Influence on bacterial translation

Factors and feedback-loops that influence the translation in E. coli

What is encrypted under HFQ?

Host Factor for Phage Q-beta

What is the function HFQ?

It serves as RNA chaperone, facilitating interactions between sRNA and mRNA

What is HFQ’s form?

It’s a homo-hexamer, consisting of 6 monomers with binding pockets in between them, foring a donut-like shape

Where does mRNA interact with HFQ?

In the binding pockets on the distal side with A-R-N motifs

Where does sRNA interact with HFQ?

In the binding pockets on the proximal side, via the poly-U stretches

What is encrypted under sRNA?

Small RNA

What is encrypted under srRNA?

Small regulatory RNA

What is encrypted under Fur?

Ferric Uptake Regulator

In which metabolic pathway does Fur take part?

Iron uptake pathway

Fur acts as a ________ for the iron uptake pathway.

repressor

Where does Fur bind?

To the Fur-boxes in the promotor region

What is RyhB?

Small trans-acting regulatory RNA that is controlled (repressed) by Fur

1 represses 2, which recruits 3. 2 and 3 together mark the mRNA of non-essential iron-using complexes for degradation

1 - Fur, 2 - RyhB, 3 - HFQ

What is RNAse E?

An endoribonuclease that plays a crucial role in mRNA degradation and processing in bacteria, specifically targeting RNA for cleavage

What does RNAse E recognize in mRNA?

The 5’ monophosphate (5'-P)

Where in the degradosome is RNAse E located?

At the N-terminus

What is an amphiphatic helix?

A part of the degradosome, used to attach it to the cell membrane

What are RBD and AR2?

Domains of the degradosome that capture RNA for cleavage

What is RhIB binding site?

A binding site on the degradosome for an ATP-dependant helicase that unwinds secondary mRNA structures

What role does enolase play in the degradosome?

It’s an enzyme that links degradation process with cellular metabolism

What is a PNPase-binding site?

A binding site on the degradosome that recruits additional protein, needed for RNA cleavage

What is encrypted under GSR sigma-RpoS?

General stress response sigma-factor RpoS

rpoS-mRNA is always ________ but not normally ________ due it’s ________

transcribed; translated; stem-structure

Which sRNA binds to the rpoS mRNA under stress conditions?

DsrA sRNA

What does RpoS factor influence?

RNA-Polymerase

What is RssB?

Adaptor molecule in RpoS gedragation under non-stress conditions

What is CIpXP?

A proteolytic complex that degrades RpoS under non-stress conditions

Which modification needs to happen to RssB for it to interact with RpoS?

Phosphorylation

RssB ________ CIpXP to RpoS

recruits

What is a 6S RNA?

A regulator of bacterial transcription that inhibits RNA polymerase, thereby modulating gene expression during stress conditions

What is encrypted under CB of 6S RNA?

Central Bulge

What is so special about CB of 6S RNA?

It mimics the open promoter complex, which binds to the RNA-P holoenzyme

Which factors does 6S RNA/RNA-P complex regulate?

It downregulates sigma-70-factors, inducing the stress response

What is pRNA?

Product of transcription of 6S RNA

What is transitional coupling?

Translational coupling is a mechanism where the translation of a downstream gene affects the translation of an upstream gene

What is non-overlapping translational coupling?

The Stop-codon of one gene and the Start-codon of the next gene have a spacer between them

What is overlapping translational coupling?

The Stop-codon of one gene overlaps with the Start-codon of the next gene

What is MS2?

MS2 is a bacteriophage that infects Escherichia coli and is used as an example for non-overlapping translational coupling

What is iraD?

Anti-adapter that binds to the RssB and blocks the degradation of RpoS, used as an example for overlapping translational coupling

What is translational attenuation?

Gene regulation mechanism, where a cell controls the production of a protein by altering how mRNA molecule folds during translation

What is SecA?

ATPase that helps to drive the movement of secretory proteins through the inner membrane

What is SecM?

Secretion monitoring protein that uses it’s own translational stalling as a regulatory mechanism

What are bL31A and bL31B?

Variant ribosomal proteins, which interchange during the growth phase

What does bL31A structurally posess?

Zn-binding domain

What does bL31B posess?

An additional loop