A novel DNA modification by sulphur

Abstract

SummaryStreptomyces lividans has a novel DNA modification, which sensitises its DNA to degradation during electrophoresis (the Dnd phenotype). The entire gene cluster ( dnd ) involved in this modification was localized on an 8 kb DNA fragment and was expressed in a S. lividans deletion mutant ( dnd ) and in several heterologous hosts. Disruption of the dnd locus abolishes the Dnd phenotype, and gain of the dnd locus conferred the Dnd phenotype respectively. Extensive analysis of the dnd gene cluster revealed five open reading frames, whose hypothetic functions suggested an incorporation of sulphur or a sulphurcontaining substance into S. lividans genome, yet in an unknown manner. The Dnd phenotype was also discovered to exist in DNA of widespread bacterial species of variable origin and diverse habitat. Similarly organized gene clusters were found in several bacterial genomes representing different genera and in eDNA of marine organisms, suggesting such modification as a widespread phenomenon. A coincidence between the Dnd phenotype and DNA modification by sulphur was demonstrated to occur in several representative bacterial genomes by the in vivo 35 S-labelling experiments.

Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification

“…In addition, we measured the interaction of DndE B7A-N110 with PAPS, ATP or ADP using the isothermal titration calorimetry assay (Supplementary information, Figure S3). In contrast with the early prediction [10][11]13], DndE B7A-N110 showed no binding affinities to any of them (Supplementary information, Figure S3), consistent with the fact that the DndE B7A-N110 structure includes neither a 5′-PSB motif nor a 3′-PB motif for PAPS and PAP binding [14], nor a glycine-rich P loop for ATP or ADP phosphate binding as seen in the NCAIR synthetase [15,16]. Taken together, the crystal structure of DndE B7A-N110 reveals that DndE is neither a sulfotransferase nor a NCAIR synthase analogue, but a possible nicked ds-DNA binding protein with a previously unrecognized fold.…”

“…DndD, known as SpfD in Pseudomonas fluorescens Pf0-1, has ATPase activity possibly related to DNA structure alteration or nicking during PT incorporation [5,12]. Sequence identity (46%) and similarity (61%) to phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) from Anabaena variabilis [11] suggest that DndE could be a NCAIR synthase analogue [13]. However, DndE may also act as a sulfotransferase due to a specific PAPS binding sequence AAVGK-TLLIHLHR contained in the C-terminus of DndE from Streptomyces lividans (DndE strep ) [10].…”

“…DndA works as a cysteine desulfurase and assembles DndC as a 4Fe-4S cluster protein [7]. DndC possesses ATP pyrophosphatase activity [8,9] and is predicted to have 3′-phosphoadenosine-5′-phosphosulfate (PAPS) reductase activity, whereas DndB has homology to a group of transcriptional regulators [10,11]. DndD, known as SpfD in Pseudomonas fluorescens Pf0-1, has ATPase activity possibly related to DNA structure alteration or nicking during PT incorporation [5,12].…”

Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes

“…The PT system is more complicated than methylation and entails sequence-selective and R Pstereo-specific incorporation of sulfur by five Dnd proteins (12,13). Since the original report in Streptomyces lividans, the five-member dndABCDE gene cluster has been found in diverse, taxonomically unrelated bacteria and archaea (14,15).…”

The development of biochemistry and molecular biology in China

“…(19). The entire dnd gene cluster involved in this modification was localized on an 8 kb DNA fragment.…”