Chapter 16: Gene Regulation in Bacteria

What is constitutive gene expression?

Gene expression that has essentially constant levels.

Why is constitutive gene expression important?

It is frequently for proteins that are continuously necessary for the survival of the organism.

Regulated gene expression

Expression may be increased or decreased according to the demand for the gene product.

Activator

Proteins that increase transcription.

Repressor

Proteins that inhibit transcription.

What is an inducer in the context of gene transcription?

A molecule that increases transcription.

How does an inducer increase transcription by binding to activators?

It causes activators to bind to DNA.

How does an inducer increase transcription by binding to repressors?

It prevents repressors from binding to DNA.

Co-repressor

Bind to repressors and cause them to bind to DNA, decreasing transcription.

Inhibitor

Bind to activators and prevent them from binding to DNA, decreasing transcription.

Promoter (lac operon)

Signals beginning of transcription.

CAP site

A DNA sequence recognized by an activator protein called catabolite activator protein (CAP).

Operator (lac operon)

A sequence of bases that provides a binding site for a repressor protein.

lacZ

Encodes beta-galactosidase, cleaves lactose and lactose analogues, also converts lactose into allolactose.

lacY

Encodes lactose permease.

What is lacA?

A gene that encodes a protein involved in the lac operon.

What is the function of the lac repressor protein?

It binds to the operator site and interferes with RNA polymerase binding to the promoter.

What role does allolactose play in the lac operon?

It inactivates lacI so that it cannot bind to the operator.

Terminator (lac operon)

Signals end of transcription.

Negative regulation of the lac operon by LacI

When no lactose is present, LacI forms a homotetramer, binds to operator, and blocks RNA polymerase from transcribing the lac operon.

Positive regulation of the lac operon by cAMP-CAP

When glucose runs out and lactose is present, the cAMP-CAP complex binds to the CAP site near the lac promoter and increases transcription rate.

Status of LacI and CAP with no lactose or glucose

LacI binds to operator, cAMP binds to CAP, binds to CAP site; transcription is very low.

Status of LacI and CAP with lactose only present

cAMP-CAP complex binds to CAP site, resulting in a high rate of transcription.

Status of LacI and CAP with glucose only present

LacI binds to operator, resulting in very low transcription.

Status of LacI and CAP with lactose and glucose present

No CAP site binding; low transcription rate.

How many operator sites are involved in lac operon regulation?

Three (O1, O2, O3)

What must the lac repressor do to cause repression in the lac operon?

Bind to two of the three operators

What happens if either O2 or O3 is missing in the lac operon?

The lac operon is not fully repressed

Promoter (trp operon)

DNA sequence where RNA polymerase binds to begin transcription.

What is the function of the operator in gene regulation?

It serves as a binding site for the trp repressor.

What happens when tryptophan levels are high?

The trp repressor binds to the operator and blocks RNA polymerase.

What is the result of the trp repressor binding to the operator?

Transcription is turned off.

What does trpL code for?

A 14-amino acid leader peptide.

What role does the leader peptide play?

It plays a key role in attenuation.

How many trp codons are in the leader peptide transcript?

Two trp codons.

What factor influences the translation speed of the leader peptide?

The amount of tryptophan (trp) in the cell.

What is attenuation in bacteria?

Attenuation occurs in bacteria because of the coupling of transcription and translation.

When does transcription terminate during attenuation?

Transcription is terminated before the entire mRNA is made.

What is the role of the attenuator sequence?

The attenuator sequence is important in facilitating the termination of transcription.

Where is the attenuator sequence located in the trp operon?

Right after trpL in the trp operon.

What does attenuation inhibit in bacteria?

further production of tryptophan.

trpE, trpD, trpC, trpB, and trpA

These genes encode enzymes involved in tryptophan biosynthesis.

Negative regulation of the trp operon

The trp operon is a repressible gene under negative control of the trp repressor. Repression is achieved when the amino acid tryptophan binds to the repressor protein. Complex then binds to operator region to block transcription.

What is attenuation in the context of transcription?

the process where transcription is terminated before the entire mRNA is made.

What regulates attenuation in the trp operon?

leader peptide (trpL) in the trp operon.

Leader peptide regulation - No translation

Translation is not coupled with transcription. 1 binds to 2, 3 binds to 4, and transcription is terminated just past the trpL gene.

Leader peptide regulation - Low tryptophan levels

Cell cannot make sufficient charged tRNATrp. Ribosome pauses at Trp codons in trpL mRNA. Stem-loop 2-3 forms, attenuation does not occur and RNA polymerase transcribes the rest of the operon.

Leader peptide regulation - High tryptophan levels

Translation of trpL mRNA progresses to stop codon. Stem-loop 3-4 forms; transcription of operon is terminated.

What type of operons are involved in catabolism?

Inducible operons

What acts as the inducer in an inducible operon?

The substance to be broken down or a related compound

What is an example of an inducible operon?

The lac operon

What type of operons are typically repressible?

Operons involved in anabolism (biosynthesis of a substance)

What is the role of the inhibitor or corepressor in a repressible gene?

The inhibitor or corepressor is the small molecule that is the product of the operon.

What is an example of a repressible operon?

The trp operon.

What is translational repression?

A process where a translational regulatory protein inhibits translation of mRNA.

How does a translational regulatory protein inhibit translation?

By recognizing sequences within the mRNA and blocking the ribosome.

What is one way translational repression can occur?

By binding next to the Shine-Dalgarno sequence and/or the start codon.

What is another way translational repression can occur?

By binding outside the Shine-Dalgarno/start codon region to stabilize mRNA secondary structure.

What are riboswitches?

RNA elements that can exist in two different conformations: active or inactive.

What is required for a riboswitch to switch from one conformation to another?

The switch relies on a small molecule.

How do riboswitches regulate translation in E. coli?

They regulate translation by controlling Thiamin pyrophosphate (TPP) biosynthesis.

How do riboswitches regulate transcription in B. subtilis?

They regulate transcription by controlling Thiamin pyrophosphate (TPP) levels.

What is the function of an anti-terminator stem loop?

It prevents the formation of the terminator stem-loop.

What happens when the anti-terminator is active in the thi operon?

Transcription of the entire thi operon occurs.

Anti-sequester stem loops

When the Shine-Dalgarno anti-sequestor loop forms, the Shine-Dalgarno sequence is accessible, which allows the mRNA to bind to the ribosome.

Allosteric enzyme

contains two binding sites: a catalytic site and a regulatory site.

What is feedback inhibition?

Feedback inhibition is a regulatory mechanism where the final product of a metabolic pathway inhibits an earlier enzyme in the pathway.

What type of enzyme is involved in feedback inhibition?

An allosteric enzyme.

What happens when the substrate binds to enzyme 1?

It creates an intermediate product that goes to enzyme 2.

What does enzyme 2 produce in the feedback inhibition process?

A second intermediate.

What does enzyme 3 produce in the feedback inhibition process?

The final product.

What occurs when the concentration of the final product is high in feedback inhibition?

The final product binds to the allosteric site of enzyme 1, inhibiting it.