1
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Edelbroek B, Westholm JO, Bergquist J, Söderbom F. Multi-omics analysis of aggregative multicellularity. iScience 2024; 27:110659. [PMID: 39224513 PMCID: PMC11367525 DOI: 10.1016/j.isci.2024.110659] [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: 03/14/2024] [Revised: 06/14/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
All organisms have to carefully regulate their gene expression, not least during development. mRNA levels are often used as proxy for protein output; however, this approach ignores post-transcriptional effects. In particular, mRNA-protein correlation remains elusive for organisms that exhibit aggregative rather than clonal multicellularity. We addressed this issue by generating a paired transcriptomics and proteomics time series during the transition from uni-to multicellular stage in the social ameba Dictyostelium discoideum. Our data reveals that mRNA and protein levels correlate highly during unicellular growth, but decrease when multicellular development is initiated. This accentuates that transcripts alone cannot accurately predict protein levels. The dataset provides a useful resource to study gene expression during aggregative multicellular development. Additionally, our study provides an example of how to analyze and visualize mRNA and protein levels, which should be broadly applicable to other organisms and conditions.
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Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, BMC, Uppsala University, 751 24 Uppsala, Sweden
| | - Jakub Orzechowski Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry and Neurochemistry, Uppsala University, Uppsala, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, BMC, Uppsala University, 751 24 Uppsala, Sweden
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2
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Edelbroek B, Kjellin J, Jerlström-Hultqvist J, Koskiniemi S, Söderbom F. Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis. Sci Data 2024; 11:678. [PMID: 38909042 PMCID: PMC11193728 DOI: 10.1038/s41597-024-03513-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Dicytostelium firmibasis is a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni- to multicellular life. The D. firmibasis genome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-level D. firmibasis genome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison to Dictyostelium discoideum, the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.
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Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Jonas Kjellin
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden.
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3
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Nishimura T, Murotani T, Sasaki H, Uekusa Y, Eguchi H, Ishigaki H, Takahashi K, Kubohara Y, Kikuchi H. Isolation and Structure Determination of New Pyrones from Dictyostelium spp. Cellular Slime Molds Coincubated with Pseudomonas spp. Molecules 2024; 29:2143. [PMID: 38731634 PMCID: PMC11085369 DOI: 10.3390/molecules29092143] [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: 04/15/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Cellular slime molds are excellent model organisms in the field of cell and developmental biology because of their simple developmental patterns. During our studies on the identification of bioactive molecules from secondary metabolites of cellular slime molds toward the development of novel pharmaceuticals, we revealed the structural diversity of secondary metabolites. Cellular slime molds grow by feeding on bacteria, such as Klebsiella aerogenes and Escherichia coli, without using medium components. Although changing the feeding bacteria is expected to affect dramatically the secondary metabolite production, the effect of the feeding bacteria on the production of secondary metabolites is not known. Herein, we report the isolation and structure elucidation of clavapyrone (1) from Dictyostelium clavatum, intermedipyrone (2) from D. magnum, and magnumiol (3) from D. intermedium. These compounds are not obtained from usual cultural conditions with Klebsiella aerogenes but obtained from coincubated conditions with Pseudomonas spp. The results demonstrate the diversity of the secondary metabolites of cellular slime molds and suggest that widening the range of feeding bacteria for cellular slime molds would increase their application potential in drug discovery.
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Affiliation(s)
- Takehiro Nishimura
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan;
| | - Takuya Murotani
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan; (T.M.); (H.S.); (H.E.)
| | - Hitomi Sasaki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan; (T.M.); (H.S.); (H.E.)
| | - Yoshinori Uekusa
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan;
| | - Hiromi Eguchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan; (T.M.); (H.S.); (H.E.)
| | - Hirotaka Ishigaki
- Department of Medical Technology, Faculty of Health Science, Gunma Paz University, Takasaki 370-0006, Japan; (H.I.); (K.T.)
| | - Katsunori Takahashi
- Department of Medical Technology, Faculty of Health Science, Gunma Paz University, Takasaki 370-0006, Japan; (H.I.); (K.T.)
| | - Yuzuru Kubohara
- Graduate School of Health and Sports Science, Juntendo University, 1-1 Hiraga-gakuendai, Inzai, Chiba 270-1695, Japan;
| | - Haruhisa Kikuchi
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan;
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan; (T.M.); (H.S.); (H.E.)
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4
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Mather RV, Larsen TJ, Brock DA, Queller DC, Strassmann JE. Paraburkholderia symbionts isolated from Dictyostelium discoideum induce bacterial carriage in other Dictyostelium species. Proc Biol Sci 2023; 290:20230977. [PMID: 37464760 PMCID: PMC10354463 DOI: 10.1098/rspb.2023.0977] [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: 05/03/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
The social amoeba Dictyostelium discoideum engages in a complex relationship with bacterial endosymbionts in the genus Paraburkholderia, which can benefit their host by imbuing it with the ability to carry prey bacteria throughout its life cycle. The relationship between D. discoideum and Paraburkholderia has been shown to take place across many strains and a large geographical area, but little is known about Paraburkholderia's potential interaction with other dictyostelid species. We explore the ability of three Paraburkholderia species to stably infect and induce bacterial carriage in other dictyostelid hosts. We found that all three Paraburkholderia species successfully infected and induced carriage in seven species of Dictyostelium hosts. While the overall behaviour was qualitatively similar to that previously observed in infections of D. discoideum, differences in the outcomes of different host/symbiont combinations suggest a degree of specialization between partners. Paraburkholderia was unable to maintain a stable association with the more distantly related host Polysphondylium violaceum. Our results suggest that the mechanisms and evolutionary history of Paraburkholderia's symbiotic relationships may be general within Dictyostelium hosts, but not so general that it can associate with hosts of other genera. Our work further develops an emerging model system for the study of symbiosis in microbes.
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Affiliation(s)
- Rory Vu Mather
- Department of Biology, Washington University in St Louis, St Louis, MO 63130-4899, USA
- Harvard Medical School, Boston, MA 02115-6027, USA
| | - Tyler J. Larsen
- Department of Biology, Washington University in St Louis, St Louis, MO 63130-4899, USA
| | - Debra A. Brock
- Department of Biology, Washington University in St Louis, St Louis, MO 63130-4899, USA
| | - David C. Queller
- Department of Biology, Washington University in St Louis, St Louis, MO 63130-4899, USA
| | - Joan E. Strassmann
- Department of Biology, Washington University in St Louis, St Louis, MO 63130-4899, USA
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5
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Forget M, Adiba S, De Monte S. Single-cell phenotypic plasticity modulates social behavior in Dictyostelium discoideum. iScience 2023; 26:106783. [PMID: 37235054 PMCID: PMC10206496 DOI: 10.1016/j.isci.2023.106783] [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: 10/11/2022] [Revised: 02/09/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
In Dictyostelium chimeras, "cheaters" are strains that positively bias their contribution to the pool of spores, i.e., the reproductive cells resulting from development. On evolutionary time scales, the selective advantage; thus, gained by cheaters is predicted to undermine collective functions whenever social behaviors are genetically determined. Genotypes; however, are not the sole determinant of spore bias, but the relative role of genetic and plastic differences in evolutionary success is unclear. Here, we study chimeras composed of cells harvested in different phases of population growth. We show that such heterogeneity induces frequency-dependent, plastic variation in spore bias. In genetic chimeras, the magnitude of such variation is not negligible and can even reverse the classification of a strain's social behavior. Our results suggest that differential cell mechanical properties can underpin, through biases emerging during aggregation, a "lottery" in strains' reproductive success that may counter the evolution of cheating.
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Affiliation(s)
- Mathieu Forget
- Institut de Biologie de l’Ecole Normale Supérieure, Département de Biologie, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plőn, Germany
| | - Sandrine Adiba
- Institut de Biologie de l’Ecole Normale Supérieure, Département de Biologie, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Silvia De Monte
- Institut de Biologie de l’Ecole Normale Supérieure, Département de Biologie, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plőn, Germany
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6
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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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7
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van der Wel H, Garcia AM, Gas-Pascual E, Willis MM, Kim HW, Bandini G, Gaye MM, Costello CE, Samuelson J, West CM. Spindly is a nucleocytosolic O-fucosyltransferase in Dictyostelium and related proteins are widespread in protists and bacteria. Glycobiology 2023; 33:225-244. [PMID: 36250576 PMCID: PMC10114647 DOI: 10.1093/glycob/cwac071] [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: 08/21/2022] [Revised: 10/09/2022] [Accepted: 10/13/2022] [Indexed: 11/15/2022] Open
Abstract
O-GlcNAcylation is a prominent modification of nuclear and cytoplasmic proteins in animals and plants and is mediated by a single O-GlcNAc transferase (OGT). Spindly (Spy), a paralog of OGT first discovered in higher plants, has an ortholog in the apicomplexan parasite Toxoplasma gondii, and both enzymes are now recognized as O-fucosyltransferases (OFTs). Here we investigate the evolution of spy-like genes and experimentally confirm OFT activity in the social amoeba Dictyostelium-a protist that is more related to fungi and metazoa. Immunofluorescence probing with the fucose-specific Aleuria aurantia lectin (AAL) and biochemical cell fractionation combined with western blotting suggested the occurrence of nucleocytoplasmic fucosylation. The absence of reactivity in mutants deleted in spy or gmd (unable to synthesize GDP-Fuc) suggested monofucosylation mediated by Spy. Genetic ablation of the modE locus, previously predicted to encode a GDP-fucose transporter, confirmed its necessity for fucosylation in the secretory pathway but not for the nucleocytoplasmic proteins. Affinity capture of these proteins combined with mass spectrometry confirmed monofucosylation of Ser and Thr residues of several known nucleocytoplasmic proteins. As in Toxoplasma, the Spy OFT was required for optimal proliferation of Dictyostelium under laboratory conditions. These findings support a new phylogenetic analysis of OGT and OFT evolution that indicates their occurrence in the last eukaryotic common ancestor but mostly complementary presence in its eukaryotic descendants with the notable exception that both occur in red algae and plants. Their generally exclusive expression, high degree of conservation, and shared monoglycosylation targets suggest overlapping roles in physiological regulation.
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Affiliation(s)
- Hanke van der Wel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Ana Maria Garcia
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Obstetrics and Gynecology (OBGYN), 1951 SW 172nd Ave, Hollywood, FL 33029, USA
| | - Elisabet Gas-Pascual
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Macy M Willis
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Hyun W Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Giulia Bandini
- Department of Molecular and Cell Biology, Boston University Henry Goldman School of Dental Medicine, Boston, MA 02118, USA
- Clarivate Analytics (UK) Ltd., 70 St. Mary Axe, London, EC3A 8BE
| | - Maissa Mareme Gaye
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, USA
- Chemistry Technology Center, Waters Corporation, Milford, MA 01757, USA
| | - Catherine E Costello
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, USA
| | - John Samuelson
- Department of Molecular and Cell Biology, Boston University Henry Goldman School of Dental Medicine, Boston, MA 02118, USA
| | - Christopher M West
- Department of Biochemistry and Molecular Biology, Center for Tropical and Emerging Global Diseases, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
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8
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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 RESEARCH EUROPE 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] [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.
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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
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9
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Saito T, Iijima T, Koyama K, Shinagawa T, Yamanaka A, Araki T, Suzuki N, Usuki T, Kay RR. Generating polyketide diversity in Dictyostelium: a Steely hybrid polyketide synthase produces alternate products at different developmental stages. Proc Biol Sci 2022; 289:20221176. [PMID: 36126683 PMCID: PMC9489281 DOI: 10.1098/rspb.2022.1176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The soil is a rich ecosystem where many ecological interactions are mediated by small molecules, and in which amoebae are low-level predators and also prey. The social amoeba Dictyostelium discoideum has a high genomic potential for producing polyketides to mediate its ecological interactions, including the unique 'Steely' enzymes, consisting of a fusion between a fatty acid synthase and a chalcone synthase. We report here that D. discoideum further increases its polyketide potential by using the StlB Steely enzyme, and a downstream chlorinating enzyme, to make both a chlorinated signal molecule, DIF-1, during its multi-cellular development, and a set of abundant polyketides in terminally differentiated stalk cells. We identify one of these as a chlorinated dibenzofuran with potent anti-bacterial activity. To do this, StlB switches expression from prespore to stalk cells in late development and is cleaved to release the chalcone synthase domain. Expression of this domain alone in StlB null cells allows synthesis of the stalk-associated, chlorinated polyketides. Thus, by altered expression and processing of StlB, cells make first a signal molecule, and then abundant secondary metabolites, which we speculate help to protect the mature spores from bacterial infection.
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Affiliation(s)
- Tamao Saito
- Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan
| | - Tomoyuki Iijima
- Graduate School of Science and Technology, Sophia University, Tokyo 102-8554, Japan
| | - Kohei Koyama
- Graduate School of Science and Technology, Sophia University, Tokyo 102-8554, Japan
| | - Tomonori Shinagawa
- Graduate School of Science and Technology, Sophia University, Tokyo 102-8554, Japan
| | - Ayaka Yamanaka
- Graduate School of Science and Technology, Sophia University, Tokyo 102-8554, Japan
| | - Tsuyoshi Araki
- Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan
| | - Noriyuki Suzuki
- Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan
| | - Toyonobu Usuki
- Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan
| | - Robert R. Kay
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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10
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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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11
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Role of an FNIP Repeat Domain-Containing Protein Encoded by Megavirus Baoshan during Viral Infection. J Virol 2022; 96:e0081322. [PMID: 35762756 PMCID: PMC9327691 DOI: 10.1128/jvi.00813-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
FNIP repeat domain-containing protein (FNIP protein) is a little-studied atypical leucine-rich repeat domain-containing protein found in social amoebae and mimiviruses. Here, a recently reported mimivirus of lineage C, Megavirus baoshan, was analyzed for FNIP protein genes. A total of 82 FNIP protein genes were identified, each containing up to 26 copies of the FNIP repeat, and mostly having an F-box domain at the N terminus. Both nucleotide and amino acid sequences of FNIP repeat were highly conserved. Most of the FNIP protein genes clustered together tandemly in groups of two to 14 genes. Nearly all FNIP protein genes shared similar expression patterns and were expressed 4 to 9 h postinfection. A typical viral FNIP protein, Mb0983, was selected for functional analysis. Protein interactome analysis identified two small GTPases, Rap1B and Rab7A, that interacted with Mb0983 in cytoplasm. The overexpression of Mb0983 in Acanthamoeba castellanii accelerated the degradation of Rap1B and Rab7A during viral infection. Mb0983 also interacted with host SKP1 and cullin-1, which were conserved components of the SKP1-cullin-1-F-box protein (SCF)-type ubiquitin E3 ligase complex. Deletion of the F-box domain of Mb0983 not only abolished its interaction with SKP1 and cullin-1 but also returned the speed of Rap1B and Rab7A degradation to normal in infected A. castellanii. These results suggested that Mb0983 is a part of the SCF-type ubiquitin E3 ligase complex and plays a role in the degradation of Rap1B and Rab7A. They also implied that other viral F-box-containing FNIP proteins might have similar effects on various host proteins. IMPORTANCE Megavirus baoshan encodes 82 FNIP proteins, more than any other reported mimiviruses. Their genetic and transcriptional features suggest that they are important for virus infection and adaption. Since most mimiviral FNIP proteins have the F-box domain, they were predicted to be involved in protein ubiquitylation. FNIP protein Mb0983 interacted with host SKP1 and cullin-1 through the F-box domain, supporting the idea that it is a part of the SCF-type ubiquitin E3 ligase complex. The substrates of Mb0983 for degradation were identified as the host small GTPases Rap1B and Rab7A. Combining the facts of the presence of a large number of FNIP genes in megavirus genomes, the extremely high expression level of the viral ubiquitin gene, and the reported observation that 35% of megavirus-infected amoeba cells died without productive infection, it is likely that megavirus actively explores the host ubiquitin-proteasome pathway in infection and that viral FNIP proteins play roles in the process.
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12
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Forbes G, Schilde C, Lawal H, Kin K, Du Q, Chen ZH, Rivero F, Schaap P. Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators. Small GTPases 2022; 13:239-254. [PMID: 34565293 PMCID: PMC8923023 DOI: 10.1080/21541248.2021.1984829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
GTP binding proteins known as small GTPases make up one of the largest groups of regulatory proteins and control almost all functions of living cells. Their activity is under, respectively, positive and negative regulation by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which together with their upstream regulators and the downstream targets of the small GTPases form formidable signalling networks. While genomics has revealed the large size of the GTPase, GEF and GAP repertoires, only a small fraction of their interactions and functions have yet been experimentally explored. Dictyostelid social amoebas have been particularly useful in unravelling the roles of many proteins in the Rac-Rho and Ras-Rap families of GTPases in directional cell migration and regulation of the actin cytoskeleton. Genomes and cell-type specific and developmental transcriptomes are available for Dictyostelium species that span the 0.5 billion years of evolution of the group from their unicellular ancestors. In this work, we identified all GTPases, GEFs and GAPs from genomes representative of the four major taxon groups and investigated their phylogenetic relationships and evolutionary conservation and changes in their functional domain architecture and in their developmental and cell-type specific expression. We performed a hierarchical cluster analysis of the expression profiles of the ~2000 analysed genes to identify putative interacting sets of GTPases, GEFs and GAPs, which highlight sets known to interact experimentally and many novel combinations. This work represents a valuable resource for research into all fields of cellular regulation.
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Affiliation(s)
- Gillian Forbes
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Hajara Lawal
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Koryu Kin
- School of Life Sciences, University of Dundee, Dundee, UK,CSIC-Universitat Pompeu Fabra, Institut de Biologia Evolutiva (Csic-universitat Pompeu Fabra), Barcelona, Spain
| | - Qingyou Du
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Zhi-hui Chen
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Francisco Rivero
- Centre for Atherothrombosis and Metabolic Disease, Hull York Medical School, Faculty of Health Sciences, University of Hull, Hull, UK
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee, UK,CONTACT Pauline Schaap ; School of Life Sciences, University of Dundee, Msi/wtb Complex, Dundee, DD15EH, UK
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13
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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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14
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Herman EK, Greninger A, van der Giezen M, Ginger ML, Ramirez-Macias I, Miller HC, Morgan MJ, Tsaousis AD, Velle K, Vargová R, Záhonová K, Najle SR, MacIntyre G, Muller N, Wittwer M, Zysset-Burri DC, Eliáš M, Slamovits CH, Weirauch MT, Fritz-Laylin L, Marciano-Cabral F, Puzon GJ, Walsh T, Chiu C, Dacks JB. Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri. BMC Biol 2021; 19:142. [PMID: 34294116 PMCID: PMC8296547 DOI: 10.1186/s12915-021-01078-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. RESULTS Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system. CONCLUSIONS In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.
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Affiliation(s)
- Emily K Herman
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Alex Greninger
- Laboratory Medicine and Medicine / Infectious Diseases, UCSF-Abbott Viral Diagnostics and Discovery Center, UCSF Clinical Microbiology Laboratory UCSF School of Medicine, San Francisco, USA
- Department of Laboratory Medicine, University of Washington Medical Center, Montlake, USA
| | - Mark van der Giezen
- Centre for Organelle Research, Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Michael L Ginger
- School of Applied Sciences, Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, UK
| | - Inmaculada Ramirez-Macias
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Department of Cardiology, Hospital Clinico Universitario Virgen de la Arrixaca. Instituto Murciano de Investigación Biosanitaria. Centro de Investigación Biomedica en Red-Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Haylea C Miller
- CSIRO Land and Water, Centre for Environment and Life Sciences, Private Bag No.5, Wembley, Western Australia 6913, Australia
- CSIRO, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, WA, Australia
| | - Matthew J Morgan
- CSIRO Land and Water, Black Mountain Laboratories, Canberra, Australia
| | | | - Katrina Velle
- Department of Biology, University of Massachusetts, Amherst, UK
| | - Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Kristína Záhonová
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Sebastian Rodrigo Najle
- Institut de Biologia Evolutiva (UPF-CSIC), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Catalonia, Spain
| | - Georgina MacIntyre
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Norbert Muller
- Institute of Parasitology, Vetsuisse Faculty Bern, University of Bern, Bern, Switzerland
| | - Mattias Wittwer
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, Spiez, Switzerland
| | - Denise C Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | | | - Francine Marciano-Cabral
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Geoffrey J Puzon
- CSIRO Land and Water, Centre for Environment and Life Sciences, Private Bag No.5, Wembley, Western Australia 6913, Australia
| | - Tom Walsh
- CSIRO Land and Water, Black Mountain Laboratories, Canberra, Australia
| | - Charles Chiu
- Laboratory Medicine and Medicine / Infectious Diseases, UCSF-Abbott Viral Diagnostics and Discovery Center, UCSF Clinical Microbiology Laboratory UCSF School of Medicine, San Francisco, USA
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
- Department of Life Sciences, The Natural History Museum, London, UK.
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15
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Kjellin J, Avesson L, Reimegård J, Liao Z, Eichinger L, Noegel A, Glöckner G, Schaap P, Söderbom F. Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas. Genome Res 2021; 31:436-447. [PMID: 33479022 PMCID: PMC7919456 DOI: 10.1101/gr.272856.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/15/2021] [Indexed: 01/26/2023]
Abstract
Aggregative multicellularity has evolved multiple times in diverse groups of eukaryotes, exemplified by the well-studied development of dictyostelid social amoebas, for example, Dictyostelium discoideum However, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of Amoebozoa are unicellular. Previously, a novel type of noncoding RNA, Class I RNAs, was identified in D. discoideum and shown to be important for normal multicellular development. Here, we investigated Class I RNA evolution and its connection to multicellular development. We identified a large number of new Class I RNA genes by constructing a covariance model combined with a scoring system based on conserved upstream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis confirmed that our search approach identifies expressed Class I RNA genes with high accuracy and sensitivity and that the RNAs are developmentally regulated. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share highly conserved structure and sequence motifs. In addition, Class I RNA genes appear to be unique to dictyostelid social amoebas because they could not be identified in outgroup genomes, including their closest known relatives. Our results show that Class I RNA is an ancient class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Based on previous functional analyses and the presented evolutionary investigation, we hypothesize that Class I RNAs were involved in evolution of multicellularity in Dictyostelia.
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Affiliation(s)
- Jonas Kjellin
- Department of Cell and Molecular Biology, Uppsala University, Uppsala S-75124, Sweden
| | - Lotta Avesson
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Uppsala S-75124, Sweden
| | - Johan Reimegård
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala S-75124, Sweden
| | - Zhen Liao
- Department of Cell and Molecular Biology, Uppsala University, Uppsala S-75124, Sweden
| | - Ludwig Eichinger
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Angelika Noegel
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Gernot Glöckner
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Pauline Schaap
- College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, Uppsala University, Uppsala S-75124, Sweden
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16
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West CM, Malzl D, Hykollari A, Wilson IBH. Glycomics, Glycoproteomics, and Glycogenomics: An Inter-Taxa Evolutionary Perspective. Mol Cell Proteomics 2021; 20:100024. [PMID: 32994314 PMCID: PMC8724618 DOI: 10.1074/mcp.r120.002263] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 12/23/2022] Open
Abstract
Glycosylation is a highly diverse set of co- and posttranslational modifications of proteins. For mammalian glycoproteins, glycosylation is often site-, tissue-, and species-specific and diversified by microheterogeneity. Multitudinous biochemical, cellular, physiological, and organismic effects of their glycans have been revealed, either intrinsic to the carrier proteins or mediated by endogenous reader proteins with carbohydrate recognition domains. Furthermore, glycans frequently form the first line of access by or defense from foreign invaders, and new roles for nucleocytoplasmic glycosylation are blossoming. We now know enough to conclude that the same general principles apply in invertebrate animals and unicellular eukaryotes-different branches of which spawned the plants or fungi and animals. The two major driving forces for exploring the glycomes of invertebrates and protists are (i) to understand the biochemical basis of glycan-driven biology in these organisms, especially of pathogens, and (ii) to uncover the evolutionary relationships between glycans, their biosynthetic enzyme genes, and biological functions for new glycobiological insights. With an emphasis on emerging areas of protist glycobiology, here we offer an overview of glycan diversity and evolution, to promote future access to this treasure trove of glycobiological processes.
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Affiliation(s)
- Christopher M West
- Department of Biochemistry & Molecular Biology, Center for Tropical and Emerging Global Diseases, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
| | - Daniel Malzl
- Department für Chemie, Universität für Bodenkultur, Wien, Austria
| | - Alba Hykollari
- Department für Chemie, Universität für Bodenkultur, Wien, Austria; VetCore Facility for Research/Proteomics Unit, Veterinärmedizinische Universität, Vienna, Austria
| | - Iain B H Wilson
- Department für Chemie, Universität für Bodenkultur, Wien, Austria
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17
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Aoki MM, Emery RJN, Anjard C, Brunetti CR, Huber RJ. Cytokinins in Dictyostelia - A Unique Model for Studying the Functions of Signaling Agents From Species to Kingdoms. Front Cell Dev Biol 2020; 8:511. [PMID: 32714926 PMCID: PMC7316887 DOI: 10.3389/fcell.2020.00511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
Cytokinins (CKs) are a diverse group of evolutionarily significant growth-regulating molecules. While the CK biosynthesis and signal transduction pathways are the most well-understood in plant systems, these molecules have been identified in all kingdoms of life. This review follows the recent discovery of an expanded CK profile in the social amoeba, Dictyostelium discoideum. A comprehensive review on the present knowledge of CK biosynthesis, signal transduction, and CK-small molecule interactions within members of Dictyostelia will be summarized. In doing so, the utility of social amoebae will be highlighted as a model system for studying the evolution of these hormone-like signaling agents, which will set the stage for future research in this area.
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Affiliation(s)
- Megan M Aoki
- Department of Biology, Trent University, Peterborough, ON, Canada
| | - R J Neil Emery
- Department of Biology, Trent University, Peterborough, ON, Canada
| | - Christophe Anjard
- Institut Lumière Matière, CNRS UMR 5306, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Craig R Brunetti
- Department of Biology, Trent University, Peterborough, ON, Canada
| | - Robert J Huber
- Department of Biology, Trent University, Peterborough, ON, Canada
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18
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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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19
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Hasni I, Andréani J, Colson P, La Scola B. Description of Virulent Factors and Horizontal Gene Transfers of Keratitis-Associated Amoeba Acanthamoeba Triangularis by Genome Analysis. Pathogens 2020; 9:pathogens9030217. [PMID: 32188120 PMCID: PMC7157575 DOI: 10.3390/pathogens9030217] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/10/2020] [Accepted: 03/13/2020] [Indexed: 02/02/2023] Open
Abstract
Acanthamoeba triangularis strain SH 621 is a free-living amoeba belonging to Acanthamoeba ribo-genotype T4. This ubiquitous protist is among the free-living amoebas responsible for Acanthamoeba keratitis, a severe infection of human cornea. Genome sequencing and genomic comparison were carried out to explore the biological functions and to better understand the virulence mechanism related to the pathogenicity of Acanthamoeba keratitis. The genome assembly harbored a length of 66.43 Mb encompassing 13,849 scaffolds. The analysis of predicted proteins reported the presence of 37,062 ORFs. A complete annotation revealed 33,168 and 16,605 genes that matched with NCBI non-redundant protein sequence (nr) and Cluster of Orthologous Group of proteins (COG) databases, respectively. The Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) annotation reported a great number of genes related to carbohydrate, amino acid and lipid metabolic pathways. The pangenome performed with 8 available amoeba genomes belonging to genus Acanthamoeba revealed a core genome containing 843 clusters of orthologous genes with a ratio core genome/pangenome of less than 0.02. We detected 48 genes related to virulent factors of Acanthamoeba keratitis. Best hit analyses in nr database identified 99 homologous genes shared with amoeba-resisting microorganisms. This study allows the deciphering the genome of a free-living amoeba with medical interest and provides genomic data to better understand virulence-related Acanthamoeba keratitis.
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Affiliation(s)
- Issam Hasni
- Institut de Recherche pour le Développement IRD 198, Aix-Marseille Université UM63, Assistance Publique – Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, 13005 Marseille, France; (I.H.); (J.A.); (P.C.)
- R&D Department, Amoéba, 38 Avenue des Frères Montgolfier, 69680 Chassieu, France
| | - Julien Andréani
- Institut de Recherche pour le Développement IRD 198, Aix-Marseille Université UM63, Assistance Publique – Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, 13005 Marseille, France; (I.H.); (J.A.); (P.C.)
| | - Philippe Colson
- Institut de Recherche pour le Développement IRD 198, Aix-Marseille Université UM63, Assistance Publique – Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, 13005 Marseille, France; (I.H.); (J.A.); (P.C.)
| | - Bernard La Scola
- Institut de Recherche pour le Développement IRD 198, Aix-Marseille Université UM63, Assistance Publique – Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, 13005 Marseille, France; (I.H.); (J.A.); (P.C.)
- Correspondence: ; Tel.: +33-4-13-73-24-01; Fax: +33-4-13-73-24-02
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20
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Hasni I, Chelkha N, Baptiste E, Mameri MR, Lachuer J, Plasson F, Colson P, La Scola B. Investigation of potential pathogenicity of Willaertia magna by investigating the transfer of bacteria pathogenicity genes into its genome. Sci Rep 2019; 9:18318. [PMID: 31797948 PMCID: PMC6892926 DOI: 10.1038/s41598-019-54580-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 11/10/2019] [Indexed: 12/14/2022] Open
Abstract
Willaertia magna c2c maky is a thermophilic amoeba closely related to the genus Naegleria. This free-living amoeba has the ability to eliminate Legionella pneumophila, which is an amoeba-resisting bacterium living in an aquatic environment. To prevent the proliferation of L. pneumophila in cooling towers, the use of W. magna as natural biocide has been proposed. To provide a better understanding of the W. magna genome, whole-genome sequencing was performed through the study of virulence factors and lateral gene transfers. This amoeba harbors a genome of 36.5 megabases with 18,519 predicted genes. BLASTp analyses reported protein homology between 136 W. magna sequences and amoeba-resistant microorganisms. Horizontal gene transfers were observed based on the basis of the phylogenetic reconstruction hypothesis. We detected 15 homologs of N. fowleri genes related to virulence, although these latter were also found in the genome of N. gruberi, which is a non-pathogenic amoeba. Furthermore, the cytotoxicity test performed on human cells supports the hypothesis that the strain c2c maky is a non-pathogenic amoeba. This work explores the genomic repertory for the first draft genome of genus Willaertia and provides genomic data for further comparative studies on virulence of related pathogenic amoeba, N. fowleri.
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Affiliation(s)
- Issam Hasni
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.,Amoéba, Chassieu, France
| | - Nisrine Chelkha
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Emeline Baptiste
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | | | - Joel Lachuer
- ProfileXpert/Viroscan3D, UCBL UMS 3453 CNRS - US7 INSERM, Lyon, France.,Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France
| | | | - Philippe Colson
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.
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21
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Conditional expression explains molecular evolution of social genes in a microbe. Nat Commun 2019; 10:3284. [PMID: 31337766 PMCID: PMC6650454 DOI: 10.1038/s41467-019-11237-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 06/25/2019] [Indexed: 12/30/2022] Open
Abstract
Conflict is thought to play a critical role in the evolution of social interactions by promoting diversity or driving accelerated evolution. However, despite our sophisticated understanding of how conflict shapes social traits, we have limited knowledge of how it impacts molecular evolution across the underlying social genes. Here we address this problem by analyzing the genome-wide impact of social interactions using genome sequences from 67 Dictyostelium discoideum strains. We find that social genes tend to exhibit enhanced polymorphism and accelerated evolution. However, these patterns are not consistent with conflict driven processes, but instead reflect relaxed purifying selection. This pattern is most likely explained by the conditional nature of social interactions, whereby selection on genes expressed only in social interactions is diluted by generations of inactivity. This dilution of selection by inactivity enhances the role of drift, leading to increased polymorphism and accelerated evolution, which we call the Red King process.
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22
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West CM, Kim HW. Nucleocytoplasmic O-glycosylation in protists. Curr Opin Struct Biol 2019; 56:204-212. [PMID: 31128470 DOI: 10.1016/j.sbi.2019.03.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/19/2019] [Accepted: 03/31/2019] [Indexed: 12/17/2022]
Abstract
O-Glycosylation is an increasingly recognized modification of intracellular proteins in all kingdoms of life, and its occurrence in protists has been investigated to understand its evolution and its roles in the virulence of unicellular pathogens. We focus here on two kinds of glycoregulation found in unicellular eukaryotes: one is a simple O-fucose modification of dozens if not hundreds of Ser/Thr-rich proteins, and the other a complex pentasaccharide devoted to a single protein associated with oxygen sensing and the assembly of polyubiquitin chains. These modifications are not required for life but contingently modulate biological processes in the social amoeba Dictyostelium and the human pathogen Toxoplasma gondii, and likely occur in diverse unicellular protists. O-Glycosylation that is co-localized in the cytoplasm allows for glycoregulation over the entire life of the protein, contrary to the secretory pathway where glycosylation usually occurs before its delivery to its site of function. Here, we interpret cellular roles of nucleocytoplasmic glycans in terms of current evidence for their effects on the conformation and dynamics of protist proteins, to serve as a guide for future studies to examine their broader significance.
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Affiliation(s)
- Christopher M West
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602 USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602 USA; Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA.
| | - Hyun W Kim
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602 USA
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23
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Abstract
In macropinocytosis, cells take up micrometre-sized droplets of medium into internal vesicles. These vesicles are acidified and fused to lysosomes, their contents digested and useful compounds extracted. Indigestible contents can be exocytosed. Macropinocytosis has been known for approaching 100 years and is described in both metazoa and amoebae, but not in plants or fungi. Its evolutionary origin goes back to at least the common ancestor of the amoebozoa and opisthokonts, with apparent secondary loss from fungi. The primary function of macropinocytosis in amoebae and some cancer cells is feeding, but the conserved processing pathway for macropinosomes, which involves shrinkage and the retrieval of membrane to the cell surface, has been adapted in immune cells for antigen presentation. Macropinocytic cups are large actin-driven processes, closely related to phagocytic cups and pseudopods and appear to be organized around a conserved signalling patch of PIP3, active Ras and active Rac that directs actin polymerization to its periphery. Patches can form spontaneously and must be sustained by excitable kinetics with strong cooperation from the actin cytoskeleton. Growth-factor signalling shares core components with macropinocytosis, based around phosphatidylinositol 3-kinase (PI3-kinase), and we suggest that it evolved to take control of ancient feeding structures through a coupled growth factor receptor. This article is part of the Theo Murphy meeting issue 'Macropinocytosis'.
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Affiliation(s)
- Jason S. King
- Department of Biomedical Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Robert R. Kay
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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24
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Schilde C, Lawal HM, Kin K, Shibano-Hayakawa I, Inouye K, Schaap P. A well supported multi gene phylogeny of 52 dictyostelia. Mol Phylogenet Evol 2019; 134:66-73. [PMID: 30711536 PMCID: PMC6430600 DOI: 10.1016/j.ympev.2019.01.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/09/2019] [Accepted: 01/21/2019] [Indexed: 12/22/2022]
Abstract
The Dictyostelid social amoebas are a popular model system for cell- and developmental biology and for evolution of sociality. Small subunit (SSU) ribosomal DNA-based phylogenies subdivide the known 150 species into four major and some minor groups, but lack resolution within groups, particularly group 4, and, as shown by genome-based phylogenies of 11 species, showed errors in the position of the root and nodes separating major clades. We are interested in the evolution of cell-type specialization, which particularly expanded in group 4. To construct a more robust phylogeny, we first included 7 recently sequenced genomes in the genome-based phylogeny of 47 functionally divergent proteins and next selected 6 proteins (Agl, AmdA, PurD, PurL, RpaA, SmdA) that independently or in sets of two fully reproduced the core-phylogeny. We amplified their coding regions from 34 Dictyostelium species and combined their concatenated sequences with those identified in the 18 genomes to generate a fully resolved phylogeny. The new AAPPRS based phylogeny (after the acronym of the 6 proteins) subdivides group 4 into 2 branches. These branches further resolve into 5 clades, rather than the progressively nested group 4 topology of the SSU rDNA tree, and also re-orders taxa in the other major groups. Ancestral state reconstruction of 25 phenotypic traits returned higher "goodness of fit" metrics for evolution of 19 of those traits over the AAPPRS tree, than over the SSU rDNA tree. The novel tree provides a solid framework for studying the evolution of cell-type specialization, signalling and other cellular processes in particularly group 4, which contains the model Dictyostelid D. discoideum.
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Affiliation(s)
| | - Hajara M Lawal
- School of Life Sciences, University of Dundee, Dundee DD15EH, UK
| | - Koryu Kin
- School of Life Sciences, University of Dundee, Dundee DD15EH, UK
| | - Ikumi Shibano-Hayakawa
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kei Inouye
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee DD15EH, UK.
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25
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Kundert P, Shaulsky G. Cellular allorecognition and its roles in Dictyostelium development and social evolution. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2019; 63:383-393. [PMID: 31840777 PMCID: PMC6919275 DOI: 10.1387/ijdb.190239gs] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The social amoeba Dictyostelium discoideum is a tractable model organism to study cellular allorecognition, which is the ability of a cell to distinguish itself and its genetically similar relatives from more distantly related organisms. Cellular allorecognition is ubiquitous across the tree of life and affects many biological processes. Depending on the biological context, these versatile systems operate both within and between individual organisms, and both promote and constrain functional heterogeneity. Some of the most notable allorecognition systems mediate neural self-avoidance in flies and adaptive immunity in vertebrates. D. discoideum's allorecognition system shares several structures and functions with other allorecognition systems. Structurally, its key regulators reside at a single genomic locus that encodes two highly polymorphic proteins, a transmembrane ligand called TgrC1 and its receptor TgrB1. These proteins exhibit isoform-specific, heterophilic binding across cells. Functionally, this interaction determines the extent to which co-developing D. discoideum strains co-aggregate or segregate during the aggregation phase of multicellular development. The allorecognition system thus affects both development and social evolution, as available evidence suggests that the threat of developmental cheating represents a primary selective force acting on it. Other significant characteristics that may inform the study of allorecognition in general include that D. discoideum's allorecognition system is a continuous and inclusive trait, it is pleiotropic, and it is temporally regulated.
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Affiliation(s)
- Peter Kundert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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26
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Kabbara S, Hérivaux A, Dugé de Bernonville T, Courdavault V, Clastre M, Gastebois A, Osman M, Hamze M, Cock JM, Schaap P, Papon N. Diversity and Evolution of Sensor Histidine Kinases in Eukaryotes. Genome Biol Evol 2019; 11:86-108. [PMID: 30252070 PMCID: PMC6324907 DOI: 10.1093/gbe/evy213] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2018] [Indexed: 12/20/2022] Open
Abstract
Histidine kinases (HKs) are primary sensor proteins that act in cell signaling pathways generically referred to as "two-component systems" (TCSs). TCSs are among the most widely distributed transduction systems used by both prokaryotic and eukaryotic organisms to detect and respond to a broad range of environmental cues. The structure and distribution of HK proteins are now well documented in prokaryotes, but information is still fragmentary for eukaryotes. Here, we have taken advantage of recent genomic resources to explore the structural diversity and the phylogenetic distribution of HKs in the prominent eukaryotic supergroups. Searches of the genomes of 67 eukaryotic species spread evenly throughout the phylogenetic tree of life identified 748 predicted HK proteins. Independent phylogenetic analyses of predicted HK proteins were carried out for each of the major eukaryotic supergroups. This allowed most of the compiled sequences to be categorized into previously described HK groups. Beyond the phylogenetic analysis of eukaryotic HKs, this study revealed some interesting findings: 1) characterization of some previously undescribed eukaryotic HK groups with predicted functions putatively related to physiological traits; 2) discovery of HK groups that were previously believed to be restricted to a single kingdom in additional supergroups, and 3) indications that some evolutionary paths have led to the appearance, transfer, duplication, and loss of HK genes in some phylogenetic lineages. This study provides an unprecedented overview of the structure and distribution of HKs in the Eukaryota and represents a first step toward deciphering the evolution of TCS signaling in living organisms.
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Affiliation(s)
- Samar Kabbara
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
| | - Anaïs Hérivaux
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
| | | | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université François Rabelais de Tours, France
| | - Marc Clastre
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université François Rabelais de Tours, France
| | - Amandine Gastebois
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - J Mark Cock
- Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Université Paris 06, CNRS, Roscoff, France
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, United Kingdom
| | - Nicolas Papon
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
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27
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Kubohara Y, Kikuchi H. Dictyostelium: An Important Source of Structural and Functional Diversity in Drug Discovery. Cells 2018; 8:E6. [PMID: 30583484 PMCID: PMC6356392 DOI: 10.3390/cells8010006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
The cellular slime mold Dictyostelium discoideum is an excellent model organism for the study of cell and developmental biology because of its simple life cycle and ease of use. Recent findings suggest that Dictyostelium and possibly other genera of cellular slime molds, are potential sources of novel lead compounds for pharmacological and medical research. In this review, we present supporting evidence that cellular slime molds are an untapped source of lead compounds by examining the discovery and functions of polyketide differentiation-inducing factor-1, a compound that was originally isolated as an inducer of stalk-cell differentiation in D. discoideum and, together with its derivatives, is now a promising lead compound for drug discovery in several areas. We also review other novel compounds, including secondary metabolites, that have been isolated from cellular slime molds.
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Affiliation(s)
- Yuzuru Kubohara
- Laboratory of Health and Life Science, Graduate School of Health and Sports Science, Juntendo University, Inzai, Chiba 270-1695, Japan.
| | - Haruhisa Kikuchi
- Laboratory of Natural Product Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.
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28
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Hayakawa IS, Inouye K. Species recognition in social amoebae. J Biosci 2018; 43:1025-1036. [PMID: 30541961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Aggregative multicellularity requires the ability of cells to recognise conspecifics. Social amoebae are among the best studied of such organisms, but the mechanism and evolutionary background of species recognition remained to be investigated. Here we show that heterologous expression of a single Dictyostelium purpureum gene is sufficient for D. discoideum cells to efficiently make chimaeric fruiting bodies with D. purpureum cells. This gene forms a bidirectional pair with another gene on the D. purpureum genome, and they are both highly polymorphic among independent wild isolates of the same mating group that do not form chimaeric fruiting bodies with each other. These paired genes are both structurally similar to D. discoideum tgrB1/C1 pair, which is responsible for clonal discrimination within that species, suggesting that these tgr genes constitute the species recognition system that has attained a level of precision capable of discriminating between clones within a species. Analysis of the available genome sequences of social amoebae revealed that such gene pairs exist only within the clade composed of species that produce precursors of sterile stalk cells (prestalk cells), suggesting concurrent evolution of a precise allorecognition system and a new 'worker' cell-type dedicated to transporting and supporting the reproductive cells.
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Affiliation(s)
- Ikumi Shibano Hayakawa
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan,
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29
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Gas-Pascual E, Ichikawa HT, Sheikh MO, Serji MI, Deng B, Mandalasi M, Bandini G, Samuelson J, Wells L, West CM. CRISPR/Cas9 and glycomics tools for Toxoplasma glycobiology. J Biol Chem 2018; 294:1104-1125. [PMID: 30463938 DOI: 10.1074/jbc.ra118.006072] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/12/2018] [Indexed: 01/25/2023] Open
Abstract
Infection with the protozoan parasite Toxoplasma gondii is a major health risk owing to birth defects, its chronic nature, ability to reactivate to cause blindness and encephalitis, and high prevalence in human populations. Unlike most eukaryotes, Toxoplasma propagates in intracellular parasitophorous vacuoles, but like nearly all other eukaryotes, Toxoplasma glycosylates many cellular proteins and lipids and assembles polysaccharides. Toxoplasma glycans resemble those of other eukaryotes, but species-specific variations have prohibited deeper investigations into their roles in parasite biology and virulence. The Toxoplasma genome encodes a suite of likely glycogenes expected to assemble N-glycans, O-glycans, a C-glycan, GPI-anchors, and polysaccharides, along with their precursors and membrane transporters. To investigate the roles of specific glycans in Toxoplasma, here we coupled genetic and glycomics approaches to map the connections between 67 glycogenes, their enzyme products, the glycans to which they contribute, and cellular functions. We applied a double-CRISPR/Cas9 strategy, in which two guide RNAs promote replacement of a candidate gene with a resistance gene; adapted MS-based glycomics workflows to test for effects on glycan formation; and infected fibroblast monolayers to assess cellular effects. By editing 17 glycogenes, we discovered novel Glc0-2-Man6-GlcNAc2-type N-glycans, a novel HexNAc-GalNAc-mucin-type O-glycan, and Tn-antigen; identified the glycosyltransferases for assembling novel nuclear O-Fuc-type and cell surface Glc-Fuc-type O-glycans; and showed that they are important for in vitro growth. The guide sequences, editing constructs, and mutant strains are freely available to researchers to investigate the roles of glycans in their favorite biological processes.
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Affiliation(s)
- Elisabet Gas-Pascual
- Department of Biochemistry and Molecular Biology, Athens, Georgia 30602; Center for Tropical and Emerging Global Diseases, Athens, Georgia 30602
| | | | | | | | - Bowen Deng
- Department of Biochemistry and Molecular Biology, Athens, Georgia 30602; Center for Tropical and Emerging Global Diseases, Athens, Georgia 30602
| | - Msano Mandalasi
- Department of Biochemistry and Molecular Biology, Athens, Georgia 30602; Center for Tropical and Emerging Global Diseases, Athens, Georgia 30602
| | - Giulia Bandini
- Department of Molecular and Cell Biology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Massachusetts 02118
| | - John Samuelson
- Department of Molecular and Cell Biology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Massachusetts 02118
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Athens, Georgia 30602; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Christopher M West
- Department of Biochemistry and Molecular Biology, Athens, Georgia 30602; Center for Tropical and Emerging Global Diseases, Athens, Georgia 30602; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602.
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30
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Species recognition in social amoebae. J Biosci 2018. [DOI: 10.1007/s12038-018-9810-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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31
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Saito YF, Miyazaki SH, Bartlem DG, Nagamatsu Y, Saito T. Chemical compounds from Dictyostelium discoideum repel a plant-parasitic nematode and can protect roots. PLoS One 2018; 13:e0204671. [PMID: 30261017 PMCID: PMC6160129 DOI: 10.1371/journal.pone.0204671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/12/2018] [Indexed: 11/18/2022] Open
Abstract
Slime mold species in the genus Dictyostelium are considered to have a close relationship with non-parasitic nematodes; they are sympatric in soils and can exhibit interspecific competition for food. We investigated whether this relationship extends to a plant-parasitic nematode that is active in the rhizosphere and has broad host specificity, damaging crops worldwide. Using a novel assay to examine the interaction between the cellular slime mold, Dictyostelium discoideum, and the plant-parasitic nematodes, Meloidogyne spp., we found that cellular slime molds can repel plant parasitic nematodes. Specifically, the repulsion activity was in response to chemical compounds released by cellular slime mold fruiting bodies. Under laboratory conditions, these soluble chemical extracts from fruiting bodies of D. discoideum showed repulsion activity strong enough to protect plant roots. The fruiting body cell extracts repelled but were not toxic to the plant-parasitic nematodes.
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Affiliation(s)
- Yumiko F. Saito
- Graduate School of Science and Technology, Sophia University, Tokyo, Japan
| | - Saki H. Miyazaki
- Graduate School of Science and Technology, Sophia University, Tokyo, Japan
| | - Derek G. Bartlem
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yukiko Nagamatsu
- Institute of Environmental Science, Panefri Industrial Company, Okinawa, Japan
| | - Tamao Saito
- Faculty of Science and Technology, Sophia University, Tokyo, Japan
- * E-mail:
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32
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Chen X, Köllner TG, Shaulsky G, Jia Q, Dickschat JS, Gershenzon J, Chen F. Diversity and Functional Evolution of Terpene Synthases in Dictyostelid Social Amoebae. Sci Rep 2018; 8:14361. [PMID: 30254228 PMCID: PMC6156593 DOI: 10.1038/s41598-018-32639-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/12/2018] [Indexed: 11/23/2022] Open
Abstract
Dictyostelids, or social amoebae, have a unique life style in forming multicellular fruiting bodies from unicellular amoeboids upon starvation. Recently, dictyostelids were found to contain terpene synthase (TPS) genes, a gene type of secondary metabolism previously known to occur only in plants, fungi and bacteria. Here we report an evolutionary functional study of dictyostelid TPS genes. The number of TPS genes in six species of dictyostelids examined ranges from 1 to 19; and the model species Dictyostelium purpureum contains 12 genes. Using in vitro enzyme assays, the 12 TPS genes from D. purpureum were shown to encode functional enzymes with distinct product profiles. The expression of the 12 TPS genes in D. purpureum is developmentally regulated. During multicellular development, D. purpureum releases a mixture of volatile terpenes dominated by sesquiterpenes that are the in vitro products of a subset of the 12 TPS genes. The quality and quantity of the terpenes released from D. purpureum, however, bear little resemblance to those of D. discoideum, a closely related dictyostelid. Despite these variations, the conserved clade of dictyostelid TPSs, which have an evolutionary distance of more than 600 million years, has the same biochemical function, catalyzing the formation of a sesquiterpene protoillud-7-ene. Taken together, our results indicate that the dynamic evolution of dictyostelid TPS genes includes both purifying selection of an orthologous group and species-specific expansion with functional divergence. Consequently, the terpenes produced by these TPSs most likely have conserved as well as species-adaptive biological functions as chemical languages in dictyostelids.
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Affiliation(s)
- Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Qidong Jia
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
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De novo assembly and annotation of Didymium iridis transcriptome and identification of stage-specfic genes. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0037-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Sex in social amoebae (or dictyostelids) has a number of striking features. Dictyostelid zygotes do not proliferate but grow to a large size by feeding on other cells of the same species, each zygote ultimately forming a walled structure called a macrocyst. The diploid macrocyst nucleus undergoes meiosis, after which a single meiotic product survives to restart haploid vegetative growth. Meiotic recombination is generally initiated by the Spo11 enzyme, which introduces DNA double-strand breaks. Uniquely, as far as is known among sexual eukaryotes, dictyostelids lack a SPO11 gene. Despite this, recombination occurs at high frequencies during meiosis in dictyostelids, through unknown mechanisms. The molecular processes underlying these events, and the evolutionary drivers that brought them into being, may shed light on the genetic conflicts that occur within and between genomes, and how they can be resolved.
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Yamada Y, Cassidy A, Schaap P. The transcription factor Spores Absent A is a PKA dependent inducer of Dictyostelium sporulation. Sci Rep 2018; 8:6643. [PMID: 29704004 PMCID: PMC5923282 DOI: 10.1038/s41598-018-24915-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/11/2018] [Indexed: 11/09/2022] Open
Abstract
Sporulation in Dictyostelium fruiting bodies evolved from amoebozoan encystation with both being induced by cAMP acting on PKA, but with downstream components still being unknown. Using tagged mutagenesis to find missing pathway components, we identified a sporeless mutant defective in a nuclear protein, SpaA. Expression of prespore genes was strongly reduced in spaA- cells, while expression of many spore stage genes was absent. Chromatin immunoprecipitation (ChIP) of a SpaA-YFP gene fusion showed that (pre)spore gene promoters bind directly to SpaA, identifying SpaA as a transcriptional regulator. SpaA dependent spore gene expression required PKA in vivo and was stimulated in vitro by the membrane-permeant PKA agonist 8Br-cAMP. The PKA agonist also promoted SpaA binding to (pre)spore promoters, placing SpaA downstream of PKA. Sequencing of SpaA-YFP ChIPed DNA fragments revealed that SpaA binds at least 117 (pre)spore promoters, including those of other transcription factors that activate some spore genes. These factors are not in turn required for spaA expression, identifying SpaA as the major trancriptional inducer of sporulation.
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Affiliation(s)
- Yoko Yamada
- School of Life Sciences, University of Dundee, Dundee, DD15EH, Angus, UK
| | - Andrew Cassidy
- Tayside Centre for Genomic Analysis, University of Dundee, Dundee, DD19SY, Angus, UK
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee, DD15EH, Angus, UK.
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Dunn JD, Bosmani C, Barisch C, Raykov L, Lefrançois LH, Cardenal-Muñoz E, López-Jiménez AT, Soldati T. Eat Prey, Live: Dictyostelium discoideum As a Model for Cell-Autonomous Defenses. Front Immunol 2018; 8:1906. [PMID: 29354124 PMCID: PMC5758549 DOI: 10.3389/fimmu.2017.01906] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/13/2017] [Indexed: 12/11/2022] Open
Abstract
The soil-dwelling social amoeba Dictyostelium discoideum feeds on bacteria. Each meal is a potential infection because some bacteria have evolved mechanisms to resist predation. To survive such a hostile environment, D. discoideum has in turn evolved efficient antimicrobial responses that are intertwined with phagocytosis and autophagy, its nutrient acquisition pathways. The core machinery and antimicrobial functions of these pathways are conserved in the mononuclear phagocytes of mammals, which mediate the initial, innate-immune response to infection. In this review, we discuss the advantages and relevance of D. discoideum as a model phagocyte to study cell-autonomous defenses. We cover the antimicrobial functions of phagocytosis and autophagy and describe the processes that create a microbicidal phagosome: acidification and delivery of lytic enzymes, generation of reactive oxygen species, and the regulation of Zn2+, Cu2+, and Fe2+ availability. High concentrations of metals poison microbes while metal sequestration inhibits their metabolic activity. We also describe microbial interference with these defenses and highlight observations made first in D. discoideum. Finally, we discuss galectins, TNF receptor-associated factors, tripartite motif-containing proteins, and signal transducers and activators of transcription, microbial restriction factors initially characterized in mammalian phagocytes that have either homologs or functional analogs in D. discoideum.
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Affiliation(s)
- Joe Dan Dunn
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Cristina Bosmani
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Caroline Barisch
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Lyudmil Raykov
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Louise H Lefrançois
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Elena Cardenal-Muñoz
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | | | - Thierry Soldati
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
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Wojtkowska M, Buczek D, Suzuki Y, Shabardina V, Makałowski W, Kmita H. The emerging picture of the mitochondrial protein import complexes of Amoebozoa supergroup. BMC Genomics 2017; 18:997. [PMID: 29284403 PMCID: PMC5747110 DOI: 10.1186/s12864-017-4383-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/14/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The existence of mitochondria-related organelles (MROs) is proposed for eukaryotic organisms. The Amoebozoa includes some organisms that are known to have mitosomes but also organisms that have aerobic mitochondria. However, the mitochondrial protein apparatus of this supergroup remains largely unsampled, except for the mitochondrial outer membrane import complexes studied recently. Therefore, in this study we investigated the mitochondrial inner membrane and intermembrane space complexes, using the available genome and transcriptome sequences. RESULTS When compared with the canonical cognate complexes described for the yeast Saccharomyces cerevisiae, amoebozoans with aerobic mitochondria, display lower differences in the number of subunits predicted for these complexes than the mitochondrial outer membrane complexes, although the predicted subunits appear to display different levels of diversity in regard to phylogenetic position and isoform numbers. For the putative mitosome-bearing amoebozoans, the number of predicted subunits suggests the complex elimination distinctly more pronounced than in the case of the outer membrane ones. CONCLUSION The results concern the problem of mitochondrial and mitosome protein import machinery structural variability and the reduction of their complexity within the currently defined supergroup of Amoebozoa. This results are crucial for better understanding of the Amoebozoa taxa of both biomedical and evolutionary importance.
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Affiliation(s)
- Małgorzata Wojtkowska
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Dorota Buczek
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Strasse 14, 48149 Muenster, Germany
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562 Japan
| | - Victoria Shabardina
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Strasse 14, 48149 Muenster, Germany
| | - Wojciech Makałowski
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Strasse 14, 48149 Muenster, Germany
| | - Hanna Kmita
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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Abstract
Natural products are invaluable sources of structural diversity and complexity ideally suited for the development of therapeutic agents. The search for novel bioactive molecules has prompted scientists to explore various ecological niches. Microorganisms have been shown to constitute such an important source. Despite their biosynthetic potential, social amoebae, that is, microorganisms with both a uni- and multicellular lifestyle, are underexplored regarding their secreted secondary metabolome. In this review, we present the structural diversity of amoebal natural products and discuss their biological functions as well as their total syntheses.
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Affiliation(s)
- Robert Barnett
- Junior Research Group Chemistry of Microbial Communication, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, HKI Jena, Beutenbergstrasse 11, 07745, Jena, Germany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial Communication, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, HKI Jena, Beutenbergstrasse 11, 07745, Jena, Germany
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Kikuchi H, Ito I, Takahashi K, Ishigaki H, Iizumi K, Kubohara Y, Oshima Y. Isolation, Synthesis, and Biological Activity of Chlorinated Alkylresorcinols from Dictyostelium Cellular Slime Molds. JOURNAL OF NATURAL PRODUCTS 2017; 80:2716-2722. [PMID: 28921976 DOI: 10.1021/acs.jnatprod.7b00456] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Eight chlorinated alkylresorcinols, monochasiol A-H (1-8), were isolated from the fruiting bodies of Dictyostelium monochasioides. Compounds 1-8 were synthesized to confirm their structures and to obtain sufficient material for performing biological tests. Monochasiol A (1) selectively inhibited the concanavalin A-induced interleukin-2 production in Jurkat cells, a human T lymphocyte cell line. Monochasiols were biogenetically synthesized by the combination of biosynthetic enzymes relating to the principal polyketides, MPBD and DIF-1, produced by Dictyostelium discoideum.
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Affiliation(s)
- Haruhisa Kikuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Ikuko Ito
- Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Katsunori Takahashi
- Department of Medical Technology, Faculty of Health Science, Gunma Paz University , 1-7-1, Tonyamachi, Takasaki 370-0006, Japan
| | - Hirotaka Ishigaki
- Department of Medical Technology, Faculty of Health Science, Gunma Paz University , 1-7-1, Tonyamachi, Takasaki 370-0006, Japan
| | - Kyoichi Iizumi
- Graduate School of Health and Sports Science, Juntendo University , 1-1 Hiraga-gakuendai, Inzai, Chiba 270-1695, Japan
| | - Yuzuru Kubohara
- Graduate School of Health and Sports Science, Juntendo University , 1-1 Hiraga-gakuendai, Inzai, Chiba 270-1695, Japan
| | - Yoshiteru Oshima
- Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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Brunet T, King N. The Origin of Animal Multicellularity and Cell Differentiation. Dev Cell 2017; 43:124-140. [PMID: 29065305 PMCID: PMC6089241 DOI: 10.1016/j.devcel.2017.09.016] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/31/2017] [Accepted: 09/19/2017] [Indexed: 12/14/2022]
Abstract
Over 600 million years ago, animals evolved from a unicellular or colonial organism whose cell(s) captured bacteria with a collar complex, a flagellum surrounded by a microvillar collar. Using principles from evolutionary cell biology, we reason that the transition to multicellularity required modification of pre-existing mechanisms for extracellular matrix synthesis and cytokinesis. We discuss two hypotheses for the origin of animal cell types: division of labor from ancient plurifunctional cells and conversion of temporally alternating phenotypes into spatially juxtaposed cell types. Mechanistic studies in diverse animals and their relatives promise to deepen our understanding of animal origins and cell biology.
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Affiliation(s)
- Thibaut Brunet
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Nicole King
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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41
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Votaw HR, Ostrowski EA. Stalk size and altruism investment within and among populations of the social amoeba. J Evol Biol 2017; 30:2017-2030. [DOI: 10.1111/jeb.13172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/13/2017] [Accepted: 08/20/2017] [Indexed: 11/26/2022]
Affiliation(s)
- H. R. Votaw
- Department of Biology and Biochemistry University of Houston Houston TX USA
| | - E. A. Ostrowski
- Department of Biology and Biochemistry University of Houston Houston TX USA
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Stumpf M, Müller R, Gaßen B, Wehrstedt R, Fey P, Karow MA, Eichinger L, Glöckner G, Noegel AA. A tripeptidyl peptidase 1 is a binding partner of the Golgi pH regulator (GPHR) in Dictyostelium. Dis Model Mech 2017; 10:897-907. [PMID: 28546289 PMCID: PMC5536908 DOI: 10.1242/dmm.029280] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/17/2017] [Indexed: 02/02/2023] Open
Abstract
Mutations in tripeptidyl peptidase 1 (TPP1) have been associated with late infantile neuronal ceroid lipofuscinosis (NCL), a neurodegenerative disorder. TPP1 is a lysosomal serine protease, which removes tripeptides from the N-terminus of proteins and is composed of an N-terminal prodomain and a catalytic domain. It is conserved in mammals, amphibians, fish and the amoeba Dictyostelium discoideum. D. discoideum harbors at least six genes encoding TPP1, tpp1A to tpp1F. We identified TPP1F as binding partner of Dictyostelium GPHR (Golgi pH regulator), which is an evolutionarily highly conserved intracellular transmembrane protein. A region encompassing the DUF3735 (GPHR_N) domain of GPHR was responsible for the interaction. In TPP1F, the binding site is located in the prodomain of the protein. The tpp1F gene is transcribed throughout development and translated into a polypeptide of ∼65 kDa. TPP1 activity was demonstrated for TPP1F-GFP immunoprecipitated from D. discoideum cells. Its activity could be inhibited by addition of the recombinant DUF3735 domain of GPHR. Knockout tpp1F mutants did not display any particular phenotype, and TPP1 activity was not abrogated, presumably because tpp1B compensates as it has the highest expression level of all the TPP1 genes during growth. The GPHR interaction was not restricted to TPP1F but occurred also with TPP1B. As previous reports show that the majority of the TPP1 mutations in NCL resulted in reduction or loss of enzyme activity, we suggest that Dicyostelium could be used as a model system in which to test new reagents that could affect the activity of the protein and ameliorate the disease. Summary: Interaction of Dictyostelium tripeptidyl peptidase 1 with GPHR could be relevant for studies of the human enzyme, which is associated with a neurodegenerative disorder.
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Affiliation(s)
- Maria Stumpf
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Rolf Müller
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Berthold Gaßen
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Regina Wehrstedt
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Petra Fey
- Dicty Base, Northwestern University, Biomedical Informatics Center and Center for Genetic Medicine, Chicago, IL 60611, USA
| | - Malte A Karow
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Ludwig Eichinger
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Gernot Glöckner
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
| | - Angelika A Noegel
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, Köln 50931, Germany
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Traynor D, Kay RR. A polycystin-type transient receptor potential (Trp) channel that is activated by ATP. Biol Open 2017; 6:200-209. [PMID: 28011630 PMCID: PMC5312093 DOI: 10.1242/bio.020685] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ATP and ADP are ancient extra-cellular signalling molecules that in Dictyostelium amoebae cause rapid, transient increases in cytosolic calcium due to an influx through the plasma membrane. This response is independent of hetero-trimeric G-proteins, the putative IP3 receptor IplA and all P2X channels. We show, unexpectedly, that it is abolished in mutants of the polycystin-type transient receptor potential channel, TrpP. Responses to the chemoattractants cyclic-AMP and folic acid are unaffected in TrpP mutants. We report that the DIF morphogens, cyclic-di-GMP, GABA, glutamate and adenosine all induce strong cytoplasmic calcium responses, likewise independently of TrpP. Thus, TrpP is dedicated to purinergic signalling. ATP treatment causes cell blebbing within seconds but this does not require TrpP, implicating a separate purinergic receptor. We could detect no effect of ATP on chemotaxis and TrpP mutants grow, chemotax and develop almost normally in standard conditions. No gating ligand is known for the human homologue of TrpP, polycystin-2, which causes polycystic kidney disease. Our results now show that TrpP mediates purinergic signalling in Dictyostelium and is directly or indirectly gated by ATP. Summary: We show that a Trp channel related to the mammalian polycystin channel, rather than a P2X receptor, is responsible for the purinergic stimulation of cytosolic calcium levels in Dictyostelium cells.
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Affiliation(s)
- David Traynor
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB1 0QH, UK
| | - Robert R Kay
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB1 0QH, UK
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Nguyen VH, Kikuchi H, Sasaki H, Iizumi K, Kubohara Y, Oshima Y. Production of novel bispyrone metabolites in the cellular slime mold Dictyostelium giganteum induced by zinc(II) ion. Tetrahedron 2017. [DOI: 10.1016/j.tet.2016.12.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Singh R, Schilde C, Schaap P. A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group. BMC Evol Biol 2016; 16:251. [PMID: 27855631 PMCID: PMC5114724 DOI: 10.1186/s12862-016-0825-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa. RESULTS We retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification. CONCLUSIONS The multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum branching at the base of that whole clade. Given the data, the approximately unbiased test rejects all alternative topologies favoured by SSU rDNA and individual proteins with high statistical support. The test also rejects monophyletic origins for the genera Acytostelium, Polysphondylium and Dictyostelium. The current position of Acytostelium ellipticum in the consensus phylogeny indicates that somatic cells were lost twice in Dictyostelia.
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Affiliation(s)
- Reema Singh
- School of Life Sciences, University of Dundee, MSI complex, Dow Street, Dundee, DD15EH, UK
| | - Christina Schilde
- School of Life Sciences, University of Dundee, MSI complex, Dow Street, Dundee, DD15EH, UK
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, MSI complex, Dow Street, Dundee, DD15EH, UK.
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46
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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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Gong M, Zhu Q, Tan Q. Evolutionary analyses of mitochondrial carrier family of dictyostelids. SPRINGERPLUS 2016; 5:1465. [PMID: 27652040 PMCID: PMC5007236 DOI: 10.1186/s40064-016-3146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 08/24/2016] [Indexed: 11/25/2022]
Abstract
The transportation of solutes across the inner membrane of the mitochondria is catalyzed by a nuclear-coded family of transport proteins called mitochondrial carriers (MCs). Sequences from dictyostelid genome projects have facilitated analysis of the evolution of the dictyostelid mitochondrial carrier family (MCF). The average evolutionary distances between various regions in the MCF shows that the transmembrane region (TR) and conical pit region (CPR) are the only two conserved structural regions. A phylogenetic tree built using the concatenated orthologous TR and CPR sequences of 7 MCs showed that dictyostelids are similar to metazoans in this way. A close evolutionary relationship was observed between dictyostelids and metazoans in 4 MCs known to be related to ADP/ATP transport (MAA). This was further evidenced by the fact that dictyostelids have undergone gene expansion similar to that of metazoans during the evolution of MAA. Sequence logo analysis of CPR in MAA showed that dictyostelids have motifs similar to those of Metazoa. Combined with the conserved substrate binding site of 7 MCs in eukaryotes, it is postulated that dictyostelids are closely related to Metazoa with respect to the evolution of MAA.
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Affiliation(s)
- Ming Gong
- National Engineering Research Center of Edible Fungi; Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture; Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 People's Republic of China ; Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182 USA
| | - Qiuming Zhu
- Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182 USA
| | - Qi Tan
- National Engineering Research Center of Edible Fungi; Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture; Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 People's Republic of China
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Kuburich NA, Adhikari N, Hadwiger JA. Acanthamoeba and Dictyostelium Use Different Foraging Strategies. Protist 2016; 167:511-525. [PMID: 27693864 DOI: 10.1016/j.protis.2016.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/15/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
Abstract
Amoeba often use cell movement as a mechanism to find food, such as bacteria, in their environment. The chemotactic movement of the soil amoeba Dictyostelium to folate or other pterin compounds released by bacteria is a well-documented foraging mechanism. Acanthamoeba can also feed on bacteria but relatively little is known about the mechanism(s) by which this amoeba locates bacteria. Acanthamoeba movement in the presence of folate or bacteria was analyzed in above agar assays and compared to that observed for Dictyostelium. The overall mobility of Acanthamoeba was robust like that of Dictyostelium but Acanthamoeba did not display a chemotactic response to folate. In the presence of bacteria, Acanthamoeba only showed a marginal bias in directed movement whereas Dictyostelium displayed a strong chemotactic response. A comparison of genomes revealed that Acanthamoeba and Dictyostelium share some similarities in G protein signaling components but that specific G proteins used in Dictyostelium chemotactic responses were not present in current Acanthamoeba genome sequence data. The results of this study suggest that Acanthamoeba does not use chemotaxis as the primary mechanism to find bacterial food sources and that the chemotactic responses of Dictyostelium to bacteria may have co-evolved with chemotactic responses that facilitate multicellular development.
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Affiliation(s)
- Nick A Kuburich
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, OK 74078-3020, USA
| | - Nirakar Adhikari
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, OK 74078-3020, USA
| | - Jeffrey A Hadwiger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, OK 74078-3020, USA
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Spaller T, Kling E, Glöckner G, Hillmann F, Winckler T. Convergent evolution of tRNA gene targeting preferences in compact genomes. Mob DNA 2016; 7:17. [PMID: 27583033 PMCID: PMC5006619 DOI: 10.1186/s13100-016-0073-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/20/2016] [Indexed: 11/30/2022] Open
Abstract
Background In gene-dense genomes, mobile elements are confronted with highly selective pressure to amplify without causing excessive damage to the host. The targeting of tRNA genes as potentially safe integration sites has been developed by retrotransposons in various organisms such as the social amoeba Dictyostelium discoideum and the yeast Saccharomyces cerevisiae. In D. discoideum, tRNA gene-targeting retrotransposons have expanded to approximately 3 % of the genome. Recently obtained genome sequences of species representing the evolutionary history of social amoebae enabled us to determine whether the targeting of tRNA genes is a generally successful strategy for mobile elements to colonize compact genomes. Results During the evolution of dictyostelids, different retrotransposon types independently developed the targeting of tRNA genes at least six times. DGLT-A elements are long terminal repeat (LTR) retrotransposons that display integration preferences ~15 bp upstream of tRNA gene-coding regions reminiscent of the yeast Ty3 element. Skipper elements are chromoviruses that have developed two subgroups: one has canonical chromo domains that may favor integration in centromeric regions, whereas the other has diverged chromo domains and is found ~100 bp downstream of tRNA genes. The integration of D. discoideum non-LTR retrotransposons ~50 bp upstream (TRE5 elements) and ~100 bp downstream (TRE3 elements) of tRNA genes, respectively, likely emerged at the root of dictyostelid evolution. We identified two novel non-LTR retrotransposons unrelated to TREs: one with a TRE5-like integration behavior and the other with preference ~4 bp upstream of tRNA genes. Conclusions Dictyostelid retrotransposons demonstrate convergent evolution of tRNA gene targeting as a probable means to colonize the compact genomes of their hosts without being excessively mutagenic. However, high copy numbers of tRNA gene-associated retrotransposons, such as those observed in D. discoideum, are an exception, suggesting that the targeting of tRNA genes does not necessarily favor the amplification of position-specific integrating elements to high copy numbers under the repressive conditions that prevail in most host cells. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0073-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Spaller
- Institute of Pharmacy, Department of Pharmaceutical Biology, Friedrich Schiller University Jena, Semmelweisstraße 10, Jena, 07743 Germany
| | - Eva Kling
- Institute of Pharmacy, Department of Pharmaceutical Biology, Friedrich Schiller University Jena, Semmelweisstraße 10, Jena, 07743 Germany
| | - Gernot Glöckner
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Berlin, Germany ; Institute for Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interaction, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Thomas Winckler
- Institute of Pharmacy, Department of Pharmaceutical Biology, Friedrich Schiller University Jena, Semmelweisstraße 10, Jena, 07743 Germany
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The multicellularity genes of dictyostelid social amoebas. Nat Commun 2016; 7:12085. [PMID: 27357338 PMCID: PMC4931340 DOI: 10.1038/ncomms12085] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/27/2016] [Indexed: 11/09/2022] Open
Abstract
The evolution of multicellularity enabled specialization of cells, but required novel signalling mechanisms for regulating cell differentiation. Early multicellular organisms are mostly extinct and the origins of these mechanisms are unknown. Here using comparative genome and transcriptome analysis across eight uni- and multicellular amoebozoan genomes, we find that 80% of proteins essential for the development of multicellular Dictyostelia are already present in their unicellular relatives. This set is enriched in cytosolic and nuclear proteins, and protein kinases. The remaining 20%, unique to Dictyostelia, mostly consists of extracellularly exposed and secreted proteins, with roles in sensing and recognition, while several genes for synthesis of signals that induce cell-type specialization were acquired by lateral gene transfer. Across Dictyostelia, changes in gene expression correspond more strongly with phenotypic innovation than changes in protein functional domains. We conclude that the transition to multicellularity required novel signals and sensors rather than novel signal processing mechanisms. Unicellular social amoebae aggregate to form a multicellular life stage, making them a model system for the evolution of multicellularity. Here, Glöckner et al. use a comparative genomic and transcriptomic approach to determine the origin of the genes essential for multicellularity in the social amoebae.
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