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Bacterial methylome

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https://www.readbyqxmd.com/read/29587528/diet-dependent-changes-in-the-intestinal-dna-methylome-after-introduction-of-enteral-feeding-in-preterm-pigs
#1
Xiaoyu Pan, Desheng Gong, Fei Gao, Per Torp Sangild
AIM: To examine how enteral feeding affects the intestinal epigenome and gene expression just after preterm birth. MATERIALS & METHODS: Intestinal tissue from preterm pigs, modeling preterm infants, was collected at birth and 5 days after gradual introduction of infant formula or bovine colostrum. The intestinal tissue was analyzed by reduced representation bisulfite sequencing and real-time qPCR. RESULTS: Relative to colostrum, formula increased bacterial epithelial adherence and lipopolysaccharide binding protein (LBP) expression, which was regulated by promoter methylation...
April 1, 2018: Epigenomics
https://www.readbyqxmd.com/read/29452952/phasevarions-of-bacterial-pathogens-methylomics-sheds-new-light-on-old-enemies
#2
REVIEW
John M Atack, Aimee Tan, Lauren O Bakaletz, Michael P Jennings, Kate L Seib
A wide variety of bacterial pathogens express phase-variable DNA methyltransferases that control expression of multiple genes via epigenetic mechanisms. These randomly switching regulons - phasevarions - regulate genes involved in pathogenesis, host adaptation, and antibiotic resistance. Individual phase-variable genes can be identified in silico as they contain easily recognized features such as simple sequence repeats (SSRs) or inverted repeats (IRs) that mediate the random switching of expression. Conversely, phasevarion-controlled genes do not contain any easily identifiable features...
February 13, 2018: Trends in Microbiology
https://www.readbyqxmd.com/read/29365082/early-microbial-colonization-affects-dna-methylation-of-genes-related-to-intestinal-immunity-and-metabolism-in-preterm-pigs
#3
Xiaoyu Pan, Desheng Gong, Duc Ninh Nguyen, Xinxin Zhang, Qi Hu, Hanlin Lu, Merete Fredholm, Per T Sangild, Fei Gao
Epigenetic regulation may play an important role in mediating microbe-host interactions and adaptation of intestinal gene expression to bacterial colonization just after birth. This is particularly important after preterm birth because the immature intestine is hypersensitive to invading bacteria. We compared the intestinal DNA methylome and microbiome between conventional (CON) and antibiotics-treated (AB) preterm pigs, used as a model for preterm infants. Oral AB treatment reduced bacterial density (∼100-fold), diversity and fermentation, improved the resistance to necrotizing enterocolitis (NEC) and changed the genome-wide DNA methylation in the distal small intestine...
January 19, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28925547/biogeographic-conservation-of-the-cytosine-epigenome-in-the-globally-important-marine-nitrogen-fixing-cyanobacterium-trichodesmium
#4
Nathan G Walworth, David A Hutchins, Egor Dolzhenko, Michael D Lee, Feixue Fu, Andrew D Smith, Eric A Webb
Cytosine methylation has been shown to regulate essential cellular processes and impact biological adaptation. Despite its evolutionary importance, only a handful of bacterial, genome-wide cytosine studies have been conducted, with none for marine bacteria. Here, we examine the genome-wide, C5 -Methyl-cytosine (m5C) methylome and its correlation to global transcription in the marine nitrogen-fixing cyanobacterium Trichodesmium. We characterize genome-wide methylation and highlight conserved motifs across three Trichodesmium isolates and two Trichodesmium metagenomes, thereby identifying highly conserved, novel genomic signatures of potential gene regulation in Trichodesmium...
November 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28575160/dynamic-changes-in-methylome-and-transcriptome-patterns-in-response-to-methyltransferase-inhibitor-5-azacytidine-treatment-in-citrus
#5
Jidi Xu, Xia Wang, Hongbo Cao, Haidan Xu, Qiang Xu, Xiuxin Deng
DNA methylation is known to play an important role in various developmental processes in plants. However, there is a general lack of understanding about the possible functions of DNA methylation in fruit trees. Using callus as a model, methylome, transcriptome and metabolite changes were assessed after treatment with the DNA methyltransferase inhibitor 5-azacytidine (5azaC). Genome-wide methylome analysis revealed the demethylation of a diverse of genes, including many genes encoding transcription factors (TFs), genes involved in biological processes, and the up-regulation of a wide range of transposable elements (TEs)...
October 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28302790/complete-genome-and-methylome-analysis-of-psychrotrophic-bacterial-isolates-from-lake-untersee-in-antarctica
#6
Alexey Fomenkov, Vladimir N Akimov, Lina V Vasilyeva, Dale T Andersen, Tamas Vincze, Richard J Roberts
This paper describes the complete genome sequences and methylome analysis of six psychrotrophic strains isolated from perennially ice-covered Lake Untersee in Antarctica.
March 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/27904456/methylome-analysis-of-two-xanthomonas-spp-using-single-molecule-real-time-sequencing
#7
Hoon Je Seong, Hye-Jee Park, Eunji Hong, Sung Chul Lee, Woo Jun Sul, Sang-Wook Han
Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and methylation patterns/motifs at the genome level. Using SMRT sequencing, diverse bacterial methylomes including those of Helicobacter pylori, Lactobacillus spp., and Escherichia coli have been determined, and previously unreported DNA methylation motifs have been identified. However, the methylomes of Xanthomonas species, which belong to the most important plant pathogenic bacterial genus, have not been documented. Here, we report the methylomes of Xanthomonas axonopodis pv...
December 2016: Plant Pathology Journal
https://www.readbyqxmd.com/read/27885609/methods-for-genome-wide-methylome-profiling-of-campylobacter-jejuni
#8
Kathy T Mou, Tyson A Clark, Usha K Muppirala, Andrew J Severin, Paul J Plummer
Methylation has a profound role in the regulation of numerous biological processes in bacteria including virulence. The study of methylation in bacteria has greatly advanced thanks to next-generation sequencing technologies. These technologies have expedited the process of uncovering unique features of many bacterial methylomes such as characterizing previously uncharacterized methyltransferases, cataloging genome-wide DNA methylations in bacteria, identifying the frequency of methylation at particular genomic loci, and revealing regulatory roles of methylation in the biology of various bacterial species...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27836852/comparative-genomics-reveals-the-diversity-of-restriction-modification-systems-and-dna-methylation-sites-in-listeria-monocytogenes
#9
Poyin Chen, Henk C den Bakker, Jonas Korlach, Nguyet Kong, Dylan B Storey, Ellen E Paxinos, Meredith Ashby, Tyson Clark, Khai Luong, Martin Wiedmann, Bart C Weimer
Listeria monocytogenes is a bacterial pathogen that is found in a wide variety of anthropogenic and natural environments. Genome sequencing technologies are rapidly becoming a powerful tool in facilitating our understanding of how genotype, classification phenotypes, and virulence phenotypes interact to predict the health risks of individual bacterial isolates. Currently, 57 closed L. monocytogenes genomes are publicly available, representing three of the four phylogenetic lineages, and they suggest that L...
February 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27826834/bacterial-dna-methylation-and-methylomes
#10
Josep Casadesús
Formation of C5-methylcytosine, N4-methylcytosine, and N6-methyladenine in bacterial genomes is postreplicative and involves transfer of a methyl group from S-adenosyl-methionine to a base embedded in a specific DNA sequence context. Most bacterial DNA methyltransferases belong to restriction-modification systems; in addition, "solitary" or "orphan" DNA methyltransferases are frequently found in the genomes of bacteria and phage. Base methylation can affect the interaction of DNA-binding proteins with their cognate sites, either by a direct effect (e...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27484700/mapping-epigenetic-changes-to-the-host-cell-genome-induced-by-burkholderia-pseudomallei-reveals-pathogen-specific-and-pathogen-generic-signatures-of-infection
#11
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...
August 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/26998690/a-role-for-the-bacterial-gatc-methylome-in-antibiotic-stress-survival
#12
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
https://www.readbyqxmd.com/read/26786317/phase-variation-of-a-type-iig-restriction-modification-enzyme-alters-site-specific-methylation-patterns-and-gene-expression-in-campylobacter-jejuni-strain-nctc11168
#13
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
https://www.readbyqxmd.com/read/26779304/complete-genome-sequence-of-the-potato-pathogen-ralstonia-solanacearum-uy031
#14
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
https://www.readbyqxmd.com/read/26689587/smrt-sequencing-of-the-campylobacter-coli-bfr-ca-9557-genome-sequence-reveals-unique-methylation-motifs
#15
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
https://www.readbyqxmd.com/read/26578678/lineage-specific-methyltransferases-define-the-methylome-of-the-globally-disseminated-escherichia-coli-st131-clone
#16
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
https://www.readbyqxmd.com/read/26567582/role-of-restriction-modification-systems-in-prokaryotic-evolution-and-ecology
#17
REVIEW
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
https://www.readbyqxmd.com/read/26377311/potential-mechanisms-of-attenuation-for-rifampicin-passaged-strains-of-flavobacterium-psychrophilum
#18
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
https://www.readbyqxmd.com/read/26225157/global-dna-methylation-changes-and-differential-gene-expression-in-anaplasma-phagocytophilum-infected-human-neutrophils
#19
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
https://www.readbyqxmd.com/read/26215614/a-biphasic-epigenetic-switch-controls-immunoevasion-virulence-and-niche-adaptation-in-non-typeable-haemophilus-influenzae
#20
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
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