Structural characterization of two tandemly arranged DNA methyltransferase genes from Neisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P

Beyond Restriction Modification: Epigenomic Roles of DNA Methylation in Prokaryotes

The amount of bacterial and archaeal genome sequence and methylome data has greatly increased over the last decade, enabling new insights into the functional roles of DNA methylation in these organisms. Methyltransferases (MTases), the enzymes responsible for DNA methylation, are exchanged between prokaryotes through horizontal gene transfer and can function either as part of restriction-modification systems or in apparent isolation as single (orphan) genes. The patterns of DNA methylation they confer on the host chromosome can have significant effects on gene expression, DNA replication, and other cellular processes. Some processes require very stable patterns of methylation, resulting in conservation of persistent MTases in a particular lineage. Other processes require patterns that are more dynamic yet more predictable than what is afforded by horizontal gene transfer and gene loss, resulting in phase-variable or recombination-driven MTase alleles. In this review, we discuss what is currently known about the functions of DNA methylation in prokaryotes in light of these evolutionary patterns. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Genome sequence of the temperate bacteriophage PH10 from Streptococcus oralis

Exponential growing cultures of Streptococcus oralis strain OMZ 1038, isolated from human supragingival dental plaque, were found to release a bacteriophage (designated PH10) upon treatment with mitomycin C. The complete genome sequence of phage PH10 was determined. The genome was 31276 bp in size and contained 54 open reading frames. The module encoding structural proteins was highly similar to that of Streptococcus pneumoniae prophage PhiSpn_3. The most abundant phage structural protein was encoded by ORF35 and was likely processed by proteolytic cleavage. The putative endolysin from PH10, which contained a muramidase domain and a choline-binding domain, was purified and shown to have lytic activity with S. oralis, S. pneumoniae and Streptococcus mitis, but not with other streptococcal species.

Recent trends on the molecular biology of pneumococcal capsules, lytic enzymes, and bacteriophage

Streptococcus pneumoniae has re-emerged as a major cause of morbidity and mortality throughout the world and its continuous increase in antimicrobial resistance is rapidly becoming a leading cause of concern for public health. This review is focussed on the analysis of recent insights on the study of capsular polysaccharide biosynthesis, and cell wall (murein) hydrolases, two fundamental pneumococcal virulence factors. Besides, we have also re-evaluated the molecular biology of the pneumococcal phage, their possible role in pathogenicity and in the shaping of natural populations of S. pneumoniae. Precise knowledge of the topics reviewed here should facilitate the rationale to move towards the design of alternative ways to combat pneumococcal disease.

VO1, a temperate bacteriophage of the type 19A multiresistant epidemic 8249 strain of Streptococcus pneumoniae: analysis of variability of lytic and putative C5 methyltransferase genes

A temperate bacteriophage (VO1) has been isolated from the Streptococcus pneumoniae type 19F multiresistant epidemic 8249 strain (South African strain). Structural analysis of the specific integration site, protein composition, restriction patterns, and molecular dissection of the lytic system of this phage revealed high sequence similarity with MM1, a temperate phage from the Spain23F-1 strain of pneumococcus, another multiresistant epidemic clone. The different pneumococcal strains sequenced so far exhibit an identical and single attB located in the same site of the genome. Remarkably, the LytA amidase coded by VO1 showed clear differences with that of the host bacterium in contrast with the situation previously documented for bacterial- and phage-coded amidases of pneumococcus. In addition, a new gene (orfmet) putatively coding for a C5 methyltransferase has been identified. A noticeable variability affecting the presence (or absence) of this supernumerary gene(s) in the same region of the genomes of three otherwise highly similar phages (i.e., VO1, MM1, and HB-3) suggests frequent recombinational events leading to introduce variability in this genome region. The peculiarities of genes like lytA and orfmet in VO1 provide interesting insights on mechanisms of horizontal transfer and lysogenic state co-evolution.

Sequence permutations in the molecular evolution of DNA methyltransferases

BACKGROUND

DNA methyltransferases (MTases), unlike MTases acting on other substrates, exhibit sequence permutation. Based on the sequential order of the cofactor-binding subdomain, the catalytic subdomain, and the target recognition domain (TRD), several classes of permutants have been proposed. The majority of known DNA MTases fall into the alpha, beta, and gamma classes. There is only one member of the zeta class known and no members of the delta and epsilon classes have been identified to date. Two mechanisms of permutation have been proposed: one involving gene duplication and in-frame fusion, and the other involving inter- and intragenic shuffling of gene segments.

RESULTS

Two novel cases of sequence permutation in DNA MTases implicated in restriction-modification systems have been identified, which suggest that members of the delta and zeta classes (M.MwoI and M.TvoORF1413P, respectively) evolved from beta-class MTases. This is the first identification of the delta-class MTase and the second known zeta-class MTase (the first zeta-class member among DNA:m4C and m6A-MTases).

CONCLUSIONS

Fragmentation of a DNA MTase gene may result from attack of nucleases, for instance when the RM system invades a new cell. Its reassembly into a functional form, the order of motifs notwithstanding, may be strongly selected for, if the cognate ENase gene remains active and poses a threat to the host's chromosome. The "cut-and-paste" mechanism is proposed for beta-delta permutation, which is non-circular and involves relocation of one segment of a gene. The circular beta-zeta permutation may be explained both by gene duplication or shuffling of gene fragments. These two mechanisms are not mutually exclusive and probably both played a role in the evolution of permuted DNA MTases.

Homology modelling of the DNA 5mC methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases?

This work presents a full tertiary model of the M.BssHII methyltransferase (MTase) complexed with substrate DNA and cofactor S-adenosyl-L-methionine, built by homology modelling based on previously solved complete structures of DNA MTases M.HaeIII and M. HhaI. M.BssHII and the template proteins show high sequence similarity, which indicates that they are evolutionary related. However, they are topologically different: M.BssHII is a circularly permuted variant of template MTases (Xu et al. Nucleic Acids Res 1997;25:3991). The model developed in this work will be a good starting point and valuable help in designing mutagenesis experiments to better understand the biological function of methyltransferases and the process of domain swapping.