Chapter 16: Gene Regulation in Bacteria

unregulated/constitutive gene expression

constant levels of expression

• 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

  • Encoded proteins will be produced only when required 

repressors

• proteins that inhibit transcription

activators

• proteins that increase transcription 

inducers

increase transcription

• Bind activators and cause them to bind to DNA

• Bind repressors and prevent them from binding DNA

inhibitors/corepressors

decrease transcription

corepressor

• bind to repressors and cause them to bind to DNA

inhibitors

• bind to activators and prevent them from binding to DNA 

lac operon structure

• Promoter

• CAP site (catabolite activator protein)

• Operator: bound by lacI (repressor) 

• Protein-coding genes: lac Z, lac Y and lac A

• Terminator

lac z

• encodes beta-galactosidase 

  • Cleaves lactose and lactose analogous

  • Converts lactose into allolactose (isomer) 

lac Y

encodes lactose permease

lac A

encodes galactoside transacetylase

• Acetylation of nonmetabolizable lactose analogs prevents their toxic buildup so they can diffuse out of the cell 

lacl

lac repressor protein

• Binds to operator site and interferes with RNA polymerase binding to promoter 

• Allolactose inactivates lacl so that it can not bind to the operator 

negative control of lac operon

1. no lactose present

2. lactose is present, beta-galactosidase makes some allolactose

no lactose present

• Lacl forms a homotetramer

• Lacl binds to operator and blocks RNA polymerase from transcribing the lac operon 

• Lac operon transcription is very low

Lactose is present, beta-galactosidase makes some allolactose 

• Allolactose binds to lacl and prevents it from binding to operator

• RNA polymerase transcribes lac operon at high level

• Lac operon is inducible, allolactose is an inducer

Trans-effect or trans-acting factor

• genetic regulation that can occur even though DNA segments are not physically adjacent 

  • Mediated by genes that encode regulatory proteins 

  • Ex: lac repressor on lac operon 

Cis- effect or cis-acting element

• DNA sequence that must be adjacent to the genes it regulates

  • Mediated by sequences that are bound by regulatory proteins 

  • Ex: lac operator 

positive control of the operon

1. lactose and glucose are present

2. only lactose present

3. only glucose present

4. no glucose or lactose present

lactose and glucose are present

• E. coli uses glucose first and catabolite repression prevents the use of lactose 

• Cyclic AMP (cAMP) binds an activator protein CAP 

• Glucose → adenylyl cyclase → cAMP

only lactose present

cAMP-CAP complex binds to the CAP site near the lac promoter and transcription rate increases

only glucose present

No lactose available to form allolactose, Lacl binds to operator

no glucose or lactose present

• No lactose available to form allolactose, Lacl binds to operator 

• cAMP binds to CAP which binds to CAP site

operator sites for lac repressor

• O1 - slightly downstream from the promoter

• O2 - downstream in the lacZ coding region

• O3 - slightly upstream from the promoter 

lac operon repression

• Lac repressor must bind to 2 of the 3 operators to cause repression 

• Possible combinations 

  • O1 and O2

  • O1 and O3

  • NOT O2 and O3 

• If either O2 or O3 is missing, the lac operon is not fully repressed

trp operon

• encodes genes involved in the biosynthesis of the amino acid tryptophan

trp structure

• Regulatory region 

  • Operator

  • Promotor

•  Structural genes → genes trpE, trpD, trpC, trpB and trpA encode enzymes involved in tryptophan biosynthesis 

• trpR is a gene that encodes the trp repressor protein 

inducible regulation

• Operons involved in catabolism (breakdown of a substance) are typically inducible 

  • Substance to be broken down (or a related compound) acts as the inducer 

  • Ex: the lac operon

repressible regulation

• Operons involved in anabolism (biosynthesis of a substance) are typically repressible

  • Inhibitor or corepressor is the small molecule that is the product of the operon 

  • Ex: trp operon 

Translational regulatory protein

• recognizes sequences within the mRNA and inhibit translation 

  • Bind next to the Schine-Dalgarno sequence and/or the start codon to block ribosome 

  • Bind outside the Schine-Dalgarno/start codon region to stabilize mRNA secondary structure 

antisense RNA

• RNA strand that is complementary to mRNA 

  • Ex: protein ompF in E. coli is important in osmoregulation 

    • At high osmolarity, micF is transcribed

riboswitches

• RNA can exist in 2 different confirmations (active or inactive)

  • Switch from one confirmation to the other relies on a small molecule