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Taylor A, Prasad A, Mueller RL. Amphibian Segmentation Clock Models Suggest How Large Genome and Cell Sizes Slow Developmental Rate. Integr Org Biol 2024; 6:obae021. [PMID: 39006893 PMCID: PMC11245677 DOI: 10.1093/iob/obae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/20/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
Evolutionary increases in genome size, cell volume, and nuclear volume have been observed across the tree of life, with positive correlations documented between all three traits. Developmental tempo slows as genomes, nuclei, and cells increase in size, yet the driving mechanisms are poorly understood. To bridge this gap, we use a mathematical model of the somitogenesis clock to link slowed developmental tempo with changes in intra-cellular gene expression kinetics induced by increasing genome size and nuclear volume. We adapt a well-known somitogenesis clock model to two model amphibian species that vary 10-fold in genome size: Xenopus laevis (3.1 Gb) and Ambystoma mexicanum (32 Gb). Based on simulations and backed by analytical derivations, we identify parameter changes originating from increased genome and nuclear size that slow gene expression kinetics. We simulate biological scenarios for which these parameter changes mathematically recapitulate slowed gene expression in A. mexicanum relative to X. laevis, and we consider scenarios for which additional alterations in gene product stability and chromatin packing are necessary. Results suggest that slowed degradation rates as well as changes induced by increasing nuclear volume and intron length, which remain relatively unexplored, are significant drivers of slowed developmental tempo.
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Affiliation(s)
- A Taylor
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - A Prasad
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - R Lockridge Mueller
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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Garfinkel AM, Ilker E, Miyazawa H, Schmeisser K, Tennessen JM. Historic obstacles and emerging opportunities in the field of developmental metabolism - lessons from Heidelberg. Development 2024; 151:dev202937. [PMID: 38912552 PMCID: PMC11299503 DOI: 10.1242/dev.202937] [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] [Indexed: 06/25/2024]
Abstract
The field of developmental metabolism is experiencing a technological revolution that is opening entirely new fields of inquiry. Advances in metabolomics, small-molecule sensors, single-cell RNA sequencing and computational modeling present new opportunities for exploring cell-specific and tissue-specific metabolic networks, interorgan metabolic communication, and gene-by-metabolite interactions in time and space. Together, these advances not only present a means by which developmental biologists can tackle questions that have challenged the field for centuries, but also present young scientists with opportunities to define new areas of inquiry. These emerging frontiers of developmental metabolism were at the center of a highly interactive 2023 EMBO workshop 'Developmental metabolism: flows of energy, matter, and information'. Here, we summarize key discussions from this forum, emphasizing modern developmental biology's challenges and opportunities.
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Affiliation(s)
- Alexandra M. Garfinkel
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT 06510, USA
| | - Efe Ilker
- Max Planck Institute for the Physics of Complex Systems, Dresden 01187, Germany
| | - Hidenobu Miyazawa
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Kathrin Schmeisser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
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Diaz-Cuadros M. Mitochondrial metabolism and the continuing search for ultimate regulators of developmental rate. Curr Opin Genet Dev 2024; 86:102178. [PMID: 38461774 DOI: 10.1016/j.gde.2024.102178] [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: 11/30/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
The rate of embryonic development is a species-specific trait that depends on the properties of the intracellular environment, namely, the rate at which gene products flow through the central dogma of molecular biology. Although any given step in the production and degradation of gene products could theoretically be co-opted by evolution to modulate developmental speed, species are observed to accelerate or slow down all steps simultaneously. This suggests the rate of these molecular processes is jointly regulated by an upstream, ultimate factor. Mitochondrial metabolism was recently proposed to act as an ultimate regulator by controlling the pace of protein synthesis upstream of developmental tempo. Alternative candidates for ultimate regulators include species-specific gene expression levels of factors involved in the central dogma, as well as species-specific cell size. Overall, much work remains to be done before we can confidently identify the ultimate causes of species-specific developmental rates.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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Sidhu JS, Lynch JP. Cortical cell size regulates root metabolic cost. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1343-1357. [PMID: 38340035 DOI: 10.1111/tpj.16672] [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: 09/21/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
It has been hypothesized that vacuolar occupancy in mature root cortical parenchyma cells regulates root metabolic cost and thereby plant fitness under conditions of drought, suboptimal nutrient availability, and increased soil mechanical impedance. However, the mechanistic role of vacuoles in reducing root metabolic cost was unproven. Here we provide evidence to support this hypothesis. We first show that root cortical cell size is determined by both cortical cell diameter and cell length. Significant genotypic variation for both cortical cell diameter (~1.1- to 1.5-fold) and cortical cell length (~ 1.3- to 7-fold) was observed in maize and wheat. GWAS and QTL analyses indicate cortical cell diameter and length are heritable and under independent genetic control. We identify candidate genes for both phenes. Empirical results from isophenic lines contrasting for cortical cell diameter and length show that increased cell size, due to either diameter or length, is associated with reduced root respiration, nitrogen content, and phosphorus content. RootSlice, a functional-structural model of root anatomy, predicts that an increased vacuolar: cytoplasmic ratio per unit cortical volume causes reduced root respiration and nutrient content. Ultrastructural imaging of cortical parenchyma cells with varying cortical diameter and cortical cell length confirms the in silico predictions and shows that an increase in cell size is correlated with increased vacuolar volume and reduced cytoplasmic volume. Vacuolar occupancy and its relationship with cell size merits further investigation as a phene for improving crop adaptation to edaphic stress.
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Affiliation(s)
- Jagdeep Singh Sidhu
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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Pinto SC, Stojilković B, Zhang X, Sablowski R. Plant cell size: Links to cell cycle, differentiation and ploidy. CURRENT OPINION IN PLANT BIOLOGY 2024; 78:102527. [PMID: 38484440 DOI: 10.1016/j.pbi.2024.102527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/07/2024]
Abstract
Cell size affects many processes, including exchange of nutrients and external signals, cell division and tissue mechanics. Across eukaryotes, cells have evolved mechanisms that assess their own size to inform processes such as cell cycle progression or gene expression. Here, we review recent progress in understanding plant cell size regulation and its implications, relating these findings to work in other eukaryotes. Highlights include use of DNA contents as reference point to control the cell cycle in shoot meristems, a size-dependent cell fate decision during stomatal development and insights into the interconnection between ploidy, cell size and cell wall mechanics.
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Affiliation(s)
- Sara C Pinto
- Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | | | - Xinyu Zhang
- Cell and Developmental Biology, John Innes Centre, Norwich, UK
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Glazier DS, Gjoni V. Interactive effects of intrinsic and extrinsic factors on metabolic rate. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220489. [PMID: 38186280 PMCID: PMC10772614 DOI: 10.1098/rstb.2022.0489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/16/2023] [Indexed: 01/09/2024] Open
Abstract
Metabolism energizes all biological processes, and its tempo may importantly influence the ecological success and evolutionary fitness of organisms. Therefore, understanding the broad variation in metabolic rate that exists across the living world is a fundamental challenge in biology. To further the development of a more reliable and holistic picture of the causes of this variation, we review several examples of how various intrinsic (biological) and extrinsic (environmental) factors (including body size, cell size, activity level, temperature, predation and other diverse genetic, cellular, morphological, physiological, behavioural and ecological influences) can interactively affect metabolic rate in synergistic or antagonistic ways. Most of the interactive effects that have been documented involve body size, temperature or both, but future research may reveal additional 'hub factors'. Our review highlights the complex, intimate inter-relationships between physiology and ecology, knowledge of which can shed light on various problems in both disciplines, including variation in physiological adaptations, life histories, ecological niches and various organism-environment interactions in ecosystems. We also discuss theoretical and practical implications of interactive effects on metabolic rate and provide suggestions for future research, including holistic system analyses at various hierarchical levels of organization that focus on interactive proximate (functional) and ultimate (evolutionary) causal networks. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.
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Affiliation(s)
| | - Vojsava Gjoni
- Department of Biology, University of South Dakota, Vermillion, SD 57609, USA
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Wang Y, Tamori Y. Polyploid Cancer Cell Models in Drosophila. Genes (Basel) 2024; 15:96. [PMID: 38254985 PMCID: PMC10815460 DOI: 10.3390/genes15010096] [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: 11/06/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Cells with an abnormal number of chromosomes have been found in more than 90% of solid tumors, and among these, polyploidy accounts for about 40%. Polyploidized cells most often have duplicate centrosomes as well as genomes, and thus their mitosis tends to promote merotelic spindle attachments and chromosomal instability, which produces a variety of aneuploid daughter cells. Polyploid cells have been found highly resistant to various stress and anticancer therapies, such as radiation and mitogenic inhibitors. In other words, common cancer therapies kill proliferative diploid cells, which make up the majority of cancer tissues, while polyploid cells, which lurk in smaller numbers, may survive. The surviving polyploid cells, prompted by acute environmental changes, begin to mitose with chromosomal instability, leading to an explosion of genetic heterogeneity and a concomitant cell competition and adaptive evolution. The result is a recurrence of the cancer during which the tenacious cells that survived treatment express malignant traits. Although the presence of polyploid cells in cancer tissues has been observed for more than 150 years, the function and exact role of these cells in cancer progression has remained elusive. For this reason, there is currently no effective therapeutic treatment directed against polyploid cells. This is due in part to the lack of suitable experimental models, but recently several models have become available to study polyploid cells in vivo. We propose that the experimental models in Drosophila, for which genetic techniques are highly developed, could be very useful in deciphering mechanisms of polyploidy and its role in cancer progression.
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Affiliation(s)
| | - Yoichiro Tamori
- Department of Molecular Oncology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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Agarwala S, Dhabal S, Mitra K. Significance of quantitative analyses of the impact of heterogeneity in mitochondrial content and shape on cell differentiation. Open Biol 2024; 14:230279. [PMID: 38228170 PMCID: PMC10791538 DOI: 10.1098/rsob.230279] [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: 08/13/2023] [Accepted: 12/15/2023] [Indexed: 01/18/2024] Open
Abstract
Mitochondria, classically known as the powerhouse of cells, are unique double membrane-bound multifaceted organelles carrying a genome. Mitochondrial content varies between cell types and precisely doubles within cells during each proliferating cycle. Mitochondrial content also increases to a variable degree during cell differentiation triggered after exit from the proliferating cycle. The mitochondrial content is primarily maintained by the regulation of mitochondrial biogenesis, while damaged mitochondria are eliminated from the cells by mitophagy. In any cell with a given mitochondrial content, the steady-state mitochondrial number and shape are determined by a balance between mitochondrial fission and fusion processes. The increase in mitochondrial content and alteration in mitochondrial fission and fusion are causatively linked with the process of differentiation. Here, we critically review the quantitative aspects in the detection methods of mitochondrial content and shape. Thereafter, we quantitatively link these mitochondrial properties in differentiating cells and highlight the implications of such quantitative link on stem cell functionality. Finally, we discuss an example of cell size regulation predicted from quantitative analysis of mitochondrial shape and content. To highlight the significance of quantitative analyses of these mitochondrial properties, we propose three independent rationale based hypotheses and the relevant experimental designs to test them.
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Affiliation(s)
- Swati Agarwala
- Department of Biology, Ashoka University, Delhi (NCR), India
| | - Sukhamoy Dhabal
- Department of Biology, Ashoka University, Delhi (NCR), India
| | - Kasturi Mitra
- Department of Biology, Ashoka University, Delhi (NCR), India
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
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Agarwal P, Cadart C, Fort L, Gahan J, Greenspan L, Juan T, Kameneva P, Miao Y. Pathway to Independence: the future of developmental biology. Development 2023; 150:dev202360. [PMID: 37812057 DOI: 10.1242/dev.202360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
In 2022, Development launched its Pathway to Independence (PI) Programme, aimed at supporting postdocs as they transition to their first independent position. We selected eight talented researchers as the first cohort of PI Fellows. In this article, each of our Fellows provides their perspective on the future of their field. Together, they paint an exciting picture of the current state of and open questions in developmental biology.
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Affiliation(s)
- Priti Agarwal
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Clotilde Cadart
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Loic Fort
- Vanderbilt University School of Medicine, 465 21st Avenue South, U 3200 MRB III, Nashville, TN 37240-7935, USA
| | - James Gahan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Leah Greenspan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Thomas Juan
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - Polina Kameneva
- The Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Yuchuan Miao
- Department of Genetics, Harvard Medical School and Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
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