DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome

Abstract

The DNA phosphorothioate (PT) modification existing in many prokaryotes, including bacterial pathogens and commensals, confers multiple characteristics, including restricting gene transfer, influencing the global transcriptional response, and reducing fitness during exposure to chemical mediators of inflammation. While PT-containing bacteria have been investigated in a variety of environments, they have not been studied in the human microbiome. Here, we investigated the distribution of PT-harboring strains and verified their existence in the human microbiome. We found over 2000 PT gene-containing strains distributed in different body sites, especially in the gastrointestinal tract. PT-modifying genes are preferentially distributed within several genera, including Pseudomonas, Clostridioides, and Escherichia, with phylogenic diversities. We also assessed the PT modification patterns and found six new PT-linked dinucleotides (CpsG, CpsT, ApsG, TpsG, GpsC, ApsT) in human fecal DNA. To further investigate the PT in the human gut microbiome, we analyzed the abundance of PT-modifying genes and quantified the PT-linked dinucleotides in the fecal DNA. These results confirmed that human microbiome is a rich reservoir for PT-containing microbes and contains a wide variety of PT modification patterns.

Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification

“…Intriguingly, we observe that nucleic acid binding by SAMHD1 is enhanced by phosphorothioate linkages of Rp stereochemistry located 3′ to guanine nucleotides in nucleic acids. The phosphorothioation pattern recognized by SAMHD1, GpsN, matches modifications generated by the Dnd gene cluster in the enzymatic DNA phosphorothioation in bacteria and archea 50 – 52 that are widespread in the human microbiome 53 and the GpsG linkages recently detected in human RNA 54 , which suggests that the immune function of SAMHD1 in humans may have something in common with the unusual phosphorothioation-dependent mechanism of antiviral defense in prokaryotes.…”

“…The exact functional impact of these putative ligands is difficult to predict from our data with short GpsN-containing oligos, because the physiological nucleic acid-binding partners of SAMHD1 may have multiple binding sites and may engage additional interaction surfaces as suggested by the earlier cross-linking studies. Identification of specific nucleic acid modulators of SAMHD1 is therefore of great interest and will also reveal whether the GpsN modification is the physiologically relevant determinant of SAMHD1 specificity 53 , 54 (see below) or whether it simply mimics some other structural feature present in these ligands.…”

“…Finally, two recent publications raise an intriguing possibility that GpsN recognition by SAMHD1 described here contributes to its immune function in humans. First, the GpsG modification has been detected in human RNA 54 and, second, DNA phosphorothioation has been found widespread in the human microbiome 53 .…”

Strategies to Avoid Artifacts in Mass Spectrometry‐Based Epitranscriptome Analyses

“…In other bacteria, PTs are involved in an epigenetic interplay with the 6‐methyladenosine introduced by the DNA methyltransferase Dam [11] . The genomic insertion of PT is beneficial to microorganisms and thus a wide distribution of PT in the human microbiome is not surprising [12] …”

Strategien zur Vermeidung von Artefakten in der massenspektrometrischen Epitranskriptomanalytik

“…ganismen von Vorteil und von daher ist eine weite Verbreitung von PT im menschlichen Mikrobiom nicht überraschend. [12] Die Entdeckung der letzten RNA-Modifikationen, einschließlich PT in RNA, wurde durch detektionsempfindliche MS-Analyse ermçglicht. Obwohl dieser Ansatz verhältnismäßig einfach ist und regelmäßig über Fortschritte berichtet wird, [13] bietet die enorme Sensitivitätd er modernen MS Instrumente einige Fallstricke,w elche überwunden werden müssen, um neuartige Strukturen in Nukleinsäuren aufzuklären.…”