Research group of Tore Samuelsson
| Tore Samuelsson, Professor
Department of Medical Biochemistry
University of Goteborg , Medicinareg. 9A
Box 440 , S-405 30 Goteborg, SWEDEN
Tel. + 46 31 786 34 68 , Mob 073 616 9629
Fax + 46 31 41 61 08
Evolution of RNA and protein genes as studied by comparative
A huge amount of sequence information is being generated world-wide as part of projects to sequence genomes and transcriptomes of a large number of organisms. This information is a highly valuable source of information to exploit fundamental biological processes such as gene function, transcriptional regulation, and molecular evolution at the level of DNA and protein sequences. Comparative genomics is a science where species are being compared with respect to their genomes, for instance to better understand the evolution of genomes. Comparative genomics is also useful in many computational methods, such as prediction of gene structure, prediction of non-coding RNAs and prediction of regulatory sites in the genome.
We are using comparative genomics and DNA and protein sequence analysis to examine the structure, function and evolution of genes. We have considered protein genes as well as non-coding RNAs (nc-RNA), i.e RNA that do not code for proteins but have other functions. The evolution of proteins is being studied in a number of projects where we make use of tools such as gene prediction, profile-based searches and methods of phylogenetic analysis. We have developed methods to effectively identify ncRNAs in genomic sequences and have applied these methods on a large number of ncRNA families. We have identified a large number of previously unrecognized homologues and these results have allowed a better understanding of the secondary structure and evolution of these RNAs.
- SRP RNA
- P and MRP RNA
- Iron responsive element
- Stem-loop motif of histone mRNA
- Evolution of U12 introns
The evolution of proteins and protein domains.
- Carlsten JO, Zhu X, López MD, Samuelsson T, Gustafsson CM.
Loss of the Mediator subunit Med20 affects transcription of tRNA and other non-coding RNA genes in fission yeast.Biochim Biophys Acta. 2015 Nov 19.
- Gao J, Yang X, Zhao W, Lang T, Samuelsson T. Evolution, diversification, and expression of KNOX proteins in plants.
Front Plant Sci. 2015 Oct 23
- Dumesic PA, Rosenblad MA, Samuelsson T, Nguyen T, Moresco JJ, Yates JR 3rd, Madhani HD. Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans.
Nucleic Acids Res. 2015 Oct 15.
- Jemt E, Persson Ö, Shi Y, Mehmedovic M, Uhler JP, Dávila López M, Freyer C, Gustafsson CM, Samuelsson T, Falkenberg M. Regulation of DNA replication at the end of the mitochondrial D-loop involves the helicase TWINKLE and a conserved sequence element
Nucleic Acids Res. 2015 Oct 30.
- Stewart JB, Alaei-Mahabadi B, Sabarinathan R, Samuelsson T, Gorodkin J, Gustafsson CM, Larsson E. Simultaneous DNA and RNA Mapping of Somatic Mitochondrial Mutations across Diverse Human Cancers. PLoS Genet. 2015 Jun 30.
Jevtov, I., Samuelsson, T., Yao, G., Amsterdam, A., Ribbeck, K. Zebrafish as a model to study live mucus physiology Scientific Reports 2014 (in press).
Uhler JP, Spåhr H, Farge G, Clavel S, Larsson NG, Falkenberg M, Samuelsson T, Gustafsson CM The UbL protein UBTD1 stably interacts with the UBE2D family of E2 ubiquitin conjugating enzymes. Biochem Biophys Res Commun. 2013 Nov 6.
& Larsson, E. The landscape of viral expression and host gene fusion and adaptation in human cancer. Nature Communications 4 doi:10.1038/ncomms3513
Wanrooij, S., Fusté, J.M., Stewart, J.B., Wanrooij, P.H., Samuelsson, T., Larsson N-G., Gustafsson, C.M. and Falkenberg, M.
In vivo mutagenesis reveals that OriL is essential for mitochondrial DNA replication. EMBO Reports 2012. Dec;13(12):1130-7.
Genomics and Bioinformatics - An Introduction to Programming Tools for Life Scientists Cambridge University Press 2012 (available from May 2012). Web resources to book.
- Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C.
RNAcentral: A vision for an international database of RNA sequences. RNA. 2011 Sep 22
- Davila Lopez, M., and Samuelsson, T. eGOB : Eukaryotic Gene Order Browser Bioinformatics 2011 Apr 15;27(8):1150-1.
Sterky FH, Ruzzenente B, Gustafsson CM, Samuelsson T, Larsson NG
LRPPRC is a mitochondrial matrix protein that is conserved in metazoans
- Spår, H, Samuelsson T, Martin Hällberg B, Gustafsson CM.
Structure of Mitochondrial Transcription Termination Factor 3 reveals a novel nucleic acid-binding domain BBRC 2010.
- Davila Lopez, M., Martinez Guerra, J.J., Samuelsson, T. Analysis of gene order conservation in eukaryotes identifies
transcriptionally and functionally linked genes. 2010 PLOS ONE.
- Bartschat S, Samuelsson T. U12 type
introns were lost at multiple occasions during evolution
. 2010 BMC Genomics.
- Rosenblad MA, Larsen N, Samuelsson T, Zwieb C
Kinship in the SRP RNA familyi 2009. RNA biology
- Davila Lopez, M., Alm Rosenblad, M., and Samuelsson, T. Conserved and variable domains of RNase MRP RNA. 2009. RNA Biology.
- Kalen,M, Wallgard E, Asker N, Nasevicius A, Athley E, Billgren E, Larson JD, Wadman SA, Norseng E, Clark KJ, He L, Karlsson-Lindahl L, Häger AK, Weber H, Augustin H, Samuelsson T, Kemmet CK, Utesch CM, Essner JJ, Hackett PB, Hellström
Combination of reverse and chemical genetic screens reveals angiogenesis inhibitors and targets.
Chem Biol. 2009 Apr 24;16(4):432-41
- Davila Lopez, M., Alm Rosenblad, M., and Samuelsson, T. Computational screen for spliceosomal RNA genes aids in defining the
phylogenetic distribution of major and minor spliceosomal components. 2008 May;36(9):3001-10.
Davila Lopez, M., Samuelsson, T. Early evolution of histone
mRNA 3' end processing RNA. 2008 Jan;14(1):1-10.
- He L, Sun Y, Takemoto M, Norlin J, Tryggvason K, Samuelsson T and Betsholtz C:
From cataloguing glomerulus-enriched gene transcripts towards systematic understanding of kidney glomeruli. Journal of American S
ociety of Nephrology 2008 Feb;19(2):260-8
- Lang, T., Hansson, GC., Samuelsson T. Gel-forming mucins
appeared early in metazoan evolution.
Proc Natl Acad Sci U S A. 2007 104, 16209-16214
P. and Samuelsson, T.
Evolution of the iron responsive elementi
2007 RNA 13(7):952-66.
J., Samuelsson, T., Strub, K.
Useful junk: Alu RNAs in the human
transcriptome. 2007 Cellular and Molecular Life Sciences
A, Berggren M, Ekeland-Sjoberg K, Samuelsson T, Ricksten A.
specific internal translation efficiency of Epstein-Barr virus present
in solid organ transplant patients.
J Med Virol. 2007 Mar 26;79(5):573-581
L, Sun Y, Patrakka J, Mostad P, Norlin J, Xiao Z, Andrae J, Tryggvason
K, Samuelsson T, Betsholtz C, Takemoto M.
Glomerulus-specific mRNA transcripts and proteins identified
through kidney expressed sequence tag database analysis.
Kidney Int. 2007 Feb 28
López, MD., Piccinelli, P. and Samuelsson, T.
Inventory and analysis of the protein subunits of the ribonucleases P
and MRP provides further evidence
of homology between the yeast and human enzymes. Nucleic
Acids Res. 2006;34(18):5145-56.
T, Hansson GC, Samuelsson T.
An inventory of mucin genes in the
chicken genome shows that the mucin domain of Muc13 is encoded by
multiple exons and that ovomucin is part of a locus of related
BMC Genomics. 2006 Aug 3;7(1):197
- Takemoto M, He L, Norlin J, Patrakka J, Xiao Z, Petrova T, Bondjers C,
Asp J, Wallgard E, Sun Y, Samuelsson T, Mostad P, Lundin S, Miura N,
Sado Y, Alitalo K, Quaggin SE, Tryggvason K, Betsholtz C.
Large-scale identification of genes implicated in kidney
glomerulus development and function.
EMBO J. 2006 Mar 8;25(5):1160-74.
- Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK,
Wower J, Gorodkin J, Samuelsson T, Zwieb C.
The tmRDB and SRPDB
resources. Nucleic Acids Res. 2006 Jan 1;34(Database
T, Samuelsson T, Sauer-Eriksson AE.
Conformational variability of the GTPase domain of the
signal recognition particle receptor FtsY.
J Struct Biol. 2006 Jan;153(1):85-96.
Previous PhD students
Marcela Dávila López
Magnus Alm Rosenblad
Liqun He (co-supervisor)