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Series GSE69872 Query DataSets for GSE69872
Status Public on Jan 20, 2016
Title The Epigenomic Landscape of Prokaryotes
Organisms Streptococcus equinus; Enterococcus gallinarum; Lactococcus lactis subsp. lactis; Lactiplantibacillus plantarum; Teredinibacter turnerae; Clostridium algidicarnis; Salmonella enterica subsp. arizonae serovar 62:z4,z23:-; Pyrococcus horikoshii OT3; Methylocystis sp. LW5; Lachnobacterium bovis; Agrobacterium fabrum str. C58; Persephonella; Xylella fastidiosa Temecula1; Clostridium perfringens ATCC 13124; Escherichia coli CFT073; Acetivibrio thermocellus ATCC 27405; Salmonella bongori NCTC 12419; Mastigocladopsis repens PCC 10914; Neisseria gonorrhoeae FA 1090; Methanocaldococcus jannaschii DSM 2661; Treponema denticola ATCC 35405; Rhodopseudomonas palustris CGA009; Clostridioides difficile 630; Methylorubrum extorquens AM1; Neisseria meningitidis FAM18; Thermoplasma acidophilum DSM 1728; Thermoplasma volcanium GSS1; Acidobacteriaceae bacterium TAA 166; Mycoplasmopsis bovis PG45; Thiobacillus denitrificans ATCC 25259; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Hydrogenovibrio crunogenus XCL-2; Methanospirillum hungatei JF-1; Sulfurimonas denitrificans DSM 1251; Chloroflexus aggregans DSM 9485; Sulfolobus acidocaldarius DSM 639; Actinobacillus succinogenes 130Z; Akkermansia muciniphila ATCC BAA-835; Fervidobacterium nodosum Rt17-B1; Thermosipho melanesiensis BI429; Phaeobacter inhibens DSM 17395; Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088; Shewanella woodyi ATCC 51908; Bradyrhizobium elkanii USDA 76; Dinoroseobacter shibae DFL 12 = DSM 16493; Staphylothermus marinus F1; Thermoanaerobacter sp. X514; Flavobacterium psychrophilum JIP02/86; Xenorhabdus nematophila ATCC 19061; Methanocorpusculum labreanum Z; Cronobacter; Parabacteroides distasonis ATCC 8503; Actinosynnema mirum DSM 43827; Staphylococcus aureus subsp. aureus USA300_TCH1516; Pseudarthrobacter chlorophenolicus A6; Galbibacter orientalis; Dyadobacter fermentans DSM 18053; Saccharomonospora viridis DSM 43017; Verrucomicrobia bacterium LP2A; Streptosporangium roseum DSM 43021; Sphaerobacter thermophilus DSM 20745; Veillonella parvula DSM 2008; Pedobacter heparinus DSM 2366; Anoxybacillus flavithermus WK1; Rhizobium etli CIAT 652; Meiothermus ruber DSM 1279; Escherichia coli str. K-12 substr. MG1655; Streptobacillus moniliformis DSM 12112; Capnocytophaga ochracea DSM 7271; Planctopirus limnophila DSM 3776; Methanothermus fervidus DSM 2088; Thermanaerovibrio acidaminovorans DSM 6589; Sebaldella termitidis ATCC 33386; Allomeiothermus silvanus DSM 9946; Haloterrigena turkmenica DSM 5511; Methanohalophilus mahii DSM 5219; Corynebacterium aurimucosum ATCC 700975; Sedimentitalea nanhaiensis DSM 24252; Aminobacterium colombiense DSM 12261; Sediminispirochaeta smaragdinae DSM 11293; Zymomonas mobilis subsp. pomaceae ATCC 29192; Hirschia baltica ATCC 49814; Coraliomargarita akajimensis DSM 45221; Palaeococcus ferrophilus DSM 13482; Acetivibrio thermocellus DSM 1313; Acidobacteriaceae bacterium KBS 146; Syntrophothermus lipocalidus DSM 12680; Stutzerimonas stutzeri RCH2; Syntrophobotulus glycolicus DSM 8271; Bacillus spizizenii str. W23; Phocaeicola salanitronis DSM 18170; Pseudofrankia sp. DC12; Klebsiella aerogenes FGI35; Cellulophaga algicola DSM 14237; Pontibacter actiniarum DSM 19842; Flexistipes sinusarabici DSM 4947; Thermobacillus composti KWC4; Gracilinema caldarium DSM 7334; Nitratifractor salsuginis DSM 16511; Sulfurospirillum barnesii SES-3; Gillisia limnaea DSM 15749; Cellulophaga lytica DSM 7489; Treponema succinifaciens DSM 2489; Marinithermus hydrothermalis DSM 14884; Spirochaeta thermophila DSM 6578; Ruminococcus sp. NK3A76; Bernardetia litoralis DSM 6794; Desulfobacca acetoxidans DSM 11109; Caldithrix abyssi DSM 13497; Rikenella microfusus DSM 15922; Spirochaeta africana DSM 8902; Holophaga foetida DSM 6591; Asinibacterium sp. OR53; Echinicola vietnamensis DSM 17526; Calidithermus chliarophilus DSM 9957; Orenia marismortui DSM 5156; Sporocytophaga myxococcoides DSM 11118; Solitalea canadensis DSM 3403; Patulibacter minatonensis DSM 18081; Niabella soli DSM 19437; Acetobacterium woodii DSM 1030; Sinorhizobium medicae WSM1115; Hippea alviniae EP5-r; Hippea sp. KM1; Cohnella panacarvi Gsoil 349; Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7; Acetivibrio clariflavus 4-2a; Nocardia sp. BMG51109; Halomicrobium katesii DSM 19301; Nitriliruptor alkaliphilus DSM 45188; Thermacetogenium phaeum DSM 12270; Sphingomonas melonis C3; Methylobacterium sp. 10; Methylophilaceae bacterium 11; Methylophilus sp. 1; Methylophilus sp. 5; Arthrobacter sp. 31Y; Methylophilus sp. 42; Methylotenera versatilis 79; Xanthobacter sp. 91; Pseudomonas aeruginosa NCAIM B.001380; Geopsychrobacter electrodiphilus DSM 16401; Kangiella aquimarina DSM 16071; Pelobacter seleniigenes DSM 18267; Psychrilyobacter atlanticus DSM 19335; Hydrogenovibrio marinus DSM 11271; Thiomicrospira pelophila DSM 1534; Thioalkalivibrio sp. ARh3; Thiomonas sp. FB-6; Oxalobacteraceae bacterium AB_14; Prevotella sp. 10(H); Desulfurobacterium sp. TC5-1; Nocardia sp. BMG111209; Bacteroides sp. 14(A); Clostridium sp. 12(A); Methylotenera sp. 73s; Hydrogenovibrio kuenenii DSM 12350; Klebsiella oxytoca BRL6-2; Leptolyngbya sp. PCC 6406; Maribacter sp. Hel_I_7; Polaribacter sp. Hel_I_88; Desulfospira joergensenii DSM 10085; Acidovorax sp. JHL-3; Tolumonas lignilytica; Gillisia sp. JM1; Methylohalobius crimeensis 10Ki; Cellvibrionaceae bacterium 1162T.S.0a.05; [Clostridium] methoxybenzovorans SR3; Streptomyces sp. WMMB 714; Ruminiclostridium josui JCM 17888; Alteromonas sp. ALT199; Cellulomonas sp. KRMCY2; Clostridium sp. ASBs410; Solidesulfovibrio cf. magneticus IFRC170; Aminiphilus circumscriptus DSM 16581; Caldicoprobacter oshimai DSM 21659; [Clostridium] indolis DSM 755; Desulforegula conservatrix Mb1Pa; Desulfotignum balticum DSM 7044; Limisalsivibrio acetivorans; Methylobacterium sp. EUR3 AL-11; Microbacterium sp. KROCY2; Polaromonas sp. EUR3 1.2.1; Oceanicola sp. HL-35; Algoriphagus marincola HL-49; Desulfohalovibrio reitneri; Kallotenue papyrolyticum; Bryobacter aggregatus MPL3; Alicyclobacillus macrosporangiidus CPP55; Thermogemmatispora carboxidivorans; Pseudacidobacterium ailaaui; Mediterraneibacter gnavus AGR2154; Levilactobacillus brevis AG48; Ruminococcus albus AD2013; Ruminococcus flavefaciens AE3010; Pediococcus acidilactici AGR20; Exiguobacterium chiriqhucha; Prevotella sp. HUN102; Eubacterium sp. AB3007; Flavimarina sp. Hel_I_48; Sediminibacter sp. Hel_I_10; Ruminococcaceae bacterium AE2021; Lachnospiraceae bacterium AC2031; Lachnospiraceae bacterium AC2012; Clostridioides mangenotii LM2; Selenomonas ruminantium AC2024; Selenomonas ruminantium AB3002; Exiguobacterium aurantiacum DSM 6208; Exiguobacterium acetylicum DSM 20416; Exiguobacterium oxidotolerans JCM 12280; Exiguobacterium antarcticum DSM 14480; Butyrivibrio sp. FCS014; Methylobacter tundripaludum 21/22; Polycyclovorans algicola TG408; Clostridium sp. KNHs205; Hydrogenovibrio sp. MA2-6; Lachnospiraceae bacterium AC2029; Enterococcus faecalis 68A; Lachnoclostridium phytofermentans KNHs2132; Pseudobutyrivibrio ruminis HUN009; Staphylococcus epidermidis AG42; Lachnoclostridium phytofermentans KNHs212; Robinsoniella sp. KNHs210; Peptostreptococcaceae bacterium VA2; Butyrivibrio sp. AE3003; Butyrivibrio sp. AE3004; Ruminococcus sp. HUN007; Teredinibacter purpureus
Experiment type Methylation profiling by high throughput sequencing
Summary DNA methylation is an important regulator of genome function in the eukaryotes, but it is currently unclear if the same is true in prokaryotes. While regulatory functions have been demonstrated for a small number of bacteria, there have been no large-scale studies of prokaryotic methylomes and the full repertoire of targets and biological functions of DNA methylation remains unclear. Here we applied single-molecule, real-time sequencing to directly study the methylomes of 232 phylogenetically diverse prokaryotes. Collectively, we identified 834 methylated motifs, enabling the specific annotation of 415 DNA methyltransferases (MTases), and adding substantially to existing databases of MTase specificities. While the majority of MTases function as components of restriction-modification systems, 139 MTases have no cognate restriction enzyme in the genome, suggesting some other functional role. Several of these ‘orphan’ MTases are conserved across species and exhibit patterns of DNA methylation consistent with known regulatory MTases. Based on these patterns of methylation, we identify candidate novel regulators of gene expression in several phyla of bacteria, and candidate regulators of DNA replication in Haloarchaea. Together these data substantially advance our knowledge of DNA restriction-modification systems, and hint at a wider role for methylation in prokaryotic genome regulation.
 
Overall design Single-molecule, real-time sequencing of DNA modifications across 232 diverse prokaryotic genomes.
 
Contributor(s) Blow MJ, Roberts RJ
Citation(s) 26870957
Submission date Jun 15, 2015
Last update date May 15, 2019
Contact name Matthew James Blow
E-mail(s) mjblow@lbl.gov
Phone 510-486-6590
Fax 510-486-7004
Organization name Lawrence Berkeley National Laboratory
Department Genomics Division
Lab Rubin / Pennacchio
Street address 1 Cyclotron Road
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platforms (228)
GPL20335 PacBio RS II (Acetobacterium woodii DSM 1030)
GPL20336 PacBio RS II (Acidobacteriaceae bacterium TAA166)
GPL20337 PacBio RS II (Acidobacteria bacterium KBS 146)
Samples (237)
GSM1711560 Acetobacterium_woodii_DSM1030_native
GSM1711561 Acidobacteriaceae_sp_DSM24188_native
GSM1711562 Acidobacteriaceae_sp_KBS_146_native
Relations
BioProject PRJNA287040
SRA SRP059508

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Supplementary file Size Download File type/resource
GSE69872_RAW.tar 28.1 Gb (http)(custom) TAR (of CSV, GFF)
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Raw data are available in SRA
Processed data provided as supplementary file
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