Evolution of catalytic RNAs, and the Origin of Life
University of Technology Darmstadt, Germany
LMU Munich, Germany
UC San Diego
UC San Diego
Whitehead Institute, Cambridge, MA
Awards and Academic Honors
NASA research award
NASA research award
NSF research award
NRSA fellowship from the NIH
Postdoctoral award from the German Research Council (DFG)
The Muller lab is interested in catalytic RNA molecules (ribozymes). We address two very different questions: (1) How did the RNA world, an early stage of life, function? To do this we develop catalytic RNAs by in vitro selection from random RNA sequences. Our long-term aim is to generate an RNA world organism and thereby recapitulate an early stage of life in the lab. (2) How can experimental evolution improve trans-splicing ribozymes? This question is important because such experimental evolution could recapitulate biochemical steps in the evolution of the spliceosome, and because evolved trans-splicing ribozymes may be useful for therapeutic applications.
Ribozymes and the origin of life
The earliest evolutionary stages of life most likely included a stage called the RNA world. In this scenario, RNA served both as genome and as the only genome-encoded catalyst; these functions were later mostly overtaken by DNA and by proteins. We are trying to generate a self-replicating system of catalytic RNAs, mimicking an RNA world. If we were able to generate such a system, it could show us how an RNA world could function, and how an RNA world was able to evolve into today's DNA/RNA/protein life forms. The focus of our work is on ribozymes that generate chemically activated nucleotides, and polymerize chemically activated nucleotides. Both activities are essential for the self-replication of an RNA world organism. Using in vitro selection from more than 10^14 sequences, we identified ribozymes that are able to catalyze the triphosphorylation of RNA 5'-hydroxyl groups using trimetaphosphate. Because trimetaphosphate likely existed on early Earth, our findings show that trimetaphosphate could have been used as energy source for RNA world organisms. Current research in our lab aims to generate variants of these ribozymes that could fuel a primitive energy metabolism, and ultimately integrate them into a larger system of self-replicating ribozymes, an RNA world organism.
Evolution of trans-splicing ribozymes in cells
Group I intron ribozymes are among the most well-studied and versatile ribozymes. In contrast to the natural, cis-splicing versions of group I intron ribozymes we are using engineered, trans-splicing group I introns. These ribozymes can specifically recognize target sites on mRNAs by base pairing and remove or replace sequences in the target mRNA. We engineered ribozyme variants that splice efficiently on two splice sites, and termed them 'spliceozymes'. Analogous to the spliceosome, these spliceozymes remove an internal sequence from a target RNA and join the flanking sequences, resulting in a translatable mRNA. Because self-splicing group II introns share a common ribozyme ancestor with the spliceosome we are now using the 'group I intron spliceozymes' as model system for biochemical steps in the evolution of the spliceosome. To do that we developed an evolution scheme that repeatedly generates about 1 million ribozyme variants and selects them for efficient splicing in cells. After about a dozen cycles, this evolution system generated spliceozyme variants that used several mechanisms to increase product formation and decrease side product formation. Future evolution and optimization may show how specific biochemical steps could have been taken in the evolution of the spliceosome, and may make these ribozymes useful as tools in therapy.
Primary Research Area
Advisory Service - Active participant in developing the GE curriculum at Thurgood Marshall College in 2009. Thurgood Marshall College places an especially high importance on promoting diversity, for example in its specifically designed program Dimensions of Culture (DOC).
Recruitment Efforts - Assist in the recruitment efforts of the Thurgood-Marshall College, in two recruitment seasons.
Mentoring Efforts - Involvement in the Thurgood-Marshall mentorship program for transfer students, specifically aimed at helping disadvantaged transfer students.
My lab is dedicated to supporting an equal opportunity environment. This is reflected in the numbers of students in my lab: Three of the seven PhD students from my lab who have so far defended their thesis are female. Five of twelve undergraduate researchers who worked in my lab were female, and five of them were from an ethnic background (Asian/Hawaiian/African American).
- Akoopie, A., Müller, U.F. "Lower temperature optimum of a smaller, fragmented triphosphorylation ribozyme", Physical Chemistry Chemical Physics, 2016, Vol. 18, 20118-20125
- Amini, Z.N., Müller, U.F. "Increased efficiency of evolved group I intron spliceozymes by decreased side product formation", RNA, 2015, Vol. 21, Issue 8, 1480-1489
- Dolan, G.F., Akoopie, A., Müller, U.F. "A faster triphosphorylation ribozyme", PLoS ONE, 2015, Vol. 10, Issue 11, e0142559
- Martin, L.L., Unrau, P.J., Müller, U.F. "RNA synthesis by in vitro selected ribozymes for recreating an RNA world", Life (Basel), 2015, Vol. 5, Issue 1, 247-268
- Amini ZN, Olson KE, Müller UF, "Spliceozymes: Ribozymes that Remove Introns from Pre-mRNAs in Trans.", PLoS One, 2014, Vol. 9, Issue 7, e101932
- Dolan G.F., Müller U.F. "Trans-splicing with the group I intron ribozyme from Azoarcus", RNA, 2014, Vol. 20, Issue 2, 202-213
- Moretti J.E., Müller U.F., "A ribozyme that triphosphorylates RNA 5'-hydroxyl groups.", Nucleic Acids Res., 2014, Vol. 42, Issue 7, 4767-4778
- Müller UF, Tor Y, "Citric acid and the RNA world.", Angew Chem Int Ed Engl, 2014, Vol. 53, Issue 21, 5245-7
- Olson KE, Dolan GF, Müller UF, "In vivo evolution of a catalytic RNA couples trans-splicing to translation.", PLoS One, 2014, Vol. 9, Issue 1, e86473
- Amini ZN, Müller UF, "Low selection pressure aids the evolution of cooperative ribozyme mutations in cells.", J Biol Chem, 2013, Vol. 288, Issue 46, 33096-106
- Meluzzi D, Olson KE, Dolan GF, Arya G, Müller UF, "Computational prediction of efficient splice sites for trans-splicing ribozymes.", RNA, 2012, Vol. 18, Issue 3, 590-602
- Olson KE, Müller UF, "An in vivo selection method to optimize trans-splicing ribozymes.", RNA, 2012, Vol. 18, Issue 3, 581-9
- Yao C, Moretti JE, Struss PE, Spall JA, Müller UF, "Arginine cofactors on the polymerase ribozyme.", PLoS One, 2011, Vol. 6, Issue 9, e25030
- Yao C, Müller UF, "Polymerase ribozyme efficiency increased by G/T-rich DNA oligonucleotides.", RNA, 2011, Vol. 17, Issue 7, 1274-81
- Müller UF, "Evolution of ribozymes in an RNA world.", Chem Biol, 2009, Vol. 16, Issue 8, 797-8
- Müller UF, Bartel DP, "Improved polymerase ribozyme efficiency on hydrophobic assemblies.", RNA, 2008, Vol. 14, Issue 3, 552-62
- Müller UF, "Re-creating an RNA world.", Cell Mol Life Sci, 2006, Vol. 63, Issue 11, 1278-93
- Müller UF, Bartel DP, "Substrate 2'-hydroxyl groups required for ribozyme-catalyzed polymerization.", Chem Biol, 2003, Vol. 10, Issue 9, 799-806
- Müller UF, Göringer HU, "Mechanism of the gBP21-mediated RNA/RNA annealing reaction: matchmaking and charge reduction.", Nucleic Acids Res, 2002, Vol. 30, Issue 2, 447-55
- Müller UF, Lambert L, Göringer HU, "Annealing of RNA editing substrates facilitated by guide RNA-binding protein gBP21.", EMBO J, 2001, Vol. 20, Issue 6, 1394-404