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Zhang Z, Yang Y, Zhao J, Li Y, Stephenson SL, Qiu J, Liu P. Environmental factors influencing the diversity and distribution of dictyostelid cellular slime molds in forest and farmland soils of western China. Microbiol Spectr 2023; 11:e0173223. [PMID: 37962389 PMCID: PMC10715086 DOI: 10.1128/spectrum.01732-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Soil protists are an essential yet seriously understudied component of the soil microbiome. In this study, 11 new records of dictyostelids belonging to 2 orders, 3 families, and 4 genera were identified from 99 soil samples collected from different elevations and habitats in central Gansu and the southeastern and southcentral portions of Guizhou Province, China. We found that dictyostelid communities were significantly different between Gansu and Guizhou Provinces, apparently in response to different environmental factors. Moreover, dictyostelids were found to have the highest species diversity in mixed forests. Soil pH, temperature, and elevation were determined to be the primary factors that affect the distribution and occurrence of dictyostelids in Guizhou and Gansu Provinces. This work supplements the survey data available for dictyostelids elsewhere in China. These new findings have significant implications for our understanding of the diversity of soil microorganisms.
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Affiliation(s)
- Zhaojuan Zhang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yingkun Yang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jing Zhao
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Steven L. Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Junzhi Qiu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Pu Liu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
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2
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Ide H, Hayashida Y, Morimoto YV. Visualization of c-di-GMP in multicellular Dictyostelium stages. Front Cell Dev Biol 2023; 11:1237778. [PMID: 37547475 PMCID: PMC10399225 DOI: 10.3389/fcell.2023.1237778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023] Open
Abstract
The bacterial signaling molecule cyclic diguanosine monophosphate (c-di-GMP) is only synthesized and utilized by the cellular slime mold Dictyostelium discoideum among eukaryotes. Dictyostelium cells undergo a transition from a unicellular to a multicellular state, ultimately forming a stalk and spores. While Dictyostelium is known to employ c-di-GMP to induce differentiation into stalk cells, there have been no reports of direct observation of c-di-GMP using fluorescent probes. In this study, we used a fluorescent probe used in bacteria to visualize its localization within Dictyostelium multicellular bodies. Cytosolic c-di-GMP concentrations were significantly higher at the tip of the multicellular body during stalk formation.
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Affiliation(s)
- Hayato Ide
- Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka, Japan
| | - Yukihisa Hayashida
- Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka, Japan
| | - Yusuke V. Morimoto
- Department of Physics and Information Technology, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka, Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi, Japan
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3
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Kin K, Chen ZH, Forbes G, Lawal H, Schilde C, Singh R, Cole C, Barton GJ, Schaap P. The protein kinases of Dictyostelia and their incorporation into a signalome. Cell Signal 2023; 108:110714. [PMID: 37187217 DOI: 10.1016/j.cellsig.2023.110714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/02/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023]
Abstract
Protein kinases are major regulators of cellular processes, but the roles of most kinases remain unresolved. Dictyostelid social amoebas have been useful in identifying functions for 30% of its kinases in cell migration, cytokinesis, vesicle trafficking, gene regulation and other processes but their upstream regulators and downstream effectors are mostly unknown. Comparative genomics can assist to distinguish between genes involved in deeply conserved core processes and those involved in species-specific innovations, while co-expression of genes as evident from comparative transcriptomics can provide cues to the protein complement of regulatory networks. Genomes and developmental and cell-type specific transcriptomes are available for species that span the 0.5 billion years of evolution of Dictyostelia from their unicellular ancestors. In this work we analysed conservation and change in the abundance, functional domain architecture and developmental regulation of protein kinases across the 4 major taxon groups of Dictyostelia. All data are summarized in annotated phylogenetic trees of the kinase subtypes and accompanied by functional information of all kinases that were experimentally studied. We detected 393 different protein kinase domains across the five studied genomes, of which 212 were fully conserved. Conservation was highest (71%) in the previously defined AGC, CAMK, CK1, CMCG, STE and TKL groups and lowest (26%) in the "other" group of typical protein kinases. This was mostly due to species-specific single gene amplification of "other" kinases. Apart from the AFK and α-kinases, the atypical protein kinases, such as the PIKK and histidine kinases were also almost fully conserved. The phylogeny-wide developmental and cell-type specific expression profiles of the protein kinase genes were combined with profiles from the same transcriptomic experiments for the families of G-protein coupled receptors, small GTPases and their GEFs and GAPs, the transcription factors and for all genes that upon lesion generate a developmental defect. This dataset was subjected to hierarchical clustering to identify clusters of co-expressed genes that potentially act together in a signalling network. The work provides a valuable resource that allows researchers to identify protein kinases and other regulatory proteins that are likely to act as intermediates in a network of interest.
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Affiliation(s)
- Koryu Kin
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
| | - Zhi-Hui Chen
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Gillian Forbes
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS, École Normale Supérieure de Lyon and Université Claude Bernard Lyon-1, Lyon 69007, France.
| | - Hajara Lawal
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Christina Schilde
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; D'Arcy Thompson Unit, School of Life Sciences, University of Dundee, DD1 4HN, United Kingdom.
| | - Reema Singh
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; Vaccine and Infectious Disease Organization, University of Saskatchewan,120 Veterinary Road, Saskatoon, SK S7N 5E3, Canada.
| | - Christian Cole
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; Population Health and Genomics, School of Medicine, University of Dundee, Ninewells Hospital, Dundee DD1 9SY, United Kingdom
| | - Geoffrey J Barton
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Pauline Schaap
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
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Archer RJ, Hamada S, Shimizu R, Nomura SIM. Scalable Synthesis of Planar Macroscopic Lipid-Based Multi-Compartment Structures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4863-4871. [PMID: 36973945 PMCID: PMC10100540 DOI: 10.1021/acs.langmuir.2c02859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/28/2023] [Indexed: 06/18/2023]
Abstract
As life evolved, the path from simple single cell organisms to multicellular enabled increasingly complex functionalities. The spatial separation of reactions at the micron scale achieved by cellular structures allowed diverse and scalable implementation in biomolecular systems. Mimicking such spatially separated domains in a scalable approach could open a route to creating synthetic cell-like structured systems. Here, we report a facile and scalable method to create multicellular-like, multi-compartment (MC) structures. Aqueous droplet-based compartments ranging from 50 to 400 μm were stabilized and connected together by hydrophobic layers composed of phospholipids and an emulsifier. Planar centimeter-scale MC structures were formed by droplet deposition on a water interface. Further, the resulting macroscopic shapes were shown to be achieved by spatially controlled deposition. To demonstrate configurability and potential versatility, MC assemblies of both homogeneous and mixed compartment types were shown. Notably, magnetically heterogeneous systems were achieved by the inclusion of magnetic nanoparticles in defined sections. Such structures demonstrated actuated motion with structurally imparted directionality. These novel and functionalized structures exemplify a route toward future applications including compartmentally assembled "multicellular" molecular robots.
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Kawabe Y, Schaap P. Development of the dictyostelid Polysphondylium violaceum does not require secreted cAMP. Biol Open 2023; 12:286712. [PMID: 36688866 PMCID: PMC9922732 DOI: 10.1242/bio.059728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/12/2023] [Indexed: 01/24/2023] Open
Abstract
Group 4 Dictyostelia, like Dictyostelium discoideum, self-organize into aggregates and fruiting bodies using propagating waves of the chemoattractant cAMP, which are produced by a network containing the adenylate cyclase AcaA, cAMP receptors (Cars) and the extracellular cAMP phosphodiesterase PdsA. Additionally, AcaA and the adenylate cyclases AcrA and AcgA produce secreted cAMP for induction of aggregative and prespore gene expression and intracellular cAMP for PKA activation, with PKA triggering initiation of development and spore and stalk maturation. Non-group 4 species also use secreted cAMP to coordinate post-aggregative morphogenesis and prespore induction but use other attractants to aggregate. To understand how cAMP's role in aggregation evolved, we deleted the acaA, carA and pdsA genes of Polysphondylium violaceum, a sister species to group 4. acaA- fruiting bodies had thinner stalks but otherwise developed normally. Deletion of acrA, which was similarly expressed as acaA, reduced aggregation centre initiation and, as also occurred after D. discoideum acrA deletion, caused spore instability. Double acaA-acrA- mutants failed to form stable aggregates, a defect that was overcome by exposure to the PKA agonist 8Br-cAMP, and therefore likely due to reduced intracellular cAMP. The carA- and pdsA- mutants showed normal aggregation and fruiting body development. Together, the data showed that P. violaceum development does not critically require secreted cAMP, while roles of intracellular cAMP in initiation of development and spore maturation are conserved. Apparently, cell-cell communication underwent major taxon-group specific innovation in Dictyostelia.
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Affiliation(s)
- Yoshinori Kawabe
- School of Life Sciences, Molecular, Cell and Developmental Biology, University of Dundee, Dundee DD15EH, UK
| | - Pauline Schaap
- School of Life Sciences, Molecular, Cell and Developmental Biology, University of Dundee, Dundee DD15EH, UK,Author for correspondence ()
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Yamasaki DT, Araki T, Narita TB. The polyketide synthase StlA is involved in inducing aggregation in Polysphondylium violaceum. Biosci Biotechnol Biochem 2022; 86:1590-1598. [PMID: 35998316 DOI: 10.1093/bbb/zbac144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022]
Abstract
In the social amoeba Dictyostelium discoideum, the polyketide MPBD (4-methyl-5-pentylbenzene-1,3-diol) regulates the gene expressions of cAMP signaling to make cells aggregation-competent and also induces spore maturation. The polyketide synthase StlA is responsible for MPBD biosynthesis in D. discoideum and appears to be conserved throughout the major groups of the social amoeba (Dictyostelia). In this study, we analyzed the function of StlA in Polysphondylium violaceum by identifying the gene sequence and creating the knockout mutants. We found that Pv-stlA- mutants had defects only in cell aggregation but not in spore maturation, indicating that the function of StlA in inducing spore maturation is species-specific. We also found that MPBD could rescue the aggregation defect in Pv-stlA- mutants whereas the mutants normally exhibited chemotaxis to their chemoattractant, glorin. Our data suggest that StlA is involved in inducing aggregation in P. violaceum by acting on signaling pathways other than chemotaxis in P. violaceum.
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Affiliation(s)
- Daiki T Yamasaki
- Graduate School of Engineering, Chiba Institute of Technology, Chiba, Japan
| | - Tsuyoshi Araki
- Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Takaaki B Narita
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba, Japan
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Love A, Wagner GP. Co-option of stress mechanisms in the origin of evolutionary novelties. Evolution 2021; 76:394-413. [PMID: 34962651 PMCID: PMC9303342 DOI: 10.1111/evo.14421] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/19/2021] [Accepted: 10/24/2021] [Indexed: 11/30/2022]
Abstract
It is widely accepted that stressful conditions can facilitate evolutionary change. The mechanisms elucidated thus far accomplish this with a generic increase in heritable variation that facilitates more rapid adaptive evolution, often via plastic modifications of existing characters. Through scrutiny of different meanings of stress in biological research, and an explicit recognition that stressors must be characterized relative to their effect on capacities for maintaining functional integrity, we distinguish between: (1) previously identified stress‐responsive mechanisms that facilitate evolution by maintaining an adaptive fit with the environment, and (2) the co‐option of stress‐responsive mechanisms that are specific to stressors leading to the origin of novelties via compensation. Unlike standard accounts of gene co‐option that identify component sources of evolutionary change, our model documents the cost‐benefit trade‐offs and thereby explains how one mechanism—an immediate response to acute stress—is transformed evolutionarily into another—routine protection from recurring stressors. We illustrate our argument with examples from cell type origination as well as processes and structures at higher levels of organization. These examples suggest a general principle of evolutionary origination based on the capacity to switch between regulatory states related to reproduction and proliferation versus survival and differentiation.
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Affiliation(s)
- Alan Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT-06520.,Yale Systems Biology Institute, West Haven, CT-06516.,Department of Evolutionary Biology, University of Vienna, Austria
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Daignan-Fornier B, Laporte D, Sagot I. Quiescence Through the Prism of Evolution. Front Cell Dev Biol 2021; 9:745069. [PMID: 34778256 PMCID: PMC8586652 DOI: 10.3389/fcell.2021.745069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/11/2021] [Indexed: 01/13/2023] Open
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.
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Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development. Genes (Basel) 2021; 12:genes12101628. [PMID: 34681022 PMCID: PMC8535579 DOI: 10.3390/genes12101628] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/23/2022] Open
Abstract
Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-specific expansions in particular had biased genes with both molecular signals of positive selection and high expression, suggesting adaptive genetic and transcriptional diversification following duplication. Our results present insights into the potential contributions of lineage-specific genes and families in generating species-specific phenotypes during multicellular development in dictyostelids.
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A topological look into the evolution of developmental programs. Biophys J 2021; 120:4193-4201. [PMID: 34480926 PMCID: PMC8516677 DOI: 10.1016/j.bpj.2021.08.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 07/13/2021] [Accepted: 08/30/2021] [Indexed: 01/06/2023] Open
Abstract
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and inventing new cell types. A hurdle to understanding developmental evolution is the difficulty of even describing the intertwined network of spatiotemporal processes underlying the development of complex multicellular organisms. Nonetheless, an overview of developmental trajectories can be obtained from cell type lineage maps. Here, we propose that these lineage maps can also reveal how developmental programs evolve: the modes of evolving new cell types in an organism should be visible in its developmental trajectories and therefore in the geometry of its cell type lineage map. This idea is demonstrated using a parsimonious generative model of developmental programs, which allows us to reliably survey the universe of all possible programs and examine their topological features. We find that, contrary to belief, tree-like lineage maps are rare, and lineage maps of complex multicellular organisms are likely to be directed acyclic graphs in which multiple developmental routes can converge on the same cell type. Although cell type evolution prescribes what developmental programs come into existence, natural selection prunes those programs that produce low-functioning organisms. Our model indicates that additionally, lineage map topologies are correlated with such a functional property: the ability of organisms to regenerate.
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Evolution of Multicellularity. Genes (Basel) 2021; 12:genes12101532. [PMID: 34680926 PMCID: PMC8535607 DOI: 10.3390/genes12101532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022] Open
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