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Bacterial methylome

Deniz Cizmeci, Emma L Dempster, Olivia L Champion, Sariqa Wagley, Ozgur E Akman, Joann L Prior, Orkun S Soyer, Jonathan Mill, Richard W Titball
The potential for epigenetic changes in host cells following microbial infection has been widely suggested, but few examples have been reported. We assessed genome-wide patterns of DNA methylation in human macrophage-like U937 cells following infection with Burkholderia pseudomallei, an intracellular bacterial pathogen and the causative agent of human melioidosis. Our analyses revealed significant changes in host cell DNA methylation, at multiple CpG sites in the host cell genome, following infection. Infection induced differentially methylated probes (iDMPs) showing the greatest changes in DNA methylation were found to be in the vicinity of genes involved in inflammatory responses, intracellular signalling, apoptosis and pathogen-induced signalling...
2016: Scientific Reports
Nadia R Cohen, Christian A Ross, Saloni Jain, Rebecca S Shapiro, Arnaud Gutierrez, Peter Belenky, Hu Li, James J Collins
Antibiotic resistance is an increasingly serious public health threat. Understanding pathways allowing bacteria to survive antibiotic stress may unveil new therapeutic targets. We explore the role of the bacterial epigenome in antibiotic stress survival using classical genetic tools and single-molecule real-time sequencing to characterize genomic methylation kinetics. We find that Escherichia coli survival under antibiotic pressure is severely compromised without adenine methylation at GATC sites. Although the adenine methylome remains stable during drug stress, without GATC methylation, methyl-dependent mismatch repair (MMR) is deleterious and, fueled by the drug-induced error-prone polymerase Pol IV, overwhelms cells with toxic DNA breaks...
May 2016: Nature Genetics
Awais Anjum, Kelly J Brathwaite, Jack Aidley, Phillippa L Connerton, Nicola J Cummings, Julian Parkhill, Ian Connerton, Christopher D Bayliss
Phase-variable restriction-modification systems are a feature of a diverse range of bacterial species. Stochastic, reversible switches in expression of the methyltransferase produces variation in methylation of specific sequences. Phase-variable methylation by both Type I and Type III methyltransferases is associated with altered gene expression and phenotypic variation. One phase-variable gene of Campylobacter jejuni encodes a homologue of an unusual Type IIG restriction-modification system in which the endonuclease and methyltransferase are encoded by a single gene...
June 2, 2016: Nucleic Acids Research
Rodrigo Guarischi-Sousa, Marina Puigvert, Núria S Coll, María Inés Siri, María Julia Pianzzola, Marc Valls, João C Setubal
Ralstonia solanacearum is the causative agent of bacterial wilt of potato. Ralstonia solanacearum strain UY031 belongs to the American phylotype IIB, sequevar 1, also classified as race 3 biovar 2. Here we report the completely sequenced genome of this strain, the first complete genome for phylotype IIB, sequevar 1, and the fourth for the R. solanacearum species complex. In addition to standard genome annotation, we have carried out a curated annotation of type III effector genes, an important pathogenicity-related class of genes for this organism...
2016: Standards in Genomic Sciences
Andreas E Zautner, Anne-Marie Goldschmidt, Andrea Thürmer, Jörg Schuldes, Oliver Bader, Raimond Lugert, Uwe Groß, Kerstin Stingl, Gabriela Salinas, Thomas Lingner
BACKGROUND: Campylobacter species are the most prevalent bacterial pathogen causing acute enteritis worldwide. In contrast to Campylobacter jejuni, about 5 % of Campylobacter coli strains exhibit susceptibility to restriction endonuclease digestion by DpnI cutting specifically 5'-G(m)ATC-3' motifs. This indicates significant differences in DNA methylation between both microbial species. The goal of the study was to analyze the methylome of a C. coli strain susceptible to DpnI digestion, to identify its methylation motifs and restriction modification systems (RM-systems), and compare them to related organisms like C...
2015: BMC Genomics
Brian M Forde, Minh-Duy Phan, Jayde A Gawthorne, Melinda M Ashcroft, Mitchell Stanton-Cook, Sohinee Sarkar, Kate M Peters, Kok-Gan Chan, Teik Min Chong, Wai-Fong Yin, Mathew Upton, Mark A Schembri, Scott A Beatson
UNLABELLED: Escherichia coli sequence type 131 (ST131) is a clone of uropathogenic E. coli that has emerged rapidly and disseminated globally in both clinical and community settings. Members of the ST131 lineage from across the globe have been comprehensively characterized in terms of antibiotic resistance, virulence potential, and pathogenicity, but to date nothing is known about the methylome of these important human pathogens. Here we used single-molecule real-time (SMRT) PacBio sequencing to determine the methylome of E...
2015: MBio
A S Ershova, I S Rusinov, S A Spirin, A S Karyagina, A V Alexeevski
Restriction-modification (R-M) systems are able to methylate or cleave DNA depending on methylation status of their recognition site. It allows them to protect bacterial cells from invasion by foreign DNA. Comparative analysis of a large number of available bacterial genomes and methylomes clearly demonstrates that the role of R-M systems in bacteria is wider than only defense. R-M systems maintain heterogeneity of a bacterial population and are involved in adaptation of bacteria to change in their environmental conditions...
October 2015: Biochemistry. Biokhimii︠a︡
Karol Gliniewicz, Mark Wildung, Lisa H Orfe, Gregory D Wiens, Kenneth D Cain, Kevin K Lahmers, Kevin R Snekvik, Douglas R Call
BACKGROUND: Flavobacterium psychrophilum is the etiologic agent of bacterial coldwater disease in salmonids. Earlier research showed that a rifampicin-passaged strain of F. psychrophilum (CSF 259-93B.17) caused no disease in rainbow trout (Oncorhynchus mykiss, Walbaum) while inducing a protective immune response against challenge with the virulent CSF 259-93 strain. We hypothesized that rifampicin passage leads to an accumulation of genomic mutations that, by chance, reduce virulence...
2015: BMC Microbiology
Sara H G Sinclair, Srinivasan Yegnasubramanian, J Stephen Dumler
BACKGROUND: Anaplasma phagocytophilum is an obligate intracellular prokaryotic pathogen that both infects and replicates within human neutrophils. The bacterium represses multiple antimicrobial functions while simultaneously increasing proinflammatory functions by reprogramming the neutrophil genome. Previous reports show that many observed phenotypic changes are in part explained by altered gene transcription. We recently identified that large chromosomal regions of the neutrophil genome are differentially expressed during A...
2015: Clinical Epigenetics
John M Atack, Yogitha N Srikhanta, Kate L Fox, Joseph A Jurcisek, Kenneth L Brockman, Tyson A Clark, Matthew Boitano, Peter M Power, Freda E-C Jen, Alastair G McEwan, Sean M Grimmond, Arnold L Smith, Stephen J Barenkamp, Jonas Korlach, Lauren O Bakaletz, Michael P Jennings
Non-typeable Haemophilus influenzae contains an N(6)-adenine DNA-methyltransferase (ModA) that is subject to phase-variable expression (random ON/OFF switching). Five modA alleles, modA2, modA4, modA5, modA9 and modA10, account for over two-thirds of clinical otitis media isolates surveyed. Here, we use single molecule, real-time (SMRT) methylome analysis to identify the DNA-recognition motifs for all five of these modA alleles. Phase variation of these alleles regulates multiple proteins including vaccine candidates, and key virulence phenotypes such as antibiotic resistance (modA2, modA5, modA10), biofilm formation (modA2) and immunoevasion (modA4)...
2015: Nature Communications
John Beaulaurier, Xue-Song Zhang, Shijia Zhu, Robert Sebra, Chaggai Rosenbluh, Gintaras Deikus, Nan Shen, Diana Munera, Matthew K Waldor, Andrew Chess, Martin J Blaser, Eric E Schadt, Gang Fang
Beyond its role in host defense, bacterial DNA methylation also plays important roles in the regulation of gene expression, virulence and antibiotic resistance. Bacterial cells in a clonal population can generate epigenetic heterogeneity to increase population-level phenotypic plasticity. Single molecule, real-time (SMRT) sequencing enables the detection of N6-methyladenine and N4-methylcytosine, two major types of DNA modifications comprising the bacterial methylome. However, existing SMRT sequencing-based methods for studying bacterial methylomes rely on a population-level consensus that lacks the single-cell resolution required to observe epigenetic heterogeneity...
2015: Nature Communications
Xin Deng, Kai Chen, Guan-Zheng Luo, Xiaocheng Weng, Quanjiang Ji, Tianhong Zhou, Chuan He
N(6)-methyladenosine (m(6)A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA). Recent discoveries of demethylases and specific binding proteins of m(6)A as well as m(6)A methylomes obtained in mammals, yeast and plants have revealed regulatory functions of this RNA modification. Although m(6)A is present in the ribosomal RNA of bacteria, its occurrence in mRNA still remains elusive. Here, we have employed ultra-high pressure liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (UHPLC-QQQ-MS/MS) to calculate the m(6)A/A ratio in mRNA from a wide range of bacterial species, which demonstrates that m(6)A is an abundant mRNA modification in tested bacteria...
July 27, 2015: Nucleic Acids Research
Yoshikazu Furuta, Mutsuko Konno, Takako Osaki, Hideo Yonezawa, Taichiro Ishige, Misaki Imai, Yuh Shiwa, Mari Shibata-Hatta, Yu Kanesaki, Hirofumi Yoshikawa, Shigeru Kamiya, Ichizo Kobayashi
Helicobacter pylori, a bacterial pathogen that can infect human stomach causing gastritis, ulcers and cancer, is known to have a high degree of genome/epigenome diversity as the result of mutation and recombination. The bacteria often infect in childhood and persist for the life of the host. One of the reasons of the rapid evolution of H. pylori is that it changes its genome drastically for adaptation to a new host. To investigate microevolution and adaptation of the H. pylori genome, we undertook whole genome sequencing of the same or very similar sequence type in multi-locus sequence typing (MLST) with seven genes in members of the same family consisting of parents and children in Japan...
2015: PloS One
María A Sánchez-Romero, Ignacio Cota, Josep Casadesús
Formation of C(5)-methyl-cytosine, N(4)-methyl-cytosine, and N(6)-methyl-adenine in bacterial genomes is postreplicative, and occurs at specific targets. Base methylation can modulate the interaction of DNA-binding proteins with their cognate sites, and controls chromosome replication, correction of DNA mismatches, cell cycle-coupled transcription, and formation of epigenetic lineages by phase variation. During four decades, the roles of DNA methylation in bacterial physiology have been investigated by analyzing the contribution of individual methyl groups or small methyl group clusters to the control of DNA-protein interactions...
June 2015: Current Opinion in Microbiology
Himanshu Kumar, Riikka Lund, Asta Laiho, Krista Lundelin, Ruth E Ley, Erika Isolauri, Seppo Salminen
UNLABELLED: The core human gut microbiota contributes to the developmental origin of diseases by modifying metabolic pathways. To evaluate the predominant microbiota as an epigenetic modifier, we classified 8 pregnant women into two groups based on their dominant microbiota, i.e., Bacteroidetes, Firmicutes, and Proteobacteria. Deep sequencing of DNA methylomes revealed a clear association between bacterial predominance and epigenetic profiles. The genes with differentially methylated promoters in the group in which Firmicutes was dominant were linked to risk of disease, predominantly to cardiovascular disease and specifically to lipid metabolism, obesity, and the inflammatory response...
2014: MBio
Ana Sousa Manso, Melissa H Chai, John M Atack, Leonardo Furi, Megan De Ste Croix, Richard Haigh, Claudia Trappetti, Abiodun D Ogunniyi, Lucy K Shewell, Matthew Boitano, Tyson A Clark, Jonas Korlach, Matthew Blades, Evgeny Mirkes, Alexander N Gorban, James C Paton, Michael P Jennings, Marco R Oggioni
Streptococcus pneumoniae (the pneumococcus) is the world's foremost bacterial pathogen in both morbidity and mortality. Switching between phenotypic forms (or 'phases') that favour asymptomatic carriage or invasive disease was first reported in 1933. Here, we show that the underlying mechanism for such phase variation consists of genetic rearrangements in a Type I restriction-modification system (SpnD39III). The rearrangements generate six alternative specificities with distinct methylation patterns, as defined by single-molecule, real-time (SMRT) methylomics...
2014: Nature Communications
Shuguang Lu, Shuai Le, Yinling Tan, Ming Li, Chang Liu, Kebin Zhang, Jianjun Huang, Haimei Chen, Xiancai Rao, Junmin Zhu, Lingyun Zou, Qingshan Ni, Shu Li, Jing Wang, Xiaolin Jin, Qiwen Hu, Xinyue Yao, Xia Zhao, Lin Zhang, Guangtao Huang, Fuquan Hu
BACKGROUND: Whole-genome sequencing is an important method to understand the genetic information, gene function, biological characteristics and survival mechanisms of organisms. Sequencing large genomes is very simple at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. Shotgun sequencing method failed to complete the sequence of this genome. RESULTS: After persevering for 10 years and going over three generations of sequencing techniques, we successfully completed the sequence of the PaP1 genome with a length of 91,715 bp...
2014: BMC Genomics
Michael T Leonard, Austin G Davis-Richardson, Alexandria N Ardissone, Kaisa M Kemppainen, Jennifer C Drew, Jorma Ilonen, Mikael Knip, Olli Simell, Jorma Toppari, Riitta Veijola, Heikki Hyöty, Eric W Triplett
Despite the large interest in the human microbiome in recent years, there are no reports of bacterial DNA methylation in the microbiome. Here metagenomic sequencing using the Pacific Biosciences platform allowed for rapid identification of bacterial GATC methylation status of a bacterial species in human stool samples. For this work, two stool samples were chosen that were dominated by a single species, Bacteroides dorei. Based on 16S rRNA analysis, this species represented over 45% of the bacteria present in these two samples...
2014: Frontiers in Microbiology
Kerry K Cooper, Robert E Mandrell, Jacqueline W Louie, Jonas Korlach, Tyson A Clark, Craig T Parker, Steven Huynh, Patrick S Chain, Sanaa Ahmed, Michelle Qiu Carter
BACKGROUND: Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne illness, including hemolytic uremic syndrome have increased worldwide. In fact, non-O157 serotypes are now estimated to cause over half of all the Shiga toxin-producing Escherichia coli (STEC) cases, and outbreaks of non-O157 EHEC infections are frequently associated with serotypes O26, O45, O103, O111, O121, and O145. Currently, there are no complete genomes for O145 in public databases...
2014: BMC Genomics
Juliane Krebes, Richard D Morgan, Boyke Bunk, Cathrin Spröer, Khai Luong, Raphael Parusel, Brian P Anton, Christoph König, Christine Josenhans, Jörg Overmann, Richard J Roberts, Jonas Korlach, Sebastian Suerbaum
The genome of Helicobacter pylori is remarkable for its large number of restriction-modification (R-M) systems, and strain-specific diversity in R-M systems has been suggested to limit natural transformation, the major driving force of genetic diversification in H. pylori. We have determined the comprehensive methylomes of two H. pylori strains at single base resolution, using Single Molecule Real-Time (SMRT®) sequencing. For strains 26695 and J99-R3, 17 and 22 methylated sequence motifs were identified, respectively...
February 2014: Nucleic Acids Research
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