Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales

Abstract

ssDNA-binding proteins (SSBs) based on the oligonucleotide-binding fold are considered ubiquitous in nature and play a central role in many DNA transactions including replication, recombination, and repair. We demonstrate that the Thermoproteales, a clade of hyperthermophilic Crenarchaea, lack a canonical SSB. Instead, they encode a distinct ssDNA-binding protein that we term “ThermoDBP,” exemplified by the protein Ttx1576 from Thermoproteus tenax . ThermoDBP binds specifically to ssDNA with low sequence specificity. The crystal structure of Ttx1576 reveals a unique fold and a mechanism for ssDNA binding, consisting of an extended cleft lined with hydrophobic phenylalanine residues and flanked by basic amino acids. Two ssDNA-binding domains are linked by a coiled-coil leucine zipper. ThermoDBP appears to have displaced the canonical SSB during the diversification of the Thermoproteales, a highly unusual example of the loss of a “ubiquitous” protein during evolution.

Molecular Genetic and Biochemical Characterization of the Vaccinia Virus I3 Protein, the Replicative Single-Stranded DNA Binding Protein

“…Although structural prediction programs failed to identify an OB fold in the herpes simplex virus (HSV)-encoded SSB (ICP8), a region containing a similar set of ß-sheets and a motif of aromatic and basic residues was identified in the solved structure (30). The SSB from the bacterium Thermoproteus tenax (38) lacks an OB fold and binds DNA through a unique sequence that resides immediately upstream of a C-terminal multimerization domain. The DNA binding cleft of this SSB is also lined with phenylalanine residues and flanked by basic residues.…”

Archaeology of Eukaryotic DNA Replication

“…ThermoSSB (arCOG05578) contains an ssDNAbinding domain with a novel fold and a leucinezipperdomain that mediates dimerization of this protein (Paytubi et al 2012). ThermoSSB is present in all Thermoproteales with the exception of T. pendens, which encodes two RPA-like proteins.…”

“…In particular, an uncharacterized paralog of ThermoSSB (arCOG03772) shows a broader phyletic distribution being present, in addition to Thermoproteales, in Sulfolobales/ Desulfurococcales, Thermococcales, and Archaeoglobi (Paytubi et al 2012). In addition, there is at least one more protein family containing OB-fold domains and distantly similar to archaeal RPA2 (arCOG02261) that is present in most Methanococcales and Nanoarchaeum equitans.…”

“…The apparent absence of a canonical RPA/ SSB in Thermoproteales stimulated the search for an alternative, which resulted in the identification of a distinct ssDNA-binding protein in T. tenax that is unrelated to RPA and has been denoted ThermoSSB (Paytubi et al 2012). ThermoSSB (arCOG05578) contains an ssDNAbinding domain with a novel fold and a leucinezipperdomain that mediates dimerization of this protein (Paytubi et al 2012).…”

Functional Characterization of a Conserved Archaeal Viral Operon Revealing Single-Stranded DNA Binding, Annealing and Nuclease Activities

“…Recently a group of hyperthermophilic archaeal organisms were found to lack a classical ssDNA binding protein and instead to harbour a distinct ssDNA binding protein termed ThermoDBP (37).…”