Bacterial Genetics & Operons

1. The Chromosome and Replication

Replication initiates at the unique oriC site (~245 bp in E. coli) where DnaA loads, melts the AT-rich region, and recruits the replicative helicase DnaB. Two replisomes proceed bidirectionally at ~1000 bp/s. The whole 4.6 Mbp genome replicates in ~40 minutes — but E. coli can divide every 20 minutes by overlapping rounds of replication (multiple replisomes per chromosome).

Termination at ter sites uses a polar replication-fork-arrest factor (Tus); resolution of catenated daughter chromosomes uses topoisomerase IV. FtsZ, the bacterial tubulin homologue, polymerises into the Z-ring at midcell to drive cytokinesis.

2. RNA Polymerase & Sigma Factors

Bacteria have a single, multi-subunit RNA polymerase — core enzyme\(\alpha_2\beta\beta'\omega\) plus a dissociable σ factor that selects promoters. The major housekeeping factor in E. coli is σ⁷⁰ recognising the −10 (TATAAT) and −35 (TTGACA) promoter elements.

Alternative sigmas reprogramme transcription in response to specific stresses: σ³² (heat shock), σ²⁸ (flagellar genes), σ^S (stationary phase), σ⁵⁴ (nitrogen limitation), σ^E (envelope stress). Sigma-factor cascades give bacteria eukaryotic-grade combinatorial regulation with a tiny number of pieces.

3. The lac Operon (Jacob & Monod 1961)

The lac operon contains three genes — lacZ (β-galactosidase), lacY (lactose permease), lacA (transacetylase) — transcribed from a single promoter as one polycistronic mRNA. Two layers of regulation:

• Negative control: LacI repressor binds the operator lacO, blocking RNA-pol elongation. Allolactose (a metabolic side-product of β-galactosidase) binds LacI and induces a conformational change that releases it from DNA.
• Positive control: when glucose is low, cAMP rises and binds CAP (catabolite-activator protein); CAP-cAMP binds upstream of the lac promoter and recruits RNA pol. This implements glucose preference (“diauxie”).

The lac operon expressed at full induction provides >1000-fold regulation. Its dynamics — particularly the all-or-none bistability under IPTG — gave Novick & Weiner’s 1957 paper its place as the first quantitative model of cellular memory.

4. The trp Operon and Attenuation

Tryptophan biosynthesis is regulated by TrpR repression (modest, ~70-fold) and a second elegant mechanism, attenuation: the leader region of the operon contains a short ORF rich in tryptophan codons. When tryptophan is abundant, the ribosome translates the leader rapidly, RNA folds into a 3:4 hairpin terminator, and transcription aborts. When tryptophan is scarce, the ribosome stalls at the Trp codons, RNA folds into the alternative 2:3 hairpin (anti-terminator), and transcription proceeds.

Attenuation is possible only because bacterial transcription and translation are coupled — ribosomes engage nascent mRNA before transcription completes. This coupling is impossible in eukaryotes (the nuclear envelope prevents it).

5. Two-Component Systems

Bacteria use a stereotyped 2-protein architecture for sensing the environment:

• Sensor histidine kinase — usually transmembrane; senses a stimulus, autophosphorylates a conserved His residue.
• Response regulator — cytoplasmic; receives the phosphate on a conserved Asp, activates DNA-binding output.

Examples: EnvZ–OmpR (osmolarity, regulates outer-membrane porins); PhoR–PhoB (phosphate starvation); CheA–CheY (chemotaxis, Module 4); KdpD–KdpE (potassium); VirA–VirG (Agrobacterium virulence). E. colihas ~30 two-component systems; Mycobacterium has ~12. They are absent from animals (a few in plants and yeast), making them potential antibiotic targets.

6. Horizontal Gene Transfer

Three classical mechanisms move DNA between bacteria, often across species:

• Transformation (Griffith 1928, Avery–MacLeod–McCarty 1944) — uptake of free environmental DNA. ~80 species are naturally competent (Bacillus, Streptococcus, Neisseria, Haemophilus).
• Transduction — phage-mediated DNA transfer. Generalised (random packaging accidents) or specialised (excisional errors of integrated prophages).
• Conjugation — F-plasmid encoded type-IV secretion machinery; cell-to-cell DNA passage through a conjugation pilus. The major route of antibiotic-resistance gene spread.

CRISPR-Cas, the bacterial adaptive immune system, evolved primarily to defend against phages and conjugative plasmids. The same system, repurposed by Doudna and Charpentier, gave eukaryotic biology its most powerful gene-editing tool and earned the 2020 Nobel Prize in Chemistry.