Regulatory RNA- Bacteria

Antisense RNAs

Another set of examples of regulatory RNAs in bacteria Encoded by the strand opposite the coding strand of a gene and act through homologous base pairing to inhibit expression of teh mRNA produced from that gene

Rho-dependent termination

Bacterial termination sequences have to main features: - An inverted repeat sequence that, when transcribed, forms a stem-loop in the RNA - A stretch of A residues; this pairs with the transcribed poly-U in the transcription bubble (a weak, unstable structure) The weak base pairing in the transcription bubble is thought to arrest transcription and the RNA hairpin is thought to interact with RNAP and help pull the RNA out of the active site

Riboswitches

Cis-acting Control expression of the genes within whose mRNAs they reside Found upstream of genes involved in teh synthesis of the metabolite ligand recognized by the riboswitch To components: aptamer and expression platform In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. Typically in the 5'UTR Most found in bacteria, some in plants/fungi

Toehold switch

De-novo-designed regulators of gene expression Detect Ebola viral RNA

SAM-sensing riboswitch

Example of transcription terminator riboswitch Genes involved in methionien metabolism use SAM-sensinging to regulate transcription

sRNAs

One class of bacterial regulatory RNAs Act in trans to control translation of target genes; larger than euk regulatory RNAs (90NT vs. 25NT) and are not generally formed by processing of larger dsRNA precursors (like euk regulatros are) Encoded in thier final form by small genes Binding of an sRNA to target mRNA is usually aided by bacterial protein Hfq (chaperone); aids stability of regulators and stronger interaction between sRNA and target mRNA

Expression platform

Part of riboswitch Activity altered by aptamer Can be regulated at the level of either translation or transcription

Aptamer

Part of riboswitch Binds to the small-molecule ligand and, in response, undergoes a conformation change of the secondary structure, altering the activity of the epxression platform

Degradation of RNA

RNAi

Riboswitches: two states

State 1: For an "OFF" switch, ligand binding stabilizes aptamer structure, permitting terminator to form and transcription to cease State 2: Absence of ligand permits an antiterminator to form and transcription to proceed

Riboswitches w/ translation

The SD-interaction positions the initiating 5'AUG of the mRNA in the P site of the 30S subunit Activation & repression of translation by sRNAs in bacteria regulate the accessibility of the RBS