The extremophile Picrophilus torridus carries a DNA adenine methylase M.PtoI that is part of a Type I restriction-modification system

Abstract

DNA methylation events mediated by orphan methyltransferases modulate various cellular processes like replication, repair and transcription. Bacteria and archaea also harbor DNA methyltransferases that are part of restriction-modification systems, which serve to protect the host genome from being cleaved by the cognate restriction enzyme. While DNA methylation has been exhaustively investigated in bacteria it remains poorly understood in archaea. Picrophilus torridus is a euryarchaeon that can thrive under conditions of extremely low pH (0.7), and thus far no reports have been published regarding DNA methylation in this extremophile. This study reports the first experimentation examining DNA methylation in P. torridus. We find the genome to carry methylated adenine (m6A) but not methylated cytosine (m5C) residues. The m6A modification is absent at GATC sites, indicating the absence of an active Dam methylase even though the dam gene has been annotated in the genome sequence. Two other methylases have also been annotated in the P. torridus genome sequence. One of these is a part of a Type I restriction-modification system. Considering that all Type I modification methylases characterized to date target adenine residues, the modification methylase of this Type I system has been examined. The genes encoding the S subunit (that is responsible for DNA recognition) and M subunit (that is responsible for DNA methylation) have been cloned and the recombinant protein purified from E.coli, and regions involved in M-S interactions have been identified. The M.PtoI enzyme harbors all the motifs that typify Type I modification methylases, and displays robust adenine methylation in in vitro assays under a variety of conditions. Interestingly, magnesium is essential for enzyme activity. The enzyme displays substrate inhibition at higher concentrations of AdoMet. Mutational analyses reveal that Motif I plays a role in AdoMet binding, and Motif IV is critical for methylation activity. The data presented here lays the foundation for further research in the area of DNA methylation and restriction-modification research in this most unusual microorganism.

Restriction modification systems in archaea: A panoramic outlook

“…M.PtoI was found to methylate adenine at pH 0.7 and temperature 55–60 °C, reflecting the natural habitat of dry solfataric fields wherein Picrophilus dwells. Notably, this study marks the first comprehensive examination of a methyltransferase enzyme originating from an organism adapted to such extreme conditions [ 43 ].…”

“…OT3, Methanococcus maripaludis and Methanothermococcus jannashii. Interestingly, while Picrophilus torridus harbors a homolog of Dam methylase, it doesn't contain methylated GATC sites in its genome [ 43 ].…”

“…RM genes are found to be tightly linked to each other. For instance, in Picrophilus torridus restriction (PTO0076), modification (PTO0078) and specificity (PTO0077) genes are arranged in the linear order [ 43 ]. This tight linkage ensures the simultaneous loss of RM genes and is particularly critical for their maintenance by the virtue of post segregational killing [ 84 ].…”

Regulatory sequence-based discovery of anti-defense genes in archaeal viruses

“…The study of archaeal defense mechanisms has been more limited, with only surface resistance (Deng et al, 2014;Rowland et al, 2020), argonaute (Lee et al, 2021;Wang et al, 2009;Zander et al, 2017;Zeng et al, 2022), restriction-modification (Gulati et al, 2023;Ouellette et al, 2018;Zatopek et al, 2021) and diverse CRISPR-Cas (Makarova et al, 2020;Shah et al, 2019;Zink et al, 2020) characterized so far. Moreover, despite the near ubiquity of CRISPR-Cas systems in archaea, only four Acrs have been experimentally identified in archaeal viruses, in contrast to more than 100 Acrs identified in bacteriophages (Bondy-Denomy et al, 2018;Lin et al, 2023;Peng et al, 2020).…”