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Chen H, Sosa A, Chen F. Growth and Cell Size of Microalga Auxenochlorella protothecoides AS-1 under Different Trophic Modes. Microorganisms 2024; 12:835. [PMID: 38674779 PMCID: PMC11052296 DOI: 10.3390/microorganisms12040835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Certain microalgal species can grow with different trophic strategies depending on the availability of nutrient resources. They can use the energy from light or an organic substrate, or both, and can therefore be called autotrophs, heterotrophs, or mixotrophs. We recently isolated a microalgal strain from the microplastic biofilm, which was identified as Auxenochlorella protothecoides, AS-1. Strain AS-1 grew rapidly in bacterial culture media and exhibited different growth rates and cell sizes under different trophic conditions. We compared the growth performance of AS-1 under the three different trophic modes. AS-1 reached a high biomass (>4 g/L) in 6 days under mixotrophic growth conditions with a few organic carbons as a substrate. In contrast, poor autotrophic growth was observed for AS-1. Different cell sizes, including daughter and mother cells, were observed under the different growth modes. We applied a Coulter Counter to measure the size distribution patterns of AS-1 under different trophic modes. We showed that the cell size distribution of AS-1 was affected by different growth modes. Compared to the auto-, hetero- and mixotrophic modes, AS-1 achieved higher biomass productivity by increasing cell number and cell size in the presence of organic substrate. The mechanisms and advantages of having more mother cells with organic substrates are still unclear and warrant further investigations. The work here provides the growth information of a newly isolated A. protothecoides AS-1 which will be beneficial to future downstream applications.
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Affiliation(s)
- Haoyu Chen
- Institute of Marine & Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21613, USA; (H.C.); (A.S.)
| | - Ana Sosa
- Institute of Marine & Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21613, USA; (H.C.); (A.S.)
- Maryland Sea Grant College, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA
| | - Feng Chen
- Institute of Marine & Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21613, USA; (H.C.); (A.S.)
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2
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Neyret M, Le Provost G, Boesing AL, Schneider FD, Baulechner D, Bergmann J, de Vries FT, Fiore-Donno AM, Geisen S, Goldmann K, Merges A, Saifutdinov RA, Simons NK, Tobias JA, Zaitsev AS, Gossner MM, Jung K, Kandeler E, Krauss J, Penone C, Schloter M, Schulz S, Staab M, Wolters V, Apostolakis A, Birkhofer K, Boch S, Boeddinghaus RS, Bolliger R, Bonkowski M, Buscot F, Dumack K, Fischer M, Gan HY, Heinze J, Hölzel N, John K, Klaus VH, Kleinebecker T, Marhan S, Müller J, Renner SC, Rillig MC, Schenk NV, Schöning I, Schrumpf M, Seibold S, Socher SA, Solly EF, Teuscher M, van Kleunen M, Wubet T, Manning P. A slow-fast trait continuum at the whole community level in relation to land-use intensification. Nat Commun 2024; 15:1251. [PMID: 38341437 PMCID: PMC10858939 DOI: 10.1038/s41467-024-45113-5] [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: 07/17/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a 'slow-fast' axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that 'slow' and 'fast' strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.
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Affiliation(s)
- Margot Neyret
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Laboratoire d'Écologie Alpine, Université Grenoble Alpes - CNRS - Université Savoie Mont Blanc, Grenoble, France.
| | | | | | - Florian D Schneider
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
- ISOE - Institute for social-ecological research, Frankfurt am Main, Germany
| | - Dennis Baulechner
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
| | - Joana Bergmann
- Leibniz Center for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Stefan Geisen
- Laboratory of Nematology, Wageningen University and Research, Wageningen, The Netherlands
| | - Kezia Goldmann
- Helmholtz Centre for Environmental Research (UFZ), Soil Ecology Department, Halle/Saale, Germany
| | - Anna Merges
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
| | - Ruslan A Saifutdinov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Nadja K Simons
- Ecological Networks, Technical University Darmstadt, Darmstadt, Germany
- Applied Biodiversity Sciences, University of Würzburg, Würzburg, Germany
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Andrey S Zaitsev
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- Senckenberg Museum for Natural History Görlitz, Görlitz, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
| | - Kirsten Jung
- Institut of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Ellen Kandeler
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Jochen Krauss
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Caterina Penone
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Michael Schloter
- Helmholtz Zentrum Muenchen, Research Unit for Comparative Microbiome Analysis, Oberschleissheim, Germany
- Chair of Environmental Microbiology, Technical University of Munich, Freising, Germany
| | - Stefanie Schulz
- Helmholtz Zentrum Muenchen, Research Unit for Comparative Microbiome Analysis, Oberschleissheim, Germany
| | - Michael Staab
- Ecological Networks, Technical University Darmstadt, Darmstadt, Germany
| | - Volkmar Wolters
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
| | - Antonios Apostolakis
- Department of Biogeochemical Processes, Max-Planck-Institute for Biogeochemistry, Jena, Germany
- Department of Crop Sciences, University of Göttingen, Göttingen, Germany
| | - Klaus Birkhofer
- Department of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Steffen Boch
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Runa S Boeddinghaus
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
- Department Plant Production and Production Related Environmental Protection, Center for Agricultural Technology Augustenberg (LTZ), Karlsruhe, Germany
| | - Ralph Bolliger
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Köln, Germany
| | - François Buscot
- Helmholtz Centre for Environmental Research (UFZ), Soil Ecology Department, Halle/Saale, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle - Jena-, Leipzig, Germany
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Köln, Germany
| | - Markus Fischer
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Huei Ying Gan
- Senckenberg Centre for Human Evolution and Palaeoenvironments Tübingen (SHEP), Tübingen, Germany
| | - Johannes Heinze
- Department of Biodiversity, Heinz Sielmann Foundation, Wustermark, Germany
| | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Katharina John
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
| | - Valentin H Klaus
- Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
- Forage Production and Grassland Systems, Agroscope, Zürich, Switzerland
| | - Till Kleinebecker
- Institute for Landscape Ecology and Resources Management (ILR), Research Centre for BioSystems, Land Use and Nutrition (iFZ), Justus Liebig University Giessen, Giessen, Germany
- Centre for International Development and Environmental Research (ZEU), Justus Liebig University Giessen, Giessen, Germany
| | - Sven Marhan
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Jörg Müller
- Department of Nature Conservation, Heinz Sielmann Foundation, Wustermark, Germany
| | - Swen C Renner
- Ornithology, Natural History Museum Vienna, Vienna, Autria, Germany
| | | | - Noëlle V Schenk
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Ingo Schöning
- Department of Biogeochemical Processes, Max-Planck-Institute for Biogeochemistry, Jena, Germany
| | - Marion Schrumpf
- Department of Biogeochemical Processes, Max-Planck-Institute for Biogeochemistry, Jena, Germany
| | - Sebastian Seibold
- Technical University of Munich, TUM School of Life Sciences, Freising, Germany
- TUD Dresden University of Technology, Forest Zoology, Tharandt, Germany
| | - Stephanie A Socher
- Paris Lodron University Salzburg, Department Environment and Biodiversity, Salzburg, Austria
| | - Emily F Solly
- Helmholtz Centre for Environmental Research (UFZ), Computation Hydrosystems Department, Leipzig, Germany
| | - Miriam Teuscher
- University of Göttingen, Centre of Biodiversity and Sustainable Land Use, Göttingen, Germany
| | - Mark van Kleunen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle - Jena-, Leipzig, Germany
- Helmholtz Centre for Environmental Research (UFZ), Community Ecology Department, Halle/Saale, Germany
| | - Peter Manning
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
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3
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Li S, Qi B, Peng X, Wang W, Wang W, Liu P, Liu B, Peng Z, Wang Q, Li Y. Genome size and GC content of myxomycetes. Eur J Protistol 2023; 90:125991. [PMID: 37331249 DOI: 10.1016/j.ejop.2023.125991] [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: 01/04/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/20/2023]
Abstract
More than 1272 myxomycetes species have been described, accounting for more than half of all Amoebozoa species. However, the genome size of only three myxomycetes species has been reported. Therefore, we used flow cytometry to present an extensive survey and a phylogeny-based analysis of genome size and GC content evolution in 144 myxomycetes species. The genome size of myxomycetes ranged from 18.7 Mb to 470.3 Mb, and the GC content ranged from 38.7% to 70.1%. Bright-spored clade showed larger genome sizes and more intra-order genome size variations than the dark-spored clade. GC content and genome size were positively correlated in both bright-spored and dark-spored clades, and spore size was positively correlated with genome size and GC content in the bright-spored clade. We provided the first genome size data set in Myxomycetes, and our results will provide helpful information for future Myxomycetes studies, such as genome sequencing.
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Affiliation(s)
- Shu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Bao Qi
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Xueyan Peng
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Wei Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Wan Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Pu Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun, China.
| | - Qi Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
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4
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von der Dunk SHA, Hogeweg P, Snel B. Obligate endosymbiosis enables genome expansion during eukaryogenesis. Commun Biol 2023; 6:777. [PMID: 37491455 PMCID: PMC10368719 DOI: 10.1038/s42003-023-05153-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/18/2023] [Indexed: 07/27/2023] Open
Abstract
The endosymbiosis of an alpha-proteobacterium that gave rise to mitochondria was one of the key events in eukaryogenesis. One striking outcome of eukaryogenesis was a much more complex cell with a large genome. Despite the existence of many alternative hypotheses for this and other patterns potentially related to endosymbiosis, a constructive evolutionary model in which these hypotheses can be studied is still lacking. Here, we present a theoretical approach in which we focus on the consequences rather than the causes of mitochondrial endosymbiosis. Using a constructive evolutionary model of cell-cycle regulation, we find that genome expansion and genome size asymmetry arise from emergent host-symbiont cell-cycle coordination. We also find that holobionts with large host and small symbiont genomes perform best on long timescales and mimic the outcome of eukaryogenesis. By designing and studying a constructive evolutionary model of obligate endosymbiosis, we uncovered some of the forces that may drive the patterns observed in nature. Our results provide a theoretical foundation for patterns related to mitochondrial endosymbiosis, such as genome size asymmetry, and reveal evolutionary outcomes that have not been considered so far, such as cell-cycle coordination without direct communication.
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Affiliation(s)
- Samuel H A von der Dunk
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.
| | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
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5
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Aida H, Hashizume T, Ashino K, Ying BW. Machine learning-assisted discovery of growth decision elements by relating bacterial population dynamics to environmental diversity. eLife 2022; 11:76846. [PMID: 36017903 PMCID: PMC9417415 DOI: 10.7554/elife.76846] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 08/15/2022] [Indexed: 12/30/2022] Open
Abstract
Microorganisms growing in their habitat constitute a complex system. How the individual constituents of the environment contribute to microbial growth remains largely unknown. The present study focused on the contribution of environmental constituents to population dynamics via a high-throughput assay and data-driven analysis of a wild-type Escherichia coli strain. A large dataset constituting a total of 12,828 bacterial growth curves with 966 medium combinations, which were composed of 44 pure chemical compounds, was acquired. Machine learning analysis of the big data relating the growth parameters to the medium combinations revealed that the decision-making components for bacterial growth were distinct among various growth phases, e.g., glucose, sulfate, and serine for maximum growth, growth rate, and growth delay, respectively. Further analyses and simulations indicated that branched-chain amino acids functioned as global coordinators for population dynamics, as well as a survival strategy of risk diversification to prevent the bacterial population from undergoing extinction.
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Affiliation(s)
- Honoka Aida
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Takamasa Hashizume
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kazuha Ashino
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Bei-Wen Ying
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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6
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Hitomi K, Weng J, Ying BW. Contribution of the genomic and nutritional differentiation to the spatial distribution of bacterial colonies. Front Microbiol 2022; 13:948657. [PMID: 36081803 PMCID: PMC9448356 DOI: 10.3389/fmicb.2022.948657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Colony growth is a common phenomenon of structured populations dispersed in nature; nevertheless, studies on the spatial distribution of colonies are largely insufficient. Here, we performed a systematic survey to address the questions of whether and how the spatial distribution of colonies was influenced by the genome and environment. Six Escherichia coli strains carrying either the wild-type or reduced genomes and eight media of varied nutritional richness were used to evaluate the genomic and environmental impacts, respectively. The genome size and nutritional variation contributed to the mean size and total area but not the variation and shape of size distribution of the colonies formed within the identical space and of equivalent spatial density. The spatial analysis by means of the Voronoi diagram found that the Voronoi correlation remained nearly constant in common, in comparison to the Voronoi response decreasing in correlation to genome reduction and nutritional enrichment. Growth analysis at the single colony level revealed positive correlations of the relative growth rate to both the maximal colony size and the Voronoi area, regardless of the genomic and nutritional variety. This result indicated fast growth for the large space assigned and supported homeostasis in the Voronoi correlation. Taken together, the spatial distribution of colonies might benefit efficient clonal growth. Although the mechanisms remain unclear, the findings provide quantitative insights into the genomic and environmental contributions to the growth and distribution of spatially or geographically isolated populations.
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7
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Kornaliková M, Hampl V, Treitli SC. Investigation of the Genome Sizes and Ploidy Within the Genus
Monocercomonoides. J Eukaryot Microbiol 2022; 69:e12925. [DOI: 10.1111/jeu.12925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martina Kornaliková
- Department of Parasitology, Faculty of Science Charles University, BIOCEV Vestec Czech Republic
| | - Vladimir Hampl
- Department of Parasitology, Faculty of Science Charles University, BIOCEV Vestec Czech Republic
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Zou S, Fu R, Deng H, Zhang Q, Gentekaki E, Gong J. Coupling between Ribotypic and Phenotypic Traits of Protists across Life Cycle Stages and Temperatures. Microbiol Spectr 2021; 9:e0173821. [PMID: 34817220 PMCID: PMC8612162 DOI: 10.1128/spectrum.01738-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/16/2021] [Indexed: 01/04/2023] Open
Abstract
Relationships between ribotypic and phenotypic traits of protists across life cycle stages remain largely unknown. Herein, we used single cells of two soil and two marine ciliate species to examine phenotypic and ribotypic traits and their relationships across lag, log, plateau, cystic stages and temperatures. We found that Colpoda inflata and Colpoda steinii demonstrated allometric relationships between 18S ribosomal DNA (rDNA) copy number per cell (CNPC), cell volume (CV), and macronuclear volume across all life cycle stages. Integrating previously reported data of Euplotes vannus and Strombidium sulcatum indicated taxon-dependent rDNA CNPC-CV functions. Ciliate and prokaryote data analysis revealed that the rRNA CNPC followed a unified power-law function only if the rRNA-deficient resting cysts were not considered. Hence, a theoretical framework was proposed to estimate the relative quantity of resting cysts in the protistan populations with total cellular rDNA and rRNA copy numbers. Using rDNA CNPC was a better predictor of growth rate at a given temperature than rRNA CNPC and CV, suggesting replication of redundant rDNA operons as a key factor that slows cell division. Single-cell high-throughput sequencing and analysis after correcting sequencing errors revealed multiple rDNA and rRNA variants per cell. Both encystment and temperature affected the number of rDNA and rRNA variants in several cases. The divergence of rDNA and rRNA sequence in a single cell ranged from 1% to 10% depending on species. These findings have important implications for inferring cell-based biological traits (e.g., species richness, abundance and biomass, activity, and community structure) of protists using molecular approaches. IMPORTANCE Based on phenotypic traits, traditional surveys usually characterize organismal richness, abundance, biomass, and growth potential to describe diversity, organization, and function of protistan populations and communities. The rRNA gene (rDNA) and its transcripts have been widely used as molecular markers in ecological studies of protists. Nevertheless, the manner in which these molecules relate to cellular (organismal) and physiological traits remains poorly understood, which could lead to misinterpretations of protistan diversity and ecology. The current research highlights the dynamic nature of cellular rDNA and rRNA contents, which tightly couple with multiple phenotypic traits in ciliated protists. We demonstrate that quantity of resting cysts and maximum growth rate of a population can be theoretically estimated using ribotypic trait-based models. The intraindividual sequence polymorphisms of rDNA and rRNA can be influenced by encystment and temperature, which should be considered when interpreting species-level diversity and community structure of microbial eukaryotes.
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Affiliation(s)
- Songbao Zou
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Huzhou, China
- Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Rao Fu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Huiwen Deng
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | - Jun Gong
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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Jong LW, Fujiwara T, Hirooka S, Miyagishima SY. Cell size for commitment to cell division and number of successive cell divisions in cyanidialean red algae. PROTOPLASMA 2021; 258:1103-1118. [PMID: 33675395 DOI: 10.1007/s00709-021-01628-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Several eukaryotic cell lineages proliferate by multiple fission cell cycles, during which cells grow to manyfold of their original size, then undergo several rounds of cell division without intervening growth. A previous study on volvocine green algae, including both unicellular and multicellular (colonial) species, showed a correlation between the minimum number of successive cell divisions without intervening cellular growth, and the threshold cell size for commitment to the first round of successive cell divisions: two times the average newly born daughter cell volume for unicellular Chlamydomonas reinhardtii, four times for four-celled Tetrabaena socialis, in which each cell in the colony produces a daughter colony by two successive cell divisions, and eight times for the eight-celled Gonium pectorale, in which each cell produces a daughter colony by three successive cell divisions. To assess whether this phenomenon is also applicable to other lineages, we have characterized cyanidialean red algae, namely, Cyanidioschyzon merolae, which proliferates by binary fission, as well as Cyanidium caldarium and Galdieria sulphuraria, which form up to four and 32 daughter cells (autospores), respectively, in a mother cell before hatching out. The result shows that there is also a correlation between the number of successive cell divisions and the threshold cell size for cell division or the first round of the successive cell divisions. In both C. merolae and C. caldarium, the cell size checkpoint for cell division(s) exists in the G1-phase, as previously shown in volvocine green algae. When C. merolae cells were arrested in the G1-phase and abnormally enlarged by conditional depletion of CDKA, the cells underwent two or more successive cell divisions without intervening cellular growth after recovery of CDKA, similarly to C. caldarium and G. sulphuraria. These results suggest that the threshold size for cell division is a major factor in determining the number of successive cell divisions and that evolutionary changes in the mechanism of cell size monitoring resulted in a variation of multiple fission cell cycle in eukaryotic algae.
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Affiliation(s)
- Lin Wei Jong
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan.
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan.
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10
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Glazier DS. Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem. BIOLOGY 2021; 10:270. [PMID: 33810583 PMCID: PMC8067107 DOI: 10.3390/biology10040270] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.
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Predicting the decision making chemicals used for bacterial growth. Sci Rep 2019; 9:7251. [PMID: 31076576 PMCID: PMC6510730 DOI: 10.1038/s41598-019-43587-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/24/2019] [Indexed: 01/01/2023] Open
Abstract
Predicting the contribution of media components to bacterial growth was first initiated by introducing machine learning to high-throughput growth assays. A total of 1336 temporal growth records corresponding to 225 different media, which were composed of 13 chemical components, were generated. The growth rate and saturated density of each growth curve were automatically calculated with the newly developed data processing program. To identify the decision making factors related to growth among the 13 chemicals, big datasets linking the growth parameters to the chemical combinations were subjected to decision tree learning. The results showed that the only carbon source, glucose, determined bacterial growth, but it was not the first priority. Instead, the top decision making chemicals in relation to the growth rate and saturated density were ammonium and ferric ions, respectively. Three chemical components (NH4+, Mg2+ and glucose) commonly appeared in the decision trees of the growth rate and saturated density, but they exhibited different mechanisms. The concentration ranges for fast growth and high density were overlapped for glucose but distinguished for NH4+ and Mg2+. The results suggested that these chemicals were crucial in determining the growth speed and growth maximum in either a universal use or a trade-off manner. This differentiation might reflect the diversity in the resource allocation mechanisms for growth priority depending on the environmental restrictions. This study provides a representative example for clarifying the contribution of the environment to population dynamics through an innovative viewpoint of employing modern data science within traditional microbiology to obtain novel findings.
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Umen JG. Sizing up the cell cycle: systems and quantitative approaches in Chlamydomonas. CURRENT OPINION IN PLANT BIOLOGY 2018; 46:96-103. [PMID: 30212737 PMCID: PMC6269190 DOI: 10.1016/j.pbi.2018.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/14/2018] [Accepted: 08/16/2018] [Indexed: 05/06/2023]
Abstract
The unicellular green alga Chlamydomonas provides a simplified model for defining core cell cycle functions conserved in the green lineage and for understanding multiple fission, a common cell cycle variation found in many algae. Systems-level approaches including a recent groundbreaking screen for conditional lethal cell cycle mutants and genome-wide transcriptome analyses are revealing the complex relationships among cell cycle regulators and helping define roles for CDKA/CDK1 and CDKB, the latter of which is unique to the green lineage and plays a central role in mitotic regulation. Genetic screens and quantitative single-cell analyses have provided insight into cell-size control during multiple fission including the identification of a candidate `sizer' protein. Quantitative single-cell tracking and modeling are promising approaches for gaining additional insight into regulation of cellular and subcellular scaling during the Chlamydomonas cell cycle.
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Affiliation(s)
- James G Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA.
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Cavalier-Smith T, Chao EE, Lewis R. Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria. PROTOPLASMA 2018; 255:1517-1574. [PMID: 29666938 PMCID: PMC6133090 DOI: 10.1007/s00709-018-1241-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/12/2018] [Indexed: 05/18/2023]
Abstract
Infrakingdom Rhizaria is one of four major subgroups with distinct cell body plans that comprise eukaryotic kingdom Chromista. Unlike other chromists, Rhizaria are mostly heterotrophic flagellates, amoebae or amoeboflagellates, commonly with reticulose (net-like) or filose (thread-like) feeding pseudopodia; uniquely for eukaryotes, cilia have proximal ciliary transition-zone hub-lattices. They comprise predominantly flagellate phylum Cercozoa and reticulopodial phylum Retaria, whose exact phylogenetic relationship has been uncertain. Given even less clear relationships amongst cercozoan classes, we sequenced partial transcriptomes of seven Cercozoa representing five classes and endomyxan retarian Filoreta marina to establish 187-gene multiprotein phylogenies. Ectoreta (retarian infraphyla Foraminifera, Radiozoa) branch within classical Cercozoa as sister to reticulose Endomyxa. This supports recent transfer of subphylum Endomyxa from Cercozoa to Retaria alongside subphylum Ectoreta which embraces classical retarians where capsules or tests subdivide cells into organelle-containing endoplasm and anastomosing pseudopodial net-like ectoplasm. Cercozoa are more homogeneously filose, often with filose pseudopodia and/or posterior ciliary gliding motility: zooflagellate Helkesimastix and amoeboid Guttulinopsis form a strongly supported clade, order Helkesida. Cercomonads are polyphyletic (Cercomonadida sister to glissomonads; Paracercomonadida deeper). Thecofilosea are a clade, whereas Imbricatea may not be; Sarcomonadea may be paraphyletic. Helkesea and Metromonadea are successively deeper outgroups within cercozoan subphylum Monadofilosa; subphylum Reticulofilosa (paraphyletic on site-heterogeneous trees) branches earliest, Granofilosea before Chlorarachnea. Our multiprotein trees confirm that Rhizaria are sisters of infrakingdom Halvaria (Alveolata, Heterokonta) within chromist subkingdom Harosa (= SAR); they further support holophyly of chromist subkingdom Hacrobia, and are consistent with holophyly of Chromista as sister of kingdom Plantae. Site-heterogeneous rDNA trees group Kraken with environmental DNA clade 'eSarcomonad', not Paracercomonadida. Ectoretan fossil dates evidence ultrarapid episodic stem sequence evolution. We discuss early rhizarian cell evolution and multigene tree coevolutionary patterns, gene-paralogue evidence for chromist monophyly, and integrate this with fossil evidence for the age of Rhizaria and eukaryote cells, and revise rhizarian classification.
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Affiliation(s)
| | - Ema E Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Rhodri Lewis
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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Shelton DE, Leslie MP, Michod RE. Models of cell division initiation in Chlamydomonas: A challenge to the consensus view. J Theor Biol 2017; 412:186-197. [PMID: 27816674 DOI: 10.1016/j.jtbi.2016.10.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 09/19/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022]
Abstract
We develop and compare two models for division initiation in cells of the unicellular green alga Chlamydomonas reinhardtii, a topic that has remained controversial in spite of years of empirical work. Achieving a better understanding of C. reinhardtii cell cycle regulation is important because this species is used in studies of fundamental eukaryotic cell features and in studies of the evolution of multicellularity. C. reinhardtii proliferates asexually by multiple fission, interspersing rapid rounds of symmetric division with prolonged periods of growth. Our Model 1 reflects major elements of the current consensus view on C. reinhardtii division initiation, with cells first growing to a specific size, then waiting for a particular time prior to division initiation. In Model 2, our proposed alternative, growing cells divide when they have reached a growth-rate-dependent target size. The two models imply a number of different empirical patterns. We highlight these differences alongside published data, which currently fall short of unequivocally distinguishing these differences in predicted cell behavior. Nevertheless, several lines of evidence are suggestive of more Model 2-like behavior than Model 1-like behavior. Our specification of these models adds rigor to issues that have too often been worked out in relation to loose, verbal models and is directly relevant to future development of informative experiments.
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Affiliation(s)
- Deborah E Shelton
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St. Tucson, AZ 85721, United States.
| | - Martin P Leslie
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St. Tucson, AZ 85721, United States
| | - Richard E Michod
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St. Tucson, AZ 85721, United States; Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, CA 93106, United States
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Matt G, Umen J. Volvox: A simple algal model for embryogenesis, morphogenesis and cellular differentiation. Dev Biol 2016; 419:99-113. [PMID: 27451296 PMCID: PMC5101179 DOI: 10.1016/j.ydbio.2016.07.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 11/20/2022]
Abstract
Patterning of a multicellular body plan involves a coordinated set of developmental processes that includes cell division, morphogenesis, and cellular differentiation. These processes have been most intensively studied in animals and land plants; however, deep insight can also be gained by studying development in simpler multicellular organisms. The multicellular green alga Volvox carteri (Volvox) is an excellent model for the investigation of developmental mechanisms and their evolutionary origins. Volvox has a streamlined body plan that contains only a few thousand cells and two distinct cell types: reproductive germ cells and terminally differentiated somatic cells. Patterning of the Volvox body plan is achieved through a stereotyped developmental program that includes embryonic cleavage with asymmetric cell division, morphogenesis, and cell-type differentiation. In this review we provide an overview of how these three developmental processes give rise to the adult form in Volvox and how developmental mutants have provided insights into the mechanisms behind these events. We highlight the accessibility and tractability of Volvox and its relatives that provide a unique opportunity for studying development.
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Affiliation(s)
- Gavriel Matt
- Donald Danforth Plant Science Center, 975 N Warson Rd, St. Louis, MO 63132, USA; Washington University in St. Louis, Division of Biology & Biomedical Science, Campus Box 8226, 660 South Euclid Ave, St. Louis, MO 63110, USA.
| | - James Umen
- Donald Danforth Plant Science Center, 975 N Warson Rd, St. Louis, MO 63132, USA.
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Li Y, Liu D, López-Paz C, Olson BJ, Umen JG. A new class of cyclin dependent kinase in Chlamydomonas is required for coupling cell size to cell division. eLife 2016; 5:e10767. [PMID: 27015111 PMCID: PMC4841777 DOI: 10.7554/elife.10767] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 03/24/2016] [Indexed: 01/04/2023] Open
Abstract
Proliferating cells actively control their size by mechanisms that are poorly understood. The unicellular green alga Chlamydomonas reinhardtii divides by multiple fission, wherein a ‘counting’ mechanism couples mother cell-size to cell division number allowing production of uniform-sized daughters. We identified a sizer protein, CDKG1, that acts through the retinoblastoma (RB) tumor suppressor pathway as a D-cyclin-dependent RB kinase to regulate mitotic counting. Loss of CDKG1 leads to fewer mitotic divisions and large daughters, while mis-expression of CDKG1 causes supernumerous mitotic divisions and small daughters. The concentration of nuclear-localized CDKG1 in pre-mitotic cells is set by mother cell size, and its progressive dilution and degradation with each round of cell division may provide a link between mother cell-size and mitotic division number. Cell-size-dependent accumulation of limiting cell cycle regulators such as CDKG1 is a potentially general mechanism for size control. DOI:http://dx.doi.org/10.7554/eLife.10767.001 Most cells are programmed to maintain a certain size. This property, known as size control, is achieved by balancing growth and division, such that a cell will only divide after it reaches a certain size. However, and despite years of research, it is largely unknown how cells sense their size (or growth) to be able to divide accordingly. One theory proposes that there is a “sizer” protein inside cells, and that cells measure the abundance of this protein and use it to link cell size to the process of division. However, the existence of such a protein remained unproven. Li, Liu et al. have now used the cells of the green alga Chlamydomonas to identify a candidate sizer protein. Chlamydomonas cells, like many other algae, can grow to become very large mother cells that then divide one or more times in succession to produce many daughter cells. Larger mother cells undergo more divisions than smaller mother cells in order to produce daughter cells of a correct size. Using a range of genetic and biochemical techniques, Li, Liu et al. identified a protein that is produced in Chlamydomonas cells just before they begin to divide. Larger mother cells contain more of this protein than smaller cells and the protein encourages cells to divide. For example, mutant cells that lack this protein divided too few times, while cells that produce too much of it divided too many times. The protein, called CDKG1, belongs to a family of proteins that regulate cell division in many organisms. CDKG1 is a kinase – an enzyme that alters the activity of other proteins by adding a phosphate group on to them. In Chlamydomonas, CDKG1 couples cell size to cell division by altering the activity of an important protein called the retinoblastoma-related protein that controls cell division in numerous organisms. This protein is also frequently disrupted in cancers in humans. These findings shed new light on a molecular pathway for size control. Future work will need to determine how the accumulation of CDKG1 links to the size of a mother cell and how it is inactivated once daughter cells reach the appropriate size. DOI:http://dx.doi.org/10.7554/eLife.10767.002
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Affiliation(s)
- Yubing Li
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Plant Molecular and Cell Biology Program, the Horticultural and Plant Science Department, University of Florida, Gainesville, United States
| | - Dianyi Liu
- Donald Danforth Plant Science Center, St. Louis, United States
| | - Cristina López-Paz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Donald Danforth Plant Science Center, St. Louis, United States
| | - Bradley Jsc Olson
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - James G Umen
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Donald Danforth Plant Science Center, St. Louis, United States
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Cross FR, Umen JG. The Chlamydomonas cell cycle. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:370-392. [PMID: 25690512 PMCID: PMC4409525 DOI: 10.1111/tpj.12795] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 05/18/2023]
Abstract
The position of Chlamydomonas within the eukaryotic phylogeny makes it a unique model in at least two important ways: as a representative of the critically important, early-diverging lineage leading to plants; and as a microbe retaining important features of the last eukaryotic common ancestor (LECA) that has been lost in the highly studied yeast lineages. Its cell biology has been studied for many decades and it has well-developed experimental genetic tools, both classical (Mendelian) and molecular. Unlike land plants, it is a haploid with very few gene duplicates, making it ideal for loss-of-function genetic studies. The Chlamydomonas cell cycle has a striking temporal and functional separation between cell growth and rapid cell division, probably connected to the interplay between diurnal cycles that drive photosynthetic cell growth and the cell division cycle; it also exhibits a highly choreographed interaction between the cell cycle and its centriole-basal body-flagellar cycle. Here, we review the current status of studies of the Chlamydomonas cell cycle. We begin with an overview of cell-cycle control in the well-studied yeast and animal systems, which has yielded a canonical, well-supported model. We discuss briefly what is known about similarities and differences in plant cell-cycle control, compared with this model. We next review the cytology and cell biology of the multiple-fission cell cycle of Chlamydomonas. Lastly, we review recent genetic approaches and insights into Chlamydomonas cell-cycle regulation that have been enabled by a new generation of genomics-based tools.
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Affiliation(s)
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
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Abstract
UNLABELLED • PREMISE OF THE STUDY Zygotes of Coleochaete are provisioned by the maternal thallus before undergoing 3-5 rounds of division to produce 8-32 zoospores. An understanding of the selective forces favoring postzygotic divisions would be relevant not only to the interpretation of Coleochaete life history but also to the origin of a multicellular diploid phase in embryophytes.• METHODS Simple optimization models are developed of the number of zygotes per maternal thallus and number of zoospores per zygote.• KEY RESULTS Zygotic mitosis is favored once zygotic size exceeds a threshold, but natural selection usually promotes investment in additional zygotes before zygotes reach this threshold. Factors that favor production of fewer, larger zygotes include multiple paternity, low fecundity, and accessory costs of zygote production. Such factors can result in zygotes exceeding the size at which zygotic mitosis becomes profitable.• CONCLUSIONS Coleochaete may possess large zygotes that undergo multiple fission because of accessory costs associated with matrotrophy, including costs of cortical cells and unfertilized oogonia. The unpredictability of fertilization on land is proposed to have increased accessory costs from unfertilized ova and, as a consequence, to have favored the production of larger zygotes that underwent postzygotic division to produce diploid sporophytes.
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Affiliation(s)
- David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138 USA
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Cavalier-Smith T. Gregarine site-heterogeneous 18S rDNA trees, revision of gregarine higher classification, and the evolutionary diversification of Sporozoa. Eur J Protistol 2014; 50:472-95. [DOI: 10.1016/j.ejop.2014.07.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/19/2014] [Accepted: 07/21/2014] [Indexed: 10/25/2022]
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Abstract
Mutation rates vary significantly within the genome and across species. Recent studies revealed a long suspected replication-timing effect on mutation rate, but the mechanisms that regulate the increase in mutation rate as the genome is replicated remain unclear. Evidence is emerging, however, that DNA repair systems, in general, are less efficient in late replicating heterochromatic regions compared to early replicating euchromatic regions of the genome. At the same time, mutation rates in both vertebrates and invertebrates have been shown to vary with generation time (GT). GT is correlated with genome size, which suggests a possible nucleotypic effect on species-specific mutation rates. These and other observations all converge on a role for DNA replication checkpoints in modulating generation times and mutation rates during the DNA synthetic phase (S phase) of the cell cycle. The following will examine the potential role of the intra-S checkpoint in regulating cell cycle times (GT) and mutation rates in eukaryotes. This article was published online on August 5, 2011. An error was subsequently identified. This notice is included in the online and print versions to indicate that both have been corrected October 4, 2011.
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Affiliation(s)
- John Herrick
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada.
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Cavalier-Smith T. Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct 2010; 5:7. [PMID: 20132544 PMCID: PMC2837639 DOI: 10.1186/1745-6150-5-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/04/2010] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. RESULTS I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate. CONCLUSION Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.
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Genome size variation in the North American sunfish genusLepomis(Pisces: Centrarchidae). Genet Res (Camb) 2009. [DOI: 10.1017/s0016672300028135] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
SummaryGenome sizes (nuclear DNA contents) were documented spectrophotometrically from individuals of each of nine species of the North American centrarchid (sunfish) genusLepomis. The distributions of DNA values within and among the nine species were essentially normal and continuous, suggesting that changes in DNA quantity inLepomisare small in amount, involve both gains and losses of DNA, and are cumulative and independent in effect. Significant differences in mean genome size were found between individuals within populations in all nine species and between species. Nested analysis of variance and comparisons of average genome size difference or distance between individuals drawn from different levels of taxonomic organization revealed that the majority of genome size divergence inLepomisoccurs above the hierarchical level of individuals within populations. TheLepomisdata when compared to similar data from North American cyprinid fishes appear to suggest that: (i) genome size evolution in these fishes at least follows a continuous rather than a discontinuous mode; (ii) the general predictions of hypothetical models relating genome size variation as a function of organismal position along adaptive continua may be oversimplified, or not applicable to complex, higher eukaryotes; and (iii) changes in genome size in these fishes may be concentrated in speciation episodes.
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Lam CMC, Yeung PKK, Lee HC, Wong JTY. Cyclic ADP-ribose links metabolism to multiple fission in the dinoflagellate Crypthecodinium cohnii. Cell Calcium 2009; 45:346-57. [PMID: 19201464 DOI: 10.1016/j.ceca.2008.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Revised: 11/27/2008] [Accepted: 12/31/2008] [Indexed: 12/19/2022]
Abstract
Cellular metabolism is required for cell proliferation. However, the way in which metabolic signals are conveyed to cell cycle decisions is unclear. Cyclic ADP-ribose (cADPR), the NAD(+) metabolite, mobilizes calcium from calcium stores in many cells. We found that dinoflagellate cells with higher metabolic rate underwent multiple fission (MF), a division mode in which cells can exceed twice their sizes at G1. A temperature shift-down experiment suggested that MF involves a commitment point at late G1. In fast-growing cells, cADPR level peaked in G(1) and increased with increasing concentrations of glucose in the medium. Addition of glycolytic poison iodoacetate inhibited cell growth, reduced cADPR levels as well as the commitment of cell cycles in fast-growing cells. Commitment of MF cell cycles was induced by a cell permeant cADPR agonist, but blocked by a specific antagonist of cADPR-induced Ca(2+) release. Our results establish cADPR as a link between cellular metabolism and cell cycle control.
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Affiliation(s)
- Connie M C Lam
- Department of Biology, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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GREGORY TRYAN. Coincidence, coevolution, or causation? DNA content, cellsize, and the C-value enigma. Biol Rev Camb Philos Soc 2007. [DOI: 10.1111/j.1469-185x.2000.tb00059.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
There is increasing evidence that the environment experienced early in life can strongly influence adult life histories. It is largely unknown, however, how past and present conditions influence suites of life-history traits regarding major life-history trade-offs. Especially in animals with indeterminate growth, we may expect that environmental conditions of juveniles and adults independently or interactively influence the life-history trade-off between growth and reproduction after maturation. Juvenile growth conditions may initiate a feedback loop determining adult allocation patterns, triggered by size-dependent mortality risk. I tested this possibility in a long-term growth experiment with mouthbrooding cichlids. Females were raised either on a high-food or low-food diet. After maturation half of them were switched to the opposite treatment, while the other half remained unchanged. Adult growth was determined by current resource availability, but key reproductive traits like reproductive rate and offspring size were only influenced by juvenile growth conditions, irrespective of the ration received as adults. Moreover, the allocation of resources to growth versus reproduction and to offspring number versus size were shaped by juvenile rather than adult ecology. These results indicate that early individual history must be considered when analysing causes of life-history variation in natural populations.
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Affiliation(s)
- Barbara Taborsky
- Behavioural ecology, University of Bern, Wohlenstrasse 50 A, CH-3032 Hinterkappelen, Swizerland.
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Hardie DC, Hebert PDN. The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes. Genome 2003; 46:683-706. [PMID: 12897876 DOI: 10.1139/g03-040] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytological and organismal characteristics associated with cellular DNA content underpin most adaptionist interpretations of genome size variation. Since fishes are the only group of vertebrate for which relationships between genome size and key cellular parameters are uncertain, the cytological correlates of genome size were examined in this group. The cell and nuclear areas of erythrocytes showed a highly significant positive correlation with each other and with genome size across 22 cartilaginous and 201 ray-finned fishes. Regressions remained significant at all taxonomic levels, as well as among different fish lineages. However, the results revealed that cartilaginous fishes possess higher cytogenomic ratios than ray-finned fishes, as do cold-water fishes relative to their warm-water counterparts. Increases in genome size owing to ploidy shifts were found to influence cell and nucleus size in an immediate and causative manner, an effect that persists in ancient polyploid lineages. These correlations with cytological parameters known to have important influences on organismal phenotypes support an adaptive interpretation for genome size variation in fishes.
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Affiliation(s)
- David C Hardie
- Department of Zoology, University of Guelph, Guelph, ON, Canada.
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Chikatsu N, Nakamura Y, Sato H, Fujita T, Asano S, Motokura T. p53 mutations and tetraploids under r- and K-selection. Oncogene 2002; 21:3043-9. [PMID: 12082535 DOI: 10.1038/sj.onc.1205413] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2001] [Revised: 02/06/2002] [Accepted: 02/20/2002] [Indexed: 12/20/2022]
Abstract
Cotransfection of rat embryo fibroblasts with c-myc and activated H-ras oncogenes is one experimental model of the multistep oncogenesis associated with p53 mutations and aneuploidy. Using the model, we found that selection processes, e.g., r- and K-selection, affect emergence of p53 mutants and tetraploids. Culture optimum for logarithmic growth (r-selection) selected p53 mutants as they proliferated rapidly, while in confluent culture (K-selection) tetraploids emerged regardless of the p53 status. Transfection of the mutated p53 gene with dominant negative functions eradicated untransfected cells under both r- and K-selection. However, these p53 mutants can be eradicated under K-selection by cells with normal p53 function and that had been selected under prolonged K-selection. The presence of competitors and the type of selection should determine whether or not p53 mutants and/or tetraploids predominate. These observations strengthen the importance of selection processes in case of cancer.
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Affiliation(s)
- Norio Chikatsu
- Department of Internal Medicine, Faculty of Medicine, the University of Tokyo, 3-28-6 Mejirodai, Bunkyo-ku, Tokyo 112-8688, Japan
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Lam CM, Chong C, Wong JT. A dinoflagellate mutant with higher frequency of multiple fission. PROTOPLASMA 2001; 216:75-79. [PMID: 11732200 DOI: 10.1007/bf02680134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The dinoflagellate Crypthecodinium cohnii Biecheler propagates by both binary and multiple fission. By a newly developed mutagenesis protocol based on using ethyl methanesulfonate and a cell size screening method, a cell cycle mutant, mf2, was isolated with giant cells which predominantly divide by multiple fission. The average cell size of the mutant mf2 is larger than the control C. cohnii. Cell cycle synchronization experiments suggest that mutant mf2, when compared with the control strain, has a prolonged G1 phase with a corresponding delay of the G2 + M phase.
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Affiliation(s)
- C M Lam
- Biology Department, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong
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Beaton MJ, Cavalier-Smitht T. Eukaryotic non-coding DNA is functional: evidence from the differential scaling of cryptomonad genomes. Proc Biol Sci 1999; 266:2053-9. [PMID: 10902541 PMCID: PMC1690321 DOI: 10.1098/rspb.1999.0886] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genic DNA functions are commonplace: coding for proteins and specifying non-messenger RNA structure. Yet most DNA in the biosphere is non-genic, existing in nuclei as non-coding or secondary DNA. Why so much secondary DNA exists and why its amount per genome varies over orders of magnitude (correlating positively with cell volume) are central biological problems. A novel perspective on secondary DNA function comes from natural eukaryote eukaryote chimaeras (cryptomonads and chlorarachneans) where two phylogenetically distinct nuclei have coevolved within one cell for hundreds of millions of years. By comparing cryptomonad species differing 13-fold in cell volume, we show that nuclear and nucleomorph genome sizes obey fundamentally different scaling laws. Following a more than 125-fold reduction in DNA content, nucleomorph genomes exhibit little variation in size. Furthermore, the present lack of significant amounts of nucleomorph secondary DNA confirms that selection can readily eliminate functionless nuclear DNA, refuting 'selfish' and 'junk' theories of secondary DNA. Cryptomonad nuclear DNA content varied 12-fold: as in other eukaryotes, larger cells have extra DNA, which is almost certainly secondary DNA positively selected for a volume-related function. The skeletal DNA theory explains why nuclear genome size increases with cell volume and, using new evidence on nucleomorph gene functions, why nucleomorph genomes do not.
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Affiliation(s)
- M J Beaton
- Department of Botany, University of British Columbia, Vancouver. Canada .
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Desnitski AG. A review on the evolution of development in Volvox — morphological and physiological aspects. Eur J Protistol 1995. [DOI: 10.1016/s0932-4739(11)80087-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
In this paper an attempt is made to consider the significance of recent data on the organization and development of Volvox, a multicellular spheroidal green alga, for the unsolved problem of metazoan origins. A brief analysis is made of differences and similarities in some trends and principles during the establishment of metazoan and volvocalean multicellularity.
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Affiliation(s)
- A G Desnitski
- Biological Institute, St. Petersburg State University, Russia
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Orias E. Evolution of amitosis of the ciliate macronucleus: gain of the capacity to divide. THE JOURNAL OF PROTOZOOLOGY 1991; 38:217-21. [PMID: 1908902 DOI: 10.1111/j.1550-7408.1991.tb04431.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ciliates exhibit nuclear dimorphism, i.e. they have a germline micronucleus and a somatic macronucleus. Macronuclei are differentiated from mitotic sisters of micronuclei. The macronuclei of "higher ciliates" are polyploid and divide acentromerically ("amitotically"); they differentiate once per life cycle. By contrast, Karyorelict (KR) ciliate macronuclei are nearly diploid and cannot divide; they must differentiate at every cell cycle. Diverse lines of evidence are presented to support the hypothesis that ancestral ciliate macronuclei were incapable of division (as in living karyorelict ciliates) and that higher ciliates gained, perhaps independently more than once, the ability to divide the macronucleus. Selective pressures that could have driven the evolution and macronuclear division and two plausible step-wise pathways for the evolution of macronuclear division are proposed. These hypotheses are relevant to our understanding of amitosis mechanisms, evolution of nuclear dimorphism, and phylogenetic classification of ciliates.
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Affiliation(s)
- E Orias
- Department of Biological Sciences, University of California, Santa Barbara 93106
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Stingo V, Rocco L, Improta R. Chromosome markers and karyology of selachians. THE JOURNAL OF EXPERIMENTAL ZOOLOGY. SUPPLEMENT : PUBLISHED UNDER AUSPICES OF THE AMERICAN SOCIETY OF ZOOLOGISTS AND THE DIVISION OF COMPARATIVE PHYSIOLOGY AND BIOCHEMISTRY 1989; 2:175-85. [PMID: 2575648 DOI: 10.1002/jez.1402520419] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Among vertebrates, chondrichthyans exhibit peculiar karyotypes and total amount and composition of DNA very different from those of tetrapods and teleosteans. Selachians have relatively large genome sizes (more than 30 pg/N), which are inversely related to the fraction rich in adenine-thymine. Moreover, they show a high chromosome number (2n = 60-100), decreasing in the most specialized species. The karyotypes of Scyliorhinus stellaris, Torpedo ocellata, and T. marmorata have been investigated by several techniques in order to distinguish particular genome fractions along the chromosome arms. C-banding appears to be positive in most telomeric regions in Scyliorhinus and at the interstitial level in the two torpedo species. Studies with restriction enzymes (RE) have just been started in selachians, employing ALU I and HIND III in Scyliorhinus stellaris. The former digests the whole chromosome except the telomeric regions, revealing patterns similar to the C-bands. The latter cuts the chromosomes into several interstitial regions, producing G-bands. Other RE are being studied, which will allow identification in situ of qualitative differences in the various DNAs.
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Affiliation(s)
- V Stingo
- Department of Evolutive and Comparative Biology, University of Naples, Italy
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Adamson ML. Evolutionary biology of the Oxyurida (Nematoda): biofacies of a haplodiploid taxon. ADVANCES IN PARASITOLOGY 1989; 28:175-228. [PMID: 2683615 DOI: 10.1016/s0065-308x(08)60333-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- M L Adamson
- Department of Zoology, University of British Columbia, Vancouver, Canada
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Santangelo G, Barone E. Experimental results on cell volume, growth rate, and macronuclear DNA variation in a ciliated protozoan. ACTA ACUST UNITED AC 1987. [DOI: 10.1002/jez.1402430306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Lynn DH, Montagnes DJ, Riggs W. Divider size and the cell cycle after prolonged starvation ofTetrahymena corlissi. MICROBIAL ECOLOGY 1987; 13:115-127. [PMID: 24213210 DOI: 10.1007/bf02011248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Cell growth and division of the ciliateTetrahymena corlissi were examined upon refeeding after prolonged starvation of up to 12 days. Division did not automatically occur when a certain critical cell size was reached. Rather, it varied both with the nutritional history of the cell and the nutrient conditions in which the cell was growing. Upon refeeding, cells starved for 12 days divided at a smaller size and later than cells starved for 6 days. Cells refed at high density took longer to begin division than cells refed at low density. The results are discussed with respect to the "relative starvation" and "critical constituent" models of the cell cycle and in terms of the polymorphic life cycle ofTetrahymena species.
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Affiliation(s)
- D H Lynn
- Department of Zoology, University of Guelph, N1G 2W1, Guelph, Ontario, Canada
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Hally MK, Rasch EM, Mainwaring HR, Bruce RC. Cytophotometric evidence of variation in genome size of desmognathine salamanders. HISTOCHEMISTRY 1986; 85:185-92. [PMID: 3744902 DOI: 10.1007/bf00494802] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The amount of DNA per haploid genome, the C-value, is often directly correlated with nuclear and cell volume, but inversely correlated with cell replication rate. Also, rates of cellular growth sometimes appear to be correlated with organismal developmental rates and life history patterns. Among vertebrates, salamanders exhibit the greatest variation in genome size. In the present study we have examined interspecific and intraspecific variation in blood cell DNA levels in the genus Desmognathus, which shows greater variation in life history traits than any other salamander genus. Specimens of Desmognathus quadramaculatus, D. monticola, D. ochrophaeus and D. wrighti were collected from nature at two localities in the southern Appalachian Mountains. Estimates of genome size in pg of DNA were obtained from blood smears by DNA-Feulgen cytophotometry, using erythrocyte nuclei of Xenopus laevis as an internal reference standard of 6.35 pg DNA per cell. C-values of Desmognathus are the smallest in the order Caudata. Although significant variation in DNA levels was found among the four species, the differences were small, and do not support previously proposed relationships between C-value and life-history variation.
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Gold JR, Price HJ. Genome size variation among north american minnows (Cyprinidae). I. Distribution of the variation in five species. Heredity (Edinb) 1985; 54 ( Pt 3):297-305. [PMID: 4019217 DOI: 10.1038/hdy.1985.40] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Genome sizes (nuclear DNA contents) were examined spectrophotometrically from ten individuals of each of five species of North American cyprinid fishes (minnows). The distributions of DNA values both within and between the five species were essentially continuous and normal. Differences between individuals within populations were significant and contributed to approximately 16 per cent of the total variation. Variation between individuals within species ranged from 4.7-13.5 per cent and averaged ca. 7.4 per cent. Variation between species ranged from 0-9.5 per cent and the average difference between any species pair was ca. 4.6 per cent. Statistical analyses showed that the methodology used was sufficient to detect significant differences in genome size as small as 2-3 per cent. Consideration of these data lead to the following tentative conclusions: (i) changes in genome size in cyprinids appear small in amount, frequent in occurrence, to involve both gains and losses of DNA, and to be cumulative and independent in effect; (ii) differences within and between cyprinid taxa are likely the result of accumulations of small changes in DNA quantity; and (iii) the primary focus of quantitative DNA variation in cyprinids is between individuals within populations. The extent of DNA quantity variation which occurs within species would appear to preclude any direct relationship between genome size variation and many of the organismal parameters (including speciation) which differentiate the five species. In short, the data suggest that a significant fraction of the cyprinid genome, perhaps more than 10 per cent, is free to vary quantitatively without phenotypic constraint or biological consequence. This fraction is considerably larger than that theoretically needed for the structural gene component.
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Abstract
It has been proposed by Cavalier-Smith that genome and cell size is controlled by the influence of r- and K-selection. This hypothesis, though explaining many regularities is unable to account for the enormous cells of some vertebrates, namely dipnoan fishes and caudate amphibians. The introduction of the concept of wasteful and frugal strategies unravels this problem. Wasteful strategy consists of evolution toward high metabolism, which is a prerequisite for high mobility and a large and complicated nervous system. Frugal strategy leads to economies of energy and material but constrains several evolutionary tendencies. It is much less common than the wasteful one and is especially prominent in fishes and amphibians living in tropical and temperate fresh waters where the respiratory conditions may force these animals to reduce their metabolism to a minimal level, or even to enter a period of aestivation. Since the increase in cell size diminishes the overall energy cost for the maintenance of ionic gradients between the cell interior and the intercellular solutions, it was favoured in dipnoans and in such caudate amphibians as inhabit fresh waters where an oxygen deficiency sometimes develops. The selection forces working for the diminution of genome and cell size may be very powerful and may change these cell characters in a comparatively short time, whereas small cells and genomes may be tolerated even in environments favouring a cell increase.
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Mahler HR. The exon:intron structure of some mitochondrial genes and its relation to mitochondrial evolution. INTERNATIONAL REVIEW OF CYTOLOGY 1983; 82:1-98. [PMID: 6352548 DOI: 10.1016/s0074-7696(08)60823-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Miklos GL, Gill AC. Nucleotide sequences of highly repeated DNAs; compilation and comments. Genet Res (Camb) 1982; 39:1-30. [PMID: 7040165 DOI: 10.1017/s0016672300020711] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
SummaryThe nucleotide sequence data from highly repeated DNAs of inverte-brates and mammals are summarized and briefly discussed. Very similar conclusions can be drawn from the two data bases. Sequence complexities can vary from 2 bp to at least 359 bp in invertebrates and from 3 bp to at least 2350 bp in mammals. The larger sequences may or may not exhibit a substructure. Significant sequence variation occurs for any given repeated array within a species, but the sources of this heterogeneity have not been systematically partitioned. The types of alterations in a basic repeating unit can involve base changes as well as deletions or additions which can vary from 1 bp to at least 98 bp in length. These changes indicate that sequenceper seis unlikely to be under significant biological constraints and may sensibly be examined by analogy to Kimura's neutral theory for allelic variation. It is not possible with the present evidence to discriminate between the roles ofneutralandselectivemechanisms in the evolution of highly repeated DNA.Tandemly repeated arrays are constantly subjected to cycles of amplification and deletion by mechanisms for which the available data stem largely from ribosomal genes. It is a matter of conjecture whether the solutions to the mechanistic puzzles involved in amplification or rapid redeployment of satellite sequences throughout a genome will necessarily give any insight into biological functions.The lack of significant somatic effects when the satellite DNA content of a genome is significantly perturbed indicates that the hunt for specific functions at thecellularlevel is unlikely to prove profitable.The presence or in some cases theamountof satellite DNA on a chromosome, however, can have significant effects in the germ line. There the data show that localized condensed chromatin, rich in satellite DNA, can have the effect of rendering adjacent euchromatic regionsrec−, or of altering levels of recombination on different chromosomes. No data stemming from natural populations however are yet available to tell us if these effects are of adaptive or evolutionary significance.
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