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Groussman RD, Blaskowski S, Coesel SN, Armbrust EV. MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes. Sci Data 2023; 10:926. [PMID: 38129449 PMCID: PMC10739892 DOI: 10.1038/s41597-023-02842-4] [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: 06/07/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.
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Affiliation(s)
- R D Groussman
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA.
| | - S Blaskowski
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Molecular Engineering & Sciences Building 3946 W Stevens Way NE, Seattle, WA, 98195, USA
| | - S N Coesel
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA
| | - E V Armbrust
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA.
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2
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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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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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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: 2] [Impact Index Per Article: 0.7] [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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Kawabe Y, Du Q, Schilde C, Schaap P. Evolution of multicellularity in Dictyostelia. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2020; 63:359-369. [PMID: 31840775 PMCID: PMC6978153 DOI: 10.1387/ijdb.190108ps] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The well-orchestrated multicellular life cycle of Dictyostelium discoideum has fascinated biologists for over a century. Self-organisation of its amoebas into aggregates, migrating slugs and fruiting structures by pulsatile cAMP signalling and their ability to follow separate differentiation pathways in well-regulated proportions continue to be topics under investigation. A striking aspect of D. discoideum development is the recurrent use of cAMP as chemoattractant, differentiation inducing signal and second messenger for other signals that control the developmental programme. D. discoideum is one of >150 species of Dictyostelia and aggregative life styles similar to those of Dictyostelia evolved many times in eukaryotes. Here we review experimental studies investigating how phenotypic complexity and cAMP signalling co-evolved in Dictyostelia. In addition, we summarize comparative genomic studies of multicellular Dictyostelia and unicellular Amoebozoa aimed to identify evolutionary conservation and change in all genes known to be essential for D. discoideum development.
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Green CM, Li Z, Smith AD, Novikova O, Bacot-Davis VR, Gao F, Hu S, Banavali NK, Thiele DJ, Li H, Belfort M. Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing. PLoS Biol 2019; 17:e3000104. [PMID: 31600193 PMCID: PMC6805012 DOI: 10.1371/journal.pbio.3000104] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 10/22/2019] [Accepted: 09/13/2019] [Indexed: 01/07/2023] Open
Abstract
The spliceosome is a large ribonucleoprotein complex that removes introns from pre-mRNAs. At its functional core lies the essential pre-mRNA processing factor 8 (Prp8) protein. Across diverse eukaryotes, this protein cofactor of RNA catalysis harbors a self-splicing element called an intein. Inteins in Prp8 are extremely pervasive and are found at 7 different sites in various species. Here, we focus on the Prp8 intein from Cryptococcus neoformans (Cne), a human fungal pathogen. We solved the crystal structure of this intein, revealing structural homology among protein splicing sequences in eukaryotes, including the Hedgehog C terminus. Working with the Cne Prp8 intein in a reporter assay, we find that the biologically relevant divalent metals copper and zinc inhibit intein splicing, albeit by 2 different mechanisms. Copper likely stimulates reversible modifications on a catalytically important cysteine, whereas zinc binds at the terminal asparagine and the same critical cysteine. Importantly, we also show that copper treatment inhibits Prp8 protein splicing in Cne. Lastly, an intein-containing Prp8 precursor model is presented, suggesting that metal-induced protein splicing inhibition would disturb function of both Prp8 and the spliceosome. These results indicate that Prp8 protein splicing can be modulated, with potential functional implications for the spliceosome.
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Affiliation(s)
- Cathleen M. Green
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
| | - Zhong Li
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Aaron D. Smith
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
| | - Valjean R. Bacot-Davis
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
| | - Fengshan Gao
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Saiyang Hu
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Nilesh K. Banavali
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
| | - Dennis J. Thiele
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America,Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hongmin Li
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America,* E-mail: (MB); (HL)
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America,* E-mail: (MB); (HL)
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7
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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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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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Hillmann F, Forbes G, Novohradská S, Ferling I, Riege K, Groth M, Westermann M, Marz M, Spaller T, Winckler T, Schaap P, Glöckner G. Multiple Roots of Fruiting Body Formation in Amoebozoa. Genome Biol Evol 2018; 10:591-606. [PMID: 29378020 PMCID: PMC5804921 DOI: 10.1093/gbe/evy011] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2018] [Indexed: 02/03/2023] Open
Abstract
Establishment of multicellularity represents a major transition in eukaryote evolution. A subgroup of Amoebozoa, the dictyosteliids, has evolved a relatively simple aggregative multicellular stage resulting in a fruiting body supported by a stalk. Protosteloid amoeba, which are scattered throughout the amoebozoan tree, differ by producing only one or few single stalked spores. Thus, one obvious difference in the developmental cycle of protosteliids and dictyosteliids seems to be the establishment of multicellularity. To separate spore development from multicellular interactions, we compared the genome and transcriptome of a Protostelium species (Protostelium aurantium var. fungivorum) with those of social and solitary members of the Amoebozoa. During fruiting body formation nearly 4,000 genes, corresponding to specific pathways required for differentiation processes, are upregulated. A comparison with genes involved in the development of dictyosteliids revealed conservation of >500 genes, but most of them are also present in Acanthamoeba castellanii for which fruiting bodies have not been documented. Moreover, expression regulation of those genes differs between P. aurantium and Dictyostelium discoideum. Within Amoebozoa differentiation to fruiting bodies is common, but our current genome analysis suggests that protosteliids and dictyosteliids used different routes to achieve this. Most remarkable is both the large repertoire and diversity between species in genes that mediate environmental sensing and signal processing. This likely reflects an immense adaptability of the single cell stage to varying environmental conditions. We surmise that this signaling repertoire provided sufficient building blocks to accommodate the relatively simple demands for cell-cell communication in the early multicellular forms.
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Affiliation(s)
- Falk Hillmann
- Junior Research Group Evolution of Microbial Interaction, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Gillian Forbes
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, United Kingdom
| | - Silvia Novohradská
- Junior Research Group Evolution of Microbial Interaction, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Iuliia Ferling
- Junior Research Group Evolution of Microbial Interaction, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Konstantin Riege
- Bioinformatics/High Throughput Analysis, Friedrich Schiller University Jena, Germany
| | - Marco Groth
- CF DNA-Sequencing, Leibniz Institute on Aging Research, Jena, Germany
| | | | - Manja Marz
- Bioinformatics/High Throughput Analysis, Friedrich Schiller University Jena, Germany
| | - Thomas Spaller
- Pharmaceutical Biology, Institute of Pharmacy, Friedrich Schiller University Jena, Germany
| | - Thomas Winckler
- Pharmaceutical Biology, Institute of Pharmacy, Friedrich Schiller University Jena, Germany
| | - Pauline Schaap
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, United Kingdom
| | - Gernot Glöckner
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Germany
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Abstract
Fungi belong to one of the largest and most diverse kingdoms of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information-based trees ("gene trees"), constructed commonly based on the degree of differences of proteins or DNA sequences of a small number of highly conserved genes common among the population by a multiple sequence alignment (MSA) method. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population depending on the subjective selection of the genes. Within the last decade, a large number of whole-genome sequences of fungi have become publicly available, which represent, at present, the most fundamental and complete information about each fungal organism. This presents an opportunity to infer kinship among fungi using a whole-genome information-based tree ("genome tree"). The method we used allows comparison of whole-genome information without MSA, and is a variation of a computational algorithm developed to find semantic similarities or plagiarism in two books, where we represent whole-genomic information of an organism as a book of words without spaces. The genome tree reveals several significant and notable differences from the gene trees, and these differences invoke new discussions about alternative narratives for the evolution of some of the currently accepted fungal groups.
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Affiliation(s)
- JaeJin Choi
- Department of Chemistry, University of California, Berkeley, CA 94720
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Integrated Omics for Biomedical Sciences, Yonsei University, Seoul 03722, Republic of Korea
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Sung-Hou Kim
- Department of Chemistry, University of California, Berkeley, CA 94720;
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Integrated Omics for Biomedical Sciences, Yonsei University, Seoul 03722, Republic of Korea
- Center for Computational Biology, University of California, Berkeley, CA 94720
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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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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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Du Q, Kawabe Y, Schilde C, Chen ZH, Schaap P. The Evolution of Aggregative Multicellularity and Cell-Cell Communication in the Dictyostelia. J Mol Biol 2015; 427:3722-33. [PMID: 26284972 PMCID: PMC5055082 DOI: 10.1016/j.jmb.2015.08.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/30/2015] [Accepted: 08/03/2015] [Indexed: 10/30/2022]
Abstract
Aggregative multicellularity, resulting in formation of a spore-bearing fruiting body, evolved at least six times independently amongst both eukaryotes and prokaryotes. Amongst eukaryotes, this form of multicellularity is mainly studied in the social amoeba Dictyostelium discoideum. In this review, we summarise trends in the evolution of cell-type specialisation and behavioural complexity in the four major groups of Dictyostelia. We describe the cell-cell communication systems that control the developmental programme of D. discoideum, highlighting the central role of cAMP in the regulation of cell movement and cell differentiation. Comparative genomic studies showed that the proteins involved in cAMP signalling are deeply conserved across Dictyostelia and their unicellular amoebozoan ancestors. Comparative functional analysis revealed that cAMP signalling in D. discoideum originated from a second messenger role in amoebozoan encystation. We highlight some molecular changes in cAMP signalling genes that were responsible for the novel roles of cAMP in multicellular development.
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Affiliation(s)
- Qingyou Du
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Yoshinori Kawabe
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Christina Schilde
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Zhi-Hui Chen
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Pauline Schaap
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom.
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Root of Dictyostelia based on 213 universal proteins. Mol Phylogenet Evol 2015; 92:53-62. [PMID: 26048704 DOI: 10.1016/j.ympev.2015.05.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 01/03/2023]
Abstract
Dictyostelia are common soil microbes that can aggregate when starved to form multicellular fruiting bodies, a characteristic that has also led to their long history of study and widespread use as model systems. Ribosomal RNA phylogeny of Dictyostelia identified four major divisions (Groups 1-4), none of which correspond to traditional genera. Group 1 was also tentatively identified as sister lineage to the other three Groups, although not consistently or with strong support. We tested the dictyostelid root using universal protein-coding genes identified by exhaustive comparison of six completely sequenced dictyostelid genomes, which include representatives of all four major molecular Groups. A set of 213 genes are low-copy number in all genomes, present in at least one amoebozoan outgroup taxon (Acanthamoeba castellanii or Physarum polycephalum), and phylogenetically congruent. Phylogenetic analysis of a concatenation of the deduced protein sequences produces a single topology dividing Dictyostelia into two major divisions: Groups 1+2 and Groups 3+4. All clades in the tree are fully supported by maximum likelihood and Bayesian inference, and all alternative roots are unambiguously rejected by the approximately unbiased (AU) test. The 1+2, 3+4 root is also fully supported even after deleting clusters with strong individual support for this root, or concatenating all clusters with low support for alternative roots. The 213 putatively ancestral amoebozoan proteins encode a wide variety of functions including 21 KOG categories out of a total of 25. These comprehensive analyses and consistent results indicate that it is time for full taxonomic revision of Dictyostelia, which will also enable more effective exploitation of its unique potential as an evolutionary model system.
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