Difference between revisions of "Forster Lab"
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1MB433: Synthetic Biology (10 hp, weeks 7-12)<br>
1MB433: Synthetic Biology (10 hp, weeks 7-12)<br>
Revision as of 09:55, 26 March 2014
SynBio links above
Professor Anthony C. Forster, M.D., Ph.D.
University Chair in Chemical Biology
Program in Structural and Molecular Biology
Department of Cell and Molecular Biology
office and mailing address:
ICM Dept., Room D9:216b
Husargatan 3, Box 596
75124 Uppsala, Sweden
office and cell phone: +46-18-471 4618
lab web: http://openwetware.org/wiki/Forster_Lab
Department web: http://www.icm.uu.se/
Uppsala University web: http://www.uu.se/en/
Meet the rest of our lab group:
File:2013 06 09 Forster lab.tif
phones in lab:
+46-18-471 4387, 471 4651 and 471 4204
iGEM 2011 Uppsala University Team Members:
Congratulations on qualifying at the European competition in Amsterdam for the world championships at MIT!
iGEM 2012 Uppsala University Team Members:
Congratulations on the top score for a Scandinavian team!
iGEM 2013 Uppsala University Team Members:
Congratulations on qualifying at the European competition in Lyon for the world championships at MIT!
1MB381, 1MB382 and 1MB383: iGEM and Synthetic Biology (Öppen fördjupningskurs i molekylär bioteknik och bioinformatik
I, II and III, 10 hp, weeks 23-30)
1MB433: Synthetic Biology (10 hp, weeks 7-12)
Japanese Exploratory Research for Advance Technology (ERATO)
Science for Life Laboratory project grant, Uppsala
Swedish Research Council Linnaeus Uppsala RNA Research Centre
Swedish Research Council Natural and Engineering Sciences project grant
Uppsala University Rektorsmedel
Minimal qualifications include expertise in molecular biology and 2 first-authored research papers in international peer-reviewed journals. Experience with bacterial translation or RNA is a plus. Please mail a letter of interest, C.V. and names/e-mail addresses/phone #'s of 3 references.
Synthetic biology, protein synthesis, drug discovery, directed evolution, translation, unnatural amino acid, ribosome, RNA, mRNA, tRNA, codon bias, E. coli, bacteria, microbiology, biochemistry, modification enzyme, transcription termination, Tony Forster, Anthony Forster, A. C. Forster
Synthetic biology, protein synthesis and drug discovery:
Synthetic biology is a new field that may be defined as the complex engineering of replicating systems ( http://syntheticbiology.org/ ). Protein synthesis is central to this field and also to antibiotic development. Important questions remain unanswered. For example,
1. What are the mechanisms of substrate recognition and peptide bond formation?
2. Can cell-free protein production be improved to rival inherently less-flexible in vivo systems?
3. What genes are required to completely reconstitute translation (the "translatome")?
4. What are the functions of ribosomal RNA modifications?
5. Can new protein synthesis inhibitors be developed to combat rising bacterial resistance?
Ironically, in addition to being a target for antibiotic development, we envisioned that the translation apparatus could also be engineered to generate drug leads against translation or any other target molecules.
Where we are:
We've reconstituted a simplified, purified translation system that has enabled:
1. Modular alteration of aminoacyl-tRNA substrates using chemical synthesis to reveal key elements for substrate function in translation,
2. Overturning of dogma on the rate-limiting step in translation,
3. Explaining why the genetic code evolved to contain proline,
4. Creation of rudimentary genetic codes de novo, and
5. Genetic screening of a model library of polypeptides in a purified system, termed "pure translation display."
6. Proposed a list of genes essential for reconstitution of translation (a "minimal translatome") and have begun synthesizing and testing the genes using "BioBricks", revealing unexpected properties of transcription terminators.
Where we're going:
We aim to exploit our purified translation system to:
1. Determine the rules of substrate recognition by the translation apparatus,
2. Enable ligand discovery using pure translation display of peptides containing multiple, protease-resistant, unnatural amino acids,
3. Synthesize active 23 rRNA in vitro using rRNA modification enzymes associated with antibiotic resistance,
4. Optimize in vitro translation systems,
5. Determine the genes necessary for reconstitution of translation, and
6. Synthesize a life-like replicating system (a minimal cell project) dependent only on small molecules for food.
B.Sc.Hons., University of Adelaide, Australia
Ph.D., Biochemistry, University of Adelaide, Australia (discovered hammerhead ribozyme structure).
M.D., Harvard University.
Residency, Anatomical Pathology, Brigham and Women's Hospital, Boston.
Forster, A C, Blacklow, S C. Process and compositions for peptide, protein and peptidomimetic synthesis. US6977150
(founding I.P. for Ra Pharmaceuticals, Inc., Boston).
Altman, S, Forster, A C, Guerrier-Takada, C L. Cleavage of targeted RNA by RNAase P. US5168053
(founding I.P. for Innovir Laboratories, Inc., NY).
Almost all pubs indexed by and available from PubMed:
http://www.ncbi.nlm.nih.gov/pubmed/ (type "Forster AC")
Citations per paper are available from Google Scholar:
http://scholar.google.com/ (type "Forster AC")
Kwiatkowski, M, Wang, J, Forster, A C. Manuscript in preparation on improved synthesis of unnatural aminoacyl-tRNAs.
Edlund, A, Jamal, S, Elofsson, H, Yuen, P, Dyrhagen, K, Marklund, E, Liljeruhm, J, Nissbeck, M, Gynnå, A, Ahlström, C, Alexis, L, Anlind, N, Ascue Avalos, G A, Berglund, A, Bergman, M, Beyan, M, Blomkvist, V, Borg, M, Boström, F, Braesch-Andersen, K, Bransell, L, Brisvåg, J, Cederberg, P, Ciftci, S, Dalmo, T, Danielsson, P, Frisk, C, Gavali, H, Gunja, S, Gustafsson, A, Herman, S, Holdar, K, Hong, M, Karlsson, J, Lundmark, K, Löwe, T, Nordsjö, O, Nyberg, A, Pello-Esso, L, Pettersson, L, Saffari, A, Sandberg, N, Sidibeh, C, Sjöstedt, V, Spaak, J, Srivastava, A, Strandgren, M, Sun, L, Törnblom, V, Vu, E, Wirtanen, A, Wärn, C, Ås, J, Östlin, C, Virtanen, A, Forster, A C, Lundin, E, Gullberg, E. Optimizing chromoproteins and tyrosine ammonia-lyase for use in Escherichia coli. Under revision for ACS Synthetic Biology.
Liljeruhm, J, Gullberg, E, Forster A C. Synthetic biology: A lab manual. Forthcoming manual from World Scientific press, 2014.
Wang, J, Kwiatkowski, M, Pavlov, M Y, Ehrenberg, M, Forster, A C. Peptide formation by N-methyl amino acids in translation is hastened by higher pH and tRNAPro. ACS Chem. Biol., in press, 2014.
Ieong, K-W, Pavlov, M Y, Kwiatkowski, M, Ehrenberg, M., Forster, A C. A tRNA body with high affinity for EF-Tu hastens ribosomal incorporation of unnatural amino acids. RNA, in press, 2014.
Punekar, A, Liljeruhm, J, Shepherd, T R, Forster, A C, Selmer, M. Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ. Nucleic Acids Res 41, 9537-9548, 2013.
Quax, T E F, Wolf, Y I, Koehorst, J J, Wurtzel, O, van der Oost, R, Ran, W, Blombach, F, Makarova, K S, Brouns, S J J, Forster, A C, Wagner, E G H, Sorek, R, Koonin, E V, van der Oost, J. Differential translation tunes uneven production of operon-encoded proteins. Cell Reports 4, 938-944, 2013.
Ieong, K-W, Pavlov, M Y, Kwiatkowski, M, Forster, A C(corresponding author), Ehrenberg, M. Inefficient delivery but fast peptide bond formation of unnatural L-aminoacyl-tRNAs in translation, J Am Chem Soc 134, 17955-17962, 2012.
Punekar, A, Shepherd, T R, Liljeruhm, J, Forster, A C, Selmer, M. Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of E. coli 23S rRNA. Nucleic Acids Res, 40, 10507-10520, 2012.
Forster, A C. Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription. Biotech J, 7, 835-845, 2012.
Forster, A C, Lee, S Y. Editorial: NextGen SynBio has arrived... Biotech J, 7, 827, 2012.
Du, L, Villarreal, S, Forster, A C. Multigene expression in vivo: supremacy of large versus small terminators for T7 RNA polymerase. Biotechnol Bioeng, 109, 1043-1050, 2012.
Wang, H H, Huang P-Y, Xu G, Haas W, Marblestone A, Li J, Gygi S P, Forster A C, Jewett M C, Church G M. Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. ACS Synthetic Biology, 1, 43-52, 2012
Watts, R E, Forster A C. Update on pure translation display with unnatural amino acid incorporation. Methods in Molecular Biology, 805, 349-365, 2012
Gao, R, Forster, A C. Changeability of individual domains of an aminoacyl-tRNA in polymerization by the ribosome. FEBS Lett, 584(1), 99-105, 2010
Jewett, M C, Forster, A C. Update on designing and building minimal cells. Current Opinion in Biotechnology, 21, 697-703, 2010
Watts, R E, Forster, A C. Chemical models of peptide formation in translation. Biochemistry, 49, 2177-2185, 2010
Du, L, Gao, R, Forster, A C. Engineering multigene expression in vitro and in vivo with small terminators for T7 RNA polymerase. Biotechnol Bioeng, 104, 1189-1196, 2009
Forster, A C. Low modularity of aminoacyl-tRNA substrates in polymerization by the ribosome. Nucleic Acids Res, 37, 3747-3755, 2009 PMCID:2699524
Pavlov, M Y, Watts, R E, Tan, Z, Cornish, V W, Ehrenberg, M, Forster, A C. Slow peptide bond formation by proline and other N-alkylamino acids in translation. Proc Natl Acad Sci U S A, 106(1), 50-4, 2009 PMCID:2629218
Forster, A C, Church, G M. Synthetic biology projects in vitro. Genome Res, 17(1), 1-6, 2007
Zhang, B, Tan, Z, Gartenmann Dickson, L, Nalam, M N L, Cornish, V W, Forster, A C. Specificity of Translation for N-Alkyl Amino Acids. J Am Chem Soc, 129(37), 11316-11317, 2007 PMCID:2275119
Forster, A C, Church, G M. Towards synthesis of a minimal cell. Mol Syst Biol, 2(45), 1-10, 2006 PMCID:1681520
Forster, A C. Engineering translation: A nano-review. Methods, 36(3), 225-6, 2005
Tan, Z, Blacklow, S C, Cornish, V W, Forster, A C. De novo genetic codes and pure translation display. Methods, 36(3), 279-90, 2005
Forster, A C, Cornish, V W, Blacklow, S C. Pure translation display. Anal Biochem, 333(2), 358-64, 2004
Tan, Z, Forster, A C, Blacklow, S C, Cornish, V W. Amino acid backbone specificity of the Escherichia coli translation machinery. J Am Chem Soc, 126(40), 12752-3, 2004
Forster, A C, Tan, Z, Nalam, M N L, Lin, H, Qu, H, Cornish, V W, Blacklow, S C. Programming peptidomimetic syntheses by translating genetic codes designed de novo. Proc Natl Acad Sci U S A, 100(11), 6353-7, 2003 PMCID:164450
Forster, A C, Weissbach, H, Blacklow, S C. A simplified reconstitution of mRNA-directed peptide synthesis: activity of the epsilon enhancer and an unnatural amino acid. Anal Biochem, 297(1), 60-70, 2001
Li, E, Beard, C, Forster, A C, Bestor, T H, Jaenisch, R. DNA methylation, genomic imprinting, and mammalian development. Cold Spring Harb Symp Quant Biol, 58, 297-305, 1993
Forster, A C, Altman, S. External guide sequences for an RNA enzyme. Science, 249(4970), 783-6, 1990
Forster, A C, Altman, S. Similar cage-shaped structures for the RNA components of all ribonuclease P and ribonuclease MRP enzymes. Cell, 62(3), 407-9, 1990
Forster, A C, Davies, C, Hutchins, C J, Symons, R H. Characterization of self-cleavage of viroid and virusoid RNAs. Methods Enzymol, 181, 583-607, 1990
McInnes, J L, Forster, A C, Skingle, D C, Symons, R H. Preparation and uses of photobiotin. Methods Enzymol, 184, 588-600, 1990
Forster, A C, Davies, C, Sheldon, C C, Jeffries, A C, Symons, R H. Self-cleaving viroid and newt RNAs may only be active as dimers. Nature, 334(6179), 265-7, 1988
McInnes, J L, Forster, A C, Symons, R H. Photobiotin-labelled DNA and RNA hybridization probes. Methods in Molecular Biology, 4, 401-414, 1988
Forster, A C, Jeffries, A C, Sheldon, C C, Symons, R H. Structural and ionic requirements for self-cleavage of virusoid RNAs and trans self-cleavage of viroid RNA. Cold Spring Harb Symp Quant Biol, 52, 249-59, 1987
Forster, A C, Symons, R H. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell, 49(2), 211-20, 1987
Forster, A C, Symons, R H. Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site. Cell, 50(1), 9-16, 1987
Symons, R H, Hutchins, C J, Forster, A C, Rathjen, P D, Keese, P, Visvader, J E. Self-cleavage of RNA in the replication of viroids and virusoids. J Cell Sci Suppl, 7, 303-18, 1987
Hutchins, C J, Rathjen, P D, Forster, A C, Symons, R H. Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Nucleic Acids Res, 14(9), 3627-40, 1986 PMCID:339804
Forster, A C, McInnes, J L, Skingle, D C, Symons, R H. Non-radioactive hybridization probes prepared by the chemical labelling of DNA and RNA with a novel reagent, photobiotin. Nucleic Acids Res, 13(3), 745-61, 1985 PMCID:341032
Visvader, J E, Forster, A C, Symons, R H. Infectivity and in vitro mutagenesis of monomeric cDNA clones of citrus exocortis viroid indicates the site of processing of viroid precursors. Nucleic Acids Res, 13(16), 5843-56, 1985 PMCID:321916