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Convergent evolution in two bacterial replicative helicase loaders

2022; Elsevier BV; Volume: 47; Issue: 7 Linguagem: Inglês

10.1016/j.tibs.2022.02.005

1362-4326

Jillian Chase, James M. Berger, David Jeruzalmi,

Bacteriophages and microbial interactions

The initiation of DNA replication is a tightly regulated process in all cellular domains of life and involves regulated recruitment and assembly of essential factors, including the replicative hexameric helicase complex, to replication origins. A crucial step during the replication initiation phase of DNA replication is loading of hexameric, ring-shaped replicative helicases onto DNA. In bacteria, the DnaB family of replicative helicases comprise six identical subunits, which collectively create a central chamber to bind one of the ssDNA strands of double-stranded DNA; the translocation of DnaB on ssDNA ahead of DNA polymerase in the replisome separates the two strands to provide substrates for DNA synthesis. Recent structure determinations of two bacterial helicase loaders bound to the same DnaB helicase offer an opportunity to extract fundamental principles associated with DnaB opening and loading onto ssDNA. Escherichia coli DnaC and bacteriophage λ P evolved independently to converge, through molecular mimicry, on a common helicase-opening mechanism. Dedicated loader proteins play essential roles in bacterial DNA replication by opening ring-shaped DnaB-family helicases and chaperoning single-stranded (ss)DNA into a central motor chamber as a prelude to DNA unwinding. Although unrelated in sequence, the Escherichia coli DnaC and bacteriophage λ P loaders feature a similar overall architecture: a globular domain linked to an extended lasso/grappling hook element, located at their N and C termini, respectively. Both loaders remodel a closed DnaB ring into nearly identical right-handed open conformations. The sole element shared by the loaders is a single alpha helix, which binds to the same site on the helicase. Physical features of the loaders establish that DnaC and λ P evolved independently to converge, through molecular mimicry, on a common helicase-opening mechanism. Dedicated loader proteins play essential roles in bacterial DNA replication by opening ring-shaped DnaB-family helicases and chaperoning single-stranded (ss)DNA into a central motor chamber as a prelude to DNA unwinding. Although unrelated in sequence, the Escherichia coli DnaC and bacteriophage λ P loaders feature a similar overall architecture: a globular domain linked to an extended lasso/grappling hook element, located at their N and C termini, respectively. Both loaders remodel a closed DnaB ring into nearly identical right-handed open conformations. The sole element shared by the loaders is a single alpha helix, which binds to the same site on the helicase. Physical features of the loaders establish that DnaC and λ P evolved independently to converge, through molecular mimicry, on a common helicase-opening mechanism. distinct subdivision of the P-loop NTPases. AAA+ (ATPases associated with various activities) are a large family of oligomeric, often ring-shaped, motors and switches with crucial functions in biology. The core AAA+ fold encompasses the P-loop NTPase structural element to feature a two-domain structure and several conserved sequence motifs. ATP binds at subunit interfaces, with contacts with nucleotides arising from both subunits. helicase loader protein used by phage λ. form of molecular evolution in which unrelated molecules independently evolve similar shapes or properties that reflect intrinsic structural or chemical constraints. A common ancestor is not a feature of convergent evolution; by contrast, a common ancestor is an essential feature of divergent evolution. replication initiator protein for bacterial chromosomal DNA replication. The λ O protein provides the replication initiation function for the phage λ genome. replicative helicase found in Gram-negative bacteria. It is related to the DnaC helicase found in Gram-positive organisms. replicative helicase loader found in certain Gram-negative bacteria. The analog in Gram-positive species is DnaI. An unusual architectural feature of some protein oligomers wherein participating protomers exchange a structural domain in a manner akin to a handshake between two people. Swapping involves replacement of intramonomer interactions between two sub-domains with nearly identical intermonomer contacts. several types have been described: ring-breakers (e.g., Escherichia coli DnaC and λ P), which physically open hexameric helicase rings to enable ssDNA to enter an internal chamber; and ring-makers (e.g., Bacillus subtilis DnaI), which assemble hexameric rings on DNA from monomers. The mechanisms of other bacterial (e.g., DciA/DopE) helicase loaders remain to be established. Other loading mechanisms have also been described, including self-regulated ring closure for the transcription terminator Rho ATPase and chaperoned ring-closure for the MCM2-7 complex in eukaryotic DNA replication. close structural resemblance between two molecular entities. Mimicry can arise from divergent or convergent evolution. A family of nucleotide-handling proteins that encompasses 10–20% of all proteins; these proteins couple the energy of nucleotide binding and hydrolysis to chemical or mechanical transformation. Members share a conserved fold, and two conserved amino acid sequence motifs termed 'Walker A' and 'Walker B'. The Walker A/P-loop sequence motif is a glycine-rich loop terminated by a threonine or serine (GxxGxGK[T/S], where x = any residue); this element closely approaches the β and γ phosphates of ATP, while the lysine and the threonine/serine contact the β phosphate and the Mg2+ ion, respectively. The Walker B sequence motif (hhhhD; h = hydrophobic residue) includes an aspartate residue that positions the Mg2+ ion and its associated water molecules. distinct subdivision of the P-loop NTPases. Members adopt oligomeric configurations and include the RecA recombinase, the DnaB replicative helicase, the F1 sub-structure of ATP synthase, and the Rho helicase. In addition to structural elements in P-loop NTPases, the RecA-like ATPases feature an arginine finger that enables stimulation of ATP hydrolysis in trans of nucleotide bound primarily by a neighboring subunit of the oligomer. DNA sequence on a chromosome where DNA synthesis will begin. large multiprotein complex that mediates synthesis of both strands (leading and lagging) of DNA.