folding of riboswitches during rna transcription
Post on 30-Jan-2016
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Folding of riboswitches during RNA transcription
•Background information
•What are riboswitches?
•Folding of riboswitch terminatorsEfficient folding of hairpins
Evolution of terminator sequences
withBen Sauerwine (Carnegie Mellon, Physics)
“Central Dogma” of Molecular Biology
DNA
RNA
5’ untranslated untranslated 3’Coding Region
Transcription
Translation
Transcriptionstart
Transcriptionstop
... ...
Protein
(RNA World hypothesis)
messenger RNA structure
Primary structure (sequence):UUACAAUAUAAUAGGAACACUCAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACUAUGGGUGAGCAAUGGAACCGCACGUGUACGGUUUUUUGUGAUAUCAGCAUUGCUUGCUCUUUAUUUGAGCGGGCAAUGCUUUUUUUAUUCUCAUAACGGAGGUAGACAGGAUGGAAGCACUGAAACGGAAAAUAGAGGAAGAAGGCGUCGUAUUAUCUGAUCAGGUAUUGAAAGUGGAUUCUUUUUUGAAUCACCAAAUUGAUCCGCUGCUUAUGCAGAGAAUUGGUGAUGAAUUUGCGUCUAGGUUUGCAAAAGACGGUAUUACCAAAAUUGUGACAAUCGAAUCAUCAGGUAUCGCUCCCGCUGUAAUGACGGGCUUGAAGCUGGGUGUGCCAGUUGUCUUCGCGAGAAAGCAUAAAUCGUUAACACUCACCGACAACUUGCUGACAGCGUCUGUUUAUUCCUUUACGAAGCAAACAGAAAGCCAAAUCGCAGUGUCUGGGACCCACCUGUCGGAUCAGGAUCAUGUGCUGAUUAUCGAUGAUUUUUUGGCAAAUGGACAGGCAGCGCACGGGCUUGUGUCGAUUGUGAAGCAAGCGGGAGCUUCUAUUGCGGGAAUCGGCAUUGUUAUUGAAAAGUCAUUUCAGCCGGGAAGAGAUGAACUUGUAAAACUGGGCUACCGAGUGGAAUCUUUGGCAAGAAUUCAGUCUUUAGAAGAAGGAAAAGUGUCCUUCGUACAGGAGGUUCAUUCAUGA
(Bacillus Subtilis XPT gene)
•Folded secondary structure•Complementary base pairing•Can this really matter ?!?
Representations of Secondary Structure
....((((((((.....(((((.......)))))..........((((((.......))))))..))))))))....
TertiaryStructure
AU CG(GU)
Riboswitch folding during transcription
Terminatorstem
Aptamerstem
Guanine in solution, stabilizes aptamerTerminator forms, stalling polymeraseTranscription halts, Guanine not synthesized“XPT switched off”
G Guanine absentAntiterminator formsTranscription proceeds, Gaunine synthesized“XPT switched on”
GG
Anti-terminator
“Gene Regulation by Riboswitches”Mandal & Breaker Nature Reviews (2004)
Work in progress
1. Antiterminator lifetimeFirst passage time for escape from
metastable state(Ben Sauerwine, short talk)
2. Natural selection of terminator sequencesEvidence that terminators are selected for reliable folding(This talk)
Sequence length 43 ntTranscription rate 50 nt/second
RealSequence
Typical ShuffledSequence
Atypical ShuffledSequence
MetastableG=-7.9 kCal/mol
StableG=-25.0 kCal/mol
MetastableG=-3.4 kCal/mol
Atypical shuffled sequenceAlternate folds
Conclusions
RNA secondary structure does matter (sometimes)
Operation of riboswitch successfully modeled with Kinfold
Evidence for natural selection of efficiently folding sequences
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