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Erickson JL, Prautsch J, Reynvoet F, Niemeyer F, Hause G, Johnston IG, Schattat MH. Stromule Geometry Allows Optimal Spatial Regulation of Organelle Interactions in the Quasi-2D Cytoplasm. PLANT & CELL PHYSIOLOGY 2024; 65:618-630. [PMID: 37658689 PMCID: PMC11094753 DOI: 10.1093/pcp/pcad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/25/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
In plant cells, plastids form elongated extensions called stromules, the regulation and purposes of which remain unclear. Here, we quantitatively explore how different stromule structures serve to enhance the ability of a plastid to interact with other organelles: increasing the effective space for interaction and biomolecular exchange between organelles. Interestingly, electron microscopy and confocal imaging showed that the cytoplasm in Arabidopsis thaliana and Nicotiana benthamiana epidermal cells is extremely thin (around 100 nm in regions without organelles), meaning that inter-organelle interactions effectively take place in 2D. We combine these imaging modalities with mathematical modeling and new in planta experiments to demonstrate how different stromule varieties (single or multiple, linear or branching) could be employed to optimize different aspects of inter-organelle interaction capacity in this 2D space. We found that stromule formation and branching provide a proportionally higher benefit to interaction capacity in 2D than in 3D. Additionally, this benefit depends on optimal plastid spacing. We hypothesize that cells can promote the formation of different stromule architectures in the quasi-2D cytoplasm to optimize their interaction interface to meet specific requirements. These results provide new insight into the mechanisms underlying the transition from low to high stromule numbers, the consequences for interaction with smaller organelles, how plastid access and plastid to nucleus signaling are balanced and the impact of plastid density on organelle interaction.
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Affiliation(s)
- Jessica Lee Erickson
- Department of Plant Physiology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, Halle 06120, Germany
- Department of Biochemistry of Plant Interactions, Leibniz Institute for Plant Biochemistry, Weinbergweg 10, Halle 06120, Germany
| | - Jennifer Prautsch
- Department of Plant Physiology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, Halle 06120, Germany
| | - Frisine Reynvoet
- Department of Plant Physiology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, Halle 06120, Germany
| | - Frederik Niemeyer
- Department of Plant Physiology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, Halle 06120, Germany
| | - Gerd Hause
- Department of Plant Physiology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, Halle 06120, Germany
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Realfagbygget, Bergen, Vestland 5007, Norway
- Computational Biology Unit, University of Bergen, Høyteknologisenteret, Bergen, Vestland 5006, Norway
| | - Martin Harmut Schattat
- Department of Plant Physiology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, Halle 06120, Germany
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Chustecki JM, Johnston IG. Collective mitochondrial dynamics resolve conflicting cellular tensions: From plants to general principles. Semin Cell Dev Biol 2024; 156:253-265. [PMID: 38043948 DOI: 10.1016/j.semcdb.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/18/2023] [Accepted: 09/15/2023] [Indexed: 12/05/2023]
Abstract
Mitochondria play diverse and essential roles in eukaryotic cells, and plants are no exception. Plant mitochondria have several differences from their metazoan and fungal cousins: they often exist in a fragmented state, move rapidly on actin rather than microtubules, have many plant-specific metabolic features and roles, and usually contain only a subset of the complete mtDNA genome, which itself undergoes frequent recombination. This arrangement means that exchange and complementation is essential for plant mitochondria, and recent work has begun to reveal how their collective dynamics and resultant "social networks" of encounters support this exchange, connecting plant mitochondria in time rather than in space. This review will argue that this social network perspective can be extended to a "societal network", where mitochondrial dynamics are an essential part of the interacting cellular society of organelles and biomolecules. Evidence is emerging that mitochondrial dynamics allow optimal resolutions to competing cellular priorities; we will survey this evidence and review potential future research directions, highlighting that plant mitochondria can help reveal and test principles that apply across other kingdoms of life. In parallel with this fundamental cell biology, we also highlight the translational "One Health" importance of plant mitochondrial behaviour - which is exploited in the production of a vast amount of crops consumed worldwide - and the potential for multi-objective optimisation to understand and rationally re-engineer the evolved resolutions to these tensions.
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Affiliation(s)
- Joanna M Chustecki
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway; Computational Biology Unit, University of Bergen, Bergen, Norway.
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Zwonitzer KD, Tressel LG, Wu Z, Kan S, Broz AK, Mower JP, Ruhlman TA, Jansen RK, Sloan DB, Havird JC. Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA. Proc Natl Acad Sci U S A 2024; 121:e2317240121. [PMID: 38427600 DOI: 10.1073/pnas.2317240121] [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: 10/12/2023] [Accepted: 01/22/2024] [Indexed: 03/03/2024] Open
Abstract
Nuclear and organellar genomes can evolve at vastly different rates despite occupying the same cell. In most bilaterian animals, mitochondrial DNA (mtDNA) evolves faster than nuclear DNA, whereas this trend is generally reversed in plants. However, in some exceptional angiosperm clades, mtDNA substitution rates have increased up to 5,000-fold compared with closely related lineages. The mechanisms responsible for this acceleration are generally unknown. Because plants rely on homologous recombination to repair mtDNA damage, we hypothesized that mtDNA copy numbers may predict evolutionary rates, as lower copy numbers may provide fewer templates for such repair mechanisms. In support of this hypothesis, we found that copy number explains 47% of the variation in synonymous substitution rates of mtDNA across 60 diverse seed plant species representing ~300 million years of evolution. Copy number was also negatively correlated with mitogenome size, which may be a cause or consequence of mutation rate variation. Both relationships were unique to mtDNA and not observed in plastid DNA. These results suggest that homologous recombinational repair plays a role in driving mtDNA substitution rates in plants and may explain variation in mtDNA evolution more broadly across eukaryotes. Our findings also contribute to broader questions about the relationships between mutation rates, genome size, selection efficiency, and the drift-barrier hypothesis.
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Affiliation(s)
- Kendra D Zwonitzer
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Lydia G Tressel
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Marine College, Shandong University, Weihai 264209, China
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Tracey A Ruhlman
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Robert K Jansen
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
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Pain C, Tynan C, Botchway SW, Kriechbaumer V. Variable-Angle Epifluorescence Microscopy for Single-Particle Tracking in the Plant ER. Methods Mol Biol 2024; 2772:273-283. [PMID: 38411821 DOI: 10.1007/978-1-0716-3710-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Single-particle tracking (SPT) of biomolecules in the plant endoplasmic reticulum has the potential to inform on the formation of protein-protein complexes, metabolons, and the transport of molecules through both the ER membrane and lumen. Plant cells are particularly challenging for observing and tracking single molecules due to their unique structure, size, and considerable autofluorescence. However, by using variable-angle or highly inclined epifluorescence microscopy (VAEM) and transient expression in tobacco, it is possible to observe single-particle dynamics in the ER. Selecting the appropriate fluorophore, and ensuring the correct fluorophore density in the ER, is essential for successful SPT. By using tuneable fluorophores, which can be photoconverted and photoactivated, it is possible to vary the density of visible fluorophores in the ER dynamically. Here we describe methods to prepare plant samples for VAEM and two methods for determining and analyzing single-particle tracks from VAEM time series.
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Affiliation(s)
- Charlotte Pain
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Christopher Tynan
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
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Broz AK, Sloan DB, Johnston IG. Stochastic organelle genome segregation through Arabidopsis development and reproduction. THE NEW PHYTOLOGIST 2024; 241:896-910. [PMID: 37925790 PMCID: PMC10841260 DOI: 10.1111/nph.19288] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 09/07/2023] [Indexed: 11/07/2023]
Abstract
Organelle DNA (oDNA) in mitochondria and plastids is vital for plant (and eukaryotic) life. Selection against damaged oDNA is mediated in part by segregation - sorting different oDNA types into different cells in the germline. Plants segregate oDNA very rapidly, with oDNA recombination protein MSH1 a key driver of this segregation, but we have limited knowledge of the dynamics of this segregation within plants and between generations. Here, we reveal how oDNA evolves through Arabidopsis thaliana development and reproduction. We combine stochastic modelling, Bayesian inference, and model selection with new and existing tissue-specific oDNA measurements from heteroplasmic Arabidopsis plant lines through development and between generations. Segregation proceeds gradually but continually during plant development, with a more rapid increase between inflorescence formation and the next generation. When MSH1 is compromised, the majority of observed segregation can be achieved through partitioning at cell divisions. When MSH1 is functional, mtDNA segregation is far more rapid; we show that increased oDNA gene conversion is a plausible mechanism quantitatively explaining this acceleration. These findings reveal the quantitative, time-dependent details of oDNA segregation in Arabidopsis. We also discuss the support for different models of the plant germline provided by these observations.
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Affiliation(s)
- Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, 5007, Norway
- Computational Biology Unit, University of Bergen, Bergen, 5007, Norway
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Shao X, Meng C, Song W, Zhang T, Chen Q. Subcellular visualization: Organelle-specific targeted drug delivery and discovery. Adv Drug Deliv Rev 2023; 199:114977. [PMID: 37391014 DOI: 10.1016/j.addr.2023.114977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023]
Abstract
Organelles perform critical biological functions due to their distinct molecular composition and internal environment. Disorders in organelles or their interacting networks have been linked to the incidence of numerous diseases, and the research of pharmacological actions at the organelle level has sparked pharmacists' interest. Currently, cell imaging has evolved into a critical tool for drug delivery, drug discovery, and pharmacological research. The introduction of advanced imaging techniques in recent years has provided researchers with richer biological information for viewing and studying the ultrastructure of organelles, protein interactions, and gene transcription activities, leading to the design and delivery of precision-targeted drugs. Therefore, this reviews the research on organelles-targeted drugs based upon imaging technologies and development of fluorescent molecules for medicinal purposes. We also give a thorough analysis of a number of subcellular-level elements of drug development, including subcellular research instruments and methods, organelle biological event investigation, subcellular target and drug identification, and design of subcellular delivery systems. This review will make it possible to promote drug research from the individual/cellular level to the subcellular level, as well as give a new focus based on newly found organelle activities.
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Affiliation(s)
- Xintian Shao
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China
| | - Caicai Meng
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China
| | - Wenjing Song
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China; School of Pharmaceutical Sciences & Institute of Materia Medica, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Key Laboratory for Biotechnology Drugs of National Health Commission, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China
| | - Tao Zhang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong Province 250014, PR China
| | - Qixin Chen
- School of Pharmaceutical Sciences & Institute of Materia Medica, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Key Laboratory for Biotechnology Drugs of National Health Commission, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China.
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Rodriguez M, Martinez-Hottovy A, Christensen AC. Social networks in the single cell. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5355-5357. [PMID: 36095660 PMCID: PMC9467649 DOI: 10.1093/jxb/erac284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
This article comments on: Chustecki JM, Etherington RD, Gibbs DJ, Johnston IG. 2022. Altered collective mitochondrial dynamics in the Arabidopsis msh1 mutant compromising organelle DNA maintenance. Journal of Experimental Botany 73, 5428-5439. Plant mitochondrial DNA (mtDNA) can become damaged in many ways. A major repair mechanism is homologous recombination, which requires an undamaged DNA template. Presumably, this template comes from a different mitochondrion in the same cell. Plant mitochondria undergo fission and fusion to form transient networks which could allow the exchange of genetic information. To test this hypothesis, Chustecki et al. (2022) used msh1 mutants with defective DNA repair, and showed that mitochondrial interactions increased, revealing a link between the physical and genetic behavior of mitochondria.
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Affiliation(s)
- Moira Rodriguez
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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Giannakis K, Chustecki JM, Johnston IG. Exchange on dynamic encounter networks allows plant mitochondria to collect complete sets of mitochondrial DNA products despite their incomplete genomes. QUANTITATIVE PLANT BIOLOGY 2022; 3:e18. [PMID: 37077986 PMCID: PMC10095876 DOI: 10.1017/qpb.2022.15] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 05/03/2023]
Abstract
Mitochondria in plant cells usually contain less than a full copy of the mitochondrial DNA (mtDNA) genome. Here, we asked whether mitochondrial dynamics may allow individual mitochondria to 'collect' a full set of mtDNA-encoded gene products over time, by facilitating exchange between individuals akin to trade on a social network. We characterise the collective dynamics of mitochondria in Arabidopsis hypocotyl cells using a recent approach combining single-cell time-lapse microscopy, video analysis and network science. We use a quantitative model to predict the capacity for sharing genetic information and gene products through the networks of encounters between mitochondria. We find that biological encounter networks support the emergence of gene product sets over time more readily than a range of other possible network structures. Using results from combinatorics, we identify the network statistics that determine this propensity, and discuss how features of mitochondrial dynamics observed in biology facilitate the collection of mtDNA-encoded gene products.
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Affiliation(s)
| | | | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
- Author for correspondence: I. G. Johnston, E-mail:
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