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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: 1.0] [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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The Long Noncoding RNA Transcriptome of Dictyostelium discoideum Development. G3-GENES GENOMES GENETICS 2017; 7:387-398. [PMID: 27932387 PMCID: PMC5295588 DOI: 10.1534/g3.116.037150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long noncoding RNAs (ncRNAs) in D. discoideum To characterize the antisense and long intergenic noncoding RNA (lncRNA) transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing (RNA-seq) library preparation method that selectively depletes ribosomal RNAs (rRNAs). We detected the accumulation of transcripts for 9833 protein-coding messenger RNAs (mRNAs), 621 lncRNAs, and 162 putative antisense RNAs (asRNAs). The noncoding RNAs were interspersed throughout the genome, and were distinct in expression level, length, and nucleotide composition. The noncoding transcriptome displayed a temporal profile similar to the coding transcriptome, with stages of gradual change interspersed with larger leaps. The transcription profiles of some noncoding RNAs were strongly correlated with known differentially expressed coding RNAs, hinting at a functional role for these molecules during development. Examining the mitochondrial transcriptome, we modeled two novel antisense transcripts. We applied yet another ribosomal depletion method to a subset of the samples to better retain transfer RNA (tRNA) transcripts. We observed polymorphisms in tRNA anticodons that suggested a post-transcriptional means by which D. discoideum compensates for codons missing in the genomic complement of tRNAs. We concluded that the prevalence and characteristics of long ncRNAs indicate that these molecules are relevant to the progression of molecular and cellular phenotypes during development.
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Long Y, Abad MG, Olson ED, Carrillo EY, Jackman JE. Identification of distinct biological functions for four 3'-5' RNA polymerases. Nucleic Acids Res 2016; 44:8395-406. [PMID: 27484477 PMCID: PMC5041481 DOI: 10.1093/nar/gkw681] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/22/2016] [Indexed: 12/19/2022] Open
Abstract
The superfamily of 3'-5' polymerases synthesize RNA in the opposite direction to all other DNA/RNA polymerases, and its members include eukaryotic tRNA(His) guanylyltransferase (Thg1), as well as Thg1-like proteins (TLPs) of unknown function that are broadly distributed, with family members in all three domains of life. Dictyostelium discoideum encodes one Thg1 and three TLPs (DdiTLP2, DdiTLP3 and DdiTLP4). Here, we demonstrate that depletion of each of the genes results in a significant growth defect, and that each protein catalyzes a unique biological reaction, taking advantage of specialized biochemical properties. DdiTLP2 catalyzes a mitochondria-specific tRNA(His) maturation reaction, which is distinct from the tRNA(His) maturation reaction typically catalyzed by Thg1 enzymes on cytosolic tRNA. DdiTLP3 catalyzes tRNA repair during mitochondrial tRNA 5'-editing in vivo and in vitro, establishing template-dependent 3'-5' polymerase activity of TLPs as a bona fide biological activity for the first time since its unexpected discovery more than a decade ago. DdiTLP4 is cytosolic and, surprisingly, catalyzes robust 3'-5' polymerase activity on non-tRNA substrates, strongly implying further roles for TLP 3'-5' polymerases in eukaryotes.
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Affiliation(s)
- Yicheng Long
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Maria G Abad
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Erik D Olson
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Elisabeth Y Carrillo
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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4
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Wiegand S, Hammann C. The 5' spreading of small RNAs in Dictyostelium discoideum depends on the RNA-dependent RNA polymerase RrpC and on the dicer-related nuclease DrnB. PLoS One 2013; 8:e64804. [PMID: 23724097 PMCID: PMC3661229 DOI: 10.1371/journal.pone.0064804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 04/16/2013] [Indexed: 11/19/2022] Open
Abstract
RNA interference (RNAi) is a gene-regulatory mechanism in eukarya that is based on the presence of double stranded RNA and that can act on both, the transcription or post-transcriptional level. In many species, RNA-dependent RNA polymerases (RdRPs) are required for RNAi. To study the function of the three RdRPs in the amoeba Dictyostelium discoideum, we have deleted the encoding genes rrpA, rrpB and rrpC in all possible combinations. In these strains, expression of either antisense or hairpin RNA constructs against the transgene lacZ resulted in a 50% reduced β-Galactosidase activity. Northern blots surprisingly revealed unchanged lacZ mRNA levels, indicative of post-transcriptional regulation. Only in rrpC knock out strains, low levels of β-gal small interfering RNAs (siRNAs) could be detected in antisense RNA expressing strains. In contrast to this, and at considerably higher levels, all hairpin RNA expressing strains featured β-gal siRNAs. Spreading of the silencing signal to mRNA sequences 5′ of the original hairpin trigger was observed in all strains, except when the rrpC gene or that of the dicer-related nuclease DrnB was deleted. Thus, our data indicate that transitivity of an RNA silencing signal exists in D. discoideum and that it requires the two enzymes RrpC and DrnB.
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Affiliation(s)
- Stephan Wiegand
- Ribogenetics@Biochemistry Lab, School of Engineering and Science, MOLIFE Research Center, Jacobs University Bremen, Bremen, Germany
| | - Christian Hammann
- Ribogenetics@Biochemistry Lab, School of Engineering and Science, MOLIFE Research Center, Jacobs University Bremen, Bremen, Germany
- * E-mail:
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Avesson L, Reimegård J, Wagner EGH, Söderbom F. MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs. RNA (NEW YORK, N.Y.) 2012; 18:1771-1782. [PMID: 22875808 PMCID: PMC3446702 DOI: 10.1261/rna.033175.112] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/11/2012] [Indexed: 06/01/2023]
Abstract
The RNA interference machinery has served as a guardian of eukaryotic genomes since the divergence from prokaryotes. Although the basic components have a shared origin, silencing pathways directed by small RNAs have evolved in diverse directions in different eukaryotic lineages. Micro (mi)RNAs regulate protein-coding genes and play vital roles in plants and animals, but less is known about their functions in other organisms. Here, we report, for the first time, deep sequencing of small RNAs from the social amoeba Dictyostelium discoideum. RNA from growing single-cell amoebae as well as from two multicellular developmental stages was sequenced. Computational analyses combined with experimental data reveal the expression of miRNAs, several of them exhibiting distinct expression patterns during development. To our knowledge, this is the first report of miRNAs in the Amoebozoa supergroup. We also show that overexpressed miRNA precursors generate miRNAs and, in most cases, miRNA* sequences, whose biogenesis is dependent on the Dicer-like protein DrnB, further supporting the presence of miRNAs in D. discoideum. In addition, we find miRNAs processed from hairpin structures originating from an intron as well as from a class of repetitive elements. We believe that these repetitive elements are sources for newly evolved miRNAs.
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Affiliation(s)
- Lotta Avesson
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, S-75124 Uppsala, Sweden
| | - Johan Reimegård
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, S-75124 Uppsala, Sweden
| | - E. Gerhart H. Wagner
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, S-75124 Uppsala, Sweden
- Science for Life Laboratory, SE-75124 Uppsala, Sweden
| | - Fredrik Söderbom
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, S-75124 Uppsala, Sweden
- Science for Life Laboratory, SE-75124 Uppsala, Sweden
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6
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Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E, Barry K, Lindquist E, Shapiro H, Bruce D, Schmutz J, Salamov A, Fey P, Gaudet P, Anjard C, Babu MM, Basu S, Bushmanova Y, van der Wel H, Katoh-Kurasawa M, Dinh C, Coutinho PM, Saito T, Elias M, Schaap P, Kay RR, Henrissat B, Eichinger L, Rivero F, Putnam NH, West CM, Loomis WF, Chisholm RL, Shaulsky G, Strassmann JE, Queller DC, Kuspa A, Grigoriev IV. Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol 2011; 12:R20. [PMID: 21356102 PMCID: PMC3188802 DOI: 10.1186/gb-2011-12-2-r20] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 12/09/2010] [Accepted: 02/28/2011] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. RESULTS We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict. CONCLUSIONS The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.
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Affiliation(s)
- Richard Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 9458, USA
| | - Xiangjun Tian
- Department of Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - William Salerno
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Anup Parikh
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Christa L Feasley
- Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, 110 N. Lindsay, Oklahoma City, OK 73104, USA
| | - Eileen Dalin
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 9458, USA
| | - Hank Tu
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 9458, USA
| | - Eryong Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 9458, USA
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 9458, USA
| | - Harris Shapiro
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 9458, USA
| | - David Bruce
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 9458, USA
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 9458, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 9458, USA
| | - Petra Fey
- dictyBase, Center for Genetic Medicine, Northwestern University, 750 N. Lake Shore Drive, Chicago, IL 60611, USA
| | - Pascale Gaudet
- dictyBase, Center for Genetic Medicine, Northwestern University, 750 N. Lake Shore Drive, Chicago, IL 60611, USA
| | - Christophe Anjard
- Section of Cell and Developmental Biology, Division of Biology, University of California, 9500 Gilman Dr, San Diego, La Jolla, CA 92093, USA
| | - M Madan Babu
- Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge CB2 2QH, UK
| | - Siddhartha Basu
- dictyBase, Center for Genetic Medicine, Northwestern University, 750 N. Lake Shore Drive, Chicago, IL 60611, USA
| | - Yulia Bushmanova
- dictyBase, Center for Genetic Medicine, Northwestern University, 750 N. Lake Shore Drive, Chicago, IL 60611, USA
| | - Hanke van der Wel
- Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, 110 N. Lindsay, Oklahoma City, OK 73104, USA
| | - Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Christopher Dinh
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universities of Aix-Marseille I & II, 13288 Marseille, France
| | - Tamao Saito
- Department of Materials and Life Sciences, Sophia University 7-1 Kioi-Cho, Chiyoda-Ku, Tokyo 102-8554, Japan
| | - Marek Elias
- Departments of Botany and Parasitology, Faculty of Science, Charles University in Prague, Albertov 6, Prague 128 43, Czech Republic
| | - Pauline Schaap
- College of Life Sciences, University of Dundee, Dow Street, Dundee, DD15EH, UK
| | - Robert R Kay
- Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge CB2 2QH, UK
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universities of Aix-Marseille I & II, 13288 Marseille, France
| | - Ludwig Eichinger
- Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Francisco Rivero
- Centre for Biomedical Research, The Hull York Medical School and Department of Biological Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Nicholas H Putnam
- Department of Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Christopher M West
- Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, 110 N. Lindsay, Oklahoma City, OK 73104, USA
| | - William F Loomis
- Section of Cell and Developmental Biology, Division of Biology, University of California, 9500 Gilman Dr, San Diego, La Jolla, CA 92093, USA
| | - Rex L Chisholm
- dictyBase, Center for Genetic Medicine, Northwestern University, 750 N. Lake Shore Drive, Chicago, IL 60611, USA
| | - Gad Shaulsky
- Department of Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, TX 77005, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Joan E Strassmann
- Department of Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - David C Queller
- Department of Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Adam Kuspa
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, TX 77005, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 9458, USA
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Stamatopoulou V, Toumpeki C, Tzakos A, Vourekas A, Drainas D. Domain Architecture of the DRpp29 Protein and Its Interaction with the RNA Subunit of Dictyostelium discoideum RNase P. Biochemistry 2010; 49:10714-27. [DOI: 10.1021/bi101297z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Chrisavgi Toumpeki
- Department of Biochemistry, School of Medicine, University of Patras, 26500 Patras, Greece
| | - Andreas Tzakos
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Anastassios Vourekas
- Department of Biochemistry, School of Medicine, University of Patras, 26500 Patras, Greece
| | - Denis Drainas
- Department of Biochemistry, School of Medicine, University of Patras, 26500 Patras, Greece
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8
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Whitney TJ, Gardner DG, Mott ML, Brandon M. Identifying the molecular basis of functions in the transcriptome of the social amoeba Dictyostelium discoideum. GENETICS AND MOLECULAR RESEARCH 2010; 9:394-415. [PMID: 20309825 DOI: 10.4238/vol9-1gmr752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The unusual life cycle of Dictyostelium discoideum, in which an extra-cellular stressor such as starvation induces the development of a multicellular fruiting body consisting of stalk cells and spores from a culture of identical amoebae, provides an excellent model for investigating the molecular control of differentiation and the transition from single- to multi-cellular life, a key transition in development. We utilized serial analysis of gene expression (SAGE), a molecular method that is unbiased by dependence on previously identified genes, to obtain a transcriptome from a high-density culture of amoebae, in order to examine the transition to multi-cellular development. The SAGE method provides relative expression levels, which allows us to rank order the expressed genes. We found that a large number of ribosomal proteins were expressed at high levels, while various components of the proteosome were expressed at low levels. The only identifiable transmembrane signaling system components expressed in amoebae are related to quorum sensing, and their expression levels were relatively low. The most highly expressed gene in the amoeba transcriptome, dutA untranslated RNA, is a molecule with unknown function that may serve as an inhibitor of translation. These results suggest that high-density amoebae have not initiated development, and they also suggest a mechanism by which the transition into the development program is controlled.
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Affiliation(s)
- T J Whitney
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
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Abstract
Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.
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10
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Larsson P, Hinas A, Ardell DH, Kirsebom LA, Virtanen A, Söderbom F. De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring. Genome Res 2008; 18:888-99. [PMID: 18347326 DOI: 10.1101/gr.069104.107] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Genome data are increasingly important in the computational identification of novel regulatory non-coding RNAs (ncRNAs). However, most ncRNA gene-finders are either specialized to well-characterized ncRNA gene families or require comparisons of closely related genomes. We developed a method for de novo screening for ncRNA genes with a nucleotide composition that stands out against the background genome based on a partial sum process. We compared the performance when assuming independent and first-order Markov-dependent nucleotides, respectively, and used Karlin-Altschul and Karlin-Dembo statistics to evaluate the significance of hits. We hypothesized that a first-order Markov-dependent process might have better power to detect ncRNA genes since nearest-neighbor models have been shown to be successful in predicting RNA structures. A model based on a first-order partial sum process (analyzing overlapping dinucleotides) had better sensitivity and specificity than a zeroth-order model when applied to the AT-rich genome of the amoeba Dictyostelium discoideum. In this genome, we detected 94% of previously known ncRNA genes (at this sensitivity, the false positive rate was estimated to be 25% in a simulated background). The predictions were further refined by clustering candidate genes according to sequence similarity and/or searching for an ncRNA-associated upstream element. We experimentally verified six out of 10 tested ncRNA gene predictions. We conclude that higher-order models, in combination with other information, are useful for identification of novel ncRNA gene families in single-genome analysis of D. discoideum. Our generalizable approach extends the range of genomic data that can be searched for novel ncRNA genes using well-grounded statistical methods.
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Affiliation(s)
- Pontus Larsson
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
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11
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Hinas A, Reimegård J, Wagner EGH, Nellen W, Ambros VR, Söderbom F. The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway. Nucleic Acids Res 2007; 35:6714-26. [PMID: 17916577 PMCID: PMC2175303 DOI: 10.1093/nar/gkm707] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Small RNAs play crucial roles in regulation of gene expression in many eukaryotes. Here, we report the cloning and characterization of 18–26 nt RNAs in the social amoeba Dictyostelium discoideum. This survey uncovered developmentally regulated microRNA candidates whose biogenesis, at least in one case, is dependent on a Dicer homolog, DrnB. Furthermore, we identified a large number of 21 nt RNAs originating from the DIRS-1 retrotransposon, clusters of which have been suggested to constitute centromeres. Small RNAs from another retrotransposon, Skipper, were significantly up-regulated in strains depleted of the second Dicer-like protein, DrnA, and a putative RNA-dependent RNA polymerase, RrpC. In contrast, the expression of DIRS-1 small RNAs was not altered in any of the analyzed strains. This suggests the presence of multiple RNAi pathways in D. discoideum. In addition, we isolated several small RNAs with antisense complementarity to mRNAs. Three of these mRNAs are developmentally regulated. Interestingly, all three corresponding genes express longer antisense RNAs from which the small RNAs may originate. In at least one case, the longer antisense RNA is complementary to the spliced but not the unspliced pre-mRNA, indicating synthesis by an RNA-dependent RNA polymerase.
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Affiliation(s)
- Andrea Hinas
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Box 590, SE-75124 Uppsala, Sweden
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