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Kawabe Y, Du Q, Narita TB, Bell C, Schilde C, Kin K, Schaap P. Emerging roles for diguanylate cyclase during the evolution of soma in dictyostelia. BMC Ecol Evol 2023; 23:60. [PMID: 37803310 PMCID: PMC10559540 DOI: 10.1186/s12862-023-02169-z] [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: 02/11/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Cyclic di-guanylate (c-di-GMP), synthesized by diguanylate cyclase, is a major second messenger in prokaryotes, where it triggers biofilm formation. The dictyostelid social amoebas acquired diguanylate cyclase (dgcA) by horizontal gene transfer. Dictyostelium discoideum (Ddis) in taxon group 4 uses c-di-GMP as a secreted signal to induce differentiation of stalk cells, the ancestral somatic cell type that supports the propagating spores. We here investigated how this role for c-di-GMP evolved in Dictyostelia by exploring dgcA function in the group 2 species Polysphondylium pallidum (Ppal) and in Polysphondylium violaceum (Pvio), which resides in a small sister clade to group 4. RESULTS Similar to Ddis, dgcA is upregulated after aggregation in Ppal and Pvio and predominantly expressed in the anterior region and stalks of emerging fruiting bodies. DgcA null mutants in Ppal and Pvio made fruiting bodies with very long and thin stalks and only few spores and showed delayed aggregation and larger aggregates, respectively. Ddis dgcA- cells cannot form stalks at all, but showed no aggregation defects. The long, thin stalks of Ppal and Pvio dgcA- mutants were also observed in acaA- mutants in these species. AcaA encodes adenylate cyclase A, which mediates the effects of c-di-GMP on stalk induction in Ddis. Other factors that promote stalk formation in Ddis are DIF-1, produced by the polyketide synthase StlB, low ammonia, facilitated by the ammonia transporter AmtC, and high oxygen, detected by the oxygen sensor PhyA (prolyl 4-hydroxylase). We deleted the single stlB, amtC and phyA genes in Pvio wild-type and dgcA- cells. Neither of these interventions affected stalk formation in Pvio wild-type and not or very mildly exacerbated the long thin stalk phenotype of Pvio dgcA- cells. CONCLUSIONS The study reveals a novel role for c-di-GMP in aggregation, while the reduced spore number in Pvio and Ppal dgcA- is likely an indirect effect, due to depletion of the cell pool by the extended stalk formation. The results indicate that in addition to c-di-GMP, Dictyostelia ancestrally used an as yet unknown factor for induction of stalk formation. The activation of AcaA by c-di-GMP is likely conserved throughout Dictyostelia.
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Affiliation(s)
- Yoshinori Kawabe
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD15EH, UK
| | - Qingyou Du
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD15EH, UK
| | - Takaaki B Narita
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD15EH, UK
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba, 275-0016, Japan
| | - Craig Bell
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD15EH, UK
- West of Scotland Innovation Hub, NHS Greater Glasgow and Clyde, Queen Elizabeth University Hospital, Glasgow, G514LB, UK
| | - Christina Schilde
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD15EH, UK
- D'Arcy Thompson Unit, School of Life Sciences, University of Dundee, Dundee, DD14HN, UK
| | - Koryu Kin
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD15EH, UK
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, 08003, Spain
| | - Pauline Schaap
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD15EH, UK.
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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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Du Q, Schaap P. Autophagy of the somatic stalk cells likely nurses the propagating spores of Dictyostelid social amoebas. OPEN RESEARCH EUROPE 2022; 2:104. [PMID: 36860212 PMCID: PMC7614253 DOI: 10.12688/openreseurope.14947.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/14/2022] [Indexed: 11/24/2022]
Abstract
Background: Autophagy (self-feeding) assists survival of starving cells by partial self-digestion, while dormancy as cysts, spores or seeds enables long-term survival. Starving Dictyostelium amoebas construct multicellular fruiting bodies with spores and stalk cells, with many Dictyostelia still able to encyst individually like their single-celled ancestors. While autophagy mostly occurs in the somatic stalk cells, autophagy gene knock-outs in Dictyostelium discoideum ( D. discoideum) formed no spores and lacked cAMP induction of prespore gene expression. Methods: To investigate whether autophagy also prevents encystation, we knocked-out autophagy genes atg5 and atg7 in the dictyostelid Polysphondylium pallidum, which forms both spores and cysts. We measured spore and cyst differentiation and viability in the knock-out as well as stalk and spore gene expression and its regulation by cAMP. We tested a hypothesis that spores require materials derived from autophagy in stalk cells. Sporulation requires secreted cAMP acting on receptors and intracellular cAMP acting on PKA. We compared the morphology and viability of spores developed in fruiting bodies with spores induced from single cells by stimulation with cAMP and 8Br-cAMP, a membrane-permeant PKA agonist. Results: Loss of autophagy in P. pallidum reduced but did not prevent encystation. Stalk cells still differentiated but stalks were disorganised. However, no spores were formed at all and cAMP-induced prespore gene expression was lost. D. discoideum spores induced in vitro by cAMP and 8Br-cAMP were smaller and rounder than spores formed multicellularly and while they were not lysed by detergent they germinated not (strain Ax2) or poorly (strain NC4), unlike spores formed in fruiting bodies. Conclusions: The stringent requirement of sporulation on both multicellularity and autophagy, which occurs mostly in stalk cells, suggests that stalk cells nurse the spores through autophagy. This highlights autophagy as a major cause for somatic cell evolution in early multicellularity.
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Affiliation(s)
- Qingyou Du
- School of Life Sciences, University of Dundee, Dundee, Angus, DD15EH, UK
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee, Angus, DD15EH, UK
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Kawabe Y, Schaap P. Adenylate cyclase A amplification and functional diversification during Polyspondylium pallidum development. EvoDevo 2022; 13:18. [PMID: 36261860 PMCID: PMC9583560 DOI: 10.1186/s13227-022-00203-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
Background In Dictyostelium discoideum (Ddis), adenylate cyclase A (ACA) critically generates the cAMP oscillations that coordinate aggregation and morphogenesis. Unlike group 4 species like Ddis, other groups do not use extracellular cAMP to aggregate. However, deletion of cAMP receptors (cARs) or extracellular phosphodiesterase (PdsA) in Polyspondylium pallidum (Ppal, group 2) blocks fruiting body formation, suggesting that cAMP oscillations ancestrally control post-aggregative morphogenesis. In group 2, the acaA gene underwent several duplications. We deleted the three Ppal aca genes to identify roles for either gene and tested whether Ppal shows transient cAMP-induced cAMP accumulation, which underpins oscillatory cAMP signalling. Results In contrast to Ddis, pre-aggregative Ppal cells did not produce a pulse of cAMP upon stimulation with the cAR agonist 2′H-cAMP, but acquired this ability after aggregation. Deletion of Ppal aca1, aca2 and aca3 yielded different phenotypes. aca1ˉ cells showed relatively thin stalks, aca2ˉ showed delayed secondary sorogen formation and aca3ˉ formed less aggregation centers. The aca1ˉaca2ˉ and aca1ˉaca3ˉ mutants combined individual defects, while aca2ˉaca3ˉ and aca1ˉaca3ˉaca2ˉ additionally showed > 24 h delay in aggregation, with only few aggregates with fragmenting streams being formed. The fragments developed into small fruiting bodies with stalk and spore cells. Aggregation was restored in aca2ˉaca3ˉ and aca1ˉaca3ˉaca2ˉ by 2.5 mM 8Br-cAMP, a membrane-permeant activator of cAMP-dependent protein kinase (PKA). Like Ddis, Ppal sorogens also express the adenylate cyclases ACR and ACG. We found that prior to aggregation, Ddis acaˉ/ACG cells produced a pulse of cAMP upon stimulation with 2′H-cAMP, indicating that cAMP oscillations may not be dependent on ACA alone. Conclusions The three Ppal replicates of acaA perform different roles in stalk morphogenesis, secondary branch formation and aggregation, but act together to enable development by activating PKA. While even an aca1ˉaca3ˉaca2ˉ mutant still forms (some) fruiting bodies, suggesting little need for ACA-induced cAMP oscillations in this process, we found that ACG also mediated transient cAMP-induced cAMP accumulation. It, therefore, remains likely that post-aggregative Ppal morphogenesis is organized by cAMP oscillations, favouring a previously proposed model, where cAR-regulated cAMP hydrolysis rather than its synthesis dominates oscillatory behaviour. Supplementary Information The online version contains supplementary material available at 10.1186/s13227-022-00203-7.
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Affiliation(s)
- Yoshinori Kawabe
- School of Life Sciences, University of Dundee, Dundee, DD15EH, UK
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee, DD15EH, UK.
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5
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Kin K, Chen ZH, Forbes G, Schaap P. Evolution of a novel cell type in Dictyostelia required gene duplication of a cudA-like transcription factor. Curr Biol 2022; 32:428-437.e4. [PMID: 34883046 PMCID: PMC8808424 DOI: 10.1016/j.cub.2021.11.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/04/2021] [Accepted: 11/17/2021] [Indexed: 10/31/2022]
Abstract
The evolution of novel cell types has been proposed to result from duplication of gene regulatory networks, but proven examples are rare. In addition to stalk cells and spores that make up the fruiting bodies of three major groups of Dictyostelia, those in group 4 additionally evolved basal disc and cup cells that respectively anchor the stalk to the substratum and the spore mass to the stalk. We noted a putative group-4-specific duplication of a cudA-like transcription factor (TF) in a comparative analysis of group-representative genomes. Using increased taxon sampling, we here confirmed that this TF, cdl1, duplicated into cdl1a and cdl1b in the common ancestor to group 4. cdl1a, but not cdl1b, showed signatures of positive selection, indicative of functional innovation. Deletion of cdl1a in Dictyostelium discoideum resulted in fruiting bodies with sagging spore heads that lacked the supporting cup cells and expression of cup-specific genes. Deletion of cdl1b resulted in thinner fruiting body stalks, while a cdl1b-cdl1a- double knockout showed more severe stalk defects, suggesting an ancestral role of cdl1 in stalk formation. This was confirmed in a closely related non-group 4 species, Polysphondylium violaceum, where cdl1 knockout caused defective stalk formation. These data indicate that the group-specific duplication of cdl1 and subsequent diversification of cdl1a played a pivotal role in the evolution of a novel somatic cell type in group 4 Dictyostelia.
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Affiliation(s)
- Koryu Kin
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Zhi-Hui Chen
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK
| | - Gillian Forbes
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK
| | - Pauline Schaap
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK.
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Schaap P. From environmental sensing to developmental control: cognitive evolution in dictyostelid social amoebas. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190756. [PMID: 33487113 PMCID: PMC7934950 DOI: 10.1098/rstb.2019.0756] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Dictyostelid social amoebas respond to starvation by self-organizing into multicellular slugs that migrate towards light to construct spore-bearing structures. These behaviours depend on excitable networks that enable amoebas to produce propagating waves of the chemoattractant cAMP, and to respond by directional movement. cAMP additionally regulates cell differentiation throughout development, with differentiation and cell movement being coordinated by interaction of the stalk inducer c-di-GMP with the adenylate cyclase that generates cAMP oscillations. Evolutionary studies indicate how the manifold roles of cAMP in multicellular development evolved from a role as intermediate for starvation-induced encystation in the unicellular ancestor. A merger of this stress response with the chemotaxis excitable networks yielded the developmental complexity and cognitive capabilities of extant Dictyostelia. This article is part of the theme issue ‘Basal cognition: conceptual tools and the view from the single cell’.
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Affiliation(s)
- Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee DD15EH, UK
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7
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Kawabe Y, Du Q, Schilde C, Schaap P. Evolution of multicellularity in Dictyostelia. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2020; 63:359-369. [PMID: 31840775 PMCID: PMC6978153 DOI: 10.1387/ijdb.190108ps] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The well-orchestrated multicellular life cycle of Dictyostelium discoideum has fascinated biologists for over a century. Self-organisation of its amoebas into aggregates, migrating slugs and fruiting structures by pulsatile cAMP signalling and their ability to follow separate differentiation pathways in well-regulated proportions continue to be topics under investigation. A striking aspect of D. discoideum development is the recurrent use of cAMP as chemoattractant, differentiation inducing signal and second messenger for other signals that control the developmental programme. D. discoideum is one of >150 species of Dictyostelia and aggregative life styles similar to those of Dictyostelia evolved many times in eukaryotes. Here we review experimental studies investigating how phenotypic complexity and cAMP signalling co-evolved in Dictyostelia. In addition, we summarize comparative genomic studies of multicellular Dictyostelia and unicellular Amoebozoa aimed to identify evolutionary conservation and change in all genes known to be essential for D. discoideum development.
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8
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Narita TB, Kawabe Y, Kin K, Gibbs RA, Kuspa A, Muzny DM, Richards S, Strassmann JE, Sucgang R, Worley KC, Schaap P. Loss of the Polyketide Synthase StlB Results in Stalk Cell Overproduction in Polysphondylium violaceum. Genome Biol Evol 2020; 12:674-683. [PMID: 32386295 PMCID: PMC7259674 DOI: 10.1093/gbe/evaa079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Major phenotypic innovations in social amoeba evolution occurred at the transition between the Polysphondylia and group 4 Dictyostelia, which comprise the model organism Dictyostelium discoideum, such as the formation of a new structure, the basal disk. Basal disk differentiation and robust stalk formation require the morphogen DIF-1, synthesized by the polyketide synthase StlB, the des-methyl-DIF-1 methyltransferase DmtA, and the chlorinase ChlA, which are conserved throughout Dictyostelia. To understand how the basal disk and other innovations evolved in group 4, we sequenced and annotated the Polysphondylium violaceum (Pvio) genome, performed cell type-specific transcriptomics to identify cell-type marker genes, and developed transformation and gene knock-out procedures for Pvio. We used the novel methods to delete the Pvio stlB gene. The Pvio stlB- mutants formed misshapen curly sorogens with thick and irregular stalks. As fruiting body formation continued, the upper stalks became more regular, but structures contained 40% less spores. The stlB- sorogens overexpressed a stalk gene and underexpressed a (pre)spore gene. Normal fruiting body formation and sporulation were restored in Pvio stlB- by including DIF-1 in the supporting agar. These data indicate that, although conserved, stlB and its product(s) acquired both a novel role in the group 4 Dictyostelia and a role opposite to that in its sister group.
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Affiliation(s)
- Takaaki B Narita
- School of Life Sciences, University of Dundee, United Kingdom,Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba, Japan
| | | | - Koryu Kin
- School of Life Sciences, University of Dundee, United Kingdom
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Adam Kuspa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas,The Welch Foundation, Houston, TX
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Stephen Richards
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,Genome Sequencing Center, University of California Davis, Davis, CA
| | | | - Richard Sucgang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Kim C Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, United Kingdom,Corresponding author: E-mail:
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Nanjundiah V. Many roads lead to Rome: Neutral phenotypes in microorganisms. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:339-348. [PMID: 31617664 DOI: 10.1002/jez.b.22909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/10/2019] [Accepted: 09/14/2019] [Indexed: 11/09/2022]
Abstract
John Bonner pointed out that microorganisms differ in several ways, some of which may reflect neutral phenotypic evolution. For making his case, Bonner referred to interspecies differences and morphological traits. Here we consider intraspecies differences and physiological traits. As a case-study, we examine the production of an extracellular cyclic 3 ' ,5 ' monophosphate phosphodiesterase in the cellular slime mold Dictyostelium discoideum. Temporal profiles of phosphodiesterase activity differ significantly between wild-type strains. From that we argue that the inference drawn initially from studies on a single wild-type, namely that the profile displayed by it pointed to an adaptive role, was mistaken. We generalize the conclusion to suggest that physiological differences exhibited by microorganisms of the same species may, but need not, reflect adaptations to different environments. Rather, the differences could be related to the fact that microorganisms live in groups whose composition can vary between homogeneous (clonal) and heterogeneous (polyclonal). More than one physiological profile is consistent with the normal development of the group in a given environment; the alternatives are neutral. When studying microbial physiology and behavior, it is expected that the observations are made on a clonal population; genetic (and so phenotypic) heterogeneity is carefully guarded against. As the example from D. discoideum shows, an unintended consequence of overlooking phenotypic heterogeneity is that one can fall into the trap of accepting a seemingly plausible, but possibly erroneous, adaptive explanation for a "normal" wild-type phenotype.
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Affiliation(s)
- Vidyanand Nanjundiah
- Centre for Human Genetics, BioTech Park, Bangalore, India.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
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10
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Kawabe Y, Morio T, Tanaka Y, Schaap P. Glycogen synthase kinase 3 promotes multicellular development over unicellular encystation in encysting Dictyostelia. EvoDevo 2018; 9:12. [PMID: 29760875 PMCID: PMC5941370 DOI: 10.1186/s13227-018-0101-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/29/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Glycogen synthase kinase 3 (GSK3) regulates many cell fate decisions in animal development. In multicellular structures of the group 4 dictyostelid Dictyostelium discoideum, GSK3 promotes spore over stalk-like differentiation. We investigated whether, similar to other sporulation-inducing genes such as cAMP-dependent protein kinase (PKA), this role of GSK3 is derived from an ancestral role in encystation of unicellular amoebas. RESULTS We deleted GSK3 in Polysphondylium pallidum, a group 2 dictyostelid which has retained encystation as an alternative survival strategy. Loss of GSK3 inhibited cytokinesis of cells in suspension, as also occurs in D. discoideum, but did not affect spore or stalk differentiation in P. pallidum. However, gsk3- amoebas entered into encystation under conditions that in wild type favour aggregation and fruiting body formation. The gsk3- cells were hypersensitive to osmolytes, which are known to promote encystation, and to cyst-inducing factors that are secreted during starvation. GSK3 was not itself regulated by these factors, but inhibited their effects. CONCLUSIONS Our data show that GSK3 has a deeply conserved role in controlling cytokinesis, but not spore differentiation in Dictyostelia. Instead, in P. pallidum, one of many Dictyostelia that like their solitary ancestors can still encyst to survive starvation, GSK3 promotes multicellular development into fruiting bodies over unicellular encystment.
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Affiliation(s)
- Yoshinori Kawabe
- 0000 0004 0397 2876grid.8241.fSchool of Life Sciences, University of Dundee, MSI/WTB Complex, Dow Street, Dundee, DD15EH UK ,0000 0001 2369 4728grid.20515.33Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572 Japan
| | - Takahiro Morio
- 0000 0001 2369 4728grid.20515.33Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572 Japan
| | - Yoshimasa Tanaka
- 0000 0001 2369 4728grid.20515.33Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572 Japan
| | - Pauline Schaap
- 0000 0004 0397 2876grid.8241.fSchool of Life Sciences, University of Dundee, MSI/WTB Complex, Dow Street, Dundee, DD15EH UK
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11
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Schilde C, Lawal HM, Noegel AA, Eichinger L, Schaap P, Glöckner G. A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae. BMC Genomics 2016; 17:871. [PMID: 27814692 PMCID: PMC5097433 DOI: 10.1186/s12864-016-3223-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/27/2016] [Indexed: 02/07/2023] Open
Abstract
Background The developmental cycle of Dictyostelid amoebae represents an early form of multicellularity with cell type differentiation. Mutant studies in the model Dictyostelium discoideum revealed that its developmental program integrates the actions of genes involved in signal transduction, adhesion, motility, autophagy and cell wall and matrix biosynthesis. However, due to functional redundancy and fail safe options not required in the laboratory, this single organism approach cannot capture all essential genes. To understand how multicellular organisms evolved, it is essential to recognize both the conserved core features of their developmental programs and the gene modifications that instigated phenotypic innovation. For complex organisms, such as animals, this is not within easy reach, but it is feasible for less complex forms, such as the Dictyostelid social amoebas. Results We compared global profiles of gene expression during the development of four social amoebae species that represent 600 mya of Dictyostelia evolution, and identified orthologous conserved genes with similar developmental up-regulation of expression using three different methods. For validation, we disrupted five genes of this core set and examined the phenotypic consequences. Conclusion At least 71 of the developmentally regulated genes that were identified with all methods were likely to be already present in the last ancestor of all Dictyostelia. The lack of phenotypic changes in null mutants indicates that even highly conserved genes either participate in functionally redundant pathways or are necessary for developmental progression under adverse, non-standard laboratory conditions. Both mechanisms provide robustness to the developmental program, but impose a limit on the information that can be obtained from deleting single genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3223-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christina Schilde
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Hajara M Lawal
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Angelika A Noegel
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
| | - Ludwig Eichinger
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
| | - Pauline Schaap
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Gernot Glöckner
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany. .,Institute for Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany.
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Huber RJ, O'Day DH. Extracellular matrix dynamics and functions in the social amoeba Dictyostelium: A critical review. Biochim Biophys Acta Gen Subj 2016; 1861:2971-2980. [PMID: 27693486 DOI: 10.1016/j.bbagen.2016.09.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/19/2016] [Accepted: 09/26/2016] [Indexed: 01/10/2023]
Abstract
BACKGROUND The extracellular matrix (ECM) is a dynamic complex of glycoproteins, proteoglycans, carbohydrates, and collagen that serves as an interface between mammalian cells and their extracellular environment. Essential for normal cellular homeostasis, physiology, and events that occur during development, it is also a key functionary in a number of human diseases including cancer. The social amoeba Dictyostelium discoideum secretes an ECM during multicellular development that regulates multicellularity, cell motility, cell differentiation, and morphogenesis, and provides structural support and protective layers to the resulting differentiated cell types. Proteolytic processing within the Dictyostelium ECM leads to specific bioactive factors that regulate cell motility and differentiation. SCOPE OF REVIEW Here we review the structure and functions of the Dictyostelium ECM and its role in regulating multicellular development. The questions and challenges that remain and how they can be answered are also discussed. MAJOR CONCLUSIONS The Dictyostelium ECM shares many of the features of mammalian and plant ECM, and thus presents an excellent system for studying the structure and function of the ECM. GENERAL SIGNIFICANCE As a genetically tractable model organism, Dictyostelium offers the potential to further elucidate ECM functions, and to possibly reveal previously unknown roles for the ECM.
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Affiliation(s)
- Robert J Huber
- Department of Biology, Trent University, Peterborough, Ontario, Canada.
| | - Danton H O'Day
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada; Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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Schaap P. Evolution of developmental signalling in Dictyostelid social amoebas. Curr Opin Genet Dev 2016; 39:29-34. [PMID: 27318097 PMCID: PMC5113120 DOI: 10.1016/j.gde.2016.05.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 05/16/2016] [Accepted: 05/26/2016] [Indexed: 11/17/2022]
Abstract
Dictyostelia represent a tractable system to resolve the evolution of cell-type specialization, with some taxa differentiating into spores only, and other taxa with additionally one or up to four somatic cell types. One of the latter forms, Dictyostelium discoideum, is a popular model system for cell biology and developmental biology with key signalling pathways controlling cell-specialization being resolved recently. For the most dominant pathways, evolutionary origins were retraced to a stress response in the unicellular ancestor, while modifications in the ancestral pathway were associated with acquisition of multicellular complexity. This review summarizes our current understanding of developmental signalling in D. discoideum and its evolution.
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Affiliation(s)
- Pauline Schaap
- School of Life Sciences, University of Dundee, DD15EH Dundee, UK.
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Du Q, Kawabe Y, Schilde C, Chen ZH, Schaap P. The Evolution of Aggregative Multicellularity and Cell-Cell Communication in the Dictyostelia. J Mol Biol 2015; 427:3722-33. [PMID: 26284972 PMCID: PMC5055082 DOI: 10.1016/j.jmb.2015.08.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/30/2015] [Accepted: 08/03/2015] [Indexed: 10/30/2022]
Abstract
Aggregative multicellularity, resulting in formation of a spore-bearing fruiting body, evolved at least six times independently amongst both eukaryotes and prokaryotes. Amongst eukaryotes, this form of multicellularity is mainly studied in the social amoeba Dictyostelium discoideum. In this review, we summarise trends in the evolution of cell-type specialisation and behavioural complexity in the four major groups of Dictyostelia. We describe the cell-cell communication systems that control the developmental programme of D. discoideum, highlighting the central role of cAMP in the regulation of cell movement and cell differentiation. Comparative genomic studies showed that the proteins involved in cAMP signalling are deeply conserved across Dictyostelia and their unicellular amoebozoan ancestors. Comparative functional analysis revealed that cAMP signalling in D. discoideum originated from a second messenger role in amoebozoan encystation. We highlight some molecular changes in cAMP signalling genes that were responsible for the novel roles of cAMP in multicellular development.
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Affiliation(s)
- Qingyou Du
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Yoshinori Kawabe
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Christina Schilde
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Zhi-Hui Chen
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Pauline Schaap
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
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A conserved signalling pathway for amoebozoan encystation that was co-opted for multicellular development. Sci Rep 2015; 5:9644. [PMID: 25881075 PMCID: PMC4399386 DOI: 10.1038/srep09644] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 03/04/2015] [Indexed: 11/08/2022] Open
Abstract
The evolution of multicellularity required novel mechanisms for intercellular communication, but their origin is unclear. Dictyostelium cells exchange signals to position specialized cell types in multicellular spore-bearing structures. These signals activate complex pathways that converge on activation of cAMP-dependent protein kinase (PKA). Genes controlling PKA were detected in the Dictyostelid unicellular ancestors, which like most protists form dormant cysts when experiencing environmental stress. We deleted PKA and the adenylate cyclases AcrA and AcgA, which synthesize cAMP for PKA activation, in the intermediate species Polysphondylium, which can develop into either cysts or into multicellular structures. Loss of PKA prevented multicellular development, but also completely blocked encystation. Loss of AcrA and AcgA, both essential for sporulation in Dictyostelium, did not affect Polysphondylium sporulation, but prevented encystation. We conclude that multicellular cAMP signalling was co-opted from PKA regulation of protist encystation with progressive refunctionalization of pathway components.
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Evolutionary reconstruction of pattern formation in 98 Dictyostelium species reveals that cell-type specialization by lateral inhibition is a derived trait. EvoDevo 2014; 5:34. [PMID: 25904998 PMCID: PMC4406040 DOI: 10.1186/2041-9139-5-34] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/22/2014] [Indexed: 02/07/2023] Open
Abstract
Background Multicellularity provides organisms with opportunities for cell-type specialization, but requires novel mechanisms to position correct proportions of different cell types throughout the organism. Dictyostelid social amoebas display an early form of multicellularity, where amoebas aggregate to form fruiting bodies, which contain only spores or up to four additional cell-types. These cell types will form the stalk and support structures for the stalk and spore head. Phylogenetic inference subdivides Dictyostelia into four major groups, with the model organism D. discoideum residing in group 4. In D. discoideum differentiation of its five cell types is dominated by lateral inhibition-type mechanisms that trigger scattered cell differentiation, with tissue patterns being formed by cell sorting. Results To reconstruct the evolution of pattern formation in Dictyostelia, we used cell-type specific antibodies and promoter-reporter fusion constructs to investigate pattern formation in 98 species that represent all groupings. Our results indicate that in all early diverging Dictyostelia and most members of groups 1–3, cells differentiate into maximally two cell types, prestalk and prespore cells, with pattern formation being dominated by position-dependent transdifferentiation of prespore cells into prestalk cells. In clade 2A, prestalk and stalk cell differentiation are lost and the prespore cells construct an acellular stalk. Group 4 species set aside correct proportions of prestalk and prespore cells early in development, and differentiate into up to three more supporting cell types. Conclusions Our experiments show that positional transdifferentiation is the ancestral mode of pattern formation in Dictyostelia. The early specification of a prestalk population equal to the number of stalk cells is a derived trait that emerged in group 4 and a few late diverging species in the other groups. Group 4 spore masses are larger than those of other groups and the differentiation of supporting cell types by lateral inhibition may have facilitated this increase in size. The signal DIF-1, which is secreted by prespore cells, triggers differentiation of supporting cell types. The synthesis and degradation of DIF-1 were shown to be restricted to group 4. This suggests that the emergence of DIF-1 signalling caused increased cell-type specialization in this group. Electronic supplementary material The online version of this article (doi:10.1186/2041-9139-5-34) contains supplementary material, which is available to authorized users.
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Du Q, Schaap P. The social amoeba Polysphondylium pallidum loses encystation and sporulation, but can still erect fruiting bodies in the absence of cellulose. Protist 2014; 165:569-79. [PMID: 25113829 PMCID: PMC4210663 DOI: 10.1016/j.protis.2014.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/08/2014] [Accepted: 07/08/2014] [Indexed: 11/24/2022]
Abstract
Amoebas and other freely moving protists differentiate into walled cysts when exposed to stress. As cysts, amoeba pathogens are resistant to biocides, preventing treatment and eradication. Lack of gene modification procedures has left the mechanisms of encystation largely unexplored. Genetically tractable Dictyostelium discoideum amoebas require cellulose synthase for formation of multicellular fructifications with cellulose-rich stalk and spore cells. Amoebas of its distant relative Polysphondylium pallidum (Ppal), can additionally encyst individually in response to stress. Ppal has two cellulose synthase genes, DcsA and DcsB, which we deleted individually and in combination. Dcsa- mutants formed fruiting bodies with normal stalks, but their spore and cyst walls lacked cellulose, which obliterated stress-resistance of spores and rendered cysts entirely non-viable. A dcsa-/dcsb- mutant made no walled spores, stalk cells or cysts, although simple fruiting structures were formed with a droplet of amoeboid cells resting on an sheathed column of decaying cells. DcsB is expressed in prestalk and stalk cells, while DcsA is additionally expressed in spores and cysts. We conclude that cellulose is essential for encystation and that cellulose synthase may be a suitable target for drugs to prevent encystation and render amoeba pathogens susceptible to conventional antibiotics.
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Affiliation(s)
- Qingyou Du
- College of Life Sciences, University of Dundee, MSI/WTB/JBC complex, Dow Street, Dundee, DD15EH, UK
| | - Pauline Schaap
- College of Life Sciences, University of Dundee, MSI/WTB/JBC complex, Dow Street, Dundee, DD15EH, UK.
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Romeralo M, Skiba A, Gonzalez-Voyer A, Schilde C, Lawal H, Kedziora S, Cavender JC, Glöckner G, Urushihara H, Schaap P. Analysis of phenotypic evolution in Dictyostelia highlights developmental plasticity as a likely consequence of colonial multicellularity. Proc Biol Sci 2013; 280:20130976. [PMID: 23782883 PMCID: PMC3712420 DOI: 10.1098/rspb.2013.0976] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Colony formation was the first step towards evolution of multicellularity in many macroscopic organisms. Dictyostelid social amoebas have used this strategy for over 600 Myr to form fruiting structures of increasing complexity. To understand in which order multicellular complexity evolved, we measured 24 phenotypic characters over 99 dictyostelid species. Using phylogenetic comparative methods, we show that the last common ancestor (LCA) of Dictyostelia probably erected small fruiting structures directly from aggregates. It secreted cAMP to coordinate fruiting body morphogenesis, and another compound to mediate aggregation. This phenotype persisted up to the LCAs of three of the four major groups of Dictyostelia. The group 4 LCA co-opted cAMP for aggregation and evolved much larger fruiting structures. However, it lost encystation, the survival strategy of solitary amoebas that is retained by many species in groups 1–3. Large structures, phototropism and a migrating intermediate ‘slug’ stage coevolved as evolutionary novelties within most groups. Overall, dictyostelids show considerable plasticity in the size and shape of multicellular structures, both within and between species. This probably reflects constraints placed by colonial life on developmental control mechanisms, which, depending on local cell density, need to direct from 10 to a million cells into forming a functional fructification.
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Affiliation(s)
- Maria Romeralo
- College of Life Sciences, University of Dundee, Dundee, UK
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Abstract
The model organism Dictyostelium discoideum is a member of the Amoebozoa, one of the six major -divisions of eukaryotes. Amoebozoa comprise a wide variety of amoeboid and flagellate organisms with single cells measuring from 5 μm to several meters across. They have adopted many different life styles and sexual behaviors and can live in all but the most extreme environments. This chapter provides an overview of Amoebozoan diversity and compares roads towards multicellularity within the Amoebozoa with inventions of multicellularity in other protist divisions. The chapter closes with a scenario for the evolution of Dictyostelid multicellularity from an Amoebozoan stress response.
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Affiliation(s)
| | - Pauline Schaap
- University of Dundee, College of Life Sciences, Dundee, UK
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