Unique Features and Anti-microbial Targeting of Folate- and Flavin-Dependent Methyltransferases Required for Accurate Maintenance of Genetic Information.

Hannu Myllykallio,Pierre Sournia,Ursula Liebl,Alice Heliou

doi:10.3389/fmicb.2018.00918

Hannu Myllykallio, Pierre Sournia + Show 2 more

Open Access

https://doi.org/10.3389/fmicb.2018.00918

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Abstract

Comparative genome analyses have led to the discovery and characterization of novel flavin- and folate-dependent methyltransferases that mainly function in DNA precursor synthesis and post-transcriptional RNA modification by forming (ribo) thymidylate and its derivatives. Here we discuss the recent literature on the novel mechanistic features of these enzymes sometimes referred to as “uracil methyltransferases,” albeit we prefer to refer to them as (ribo) thymidylate synthases. These enzyme families attest to the convergent evolution of nucleic acid methylation. Special focus is given to describing the unique characteristics of these flavin- and folate-dependent enzymes that have emerged as new models for studying the non-canonical roles of reduced flavin co-factors (FADH2) in relaying carbon atoms between enzyme substrates. This ancient enzymatic methylation mechanism with a very wide phylogenetic distribution may be more commonly used for biological methylation reactions than previously anticipated. This notion is exemplified by the recent discovery of additional substrates for these enzymes. Moreover, similar reaction mechanisms can be reversed by demethylases, which remove methyl groups e.g., from human histones. Future work is now required to address whether the use of different methyl donors facilitates the regulation of distinct methylation reactions in the cell. It will also be of great interest to address whether the low activity flavin-dependent thymidylate synthases ThyX represent ancestral enzymes that were eventually replaced by the more active thymidylate synthases of the ThyA family to facilitate the maintenance of larger genomes in fast-growing microbes. Moreover, we discuss the recent efforts from several laboratories to identify selective anti-microbial compounds that target flavin-dependent thymidylate synthase ThyX. Altogether we underline how the discovery of the alternative flavoproteins required for methylation of DNA and/or RNA nucleotides, in addition to providing novel targets for antibiotics, has provided new insight into microbial physiology and virulence.

Highlights

Methylation at the C5 position of the uracil of nucleotides occurs at high frequency per cell division during DNA biosynthesis, and during post-transcriptional RNA modification reactions
AdoMet_MTase t-RNA U54 SAMc Activated methyl groupd Not required aPercentage indicating the relative presence of the different enzymes in 711 genomes of the COG database; bCatalytic properties of TrmFO and MnmG/GidA are likely very similar, as suggested by the identification of the catalytically essential conserved cysteine residues participating in substrate activation (Osawa et al, 2009), during synthesis of 5-carboxymethylaminomethyluridine at the tRNA anticodon; cSAM dependent methyltransferases are involved in cytosine methylation participating in chromatin regulation, gene silencing and protection against DNA cleavage by restriction enzymes; dThe charged methylsulfonium center of SAM activates the methyl group, thermodynamically favoring its direct transfer; eBoth, NADH and nicotinamide adenine dinucleotide phosphate (NADPH) can reduce ThyX- and TrmFO-bound FAD co-factor (Myllykallio et al, 2002; Yamagami et al, 2012), see text for details
The optical absorption spectrum of this adduct has a broad maximum at 360 nm, which is fully consistent with an alkylated FAD that is covalently bound to the enzyme via a cysteine residue (Cys51 in Thermus thermophilus TrmFO, Figure 2B), as was demonstrated via mutagenesis studies (Hamdane et al, 2011a). These results indicate that the catalytic cysteine is required for formation of a reaction intermediate, where CH2 is transferred to tRNA using FAD as a methylating agent

Summary

Introduction

Methylation at the C5 position of the uracil of nucleotides occurs at high frequency per cell division during DNA biosynthesis, and during post-transcriptional RNA modification reactions (see below). To ThyX proteins, the TrmFO (previously Gid) flavoproteins (E.C.2.1.1.74) use CH2H4folate as donor of a carbon group that is transferred to the uracil ring.

Results

Conclusion