1
|
Ramirez Flores RO, Schäfer PSL, Küchenhoff L, Saez-Rodriguez J. Complementing Cell Taxonomies with a Multicellular Analysis of Tissues. Physiology (Bethesda) 2024; 39:0. [PMID: 38319138 DOI: 10.1152/physiol.00001.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
The application of single-cell molecular profiling coupled with spatial technologies has enabled charting of cellular heterogeneity in reference tissues and in disease. This new wave of molecular data has highlighted the expected diversity of single-cell dynamics upon shared external queues and spatial organizations. However, little is known about the relationship between single-cell heterogeneity and the emergence and maintenance of robust multicellular processes in developed tissues and its role in (patho)physiology. Here, we present emerging computational modeling strategies that use increasingly available large-scale cross-condition single-cell and spatial datasets to study multicellular organization in tissues and complement cell taxonomies. This perspective should enable us to better understand how cells within tissues collectively process information and adapt synchronized responses in disease contexts and to bridge the gap between structural changes and functions in tissues.
Collapse
Affiliation(s)
- Ricardo Omar Ramirez Flores
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Sven Lars Schäfer
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Leonie Küchenhoff
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
2
|
Tröger L, Goirand F, Alim K. Size-dependent self-avoidance enables superdiffusive migration in macroscopic unicellulars. Proc Natl Acad Sci U S A 2024; 121:e2312611121. [PMID: 38517977 DOI: 10.1073/pnas.2312611121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/18/2024] [Indexed: 03/24/2024] Open
Abstract
Many cells face search problems, such as finding food, mates, or shelter, where their success depends on their search strategy. In contrast to other unicellular organisms, the slime mold Physarum polycephalum forms a giant network-shaped plasmodium while foraging for food. What is the advantage of the giant cell on the verge of multicellularity? We experimentally study and quantify the migration behavior of P. polycephalum plasmodia on the time scale of days in the absence and presence of food. We develop a model which successfully describes its migration in terms of ten data-derived parameters. Using the mechanistic insights provided by our data-driven model, we find that regardless of the absence or presence of food, P. polycephalum achieves superdiffusive migration by performing a self-avoiding run-and-tumble movement. In the presence of food, the run duration statistics change, only controlling the short-term migration dynamics. However, varying organism size, we find that the long-term superdiffusion arises from self-avoidance determined by cell size, highlighting the potential evolutionary advantage that this macroscopically large cell may have.
Collapse
Affiliation(s)
- Lucas Tröger
- Technical University of Munich, School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Garching 85748, Germany
| | - Florian Goirand
- Technical University of Munich, School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Garching 85748, Germany
| | - Karen Alim
- Technical University of Munich, School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Garching 85748, Germany
| |
Collapse
|
3
|
Tee EE, Faulkner C. Plasmodesmata and intercellular molecular traffic control. New Phytol 2024. [PMID: 38494438 DOI: 10.1111/nph.19666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/13/2024] [Indexed: 03/19/2024]
Abstract
Plasmodesmata are plasma membrane-lined connections that join plant cells to their neighbours, establishing an intercellular cytoplasmic continuum through which molecules can travel between cells, tissues, and organs. As plasmodesmata connect almost all cells in plants, their molecular traffic carries information and resources across a range of scales, but dynamic control of plasmodesmal aperture can change the possible domains of molecular exchange under different conditions. Plasmodesmal aperture is controlled by specialised signalling cascades accommodated in spatially discrete membrane and cell wall domains. Thus, the composition of plasmodesmata defines their capacity for molecular trafficking. Further, their shape and density can likewise define trafficking capacity, with the cell walls between different cell types hosting different numbers and forms of plasmodesmata to drive molecular flux in physiologically important directions. The molecular traffic that travels through plasmodesmata ranges from small metabolites through to proteins, and possibly even larger mRNAs. Smaller molecules are transmitted between cells via passive mechanisms but how larger molecules are efficiently trafficked through plasmodesmata remains a key question in plasmodesmal biology. How plasmodesmata are formed, the shape they take, what they are made of, and what passes through them regulate molecular traffic through plants, underpinning a wide range of plant physiology.
Collapse
Affiliation(s)
- Estee E Tee
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Christine Faulkner
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| |
Collapse
|
4
|
Doré H, Eisenberg AR, Junkins EN, Leventhal GE, Ganesh A, Cordero OX, Paul BG, Valentine DL, O’Malley MA, Wilbanks EG. Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proc Natl Acad Sci U S A 2024; 121:e2316469121. [PMID: 38354254 PMCID: PMC10907252 DOI: 10.1073/pnas.2316469121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remain elusive. We find that 82% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci capable of generating 10282 different combinations of target proteins. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1's DGR target genes are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In Thiohalocapsa PB-PSB1 and other bacteria hosting this lineage of cellular DGRs, the diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified targets act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia, though this remains to be experimentally tested. These findings could have implications for understanding the evolution of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans.
Collapse
Affiliation(s)
- H. Doré
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
| | - A. R. Eisenberg
- Department of Chemical Engineering, University of California, Santa Barbara, CA93106
| | - E. N. Junkins
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
| | - G. E. Leventhal
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Anakha Ganesh
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA02543
| | - O. X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - B. G. Paul
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA02543
| | - D. L. Valentine
- Department of Earth Science, University of California, Santa Barbara, CA93106
- Marine Science Institute, University of California, Santa Barbara, CA93106
| | - M. A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA93106
- Department of Bioengineering, University of California, Santa Barbara, CA93106
| | - E. G. Wilbanks
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
- Department of Bioengineering, University of California, Santa Barbara, CA93106
| |
Collapse
|
5
|
Chai L, Shank EA, Zaburdaev V. Where bacteria and eukaryotes meet. J Bacteriol 2024; 206:e0004923. [PMID: 38289062 PMCID: PMC10882991 DOI: 10.1128/jb.00049-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
The international workshop "Interdisciplinary life of microbes: from single cells to multicellular aggregates," following a virtual preassembly in November 2021, was held in person in Dresden, from 9 to 13 November 2022. It attracted not only prominent experts in biofilm research but also researchers from broadly neighboring disciplines, such as medicine, chemistry, and theoretical and experimental biophysics, both eukaryotic and prokaryotic. Focused brainstorming sessions were the special feature of the event and are at the heart of this commentary.
Collapse
Affiliation(s)
- Liraz Chai
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Elizabeth A. Shank
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Vasily Zaburdaev
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| |
Collapse
|
6
|
Bingham EP, Ratcliff WC. A nonadaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity. Proc Natl Acad Sci U S A 2024; 121:e2319840121. [PMID: 38315855 PMCID: PMC10873551 DOI: 10.1073/pnas.2319840121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
"Complex multicellularity," conventionally defined as large organisms with many specialized cell types, has evolved five times independently in eukaryotes, but never within prokaryotes. A number of hypotheses have been proposed to explain this phenomenon, most of which posit that eukaryotes evolved key traits (e.g., dynamic cytoskeletons, alternative mechanisms of gene regulation, or subcellular compartments) which were a necessary prerequisite for the evolution of complex multicellularity. Here, we propose an alternative, nonadaptive hypothesis for this broad macroevolutionary pattern. By binning cells into groups with finite genetic bottlenecks between generations, the evolution of multicellularity greatly reduces the effective population size (Ne) of cellular populations, increasing the role of genetic drift in evolutionary change. While both prokaryotes and eukaryotes experience this phenomenon, they have opposite responses to drift: eukaryotes tend to undergo genomic expansion, providing additional raw genetic material for subsequent multicellular innovation, while prokaryotes generally face genomic erosion. Taken together, we hypothesize that these idiosyncratic lineage-specific evolutionary dynamics play a fundamental role in the long-term divergent evolution of complex multicellularity across the tree of life.
Collapse
Affiliation(s)
- Emma P. Bingham
- School of Physics, Georgia Institute of Technology, Atlanta, GA30332
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA30332
| | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
| |
Collapse
|
7
|
Habimana O, Bridier A, Giaouris E. Editorial: The ever so elusive pathogen-harboring biofilms on abiotic surfaces in the food and clinical sectors: the good, the bad and the slimy. Front Cell Infect Microbiol 2024; 14:1374693. [PMID: 38404285 PMCID: PMC10884827 DOI: 10.3389/fcimb.2024.1374693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Affiliation(s)
- Olivier Habimana
- Department of Biotechnology and Food Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, China
| | - Arnaud Bridier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougeres Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougeres, France
| | - Efstathios Giaouris
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Nutrition, School of the Environment, University of the Aegean, Myrina, Lemnos, Greece
| |
Collapse
|
8
|
Bierenbroodspot MJ, Darienko T, de Vries S, Fürst-Jansen JMR, Buschmann H, Pröschold T, Irisarri I, de Vries J. Phylogenomic insights into the first multicellular streptophyte. Curr Biol 2024; 34:670-681.e7. [PMID: 38244543 PMCID: PMC10849092 DOI: 10.1016/j.cub.2023.12.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024]
Abstract
Streptophytes are best known as the clade containing the teeming diversity of embryophytes (land plants).1,2,3,4 Next to embryophytes are however a range of freshwater and terrestrial algae that bear important information on the emergence of key traits of land plants. Among these, the Klebsormidiophyceae stand out. Thriving in diverse environments-from mundane (ubiquitous occurrence on tree barks and rocks) to extreme (from the Atacama Desert to the Antarctic)-Klebsormidiophyceae can exhibit filamentous body plans and display remarkable resilience as colonizers of terrestrial habitats.5,6 Currently, the lack of a robust phylogenetic framework for the Klebsormidiophyceae hampers our understanding of the evolutionary history of these key traits. Here, we conducted a phylogenomic analysis utilizing advanced models that can counteract systematic biases. We sequenced 24 new transcriptomes of Klebsormidiophyceae and combined them with 14 previously published genomic and transcriptomic datasets. Using an analysis built on 845 loci and sophisticated mixture models, we establish a phylogenomic framework, dividing the six distinct genera of Klebsormidiophyceae in a novel three-order system, with a deep divergence more than 830 million years ago. Our reconstructions of ancestral states suggest (1) an evolutionary history of multiple transitions between terrestrial-aquatic habitats, with stem Klebsormidiales having conquered land earlier than embryophytes, and (2) that the body plan of the last common ancestor of Klebsormidiophyceae was multicellular, with a high probability that it was filamentous whereas the sarcinoids and unicells in Klebsormidiophyceae are likely derived states. We provide evidence that the first multicellular streptophytes likely lived about a billion years ago.
Collapse
Affiliation(s)
- Maaike J Bierenbroodspot
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Janine M R Fürst-Jansen
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Technikumplatz 17, 09648 Mittweida, Germany
| | - Thomas Pröschold
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Innsbruck, Research Department for Limnology, 5310 Mondsee, Austria
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany.
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany.
| |
Collapse
|
9
|
Bowles AMC, Williamson CJ, Williams TA, Donoghue PCJ. Cryogenian Origins of Multicellularity in Archaeplastida. Genome Biol Evol 2024; 16:evae026. [PMID: 38333966 PMCID: PMC10883732 DOI: 10.1093/gbe/evae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution.
Collapse
Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| |
Collapse
|
10
|
Arbel-Goren R, Dassa B, Zhitnitsky A, Valladares A, Herrero A, Flores E, Stavans J. Spatio-temporal coherence of circadian clocks and temporal control of differentiation in Anabaena filaments. mSystems 2024; 9:e0070023. [PMID: 38079111 PMCID: PMC10805033 DOI: 10.1128/msystems.00700-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 10/18/2023] [Indexed: 01/24/2024] Open
Abstract
Circadian clock arrays in multicellular filaments of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 display remarkable spatio-temporal coherence under nitrogen-replete conditions. To shed light on the interplay between circadian clocks and the formation of developmental patterns, we followed the expression of a clock-controlled gene under nitrogen deprivation, at the level of individual cells. Our experiments showed that differentiation into heterocysts took place preferentially within a limited interval of the circadian clock cycle, that gene expression in different vegetative intervals along a developed filament was discoordinated, and that the circadian clock was active in individual heterocysts. Furthermore, Anabaena mutants lacking the kaiABC genes encoding the circadian clock core components produced heterocysts but failed in diazotrophy. Therefore, genes related to some aspect of nitrogen fixation, rather than early or mid-heterocyst differentiation genes, are likely affected by the absence of the clock. A bioinformatics analysis supports the notion that RpaA may play a role as master regulator of clock outputs in Anabaena, the temporal control of differentiation by the circadian clock and the involvement of the clock in proper diazotrophic growth. Together, these results suggest that under nitrogen-deficient conditions, the clock coherent unit in Anabaena is reduced from a full filament under nitrogen-rich conditions to the vegetative cell interval between heterocysts.IMPORTANCECircadian clocks, from unicellular organisms to animals, temporally align biological processes to day and night cycles. We study the dynamics of a circadian clock-controlled gene at the individual cell level in the multicellular filamentous cyanobacterium Anabaena, under nitrogen-stress conditions. Under these conditions, some cells along filaments differentiate to carry out atmospheric nitrogen fixation and lose their capability for oxygenic photosynthesis. We found that clock synchronization is limited to organismic units of contiguous photosynthetic cells, contrary to nitrogen-replete conditions in which clocks are synchronized over a whole filament. We provided evidence that the circadian clock regulates the process of differentiation, allowing it to occur preferentially within a limited time window during the circadian clock period. Lastly, we present evidence that the signal from the core clock to clock-regulated genes is conveyed in Anabaena as in unicellular cyanobacteria.
Collapse
Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Zhitnitsky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Ana Valladares
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
11
|
Stéger A, Palmgren M. Hypothesis paper: the development of a regulatory layer in P2B autoinhibited Ca 2+-ATPases may have facilitated plant terrestrialization and animal multicellularization. Plant Signal Behav 2023; 18:2204284. [PMID: 37096591 PMCID: PMC10132250 DOI: 10.1080/15592324.2023.2204284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
With the appearance of plants and animals, new challenges emerged. These multicellular eukaryotes had to solve for example the difficulties of multifaceted communication between cells and adaptation to new habitats. In this paper, we are looking for one piece of the puzzle that made the development of complex multicellular eukaryotes possible with a focus on regulation of P2B autoinhibited Ca2+-ATPases. P2B ATPases pump Ca2+ out of the cytosol at the expense of ATP hydrolysis, and thereby maintain a steep gradient between the extra- and intracytosolic compartments which is utilized for Ca2+-mediated rapid cell signaling. The activity of these enzymes is regulated by a calmodulin (CaM)-responsive autoinhibitory region, which can be located in either termini of the protein, at the C-terminus in animals and at the N-terminus in plants. When the cytoplasmic Ca2+ level reaches a threshold, the CaM/Ca2+ complex binds to a calmodulin-binding domain (CaMBD) in the autoinhibitor, which leads to the upregulation of pump activity. In animals, protein activity is also controlled by acidic phospholipids that bind to a cytosolic portion of the pump. Here, we analyze the appearance of CaMBDs and the phospholipid-activating sequence and show that their evolution in animals and plants was independent. Furthermore, we hypothesize that different causes may have initiated the appearance of these regulatory layers: in animals, it is linked to the appearance of multicellularity, while in plants it co-occurs with their water-to-land transition.
Collapse
Affiliation(s)
- Anett Stéger
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- CONTACT Michael Palmgren Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, FrederiksbergDK-1871, Denmark
| |
Collapse
|
12
|
Mulvey H, Dolan L. RHO of plant signaling was established early in streptophyte evolution. Curr Biol 2023; 33:5515-5525.e4. [PMID: 38039969 DOI: 10.1016/j.cub.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023]
Abstract
The algal ancestors of land plants underwent a transition from a unicellular to a multicellular body plan.1 This transition likely took place early in streptophyte evolution, sometime after the divergence of the Chlorokybophyceae/Mesostigmatophyceae lineage, but before the divergence of the Klebsormidiophyceae lineage.2 How this transition was brought about is unknown; however, it was likely facilitated by the evolution of novel mechanisms to spatially regulate morphogenesis. In land plants, RHO of plant (ROP) signaling plays a conserved role in regulating polarized cell growth and cell division orientation to orchestrate morphogenesis.3,4,5,6,7,8 ROP constitutes a plant-specific subfamily of the RHO GTPases, which are more widely conserved throughout eukaryotes.9,10 Although the RHO family originated in early eukaryotes,11,12 how and when the ROP subfamily originated had remained elusive. Here, we demonstrate that ROP signaling was established early in the streptophyte lineage, sometime after the divergence of the Chlorokybophyceae/Mesostigmatophyceae lineage, but before the divergence of the Klebsormidiophyceae lineage. This period corresponds to when the unicellular-to-multicellular transition likely took place in the streptophytes. In addition to being critical for the complex morphogenesis of extant land plants, we speculate that ROP signaling contributed to morphological evolution in early streptophytes.
Collapse
Affiliation(s)
- Hugh Mulvey
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Liam Dolan
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria.
| |
Collapse
|
13
|
Müller FD, Schüler D, Weig A. Complete genome sequencing and annotation of Rhodomicrobium vannielii strain DSM166 suggest affiliation to Rhodomicrobium lacus. Microbiol Resour Announc 2023; 12:e0069023. [PMID: 37909726 PMCID: PMC10720471 DOI: 10.1128/mra.00690-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
Rhodomicrobium vannielii is a multicellular and differentiating member of the order Hyphomicrobiales in the class Alphaproteobacteria. Here, we report the complete genome of strain DSM166 obtained by PacBio SMRT sequencing. The results suggest that this strain is closely related to Rhodomicrobium lacus.
Collapse
Affiliation(s)
- Frank D. Müller
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Alfons Weig
- Genomics and Bioinformatics, University of Bayreuth, Bayreuth, Germany
| |
Collapse
|
14
|
Lamża Ł. Diversity of 'simple' multicellular eukaryotes: 45 independent cases and six types of multicellularity. Biol Rev Camb Philos Soc 2023; 98:2188-2209. [PMID: 37475165 DOI: 10.1111/brv.13001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023]
Abstract
Multicellularity evolved multiple times in the history of life, with most reviewers agreeing that it appeared at least 20 times in eukaryotes. However, a specific list of multicellular eukaryotes with clear criteria for inclusion has not yet been published. Herein, an updated critical review of eukaryotic multicellularity is presented, based on current understanding of eukaryotic phylogeny and new discoveries in microbiology, phycology and mycology. As a result, 45 independent multicellular lineages are identified that fall into six distinct types. Functional criteria, as distinct from a purely topological definition of a cell, are introduced to bring uniformity and clarity to the existing definitions of terms such as colony, multicellularity, thallus or plasmodium. The category of clonal multicellularity is expanded to include: (i) septated multinucleated thalli found in Pseudofungi and early-branching Fungi such as Chytridiomycota and Blastocladiomycota; and (ii) multicellular reproductive structures formed by plasmotomy in intracellular parasites such as Phytomyxea. Furthermore, (iii) endogeneous budding, as found in Paramyxida, is described as a form of multicellularity. The best-known case of clonal multicellularity, i.e. (iv) non-separation of cells after cell division, as known from Metazoa and Ochrophyta, is also discussed. The category of aggregative multicellularity is expanded to include not only (v) pseudoplasmodial forms, such a sorocarp-forming Acrasida, but also (vi) meroplasmodial organisms, such as members of Variosea or Filoreta. A common set of topological, geometric, genetic and life-cycle criteria are presented that form a coherent, philosophically sound framework for discussing multicellularity. A possibility of a seventh type of multicellularity is discussed, that of multi-species superorganisms formed by protists with obligatory bacterial symbionts, such as some members of Oxymonada or Parabasalia. Its inclusion is dependent on the philosophical stance taken towards the concepts of individuality and organism in biology. Taxa that merit special attention are identified, such as colonial Centrohelea, and a new speculative form of multicellularity, possibly present in some reticulopodial amoebae, is briefly described. Because of insufficient phylogenetic and morphological data, not all lineages could be unequivocally identified, and the true total number of all multicellular eukaryotic lineages is therefore higher, likely close to a hundred.
Collapse
Affiliation(s)
- Łukasz Lamża
- Copernicus Center for Interdisciplinary Studies, Jagiellonian University, Szczepanska 1, Kraków, 31-011, Poland
| |
Collapse
|
15
|
Pentz JT, MacGillivray K, DuBose JG, Conlin PL, Reinhardt E, Libby E, Ratcliff WC. Evolutionary consequences of nascent multicellular life cycles. eLife 2023; 12:e84336. [PMID: 37889142 PMCID: PMC10611430 DOI: 10.7554/elife.84336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/08/2023] [Indexed: 10/28/2023] Open
Abstract
A key step in the evolutionary transition to multicellularity is the origin of multicellular groups as biological individuals capable of adaptation. Comparative work, supported by theory, suggests clonal development should facilitate this transition, although this hypothesis has never been tested in a single model system. We evolved 20 replicate populations of otherwise isogenic clonally reproducing 'snowflake' yeast (Δace2/∆ace2) and aggregative 'floc' yeast (GAL1p::FLO1 /GAL1p::FLO1) with daily selection for rapid growth in liquid media, which favors faster cell division, followed by selection for rapid sedimentation, which favors larger multicellular groups. While both genotypes adapted to this regime, growing faster and having higher survival during the group-selection phase, there was a stark difference in evolutionary dynamics. Aggregative floc yeast obtained nearly all their increased fitness from faster growth, not improved group survival; indicating that selection acted primarily at the level of cells. In contrast, clonal snowflake yeast mainly benefited from higher group-dependent fitness, indicating a shift in the level of Darwinian individuality from cells to groups. Through genome sequencing and mathematical modeling, we show that the genetic bottlenecks in a clonal life cycle also drive much higher rates of genetic drift-a result with complex implications for this evolutionary transition. Our results highlight the central role that early multicellular life cycles play in the process of multicellular adaptation.
Collapse
Affiliation(s)
| | - Kathryn MacGillivray
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of TechnologyAtlantaUnited States
| | - James G DuBose
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Peter L Conlin
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Emma Reinhardt
- Department of Biology, University of North Carolina at Chapel HillChapel HillUnited States
| | | | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| |
Collapse
|
16
|
Gavrilov-Zimin IA. Ancient reproductive modes and criteria of multicellularity. Comp Cytogenet 2023; 17:195-238. [PMID: 37953852 PMCID: PMC10636606 DOI: 10.3897/compcytogen.17.109671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/05/2023] [Indexed: 11/14/2023]
Abstract
It is demonstrated that the initial method of fertilization in animals (Metazoa), embryophyte plants (Embryophyta), most groups of multicellular oogamous algae, oogamous and pseudoogamous multicellular fungi was internal fertilization (in the broad meaning) in/on the body of a maternal organism. Accordingly, during the bisexual process, the initial method of formation of a daughter multicellular organism in animals was viviparity, and in embryophyte plants and most groups of oogamous multicellular algae - the germination of a zygote in/on the body of maternal organism. The reproductive criteria of multicellularity are proposed and discussed. In this regard, the multicellularity is considered to subdivide terminologically into three variants: 1) protonemal, the most simple, characteristic of multicellular prokaryotes, most groups of multicellular algae and gametophytes of some higher plants; 2) siphonoseptal, found among multicellular fungi, some groups of green and yellow-green algae; 3) embryogenic, most complicated, known in all animals (Metazoa), all sporophytes and some gametophytes of higher plants (Embryophyta), charophyte green algae Charophyceae s.s., oogamous species of green and brown algae, some genera of red algae. In addition to the well-known division of reproduction methods into sexual and asexual, it is proposed to divide the reproduction of multicellular organisms into monocytic (the emergence of a new organism from one cell sexually or asexually) and polycytic (fragmentation, longitudinal / transverse division or budding based on many cells of the body of the mother organism), since these two ways have different evolutionary and ontogenetic origins.
Collapse
Affiliation(s)
- Ilya A. Gavrilov-Zimin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg, 199034, RussiaZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
| |
Collapse
|
17
|
Shalev O, Ye X, Ratzke C. Replaying the evolution of multicellularity. Trends Ecol Evol 2023; 38:910-912. [PMID: 37586948 DOI: 10.1016/j.tree.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023]
Abstract
The first organisms on Earth were presumably unicellular. At one point, evolution shaped these individual cells into multicellular organisms, which was a significant transition in the history of life on Earth. To investigate how this change happened, Bozdag et al. re-ran evolution in the lab and observed how single-celled yeast forms large multicellular aggregates.
Collapse
Affiliation(s)
- Or Shalev
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence EXC 2124 'Controlling Microbes to Fight Infections' (CMFI), University of Tübingen, Calwerstrasse 7/1, 72076 Tübingen, Germany
| | - Xiaozhou Ye
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence EXC 2124 'Controlling Microbes to Fight Infections' (CMFI), University of Tübingen, Calwerstrasse 7/1, 72076 Tübingen, Germany
| | - Christoph Ratzke
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence EXC 2124 'Controlling Microbes to Fight Infections' (CMFI), University of Tübingen, Calwerstrasse 7/1, 72076 Tübingen, Germany.
| |
Collapse
|
18
|
Pradeu T, Daignan-Fornier B, Ewald A, Germain PL, Okasha S, Plutynski A, Benzekry S, Bertolaso M, Bissell M, Brown JS, Chin-Yee B, Chin-Yee I, Clevers H, Cognet L, Darrason M, Farge E, Feunteun J, Galon J, Giroux E, Green S, Gross F, Jaulin F, Knight R, Laconi E, Larmonier N, Maley C, Mantovani A, Moreau V, Nassoy P, Rondeau E, Santamaria D, Sawai CM, Seluanov A, Sepich-Poore GD, Sisirak V, Solary E, Yvonnet S, Laplane L. Reuniting philosophy and science to advance cancer research. Biol Rev Camb Philos Soc 2023; 98:1668-1686. [PMID: 37157910 PMCID: PMC10869205 DOI: 10.1111/brv.12971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important way forward in service of a more successful dialogue is through greater integration of applied sciences (experimental and clinical) with conceptual and theoretical approaches, informed by philosophical methods. By way of illustration, we explore six central themes: (i) the role of mutations in cancer; (ii) the clonal evolution of cancer cells; (iii) the relationship between cancer and multicellularity; (iv) the tumour microenvironment; (v) the immune system; and (vi) stem cells. In each case, we examine open questions in the scientific literature through a philosophical methodology and show the benefit of such a synergy for the scientific and medical understanding of cancer.
Collapse
Affiliation(s)
- Thomas Pradeu
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
- CNRS UMR8590, Institut d’Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris 75006, France
| | - Bertrand Daignan-Fornier
- CNRS UMR 5095 Institut de Biochimie et Génétique Cellulaires, University of Bordeaux, 1 rue Camille St Saens, Bordeaux 33077, France
| | - Andrew Ewald
- Departments of Cell Biology and Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Pierre-Luc Germain
- Department of Health Sciences and Technology, Institute for Neurosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Universitätstrasse 2, Zürich 8092, Switzerland
- Department of Molecular Life Sciences, Laboratory of Statistical Bioinformatics, Universität Zürich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Samir Okasha
- Department of Philosophy, University of Bristol, Cotham House, Bristol, BS6 6JL, UK
| | - Anya Plutynski
- Department of Philosophy, Washington University in St. Louis, and Associate with Division of Biology and Biomedical Sciences, St. Louis, MO 63105, USA
| | - Sébastien Benzekry
- Computational Pharmacology and Clinical Oncology (COMPO) Unit, Inria Sophia Antipolis-Méditerranée, Cancer Research Center of Marseille, Inserm UMR1068, CNRS UMR7258, Aix Marseille University UM105, 27, bd Jean Moulin, Marseille 13005, France
| | - Marta Bertolaso
- Research Unit of Philosophy of Science and Human Development, Università Campus Bio-Medico di Roma, Via Àlvaro del Portillo, 21-00128, Rome, Italy
- Centre for Cancer Biomarkers, University of Bergen, Bergen 5007, Norway
| | - Mina Bissell
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Joel S. Brown
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Benjamin Chin-Yee
- Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada
- Rotman Institute of Philosophy, Western University, 1151 Richmond Street North, London, ON, Canada
| | - Ian Chin-Yee
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada
| | - Hans Clevers
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel 4070, Switzerland
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands
| | - Laurent Cognet
- CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence 33400, France
| | - Marie Darrason
- Department of Pneumology and Thoracic Oncology, University Hospital of Lyon, 165 Chem. du Grand Revoyet, 69310 Pierre Bénite, Lyon, France
- Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon 69007, France
| | - Emmanuel Farge
- Mechanics and Genetics of Embryonic and Tumor Development group, Institut Curie, CNRS, UMR168, Inserm, Centre Origines et conditions d’apparition de la vie (OCAV) Paris Sciences Lettres Research University, Sorbonne University, Institut Curie, 11 rue Pierre et Marie Curie, Paris 75005, France
| | - Jean Feunteun
- INSERM U981, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
| | - Jérôme Galon
- INSERM UMRS1138, Integrative Cancer Immunology, Cordelier Research Center, Sorbonne Université, Université Paris Cité, 15 rue de l’École de Médecine, Paris 75006, France
| | - Elodie Giroux
- Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon 69007, France
| | - Sara Green
- Section for History and Philosophy of Science, Department of Science Education, University of Copenhagen, Rådmandsgade 64, Copenhagen 2200, Denmark
| | - Fridolin Gross
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Fanny Jaulin
- INSERM U1279, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, 3223 Voigt Dr, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Ezio Laconi
- Department of Biomedical Sciences, School of Medicine, University of Cagliari, Via Università 40, Cagliari 09124, Italy
| | - Nicolas Larmonier
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Carlo Maley
- Arizona Cancer Evolution Center, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287, USA
- Center for Evolution and Medicine, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Alberto Mantovani
- Department of Biomedical Sciences, Humanitas University, 4 Via Rita Levi Montalcini, 20090 Pieve Emanuele, Milan, Italy
- Department of Immunology and Inflammation, Istituto Clinico Humanitas Humanitas Cancer Center (IRCCS) Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy
- The William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Violaine Moreau
- INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux 33076, France
| | - Pierre Nassoy
- CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence 33400, France
| | - Elena Rondeau
- INSERM U1111, ENS Lyon and Centre International de Recherche en Infectionlogie (CIRI), 46 Allée d’Italie, Lyon 69007, France
| | - David Santamaria
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca 37007, Spain
| | - Catherine M. Sawai
- INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux 33076, France
| | - Andrei Seluanov
- Department of Biology and Medicine, University of Rochester, Rochester, NY 14627, USA
| | | | - Vanja Sisirak
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Eric Solary
- INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Département d’hématologie, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Université Paris-Saclay, Faculté de Médecine, 63 Rue Gabriel Péri, Le Kremlin-Bicêtre 94270, France
| | - Sarah Yvonnet
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Lucie Laplane
- CNRS UMR8590, Institut d’Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris 75006, France
- INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Center for Biology and Society, College of Liberal Arts and Sciences, Arizona State University, 1100 S McAllister Ave, Tempe, AZ 85281, USA
| |
Collapse
|
19
|
Kalambokidis M, Travisano M. Multispecies interactions shape the transition to multicellularity. Proc Biol Sci 2023; 290:20231055. [PMID: 37727086 PMCID: PMC10509594 DOI: 10.1098/rspb.2023.1055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
The origin of multicellularity transformed the adaptive landscape on Earth, opening diverse avenues for further innovation. The transition to multicellular life is understood as the evolution of cooperative groups which form a new level of individuality. Despite the potential for community-level interactions, most studies have not addressed the competitive context of this transition, such as competition between species. Here, we explore how interspecific competition shapes the emergence of multicellularity in an experimental system with two yeast species, Saccharomyces cerevisiae and Kluyveromyces lactis, where multicellularity evolves in response to selection for faster settling ability. We find that the multispecies context slows the rate of the transition to multicellularity, and the transition to multicellularity significantly impacts community composition. Multicellular K. lactis emerges first and sweeps through populations in monocultures faster than in cocultures with S. cerevisiae. Following the transition, the between-species competitive dynamics shift, likely in part to intraspecific cooperation in K. lactis. Hence, we document an eco-evolutionary feedback across the transition to multicellularity, underscoring how ecological context is critical for understanding the causes and consequences of innovation. By including two species, we demonstrate that cooperation and competition across several biological scales shapes the origin and persistence of multicellularity.
Collapse
Affiliation(s)
- Maria Kalambokidis
- Department of Ecology, Evolution, University of Minnesota, St. Paul, MN 55108, USA
- Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael Travisano
- Department of Ecology, Evolution, University of Minnesota, St. Paul, MN 55108, USA
- The BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
- Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
20
|
Aanen DK, van ’t Padje A, Auxier B. Longevity of Fungal Mycelia and Nuclear Quality Checks: a New Hypothesis for the Role of Clamp Connections in Dikaryons. Microbiol Mol Biol Rev 2023; 87:e0002221. [PMID: 37409939 PMCID: PMC10521366 DOI: 10.1128/mmbr.00022-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
This paper addresses the stability of mycelial growth in fungi and differences between ascomycetes and basidiomycetes. Starting with general evolutionary theories of multicellularity and the role of sex, we then discuss individuality in fungi. Recent research has demonstrated the deleterious consequences of nucleus-level selection in fungal mycelia, favoring cheaters with a nucleus-level benefit during spore formation but a negative effect on mycelium-level fitness. Cheaters appear to generally be loss-of-fusion (LOF) mutants, with a higher propensity to form aerial hyphae developing into asexual spores. Since LOF mutants rely on heterokaryosis with wild-type nuclei, we argue that regular single-spore bottlenecks can efficiently select against such cheater mutants. We then zoom in on ecological differences between ascomycetes being typically fast-growing but short-lived with frequent asexual-spore bottlenecks and basidiomycetes being generally slow-growing but long-lived and usually without asexual-spore bottlenecks. We argue that these life history differences have coevolved with stricter nuclear quality checks in basidiomycetes. Specifically, we propose a new function for clamp connections, structures formed during the sexual stage in ascomycetes and basidiomycetes but during somatic growth only in basidiomycete dikaryons. During dikaryon cell division, the two haploid nuclei temporarily enter a monokaryotic phase, by alternatingly entering a retrograde-growing clamp cell, which subsequently fuses with the subapical cell to recover the dikaryotic cell. We hypothesize that clamp connections act as screening devices for nuclear quality, with both nuclei continuously testing each other for fusion ability, a test that LOF mutants will fail. By linking differences in longevity of the mycelial phase to ecology and stringency of nuclear quality checks, we propose that mycelia have a constant and low lifetime cheating risk, irrespective of their size and longevity.
Collapse
Affiliation(s)
- Duur K. Aanen
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Anouk van ’t Padje
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Benjamin Auxier
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| |
Collapse
|
21
|
Ashouri A, Zhang C, Gaiti F. Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights. Genes (Basel) 2023; 14:1856. [PMID: 37895205 PMCID: PMC10606072 DOI: 10.3390/genes14101856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The development of cancer begins with cells transitioning from their multicellular nature to a state akin to unicellular organisms. This shift leads to a breakdown in the crucial regulators inherent to multicellularity, resulting in the emergence of diverse cancer cell subpopulations that have enhanced adaptability. The presence of different cell subpopulations within a tumour, known as intratumoural heterogeneity (ITH), poses challenges for cancer treatment. In this review, we delve into the dynamics of the shift from multicellularity to unicellularity during cancer onset and progression. We highlight the role of genetic and non-genetic factors, as well as tumour microenvironment, in promoting ITH and cancer evolution. Additionally, we shed light on the latest advancements in omics technologies that allow for in-depth analysis of tumours at the single-cell level and their spatial organization within the tissue. Obtaining such detailed information is crucial for deepening our understanding of the diverse evolutionary paths of cancer, allowing for the development of effective therapies targeting the key drivers of cancer evolution.
Collapse
Affiliation(s)
- Arghavan Ashouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Chufan Zhang
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Federico Gaiti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| |
Collapse
|
22
|
Wegner L, Porth ML, Ehlers K. Multicellularity and the Need for Communication-A Systematic Overview on (Algal) Plasmodesmata and Other Types of Symplasmic Cell Connections. Plants (Basel) 2023; 12:3342. [PMID: 37765506 PMCID: PMC10536634 DOI: 10.3390/plants12183342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
In the evolution of eukaryotes, the transition from unicellular to simple multicellular organisms has happened multiple times. For the development of complex multicellularity, characterized by sophisticated body plans and division of labor between specialized cells, symplasmic intercellular communication is supposed to be indispensable. We review the diversity of symplasmic connectivity among the eukaryotes and distinguish between distinct types of non-plasmodesmatal connections, plasmodesmata-like structures, and 'canonical' plasmodesmata on the basis of developmental, structural, and functional criteria. Focusing on the occurrence of plasmodesmata (-like) structures in extant taxa of fungi, brown algae (Phaeophyceae), green algae (Chlorophyta), and streptophyte algae, we present a detailed critical update on the available literature which is adapted to the present classification of these taxa and may serve as a tool for future work. From the data, we conclude that, actually, development of complex multicellularity correlates with symplasmic connectivity in many algal taxa, but there might be alternative routes. Furthermore, we deduce a four-step process towards the evolution of canonical plasmodesmata and demonstrate similarity of plasmodesmata in streptophyte algae and land plants with respect to the occurrence of an ER component. Finally, we discuss the urgent need for functional investigations and molecular work on cell connections in algal organisms.
Collapse
Affiliation(s)
- Linus Wegner
- Institute of Botany, Justus-Liebig University, D-35392 Giessen, Germany
| | | | - Katrin Ehlers
- Institute of Botany, Justus-Liebig University, D-35392 Giessen, Germany
| |
Collapse
|
23
|
Ruiz-Trillo I, Kin K, Casacuberta E. The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event. Annu Rev Microbiol 2023; 77:499-516. [PMID: 37406343 DOI: 10.1146/annurev-micro-032421-120023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The emergence of animals from their unicellular ancestors is a major evolutionary event. Thanks to the study of diverse close unicellular relatives of animals, we now have a better grasp of what the unicellular ancestor of animals was like. However, it is unclear how that unicellular ancestor of animals became the first animals. To explain this transition, two popular theories, the choanoblastaea and the synzoospore, have been proposed. We will revise and expose the flaws in these two theories while showing that, due to the limits of our current knowledge, the origin of animals is a biological black swan event. As such, the origin of animals defies retrospective explanations. Therefore, we should be extra careful not to fall for confirmation biases based on few data and, instead, embrace this uncertainty and be open to alternative scenarios. With the aim to broaden the potential explanations on how animals emerged, we here propose two novel and alternative scenarios. In any case, to find the answer to how animals evolved, additional data will be required, as will the hunt for microscopic creatures that are closely related to animals but have not yet been sampled and studied.
Collapse
Affiliation(s)
- Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
- ICREA, Barcelona, Spain
| | - Koryu Kin
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
| | - Elena Casacuberta
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
| |
Collapse
|
24
|
Ma X, Shi X, Wang Q, Zhao M, Zhang Z, Zhong B. A Reinvestigation of Multiple Independent Evolution and Triassic-Jurassic Origins of Multicellular Volvocine Algae. Genome Biol Evol 2023; 15:evad142. [PMID: 37498572 PMCID: PMC10410301 DOI: 10.1093/gbe/evad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/09/2023] [Accepted: 07/22/2023] [Indexed: 07/28/2023] Open
Abstract
The evolution of multicellular organisms is considered to be a major evolutionary transition, profoundly affecting the ecology and evolution of nearly all life on earth. The volvocine algae, a unique clade of chlorophytes with diverse cell morphology, provide an appealing model for investigating the evolution of multicellularity and development. However, the phylogenetic relationship and timescale of the volvocine algae are not fully resolved. Here, we use extensive taxon and gene sampling to reconstruct the phylogeny of the volvocine algae. Our results support that the colonial volvocine algae are not monophyletic group and multicellularity independently evolve at least twice in the volvocine algae, once in Tetrabaenaceae and another in the Goniaceae + Volvocaceae. The simulation analyses suggest that incomplete lineage sorting is a major factor for the tree topology discrepancy, which imply that the multispecies coalescent model better fits the data used in this study. The coalescent-based species tree supports that the Goniaceae is monophyletic and Crucicarteria is the earliest diverging lineage, followed by Hafniomonas and Radicarteria within the Volvocales. By considering the multiple uncertainties in divergence time estimation, the dating analyses indicate that the volvocine algae occurred during the Cryogenian to Ediacaran (696.6-551.1 Ma) and multicellularity in the volvocine algae originated from the Triassic to Jurassic. Our phylogeny and timeline provide an evolutionary framework for studying the evolution of key traits and the origin of multicellularity in the volvocine algae.
Collapse
Affiliation(s)
- Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Mengru Zhao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| |
Collapse
|
25
|
Kurakin G. Lipoxygenase in a Giant Sulfur Bacterium: An Evolutionary Solution for Size and Complexity? Biochemistry (Mosc) 2023; 88:842-845. [PMID: 37748879 DOI: 10.1134/s0006297923060111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 04/17/2023] [Accepted: 05/02/2023] [Indexed: 09/27/2023]
Abstract
Discovery of Thiomargarita magnifica - an exceptionally large giant sulfur bacterium - urges us to pay additional attention to the giant sulfur bacteria and to revisit our recent bioinformatic finding of lipoxygenases in the representatives of the genus Beggiatoa. These close relatives of Thiomargarita magnifica meet the similar size requirements by forming multicellular structures. We hypothesize that their lipoxygenases are a part of the oxylipin signaling system that provides high level of cell-to-cell signaling complexity which, in turn, enables them to reach large sizes.
Collapse
Affiliation(s)
- Georgy Kurakin
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia.
| |
Collapse
|
26
|
Yu YY, Zhang YY, Wang T, Huang TX, Tang SY, Jin Y, Mi DD, Zheng Y, Niu DD, Guo JH, Jiang CH. Kurstakin Triggers Multicellular Behaviors in Bacillus cereus AR156 and Enhances Disease Control Efficacy Against Rice Sheath Blight. Plant Dis 2023:PDIS01220078RE. [PMID: 36205689 DOI: 10.1094/pdis-01-22-0078-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Kurstakin is the latest discovered family of lipopeptides secreted by Bacillus spp. In this study, the effects of kurstakin on the direct antagonism, multicellularity, and disease control ability of Bacillus cereus AR156 were explored. An insertion mutation in the nonribosomal peptide synthase responsible for kurstakin synthesis led to a significant reduction of antagonistic ability of AR156 against the plant-pathogenic fungi Rhizoctonia solani, Ascochyta citrullina, Fusarium graminearum, and F. oxysporum f. sp. cubense. The loss of kurstakin synthesis ability significantly impaired the swarming motility of AR156 and reduced biofilm formation and amyloid protein accumulation. Although the loss of kurstakin synthesis ability did not reduce the competitiveness of AR156 under laboratory conditions, the colonization and environmental adaptability of the mutant was significantly weaker than that of wild-type AR156 on rice leaves. The cell surface of wild-type AR156 colonizing the leaf surface was covered by a thick biofilm matrix under a scanning electron microscope, but not the mutant. The colonization ability on rice roots and control efficacy against rice sheath blight disease of the mutant were also impaired. Thus, kurstakin participates in the control of plant diseases by B. cereus AR156 through directly inhibiting the growth of pathogenic fungi and improving long-term environmental adaptability and colonization of AR156 on the host surface by triggering multicellularity. This study explored the multiple functions of kurstakin in plant disease control by B. cereus.
Collapse
Affiliation(s)
- Yi-Yang Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Yi-Yuan Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Ting Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Tao-Xiang Huang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Shu-Ya Tang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Yu Jin
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Dan-Dan Mi
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Ying Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Dong-Dong Niu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Jian-Hua Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| | - Chun-Hao Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education; Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture; and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing 210095, China
| |
Collapse
|
27
|
Ros-Rocher N, Kidner RQ, Gerdt C, Davidson WS, Ruiz-Trillo I, Gerdt JP. Chemical factors induce aggregative multicellularity in a close unicellular relative of animals. Proc Natl Acad Sci U S A 2023; 120:e2216668120. [PMID: 37094139 PMCID: PMC10161120 DOI: 10.1073/pnas.2216668120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Regulated cellular aggregation is an essential process for development and healing in many animal tissues. In some animals and a few distantly related unicellular species, cellular aggregation is regulated by diffusible chemical cues. However, it is unclear whether regulated cellular aggregation was part of the life cycles of the first multicellular animals and/or their unicellular ancestors. To fill this gap, we investigated the triggers of cellular aggregation in one of animals' closest unicellular living relatives-the filasterean Capsaspora owczarzaki. We discovered that Capsaspora aggregation is induced by chemical cues, as observed in some of the earliest branching animals and other unicellular species. Specifically, we found that calcium ions and lipids present in lipoproteins function together to induce aggregation of viable Capsaspora cells. We also found that this multicellular stage is reversible as depletion of the cues triggers disaggregation, which can be overcome upon reinduction. Our finding demonstrates that chemically regulated aggregation is important across diverse members of the holozoan clade. Therefore, this phenotype was plausibly integral to the life cycles of the unicellular ancestors of animals.
Collapse
Affiliation(s)
- Núria Ros-Rocher
- Department of Functional Genomics and Evolution, Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), 08003 Barcelona, Spain
- Department of Cell Biology and Infection and Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France
| | - Ria Q Kidner
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Catherine Gerdt
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - W Sean Davidson
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH 45221
| | - Iñaki Ruiz-Trillo
- Department of Functional Genomics and Evolution, Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Joseph P Gerdt
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| |
Collapse
|
28
|
Newman PLH, Yip Q, Osteil P, Anderson TA, Sun JQJ, Kempe D, Biro M, Shin J, Tam PPL, Zreiqat H. Programming of Multicellular Patterning with Mechano-Chemically Microstructured Cell Niches. Adv Sci (Weinh) 2023; 10:e2204741. [PMID: 36998105 PMCID: PMC10214222 DOI: 10.1002/advs.202204741] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 02/13/2023] [Indexed: 05/27/2023]
Abstract
Multicellular patterning of stem-cell-derived tissue models is commonly achieved via self-organizing activities triggered by exogenous morphogenetic stimuli. However, such tissue models are prone to stochastic behavior, limiting the reproducibility of cellular composition and forming non-physiological architectures. To enhance multicellular patterning in stem cell-derived tissues, a method for creating complex tissue microenvironments endowed with programmable multimodal mechano-chemical cues, including conjugated peptides, proteins, morphogens, and Young's moduli defined over a range of stiffnesses is developed. The ability of these cues to spatially guide tissue patterning processes, including mechanosensing and the biochemically driven differentiation of selected cell types, is demonstrated. By rationally designing niches, the authors engineered a bone-fat assembly from stromal mesenchyme cells and regionalized germ layer tissues from pluripotent stem cells. Through defined niche-material interactions, mechano-chemically microstructured niches enable the spatial programming of tissue patterning processes. Mechano-chemically microstructured cell niches thereby offer an entry point for enhancing the organization and composition of engineered tissues, potentiating structures that better recapitulate their native counterparts.
Collapse
Affiliation(s)
- Peter L. H. Newman
- ARC Training Centre for Innovative BioengineeringThe University of SydneySydney2006Australia
| | - Queenie Yip
- ARC Training Centre for Innovative BioengineeringThe University of SydneySydney2006Australia
| | - Pierre Osteil
- Embryology Research UnitChildren's Medical Research InstituteSydney2145Australia
- School of Medical ScienceFaculty of Medicine and HealthThe University of SydneySydney2006Australia
- Swiss Cancer Research Institute (ISREC)School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanne1005Switzerland
| | - Tim A. Anderson
- ARC Training Centre for Innovative BioengineeringThe University of SydneySydney2006Australia
| | - Jane Q. J. Sun
- Embryology Research UnitChildren's Medical Research InstituteSydney2145Australia
- School of Medical ScienceFaculty of Medicine and HealthThe University of SydneySydney2006Australia
| | - Daryan Kempe
- EMBL AustraliaSingle Molecule Science NodeSchool of Medical SciencesUNSWSydney2052Australia
| | - Maté Biro
- EMBL AustraliaSingle Molecule Science NodeSchool of Medical SciencesUNSWSydney2052Australia
| | - Jae‐Won Shin
- Department of Pharmacology and Regenerative MedicineUniversity of Illinois at ChicagoChicagoIL60607USA
| | - Patrick P. L. Tam
- Embryology Research UnitChildren's Medical Research InstituteSydney2145Australia
- School of Medical ScienceFaculty of Medicine and HealthThe University of SydneySydney2006Australia
| | - Hala Zreiqat
- ARC Training Centre for Innovative BioengineeringThe University of SydneySydney2006Australia
| |
Collapse
|
29
|
Grochau-Wright ZI, Nedelcu AM, Michod RE. The Genetics of Fitness Reorganization during the Transition to Multicellularity: The Volvocine regA-like Family as a Model. Genes (Basel) 2023; 14:genes14040941. [PMID: 37107699 PMCID: PMC10137558 DOI: 10.3390/genes14040941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The evolutionary transition from single-celled to multicellular individuality requires organismal fitness to shift from the cell level to a cell group. This reorganization of fitness occurs by re-allocating the two components of fitness, survival and reproduction, between two specialized cell types in the multicellular group: soma and germ, respectively. How does the genetic basis for such fitness reorganization evolve? One possible mechanism is the co-option of life history genes present in the unicellular ancestors of a multicellular lineage. For instance, single-celled organisms must regulate their investment in survival and reproduction in response to environmental changes, particularly decreasing reproduction to ensure survival under stress. Such stress response life history genes can provide the genetic basis for the evolution of cellular differentiation in multicellular lineages. The regA-like gene family in the volvocine green algal lineage provides an excellent model system to study how this co-option can occur. We discuss the origin and evolution of the volvocine regA-like gene family, including regA-the gene that controls somatic cell development in the model organism Volvox carteri. We hypothesize that the co-option of life history trade-off genes is a general mechanism involved in the transition to multicellular individuality, making volvocine algae and the regA-like family a useful template for similar investigations in other lineages.
Collapse
Affiliation(s)
| | - Aurora M Nedelcu
- Biology Department, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Richard E Michod
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
30
|
Rusin LY. Evolution of homology: From archetype towards a holistic concept of cell type. J Morphol 2023; 284:e21569. [PMID: 36789784 DOI: 10.1002/jmor.21569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/10/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
The concept of homology lies in the heart of comparative biological science. The distinction between homology as structure and analogy as function has shaped the evolutionary paradigm for a century and formed the axis of comparative anatomy and embryology, which accept the identity of structure as a ground measure of relatedness. The advent of single-cell genomics overturned the classical view of cell homology by establishing a backbone regulatory identity of cell types, the basic biological units bridging the molecular and phenotypic dimensions, to reveal that the cell is the most flexible unit of living matter and that many approaches of classical biology need to be revised to understand evolution and diversity at the cellular level. The emerging theory of cell types explicitly decouples cell identity from phenotype, essentially allowing for the divergence of evolutionarily related morphotypes beyond recognition, as well as it decouples ontogenetic cell lineage from cell-type phylogeny, whereby explicating that cell types can share common descent regardless of their structure, function or developmental origin. The article succinctly summarizes current progress and opinion in this field and formulates a more generalistic view of biological cell types as avatars, transient or terminal cell states deployed in a continuum of states by the developmental programme of one and the same omnipotent cell, capable of changing or combining identities with distinct evolutionary histories or inventing ad hoc identities that never existed in evolution or development. It highlights how the new logic grounded in the regulatory nature of cell identity transforms the concepts of cell homology and phenotypic stability, suggesting that cellular evolution is inherently and massively network-like, with one-to-one homologies being rather uncommon and restricted to shallower levels of the animal tree of life.
Collapse
Affiliation(s)
- Leonid Y Rusin
- Laboratory for Mathematic Methods and Models in Bioinformatics, Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
- EvoGenome Analytics LLC, Odintsovo, Moscow Region, Russia
| |
Collapse
|
31
|
Davidescu MR, Romanczuk P, Gregor T, Couzin ID. Growth produces coordination trade-offs in Trichoplax adhaerens, an animal lacking a central nervous system. Proc Natl Acad Sci U S A 2023; 120:e2206163120. [PMID: 36897970 DOI: 10.1073/pnas.2206163120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
How collectives remain coordinated as they grow in size is a fundamental challenge affecting systems ranging from biofilms to governments. This challenge is particularly apparent in multicellular organisms, where coordination among a vast number of cells is vital for coherent animal behavior. However, the earliest multicellular organisms were decentralized, with indeterminate sizes and morphologies, as exemplified by Trichoplax adhaerens, arguably the earliest-diverged and simplest motile animal. We investigated coordination among cells in T. adhaerens by observing the degree of collective order in locomotion across animals of differing sizes and found that larger individuals exhibit increasingly disordered locomotion. We reproduced this effect of size on order through a simulation model of active elastic cellular sheets and demonstrate that this relationship is best recapitulated across all body sizes when the simulation parameters are tuned to a critical point in the parameter space. We quantify the trade-off between increasing size and coordination in a multicellular animal with a decentralized anatomy that shows evidence of criticality and hypothesize as to the implications of this on the evolution hierarchical structures such as nervous systems in larger organisms.
Collapse
|
32
|
Hall G, Kelly S, Schaap P, Schilde C. Phylogeny-wide analysis of G-protein coupled receptors in social amoebas and implications for the evolution of multicellularity. Open Res Eur 2023; 2:134. [PMID: 37645274 PMCID: PMC10445921 DOI: 10.12688/openreseurope.15250.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/07/2023] [Indexed: 08/31/2023]
Abstract
G-protein coupled receptors (GPCRs) are seven-transmembrane proteins and constitute the largest group of receptors within eukaryotes. The presence of a large set of GPCRs in the unicellular Amoebozoa was surprising and is indicative of the largely undiscovered environmental sensing capabilities in this group. Evolutionary transitions from unicellular to multicellular lifestyles, like we see in social amoebas, have occurred several times independently in the Amoebozoa, and GPCRs may have been co-opted for new functions in cell-cell communication. Methods We have analysed a set of GPCRs from fully sequenced Amoebozoan genomes by Bayesian inference, compared their phylogenetic distribution and domain composition, and analysed their temporal and spatial expression patterns in five species of dictyostelids. Results We found evidence that most GPCRs are conserved deeply in the Amoebozoa and are probably performing roles in general cell functions and complex environmental sensing. All families of GPCRs (apart from the family 4 fungal pheromone receptors) are present in dictyostelids with family 5 being the largest and family 2 the one with the fewest members. For the first time, we identify the presence of family 1 rhodopsin-like GPCRs in dictyostelids. Some GPCRs have been amplified in the dictyostelids and in specific lineages thereof and through changes in expression patterns may have been repurposed for signalling in multicellular development. Discussion Our phylogenetic analysis suggests that GPCR families 1, 2 and 6 already diverged early in the Amoebozoa, whereas families 3 and 5 expanded later within the dictyostelids. The family 6 cAMP receptors that have experimentally supported roles in multicellular development in dictyostelids ( carA-carD; tasA/B) originated at the root of all dictyostelids and only have weakly associated homologs in Physarum polycephalum. Our analysis identified candidate GPCRs which have evolved in the dictyostelids and could have been co-opted for multicellular development.
Collapse
Affiliation(s)
- Grant Hall
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Sarah Kelly
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | | |
Collapse
|
33
|
Montenegro-Rojas I, Yañez G, Skog E, Guerrero-Calvo O, Andaur-Lobos M, Dolfi L, Cellerino A, Cerda M, Concha ML, Bertocchi C, Rojas NO, Ravasio A, Rudge TJ. A computational framework for testing hypotheses of the minimal mechanical requirements for cell aggregation using early annual killifish embryogenesis as a model. Front Cell Dev Biol 2023; 11:959611. [PMID: 37020464 PMCID: PMC10067630 DOI: 10.3389/fcell.2023.959611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 02/08/2023] [Indexed: 04/07/2023] Open
Abstract
Introduction: Deciphering the biological and physical requirements for the outset of multicellularity is limited to few experimental models. The early embryonic development of annual killifish represents an almost unique opportunity to investigate de novo cellular aggregation in a vertebrate model. As an adaptation to seasonal drought, annual killifish employs a unique developmental pattern in which embryogenesis occurs only after undifferentiated embryonic cells have completed epiboly and dispersed in low density on the egg surface. Therefore, the first stage of embryogenesis requires the congregation of embryonic cells at one pole of the egg to form a single aggregate that later gives rise to the embryo proper. This unique process presents an opportunity to dissect the self-organizing principles involved in early organization of embryonic stem cells. Indeed, the physical and biological processes required to form the aggregate of embryonic cells are currently unknown. Methods: Here, we developed an in silico, agent-based biophysical model that allows testing how cell-specific and environmental properties could determine the aggregation dynamics of early Killifish embryogenesis. In a forward engineering approach, we then proceeded to test two hypotheses for cell aggregation (cell-autonomous and a simple taxis model) as a proof of concept of modeling feasibility. In a first approach (cell autonomous system), we considered how intrinsic biophysical properties of the cells such as motility, polarity, density, and the interplay between cell adhesion and contact inhibition of locomotion drive cell aggregation into self-organized clusters. Second, we included guidance of cell migration through a simple taxis mechanism to resemble the activity of an organizing center found in several developmental models. Results: Our numerical simulations showed that random migration combined with low cell-cell adhesion is sufficient to maintain cells in dispersion and that aggregation can indeed arise spontaneously under a limited set of conditions, but, without environmental guidance, the dynamics and resulting structures do not recapitulate in vivo observations. Discussion: Thus, an environmental guidance cue seems to be required for correct execution of early aggregation in early killifish development. However, the nature of this cue (e.g., chemical or mechanical) can only be determined experimentally. Our model provides a predictive tool that could be used to better characterize the process and, importantly, to design informed experimental strategies.
Collapse
Affiliation(s)
- Ignacio Montenegro-Rojas
- Laboratory for Mechanobiology of Transforming Systems, Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences. Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Guillermo Yañez
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences. Pontificia Universidad Católica de Chile, Santiago, Chile
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Emily Skog
- Laboratory for Mechanobiology of Transforming Systems, Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences. Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Oscar Guerrero-Calvo
- Laboratory for Mechanobiology of Transforming Systems, Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences. Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Martin Andaur-Lobos
- Laboratory for Mechanobiology of Transforming Systems, Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences. Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luca Dolfi
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Alessandro Cellerino
- BIO@SNS, Scuola Normale Superiore, Pisa, Italy
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Mauricio Cerda
- Integrative Biology Program, Institute of Biomedical Sciences, Facultad de Medicina. Universidad de Chile, Santiago, Chile
- Biomedical Neuroscience Institute, Santiago, Chile
- Center for Medical Informatics and Telemedicine, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Miguel L. Concha
- Integrative Biology Program, Institute of Biomedical Sciences, Facultad de Medicina. Universidad de Chile, Santiago, Chile
- Biomedical Neuroscience Institute, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Cristina Bertocchi
- Laboratory for Molecular Mechanics of Cell Adhesion, Department of Physiology Pontificia Universidad Católica de Chile, Santiago, Chile
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Nicolás O. Rojas
- Laboratory for Mechanobiology of Transforming Systems, Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences. Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrea Ravasio
- Laboratory for Mechanobiology of Transforming Systems, Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences. Pontificia Universidad Católica de Chile, Santiago, Chile
- *Correspondence: Timothy J. Rudge, ; Andrea Ravasio,
| | - Timothy J. Rudge
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences. Pontificia Universidad Católica de Chile, Santiago, Chile
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
- *Correspondence: Timothy J. Rudge, ; Andrea Ravasio,
| |
Collapse
|
34
|
Chin NE, Wu TC, O'Toole JM, Xu K, Hata T, Koehl MAR. Formation of multicellular colonies by choanoflagellates increases susceptibility to capture by amoeboid predators. J Eukaryot Microbiol 2022; 70:e12961. [PMID: 36578145 DOI: 10.1111/jeu.12961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 11/10/2022] [Accepted: 12/13/2022] [Indexed: 12/30/2022]
Abstract
Many heterotrophic microbial eukaryotes are size-selective feeders. Some microorganisms increase their size by forming multicellular colonies. We used choanoflagellates, Salpingoeca helianthica, which can be unicellular or form multicellular colonies, to study the effects of multicellularity on vulnerability to predation by the raptorial protozoan predator, Amoeba proteus, which captures prey with pseudopodia. Videomicrography used to measure the behavior of interacting S. helianthica and A. proteus revealed that large choanoflagellate colonies were more susceptible to capture than were small colonies or single cells. Swimming colonies produced larger flow fields than did swimming unicellular choanoflagellates, and the distance of S. helianthica from A. proteus when pseudopod formation started was greater for colonies than for single cells. Prey size did not affect the number of pseudopodia formed and the time between their formation, pulsatile kinematics and speed of extension by pseudopodia, or percent of prey lost by the predator. S. helianthica did not change swimming speed or execute escape maneuvers in response to being pursued by pseudopodia, so size-selective feeding by A. proteus was due to predator behavior rather than prey escape. Our results do not support the theory that the selective advantage of becoming multicellular by choanoflagellate-like ancestors of animals was reduced susceptibility to protozoan predation.
Collapse
Affiliation(s)
- Nicole E Chin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Tiffany C Wu
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - J Michael O'Toole
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Kevin Xu
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Tom Hata
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Mimi A R Koehl
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| |
Collapse
|
35
|
Liu J, Xing WY, Liu B, Zhang CC. Three-dimensional coordination of cell-division site positioning in a filamentous cyanobacterium. PNAS Nexus 2022; 2:pgac307. [PMID: 36743469 PMCID: PMC9896137 DOI: 10.1093/pnasnexus/pgac307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/23/2022] [Indexed: 12/26/2022]
Abstract
Bacterial cells mostly divide symmetrically. In the filamentous, multicellular cyanobacterium Anabaena, cell-division planes are aligned vertically relative to the long axis of every single cell. This observation suggests that both the placement and the angle of the division planes are controlled in every single cell so that the filament can grow in one single dimension along the long axis. In this study, we showed that inactivation of patU3 encoding a cell-division inhibitor led cells to divide asymmetrically in two dimensions leading to twisted filaments, indicating that PatU3 controls not only the position but also the angle of the division planes. Deletion of the conserved minC and minD genes affected cell division symmetry, but not the angle of the division planes. Remarkably, when both patU3 and minCD were inactivated, cells could divide asymmetrically over 360° angles in three dimensions across different cellular sections, producing not only cells with irregular sizes, but also branching filaments. This study demonstrated the existence of a system operating in a three-dimensional manner for the control of cell division in Anabaena. Such a regulation may have been evolved to accommodate multicellular behaviors, a hallmark in evolution.
Collapse
Affiliation(s)
| | | | - Bowen Liu
- Institut WUT-AMU, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei 430070, People's Republic of China
| | | |
Collapse
|
36
|
Wright BA, Kvansakul M, Schierwater B, Humbert PO. Cell polarity signalling at the birth of multicellularity: What can we learn from the first animals. Front Cell Dev Biol 2022; 10:1024489. [PMID: 36506100 PMCID: PMC9729800 DOI: 10.3389/fcell.2022.1024489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/31/2022] [Indexed: 11/25/2022] Open
Abstract
The innovation of multicellularity has driven the unparalleled evolution of animals (Metazoa). But how is a multicellular organism formed and how is its architecture maintained faithfully? The defining properties and rules required for the establishment of the architecture of multicellular organisms include the development of adhesive cell interactions, orientation of division axis, and the ability to reposition daughter cells over long distances. Central to all these properties is the ability to generate asymmetry (polarity), coordinated by a highly conserved set of proteins known as cell polarity regulators. The cell polarity complexes, Scribble, Par and Crumbs, are considered to be a metazoan innovation with apicobasal polarity and adherens junctions both believed to be present in all animals. A better understanding of the fundamental mechanisms regulating cell polarity and tissue architecture should provide key insights into the development and regeneration of all animals including humans. Here we review what is currently known about cell polarity and its control in the most basal metazoans, and how these first examples of multicellular life can inform us about the core mechanisms of tissue organisation and repair, and ultimately diseases of tissue organisation, such as cancer.
Collapse
Affiliation(s)
- Bree A. Wright
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Marc Kvansakul
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, VIC, Australia
| | - Bernd Schierwater
- Institute of Animal Ecology and Evolution, University of Veterinary Medicine Hannover, Foundation, Bünteweg, Hannover, Germany
| | - Patrick O. Humbert
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, VIC, Australia,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia,Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia,*Correspondence: Patrick O. Humbert,
| |
Collapse
|
37
|
Hess S, Williams SK, Busch A, Irisarri I, Delwiche CF, de Vries S, Darienko T, Roger AJ, Archibald JM, Buschmann H, von Schwartzenberg K, de Vries J. A phylogenomically informed five-order system for the closest relatives of land plants. Curr Biol 2022; 32:4473-4482.e7. [PMID: 36055238 PMCID: PMC9632326 DOI: 10.1016/j.cub.2022.08.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/01/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022]
Abstract
The evolution of streptophytes had a profound impact on life on Earth. They brought forth those photosynthetic eukaryotes that today dominate the macroscopic flora: the land plants (Embryophyta).1 There is convincing evidence that the unicellular/filamentous Zygnematophyceae-and not the morphologically more elaborate Coleochaetophyceae or Charophyceae-are the closest algal relatives of land plants.2-6 Despite the species richness (>4,000), wide distribution, and key evolutionary position of the zygnematophytes, their internal phylogeny remains largely unresolved.7,8 There are also putative zygnematophytes with interesting body plan modifications (e.g., filamentous growth) whose phylogenetic affiliations remain unknown. Here, we studied a filamentous green alga (strain MZCH580) from an Austrian peat bog with central or parietal chloroplasts that lack discernible pyrenoids. It represents Mougeotiopsis calospora PALLA, an enigmatic alga that was described more than 120 years ago9 but never subjected to molecular analyses. We generated transcriptomic data of M. calospora strain MZCH580 and conducted comprehensive phylogenomic analyses (326 nuclear loci) for 46 taxonomically diverse zygnematophytes. Strain MZCH580 falls in a deep-branching zygnematophycean clade together with some unicellular species and thus represents a formerly unknown zygnematophycean lineage with filamentous growth. Our well-supported phylogenomic tree lets us propose a new five-order system for the Zygnematophyceae and provides evidence for at least five independent origins of true filamentous growth in the closest algal relatives of land plants. This phylogeny provides a robust and comprehensive framework for performing comparative analyses and inferring the evolution of cellular traits and body plans in the closest relatives of land plants.
Collapse
Affiliation(s)
- Sebastian Hess
- Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany.
| | - Shelby K Williams
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax NS B3H 4R2, Canada
| | - Anna Busch
- Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
| | - Charles F Delwiche
- Cell Biology and Molecular Genetics, University of Maryland-College Park, College Park, MD, USA
| | - Sophie de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax NS B3H 4R2, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax NS B3H 4R2, Canada
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Technikumplatz 17, 09648 Mittweida, Germany
| | - Klaus von Schwartzenberg
- Universität Hamburg, Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg (MZCH) and Aquatic Ecophysiology and Phycology, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany.
| |
Collapse
|
38
|
Abstract
Metazoans function as individual organisms but also as “colonies” of cells whose single-celled ancestors lived and reproduced independently. Insights from evolutionary biology about multicellular group formation help us understand the behavior of cells: why they cooperate, and why cooperation sometimes breaks down. Current explanations for multicellularity focus on two aspects of development which promote cooperation and limit conflict among cells: a single-cell bottleneck, which creates organisms composed of clones, and a separation of somatic and germ cell lineages, which reduces the selective advantage of cheating. However, many obligately multicellular organisms thrive with neither, creating the potential for within-organism conflict. Here, we argue that the prevalence of such organisms throughout the Metazoa requires us to refine our preconceptions of conflict-free multicellularity. Evolutionary theory must incorporate developmental mechanisms across a broad range of organisms—such as unusual reproductive strategies, totipotency, and cell competition—while developmental biology must incorporate evolutionary principles. To facilitate this cross-disciplinary approach, we provide a conceptual overview from evolutionary biology for developmental biologists, using analogous examples in the well-studied social insects.
Collapse
|
39
|
Baselga-Cervera B, Gettle N, Travisano M. Loss-of-heterozygosity facilitates a fitness valley crossing in experimentally evolved multicellular yeast. Proc Biol Sci 2022; 289:20212722. [PMID: 36547392 PMCID: PMC9185828 DOI: 10.1098/rspb.2021.2722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Determining how adaptive possibilities do or do not become evolutionary realities is central to understanding the tempo and mode of evolutionary change. Some of the simplest evolutionary landscapes arise from underdominance at a single locus where the fitness valley consists of only one less-fit genotype. Despite their potential for rapid evolutionary change, few such examples have been investigated. We capitalized on an experimental system in which a significant evolutionary shift, the transition from uni-to-multicellularity, was observed in asexual diploid populations of Saccharomyces cerevisiae experimentally selected for increased settling rates. The multicellular phenotype results from recessive single-locus mutations that undergo loss-of-heterozygosity (LOH) events. By reconstructing the necessary heterozygous intermediate steps, we found that the evolution of multicellularity involves a decrease in size during the first steps. Heterozygous genotypes are 20% smaller in size than genotypes with functional alleles. Nevertheless, populations of heterozygotes give rise to multicellular genotypes more readily than unicellular genotypes with two functional alleles, by rapid LOH events. LOH drives adaptation that may enable rapid evolution in diploid yeast. Together these results show discordance between the phenotypic and genotypic multicellular transition. The evolutionary path to multicellularity, and the adaptive benefits of increased size, requires initial size reductions.
Collapse
Affiliation(s)
- Beatriz Baselga-Cervera
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN 55108, USA,Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Noah Gettle
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Michael Travisano
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN 55108, USA,The BioTechnology Institute, University of Minnesota, St Paul, MN 55108, USA,Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
40
|
Phillips JE, Santos M, Konchwala M, Xing C, Pan D. Genome editing in the unicellular holozoan Capsaspora owczarzaki suggests a premetazoan role for the Hippo pathway in multicellular morphogenesis. eLife 2022; 11:77598. [PMID: 35659869 PMCID: PMC9170242 DOI: 10.7554/elife.77598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022] Open
Abstract
Animal development is mediated by a surprisingly small set of canonical signaling pathways such as Wnt, Hedgehog, TGF-beta, Notch, and Hippo pathways. Although once thought to be present only in animals, recent genome sequencing has revealed components of these pathways in the closest unicellular relatives of animals. These findings raise questions about the ancestral functions of these developmental pathways and their potential role in the emergence of animal multicellularity. Here, we provide the first functional characterization of any of these developmental pathways in unicellular organisms by developing techniques for genetic manipulation in Capsaspora owczarzaki, a close unicellular relative of animals that displays aggregative multicellularity. We then use these tools to characterize the Capsaspora ortholog of the Hippo signaling nuclear effector YAP/TAZ/Yorkie (coYki), a key regulator of tissue size in animals. In contrast to what might be expected based on studies in animals, we show that coYki is dispensable for cell proliferation but regulates cytoskeletal dynamics and the three-dimensional (3D) shape of multicellular structures. We further demonstrate that the cytoskeletal abnormalities of individual coYki mutant cells underlie the abnormal 3D shape of coYki mutant aggregates. Taken together, these findings implicate an ancestral role for the Hippo pathway in cytoskeletal dynamics and multicellular morphogenesis predating the origin of animal multicellularity, which was co-opted during evolution to regulate cell proliferation.
Collapse
Affiliation(s)
- Jonathan E Phillips
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Maribel Santos
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Mohammed Konchwala
- Eugene McDermott Center for Human Growth & Development, Departments of Bioinformatics and Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development, Departments of Bioinformatics and Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, United States
| | - Duojia Pan
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| |
Collapse
|
41
|
Abstract
Multicellular life forms have evolved many times on our planet, suggesting that this is a common evolutionary innovation. Multiple advantages have been proposed for the emergence of multicellularity (MC). In this paper, we address the problem of how the first precondition for MC, namely 'stay together', might have occurred under spatially limited resources exploited by a population of unicellular agents. Using a minimal model of evolved cell-cell adhesion among growing and dividing cells that exploit a localized resource with a given size, we show that a transition occurs at a critical resource size separating a phase of evolved multicellular aggregates from a phase where unicellularity (UC) is favoured. The two phases are separated by an intermediate domain where both UC and MC can be selected by evolution. This model provides a minimal approach to the early stages that were required to transition from individuality to cohesive groups of cells associated with a physical cooperative effect: when resources are present only in a localized portion of the habitat, MC is a desirable property as it helps cells to keep close to the available local nutrients.
Collapse
Affiliation(s)
- Adriano Bonforti
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, 08003 Barcelona, Spain.,Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain
| | - Ricard Solé
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, 08003 Barcelona, Spain.,Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| |
Collapse
|
42
|
Hammond M, Dorrell RG, Speijer D, Lukeš J. Eukaryotic cellular intricacies shape mitochondrial proteomic complexity. Bioessays 2022; 44:e2100258. [PMID: 35318703 DOI: 10.1002/bies.202100258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/17/2022]
Abstract
Mitochondria have been fundamental to the eco-physiological success of eukaryotes since the last eukaryotic common ancestor (LECA). They contribute essential functions to eukaryotic cells, above and beyond classical respiration. Mitochondria interact with, and complement, metabolic pathways occurring in other organelles, notably diversifying the chloroplast metabolism of photosynthetic organisms. Here, we integrate existing literature to investigate how mitochondrial metabolism varies across the landscape of eukaryotic evolution. We illustrate the mitochondrial remodelling and proteomic changes undergone in conjunction with major evolutionary transitions. We explore how the mitochondrial complexity of the LECA has been remodelled in specific groups to support subsequent evolutionary transitions, such as the acquisition of chloroplasts in photosynthetic species and the emergence of multicellularity. We highlight the versatile and crucial roles played by mitochondria during eukaryotic evolution, extending from its huge contribution to the development of the LECA itself to the dynamic evolution of individual eukaryote groups, reflecting both their current ecologies and evolutionary histories.
Collapse
Affiliation(s)
- Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Dave Speijer
- Medical Biochemistry, UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| |
Collapse
|
43
|
Toret C, Picco A, Boiero-Sanders M, Michelot A, Kaksonen M. The cellular slime mold Fonticula alba forms a dynamic, multicellular collective while feeding on bacteria. Curr Biol 2022; 32:1961-1973.e4. [PMID: 35349792 PMCID: PMC9097593 DOI: 10.1016/j.cub.2022.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 01/04/2022] [Accepted: 03/04/2022] [Indexed: 11/25/2022]
Abstract
Multicellularity evolved in fungi and animals, or the opisthokonts, from their common amoeboflagellate ancestor but resulted in strikingly distinct cellular organizations. The origins of this multicellularity divergence are not known. The stark mechanistic differences that underlie the two groups and the lack of information about ancestral cellular organizations limits progress in this field. We discovered a new type of invasive multicellular behavior in Fonticula alba, a unique species in the opisthokont tree, which has a simple, bacteria-feeding sorocarpic amoeba lifestyle. This invasive multicellularity follows germination dependent on the bacterial culture state, after which amoebae coalesce to form dynamic collectives that invade virgin bacterial resources. This bacteria-dependent social behavior emerges from amoeba density and allows for rapid and directed invasion. The motile collectives have animal-like properties but also hyphal-like search and invasive behavior. These surprising findings enrich the diverse multicellularities present within the opisthokont lineage and offer a new perspective on fungal origins. Unexpected bacterial-state-dependent culture conditions for Fonticula alba A multicellular invasion of bacterial food resources that is distinct from fruiting A leader-led invasive collectivity that is an emergent property Insights into the origins of invasive hyphal and fruiting multicellularity in dikarya
Collapse
Affiliation(s)
- Christopher Toret
- Department of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Andrea Picco
- Department of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Micaela Boiero-Sanders
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Alphee Michelot
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Marko Kaksonen
- Department of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland.
| |
Collapse
|
44
|
Jiménez-Marín B, Olson BJSC. The Curious Case of Multicellularity in the Volvocine Algae. Front Genet 2022; 13:787665. [PMID: 35295942 PMCID: PMC8919427 DOI: 10.3389/fgene.2022.787665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
The evolution of multicellularity is a major evolutionary transition that underlies the radiation of many species in all domains of life, especially in eukaryotes. The volvocine green algae are an unconventional model system that holds great promise in the field given its genetic tractability, late transition to multicellularity, and phenotypic diversity. Multiple efforts at linking multicellularity-related developmental landmarks to key molecular changes, especially at the genome level, have provided key insights into the molecular innovations or lack thereof that underlie multicellularity. Twelve developmental changes have been proposed to explain the evolution of complex differentiated multicellularity in the volvocine algae. Co-option of key genes, such as cell cycle and developmental regulators has been observed, but with few exceptions, known co-option events do not seem to coincide with most developmental features observed in multicellular volvocines. The apparent lack of “master multicellularity genes” combined with no apparent correlation between gene gains for developmental processes suggest the possibility that many multicellular traits might be the product gene-regulatory and functional innovations; in other words, multicellularity can arise from shared genomic repertoires that undergo regulatory and functional overhauls.
Collapse
Affiliation(s)
- Berenice Jiménez-Marín
- Division of Biology, Kansas State University, Manhattan, KS, United States.,Interdepartmental Genetics Graduate Program, Kansas State University, Manhattan, KS, United States
| | | |
Collapse
|
45
|
Day TC, Höhn SS, Zamani-Dahaj SA, Yanni D, Burnetti A, Pentz J, Honerkamp-Smith AR, Wioland H, Sleath HR, Ratcliff WC, Goldstein RE, Yunker PJ. Cellular organization in lab-evolved and extant multicellular species obeys a maximum entropy law. eLife 2022; 11:72707. [PMID: 35188101 PMCID: PMC8860445 DOI: 10.7554/elife.72707] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022] Open
Abstract
The prevalence of multicellular organisms is due in part to their ability to form complex structures. How cells pack in these structures is a fundamental biophysical issue, underlying their functional properties. However, much remains unknown about how cell packing geometries arise, and how they are affected by random noise during growth - especially absent developmental programs. Here, we quantify the statistics of cellular neighborhoods of two different multicellular eukaryotes: lab-evolved ‘snowflake’ yeast and the green alga Volvox carteri. We find that despite large differences in cellular organization, the free space associated with individual cells in both organisms closely fits a modified gamma distribution, consistent with maximum entropy predictions originally developed for granular materials. This ‘entropic’ cellular packing ensures a degree of predictability despite noise, facilitating parent-offspring fidelity even in the absence of developmental regulation. Together with simulations of diverse growth morphologies, these results suggest that gamma-distributed cell neighborhood sizes are a general feature of multicellularity, arising from conserved statistics of cellular packing.
Collapse
Affiliation(s)
- Thomas C Day
- School of Physics, Georgia Institute of Technology, Atlanta, United States
| | - Stephanie S Höhn
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Seyed A Zamani-Dahaj
- School of Physics, Georgia Institute of Technology, Atlanta, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States.,Quantitative Biosciences Graduate Program, Georgia Institute of Technology, Atlanta, United States
| | - David Yanni
- School of Physics, Georgia Institute of Technology, Atlanta, United States
| | - Anthony Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | - Jennifer Pentz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Aurelia R Honerkamp-Smith
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Hugo Wioland
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Hannah R Sleath
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | - Raymond E Goldstein
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Peter J Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, United States
| |
Collapse
|
46
|
Chou KT, Lee DYD, Chiou JG, Galera-Laporta L, Ly S, Garcia-Ojalvo J, Süel GM. A segmentation clock patterns cellular differentiation in a bacterial biofilm. Cell 2022; 185:145-157.e13. [PMID: 34995513 PMCID: PMC8754390 DOI: 10.1016/j.cell.2021.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/13/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023]
Abstract
Contrary to multicellular organisms that display segmentation during development, communities of unicellular organisms are believed to be devoid of such sophisticated patterning. Unexpectedly, we find that the gene expression underlying the nitrogen stress response of a developing Bacillus subtilis biofilm becomes organized into a ring-like pattern. Mathematical modeling and genetic probing of the underlying circuit indicate that this patterning is generated by a clock and wavefront mechanism, similar to that driving vertebrate somitogenesis. We experimentally validated this hypothesis by showing that predicted nutrient conditions can even lead to multiple concentric rings, resembling segments. We additionally confirmed that this patterning mechanism is driven by cell-autonomous oscillations. Importantly, we show that the clock and wavefront process also spatially patterns sporulation within the biofilm. Together, these findings reveal a biofilm segmentation clock that organizes cellular differentiation in space and time, thereby challenging the paradigm that such patterning mechanisms are exclusive to plant and animal development.
Collapse
Affiliation(s)
- Kwang-Tao Chou
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Dong-Yeon D Lee
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Jian-Geng Chiou
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Leticia Galera-Laporta
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - San Ly
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Gürol M Süel
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California San Diego, La Jolla, CA 92093-0380, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093-0380, USA.
| |
Collapse
|
47
|
Atakhani A, Bogdziewiez L, Verger S. Characterising the mechanics of cell-cell adhesion in plants. Quant Plant Biol 2022; 3:e2. [PMID: 37077973 PMCID: PMC10095952 DOI: 10.1017/qpb.2021.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 05/03/2023]
Abstract
Cell-cell adhesion is a fundamental feature of multicellular organisms. To ensure multicellular integrity, adhesion needs to be tightly controlled and maintained. In plants, cell-cell adhesion remains poorly understood. Here, we argue that to be able to understand how cell-cell adhesion works in plants, we need to understand and quantitatively measure the mechanics behind it. We first introduce cell-cell adhesion in the context of multicellularity, briefly explain the notions of adhesion strength, work and energy and present the current knowledge concerning the mechanisms of cell-cell adhesion in plants. Because still relatively little is known in plants, we then turn to animals, but also algae, bacteria, yeast and fungi, and examine how adhesion works and how it can be quantitatively measured in these systems. From this, we explore how the mechanics of cell adhesion could be quantitatively characterised in plants, opening future perspectives for understanding plant multicellularity.
Collapse
Affiliation(s)
- Asal Atakhani
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Léa Bogdziewiez
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Stéphane Verger
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
- Author for correspondence: S. Verger, E-mail:
| |
Collapse
|
48
|
Caetano-Anollés G, Aziz MF, Mughal F, Caetano-Anollés D. Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution. Expert Rev Proteomics 2021; 18:863-880. [PMID: 34628994 DOI: 10.1080/14789450.2021.1992277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and proteomes. Molecular chronologies are series of time events describing the history of biological systems and subsystems and the rise of biological innovations. Together with time-varying networks, these chronologies provide a window into the past. AREAS COVERED Here, we review molecular chronologies and networks built with modern methods of phylogeny reconstruction. We discuss how chronologies of structural domain families uncover the explosive emergence of metabolism, the late rise of translation, the co-evolution of ribosomal proteins and rRNA, and the late development of the ribosomal exit tunnel; events that coincided with a tendency to shorten folding time. Evolving networks described the early emergence of domains and a late 'big bang' of domain combinations. EXPERT OPINION Two processes, folding and recruitment appear central to the evolutionary progression. The former increases protein persistence. The later fosters diversity. Chronologically, protein evolution mirrors folding by combining supersecondary structures into domains, developing translation machinery to facilitate folding speed and stability, and enhancing structural complexity by establishing long-distance interactions in novel structural and architectural designs.
Collapse
Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA.,C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Derek Caetano-Anollés
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| |
Collapse
|
49
|
Abstract
Being able to reproduce and survive is fundamental to all forms of life. In primitive unicellular organisms, the emergence of quiescence as a reversible proliferation arrest has most likely improved cell survival under unfavorable environmental conditions. During evolution, with the repeated appearances of multicellularity, several aspects of unicellular quiescence were conserved while new quiescent cell intrinsic abilities arose. We propose that the formation of a microenvironment by neighboring cells has allowed disconnecting quiescence from nutritional cues. In this new context, non-proliferative cells can stay metabolically active, potentially authorizing the emergence of new quiescent cell properties, and thereby favoring cell specialization. Through its co-evolution with cell specialization, quiescence may have been a key motor of the fascinating diversity of multicellular complexity.
Collapse
|
50
|
Krespach MKC, Stroe MC, Flak M, Komor AJ, Nietzsche S, Sasso S, Hertweck C, Brakhage AA. Bacterial marginolactones trigger formation of algal gloeocapsoids, protective aggregates on the verge of multicellularity. Proc Natl Acad Sci U S A 2021; 118:e2100892118. [PMID: 34740967 DOI: 10.1073/pnas.2100892118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 12/17/2022] Open
Abstract
Photosynthetic microorganisms including the green alga Chlamydomonas reinhardtii are essential to terrestrial habitats as they start the carbon cycle by conversion of CO2 to energy-rich organic carbohydrates. Terrestrial habitats are densely populated, and hence, microbial interactions mediated by natural products are inevitable. We previously discovered such an interaction between Streptomyces iranensis releasing the marginolactone azalomycin F in the presence of C. reinhardtii Whether the alga senses and reacts to azalomycin F remained unknown. Here, we report that sublethal concentrations of azalomycin F trigger the formation of a protective multicellular structure by C. reinhardtii, which we named gloeocapsoid. Gloeocapsoids contain several cells which share multiple cell membranes and cell walls and are surrounded by a spacious matrix consisting of acidic polysaccharides. After azalomycin F removal, gloeocapsoid aggregates readily disassemble, and single cells are released. The presence of marginolactone biosynthesis gene clusters in numerous streptomycetes, their ubiquity in soil, and our observation that other marginolactones such as desertomycin A and monazomycin also trigger the formation of gloeocapsoids suggests a cross-kingdom competition with ecological relevance. Furthermore, gloeocapsoids allow for the survival of C. reinhardtii at alkaline pH and otherwise lethal concentrations of azalomycin F. Their structure and polysaccharide matrix may be ancestral to the complex mucilage formed by multicellular members of the Chlamydomonadales such as Eudorina and Volvox Our finding suggests that multicellularity may have evolved to endure the presence of harmful competing bacteria. Additionally, it underlines the importance of natural products as microbial cues, which initiate interesting ecological scenarios of attack and counter defense.
Collapse
|