Novel Interaction of the Bacterial-Like DnaG Primase with the MCM Helicase in Archaea

Bauer, Robert J.; Graham, Brian W.; Trakselis, Michael A.

doi:10.1016/j.jmb.2013.01.025

Cited by 10 publications

(12 citation statements)

References 82 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The ATPase activity for all of the mutants is stimulated in the presence of DNA (ϳ1.4-fold) similar to wild type (1.8-fold) ( Fig. 8B and Table 2) and consistent with previously published data showing typical DNA-dependent ATPase stimulation of 1.2-2.0-fold (14,33,(37)(38)(39). The double mutant (K111A/R113A) has an overall reduced ATPase rate (0.5-0.6) compared with WT and the other mutants.…”

Section: External Surface Electrostatic Mutations Alter Deuterium Uptsupporting

confidence: 91%

DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase

Graham

Tao

Dodge

et al. 2016

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

The archaeal minichromosomal maintenance (MCM) helicase from Sulfolobus solfataricus (SsoMCM) is a model for understanding structural and mechanistic aspects of DNA unwinding. Although interactions of the encircled DNA strand within the central channel provide an accepted mode for translocation, interactions with the excluded strand on the exterior surface have mostly been ignored with regard to DNA unwinding. We have previously proposed an extension of the traditional steric exclusion model of unwinding to also include significant contributions with the excluded strand during unwinding, termed steric exclusion and wrapping (SEW). The SEW model hypothesizes that the displaced single strand tracks along paths on the exterior surface of hexameric helicases to protect singlestranded DNA (ssDNA) and stabilize the complex in a forward unwinding mode. Using hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance MS, we have probed the binding sites for ssDNA, using multiple substrates targeting both the encircled and excluded strand interactions. In each experiment, we have obtained >98.7% sequence coverage of SsoMCM from >650 peptides (5-30 residues in length) and are able to identify interacting residues on both the interior and exterior of SsoMCM. Based on identified contacts, positively charged residues within the external waist region were mutated and shown to generally lower DNA unwinding without negatively affecting the ATP hydrolysis. The combined data globally identify binding sites for ssDNA during SsoMCM unwinding as well as validating the importance of the SEW model for hexameric helicase unwinding.DNA unwinding by hexameric replicative helicases is required for DNA replication elongation, providing the singlestranded DNA (ssDNA) 5 templates for leading and lagging strand synthesis. These hexameric helicase complexes form ring-like structures that preferentially encircle one of the DNA strands, providing stability in DNA binding and enhancing processivity for unwinding long stretches of DNA. In the steric exclusion model for unwinding, the motor domains within the central channel translocate along the encircled ssDNA while physically excluding the complementary ssDNA on the exterior. Although DNA unwinding by helicases can be effectively measured in gel-based and fluorescence assays, the specific molecular interactions with DNA are poorly described. Previously, we have proposed that the excluded strand is not a passive component of unwinding; rather, it will interact along specific exterior paths on the hexameric helicase surface to both stabilize the complex and promote forward unwinding (1). Although structures of hexameric helicases that include small stretches of ssDNA have been solved recently (2, 3), the interactions are constrained to central channel residues, and no molecular information is available at the duplex region or with respect to the excluded strand.Hexameric DNA replication helicases are known to exist across the three domains of life, including viruses. Althou...

show abstract

Section: External Surface Electrostatic Mutations Alter Deuterium Uptsupporting

confidence: 91%

DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase

Graham

Tao

Dodge

et al. 2016

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

show abstract

“…DNA gyrase, a topoisomerase belonging to the Topo IIA family, is present in a number of euryarchaeal lineages (Forterre et al 2007). In the case of archaeal homologs of bacterial primase DnaG (Aravind and Koonin 1998), the proposal that they are involved in replication (Bauer et al 2013) is weakened by strong evidence that suggests a role in RNA metabolism (Hou et al 2013). …”

Section: Introductionmentioning

confidence: 99%

Global Phylogenomic Analysis Disentangles the Complex Evolutionary History of DNA Replication in Archaea

Raymann

Forterre

Brochier-Armanet

et al. 2014

Genome Biology and Evolution

106

View full text Add to dashboard Cite

The archaeal machinery responsible for DNA replication is largely homologous to that of eukaryotes and is clearly distinct from its bacterial counterpart. Moreover, it shows high diversity in the various archaeal lineages, including different sets of components, heterogeneous taxonomic distribution, and a large number of additional copies that are sometimes highly divergent. This has made the evolutionary history of this cellular system particularly challenging to dissect. Here, we have carried out an exhaustive identification of homologs of all major replication components in over 140 complete archaeal genomes. Phylogenomic analysis allowed assigning them to either a conserved and probably essential core of replication components that were mainly vertically inherited, or to a variable and highly divergent shell of extra copies that have likely arisen from integrative elements. This suggests that replication proteins are frequently exchanged between extrachromosomal elements and cellular genomes. Our study allowed clarifying the history that shaped this key cellular process (ancestral components, horizontal gene transfers, and gene losses), providing important evolutionary and functional information. Finally, our precise identification of core components permitted to show that the phylogenetic signal carried by DNA replication is highly consistent with that harbored by two other key informational machineries (translation and transcription), strengthening the existence of a robust organismal tree for the Archaea.

show abstract

“…It has been shown that the bacterial-type DnaG primase from the hyperthermophilic archaeon Sulfolobus solfataricus was active in primer synthesis 7 and interacted with MCM in vitro 8 . However, since archaeal DnaG was also found to be an integral part of the exosome 9 and dispensable for cell growth 10 , it is unclear if the protein is involved in primer synthesis during DNA replication.…”

mentioning

confidence: 99%

A primase subunit essential for efficient primer synthesis by an archaeal eukaryotic-type primase

et al. 2015

View full text Add to dashboard Cite

Novel Interaction of the Bacterial-Like DnaG Primase with the MCM Helicase in Archaea

Cited by 10 publications

References 82 publications

DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase

DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase

Global Phylogenomic Analysis Disentangles the Complex Evolutionary History of DNA Replication in Archaea

A primase subunit essential for efficient primer synthesis by an archaeal eukaryotic-type primase

Contact Info

Product

Resources

About