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Vagne Q, Vrel JP, Sens P. A minimal self-organisation model of the Golgi apparatus. eLife 2020; 9:47318. [PMID: 32755543 PMCID: PMC7406241 DOI: 10.7554/elife.47318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/07/2020] [Indexed: 11/29/2022] Open
Abstract
The design principles dictating the spatio-temporal organisation of eukaryotic cells, and in particular the mechanisms controlling the self-organisation and dynamics of membrane-bound organelles such as the Golgi apparatus, remain elusive. Although this organelle was discovered 120 years ago, such basic questions as whether vesicular transport through the Golgi occurs in an anterograde (from entry to exit) or retrograde fashion are still strongly debated. Here, we address these issues by studying a quantitative model of organelle dynamics that includes: de-novo compartment generation, inter-compartment vesicular exchange, and biochemical conversion of membrane components. We show that anterograde or retrograde vesicular transports are asymptotic behaviors of a much richer dynamical system. Indeed, the structure and composition of cellular compartments and the directionality of vesicular exchange are intimately linked. They are emergent properties that can be tuned by varying the relative rates of vesicle budding, fusion and biochemical conversion.
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Affiliation(s)
- Quentin Vagne
- Center for Systems Biology Dresden, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jean-Patrick Vrel
- Institut Curie, PSL Research University, CNRS, UMR 168, F-75005, Paris, France.,UPMC Univ Paris 06, CNRS, UMR 168, F-75005, Paris, France
| | - Pierre Sens
- Institut Curie, PSL Research University, CNRS, UMR 168, F-75005, Paris, France.,UPMC Univ Paris 06, CNRS, UMR 168, F-75005, Paris, France
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2
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Vagne Q, Sens P. Stochastic Model of Maturation and Vesicular Exchange in Cellular Organelles. Biophys J 2018; 114:947-957. [PMID: 29490254 PMCID: PMC5984994 DOI: 10.1016/j.bpj.2017.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/14/2017] [Accepted: 12/18/2017] [Indexed: 11/21/2022] Open
Abstract
The dynamical organization of membrane-bound organelles along intracellular transport pathways relies on vesicular exchange between organelles and on the maturation of the organelle's composition by enzymatic reactions or exchange with the cytoplasm. The relative importance of each mechanism in controlling organelle dynamics remains controversial, in particular for transport through the Golgi apparatus. Using a stochastic model, we identify two classes of dynamical behavior that can lead to full maturation of membrane-bound compartments. In the first class, maturation corresponds to the stochastic escape from a steady state in which export is dominated by vesicular exchange, and is very unlikely for large compartments. In the second class, it occurs in a quasi-deterministic fashion and is almost size independent. Whether a system belongs to the first or second class is largely controlled by homotypic fusion.
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Affiliation(s)
- Quentin Vagne
- Institut Curie, PSL Research University, CNRS, UMR 168, Paris, France
| | - Pierre Sens
- Institut Curie, PSL Research University, CNRS, UMR 168, Paris, France.
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3
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Vagne Q, Sens P. Stochastic Model of Vesicular Sorting in Cellular Organelles. PHYSICAL REVIEW LETTERS 2018; 120:058102. [PMID: 29481197 DOI: 10.1103/physrevlett.120.058102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Indexed: 06/08/2023]
Abstract
The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intracellular organization. This process relies on the budding and fusion of transport vesicles, and should be strongly influenced by stochastic fluctuations, considering the relatively small size of many organelles. We identify the perfect sorting of two membrane components initially mixed in a single compartment as a first passage process, and we show that the mean sorting time exhibits two distinct regimes as a function of the ratio of vesicle fusion to budding rates. Low ratio values lead to fast sorting but result in a broad size distribution of sorted compartments dominated by small entities. High ratio values result in two well-defined sorted compartments but sorting is exponentially slow. Our results suggest an optimal balance between vesicle budding and fusion for the rapid and efficient sorting of membrane components and highlight the importance of stochastic effects for the steady-state organization of intracellular compartments.
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Affiliation(s)
- Quentin Vagne
- Institut Curie, PSL Research University, CNRS, UMR 168, 26 rue d'Ulm, F-75005 Paris, France
| | - Pierre Sens
- Institut Curie, PSL Research University, CNRS, UMR 168, 26 rue d'Ulm, F-75005 Paris, France
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4
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Yu RY, Xing L, Cui PF, Qiao JB, He YJ, Chang X, Zhou TJ, Jin QR, Jiang HL, Xiao Y. Regulating the Golgi apparatus by co-delivery of a COX-2 inhibitor and Brefeldin A for suppression of tumor metastasis. Biomater Sci 2018; 6:2144-2155. [DOI: 10.1039/c8bm00381e] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Herein, celecoxib (CLX) and brefeldin A (BFA) were encapsulated into the biocompatible polymer PLGA-PEG to form nanoparticles that act on the Golgi apparatus to treat metastatic breast cancer.
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5
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Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Sci Rep 2016; 6:38840. [PMID: 27991496 PMCID: PMC5171829 DOI: 10.1038/srep38840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/11/2016] [Indexed: 12/11/2022] Open
Abstract
A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner–this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.
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6
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Mani S, Thattai M. Stacking the odds for Golgi cisternal maturation. eLife 2016; 5. [PMID: 27542195 PMCID: PMC5012865 DOI: 10.7554/elife.16231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 08/18/2016] [Indexed: 12/28/2022] Open
Abstract
What is the minimal set of cell-biological ingredients needed to generate a Golgi apparatus? The compositions of eukaryotic organelles arise through a process of molecular exchange via vesicle traffic. Here we statistically sample tens of thousands of homeostatic vesicle traffic networks generated by realistic molecular rules governing vesicle budding and fusion. Remarkably, the plurality of these networks contain chains of compartments that undergo creation, compositional maturation, and dissipation, coupled by molecular recycling along retrograde vesicles. This motif precisely matches the cisternal maturation model of the Golgi, which was developed to explain many observed aspects of the eukaryotic secretory pathway. In our analysis cisternal maturation is a robust consequence of vesicle traffic homeostasis, independent of the underlying details of molecular interactions or spatial stacking. This architecture may have been exapted rather than selected for its role in the secretion of large cargo. DOI:http://dx.doi.org/10.7554/eLife.16231.001
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Affiliation(s)
- Somya Mani
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Mukund Thattai
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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7
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Mani S, Thattai M. Wine glasses and hourglasses: Non-adaptive complexity of vesicle traffic in microbial eukaryotes. Mol Biochem Parasitol 2016; 209:58-63. [PMID: 27012485 PMCID: PMC5154330 DOI: 10.1016/j.molbiopara.2016.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 12/27/2022]
Abstract
We are motivated by the diversity of vesicle traffic systems in microbial parasites. We present a mathematical model of vesicle traffic in a manner accessible to a broad audience. We show that many complex features of vesicle traffic systems arise spontaneously due to molecular interactions. Traffic features such as compartmental maturation might arise non-adaptively and later be selected for function.
Microbial eukaryotes present a stunning diversity of endomembrane organization. From specialized secretory organelles such as the rhoptries and micronemes of apicomplexans, to peroxisome-derived metabolic compartments such as the glycosomes of kinetoplastids, different microbial taxa have explored different solutions to the compartmentalization and processing of cargo. The basic secretory and endocytic system, comprising the ER, Golgi, endosomes, and plasma membrane, as well as diverse taxon-specific specialized endomembrane organelles, are coupled by a complex network of cargo transport via vesicle traffic. It is tempting to connect form to function, ascribing biochemical roles to each compartment and vesicle of such a system. Here we argue that traffic systems of high complexity could arise through non-adaptive mechanisms via purely physical constraints, and subsequently be exapted for various taxon-specific functions. Our argument is based on a Boolean mathematical model of vesicle traffic: we specify rules of how compartments exchange vesicles; these rules then generate hypothetical cells with different types of endomembrane organization. Though one could imagine a large number of hypothetical vesicle traffic systems, very few of these are consistent with molecular interactions. Such molecular constraints are the bottleneck of a metaphorical hourglass, and the rules that make it through the bottleneck are expected to generate cells with many special properties. Sampling at random from among such rules represents an evolutionary null hypothesis: any properties of the resulting cells must be non-adaptive. We show by example that vesicle traffic systems generated in this random manner are reminiscent of the complex trafficking apparatus of real cells.
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Affiliation(s)
- Somya Mani
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Mukund Thattai
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bellary Road, Bangalore 560065, India.
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Griesemer M, Young C, Robinson AS, Petzold L. BiP clustering facilitates protein folding in the endoplasmic reticulum. PLoS Comput Biol 2014; 10:e1003675. [PMID: 24991821 PMCID: PMC4081015 DOI: 10.1371/journal.pcbi.1003675] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 05/03/2014] [Indexed: 12/26/2022] Open
Abstract
The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, experimental evidence revealed the spatial heterogeneity of BiP within the nuclear and peripheral ER of S. cerevisiae (commonly referred to as 'clusters'). Here, we developed a model to evaluate the potential advantages of accounting for multiple BiP molecules binding to peptides, while proposing that BiP's spatial heterogeneity may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness of binding multiple chaperone molecules to peptides. Using two metrics: folding efficiency and chaperone cost, we determined that the single binding site model achieves a higher efficiency than models characterized by multiple binding sites, in the absence of cooperativity. Due to entropic pulling, however, multiple chaperones perform in concert to facilitate the resolubilization and ultimate yield of folded proteins. As a result of cooperativity, multiple binding site models used fewer BiP molecules and maintained a higher folding efficiency than the single binding site model. These insilico investigations reveal that clusters of BiP molecules bound to unfolded proteins may enhance folding efficiency through cooperative action via entropic pulling.
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Affiliation(s)
- Marc Griesemer
- Department of Applied Mathematics, University of California, Merced, Merced, California, United States of America
- * E-mail:
| | - Carissa Young
- Department of Chemical Engineering, University of Delaware, Newark, Delaware, United States of America
| | - Anne S. Robinson
- Department of Chemical Engineering, University of Delaware, Newark, Delaware, United States of America
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana, United States of America
| | - Linda Petzold
- Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California, United States of America
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9
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Ramadas R, Thattai M. New organelles by gene duplication in a biophysical model of eukaryote endomembrane evolution. Biophys J 2014; 104:2553-63. [PMID: 23746528 DOI: 10.1016/j.bpj.2013.03.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/05/2013] [Accepted: 03/11/2013] [Indexed: 12/13/2022] Open
Abstract
Extant eukaryotic cells have a dynamic traffic network that consists of diverse membrane-bound organelles exchanging matter via vesicles. This endomembrane system arose and diversified during a period characterized by massive expansions of gene families involved in trafficking after the acquisition of a mitochondrial endosymbiont by a prokaryotic host cell >1.8 billion years ago. Here we investigate the mechanistic link between gene duplication and the emergence of new nonendosymbiotic organelles, using a minimal biophysical model of traffic. Our model incorporates membrane-bound compartments, coat proteins and adaptors that drive vesicles to bud and segregate cargo from source compartments, and SNARE proteins and associated factors that cause vesicles to fuse into specific destination compartments. In simulations, arbitrary numbers of compartments with heterogeneous initial compositions segregate into a few compositionally distinct subsets that we term organelles. The global structure of the traffic system (i.e., the number, composition, and connectivity of organelles) is determined completely by local molecular interactions. On evolutionary timescales, duplication of the budding and fusion machinery followed by loss of cross-interactions leads to the emergence of new organelles, with increased molecular specificity being necessary to maintain larger organellar repertoires. These results clarify potential modes of early eukaryotic evolution as well as more recent eukaryotic diversification.
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Affiliation(s)
- Rohini Ramadas
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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10
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Abstract
In this chapter, we summarize recent theoretical efforts to address a variety of issues in Golgi morphogenesis: de novo biogenesis of compartments with precise chemical identity, the transport of proteins through the Golgi, the maintenance of chemical identity, and the morphology of Golgi compartments, from the perspective of nonequilibrium physics.
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Affiliation(s)
- Pierre Sens
- Laboratoire Gulliver, CNRS-ESPCI, UMR 7083, 75231 Paris, France
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11
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Bressloff PC. Two-pool model of cooperative vesicular transport. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:031911. [PMID: 23030948 DOI: 10.1103/physreve.86.031911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Indexed: 06/01/2023]
Abstract
We present a model of bidirectional vesicular transport between two intracellular organelles, which takes into account intermediate stages of transport that occur between vesicular budding from one organelle and subsequent fusion with the other organelle. These are incorporated into the model by associating with each organelle a donor pool of newly budded vesicles and an acceptor pool of transported vesicles ready for fusion. By constructing a system of differential equations that keeps track of the distribution of vesicles and protein concentrations within the various pools and along cytoskeletal tracks, we show how a stable steady state can emerge that consists of organelles that maintain different protein concentrations in spite of the continuous exchange of materials. In particular, exploiting the fact that the surface area of individual vesicles is much smaller than the surface area of organelles, we use an adiabatic approximation to eliminate the vesicular variables. This results in a major simplification of the dynamics and provides a systematic procedure for deriving phenomenological models of cooperative transport.
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Affiliation(s)
- Paul C Bressloff
- Department of Mathematics, University of Utah, 155 South 1400 East, Salt Lake City, Utah 84112, USA
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12
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Golgi apparatus: Homotypic fusion maintains biochemical gradients within the Golgi and improves the accuracy of protein maturation. Int J Biochem Cell Biol 2012; 44:718-21. [DOI: 10.1016/j.biocel.2012.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 01/18/2012] [Accepted: 01/19/2012] [Indexed: 11/18/2022]
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