The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes

Abstract

Phosphorothioate (PT) modification by the dnd gene cluster is the first identified DNA backbone modification and constitute an epigenetic system with multiple functions, including antioxidant ability, restriction modification, and virus resistance. Despite these advantages for hosting dnd systems, they are surprisingly distributed sporadically among contemporary prokaryotic genomes. To address this ecological paradox, we systematically investigate the occurrence and phylogeny of dnd systems, and they are suggested to have originated in ancient Cyanobacteria after the Great Oxygenation Event. Interestingly, the occurrence of dnd systems and prophages is significantly negatively correlated. Further, we experimentally confirm that PT modification activates the filamentous phage SW1 by altering the binding affinity of repressor and the transcription level of its encoding gene. Competition assays, concurrent epigenomic and transcriptomic sequencing subsequently show that PT modification affects the expression of a variety of metabolic genes, which reduces the competitive fitness of the marine bacterium Shewanella piezotolerans WP3. Our findings strongly suggest that a series of negative effects on microorganisms caused by dnd systems limit horizontal gene transfer, thus leading to their sporadic distribution. Overall, our study reveals putative evolutionary scenario of the dnd system and provides novel insights into the physiological and ecological influences of PT modification.

The red thread between methylation and mutation in bacterial antibiotic resistance: How third-generation sequencing can help to unravel this relationship

“…Phosphorothioation (PT) is a chemical modification of the DNA that occurs not on bases, like methylation, but on DNA backbone: it is the substitution of a non-bridging oxygen on the phosphodiester bond with a sulfur atom (Wang et al, 2007 ). This oxygen–sulfur exchange is catalyzed by the cooperation of the products of the dnd gene cluster ( dnd ABCDE) that involve a cysteine desulfurase (DndA), an iron–sulfur cluster protein (DndC), a protein with ATPase activity (DndD), a protein that binds nicked dsDNA (DndE) and DndB, that seems to be not essential for PT modification (Jian et al, 2021 ). This modification occurs on 5′GAAT3′/5′GTTC3′/5′GATC3′ and similar motifs (Wu et al, 2020 ).…”

“…This modification occurs on 5′GAAT3′/5′GTTC3′/5′GATC3′ and similar motifs (Wu et al, 2020 ). Phosphorothioation is linked with some important functions: (i) it confers protection to DNA against oxidative damage; (ii) it is often coupled with dnd FGHI genes, which cleave unmodified DNA motifs (likewise RM systems) (Tong et al, 2018 ); (iii) influence or inhibit restriction enzymes that cleave close to modified sites; (iv) it changes the affinity of regulatory proteins affecting gene expression regulation (Jian et al, 2021 ). Interestingly, both PT modification and DNA methylation systems can recognize the 5′-GATC-3′ motif, and thus a hybrid 5′-GPS6mATC-3′ can be produced (Chen et al, 2017 ).…”

Involvement of the DNA Phosphorothioation System in TorR Binding and Anaerobic TMAO Respiration in Salmonella enterica

“…According to one recent report, PT modification of the fpsR - fpsA intergenic region increases the binding of the phage-borne repressor FpsR and decreases the amount of FpsR protein, thereby relieving the repression of phage gene transcription ( 45 ). In addition, several observations support the capacity of PT to interfere with protein–DNA interactions: (i) the presence of PT in DNA templates is capable of altering transcription by RNA polymerase in vitro ( 37 ) and (ii) PT modification at 5′-GATC-3′ (generating 5′-G PS ATC-3′) slows Dam-catalyzed methylation at this site ( 44 ).…”

Modification-Dependent Restriction Endonuclease-based sequencing method (EcoWI-seq) maps the genome-wide landscape of phosphorothioate modification at base resolution

“…Furthermore DndA protein can be functionally substituted by NifS-like cysteine desulfurase IscS in some bacterial strains including E.coli K12 (5). Possible biological functions of PT modifications on DNA are considered as: 1) epigenetic marker to regulate gene expression (6)(7)(8); 2) providing a resistance mechanism to restriction systems or exonuclease degradation (9,10); 3) an antioxidant to resist intracellular oxidative stress (11)(12)(13); 4) a marker for self vs non-self (here PT-modified DNA as "foreign" and subject to SBD-HNH restriction) (14,15). So far, a limited number of sequence contexts such as GpsAAC and its reverse complement GpsTTC (GpsAAC/GpsTTC), GpsGCC/GpsGCC, GpsATC/GpsATC, or CpsCA/TGG (3,4) have been found to be PT modified.…”