Bacterial Primosome

Taku Tanaka, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
Hisao Masai, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan

Published online: October 2019

DOI: 10.1002/9780470015902.a0001048.pub3

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.
close

References

Arai K, Low R and Kornberg A (1981) Movement and site selection for priming by the primosome in phage ϕX174 DNA replication. Proceedings of the National Academy of Sciences of the USA 78: 707–711.

Aramaki T, Abe Y, Ohkuri T, et al. (2013) Domain separation and characterization of PriC, a replication restart primosome factor in Escherichia coli. Genes to Cells 18: 723–732.

Bhattacharyya B, George NP, Thurmes TM, et al. (2014) Structural mechanisms of PriA‐mediated DNA replication restart. Proceedings of the National Academy of Sciences of the USA 111: 1373–1378.

Bruand C, Velten M, McGovern S, et al. (2005) Functional interplay between the Bacillus subtilis DnaD and DnaB proteins essential for initiation and reinitiation of DNA replication. Molecular Microbiology 55: 1138–1150.

Chen HW, North SH and Nakai H (2004) Properties of the PriA helicase domain and its role in binding PriA to specific DNA structures. Journal of Biological Chemistry 279: 38503–38512.

Fujiyama S, Abe Y, Tani J, et al. (2014) Structure and mechanism of the primosome protein DnaT‐functional structures for homotrimerization, dissociation of ssDNA from the PriB·ssDNA complex, and formation of the DnaT·ssDNA complex. FEBS Journal 281: 5356–5370.

Gambus A, Jones RC, Sanchez‐Diaz A, et al. (2006) GINS maintains association of Cdc45 with MCM in replisome progression complexes at eukaryotic DNA replication forks. Nature Cell Biology 8: 358–366.

Gregg AV, McGlynn P, Jaktaji RP and Lloyd RG (2002) Direct rescue of stalled DNA replication forks via the combined action of PriA and RecG helicase activities. Molecular Cell 9: 241–251.

Heller RC and Marians KJ (2005a) Unwinding of the nascent lagging strand by Rep and PriA enables the direct restart of stalled replication forks. Journal of Biological Chemistry 280: 34143–34151.

Heller RC and Marians KJ (2005b) The disposition of nascent strands at stalled replication forks dictates the pathway of replisome loading during restart. Molecular Cell 17: 733–743.

Huang YH, Lo YH, Huang W and Huang CY (2012) Crystal structure and DNA‐binding mode of Klebsiella pneumoniae primosomal PriB protein. Genes to Cells 17: 837–849.

Huang YH and Huang CY (2013) The N‐terminal domain of DnaT, a primosomal DNA replication protein, is crucial for PriB binding and self‐trimerization. Biochemical and Biophysical Research Communications 442: 147–152.

Huang CC and Huang CY (2016) DnaT is a PriC‐binding protein. Biochemical and Biophysical Research Communications 477: 988–992.

Jones JM and Nakai H (1999) Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate. Journal of Molecular Biology 289: 503–515.

Kelly T (2017) Historical perspective of eukaryotic DNA replication. Advances in Experimental Medicine and Biology 1042: 1–41.

Kogoma T (1996) Recombination by replication. Cell 85: 625–627.

Kogoma T, Cadwell GX, Barnard KG and Asai T (1996) Requirement of the DNA replication priming protein, PriA, for homologous recombination and double‐strand break repair. Journal of Bacteriology 178: 1258–1264.

Kogoma T (1997) Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Microbiology and Molecular Biology Reviews 61: 212–238.

Kornberg A and Baker TA (1992) DNA Replication, 2nd edn. Freeman: New York.

LeBowitz JH, Zylicz M, Georgopoulos C and McMacken R (1985) Initiation of DNA replication on single‐stranded DNA templates catalyzed by purified replication proteins of bacteriophage λ and Escherichia coli. Proceedings of the National Academy of Sciences of the USA 82: 3988–3992.

LeBowitz JH and McMacken R (1986) The Escherichia coli dnaB replication protein is a DNA helicase. Journal of Biological Chemistry 261: 4738–4748.

Lee EH, Masai H, Allen GC Jr and Kornberg A (1990) The priA gene encoding the primosomal replicative n' protein of Escherichia coli. Proceedings of the National Academy of Sciences of the USA 87: 4620–4624.

Lee EH and Kornberg A (1991) Replication deficiencies in priA mutants of Escherichia coli lacking the primosomal replication n' protein. Proceedings of the National Academy of Sciences of the USA 88: 3029–3032.

Li YC, Naveen V, Lin MG and Hsiao CD (2017) Structural analyses of the bacterial primosomal protein DnaB reveal that it is a tetramer and forms a complex with a primosomal re‐initiation protein. Journal of Biological Chemistry 292: 15744–15757.

Liu J, Nurse P and Marians KJ (1996) The ordered assembly of the ϕX174‐type primosome. III. PriB facilitates complex formation between PriA and DnaT. Journal of Biological Chemistry 271: 15656–15661.

Liu J and Marians KJ (1999) PriA‐directed assembly of a primosome on D‐loop DNA. Journal of Biological Chemistry 274: 25033–25041.

Liu Z, Chen P, Wang X, et al. (2014) Crystal structure of DnaT84‐153‐dT10 ssDNA complex reveals a novel single‐stranded DNA binding mode. Nucleic Acids Research 42: 9470–9483.

Lopper M, Holten JM and Kech JL (2004) Crystal structure of PriB, a component of the E. coli replication restart primosome. Structure 12: 1967–1975.

Lopper M, Boonsombat R, Sandler SJ and Keck JL (2007) A hand‐off mechanism for primosome assembly in replication restart. Molecular Cell 26: 781–793.

Masai H, Bond MW and Arai K (1986) Cloning of the Escherichia coli gene for primosomal protein i: the relationship to dnaT, essential for chromosomal DNA replication. Proceedings of the National Academy of Sciences of the USA 83: 1256–1260.

Masai H and Arai K (1988) Operon structure of dnaT and dnaC genes essential for normal and stable DNA replication of Escherichia coli chromosome. Journal of Biological Chemistry 263: 15083–15093.

Masai H, Nomura N and Arai K (1990) The ABC primosome: a novel priming system employing dnaA, dnaB, dnaC, and primase on a hairpin containing a dnaA box sequence. Journal of Biological Chemistry 265: 15124–15144.

Masai H, Asai T, Kubota Y, Arai K and Kogoma T (1994) Escherichia coli PriA protein is essential for inducible and constitutive stable DNA replication. EMBO Journal 13: 5338–5345.

Masai H, Deneke J, Furui Y, Tanaka T and Arai KI (1999) Escherichia coli and Bacillus subtilis PriA proteins essential for recombination‐dependent DNA replication: involvement of ATPase/helicase activity of PriA for inducible stable DNA replication. Biochimie 81: 847–857.

Masai H, Matsumoto S, You Z, Yoshizawa‐Sugata N and Oda M (2010a) Eukaryotic chromosome DNA replication: where, when, and how? Annual Review of Biochemistry 79: 89–130.

Masai H, Tanaka T and Kohda D (2010b) Stalled replication forks: making ends meet for recognition and stabilization. Bioessays 32: 687–697.

McGlynn P, Al‐Deib AA, Liu J, Marians KJ and Lloyd RG (1997) The DNA replication protein PriA and the recombination protein RecG bind D‐loops. Journal of Molecular Biology 270: 212–221.

Mizukoshi T, Tanaka T, Arai K, Kohda D and Masai H (2003) A critical role of the 3′ terminus of nascent DNA chains in recognition of stalled replication forks. Journal of Biological Chemistry 278: 42234–42239.

Ng JY and Marians KJ (1996a) The ordered assembly of the ϕX174‐type primosome. Journal of Biological Chemistry 271: 15642–15648.

Ng JY and Marians KJ (1996b) The ordered assembly of the ϕX174‐type primosome. II. Preservation of primosome composition from assembly through replication. Journal of Biological Chemistry 271: 15649–15655.

Nossal NG (1992) Protein‐protein interactions at a DNA replication fork: bacteriophage T4 as a model. FASEB Journal 6: 871–878.

Nurse P, DiGate RJ, Zavitz KH and Marians KJ (1990) Molecular cloning and DNA sequence analysis of Escherichia coli priA, the gene encoding the primosomal protein replication factor Y. Proceedings of the National Academy of Sciences of the USA 87: 4615–4619.

Nurse P, Zavitz KH and Marians KJ (1991) Inactivation of the Escherichia coli priA DNA replication protein induces the SOS response. Journal of Bacteriology 173: 6686–6693.

Ouzounis CA and Blencowe BJ (1991) Bacterial DNA replication initiation factor priA is related to proteins belonging to the 'DEAD‐box' family. Nucleic Acids Research 19: 6953.

Sandler SJ, Samra HS and Clark AJ (1996) Differential suppression of priA2::kan phenotypes in Escherichia coli K‐12 by mutations in priA, lexA, and dnaC. Genetics 143: 5–13.

Sandler SJ, Marians KJ, Zavitz KH, et al. (1999) dnaC mutations suppress defects in DNA replication‐ and recombination‐associated functions in priB and priC double mutants in Escherichia coli K‐12. Molecular Microbiology 34: 91–101.

Sandler SJ and Marians KJ (2000) Role of PriA in replication fork reactivation in E. coli. Journal of Bacteriology 182: 9–13.

Sasaki K, Ose T, Okamoto N, et al. (2007) Structural basis of the 3′‐end recognition of a leading strand in stalled replication forks by PriA. EMBO Journal 26: 2584–2593.

Shlomai J and Kornberg A (1980) An E. coli replication protein that recognizes a unique sequence within a hairpin region in ϕX174 DNA. Proceedings of the National Academy of Sciences of the USA 77: 799–803.

Szymanski MR, Jezewska MJ and Bujalowski W (2013a) Energetics of the Escherichia coli DnaT protein trimerization reaction. Biochemistry 52: 1858–1873.

Szymanski MR, Jezewska MJ and Bujalowski W (2013b) The Escherichia coli primosomal DnaT protein exists in solution as a monomer‐trimer equilibrium system. Biochemistry 52: 1845–1857.

Tanaka T, Mizukoshi T, Taniyama C, et al. (2002) DNA binding of PriA protein requires cooperation of the N‐ternimal D‐loop/arrested‐fork binding and C‐terminal helicase domains. Journal of Biological Chemistry 277: 38062–38071.

Tanaka T, Taniyama C, Arai K and Masai H (2003) ATPase/helicase motif mutants of Escherichia coli PriA protein essential for recombination‐dependent DNA replication. Genes to Cells 8: 251–261.

Tanaka T and Masai H (2006) Stabilization of a stalled replication fork by concerted actions of two helicases. Journal of Biological Chemistry 281: 3484–3493.

Tanaka T, Mizukoshi T, Sasaki K, Kohda D and Masai H (2007) Escherichia coli PriA protein, two modes of DNA binding and activation of ATP hydrolysis. Journal of Biological Chemistry 282: 19917–19927.

Wessel SR, Marceau AH, Massoni SC, et al. (2013) PriC‐mediated DNA replication restart requires PriC complex formation with the single‐stranded DNA‐binding protein. Journal of Biological Chemistry 288: 17569–17578.

Wessel SR, Cornilescu CC, Cornilescu G, et al. (2016) Structure and function of the PriC DNA replication restart protein. Journal of Biological Chemistry 291: 18384–18396.

Windgassen TA, Leroux M, Satyshur KA, Sandler SJ and Keck JL (2018a) Structure‐specific DNA replication‐fork recognition directs helicase and replication restart activities of the PriA helicase. Proceedings of the National Academy of Sciences of the USA 115: E9075–E9084.

Windgassen TA, Wessel SR, Bhattacharyya B and Keck JL (2018b) Mechanisms of bacterial DNA replication restart. Nucleic Acids Research 46: 504–519.

Yeeles JT, Deegan TD, Janska A, Early A and Diffley JF (2015) Regulated eukaryotic DNA replication origin firing with purified proteins. Nature 519: 431–435.

Zavitz KH and Marians KJ (1992) ATPase‐deficient mutants of the Escherichia coli DNA replication protein PriA are capable of catalyzing the assembly of active primosomes. Journal of Biological Chemistry 267: 6933–6940.

Related Sub-Topics:

Genomes and Chromosomes | Nucleic Acids: Structure, Function, Metabolism | Protein Structure | Enzymes: Structure and Action Mechanism | Chromosomes and Chromatin Modifications | Replication and Recombination | DNA Structure and Function | DNA Damage and Repair | Transcription of DNA
Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

Article Title: Bacterial Primosome
 
How to Cite close
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]