BIO 265 Bacteria and Eukaryotic Gene Regulation

Gene regulation

Control of gene expression from DNA (genotype) to functional product (phenotype)

Why regulate genes?

To conserve energy and respond to environmental changes

Most energy-efficient regulation level

Transcription (prevents unnecessary RNA/protein production)

Levels of gene regulation

Chromatin structure, transcription, mRNA processing, mRNA stability, translation, posttranslational modification

Chromatin structure regulation

Controls accessibility of DNA to transcription machinery (mainly eukaryotes)

Transcription regulation

Determines whether RNA polymerase transcribes a gene

mRNA processing

Modifications to pre-mRNA (splicing, 5' cap, poly-A tail)

mRNA stability

Determines how long mRNA is available for translation

Translation regulation

Controls protein synthesis from mRNA

Posttranslational modification

Chemical changes to proteins after synthesis (affects activity/function)

Structural genes

Encode proteins with metabolic, structural, or defensive roles

Regulatory genes

Encode proteins or RNAs that control expression of other genes

Constitutive genes

Genes that are continuously expressed regardless of conditions

Regulatory elements

DNA sequences that control gene expression but are not transcribed

Operon

Cluster of genes under one promoter, transcribed as a single mRNA (common in bacteria)

Purpose of operons

Coordinate expression of genes in the same pathway

Promoter

DNA sequence where RNA polymerase binds to begin transcription

Operator

DNA sequence where repressor binds to block transcription

Regulator gene

Encodes regulatory protein (often located outside operon)

Negative control

Repressor protein blocks transcription when active

Positive control

Activator protein enhances transcription when active

Inducible operon

Normally OFF, turned ON by inducer molecule

Repressible operon

Normally ON, turned OFF by repressor/corepressor

Negative inducible operon

Repressor active by default, inducer inactivates it → transcription ON

Negative repressible operon

Repressor inactive by default, corepressor activates it → transcription OFF

Positive inducible operon

Activator inactive by default, inducer activates it → transcription ON

Positive repressible operon

Activator active by default, inhibitor inactivates it → transcription OFF

Lac operon type

Negative inducible operon with additional positive control

lacI gene

Codes for lac repressor protein (trans-acting)

lacP (promoter)

RNA polymerase binding site for lac operon

lacO (operator)

Binding site for lac repressor

lacZ

Encodes β-galactosidase (breaks lactose into glucose + galactose and produces allolactose)

lacY

Encodes permease (transports lactose into the cell)

lacA

Encodes transacetylase (minor detoxification role)

Lac operon without lactose

Repressor binds operator → RNA polymerase blocked → transcription OFF

Basal transcription

Very low transcription due to occasional repressor dissociation

Lac operon with lactose

Lactose converted to allolactose → repressor inactivated → transcription ON

Allolactose

Inducer molecule that binds and inactivates repressor

Purpose of lac operon

Allows bacteria to use lactose as an energy source when present

Catabolite repression

Glucose inhibits lac operon via cAMP and CAP

High glucose

Low cAMP → CAP inactive → weak RNA polymerase binding → low transcription

Low glucose

High cAMP → CAP binds cAMP → CAP-cAMP binds DNA → strong transcription

CAP (catabolite activator protein)

Activator that enhances RNA polymerase binding

Requirement for maximum lac expression

Low glucose AND high lactose

lacI⁻ mutation

Nonfunctional repressor → cannot bind operator → operon always ON (constitutive)

lacIˢ mutation

Super-repressor cannot bind inducer → always bound to operator → operon always OFF

lacOᶜ mutation

Operator altered → repressor cannot bind → operon always ON

lacP⁻ mutation

Promoter defective → RNA polymerase cannot bind → operon always OFF

lacZ⁻ mutation

No β-galactosidase → lactose cannot be broken down

lacY⁻ mutation

No permease → lactose cannot efficiently enter cell

Dominance of lacI⁺ over lacI⁻

Functional repressor diffuses and regulates both operons (trans-acting)

cis-acting elements

Affect only genes on same DNA molecule (lacO, lacP)

trans-acting elements

Diffusible products affect multiple DNA molecules (lacI protein)

Partial diploid

Cell with two copies of lac operon (chromosome + plasmid)

Bacteria genome organization

Genes often in operons

Eukaryote genome organization

Genes have individual promoters (no operons)

Transcription/translation in bacteria

Occur simultaneously (coupled)

Transcription/translation in eukaryotes

Separated (nucleus vs cytoplasm)

Chromatin

DNA + histone protein complex in eukaryotes

Nucleosome

DNA wrapped around histone octamer

Histone tails

Protein extensions that can be chemically modified

Chromatin condensation

Prevents transcription (DNA inaccessible)

Chromatin decondensation

Allows transcription (DNA accessible)

Histone acetylation

Loosens chromatin → increases transcription

Histone methylation

Can increase or decrease transcription depending on context

Chromatin remodeling complexes

Move or remove nucleosomes to expose DNA

DNA methylation

Addition of methyl groups to DNA → usually represses transcription

Epigenetics

Heritable changes in gene expression without DNA sequence change

Core promoter

Region where general transcription machinery assembles (includes TATA box)

Enhancers

DNA elements that increase transcription (can be far from gene)

Silencers

DNA elements that decrease transcription

Activators

Proteins that bind enhancers and increase transcription

Repressors (eukaryotic)

Proteins that decrease transcription

Coactivators

Assist activators but do not bind DNA directly

Corepressors

Assist repressors

Coordinated gene regulation

Multiple genes share regulatory sequences and respond together

Alternative splicing

One gene produces multiple protein variants

mRNA degradation

Controls protein levels by determining mRNA lifespan

Poly-A tail shortening

Leads to mRNA degradation

5' cap removal

Leads to mRNA degradation

RNA interference (RNAi)

Small RNAs regulate gene expression post-transcriptionally

siRNA

Binds mRNA → causes cleavage and degradation

miRNA

Binds mRNA → blocks translation or promotes degradation

Translation regulation

Controlled by ribosomes, initiation factors, or mRNA structure

Posttranslational modification

Includes phosphorylation, glycosylation, cleavage → alters protein function