Department of Cell and Molecular Biology

Selected publications

Articles

A host factor supports retrotransposition of the TRE5-A population in Dictyostelium cells by suppressing an Argonaute protein. Schmith A, Spaller T, Gaube F, Fransson Å, Boesler B, Ojha S, Nellen W, Hammann C, Söderbom F, Winckler T. Mob DNA. 2015 Sep 3;6:14. doi: 10.1186/s13100-015-0045-5. eCollection 2015.

Wiegand S., Meier D., Seehafer C., Malicki M., Hofmann P., Schmith A., Winckler T., Földesi B., Boesler B., Nellen W., Reimegård J., Käller M., Hällman J., Emanuelsson, O., Avesson L., Söderbom F., Hammann C. (2013). 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, 3330-3345.

Crona M., Avesson L., Sahlin M., Lundin D., Hinas A., Klose R., Söderbom F. and Sjoberg B.M. (2013). A Rare Combination of Ribonucleotide Reductases in the Social Amoeba Dictyostelium discoideum. J. Biol. Chem. 288, 8198-8208.

Vetukuri R.R., Åsman A.K., Tellgren-Roth C., Jahan S.N., Reimegård J., Fogelqvist J., Savenkov E., Söderbom F., Avrova A.O., Whisson S.C. and Dixelius C. (2012). Evidence for small RNAs homologous to effector-encoding genes and transposable elements in the oomycete Phytophthora infestans. PLoS One 7, e51399.

Avesson, L., Reimegård, J., Wagner, E.G. and Söderbom, F. (2012) MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentlly regulated microRNAs. RNA 18, 1771-11782.

Avesson, L., Schumacher, H.T., Fechter, P., Romby, P. and Söderbom, F. (2011) Abundant Class of Non-coding RNA Regulates Development in the Social Amoeba Dictyostelium discoideum. RNA Biology 8, 1094-1104.

Ringqvist, E., Avesson, L., Söderbom, F. and Svärd, S.G. (2011) Transcriptional changes in Giardia during host-parasite interactions. Int. J. Parasitol. 41, 277-85.

Boesler C, Kruse J, Söderbom F, Hammann C. (2011) Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum. J Biol Chem. 286, 17693-17703.

Vetukuri, R.R., Avrova, A.O., Grenville-Briggs, L.J. West, P. VAN, Söderbom, F., Savenkov, E.I., Whisson, S.C. and Dixelius, C. (2011) Evidence for involvement of Dicer-like, Argonaute and histone deacetylase proteins in gene silencing in Phytophthora infestans. Mol. Plant Pathol. 12, 772-85.

Masson, P., Lundin D., Söderbom F. and Young P. (2009) Characterization of a REG/PA28 proteosome activator homolog in Dictyostelium discoideum indicates that the ubiquitin- and ATP-independent REGgamma proteosome is an ancient nuclear protease. Eukaryotic Cell 8, 844-851.

Larsson, P., Hinas, A., Ardell, D., Kirsebom, L., Virtanen, A. and Söderbom, F. (2008) De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring. Genome Research 18, 888-899.

Hinas A., Reimegård, J., Wagner E.G.H., Nellen, W., Ambros, and Söderbom, F. (2007) The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway. Nucleic Acids Research 35, 6714-26.

Sandrini, M. P. B., Söderbom F., Mikkelsen, N. E. and Piskur, J. (2007) Dictyostelium discoideum salvages purine deoxyribonucleosides by highly specific bacteria-like deoxyribonucleoside kinases. J. Mol. Biol. 369, 653-64.

Hinas, A. and Söderbom, F. (2007): Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum. CurrentGenetics 51, 141-159. (Review)

Kyriakopoulou, C., Larsson, P., Liu, L., Schuster, J., Söderbom, F., Kirsebom. L. and Virtanen, A. (2006) U1-like snRNAs lacking complementarity to canonical 5’ splice sites. RNA 12, 1603-1611.

Hinas, A., Larsson, P., Avesson, P., Kirsebom, L., Virtanen, A. and Söderbom, F. (2006) Identification of the major spliceosomal RNAs in Dictyostelium discoideum reveals developmentally regulated U2 variants and polyadenylated snRNAs. Eukaryotic Cell 5, 924-934.

Popova, B., Kuhlmann, M., Hinas, A., Söderbom, F. and Nellen, W. (2006) HelF, a putative RNA helicase acts as a nuclear suppressor of RNAi but not antisense mediated gene silencing. Nucleic Acids Research 34, 773-784.

Kuhlmann, M., Borisova, B.E., Kaller, M., Larsson, P., Stach, D., Na, J., Eichinger, L., Lyko, F., Ambros, V., Söderbom, F., Hammann, C.  and Nellen, W. (2005) Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi. Nucleic Acids Research. 33, 6405-6417.

Söderbom, F., Svärd, S.G. and Kirsebom, L.A. (2005) RNase E Cleavage in the 5' Leader of a tRNA Precursor. Journal of Molecular Biology 352, 22-27.

Aspegren, A., Hinas, A., Larsson, P., Larsson, A. and Söderbom, F. (2004) Novel non-coding RNAs in Dictyostelium discoideum and their expression during development. Nucleic Acid Research 32, 4646-4656.

Anjard, C., Söderbom, F., Fuller, D. and Loomis, W.F. (2001) Requirements for the Adenylyl Cyclase in Development of Dictyostelium. Development 128, 3649-3654.

Söderbom, F., Anjard, C., Iranfar, Fuller, D. and Loomis, W.F. (1999) An adenylyl cyclase that function during late development of Dictyostelium. Development 126, 5436-5471.

Wang, N., Söderbom, F., Anjard, C., Shaulsky, G. and Loomis, W.F. (1999) SDF-2 induction of terminal differentiation in Dictyostelium is mediated by the membrane-spanning sensor kinase DhkA. Mol Cell Biol. 15, 4750-4756.

Söderbom, F., and Loomis (1998) Cell-cell signaling during Dictyostelium development. Trends Microbiol. 6, 402-406. (Review)

Söderbom, F. and Wagner, E.G.H. (1998) Degradation pathway of CopA, the antisense RNA that controls replication of plasmid R1. Microbiology 144, 1907-1917.

Söderbom, F., Binnie, U., Masters, M. and Wagner, E.G.H. (1997) Regulation of R1 replication: PcnB and Rnase E expidite the decay of the antisense RNA CopA. Mol. Microbiol. 26, 493-504.

*L. He, *F. Söderbom, E.G.H. Wagner, U. Binnie, N. Binns, M. Masters (1993). PcnB is required for the rapid degradation of RNAI, the antisense RNA that controls the copy number of ColE1-related plasmids. Mol Microbiol. 9, 1131-1142. *First authorship shared

T. van Biesen, F. Söderbom, E.G.H. Wagner, L.S. Frost (1993). Structural and functional analyses of the FinP antisense RNA regulatory system of the F conjugative plasmid. Mol Microbiol. 10, 35-43.

Book chapters

Avesson, L., Hinas, A. and Söderbom F. (2013): Non-coding RNAs in Dictyostelium discoideum and other Dictyostelia. In Dictyostelia – Evolutionary patterns and processes in the social amoeba Edts.: Romeralo, Escalantes, R. and M., Baldauf. Springer. In press

Hällman, J., Avesson, L., Reimegård, J., Käller, M. and Söderbom, F. (2013): Identification and verification of microRNAs by high-throughput sequencing. Series “Methods in Molecular Biology” Edts.: Eichinger, L. and Rivero, F. Human Springer 983, 125-138.

Söderbom, F. (2006) Small Nucleolar RNAs: Identification, Structure, and Function. In: Small RNAs; Analysis and Regulatory Functions. Series “Nucleic Acids and Molecular Biology”, Vol. 17, Edts.: Nellen, W. and Hammann, C., Springer, Berlin Heidelberg pp 31-56.