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Malicki M, Iliopoulou M, Hammann C. Retrotransposon Domestication and Control in Dictyostelium discoideum. Front Microbiol 2017; 8:1869. [PMID: 29051748 PMCID: PMC5633606 DOI: 10.3389/fmicb.2017.01869] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/13/2017] [Indexed: 01/22/2023] Open
Abstract
Transposable elements, identified in all eukaryotes, are mobile genetic units that can change their genomic position. Transposons usually employ an excision and reintegration mechanism, by which they change position, but not copy number. In contrast, retrotransposons amplify via RNA intermediates, increasing their genomic copy number. Hence, they represent a particular threat to the structural and informational integrity of the invaded genome. The social amoeba Dictyostelium discoideum, model organism of the evolutionary Amoebozoa supergroup, features a haploid, gene-dense genome that offers limited space for damage-free transposition. Several of its contemporary retrotransposons display intrinsic integration preferences, for example by inserting next to transfer RNA genes or other retroelements. Likely, any retrotransposons that invaded the genome of the amoeba in a non-directed manner were lost during evolution, as this would result in decreased fitness of the organism. Thus, the positional preference of the Dictyostelium retroelements might represent a domestication of the selfish elements. Likewise, the reduced danger of such domesticated transposable elements led to their accumulation, and they represent about 10% of the current genome of D. discoideum. To prevent the uncontrolled spreading of retrotransposons, the amoeba employs control mechanisms including RNA interference and heterochromatization. Here, we review TRE5-A, DIRS-1 and Skipper-1, as representatives of the three retrotransposon classes in D. discoideum, which make up 5.7% of the Dictyostelium genome. We compile open questions with respect to their mobility and cellular regulation, and suggest strategies, how these questions might be addressed experimentally.
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Affiliation(s)
- Marek Malicki
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Maro Iliopoulou
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
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Schmith A, Spaller T, Gaube F, Fransson Å, Boesler B, Ojha S, Nellen W, Hammann C, Söderbom F, Winckler T. A host factor supports retrotransposition of the TRE5-A population in Dictyostelium cells by suppressing an Argonaute protein. Mob DNA 2015; 6:14. [PMID: 26339297 PMCID: PMC4559204 DOI: 10.1186/s13100-015-0045-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/26/2015] [Indexed: 11/30/2022] Open
Abstract
Background In the compact and haploid genome of Dictyostelium discoideum control of transposon activity is of particular importance to maintain viability. The non-long terminal repeat retrotransposon TRE5-A amplifies continuously in D. discoideum cells even though it produces considerable amounts of minus-strand (antisense) RNA in the presence of an active RNA interference machinery. Removal of the host-encoded C-module-binding factor (CbfA) from D. discoideum cells resulted in a more than 90 % reduction of both plus- and minus-strand RNA of TRE5-A and a strong decrease of the retrotransposition activity of the cellular TRE5-A population. Transcriptome analysis revealed an approximately 230-fold overexpression of the gene coding for the Argonaute-like protein AgnC in a CbfA-depleted mutant. Results The D. discoideum genome contains orthologs of RNA-dependent RNA polymerases, Dicer-like proteins, and Argonaute proteins that are supposed to represent RNA interference pathways. We analyzed available mutants in these genes for altered expression of TRE5-A. We found that the retrotransposon was overexpressed in mutants lacking the Argonaute proteins AgnC and AgnE. Because the agnC gene is barely expressed in wild-type cells, probably due to repression by CbfA, we employed a new method of promoter-swapping to overexpress agnC in a CbfA-independent manner. In these strains we established an in vivo retrotransposition assay that determines the retrotransposition frequency of the cellular TRE5-A population. We observed that both the TRE5-A steady-state RNA level and retrotransposition rate dropped to less than 10 % of wild-type in the agnC overexpressor strains. Conclusions The data suggest that TRE5-A amplification is controlled by a distinct pathway of the Dictyostelium RNA interference machinery that does not require RNA-dependent RNA polymerases but involves AgnC. This control is at least partially overcome by the activity of CbfA, a factor derived from the retrotransposon’s host. This unusual regulation of mobile element activity most likely had a profound effect on genome evolution in D. discoideum. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0045-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anika Schmith
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
| | - Thomas Spaller
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
| | - Friedemann Gaube
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
| | - Åsa Fransson
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Uppsala, Sweden ; Present address: Aprea AB, Karolinska Institutet Science Park, Nobels väg 3, 17175 Solna, Sweden
| | - Benjamin Boesler
- Institute of Biology - Genetics, University of Kassel, Kassel, Germany
| | - Sandeep Ojha
- Ribogenetics@Biochemistry Lab, Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Jacobs University Bremen, Bremen, Germany
| | - Wolfgang Nellen
- Institute of Biology - Genetics, University of Kassel, Kassel, Germany ; Present address: Department of Biology, Brawijaya University, Jl. Veteran, Malang, East Java Indonesia
| | - Christian Hammann
- Ribogenetics@Biochemistry Lab, Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Jacobs University Bremen, Bremen, Germany
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Thomas Winckler
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
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Conserved gene regulatory function of the carboxy-terminal domain of dictyostelid C-module-binding factor. EUKARYOTIC CELL 2013; 12:460-8. [PMID: 23355006 DOI: 10.1128/ec.00329-12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
C-module-binding factor A (CbfA) is a jumonji-type transcription regulator that is important for maintaining the expression and mobility of the retrotransposable element TRE5-A in the social amoeba Dictyostelium discoideum. CbfA-deficient cells have lost TRE5-A retrotransposition, are impaired in the ability to feed on bacteria, and do not enter multicellular development because of a block in cell aggregation. In this study, we performed Illumina RNA-seq of growing CbfA mutant cells to obtain a list of CbfA-regulated genes. We demonstrate that the carboxy-terminal domain of CbfA alone is sufficient to mediate most CbfA-dependent gene expression. The carboxy-terminal domain of CbfA from the distantly related social amoeba Polysphondylium pallidum restored the expression of CbfA-dependent genes in the D. discoideum CbfA mutant, indicating a deep conservation in the gene regulatory function of this domain in the dictyostelid clade. The CbfA-like protein CbfB displays ∼25% sequence identity with CbfA in the amino-terminal region, which contains a JmjC domain and two zinc finger regions and is thought to mediate chromatin-remodeling activity. In contrast to CbfA proteins, where the carboxy-terminal domains are strictly conserved in all dictyostelids, CbfB proteins have completely unrelated carboxy-terminal domains. Outside the dictyostelid clade, CbfA-like proteins with the CbfA-archetypical JmjC/zinc finger arrangement and individual carboxy-terminal domains are prominent in filamentous fungi but are not found in yeasts, plants, and metazoans. Our data suggest that two functional regions of the CbfA-like proteins evolved at different rates to allow the occurrence of species-specific adaptation processes during genome evolution.
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Abstract
Recent advances in quantitation of mRNA by hybridization to microarrayed gene sequences or by deep sequencing of cDNA (RNA-seq) have provided global views of the abundance of each transcript. Analyses of RNA samples taken at 2 or 4 h intervals throughout development of Dictyostelium discoideum have defined the developmental changes in transcriptional profiles. Comparisons of the transcriptome of wild-type cells to that of mutant strains lacking a gene critical to progression through the developmental stages have defined key steps in the progression. The transcriptional response to cAMP pulses depends on the expression of pulse-independent genes that have been identified by transcriptional profiling with microarrays. Similar techniques were used to discover that the DNA binding protein GBF functions in a feed-forward loop to regulate post-aggregation genes and that expression of a set of late genes during culmination is dependent on the DNA binding protein SrfA. RNA-seq is able to reliably measure individual mRNAs present as a single copy per cell as well as mRNAs present at a thousand fold higher abundance. Using this technique it was found that 65% of the genes in Dictyostelium change twofold or more during development. Many decrease during the first 8 h of development, while the rest increase at specific stages and this pattern is evolutionarily conserved as found by comparing the transcriptomes of D. discoideum and Dictyostelium purpureum. The transcriptional profile of each gene is readily available at dictyBase and more sophisticated analyses are available on DictyExpress.
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Affiliation(s)
- William F Loomis
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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The C-module-binding factor supports amplification of TRE5-A retrotransposons in the Dictyostelium discoideum genome. EUKARYOTIC CELL 2010; 10:81-6. [PMID: 21076008 DOI: 10.1128/ec.00205-10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Retrotransposable elements are molecular parasites that have invaded the genomes of virtually all organisms. Although retrotransposons encode essential proteins to mediate their amplification, they also require assistance by host cell-encoded machineries that perform functions such as DNA transcription and repair. The retrotransposon TRE5-A of the social amoeba Dictyostelium discoideum generates a notable amount of both sense and antisense RNAs, which are generated from element-internal promoters, located in the A module and the C module, respectively. We observed that TRE5-A retrotransposons depend on the C-module-binding factor (CbfA) to maintain high steady-state levels of TRE5-A transcripts and that CbfA supports the retrotransposition activity of TRE5-A elements. The carboxy-terminal domain of CbfA was found to be required and sufficient to mediate the accumulation of TRE5-A transcripts, but it did not support productive retrotransposition of TRE5-A. This result suggests different roles for CbfA protein domains in the regulation of TRE5-A retrotransposition frequency in D. discoideum cells. Although CbfA binds to the C module in vitro, the factor regulates neither C-module nor A-module promoter activity in vivo. We speculate that CbfA supports the amplification of TRE5-A retrotransposons by suppressing the expression of an as yet unidentified component of the cellular posttranscriptional gene silencing machinery.
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Galardi-Castilla M, Garciandía A, Suarez T, Sastre L. The Dictyostelium discoideum acaA gene is transcribed from alternative promoters during aggregation and multicellular development. PLoS One 2010; 5:e13286. [PMID: 20949015 PMCID: PMC2952602 DOI: 10.1371/journal.pone.0013286] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 09/15/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Extracellular cAMP is a key extracellular signaling molecule that regulates aggregation, cell differentiation and morphogenesis during multi-cellular development of the social amoeba Dictyostelium discoideum. This molecule is produced by three different adenylyl cyclases, encoded by the genes acaA, acrA and acgA, expressed at different stages of development and in different structures. METHODOLOGY/PRINCIPAL FINDINGS This article describes the characterization of the promoter region of the acaA gene, showing that it is transcribed from three different alternative promoters. The distal promoter, promoter 1, is active during the aggregation process while the more proximal promoters are active in tip-organiser and posterior regions of the structures. A DNA fragment containing the three promoters drove expression to these same regions and similar results were obtained by in situ hybridization. Analyses of mRNA expression by quantitative RT-PCR with specific primers for each of the three transcripts also demonstrated their different temporal patterns of expression. CONCLUSIONS/SIGNIFICANCE The existence of an aggregation-specific promoter can be associated with the use of cAMP as chemo-attractant molecule, which is specific for some Dictyostelium species. Expression at late developmental stages indicates that adenylyl cyclase A might play a more important role in post-aggregative development than previously considered.
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Affiliation(s)
- Maria Galardi-Castilla
- Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Cientificas/Universidad Autónoma de Madrid, Madrid, Spain
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Lucas J, Bilzer A, Moll L, Zündorf I, Dingermann T, Eichinger L, Siol O, Winckler T. The carboxy-terminal domain of Dictyostelium C-module-binding factor is an independent gene regulatory entity. PLoS One 2009; 4:e5012. [PMID: 19343174 PMCID: PMC2661138 DOI: 10.1371/journal.pone.0005012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 03/04/2009] [Indexed: 11/18/2022] Open
Abstract
The C-module-binding factor (CbfA) is a multidomain protein that belongs to the family of jumonji-type (JmjC) transcription regulators. In the social amoeba Dictyostelium discoideum, CbfA regulates gene expression during the unicellular growth phase and multicellular development. CbfA and a related D. discoideum CbfA-like protein, CbfB, share a paralogous domain arrangement that includes the JmjC domain, presumably a chromatin-remodeling activity, and two zinc finger-like (ZF) motifs. On the other hand, the CbfA and CbfB proteins have completely different carboxy-terminal domains, suggesting that the plasticity of such domains may have contributed to the adaptation of the CbfA-like transcription factors to the rapid genome evolution in the dictyostelid clade. To support this hypothesis we performed DNA microarray and real-time RT-PCR measurements and found that CbfA regulates at least 160 genes during the vegetative growth of D. discoideum cells. Functional annotation of these genes revealed that CbfA predominantly controls the expression of gene products involved in housekeeping functions, such as carbohydrate, purine nucleoside/nucleotide, and amino acid metabolism. The CbfA protein displays two different mechanisms of gene regulation. The expression of one set of CbfA-dependent genes requires at least the JmjC/ZF domain of the CbfA protein and thus may depend on chromatin modulation. Regulation of the larger group of genes, however, does not depend on the entire CbfA protein and requires only the carboxy-terminal domain of CbfA (CbfA-CTD). An AT-hook motif located in CbfA-CTD, which is known to mediate DNA binding to A+T-rich sequences in vitro, contributed to CbfA-CTD-dependent gene regulatory functions in vivo.
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Affiliation(s)
- Jörg Lucas
- School of Biology and Pharmacy, Institute of Pharmacy, Department of Pharmaceutical Biology, University of Jena, Jena, Germany
| | - Annika Bilzer
- School of Biology and Pharmacy, Institute of Pharmacy, Department of Pharmaceutical Biology, University of Jena, Jena, Germany
| | - Lorna Moll
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
| | - Ilse Zündorf
- Institute of Pharmaceutical Biology, University of Frankfurt, Frankfurt am Main, Germany
| | - Theodor Dingermann
- Institute of Pharmaceutical Biology, University of Frankfurt, Frankfurt am Main, Germany
| | - Ludwig Eichinger
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
| | - Oliver Siol
- School of Biology and Pharmacy, Institute of Pharmacy, Department of Pharmaceutical Biology, University of Jena, Jena, Germany
| | - Thomas Winckler
- School of Biology and Pharmacy, Institute of Pharmacy, Department of Pharmaceutical Biology, University of Jena, Jena, Germany
- * E-mail:
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Pilcher KE, Gaudet P, Fey P, Kowal AS, Chisholm RL. A general purpose method for extracting RNA from Dictyostelium cells. Nat Protoc 2007; 2:1329-32. [PMID: 17545970 DOI: 10.1038/nprot.2007.191] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Here we present a protocol for the extraction of RNA from Dictyostelium discoideum. Dictyostelium is a social amoeba that undergoes a basic developmental program, and therefore analysis of RNA levels over a time course is a commonly used technique. This procedure is similar to other guanidine thiocyanate-based methods; however, it has been adjusted because of the large quantities of carbohydrate and nucleases found in Dictyostelium cells. After cell lysis and phenol:chloroform extraction, the resulting high-quality RNA isolated with the described protocol allows the molecular genetic analysis of wild-type and genetically modified cells. The purified RNA can be used for analyses such as northern blotting, RT-PCR and microarrays. This procedure requires approximately 2 h to complete.
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Affiliation(s)
- Karen E Pilcher
- dictyBase, Center for Genetic Medicine, Northwestern University, 676 North Saint Clair Street Suite 1260, Chicago, Illinois 60611, USA
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Siol O, Dingermann T, Winckler T. The C-module DNA-binding factor mediates expression of the dictyostelium aggregation-specific adenylyl cyclase ACA. EUKARYOTIC CELL 2006; 5:658-64. [PMID: 16607013 PMCID: PMC1459664 DOI: 10.1128/ec.5.4.658-664.2006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Aggregation of Dictyostelium discoideum amoebae into multicellular structures is organized by cyclic AMP (cAMP), which acts as a chemoattractant, as a second messenger, and as a morphogen. Aggregation of D. discoideum cells depends on the expression of adenylyl cyclase ACA, which provides extracellular cAMP for signal relay and intracellular cAMP for the induction of genes required at multicellular stages. We have identified a DNA-binding activity specific for a highly A+T-enriched motif in the upstream region of the ACA-encoding gene, acaA. The factor shows DNA-binding characteristics very similar to those of C-module-binding factor (CbfA). Although CbfA was originally identified as a putative regulator of the activity of D. discoideum retrotransposon TRE5-A, it also was found to be essential for aggregation of D. discoideum cells. The identified DNA-binding activity was absent in mutant cells depleted of CbfA, and CbfA could be precipitated using an acaA promoter fragment. We propose that CbfA binds to the acaA promoter to provide a basal transcription activity that is required for induction of ACA expression after the onset of D. discoideum development.
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Affiliation(s)
- Oliver Siol
- Universität Jena, Lehrstuhl für Pharmazeutische Biologie, Semmelweisstrasse 10, D-07743 Jena, Germany
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Iranfar N, Fuller D, Loomis WF. Transcriptional regulation of post-aggregation genes in Dictyostelium by a feed-forward loop involving GBF and LagC. Dev Biol 2006; 290:460-9. [PMID: 16386729 DOI: 10.1016/j.ydbio.2005.11.035] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 10/24/2005] [Accepted: 11/16/2005] [Indexed: 11/28/2022]
Abstract
Expression profiles of developmental genes in Dictyostelium were determined on microarrays during development of wild type cells and mutant cells lacking either the DNA binding protein GBF or the signaling protein LagC. We found that the mutant strains developed in suspension with added cAMP expressed the pulse-induced and early adenylyl cyclase (ACA)-dependent genes, but not the later ACA-dependent, post-aggregation genes. Since expression of lagC itself is dependent on GBF, expression of the post-aggregation genes might be controlled only by signaling from LagC. However, expression of lagC in a GBF-independent manner in a gbfA- null strain did not result in expression of the post-aggregation genes. Since GBF is necessary for accumulation of LagC and both the DNA binding protein and the LagC signal transduction pathway are necessary for expression of post-aggregation genes, GBF and LagC form a feed-forward loop. Such network architecture is a common motif in diverse organisms and can act as a filter for noisy inputs. Breaking the feed-forward loop by expressing lagC in a GBF-independent manner in a gbfA+ strain does not significantly affect the patterns of gene expression for cells developed in suspension with added cAMP, but results in a significant delay at the mound stage and asynchronous development on solid supports. This feed-forward loop can integrate temporal information with morphological signals to ensure that post-aggregation genes are only expressed after cell contacts have been made.
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Affiliation(s)
- Negin Iranfar
- Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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