L15: Regulatory RNAs (Prokaryotes) Flashcards
(20 cards)
what are sRNAs
- a class of bacterial regulatory RNAs 80-110 nucleotides in size
- bind to target RNA transcripts
sRNAs - what can they result in?
- Destruction
- Prevention of Translation
- Stimulation of Translation
sRNAs - destruction
- sRNAs recognizes and binds to target mRNA due to complementarity base pairing
- it then creates a double-stranded region that is recognized by RNaseE
- the target mRNA is then degraded
sRNAs - prevention of translation
binds and occludes (obstructs) ribosome binding site (RBS)
sRNAs - stimulation of translation
sRNA binding unmasks a hidden RBS
what are riboswitches?
- they are found in the 5’ untranslated region (5’ UTR) of the gene they regulate
- they can regulate gene expression at the level of translation or transcription
- made of two components: (1) expression platform and (2) aptamer
riboswitches - expression platform
regulates gene expression
riboswitches - aptamer
it binds a small ligand and it undergoes a conformational change that influences activity of expression pattern
riboswitches - transcription termination
- it terminates transcription before the ORF
- mechanism of termination is called attenuation
riboswitches: transcription termination - attenuation
- absence of ligand: aptamer confirmation allows transcription of a complete mRNA
- presence of ligand: confirmation promotes the formation of a terminator loop in the expression platform (followed by a stretch of U’s)
rho-independent transcriptional termination vs riboswitches
- rho-independent: hair-pin and poly-U tail at 3’ and does not require a protein or a ligand
- riboswitches: involves a ligand-induced structural change and does not require a protein
riboswitches - inhibition of translation initiation
- absence of ligand: aptamer confirmation does not effect RBS accessibility in expression platform
- presence of ligand: aptamer structure promotes the formation of a hairloop that sequesters (hides) the RBS from ribosome
riboswitches - explain the function/structure of the expression platform
- it changes in repsonse to alternative intramolecular base-pairing
- ribosome can bind when the hair-pin is faced down but when its up, the ribosome cannot bind
riboswitches - where is it found
often on genes that are involved in the synthesis of the ligand that binds to the aptamer (negative feedback)
riboswitches - how does S-adenosylmethionine (SAM) impact riboswitches
riboswitches that bind SAM regulate genes involved in SAM and methionine synthesis
example of Attenuation: typtophan (Trp) operon regulation - Trp is high
- when Trp levels are high, aminoacyl tRNAs are charged with Trp are also high
- efficient progression of the ribosome on a short leader peptide (upstream open reading frame or uORF) creates an attenuation loop
- this causes transcription to be terminated prematurely
example of Attenuation: typtophan (Trp) operon regulation - why is it that when Trp is high, aminoacyl tRNAs with Trp are also high?
- bc transcription is coupled with translation in prokaryotes
- ribosomes bind to trp operon transcripts as they are released from RNA Pol
typtophan (Trp) operon regulation: Trp is high - explain the regions
- ribosome translates past region 2
- region 3 pairs with 4 to create the attenuation loop
example of Attenuation: typtophan (Trp) operon regulation - Trp is low
- aminoacyl tRNAs charged with Trp are scarce
- this causes the ribosome to stall at the “back-to-back” Trp codons in the leader sequence (region 1)
- trp operon is transcribed to support Trp biosynthesis
typtophan (Trp) operon regulation: low Trp levels - why is the trp operon transcribed?
- bc the ribosome is stalled, region 2 is free to form a hair-pin with region 3
- this causes the attenuating loop between regions 3 and 4 to not form
