mcbl 121 Lecture_13-14_molecular_regulation

Catabolic pathway activation condition

Substrate present AND preferred carbon source (e.g. glucose) absent

Catabolic pathway ON state

Genes/operon expressed and enzymes synthesized

Catabolic pathway OFF state

Substrate absent OR preferred carbon source present

Anabolic (biosynthetic) pathway activation condition

End product absent or at low concentration

Anabolic pathway ON state

Genes/operon expressed to synthesize enzymes

Anabolic pathway OFF state (repression)

End product present so transcription is turned off to conserve energy

Induction

Repressor binds DNA to keep gene off until an inducer binds repressor and releases it

Derepression

Repressor requires a corepressor to bind DNA and removal of corepressor allows gene expression

Activation

Activator must bind an induer to bind DNA and initiate transcription

Aporepressor

Inactive repressor protein produced by biosynthetic pathways

Corepressor

End product of a biosynthetic pathway that activates an aporepressor

Holorepressor

Active complex formed by aporepressor bound to its corepressor

trp operon function

Encodes enzymes required for tryptophan biosynthesis

trp operon repression trigger

High intracellular tryptophan levels

Tryptophan as a corepressor

Binds TrpR aporepressor to activate it

Holorepressor binding site

Operator sequence of the trp operon

Effect of holorepressor binding

Blocks RNA polymerase and lowers transcription

Transcriptional attenuation

Regulation that terminates transcription after initiation

trp leader sequence (trpL)

Region between operator and first structural gene containing attenuator

Attenuator RNA regions

Four RNA regions (1–4) that form alternative secondary structures

3:4 loop

Terminator structure that causes RNA polymerase to fall off

2:3 loop

Anti-attenuator structure that allows transcription to continue

Low tryptophan ribosome behavior

Ribosome stalls at adjacent trp codons in region 1

Low tryptophan RNA structure

Region 2 pairs with region 3 forming anti-attenuator

Low tryptophan transcription outcome

Structural genes trpE-A are transcribed

High tryptophan ribosome behavior

Ribosome moves quickly and stops covering regions 1 and 2

High tryptophan RNA structure

Region 3 pairs with region 4 forming terminator

High tryptophan transcription outcome

RNA polymerase dissociates before structural genes

Arabinose operon function

Converts arabinose into xylulose-P for biosynthesis

AraC protein

Dimeric regulator that acts as repressor or activator

AraC without arabinose

Elongated conformation that forms DNA loop

AraC repression mechanism

Binds araO2 and araI1 preventing RNA polymerase access

AraC with arabinose

Compact conformation that activates transcription

AraC activation mechanism

Binds araI1 and araI2 to recruit RNA polymerase

Regulon

Group of genes across chromosome controlled by one regulator

Alternative sigma factors

Specialized sigma proteins used under stress conditions

Housekeeping sigma factor

σ70

rpoH gene

Encodes heat-shock sigma factor σH

Normal temperature regulation of σH

rpoH mRNA hides RBS and σH is degraded

Anti-sigma chaperones

DnaJ DnaK and GrpE

Heat shock effect on rpoH mRNA

Secondary structure melts exposing RBS

Heat shock effect on chaperones

Chaperones bind misfolded proteins instead of σH

Heat shock transcription outcome

Free σH directs RNA polymerase to heat-shock genes

sRNA definition

Small regulatory RNAs that bind mRNAs via antisense pairing

sRNA translation inhibition

Blocks ribosome binding site

sRNA translation activation

Unfolds mRNA to expose ribosome binding site

sRNA-mediated degradation

Forms dsRNA recognized by RNase III

Quorum sensing

Cell-density dependent regulation of gene expression

Autoinducer

Small secreted molecule whose concentration reflects population size

LuxI function

Synthesizes autoinducer

LuxR function

Binds autoinducer to activate transcription

Vibrio fischeri outcome

Bioluminescence

Pseudomonas quorum sensing role

Exoenzyme production

Staphylococcus quorum sensing role

Exotoxin production

Agrobacterium quorum sensing role

Regulation of conjugation