DNA Replication in Bacteria and Eukaryotes: Key Concepts and Mechanisms

DNA Replication: Bacteria vs. Eukaryotes

Bacteria

DNA replication in bacteria is a highly regulated process that ensures accurate duplication of the genome before cell division. The process involves several steps and specialized proteins.

Multiple DNA Topological Domains

• HU/IHF role: HU and IHF are DNA-binding proteins that help organize bacterial chromosomal DNA into topological domains, facilitating replication and gene regulation.

Initiation

• Bidirectional, Semiconservative Replication: Replication begins at a single origin (OriC) and proceeds in both directions, producing two DNA molecules, each with one parental and one newly synthesized strand.

• Control of Replication Initiation: Initiation is tightly regulated to ensure replication occurs only once per cell cycle.

• Key Proteins and Their Functions:

  • OriC: The origin of replication in Escherichia coli and other bacteria.

  • DnaA: Initiator protein that binds OriC and unwinds DNA.

  • DnaB: Helicase that unwinds the DNA helix ahead of the replication fork.

  • DnaC: Loader protein that helps DnaB bind to DNA.

  • SSB proteins: Single-stranded binding proteins stabilize unwound DNA.

  • DnaG: Primase that synthesizes RNA primers for DNA polymerase.

• Replication Forks and Bubble Formation: The unwinding of DNA creates replication forks and a replication bubble where synthesis occurs.

• Interaction with OriC: DnaA binds to OriC, recruiting other proteins to initiate replication.

Elongation

• DNA Polymerases in Prokaryotes: Bacteria have several DNA polymerases, each with specific roles.

  • DNA Pol I: Removes RNA primers and fills gaps.

  • DNA Pol III: Main enzyme for DNA synthesis.

  • DNA Pol II: Involved in DNA repair.

• Direction of Synthesis: DNA polymerases synthesize DNA in the 5' to 3' direction.

• Other Key Enzymes:

  • RNase H: Removes RNA primers.

  • DNA ligase: Seals nicks between Okazaki fragments.

  • DNA gyrase: Relieves supercoiling ahead of the fork.

• Exonuclease Activity: Many polymerases have 3' to 5' exonuclease activity for proofreading, ensuring fidelity by removing mismatched nucleotides.

• Leading vs. Lagging Strand Synthesis:

  • Leading strand: Synthesized continuously.

  • Lagging strand: Synthesized discontinuously as Okazaki fragments.

Termination

• Ter and Tus Proteins: Termination occurs at specific Ter sites, where Tus proteins bind and halt replication forks.

• Catenane Linkage and Topoisomerase IV: After replication, daughter chromosomes may be interlinked (catenanes). Topoisomerase IV resolves these links to allow chromosome segregation.

Eukaryotes

Eukaryotic DNA replication is more complex due to the linear nature of chromosomes and the presence of multiple origins of replication.

Differences from Prokaryotes

• Linear Genome: Eukaryotic chromosomes are linear, not circular.

• Bidirectional and Semiconservative Replication: Replication proceeds in both directions from multiple origins, and each daughter DNA contains one parental and one new strand.

• Origin of Replication: Multiple origins are present on each chromosome, unlike the single origin in bacteria.

Initiation

• Origin Recognition Complex (ORC): A multi-protein complex that identifies replication origins and recruits other factors.

Elongation

• Polymerases and Their Roles:

  • DNA Polymerase α: Initiates synthesis by adding RNA-DNA primers.

  • DNA Polymerase δ: Synthesizes the lagging strand.

  • DNA Polymerase ε: Synthesizes the leading strand.

• RNase H: Removes RNA primers from Okazaki fragments.

Termination

• End-Replication Problem: Linear chromosomes cannot fully replicate their ends, leading to overhangs.

• Telomere Definition: Telomeres are repetitive DNA sequences at chromosome ends that protect genetic information.

• Telomerase Role: Telomerase is an enzyme that extends telomeres, preventing loss of genetic material during replication.

Comparison Table: Bacterial vs. Eukaryotic DNA Replication

Feature	Bacteria	Eukaryotes
Genome Structure	Circular	Linear
Origin of Replication	Single (OriC)	Multiple per chromosome
Main DNA Polymerase	DNA Pol III	DNA Pol δ, ε
Termination	Ter sites, Tus proteins	Telomeres, telomerase
End-Replication Problem	No	Yes

Key Equations

• Semiconservative Replication: $\text{Parental DNA} \rightarrow \text{Two daughter DNAs, each with one parental and one new strand}$

• DNA Synthesis Direction: $\text{DNA polymerase adds nucleotides in the 5' \rightarrow 3' direction}$

Example

• Application: Understanding the differences in DNA replication mechanisms is crucial for developing antibiotics that target bacterial enzymes without affecting eukaryotic cells.