscillation amplitude of a dipolar particle under combined static and oscillating fields provides a measure for the Stokes friction. From numerical studies we derive a semi-empirical analytic expression for the amplitude of the oscillation, which cannot be calculated analytically from the equation of motion. We additionally demonstrate that this expression can be used to experimentally determine the rotational friction coefficient of single particles. Here, we record the amplitudes of a field-driven dipolar Janus microsphere with optical microscopy. The presented method distinguishes itself in its experimental and conceptual simplicity. The magnetic torque leaves the local environment unchanged, which contrasts with other approaches where, for example, additional mechanical (frictional) or thermal contributions have to be regarded.
Collapse
|
8
|
Mussel M, Inzelberg L, Nevo U. Insignificance of active flow for neural diffusion weighted imaging: A negative result. Magn Reson Med 2016; 78:746-753. [DOI: 10.1002/mrm.26375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/28/2016] [Accepted: 07/19/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Matan Mussel
- The Iby and Aladar Fleischman Faculty of Engineering, Department of Biomedical Engineering, Tel Aviv University; Tel Aviv Israel
| | - Lilah Inzelberg
- The Iby and Aladar Fleischman Faculty of Engineering, Department of Biomedical Engineering, Tel Aviv University; Tel Aviv Israel
- Sagol School of Neuroscience; Tel Aviv University; Tel Aviv Israel
| | - Uri Nevo
- The Iby and Aladar Fleischman Faculty of Engineering, Department of Biomedical Engineering, Tel Aviv University; Tel Aviv Israel
- Sagol School of Neuroscience; Tel Aviv University; Tel Aviv Israel
| |
Collapse
|
9
|
Godec A, Metzler R. Signal focusing through active transport. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:010701. [PMID: 26274108 DOI: 10.1103/physreve.92.010701] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Indexed: 06/04/2023]
Abstract
The accuracy of molecular signaling in biological cells and novel diagnostic devices is ultimately limited by the counting noise floor imposed by the thermal diffusion. Motivated by the fact that messenger RNA and vesicle-engulfed signaling molecules transiently bind to molecular motors and are actively transported in biological cells, we show here that the random active delivery of signaling particles to within a typical diffusion distance to the receptor generically reduces the correlation time of the counting noise. Considering a variety of signaling particle sizes from mRNA to vesicles and cell sizes from prokaryotic to eukaryotic cells, we show that the conditions for active focusing-faster and more precise signaling-are indeed compatible with observations in living cells. Our results improve the understanding of molecular cellular signaling and novel diagnostic devices.
Collapse
Affiliation(s)
- Aljaž Godec
- Institute of Physics & Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany
- Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| |
Collapse
|