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Interplay between the trigger loop and the F loop during RNA polymerase catalysis
Nataliya Miropolskaya1, Daria Esyunina, Saulius Klimasauskas
1Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia, Molecular Biology Department, Biological Faculty, Moscow State University, Moscow 119991 Russia, Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 02241, Lithuania and Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
Nucleic Acids Research
|October 4, 2013
Summary
The trigger loop (TL) is crucial for RNA polymerase (RNAP) temperature activation and nucleotide addition. The F loop (FL) modulates the TL, influencing catalysis and adaptation in thermophilic and mesophilic bacteria.
Area of Science:
- Molecular Biology
- Enzymology
- Biochemistry
Background:
- The RNA polymerase (RNAP) active center contains a trigger loop (TL) essential for nucleotide addition and RNA cleavage.
- The adjacent F loop (FL) is hypothesized to modulate TL structural changes, impacting RNAP catalysis.
Purpose of the Study:
- Investigate the functional interplay between the TL and FL during bacterial RNAP transcription.
- Determine the roles of TL and FL in temperature activation, nucleotide addition, and RNA cleavage.
Main Methods:
- Utilized thermodynamic analysis of RNAP variants with mutations in TL and FL.
- Compared catalytic parameters between thermophilic (Thermus aquaticus) and mesophilic (Deinococcus radiodurans) RNAPs.
Main Results:
- The TL is essential for temperature activation; the FL promotes TL transitions during nucleotide addition.
- Identified the FL as an adaptable element responsible for catalytic differences between thermophilic and mesophilic RNAPs.
- FL mutations impact intrinsic RNA cleavage rates in a TL-dependent manner, unlike GreA-assisted cleavage.
Conclusions:
- Functional interplay between FL and TL is vital for RNAP catalytic activities.
- The FL plays an adaptive role in the distinct catalytic strategies of thermophilic and mesophilic RNAPs.
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