Intracellular diffusion in the cytoplasm increases with cell size in fission yeast
Posted on: 18 October 2024 , updated on: 21 October 2024
Preprint posted on 23 September 2024
Size matters: Larger yeast cells boost cytoplasmic diffusion
Selected by Leeba Ann Chacko, Sameer ThukralCategories: cell biology, genetics, microbiology
Background:
Cell size, though varying dramatically across different cell types, remains tightly regulated within a specific cell population. When this regulation breaks down, aberrant cell sizes are often associated with ageing, senescence, and various pathological conditions including cancer. However, the fundamental mechanisms by which cell size impacts cellular physiology represent a critical gap in our understanding.
The cytoplasm, far from being a simple cellular compartment, emerges as a key player in this size-dependent regulation. Acting as the matrix in which cell physiology occurs, it influences virtually all biochemical reactions through its effects on viscosity, macromolecular crowding, and phase separation. Previous studies in yeast have revealed that aberrantly sized cells exhibit various physiological defects, including decreased cytoplasmic density. Could the cytoplasm be the link between cell size and cell physiology?
One compelling hypothesis centres on the DNA-to-cytoplasm ratio. As cells grow larger without a corresponding increase in DNA content, they may lack sufficient gene copies or biosynthetic machinery to support their increased volume. This theory is supported by observations that cells with increased ploidy can achieve larger sizes without exhibiting typical size-related defects.
Despite these advances, numerous questions remain unanswered. How do changes in cell size precisely alter the biophysical properties of the cytoplasm? Which cellular components are responsible for fluctuations in cytoplasmic density? What are the molecular mechanisms that link DNA-to-cytoplasm ratio to cellular physiology? This preprint attempts to answer these questions.
Key Findings:
Nanoparticles Diffuse More in Larger Cells
By utilizing temperature-sensitive mutants (wee1-50 and cdc25-22) that significantly alter cell size, the authors demonstrated that 40 nm cytGEM nanoparticles—genetically encoded fluorescent particles designed to mimic large macromolecules—diffuse faster in larger cells and slower in smaller ones. Within each mutant strain, smaller cells exhibited reduced nanoparticle diffusion compared to their larger counterparts. Additionally, the authors employed the cdc2-asM17 strain, which can be specifically inhibited by the ATP analogue 1-NM-PP1 to arrest cells in the G2 phase and induce cell enlargement. Treatment with 1-NM-PP1 for 3 and 6 hours resulted in progressively larger cells compared to DMSO-treated controls, accompanied by increased nanoparticle diffusion. These findings reinforce the conclusion that nanoparticle diffusion and thereby possibly cytoplasmic density positively correlates with cell size.
The DNA-to-Cytoplasm Ratio is Crucial for Maintaining Nanoparticle Diffusion
To assess whether the DNA-to-cytoplasm ratio, rather than cell size alone, governs nanoparticle diffusion in the cytoplasm, the authors utilized the sid2-as and cdc11-119 mutants, which are defective in cytokinesis resulting in multinucleate cells. These mutants maintain the same DNA-to-cell length ratio as smaller, mononucleate cells. Specifically, sid2-as cells treated with the ATP analogue 1-NM-PP1 for 3 and 6 hours formed progressively larger cells with multiple nuclei. Despite the increase in cell size, the diffusion coefficients of nanoparticles in these multinucleate cells remained comparable to those in smaller, control cells. This finding indicates that maintaining the DNA-to-cytoplasm ratio is essential for regulating nanoparticle diffusion, independent of cell size.
Increased Diffusion in Larger Cells Can Be Attributed to Lower Protein Concentration
To investigate why nanoparticles diffuse more rapidly in larger cells, the authors measured protein concentrations using two probes: the Rps2-GFP marker for ribosomal proteins and FITC staining for overall protein levels. Both measurements indicated that larger cells had lower concentrations of ribosomal proteins and total proteins compared to medium-sized cells. Specifically, Rps2-GFP fluorescence was significantly reduced in cells larger than 18 µm, and FITC staining showed a modest decrease in overall protein concentration in these larger cells. These reductions in protein concentration likely decrease cytoplasmic crowding, thereby facilitating the faster diffusion of nanoparticles in larger cells.
Proteome Composition Changes with Cell Size
To investigate the molecular basis for altered nanoparticle diffusion in cells of different sizes, the authors performed SILAC-based mass spectrometry to compare the proteomes of small and large cells. They identified 3,353 proteins and found that in larger cells, proteins associated with the nucleus and ribosomes were underrepresented (sub-scaled), whereas proteins related to the endoplasmic reticulum, mitochondria, and vacuoles were overrepresented (super-scaled). Gene ontology analysis revealed that sub-scaled proteins are involved in nuclear functions and gene expression, while super-scaled proteins participate in metabolic pathways and are linked to membrane-bound organelles. Importantly, similar proteomic changes were observed in human cells, suggesting that size-dependent proteome remodelling is a conserved feature in eukaryotes. These findings demonstrate that cell size significantly influences the composition of the cytoplasmic proteome, thereby affecting the biophysical properties of the cytoplasm.
Conclusion:
Collectively, these results highlight the pivotal role of cell size in modulating the biophysical environment of the cytoplasm. Larger cells exhibit increased nanoparticle diffusion primarily due to reduced protein concentrations and specific proteomic adjustments that maintain the DNA-to-cytoplasm ratio. This study underscores the intricate relationship between cell size, protein composition, and intracellular dynamics, providing valuable insights into how cell size regulation can impact overall cellular physiology and function.
What we liked about this preprint:
Leeba: At this year’s Plant and Microbial Cytoskeleton Gordon Research Conference, I met Fred Chang and was captivated by his research on how modulating cytoplasmic properties can influence cellular dynamics within S. pombe. I was also intrigued by his work on how other fungi adjust their cytoplasmic characteristics to interact with multicellular organisms. Inspired by his insights, I was excited to discover this preprint, which shows how cell length can modulate cytoplasmic properties.
Sameer: I have been actively following Fred Chang and Jan Skotheim’s groups work. I appreciate their contributions to our understanding of long-standing fundamental questions in cell scaling through the application of novel cell biology approaches. Particularly, this work contributes to the growing body of literature suggesting that DNA-to-cell size ratio governs cytoplasmic density and thereby controls cytoplasmic diffusion (this study), nuclear size in yeast (Joël Lemière et. al) and across metazoans (Biswas et.al).
Questions for the authors:
1. Since ribosomal proteins subscales in larger fission yeast cells, can one engineer extra copies of ribosomal proteins to rescue the cytoplasmic dilution? Similarly, can overexpressing ectopic large proteins in the large cells rescue the phenotype? Conversely, would simply inhibiting protein translation lead to diluted cytoplasm in WT cells?
2. Why doesn’t the correlation between cell size and nanoparticle diffusion appear in wild-type cells, even though their cell length range is broader than that of wee1-50 mutants? Additionally, how do these results align with the observed decrease in cellular density as wild-type cells grow during the cell cycle (Odermatt et al)?
3. Have the authors confirmed that protein concentrations are similar between smaller mononucleate cells and larger multinucleate cells using Rps2-GFP or FITC probes? Alternatively, could the presence of multiple nuclei affect cytoplasmic viscosity and thereby influence diffusion measurements?
4. In Figure S2A, do DMSO-treated sid2-as cells have multiple nuclei while maintaining cell lengths comparable to wild-type cells? If not, is there a way to generate small multinucleate cells to determine if their diffusion coefficients are reduced similarly to wee1-50 mutants?
References:
- Pascal D Odermatt, Teemu P Miettinen, Joël Lemière, Joon Ho Kang, Emrah Bostan, Scott R Manalis, Kerwyn Casey Huang, Fred Chang (2021) Variations of intracellular density during the cell cycle arise from tip-growth regulation in fission yeast eLife 10:e64901
- Joël Lemière, Paula Real-Calderon, Liam J Holt, Thomas G Fai, Fred Chang (2022) Control of nuclear size by osmotic forces in Schizosaccharomyces pombe eLife 11:e76075
- Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes. Abin Biswas, Omar Muñoz, Kyoohyun Kim, Carsten Hoege, Benjamin M. Lorton, David Shechter, Jochen Guck, Vasily Zaburdaev, Simone Reber bioRxiv 2023.09.05.556409; doi: https://doi.org/10.1101/2023.09.05.556409
doi: https://doi.org/10.1242/prelights.38612
Read preprintSign up to customise the site to your preferences and to receive alerts
Register hereAlso in the cell biology category:
Leukocytes use endothelial membrane tunnels to extravasate the vasculature
Felipe Del Valle Batalla
Platelet-derived LPA16:0 inhibits adult neurogenesis and stress resilience in anxiety disorder
Harvey Roweth
Investigating Mechanically Activated Currents from Trigeminal Neurons of Non-Human Primates
Vanessa Ehlers
Also in the genetics category:
Intracellular diffusion in the cytoplasm increases with cell size in fission yeast
Leeba Ann Chacko, Sameer Thukral
HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos
Anchel De Jaime Soguero
Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA
Leeba Ann Chacko
Also in the microbiology category:
Green synthesized silver nanoparticles from Moringa: Potential for preventative treatment of SARS-CoV-2 contaminated water
Safieh Shah, Benjamin Dominik Maier
Intracellular diffusion in the cytoplasm increases with cell size in fission yeast
Leeba Ann Chacko, Sameer Thukral
The bat Influenza A virus subtype H18N11 induces nanoscale MHCII clustering upon host cell attachment
Mitchell Sarmie, Mohammed A. Jalloh
preListscell biology category:
in theNovember in preprints – the CellBio edition
This is the first community-driven preList! A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. Categories include: 1) cancer cell biology 2) cell cycle and division 3) cell migration and cytoskeleton 4) cell organelles and organisation 5) cell signalling and mechanosensing 6) genetics/gene expression
List by | Felipe Del Valle Batalla et al. |
BSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
List by | Reinier Prosee |
‘In preprints’ from Development 2022-2023
A list of the preprints featured in Development's 'In preprints' articles between 2022-2023
List by | Alex Eve, Katherine Brown |
preLights peer support – preprints of interest
This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.
List by | preLights peer support |
The Society for Developmental Biology 82nd Annual Meeting
This preList is made up of the preprints discussed during the Society for Developmental Biology 82nd Annual Meeting that took place in Chicago in July 2023.
List by | Joyce Yu, Katherine Brown |
CSHL 87th Symposium: Stem Cells
Preprints mentioned by speakers at the #CSHLsymp23
List by | Alex Eve |
Journal of Cell Science meeting ‘Imaging Cell Dynamics’
This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.
List by | Helen Zenner |
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
List by | Martin Estermann |
Alumni picks – preLights 5th Birthday
This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.
List by | Sergio Menchero et al. |
CellBio 2022 – An ASCB/EMBO Meeting
This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.
List by | Nadja Hümpfer et al. |
Fibroblasts
The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!
List by | Osvaldo Contreras |
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
List by | Alex Eve |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
List by | Ana Dorrego-Rivas |
Planar Cell Polarity – PCP
This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.
List by | Ana Dorrego-Rivas |
BioMalPar XVI: Biology and Pathology of the Malaria Parasite
[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria
List by | Dey Lab, Samantha Seah |
1
Cell Polarity
Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.
List by | Yamini Ravichandran |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
List by | Maiko Kitaoka et al. |
3D Gastruloids
A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.
List by | Paul Gerald L. Sanchez and Stefano Vianello |
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
List by | Hiral Shah |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
List by | Madhuja Samaddar et al. |
EMBL Seeing is Believing – Imaging the Molecular Processes of Life
Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019
List by | Dey Lab |
Autophagy
Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.
List by | Sandra Malmgren Hill |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
List by | Rob Hynds |
Cellular metabolism
A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.
List by | Pablo Ranea Robles |
BSCB/BSDB Annual Meeting 2019
Preprints presented at the BSCB/BSDB Annual Meeting 2019
List by | Dey Lab |
MitoList
This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.
List by | Sandra Franco Iborra |
Biophysical Society Annual Meeting 2019
Few of the preprints that were discussed in the recent BPS annual meeting at Baltimore, USA
List by | Joseph Jose Thottacherry |
ASCB/EMBO Annual Meeting 2018
This list relates to preprints that were discussed at the recent ASCB conference.
List by | Dey Lab, Amanda Haage |
Also in the genetics category:
BSDB/GenSoc Spring Meeting 2024
A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.
List by | Joyce Yu, Katherine Brown |
BSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
List by | Reinier Prosee |
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
List by | Martin Estermann |
Alumni picks – preLights 5th Birthday
This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.
List by | Sergio Menchero et al. |
Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University
This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.
List by | Nándor Lipták |
20th “Genetics Workshops in Hungary”, Szeged (25th, September)
In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf
List by | Nándor Lipták |
2nd Conference of the Visegrád Group Society for Developmental Biology
Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)
List by | Nándor Lipták |
EMBL Conference: From functional genomics to systems biology
Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020
List by | Jesus Victorino |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
List by | Maiko Kitaoka et al. |
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
List by | Hiral Shah |
Autophagy
Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.
List by | Sandra Malmgren Hill |
Zebrafish immunology
A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.
List by | Shikha Nayar |
Also in the microbiology category:
BioMalPar XVI: Biology and Pathology of the Malaria Parasite
[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria
List by | Dey Lab, Samantha Seah |
1
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
List by | Hiral Shah |
EMBL Seeing is Believing – Imaging the Molecular Processes of Life
Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019
List by | Dey Lab |
Antimicrobials: Discovery, clinical use, and development of resistance
Preprints that describe the discovery of new antimicrobials and any improvements made regarding their clinical use. Includes preprints that detail the factors affecting antimicrobial selection and the development of antimicrobial resistance.
List by | Zhang-He Goh |