Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria

Advances in Diversity, Evolutionary Dynamics and Biotechnological Potential of Restriction-Modification Systems

Restriction-modification systems (RMS) are ubiquitous in prokaryotes and serve as primitive immune-like mechanisms that safeguard microbial genomes against foreign genetic elements. Beyond their well-known role in sequence-specific defense, RMS also contribute significantly to genomic stability, drive evolutionary processes, and mitigate the deleterious effects of mutations. This review provides a comprehensive synthesis of current insights into RMS, emphasizing their structural and functional diversity, ecological and evolutionary roles, and expanding applications in biotechnology. By integrating recent advances with an analysis of persisting challenges, we highlight the critical contributions of RMS to both fundamental microbiology and practical applications in biomedicine and industrial biotechnology. Furthermore, we discuss emerging research directions in RMS, particularly in light of novel technologies and the increasing importance of microbial genetics in addressing global health and environmental issues.

Epigenetic background of lineage-specific gene expression landscapes of four Staphylococcus aureus hospital isolates

Bacteria with similar genomes can exhibit different phenotypes due to alternative gene expression patterns. In this study, we analysed four antibiotic-resistant Staphylococcus aureus hospital isolates using transcriptomics, PacBio genome sequencing, and methylomics analyses. Transcriptomic data were obtained from cultures exposed to gentamicin, the iodine-alanine complex CC-196, and their combination. We observed strain-specific expression patterns of core and accessory genes that remained stable under antimicrobial stress - a phenomenon we term the Clonal Gene Expression Stability (CGES) that is the main discovery of the paper. An involvement of epigenetic mechanisms in stabilization of the CGES was hypothesized and statistically verified. Canonical methylation patterns controlled by type I restriction-modification systems accounted for ~ 10% of epigenetically modified adenine residues, whereas multiple non-canonically modified adenines were distributed sporadically due to imperfect DNA targeting by methyltransferases. Protein-coding sequences were characterized by a significantly lower frequency of modified nucleotides. Epigenetic modifications near transcription start codons showed a statistically significant negative association with gene expression levels. While the role of epigenetic modifications in gene regulation remains debatable, variations in non-canonical modification patterns may serve as markers of CGES.

Comprehensive comparison of the third-generation sequencing tools for bacterial 6mA profiling

DNA N6-methyladenine (6mA) serves as an intrinsic and principal epigenetic marker in prokaryotes, impacting various biological processes. To date, limited advanced sequencing technologies and analyzing tools are available for bacterial DNA 6mA. Here, we evaluate eight tools designed for the 6mA identification or de novo methylation detection. This assessment includes Nanopore (R9 and R10), Single-Molecule Real-Time (SMRT) Sequencing, and cross-reference with 6mA-IP-seq and DR-6mA-seq. Our multi-dimensional evaluation report encompasses motif discovery, site-level accuracy, single-molecule accuracy, and outlier detection across six bacteria strains. While most tools correctly identify motifs, their performance varies at single-base resolution, with SMRT and Dorado consistently delivering strong performance. Our study indicates that existing tools cannot accurately detect low-abundance methylation sites. Additionally, we introduce an optimized method for advancing 6mA prediction, which substantially improves the detection performance of Dorado. Overall, our study provides a robust and detailed examination of computational tools for bacterial 6mA profiling, highlighting insights for further tool enhancement and epigenetic research.

Decoding bacterial methylomes in four public health-relevant microbial species: nanopore sequencing enables reproducible analysis of DNA modifications

Investigating bacterial methylation profiles provides essential complementary information to the native DNA sequence, significantly extending our understanding of how DNA modifications influence virulence, antibiotic resistance, and the ability of bacteria to evade the immune system. Recent advancements in real-time Nanopore sequencing and basecalling algorithms have enabled the direct detection of modified bases from raw signal data, eliminating the need for bisulfite treatment of DNA. However, decoding methylation signals remains challenging due to rapid technological and methodological progress. In this study, we focus on public health-relevant bacterial strains to analyze their methylation profiles and identify methylation motifs. Our dataset includes samples from Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecium, and Klebsiella pneumoniae, sequenced on the Nanopore GridION platform using the latest flow cell chemistry (R10.4.1) and modification basecalling models (Dorado basecalling SUP model v5). We investigated distinct methylation patterns within and between species, focusing on heavily modified genes or genomic regions. Our results reveal distinct species-specific methylation profiles, with each strain exhibiting unique modification patterns. We developed a modular pipeline using Nextflow and the Nanopore Modkit tool to streamline the detection of methylated motifs. We compared the results with outputs from MicrobeMod, a recent toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing. Our pipeline is publicly available for further use (github.com/rki-mf1/ont-methylation). We identified known methylation motifs already described in the literature and novel de novo motifs, providing deeper insights into the diversity of bacterial DNA modifications. Furthermore, we identified genomic regions that are extensively methylated, which could have implications for bacterial behavior and pathogenicity. We also assess improvements in basecalling accuracy, specifically how methylated bases can influence neighboring basecalls. Recent advances in basecalling models, particularly v5 models as part of Dorado, have reduced these issues, improving the reliability of methylation detection in bacterial genomes. In conclusion, our study highlights the potential of current nanopore sequencing tools for detecting DNA modifications in prokaryotes. By making our pipeline and results publicly available, we facilitate further research into bacterial DNA modifications and their role in microbial pathogenesis.

Unveiling the role of phages in shaping the periodontal microbial ecosystem

The oral microbiome comprises various species and plays a crucial role in maintaining the oral ecosystem and host health. Phages are an important component of the periodontal microbiome, yet our understanding of periodontal phages remains limited. Here, we investigated oral periodontal phages using various advanced bioinformatics tools based on genomes of key periodontitis pathogens. Prophages were found to encode various auxiliary genes that potentially enhance host survival and pathogenicity, including genes involved in carbohydrate metabolism, antibiotic resistance, and immune modulation. We observed cross-species transmission among prophages with a complex network of phage-bacteria interactions. Our findings suggest that prophages play a crucial role in shaping the periodontal microbial ecosystem, influencing microbial community dynamics and the progression of periodontitis.IMPORTANCEIn the context of periodontitis, the ecological dynamics of the microbiome are largely driven by interactions between bacteria and their phages. While the impact of prophages on regulating oral pathogens has been increasingly recognized, their role in modulating periodontal disease remains underexplored. This study reveals that prophages within key periodontitis pathogens contribute significantly to virulence factor dissemination, antibiotic resistance, and host metabolism. By influencing the metabolic capabilities and survival strategies of their bacterial hosts, prophages may act as critical regulators of microbial communities in the oral cavity. Understanding these prophage-mediated interactions is essential not only for unraveling the mechanisms of periodontal disease progression but also for developing innovative therapeutic approaches that target the microbial ecosystem at the genetic level. These insights emphasize the need for more comprehensive studies on the ecological risks posed by prophages in shaping microbial pathogenicity and resistance.

Decoding Adenine DNA Methylation Effects in Streptococcus Mutans: Insights Into Self-DNA Protection and Autoaggregation

Streptococcus mutans, a key player in dental caries, faces multiple environmental challenges within the oral cavity, including oxidative stress, nutrient scarcity, and acidic pH. To survive and thrive, S. mutans has evolved intricate mechanisms, including the CSP-ComDE quorum sensing system, which coordinates responses to environmental cues. The CSP-ComDE system enables S. mutans to communicate with neighboring cells via its CSP pheromone. Under stress conditions, the CSP pheromone production increases, triggering a cascade of events. Notably, our research demonstrated that the CSP pheromone activates the expression of a Type II restriction-modification (R-M) system. Type II R-M systems are well-known tools in molecular biology and genetic engineering and consist of two distinct enzymes: a restriction enzyme and a methyltransferase. An increasing number of studies have revealed that bacterial adenine methylation (Dam methylation) has a broader role beyond mere DNA protection. In fact, the marks introduced into the DNA provide signals for a variety of physiological processes. Our results highlight a conserved chromosomal locus in S. mutans encoding the DpnII R-M system. DpnII R-M methylates DNA at 5'-GATC target sites within the S. mutans genome and cleaves unmarked DNA. Furthermore, our findings suggest that Dam methylation significantly impacts foreign DNA acquisition via natural transformation and modulates mutanobactin expression-a secondary metabolite linked to oxidative stress tolerance. Collectively, our findings suggest that Dam methylation bridges epigenetics and bacterial fitness, potentially opening new avenues in bacterial epigenetics. As we explore this intricate biological process, we may uncover novel therapeutic strategies to combat bacterial infections.

Non-enzymatic methylcyclization of alkenes

Methyltransferases are a broad class of enzymes that catalyse the transfer of methyl groups onto a wide variety of substrates and functionalities. In their most striking variant, bifunctional methyltransferase-cyclases both transfer a methyl group onto alkenes and induce cyclization (methylcyclization). Although recent years have seen substantial advances in the methylation of alkenes, especially hydromethylation, the reactivity demonstrated by bifunctional methyltransferase-cyclases in nature has yet to be developed into a synthetically viable method. Here we report a silver(I)-mediated electrophilic methylcyclization that rivals selectivities found in enzymes while not being limited by their inherent substrate specificity. Our method benefits from the use of commercial reagents, is applicable to a wide range of substrates, including heterocycles, and affords unique structures that are difficult to access via conventional synthetic methods. Furthermore, computational studies have been utilized to unravel the underlying mechanism and ultimately support a stepwise cationic reaction pathway with a rate-limiting methyltransfer.

Bacterial DNA methylases as novel molecular and synthetic biology tools: recent developments

Bacterial DNA methylases are a diverse group of enzymes which have been pivotal in the development of technologies with applications including genetic engineering, bacteriology, biotechnology and agriculture. This review describes bacterial DNA methylase types, the main technologies for targeted methylation or demethylation and the recent roles of these enzymes in molecular and synthetic biology. Bacterial methylases can be exocyclic or endocyclic and can exist as orphan enzymes or as a part of the restriction-modifications (R-M) systems. As a group, they display a rich diversity of sequence-specificity. Additional technologies for targeting methylation involve using fusion proteins combining a methylase and a DNA-binding protein (DNBP) such as a zinc-finger (ZF), transcription activator-like effector (TALE) or CRISPR/dCas9. Bacterial methylases have contributed significantly to the creation of novel DNA assembly techniques, to the improvement of bacterial transformation and to crop plant engineering. Future studies to define the characteristics of more bacterial methylases have potential to identify new tools of value in synthetic and molecular biology and with widespread applications. KEY POINTS: • Bacterial methylases can be used to direct methylation to specific sequences in target DNA • DNA methylation using bacterial methylases has been applied to improve DNA assembly and to increase the efficiency of bacterial transformation • Site-selective methylation using bacterial methylases can alter plant gene expression and phenotype.

NK Cell-Microbiota Interaction Biomarker Strategy: Advancing Prostate Cancer Management

The role of natural killer (NK) cells in the management of prostate cancer (PCa) remains incompletely understood. Some have proposed that measuring NK cells in blood samples could serve as a reliable, minimally invasive tool for screening, assessing treatment effects, and predicting survival outcomes in PCa patients. However, the significance of different NK cell phenotypes remains unclear. Given the interplay between NK cells and the microbiome, we hypothesize that a combined signature of NK cell phenotypes derived from blood, along with microbiome profiles from oral, urine, and stool samples, could serve as a surrogate marker for NK cell activity in tumor and its microenvironment. Such an approach provides a practical alternative to invasive tumor biopsies by enabling the indirect assessment of NK cell function in tumors. Additionally, profiling NK cell phenotypes and their interactions with the microbiota has the potential to enhance prognostic accuracy and guide the development of personalized therapeutic strategies. Prospective studies are needed to validate the utility of NK cell and microbiome assays in personalized PCa management, with a focus on minimally invasive procedures and predictive signatures for treatment outcomes.

Differential responses of Bradyrhizobium sp. SUTN9-2 to plant extracts and implications for endophytic interactions within different host plants

Bradyrhizobium sp. strain SUTN9-2 demonstrates cell enlargement, increased DNA content, and efficient nitrogen fixation in response to rice (Oryza sativa) extract. This response is attributed to the interaction between the plant's cationic antimicrobial peptides (CAMPs) and the Bradyrhizobium BacA-like transporter (BclA), similar to bacteroid in legume nodules. The present study reveals that SUTN9-2 can also establish functional endophytic interactions with chili (Capsicum annuum) and tomato (Solanum lycopersicum) plants. When exposed to extracts from chili and tomato, SUTN9-2 exhibits cell elongation, polyploidy, and reduced cell viability, with the effects being less pronounced for tomato extract. Transcriptomic and cytological analyses revealed that genes associated with CAMP resistance, nitrogen metabolism, nitrogen fixation, defense responses, and secretion systems were upregulated, while genes related to the cell cycle and certain CAMP-resistance mechanisms were downregulated, particularly in response to chili extract. This study suggests that SUTN9-2 likely evolves resistance mechanisms against CAMPs found in rice, chili, and tomato plants through mechanisms involving the protease-chaperone DegP, AcrAB-TolC multidrug efflux pumps, and polysaccharides. These mechanisms facilitate efflux, degradation, and the formation of protective barriers to resist CAMPs. Such adaptations enable SUTN9-2 to persist and colonize host plants despite antimicrobial pressures, influencing its viability, cell differentiation, and nitrogen fixation during endophytic interactions with various plant hosts.

The Complex Epigenetic Panorama in the Multipartite Genome of the Nitrogen-Fixing Bacterium Sinorhizobium meliloti

In prokaryotes, DNA methylation plays roles in DNA repair, gene expression, cell cycle progression, and immune recognition of foreign DNA. Genome-wide methylation patterns can vary between strains, influencing phenotype, and gene transfer. However, broader evolutionary studies on bacterial epigenomic variation remain limited. In this study, we conducted an epigenomic analysis using single-molecule real-time sequencing on 21 strains of Sinorhizobium meliloti, a facultative plant nitrogen-fixing alphaproteobacterium. This species is notable for its multipartite genome structure, consisting of a chromosome, chromid, and megaplasmid, leading to significant genomic and phenotypic diversity. We identified 16 palindromic and nonpalindromic methylated DNA motifs, including N4-methylcytosine and N6-methyladenine modifications, and analyzed their associated methyltransferases. Some motifs were methylated across all strains, forming a core set of epigenomic signatures, while others exhibited variable methylation frequencies, indicating a dispensable (shell) epigenome. Additionally, we observed differences in methylation frequency between replicons and within coding sequences versus regulatory regions, suggesting that methylation patterns may reflect multipartite genome evolution and influence gene regulation. Overall, our findings reveal extensive epigenomic diversity in S. meliloti, with complex epigenomic signatures varying across replicons and genomic regions. These results enhance our understanding of multipartite genome evolution and highlight the potential role of epigenomic diversity in phenotypic variation.

Antibacterial Effects of Polycephalomyces nipponicus (Ascomycota) Mycelial Extract on Salmonella enterica Serovar Typhi

The rise of antibiotic-resistant bacteria, particularly Salmonella enterica subsp. enterica serovar Typhi (S. Typhi), poses a significant challenge to global public health. This study investigates the antibacterial potential of mycelial extract from the medicinal fungus Polycephalomyces nipponicus strain Cod-MK1201 against S. Typhi strain DMST 16122. The extract demonstrated significant inhibitory effects, with minimum inhibitory concentration and minimum bactericidal concentration values of 3.12 mg/mL and 6.25 mg/mL, respectively. Scanning and transmission electron microscopy revealed dose-dependent severe morphological damage to S. Typhi cells, including cell wall disruption, cytoplasmic leakage, and structural deformation, indicating the extract's ability to target multiple cellular structures. Additionally, proteomic analysis showed significant alterations in the bacterial proteome, with downregulation of key proteins involved in metabolism, stress response, and virulence, and upregulation of proteins related to oxidative stress response and the stringent survival pathway. These findings demonstrate the multifaceted antimicrobial mechanisms of P. nipponicus mycelial extract, indicating its potential as a natural resource for developing novel therapeutic agents to treat S. Typhi infections. This highlights its promise as a candidate for reducing antibiotic dependency and addressing the growing challenge of antimicrobial resistance.

Distribution of mercury and methylmercury in ice-water-sediments in lakes during the freezing period under the influence of ice cover

The presence of lake ice cover alters the subglacial water environment, thereby influencing the migration and transformation of mercury (Hg) and methylmercury (MeHg) within the ice-water-sediment media of lakes. This study investigated the occurrence characteristics of mercury and methylmercury in various environmental compartments within lakes located at high latitudes in cold regions during the freezing period. To this end, Wuliangsuhai Lake, the largest freshwater lake situated at 40°N in China, was selected as the study site. The contents of mercury and methylmercury in lake ice were determined for the first time. The percentage of methylmercury (MeHg%) and ice-water partition coefficient were analyzed. The pollution situation and health risk were evaluated by single factor pollution index. The results show that the ice body and water body of Wuliangsuhai are not polluted by mercury and methylmercury, but some sampling points in the sediment are slightly polluted. The mercury content in sediment is negatively correlated with the ice thickness, and the methylmercury content in water is positively correlated with the methylmercury content in sediment, but negatively correlated with the ice thickness. The migration ability of methylmercury in ice-water system is stronger than that of mercury. The MeHg% of water in ice period is higher than that in non-freezing period, which is different from other lakes without ice sheet. The results show that in the dynamic equilibrium of methylation and demethylation in the high-latitude lake water, the methylation is higher in the ice period than in the non-freezing period due to the influence of light intensity, while the mercury in the non-freezing period is more susceptible to the demethylation.

Epigenetic Mechanisms in Aging: Extrinsic Factors and Gut Microbiome

BACKGROUND/OBJECTIVES

Aging is a natural physiological process involving biological and genetic pathways. Growing evidence suggests that alterations in the epigenome during aging result in transcriptional changes, which play a significant role in the onset of age-related diseases, including cancer, cardiovascular disease, diabetes, and neurodegenerative disorders. For this reason, the epigenetic alterations in aging and age-related diseases have been reviewed, and the major extrinsic factors influencing these epigenetic alterations have been identified. In addition, the role of the gut microbiome and its metabolites as epigenetic modifiers has been addressed.

RESULTS

Long-term exposure to extrinsic factors such as air pollution, diet, drug use, environmental chemicals, microbial infections, physical activity, radiation, and stress provoke epigenetic changes in the host through several endocrine and immune pathways, potentially accelerating the aging process. Diverse studies have reported that the gut microbiome plays a critical role in regulating brain cell functions through DNA methylation and histone modifications. The interaction between genes and the gut microbiome serves as a source of adaptive variation, contributing to phenotypic plasticity. However, the molecular mechanisms and signaling pathways driving this process are still not fully understood.

CONCLUSIONS

Extrinsic factors are potential inducers of epigenetic alterations, which may have important implications for longevity. The gut microbiome serves as an epigenetic effector influencing host gene expression through histone and DNA modifications, while bidirectional interactions with the host and the underexplored roles of microbial metabolites and non-bacterial microorganisms such as fungi and viruses highlight the need for further research.

Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors

Our study investigates the effectiveness of Oxford Nanopore Technologies for accurate outbreak tracing by resequencing 33 isolates of a 3-year-long Klebsiella pneumoniae outbreak with Illumina short-read sequencing data as the point of reference. We detect considerable base errors through cgMLST and phylogenetic analysis of genomes sequenced with Oxford Nanopore Technologies, leading to the false exclusion of some outbreak-related strains from the outbreak cluster. Nearby methylation sites cause these errors and can also be found in other species besides K. pneumoniae Based on these data, we explore PCR-based sequencing and a masking strategy, which both successfully address these inaccuracies and ensure accurate outbreak tracing. We offer our masking strategy as a bioinformatic workflow (MPOA) to identify and mask problematic genome positions in a reference-free manner. Our research highlights limitations in using Oxford Nanopore Technologies for sequencing prokaryotic organisms, especially for investigating outbreaks. For time-critical projects that cannot wait for further technological developments by Oxford Nanopore Technologies, our study recommends either using PCR-based sequencing or using our provided bioinformatic workflow. We advise that read mapping-based quality control of genomes should be provided when publishing results.

Approaches for Benchmarking Single-Cell Gene Regulatory Network Methods

Gene regulatory networks are powerful tools for modeling genetic interactions that control the expression of genes driving cell differentiation, and single-cell sequencing offers a unique opportunity to build these networks with high-resolution genomic data. There are many proposed computational methods to build these networks using single-cell data, and different approaches are used to benchmark these methods. However, a comprehensive discussion specifically focusing on benchmarking approaches is missing. In this article, we lay the GRN terminology, present an overview of common gold-standard studies and data sets, and define the performance metrics for benchmarking network construction methodologies. We also point out the advantages and limitations of different benchmarking approaches, suggest alternative ground truth data sets that can be used for benchmarking, and specify additional considerations in this context.

DNA methylation activates retron Ec86 filaments for antiphage defense

Retrons are a class of multigene antiphage defense systems typically consisting of a retron reverse transcriptase, a non-coding RNA, and a cognate effector. Although triggers for several retron systems have been discovered recently, the complete mechanism by which these systems detect invading phages and mediate defense remains unclear. Here, we focus on the retron Ec86 defense system, elucidating its modes of activation and mechanisms of action. We identified a phage-encoded DNA cytosine methyltransferase (Dcm) as a trigger of the Ec86 system and demonstrated that Ec86 is activated upon multicopy single-stranded DNA (msDNA) methylation. We further elucidated the structure of a tripartite retron Ec86-effector filament assembly that is primed for activation by Dcm and capable of hydrolyzing nicotinamide adenine dinucleotide (NAD+). These findings provide insights into the retron Ec86 defense mechanism and underscore an emerging theme of antiphage defense through supramolecular complex assemblies.

Translocating bacteria in SIV infection are not stochastic and preferentially express cytosine methyltransferases

Microbial translocation is a significant contributor to chronic inflammation in people living with HIV (PLWH) and is associated with increased mortality and morbidity in individuals treated for long periods with antiretrovirals. The use of therapeutics to treat microbial translocation has yielded mixed effects, in part, because the species and mechanisms contributing to translocation in HIV remain incompletely characterized. To characterize translocating bacteria, we cultured translocators from chronically SIV-infected rhesus macaques. Proteomic profiling of these bacteria identified cytosine-specific methyltransferases as a common feature and therefore, a potential driver of translocation. Treatment of translocating bacteria with the cytosine methyltransferase inhibitor decitabine significantly impaired growth for several species in vitro. In rhesus macaques, oral treatment with decitabine led to some transient decreases in translocator taxa in the gut microbiome. These data provide mechanistic insight into bacterial translocation in lentiviral infection and explore a novel therapeutic intervention that may improve the prognosis of PLWH.

Emerging methylation-based approaches in microbiome engineering

Bacterial epigenetics, particularly through DNA methylation, exerts significant influence over various biological processes such as DNA replication, uptake, and gene regulation in bacteria. In this review, we explore recent advances in characterizing bacterial epigenomes, accompanied by emerging strategies that harness bacterial epigenetics to elucidate and engineer diverse bacterial species with precision and effectiveness. Furthermore, we delve into the potential of epigenetic modifications to steer microbial functions and influence community dynamics, offering promising opportunities for understanding and modulating microbiomes. Additionally, we investigate the extensive diversity of DNA methyltransferases and emphasize their potential utility in the context of the human microbiome. In summary, this review highlights the potential of DNA methylation as a powerful toolkit for engineering microbiomes.

Comprehensive Analysis of Antiphage Defense Mechanisms: Serovar-Specific Patterns

Leptospirosis is a major zoonotic disease caused by pathogenic spirochetes in the genus Leptospira, affecting over a million people annually and causing approximately 60,000 deaths. Leptospira interrogans, a key causative agent, likely possesses defense systems against bacteriophages (leptophages), yet these systems are not well understood. We analyzed 402 genomes of L. interrogans using the DefenseFinder tool to identify and characterize the antiphage defense systems. We detected 24 unique systems, with CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins), PrrC, Borvo, and Restriction-Modification (R-M) being the most prevalent. Notably, Cas were identified in all strains, indicating their central role in phage defense. Furthermore, there were variations in the antiphage system distribution across different serovars, suggesting unique evolutionary adaptations. For instance, Retron was found exclusively in the Canicola serovar, while prokaryotic Argonaute proteins (pAgo) were only detected in the Grippotyphosa serovar. These findings significantly enhance our understanding of Leptospira's antiphage defense mechanisms. They reveal the potential for the development of serovar-specific phage-based therapies and underscore the importance of further exploring these defense systems.

Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges

The universality of DNA methylation as an epigenetic regulatory mechanism belongs to all biological kingdoms. However, while eukaryotic systems have been the primary focus of DNA methylation studies, the molecular mechanisms in prokaryotes are less known. Nevertheless, DNA methylation in prokaryotes plays a pivotal role in many cellular processes such as defense systems against exogenous DNA, cell cycle dynamics, and gene expression, including virulence. Thanks to single-molecule DNA sequencing technologies, genome-wide identification of methylated DNA is becoming feasible on a large scale, providing the possibility to investigate more deeply the presence, variability, and roles of DNA methylation. Here, we present an overview of the multifaceted roles of DNA methylation in prokaryotes and suggest research directions and tools which can enable us to better understand the contribution of DNA methylation to prokaryotic genome evolution and adaptation. In particular, we emphasize the need to understand the presence and role of transgenerational inheritance, as well as the impact of epigenomic signatures on adaptation and genome evolution. Research directions and the importance of novel computational tools are underlined.

The complete genome sequence of unculturable Mycoplasma faucium obtained through clinical metagenomic next-generation sequencing

Introduction

Diagnosing Mycoplasma faucium poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements.

Methods

This study analyzes the complete genome sequence of M. faucium, obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing.

Results

Genome analysis revealed limited therapeutic options for the M. faucium infection, primarily susceptibility to tetracyclines. Three classes of mobile genetic elements were identified: two new insertion sequences, a new prophage (phiUMCG-1), and a species-specific variant of a mycoplasma integrative and conjugative element (MICE). Additionally, a Type I Restriction-Modification system was identified, featuring 5'-terminally truncated hsdS pseudogenes with overlapping repeats, indicating the potential for forming alternative hsdS variants through recombination.

Conclusion

This study represents the first-ever acquisition of a complete circularized bacterial genome directly from a patient sample obtained from invasive infection of a primary sterile site using culture-independent, PCR-free clinical metagenomics.

Bioinformatics Insights on Viral Gene Expression Transactivation: From HIV-1 to SARS-CoV-2

Viruses provide vital insights into gene expression control. Viral transactivators, with other viral and cellular proteins, regulate expression of self, other viruses, and host genes with profound effects on infected cells, underlying inflammation, control of immune responses, and pathogenesis. The multifunctional Tat proteins of lentiviruses (HIV-1, HIV-2, and SIV) transactivate gene expression by recruiting host proteins and binding to transacting responsive regions (TARs) in viral and host RNAs. SARS-CoV-2 nucleocapsid participates in early viral transcription, recruits similar cellular proteins, and shares intracellular, surface, and extracellular distribution with Tat. SARS-CoV-2 nucleocapsid interacting with the replication-transcription complex might, therefore, transactivate viral and cellular RNAs in the transcription and reactivation of self and other viruses, acute and chronic pathogenesis, immune evasion, and viral evolution. Here, we show, by using primary and secondary structural comparisons, that the leaders of SARS-CoV-2 and other coronaviruses contain TAR-like sequences in stem-loops 2 and 3. The coronaviral nucleocapsid C-terminal domains harbor a region of similarity to TAR-binding regions of lentiviral Tat proteins, and coronaviral nonstructural protein 12 has a cysteine-rich metal binding, dimerization domain, as do lentiviral Tat proteins. Although SARS-CoV-1 nucleocapsid transactivated gene expression in a replicon-based study, further experimental evidence for coronaviral transactivation and its possible implications is warranted.

Comparison of Yersinia enterocolitica DNA Methylation at Ambient and Host Temperatures

Pathogenic bacteria recognize environmental cues to vary gene expression for host adaptation. Moving from ambient to host temperature, Yersinia enterocolitica responds by immediately repressing flagella synthesis and inducing the virulence plasmid (pYV)-encoded type III secretion system. In contrast, shifting from host to ambient temperature requires 2.5 generations to restore motility, suggesting a link to the cell cycle. We hypothesized that differential DNA methylation contributes to temperature-regulated gene expression. We tested this hypothesis by comparing single-molecule real-time (SMRT) sequencing of Y. enterocolitica DNA from cells growing exponentially at 22 °C and 37 °C. The inter-pulse duration ratio rather than the traditional QV scoring was the kinetic metric to compare DNA from cells grown at each temperature. All 565 YenI restriction sites were fully methylated at both temperatures. Among the 27,118 DNA adenine methylase (Dam) sites, 42 had differential methylation patterns, while 17 remained unmethylated regardless of the temperature. A subset of the differentially methylated Dam sites localized to promoter regions of predicted regulatory genes including LysR-type and PadR-like transcriptional regulators and a cyclic-di-GMP phosphodiesterase. The unmethylated Dam sites localized with a bias to the replication terminus, suggesting they were protected from Dam methylase. No cytosine methylation was detected at Dcm sites.