18.4 Gene Regulation in Prokaryotes & Eukaryotes

Gene Regulation in Prokaryotes and Eukaryotes

Gene regulation determines when, where, and how much a gene is expressed. PA-CAT Bulletin of Information, rev. 20240815, Table 8, expects mastery of both prokaryotic operons and eukaryotic epigenetic mechanisms.

Prokaryotic Operons

An operon is a cluster of genes transcribed from a single promoter as one polycistronic mRNA, common in bacteria but rare in eukaryotes. Regulation integrates signals from small molecules and regulatory proteins.

Lac operon (E. coli lactose metabolism): three structural genes — lacZ (β-galactosidase), lacY (lactose permease), lacA (transacetylase) — controlled by a shared promoter and operator.

• Negative control: the lacI repressor binds the operator when lactose is absent, blocking transcription. When lactose is present, the inducer allolactose binds LacI and inactivates it, allowing transcription.
• Positive control: when glucose is low, cAMP accumulates, binds CAP (CRP), and the CAP–cAMP complex binds just upstream of the promoter to recruit RNA polymerase and boost transcription.

The lac operon is inducible — default off, turned on by lactose — and is only fully expressed when lactose is present and glucose is scarce.

Trp operon (tryptophan biosynthesis): five genes for tryptophan synthesis. It is repressible — default on, turned off when tryptophan is abundant. Tryptophan itself acts as a corepressor that enables the TrpR repressor to bind the operator. A second layer, attenuation, uses a 5' leader peptide whose translation rate (depending on tryptophan availability) determines whether a terminator hairpin or an anti-terminator hairpin forms, controlling premature termination.

Eukaryotic Transcription Factors

Eukaryotic regulation uses transcription factors (TFs):

• General (basal) TFs — required at all RNA Pol II promoters: TFIID (binds TATA), TFIIA, TFIIB, TFIIE, TFIIF, TFIIH (helicase/kinase).
• Specific TFs — bind enhancers (activators) or silencers (repressors) and are tissue- and stage-specific.
• Coactivators and corepressors — bridge specific TFs to the basal machinery; many have histone-modifying activities.

Common DNA-binding motifs include helix-turn-helix, zinc finger, leucine zipper (bZIP), and helix-loop-helix (bHLH). Regulation is combinatorial: the expression pattern of a gene reflects the combination of TFs present in a cell, the local chromatin state, and the integration of multiple signaling inputs (e.g., steroid receptors, MAPK, JAK-STAT) converging on a single promoter.

Epigenetics: DNA Methylation and Histone Modification

Epigenetics changes gene expression without altering the DNA sequence. Major mechanisms:

1. DNA methylation — addition of a methyl group to the 5-carbon of cytosine in CpG dinucleotides by DNA methyltransferases (DNMTs). Methylation of CpG islands near promoters usually silences transcription, either by blocking transcription-factor binding or by recruiting methyl-CpG-binding proteins that compact chromatin. Imprinted genes (e.g., IGF2 and H19) show parent-of-origin-specific methylation, and the pattern is reprogrammed in the germline each generation.
2. Histone modification — covalent marks on histone tails change chromatin accessibility:
   • Acetylation by histone acetyltransferases (HATs) — neutralizes lysine's positive charge, loosens DNA–histone contact, generally activates transcription.
   • Deacetylation by histone deacetylases (HDACs) — restores positive charge, tightens chromatin, generally represses transcription.
   • Methylation — residue- and state-dependent: H3K4me3 marks active promoters, whereas H3K9me3 and H3K27me3 mark repressed heterochromatin.
   • Phosphorylation and ubiquitination — additional regulatory marks.
3. Chromatin remodeling — ATP-dependent complexes (SWI/SNF, ISWI, CHD, INO80) slide, eject, or restructure nucleosomes to expose or hide regulatory DNA.
4. RNA interference (RNAi) — small RNAs silence expression post-transcriptionally:
   • miRNA (~22 nt) — imperfectly base-pair to 3' UTRs, repress translation and promote mRNA decay.
   • siRNA — fully complementary to target, leading Argonaute in the RISC complex to cleave the mRNA.
   • piRNA — protects the germline from transposon activity.

X-Inactivation and Epigenetic Inheritance

A classic epigenetic phenomenon is X-inactivation in female mammals: the long noncoding RNA XIST coats one X chromosome in each embryonic cell, recruits silencing machinery, and condenses it into a Barr body. The choice of which X is inactivated is random in most tissues, but once established it is clonally inherited, producing mosaic expression of X-linked alleles (visible in calico cat coat color). Epigenetic states are generally stable through mitosis but are reset during gametogenesis and early embryogenesis, a process called reprogramming.

Levels of Eukaryotic Regulation

Eukaryotic gene expression is regulated at many levels: chromatin accessibility → transcription initiation → RNA processing (alternative splicing, poly-A site choice) → mRNA stability and export → translation → post-translational modification. Alternative splicing allows one gene to yield many protein isoforms — an extreme example is Drosophila Dscam, which can produce more than 38,000 isoforms.

Worked Lac Operon: Glucose and Lactose Decision Matrix

The lac operon integrates two signals — lactose presence (controls the LacI repressor) and glucose level (controls CAP–cAMP activation). PA-CAT items often give a nutrient condition and ask whether lacZ, lacY, and lacA are transcribed. Use this four-state matrix.

Why each state:

• High glucose, no lactose: LacI repressor blocks the operator; even though CAP–cAMP would help, there is no lactose to induce. Transcription is off.
• High glucose + lactose: Allolactose removes LacI, but high glucose keeps cAMP low, so CAP–cAMP is scarce and RNA polymerase binds inefficiently. A small amount of transcript appears — the basal level — but expression is weak.
• Low glucose, no lactose: CAP–cAMP is abundant and would recruit polymerase, but LacI still blocks the operator. Transcription is off.
• Low glucose + lactose: Both conditions are satisfied — LacI is inactivated and CAP–cAMP recruits polymerase. The operon is fully induced.

The biological logic is energy economics: E. coli prefers glucose. When glucose is abundant it ignores lactose regardless of availability; only when glucose is depleted and lactose is present does it commit to lactose metabolism. This catabolite-repression pattern — glucose repressing alternative-sugar operons via low cAMP — generalizes to the ara and gal operons.