Bacterial Primosome

Abstract

DNA (deoxyribonucleic acid) replication requires operation of molecular machinery which efficiently elongates nucleotide chains on both strands. This process requires not only the enzymes synthesising DNA (DNA polymerases) but also those providing primer RNAs (ribonucleic acid) and continuously melting the duplex DNA. The primosome refers to a protein complex capable of processive unwinding of duplex DNA and primer RNA synthesis on the lagging strand at a replication fork. The prepriming proteins, DNA helicase and primase are sequentially assembled on the template DNA to generate a primosome. Once assembled, it, in conjunction with DNA polymerases, facilitates DNA chain elongation. The assembly of bacterial primosome is triggered by an ‘initiator’ protein including DnaA or PriA, which recognises the site of assembly. Primosome is assembled also in replication restart process at stalled or processed replication forks, triggered by PriA. Primosome constitutes an essential component for active replication fork machinery. Recent advances in this field provide structural basis regarding how these factors function during the assembly of a primosome on viral origins as well as during the restart from the stalled DNA replication forks. These new knowledges provide important insight into how replication forks are protected from various genotoxic agents in eukaryotes.

Key Concepts

  • Replication fork is the site of DNA replication where DNA synthesis occurs, and primosome is its integral component.
  • Primosome is capable of duplex DNA unwinding and primer RNA synthesis at the replication fork.
  • In bacteria, replication is normally initiated at a single locus, oriC, on the genome.
  • Bacterial DNA replication is initiated by an initiator, DnaA, which generates a oriC‐primosome.
  • The stalled DNA replication fork needs to be swiftly detected and rescued to prevent its collapse and to ensure the completion of genome replication.
  • Another primosome mediated by PriA serves for reassembly of replication fork at a stalled fork in bacteria.
  • Bacterial genomes can be replicated by an alternative mode that involves RNA‐DNA hybrids.
  • Primosomes in eukaryotes may be more complex, but essential components would be conserved.

Keywords: DnaA; PriA; DnaB helicase; DnaG primase; replication fork; stable DNA replication

Figure 1. Two representative modes of primosome assembly for DNA replication in E. coli. PriA‐dependent primosome is assembled at a small single‐stranded hairpin structure, whereas DnaA‐dependent primosome is assembled at oriC DNA as well as at a hairpin containing dnaA box (A site). These two modes differ in the requirement of proteins involved in the prepriming stage. Hypothetical structures for the preprimosomes are shown and the association of DnaG primase with them results in functional primosomes. The PriA‐dependent ‘ϕX174‐type’ primosome can be assembled at a recombination intermediate or at a stalled replication fork.
Figure 2. Stabilisation of a stalled replication fork by PriA protein. In the presence of 3′‐end of the nascent leading strand at the fork branch point (A‐fork [3′]), PriA can directly recognise and bind to the fork through the TT‐pocket to stabilise the fork. When the 3′‐end of the nascent leading strand is not positioned at the branch point (A‐fork [5′]), RecG, which has a higher affinity to A‐fork [5′] at the branch than PriA, binds to the fork and regresses the unwound fork to bring the 3′‐end of the leading strand at the branch point. PriA can now bind and stabilise the fork. This also prevents PriA from unwinding the unreplicated duplex. It should be noted that fork reversal could be conducted by other mechanisms as well. Masai et al. . Reproduced with permission of John Wiley & Sons.
Figure 3. PriB‐ and PriC‐pathway for loading of DnaB helicase at the stalled fork. After a stalled fork is stabilised by PriA, as described in Figure , lagging strand is unwound to expose single‐stranded DNA on which DnaB helicase is loaded either in PriB‐ or PriC‐dependent pathway. Both pathways requires DnaT protein. Windgassen et al. . Reproduced with permission of Oxford University Press.
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Tanaka, Taku, and Masai, Hisao(Oct 2019) Bacterial Primosome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001048.pub3]