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Söderbom, Fredrik
Publications (10 of 21) Show all publications
Liao, Z., Kjellin, J., Höppner, M. P., Grabherr, M. & Söderbom, F. (2018). Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum. RNA Biology, 15(7), 937-954
Open this publication in new window or tab >>Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum
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2018 (English)In: RNA Biology, ISSN 1547-6286, E-ISSN 1555-8584, Vol. 15, no 7, p. 937-954Article in journal (Refereed) Published
Abstract [en]

Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3’-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.

Place, publisher, year, edition, pages
UK: Taylor & Francis Group, 2018
Keywords
Dicer, microRNA, amoeba, biogenesis, evolution, transcriptional start site, intron, development, Dictyostelium discoideum
National Category
Microbiology
Research subject
Biology
Identifiers
urn:nbn:se:uu:diva-354016 (URN)10.1080/15476286.2018.1481697 (DOI)000445654400013 ()
Funder
Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning, 621-2013-4665Carl Tryggers foundation , CST12:485
Available from: 2018-06-19 Created: 2018-06-19 Last updated: 2018-10-18Bibliographically approved
Schmith, A., Spaller, T., Gaube, F., Fransson, A., Boesler, B., Ojha, S., . . . Winckler, T. (2015). A host factor supports retrotransposition of the TRE5-A population in Dictyostelium cells by suppressing an Argonaute protein. Mobile DNA, 6, Article ID 14.
Open this publication in new window or tab >>A host factor supports retrotransposition of the TRE5-A population in Dictyostelium cells by suppressing an Argonaute protein
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2015 (English)In: Mobile DNA, ISSN 1759-8753, E-ISSN 1759-8753, Vol. 6, article id 14Article in journal (Refereed) Published
Abstract [en]

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.

Keywords
Dictyostelium, Retrotransposition, siRNA, RNAi, Argonaute
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-262949 (URN)10.1186/s13100-015-0045-5 (DOI)000360527400001 ()26339297 (PubMedID)
Funder
Swedish Research Council
Available from: 2015-10-02 Created: 2015-09-23 Last updated: 2017-12-01Bibliographically approved
Wiegand, S., Meier, D., Seehafer, C., Malicki, M., Hofmann, P., Schmith, A., . . . Hammann, C. (2014). The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals. Nucleic Acids Research, 42(5), 3330-3345
Open this publication in new window or tab >>The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals
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2014 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 42, no 5, p. 3330-3345Article in journal (Refereed) Published
Abstract [en]

Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the function of centromeres, rendering tight retrotransposition control critical to maintaining chromosome integrity. We report that in deletion strains of the RNA-dependent RNA polymerase RrpC, full-length and shorter DIRS-1 messenger RNAs are strongly enriched. Shorter versions of a hitherto unknown long non-coding RNA in DIRS-1 antisense orientation are also enriched in rrpC(-) strains. Concurrent with the accumulation of long transcripts, the vast majority of small (21 mer) DIRS-1 RNAs vanish in rrpC(-) strains. RNASeq reveals an asymmetric distribution of the DIRS-1 small RNAs, both along DIRS-1 and with respect to sense and antisense orientation. We show that RrpC is required for post-transcriptional DIRS-1 silencing and also for spreading of RNA silencing signals. Finally, DIRS-1 mis-regulation in the absence of RrpC leads to retrotransposon mobilization. In summary, our data reveal RrpC as a key player in the silencing of centromeric retrotransposon DIRS-1. RrpC acts at the post-transcriptional level and is involved in spreading of RNA silencing signals, both in the 5' and 3' directions.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-224144 (URN)10.1093/nar/gkt1337 (DOI)000333093600049 ()
Available from: 2014-05-05 Created: 2014-05-05 Last updated: 2017-12-05Bibliographically approved
Crona, M., Avesson, L., Sahlin, M., Lundin, D., Hinas, A., Klose, R., . . . Sjöberg, B.-M. (2013). A Rare Combination of Ribonucleotide Reductases in the Social Amoeba Dictyostelium discoideum. Journal of Biological Chemistry, 288(12), 8198-208
Open this publication in new window or tab >>A Rare Combination of Ribonucleotide Reductases in the Social Amoeba Dictyostelium discoideum
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2013 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 288, no 12, p. 8198-208Article in journal (Refereed) Published
Abstract [en]

Ribonucleotide reductases (RNRs) catalyze the only pathway for de novo synthesis of deoxyribonucleotides needed for DNA replication and repair. The vast majority of eukaryotes encodes only a class I RNR, but interestingly some eukaryotes, including the social amoeba Dictyostelium discoideum, encode both a class I and a class II RNR. The amino acid sequence of the D. discoideum class I RNR is similar to other eukaryotic RNRs, whereas that of its class II RNR is most similar to the monomeric class II RNRs found in Lactobacillus spp. and a few other bacteria. Here we report the first study of RNRs in a eukaryotic organism that encodes class I and class II RNRs. Both classes of RNR genes were expressed in D. discoideum cells, although the class I transcripts were more abundant and strongly enriched during mid-development compared with the class II transcript. The quaternary structure, allosteric regulation, and properties of the diiron-oxo/radical cofactor of D. discoideum class I RNR are similar to those of the mammalian RNRs. Inhibition of D. discoideum class I RNR by hydroxyurea resulted in a 90% reduction in spore formation and decreased the germination viability of the surviving spores by 75%. Class II RNR could not compensate for class I inhibition during development, and an excess of vitamin B12 coenzyme, which is essential for class II activity, did not improve spore formation. We suggest that class I is the principal RNR during D. discoideum development and growth and is important for spore formation, possibly by providing dNTPs for mitochondrial replication.

National Category
Cell Biology
Identifiers
urn:nbn:se:uu:diva-198961 (URN)10.1074/jbc.M112.442434 (DOI)000316564500020 ()23372162 (PubMedID)
Funder
Swedish Research CouncilEU, European Research Council, EC005120
Available from: 2013-04-30 Created: 2013-04-30 Last updated: 2017-12-06Bibliographically approved
Hällman, J., Avesson, L., Reimegård, J., Käller, M. & Söderbom, F. (2013). Identification and verification of microRNAs by high-throughput sequencing (2ed.). In: Ludwig Eichinger and Francisco Rivero (Ed.), Dictyostelium discoideum Protocols: (pp. 125-138). Humana Press, 983
Open this publication in new window or tab >>Identification and verification of microRNAs by high-throughput sequencing
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2013 (English)In: Dictyostelium discoideum Protocols / [ed] Ludwig Eichinger and Francisco Rivero, Humana Press, 2013, 2, Vol. 983, p. 125-138Chapter in book (Other academic)
Abstract [en]

High-throughput sequencing methods have become invaluable for detection and analysis of small RNAs. The results are millions of sequences that need to be carefully analyzed by computational methods and preferentially verified by different experimental techniques. Here we describe how to use high-throughput sequencing followed by bioinformatics and northern blot to identify one particular class of small RNA, microRNAs.

Place, publisher, year, edition, pages
Humana Press, 2013 Edition: 2
Series
Methods in Molecular Biology, ISSN 1063-3745 ; 983
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-198959 (URN)10.1007/978-1-62703-302-2_7 (DOI)23494305 (PubMedID)
Available from: 2013-04-30 Created: 2013-04-30 Last updated: 2013-11-14Bibliographically approved
Vetukuri, R. R., Asman, A. K. M., Tellgren-Roth, C., Jahan, S. N., Reimegard, J., Fogelqvist, J., . . . Dixelius, C. (2012). Evidence for Small RNAs Homologous to Effector-Encoding Genes and Transposable Elements in the Oomycete Phytophthora infestans. PLoS ONE, 7(12), e51399
Open this publication in new window or tab >>Evidence for Small RNAs Homologous to Effector-Encoding Genes and Transposable Elements in the Oomycete Phytophthora infestans
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2012 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 12, p. e51399-Article in journal (Refereed) Published
Abstract [en]

Phytophthora infestans is the oomycete pathogen responsible for the devastating late blight disease on potato and tomato. There is presently an intense research focus on the role(s) of effectors in promoting late blight disease development. However, little is known about how they are regulated, or how diversity in their expression may be generated among different isolates. Here we present data from investigation of RNA silencing processes, characterized by non-coding small RNA molecules (sRNA) of 19-40 nt. From deep sequencing of sRNAs we have identified sRNAs matching numerous RxLR and Crinkler (CRN) effector protein genes in two isolates differing in pathogenicity. Effector gene-derived sRNAs were present in both isolates, but exhibited marked differences in abundance, especially for CRN effectors. Small RNAs in P. infestans grouped into three clear size classes of 21, 25/26 and 32 nt. Small RNAs from all size classes mapped to RxLR effector genes, but notably 21 nt sRNAs were the predominant size class mapping to CRN effector genes. Some effector genes, such as PiAvr3a, to which sRNAs were found, also exhibited differences in transcript accumulation between the two isolates. The P. infestans genome is rich in transposable elements, and the majority of sRNAs of all size classes mapped to these sequences, predominantly to long terminal repeat (LTR) retrotransposons. RNA silencing of Dicer and Argonaute genes provided evidence that generation of 21 nt sRNAs is Dicer-dependent, while accumulation of longer sRNAs was impacted by silencing of Argonaute genes. Additionally, we identified six microRNA (miRNA) candidates from our sequencing data, their precursor sequences from the genome sequence, and target mRNAs. These miRNA candidates have features characteristic of both plant and metazoan miRNAs. Citation: Vetukuri RR, Asman AKM, Tellgren-Roth C, Jahan SN, Reimegard J, et al. (2012) Evidence for Small RNAs Homologous to Effector-Encoding Genes and Transposable Elements in the Oomycete Phytophthora infestans.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-191768 (URN)10.1371/journal.pone.0051399 (DOI)000312386800044 ()
Available from: 2013-01-16 Created: 2013-01-14 Last updated: 2017-12-06Bibliographically approved
Avesson, L., Reimegård, J., Wagner, G. E. & Söderbom, F. (2012). MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs. RNA: A publication of the RNA Society, 18(10), 1771-1782
Open this publication in new window or tab >>MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs
2012 (English)In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 18, no 10, p. 1771-1782Article in journal (Refereed) Published
Abstract [en]

The RNA interference machinery has served as a guardian of eukaryotic genomes since the divergence from prokaryotes. Although the basic components have a common origin, silencing pathways directed by small RNAs have evolved in diverse directions in different eukaryotic lineages. One example is miRNAs. Their regulation of protein coding genes has been shown to play a vital role in plants and animals but little is known about their role in other organisms. The single cell social amoeba Dictyostelium discoideum could hold the answers to some questions regarding the evolution and function of small RNA pathways. Here we report deep sequencing of small RNAs from three developmental stages of D. discoideum. Analyses of these libraries as well as experimental data reveal the expression of a number of miRNAs, several which have distinct expression patterns during development. We also find miRNAs processed from a hairpin originating from a repetitive element that we believe could represent a pathway for the generation of new miRNAs.

Keywords
microRNA, Dictyostelium discoideum, high-throughput sequencing, small RNA, development
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-131165 (URN)10.1261/rna.033175.112 (DOI)000309002700003 ()
Available from: 2010-09-26 Created: 2010-09-26 Last updated: 2017-12-12Bibliographically approved
Boesler, C., Kruse, J., Söderbom, F. & Hammann, C. (2011). Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum. Journal of Biological Chemistry, 286(20), 17693-17703
Open this publication in new window or tab >>Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum
2011 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 286, no 20, p. 17693-17703Article in journal (Refereed) Published
Abstract [en]

The amoeba Dictyostelium discoideum is a well established model organism for studying numerous aspects of cellular and developmental functions. Its ribosomal RNA (rRNA) is encoded in an extrachromosomal palindrome that exists in ∼100 copies in the cell. In this study, we have set out to investigate the sequence of the expressed rRNA. For this, we have ligated the rRNA ends and performed RT-PCR on these circular RNAs. Sequencing revealed that the mature 26 S, 17 S, 5.8 S, and 5 S rRNAs have sizes of 3741, 1871, 162, and 112 nucleotides, respectively. Unlike the published data, all mature rRNAs of the same type uniformly display the same start and end nucleotides in the analyzed AX2 strain. We show the existence of a short lived primary transcript covering the rRNA transcription unit of 17 S, 5.8 S, and 26 S rRNA. Northern blots and RT-PCR reveal that from this primary transcript two precursor molecules of the 17 S and two precursors of the 26 S rRNA are generated. We have also determined the sequences of these precursor molecules, and based on these data, we propose a model for the maturation of the rRNAs in Dictyostelium discoideum that we compare with the processing of the rRNA transcription unit of Saccharomyces cerevisiae.

National Category
Cell Biology
Identifiers
urn:nbn:se:uu:diva-198962 (URN)10.1074/jbc.M110.208306 (DOI)21454536 (PubMedID)
Available from: 2013-04-30 Created: 2013-04-30 Last updated: 2017-12-06Bibliographically approved
Masson, P., Lundin, D., Söderbom, F. & Young, P. (2009). Characterization of a REG/PA28 proteasome activator homolog in Dictyostelium discoideum indicates that the ubiquitin- and ATP-independent REGgamma proteasome is an ancient nuclear protease. Eukaryotic Cell, 8(6), 844-851
Open this publication in new window or tab >>Characterization of a REG/PA28 proteasome activator homolog in Dictyostelium discoideum indicates that the ubiquitin- and ATP-independent REGgamma proteasome is an ancient nuclear protease
2009 (English)In: Eukaryotic Cell, ISSN 1535-9778, E-ISSN 1535-9786, Vol. 8, no 6, p. 844-851Article in journal (Refereed) Published
Abstract [en]

The nuclear proteasome activator REGgamma/PA28gamma is an ATP- and ubiquitin-independent activator of the 20S proteasome and has been proposed to degrade and thereby regulate both a key human oncogene, encoding the coactivator SRC-3/AIB1, and the cyclin-dependent kinase inhibitor p21 (Waf/Cip1). We report the identification and characterization of a PA28/REG homolog in Dictyostelium. Association of a recombinant Dictyostelium REG with the purified Dictyostelium 20S proteasome led to the preferential stimulation of the trypsin-like proteasome peptidase activity. Immunolocalization studies demonstrated that the proteasome activator is localized to the nucleus and is present in growing as well as starving Dictyostelium cells. Our results indicate that the Dictyostelium PA28/REG activator can stimulate both the trypsin-like and chymotrypsin-like activities of the 20S proteasome and supports the idea that the REGgamma-20S proteasome represents an early unique nuclear degradation pathway for eukaryotic cells.

National Category
Cell Biology
Identifiers
urn:nbn:se:uu:diva-198964 (URN)10.1128/EC.00165-08 (DOI)19411624 (PubMedID)
Available from: 2013-04-30 Created: 2013-04-30 Last updated: 2017-12-06Bibliographically approved
Sandrini, M. P., Söderbom, F., Mikkelsen, N. E. & Piskur, J. (2007). Dictyostelium discoideum salvages purine deoxyribonucleosides by highly specific bacterial-like deoxyribonucleoside kinases. Journal of Molecular Biology, 369(3), 653-664
Open this publication in new window or tab >>Dictyostelium discoideum salvages purine deoxyribonucleosides by highly specific bacterial-like deoxyribonucleoside kinases
2007 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 369, no 3, p. 653-664Article in journal (Refereed) Published
Abstract [en]

The salvage of deoxyribonucleosides in the social amoeba Dictyostelium discoideum, which has an extremely A+T-rich genome, was investigated. All native deoxyribonucleosides were phosphorylated by D. discoideum cell extracts and we subcloned three deoxyribonucleoside kinase (dNK) encoding genes. D. discoideum thymidine kinase was similar to the human thymidine kinase 1 and was specific for thymidine with a K(m) of 5.1 microM. The other two cloned kinases were phylogenetically closer to bacterial deoxyribonucleoside kinases than to the eukaryotic enzymes. D. discoideum deoxyadenosine kinase (DddAK) had a K(m) for deoxyadenosine of 22.7 microM and a k(cat) of 3.7 s(-1) and could not efficiently phosphorylate any other native deoxyribonucleoside. D. discoideum deoxyguanosine kinase was also a purine-specific kinase and phosphorylated significantly only deoxyguanosine, with a K(m) of 1.4 microM and a k(cat) of 3 s(-1). The two purine-specific deoxyribonucleoside kinases could represent ancient enzymes present in the common ancestor of bacteria and eukaryotes but remaining only in a few eukaryote lineages. The narrow substrate specificity of the D. discoideum dNKs reflects the biased genome composition and we attempted to explain the strict preference of DddAK for deoxyadenosine by modeling the active center with different substrates. Apart from its native substrate, deoxyadenosine, DddAK efficiently phosphorylated fludarabine. Hence, DddAK could be used in the enzymatic production of fludarabine monophosphate, a drug used in the treatment of chronic lymphocytic leukemia.

National Category
Cell Biology
Identifiers
urn:nbn:se:uu:diva-198965 (URN)10.1016/j.jmb.2007.03.053 (DOI)17448496 (PubMedID)
Available from: 2013-04-30 Created: 2013-04-30 Last updated: 2017-12-06Bibliographically approved
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