Abstract

In the past year, we have made progress in the subject of RNA-cation interactions and how RNA can employ cation selectivity. Our previous in vitro selection, biochemical and structural studies of the bacterial glmS ribozyme-riboswitch had demonstrated that a point mutation can convert the coenzyme-dependent wild-type RNA into a metalloenzyme. In new work, we have subjected the metalloenzyme variant to further in vitro evolution, obtaining a ribozyme with exquisite selectivity for calcium ion over magnesium ion. This RNA is over 10,000 times more active in the former than the latter. Biochemical probing suggests that calcium selectivity was acquired by a pre-existing, formerly non-specific cation binding site which functions primarily in structural stabilization in the wild-typre ribozyme. In the mutant, this site has been co-opted to participate in the transition state when bound to calcium. This is thus a clear case of molecular exaptation.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Heart, Lung, and Blood Institute (NHLBI)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIAHL006102-07
Application #
9572298
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
7
Fiscal Year
2017
Total Cost
Indirect Cost

  Institution

Name
U.S. National Heart Lung and Blood Inst
Department
Type
DUNS #
City
State
Country
Zip Code

  Publications

Chen, Michael C; Tippana, Ramreddy; Demeshkina, Natalia A et al. (2018) Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36. Nature 558:465-469
Lau, Matthew W L; Trachman 3rd, Robert J; Ferré-D'Amaré, Adrian R (2017) A divalent cation-dependent variant of the glmS ribozyme with stringent Ca(2+) selectivity co-opts a preexisting nonspecific metal ion-binding site. RNA 23:355-364
Miao, Zhichao; Adamiak, Ryszard W; Antczak, Maciej et al. (2017) RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA 23:655-672
Zhang, Jinwei; Ferré-DAmaré, Adrian R (2016) Trying on tRNA for Size: RNase P and the T-box Riboswitch as Molecular Rulers. Biomolecules 6:
Zhang, Jinwei; Ferré-D'Amaré, Adrian R (2016) The tRNA Elbow in Structure, Recognition and Evolution. Life (Basel) 6:
Lau, Matthew W L; Ferré-D'Amaré, Adrian R (2016) In vitro evolution of coenzyme-independent variants from the glmS ribozyme structural scaffold. Methods 106:76-81
Meyer, Peter A; Socias, Stephanie; Key, Jason et al. (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun 7:10882
Miao, Zhichao; Adamiak, Ryszard W; Blanchet, Marc-Frédérick et al. (2015) RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. RNA 21:1066-84
Zhang, Jinwei; Ferré-D'Amaré, Adrian R (2015) Structure and mechanism of the T-box riboswitches. Wiley Interdiscip Rev RNA 6:419-33
Ferré-D'Amaré, Adrian R (2015) On the shoulders of giants. RNA 21:504-5

Showing the most recent 10 out of 29 publications