Fricke WF

References (15)

Title : Genome sequences of 65 Helicobacter pylori strains isolated from asymptomatic individuals and patients with gastric cancer, peptic ulcer disease, or gastritis - Blanchard_2013_Pathog.Dis_68_39
Author(s) : Blanchard TG , Czinn SJ , Correa P , Nakazawa T , Keelan M , Morningstar L , Santana-Cruz I , Maroo A , McCracken C , Shefchek K , Daugherty S , Song Y , Fraser CM , Fricke WF
Ref : Pathog Dis , 68 :39 , 2013
Abstract : Helicobacter pylori, inhabitant of the gastric mucosa of over half of the world population, with decreasing prevalence in the U.S., has been associated with a variety of gastric pathologies. However, the majority of H. pylori-infected individuals remain asymptomatic, and negative correlations between H. pylori and allergic diseases have been reported. Comprehensive genome characterization of H. pylori populations from different human host backgrounds including healthy individuals provides the exciting potential to generate new insights into the open question whether human health outcome is associated with specific H. pylori genotypes or dependent on other environmental factors. We report the genome sequences of 65 H. pylori isolates from individuals with gastric cancer, preneoplastic lesions, peptic ulcer disease, gastritis, and from asymptomatic adults. Isolates were collected from multiple locations in North America (USA and Canada) as well as from Columbia and Japan. The availability of these H. pylori genome sequences from individuals with distinct clinical presentations provides the research community with a resource for detailed investigations into genetic elements that correlate either positively or negatively with the epidemiology, human host adaptation, and gastric pathogenesis and will aid in the characterization of strains that may favor the development of specific pathology, including gastric cancer.
ESTHER : Blanchard_2013_Pathog.Dis_68_39
PubMedSearch : Blanchard_2013_Pathog.Dis_68_39
PubMedID: 23661595
Gene_locus related to this paper: helpy-o25061

Title : Whole-genome sequences of Bacillus subtilis and close relatives - Earl_2012_J.Bacteriol_194_2378
Author(s) : Earl AM , Eppinger M , Fricke WF , Rosovitz MJ , Rasko DA , Daugherty S , Losick R , Kolter R , Ravel J
Ref : Journal of Bacteriology , 194 :2378 , 2012
Abstract : We sequenced four strains of Bacillus subtilis and the type strains for two closely related species, Bacillus vallismortis and Bacillus mojavensis. We report the high-quality Sanger genome sequences of B. subtilis subspecies subtilis RO-NN-1 and AUSI98, B. subtilis subspecies spizizenii TU-B-10(T) and DV1-B-1, Bacillus mojavensis RO-H-1(T), and Bacillus vallismortis DV1-F-3(T).
ESTHER : Earl_2012_J.Bacteriol_194_2378
PubMedSearch : Earl_2012_J.Bacteriol_194_2378
PubMedID: 22493193
Gene_locus related to this paper: bacsu-YBAC , bacsu-ytxm , bacsu-YVAK

Title : Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution - Fricke_2011_J.Bacteriol_193_3556
Author(s) : Fricke WF , Mammel MK , McDermott PF , Tartera C , White DG , Leclerc JE , Ravel J , Cebula TA
Ref : Journal of Bacteriology , 193 :3556 , 2011
Abstract : Despite extensive surveillance, food-borne Salmonella enterica infections continue to be a significant burden on public health systems worldwide. As the S. enterica species comprises sublineages that differ greatly in antigenic representation, virulence, and antimicrobial resistance phenotypes, a better understanding of the species' evolution is critical for the prediction and prevention of future outbreaks. The roles that virulence and resistance phenotype acquisition, exchange, and loss play in the evolution of S. enterica sublineages, which to a certain extent are represented by serotypes, remains mostly uncharacterized. Here, we compare 17 newly sequenced and phenotypically characterized nontyphoidal S. enterica strains to 11 previously sequenced S. enterica genomes to carry out the most comprehensive comparative analysis of this species so far. These phenotypic and genotypic data comparisons in the phylogenetic species context suggest that the evolution of known S. enterica sublineages is mediated mostly by two mechanisms, (i) the loss of coding sequences with known metabolic functions, which leads to functional reduction, and (ii) the acquisition of horizontally transferred phage and plasmid DNA, which provides virulence and resistance functions and leads to increasing specialization. Matches between S. enterica clustered regularly interspaced short palindromic repeats (CRISPR), part of a defense mechanism against invading plasmid and phage DNA, and plasmid and prophage regions suggest that CRISPR-mediated immunity could control short-term phenotype changes and mediate long-term sublineage evolution. CRISPR analysis could therefore be critical in assessing the evolutionary potential of S. enterica sublineages and aid in the prediction and prevention of future S. enterica outbreaks.
ESTHER : Fricke_2011_J.Bacteriol_193_3556
PubMedSearch : Fricke_2011_J.Bacteriol_193_3556
PubMedID: 21602358
Gene_locus related to this paper: salen-OPDB , salty-AES , salty-DLHH , salty-ENTF , salty-PLDB , salty-STM4506 , salty-STY3846 , salty-yafa , salty-YBFF , salty-ycfp , salty-YHET , salty-YQIA

Title : Horizontal gene transfer of a ColV plasmid has resulted in a dominant avian clonal type of Salmonella enterica serovar Kentucky - Johnson_2010_PLoS.One_5_e15524
Author(s) : Johnson TJ , Thorsness JL , Anderson CP , Lynne AM , Foley SL , Han J , Fricke WF , McDermott PF , White DG , Khatri M , Stell AL , Flores C , Singer RS
Ref : PLoS ONE , 5 :e15524 , 2010
Abstract : Salmonella enterica continues to be a significant cause of foodborne gastrointestinal illness in humans. A wide variety of Salmonella serovars have been isolated from production birds and from retail poultry meat. Recently, though, S. enterica subsp. enterica serovar Kentucky has emerged as one of the prominent Salmonella serovars isolated from broiler chickens. Recent work suggests that its emergence apparently coincides with its acquisition of a ColV virulence plasmid. In the present study, we examined 902 Salmonella isolates belonging to 59 different serovars for the presence of this plasmid. Of the serovars examined, the ColV plasmid was found only among isolates belonging to the serovars Kentucky (72.9%), Typhimurium (15.0%) and Heidelberg (1.7%). We demonstrated that a single PFGE clonal type of S. Kentucky harbors this plasmid, and acquisition of this plasmid by S. Kentucky significantly increased its ability to colonize the chicken cecum and cause extraintestinal disease. Comparison of the completed sequences of three ColV plasmids from S. Kentucky isolated from different geographical locales, timepoints and sources revealed a nearly identical genetic structure with few single nucleotide changes or insertions/deletions. Overall, it appears that the ColV plasmid was recently acquired by a single clonal type S. Kentucky and confers to its host enhanced colonization and fitness capabilities. Thus, the potential for horizontal gene transfer of virulence and fitness factors to Salmonella from other enteric bacteria exists in poultry, representing a potential human health hazard.
ESTHER : Johnson_2010_PLoS.One_5_e15524
PubMedSearch : Johnson_2010_PLoS.One_5_e15524
PubMedID: 21203520
Gene_locus related to this paper: ecoli-IROE

Title : Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide - Strittmatter_2009_Environ.Microbiol_11_1038
Author(s) : Strittmatter AW , Liesegang H , Rabus R , Decker I , Amann J , Andres S , Henne A , Fricke WF , Martinez-Arias R , Bartels D , Goesmann A , Krause L , Puhler A , Klenk HP , Richter M , Schuler M , Glockner FO , Meyerdierks A , Gottschalk G , Amann R
Ref : Environ Microbiol , 11 :1038 , 2009
Abstract : Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp(-1)) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood-Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO(2) but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII-c(3), Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2.
ESTHER : Strittmatter_2009_Environ.Microbiol_11_1038
PubMedSearch : Strittmatter_2009_Environ.Microbiol_11_1038
PubMedID: 19187283
Gene_locus related to this paper: desah-c0q9m7 , desah-c0qb70 , desah-c0qf45 , desah-c0qhm8

Title : Comparative genomics of the IncA\/C multidrug resistance plasmid family - Fricke_2009_J.Bacteriol_191_4750
Author(s) : Fricke WF , Welch TJ , McDermott PF , Mammel MK , Leclerc JE , White DG , Cebula TA , Ravel J
Ref : Journal of Bacteriology , 191 :4750 , 2009
Abstract : Multidrug resistance (MDR) plasmids belonging to the IncA/C plasmid family are widely distributed among Salmonella and other enterobacterial isolates from agricultural sources and have, at least once, also been identified in a drug-resistant Yersinia pestis isolate (IP275) from Madagascar. Here, we present the complete plasmid sequences of the IncA/C reference plasmid pRA1 (143,963 bp), isolated in 1971 from the fish pathogen Aeromonas hydrophila, and of the cryptic IncA/C plasmid pRAx (49,763 bp), isolated from Escherichia coli transconjugant D7-3, which was obtained through pRA1 transfer in 1980. Using comparative sequence analysis of pRA1 and pRAx with recent members of the IncA/C plasmid family, we show that both plasmids provide novel insights into the evolution of the IncA/C MDR plasmid family and the minimal machinery necessary for stable IncA/C plasmid maintenance. Our results indicate that recent members of the IncA/C plasmid family evolved from a common ancestor, similar in composition to pRA1, through stepwise integration of horizontally acquired resistance gene arrays into a conserved plasmid backbone. Phylogenetic comparisons predict type IV secretion-like conjugative transfer operons encoded on the shared plasmid backbones to be closely related to a group of integrating conjugative elements, which use conjugative transfer for horizontal propagation but stably integrate into the host chromosome during vegetative growth. A hipAB toxin-antitoxin gene cluster found on pRA1, which in Escherichia coli is involved in the formation of persister cell subpopulations, suggests persistence as an early broad-spectrum antimicrobial resistance mechanism in the evolution of IncA/C resistance plasmids.
ESTHER : Fricke_2009_J.Bacteriol_191_4750
PubMedSearch : Fricke_2009_J.Bacteriol_191_4750
PubMedID: 19482926

Title : Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry - Fricke_2009_Appl.Environ.Microbiol_75_5963
Author(s) : Fricke WF , McDermott PF , Mammel MK , Zhao S , Johnson TJ , Rasko DA , Fedorka-Cray PJ , Pedroso A , Whichard JM , Leclerc JE , White DG , Cebula TA , Ravel J
Ref : Applied Environmental Microbiology , 75 :5963 , 2009
Abstract : Salmonella enterica, a leading cause of food-borne gastroenteritis worldwide, may be found in any raw food of animal, vegetable, or fruit origin. Salmonella serovars differ in distribution, virulence, and host specificity. Salmonella enterica serovar Kentucky, though often found in the food supply, is less commonly isolated from ill humans. The multidrug-resistant isolate S. Kentucky CVM29188, isolated from a chicken breast sample in 2003, contains three plasmids (146,811 bp, 101,461 bp, and 46,121 bp), two of which carry resistance determinants (pCVM29188_146 [strAB and tetRA] and pCVM29188_101 [bla(CMY-2) and sugE]). Both resistance plasmids were transferable by conjugation, alone or in combination, to S. Kentucky, Salmonella enterica serovar Newport, and Escherichia coli recipients. pCVM29188_146 shares a highly conserved plasmid backbone of 106 kb (>90% nucleotide identity) with two virulence plasmids from avian pathogenic Escherichia coli strains (pAPEC-O1-ColBM and pAPEC-O2-ColV). Shared avian pathogenic E. coli (APEC) virulence factors include iutA iucABCD, sitABCD, etsABC, iss, and iroBCDEN. PCR analyses of recent (1997 to 2005) S. Kentucky isolates from food animal, retail meat, and human sources revealed that 172 (60%) contained similar APEC-like plasmid backbones. Notably, though rare in human- and cattle-derived isolates, this plasmid backbone was found at a high frequency (50 to 100%) among S. Kentucky isolates from chickens within the same time span. Ninety-four percent of the APEC-positive isolates showed resistance to tetracycline and streptomycin. Together, our findings of a resistance-conferring APEC virulence plasmid in a poultry-derived S. Kentucky isolate and of similar resistance/virulence plasmids in most recent S. Kentucky isolates from chickens and, to lesser degree, from humans and cattle highlight the need for additional research in order to examine the prevalence and spread of combined virulence and resistance plasmids in bacteria in agricultural, environmental, and clinical settings.
ESTHER : Fricke_2009_Appl.Environ.Microbiol_75_5963
PubMedSearch : Fricke_2009_Appl.Environ.Microbiol_75_5963
PubMedID: 19648374
Gene_locus related to this paper: ecoli-IROD , shidy-q67dv1

Title : The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates - Rasko_2008_J.Bacteriol_190_6881
Author(s) : Rasko DA , Rosovitz MJ , Myers GS , Mongodin EF , Fricke WF , Gajer P , Crabtree J , Sebaihia M , Thomson NR , Chaudhuri R , Henderson IR , Sperandio V , Ravel J
Ref : Journal of Bacteriology , 190 :6881 , 2008
Abstract : Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of approximately 2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.
ESTHER : Rasko_2008_J.Bacteriol_190_6881
PubMedSearch : Rasko_2008_J.Bacteriol_190_6881
PubMedID: 18676672
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C4836 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-ypt1 , ecoli-yqia , ecoli-Z2445 , ecoli-YfhR

Title : Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5 - Fricke_2008_J.Bacteriol_190_6779
Author(s) : Fricke WF , Wright MS , Lindell AH , Harkins DM , Baker-Austin C , Ravel J , Stepanauskas R
Ref : Journal of Bacteriology , 190 :6779 , 2008
Abstract : The increasing occurrence of multidrug-resistant pathogens of clinical and agricultural importance is a global public health concern. While antimicrobial use in human and veterinary medicine is known to contribute to the dissemination of antimicrobial resistance, the impact of microbial communities and mobile resistance genes from the environment in this process is not well understood. Isolated from an industrially polluted aquatic environment, Escherichia coli SMS-3-5 is resistant to a record number of antimicrobial compounds from all major classes, including two front-line fluoroquinolones (ciprofloxacin and moxifloxacin), and in many cases at record-high concentrations. To gain insights into antimicrobial resistance in environmental bacterial populations, the genome of E. coli SMS-3-5 was sequenced and compared to the genome sequences of other E. coli strains. In addition, selected genetic loci from E. coli SMS-3-5 predicted to be involved in antimicrobial resistance were phenotypically characterized. Using recombinant vector clones from shotgun sequencing libraries, resistance to tetracycline, streptomycin, and sulfonamide/trimethoprim was assigned to a single mosaic region on a 130-kb plasmid (pSMS35_130). The remaining plasmid backbone showed similarity to virulence plasmids from avian-pathogenic E. coli (APEC) strains. Individual resistance gene cassettes from pSMS35_130 are conserved among resistant bacterial isolates from multiple phylogenetic and geographic sources. Resistance to quinolones was assigned to several chromosomal loci, mostly encoding transport systems that are also present in susceptible E. coli isolates. Antimicrobial resistance in E. coli SMS-3-5 is therefore dependent both on determinants acquired from a mobile gene pool that is likely available to clinical and agricultural pathogens, as well, and on specifically adapted multidrug efflux systems. The association of antimicrobial resistance with APEC virulence genes on pSMS35_130 highlights the risk of promoting the spread of virulence through the extensive use of antibiotics.
ESTHER : Fricke_2008_J.Bacteriol_190_6779
PubMedSearch : Fricke_2008_J.Bacteriol_190_6779
PubMedID: 18708504
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C0410 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-estX , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-yqia , ecoli-YfhR , ecosm-b1lhu2

Title : The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features - Seedorf_2008_Proc.Natl.Acad.Sci.U.S.A_105_2128
Author(s) : Seedorf H , Fricke WF , Veith B , Bruggemann H , Liesegang H , Strittmatter A , Miethke M , Buckel W , Hinderberger J , Li F , Hagemeier C , Thauer RK , Gottschalk G
Ref : Proc Natl Acad Sci U S A , 105 :2128 , 2008
Abstract : Clostridium kluyveri is unique among the clostridia; it grows anaerobically on ethanol and acetate as sole energy sources. Fermentation products are butyrate, caproate, and H2. We report here the genome sequence of C. kluyveri, which revealed new insights into the metabolic capabilities of this well studied organism. A membrane-bound energy-converting NADH:ferredoxin oxidoreductase (RnfCDGEAB) and a cytoplasmic butyryl-CoA dehydrogenase complex (Bcd/EtfAB) coupling the reduction of crotonyl-CoA to butyryl-CoA with the reduction of ferredoxin represent a new energy-conserving module in anaerobes. The genes for NAD-dependent ethanol dehydrogenase and NAD(P)-dependent acetaldehyde dehydrogenase are located next to genes for microcompartment proteins, suggesting that the two enzymes, which are isolated together in a macromolecular complex, form a carboxysome-like structure. Unique for a strict anaerobe, C. kluyveri harbors three sets of genes predicted to encode for polyketide/nonribosomal peptide synthetase hybrides and one set for a nonribosomal peptide synthetase. The latter is predicted to catalyze the synthesis of a new siderophore, which is formed under iron-deficient growth conditions.
ESTHER : Seedorf_2008_Proc.Natl.Acad.Sci.U.S.A_105_2128
PubMedSearch : Seedorf_2008_Proc.Natl.Acad.Sci.U.S.A_105_2128
PubMedID: 18218779
Gene_locus related to this paper: clok1-b9e489 , clok5-a5myu5 , clok5-a5mz95 , clok5-a5n686

Title : The complete genome sequence of Yersinia pseudotuberculosis IP31758, the causative agent of Far East scarlet-like fever - Eppinger_2007_PLoS.Genet_3_e142
Author(s) : Eppinger M , Rosovitz MJ , Fricke WF , Rasko DA , Kokorina G , Fayolle C , Lindler LE , Carniel E , Ravel J
Ref : PLoS Genet , 3 :e142 , 2007
Abstract : The first reported Far East scarlet-like fever (FESLF) epidemic swept the Pacific coastal region of Russia in the late 1950s. Symptoms of the severe infection included erythematous skin rash and desquamation, exanthema, hyperhemic tongue, and a toxic shock syndrome. The term FESLF was coined for the infection because it shares clinical presentations with scarlet fever caused by group A streptococci. The causative agent was later identified as Yersinia pseudotuberculosis, although the range of morbidities was vastly different from classical pseudotuberculosis symptoms. To understand the origin and emergence of the peculiar clinical features of FESLF, we have sequenced the genome of the FESLF-causing strain Y. pseudotuberculosis IP31758 and compared it with that of another Y. pseudotuberculosis strain, IP32953, which causes classical gastrointestinal symptoms. The unique gene pool of Y pseudotuberculosis IP31758 accounts for more than 260 strain-specific genes and introduces individual physiological capabilities and virulence determinants, with a significant proportion horizontally acquired that likely originated from Enterobacteriaceae and other soil-dwelling bacteria that persist in the same ecological niche. The mobile genome pool includes two novel plasmids phylogenetically unrelated to all currently reported Yersinia plasmids. An icm/dot type IVB secretion system, shared only with the intracellular persisting pathogens of the order Legionellales, was found on the larger plasmid and could contribute to scarlatinoid fever symptoms in patients due to the introduction of immunomodulatory and immunosuppressive capabilities. We determined the common and unique traits resulting from genome evolution and speciation within the genus Yersinia and drew a more accurate species border between Y. pseudotuberculosis and Y. pestis. In contrast to the lack of genetic diversity observed in the evolutionary young descending Y. pestis lineage, the population genetics of Y. pseudotuberculosis is more heterogenous. Both Y. pseudotuberculosis strains IP31758 and the previously sequenced Y. pseudotuberculosis strain IP32953 have evolved by the acquisition of specific plasmids and by the horizontal acquisition and incorporation of different genetic information into the chromosome, which all together or independently seems to potentially impact the phenotypic adaptation of these two strains.
ESTHER : Eppinger_2007_PLoS.Genet_3_e142
PubMedSearch : Eppinger_2007_PLoS.Genet_3_e142
PubMedID: 17784789
Gene_locus related to this paper: yerpe-BIOH , yerpe-dlhh , yerpe-PIP , yerpe-PTRB , yerpe-Y0507 , yerpe-y1616 , yerpe-y3224 , yerpe-YPLA , yerpe-YPO0180 , yerpe-YPO0667 , yerpe-YPO0773 , yerpe-YPO0986 , yerpe-YPO1501 , yerpe-YPO1997 , yerpe-YPO2526 , yerpe-YPO2814

Title : The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis - Fricke_2006_J.Bacteriol_188_642
Author(s) : Fricke WF , Seedorf H , Henne A , Kruer M , Liesegang H , Hedderich R , Gottschalk G , Thauer RK
Ref : Journal of Bacteriology , 188 :642 , 2006
Abstract : Methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic archaea. This human intestinal inhabitant can generate methane only by reduction of methanol with H2 and is dependent on acetate as a carbon source. We report here the genome sequence of M. stadtmanae, which was found to be composed of 1,767,403 bp with an average G+C content of 28% and to harbor only 1,534 protein-encoding sequences (CDS). The genome lacks 37 CDS present in the genomes of all other methanogens. Among these are the CDS for synthesis of molybdopterin and for synthesis of the carbon monoxide dehydrogenase/acetyl-coenzyme A synthase complex, which explains why M. stadtmanae cannot reduce CO2 to methane or oxidize methanol to CO2 and why this archaeon is dependent on acetate for biosynthesis of cell components. Four sets of mtaABC genes coding for methanol:coenzyme M methyltransferases were found in the genome of M. stadtmanae. These genes exhibit homology to mta genes previously identified in Methanosarcina species. The M. stadtmanae genome also contains at least 323 CDS not present in the genomes of all other archaea. Seventy-three of these CDS exhibit high levels of homology to CDS in genomes of bacteria and eukaryotes. These 73 CDS include 12 CDS which are unusually long (>2,400 bp) with conspicuous repetitive sequence elements, 13 CDS which exhibit sequence similarity on the protein level to CDS encoding enzymes involved in the biosynthesis of cell surface antigens in bacteria, and 5 CDS which exhibit sequence similarity to the subunits of bacterial type I and III restriction-modification systems.
ESTHER : Fricke_2006_J.Bacteriol_188_642
PubMedSearch : Fricke_2006_J.Bacteriol_188_642
PubMedID: 16385054
Gene_locus related to this paper: metst-q2ne60 , metst-q2ngh9

Title : Genome sequence of the bioplastic-producing Knallgas bacterium Ralstonia eutropha H16 - Pohlmann_2006_Nat.Biotechnol_24_1257
Author(s) : Pohlmann A , Fricke WF , Reinecke F , Kusian B , Liesegang H , Cramm R , Eitinger T , Ewering C , Potter M , Schwartz E , Strittmatter A , Voss I , Gottschalk G , Steinbuchel A , Friedrich B , Bowien B
Ref : Nat Biotechnol , 24 :1257 , 2006
Abstract : The H(2)-oxidizing lithoautotrophic bacterium Ralstonia eutropha H16 is a metabolically versatile organism capable of subsisting, in the absence of organic growth substrates, on H(2) and CO(2) as its sole sources of energy and carbon. R. eutropha H16 first attracted biotechnological interest nearly 50 years ago with the realization that the organism's ability to produce and store large amounts of poly[R-(-)-3-hydroxybutyrate] and other polyesters could be harnessed to make biodegradable plastics. Here we report the complete genome sequence of the two chromosomes of R. eutropha H16. Together, chromosome 1 (4,052,032 base pairs (bp)) and chromosome 2 (2,912,490 bp) encode 6,116 putative genes. Analysis of the genome sequence offers the genetic basis for exploiting the biotechnological potential of this organism and provides insights into its remarkable metabolic versatility.
ESTHER : Pohlmann_2006_Nat.Biotechnol_24_1257
PubMedSearch : Pohlmann_2006_Nat.Biotechnol_24_1257
PubMedID: 16964242
Gene_locus related to this paper: alceu-catD1 , alceu-catD2 , alceu-lipas , alceu-q4w8c9 , cupne-q7wt49 , cupnh-q0jy77 , cupnh-q0k0b3 , cupnh-q0k0b5 , cupnh-q0k0g2 , cupnh-q0k0l5 , cupnh-q0k0q7 , cupnh-q0k2d0 , cupnh-q0k4q3 , cupnh-q0k4r4 , cupnh-q0k9j6 , cupnh-q0ka76 , cupnh-q0kab1 , cupnh-q0kat1 , cupnh-q0kcu9 , cupnh-q0kd98 , cupnh-q0kdv2 , cupnh-q0ke65 , cuppj-metx , cuppj-q472r0 , cuptr-b2agb4 , cuptr-b3r9z0 , cuptr-b3r543 , cupnh-acoc , cupnh-q0jyv4 , cupnh-q0jzs8 , cupnh-q0jzu9 , cupnh-q0k1a8 , cupnh-q0k1c5 , cupnh-q0k2b3 , cupnh-q0k3m7 , cupnh-q0k7y4 , cupnh-q0k9g4 , cupnh-q0k9l1 , cupnh-q0k038 , cupnh-q0k189 , cupnh-q0k199 , cupnh-q0k226 , cupnh-q0k320 , cupnh-q0k399 , cupnh-q0kbr4 , cupnh-q0kbs3 , cupnh-q0kcd2 , cupnh-q0kci6 , cupnh-q0kd51 , cupnh-q0kfc2 , ralpi-u3qr80 , cupnn-g0ewh7 , cupnh-hboh , cupnh-q0kdw6

Title : Complete genome sequence of the acetic acid bacterium Gluconobacter oxydans - Prust_2005_Nat.Biotechnol_23_195
Author(s) : Prust C , Hoffmeister M , Liesegang H , Wiezer A , Fricke WF , Ehrenreich A , Gottschalk G , Deppenmeier U
Ref : Nat Biotechnol , 23 :195 , 2005
Abstract : Gluconobacter oxydans is unsurpassed by other organisms in its ability to incompletely oxidize a great variety of carbohydrates, alcohols and related compounds. Furthermore, the organism is used for several biotechnological processes, such as vitamin C production. To further our understanding of its overall metabolism, we sequenced the complete genome of G. oxydans 621H. The chromosome consists of 2,702,173 base pairs and contains 2,432 open reading frames. In addition, five plasmids were identified that comprised 232 open reading frames. The sequence data can be used for metabolic reconstruction of the pathways leading to industrially important products derived from sugars and alcohols. Although the respiratory chain of G. oxydans was found to be rather simple, the organism contains many membrane-bound dehydrogenases that are critical for the incomplete oxidation of biotechnologically important substrates. Moreover, the genome project revealed the unique biochemistry of G. oxydans with respect to the process of incomplete oxidation.
ESTHER : Prust_2005_Nat.Biotechnol_23_195
PubMedSearch : Prust_2005_Nat.Biotechnol_23_195
PubMedID: 15665824
Gene_locus related to this paper: gluox-metx , gluox-q5fn25 , gluox-q5fn27 , gluox-q5fnv1 , gluox-q5fpe1 , gluox-q5fpq8 , gluox-q5fq41 , gluox-q5fq84 , gluox-q5fqg3 , gluox-q5fqw7 , gluox-q5fqy6 , gluox-q5fsb6 , gluox-q5fsc5 , gluox-q5fsj2 , gluox-q5fsy1 , gluox-q5fsz2 , gluox-q5ft19 , gluox-q5ft58 , gluox-q5ftj8 , gluox-q5ftp6 , gluox-q5fuk6 , gluox-q5fum7 , gluox-q5fup8

Title : The genome sequence of Clostridium tetani, the causative agent of tetanus disease - Bruggemann_2003_Proc.Natl.Acad.Sci.U.S.A_100_1316
Author(s) : Bruggemann H , Baumer S , Fricke WF , Wiezer A , Liesegang H , Decker I , Herzberg C , Martinez-Arias R , Merkl R , Henne A , Gottschalk G
Ref : Proceedings of the National Academy of Sciences of the United States of America , 100 :1316 , 2003
Abstract : Tetanus disease is one of the most dramatic and globally prevalent diseases of humans and vertebrate animals, and has been reported for over 24 centuries. The manifestation of the disease, spastic paralysis, is caused by the second most poisonous substance known, the tetanus toxin, with a human lethal dose of approximately 1 ng/kg. Fortunately, this disease is successfully controlled through immunization with tetanus toxoid; nevertheless, according to the World Health Organization, an estimated 400,000 cases still occur each year, mainly of neonatal tetanus. The causative agent of tetanus disease is Clostridium tetani, an anaerobic spore-forming bacterium, whose natural habitat is soil, dust, and intestinal tracts of various animals. Here we report the complete genome sequence of toxigenic C. tetani E88, a variant of strain Massachusetts. The genome consists of a 2,799,250-bp chromosome encoding 2,372 ORFs. The tetanus toxin and a collagenase are encoded on a 74,082-bp plasmid, containing 61 ORFs. Additional virulence-related factors could be identified, such as an array of surface-layer and adhesion proteins (35 ORFs), some of them unique to C. tetani. Comparative genomics with the genomes of Clostridium perfringens, the causative agent of gas gangrene, and Clostridium acetobutylicum, a nonpathogenic solvent producer, revealed a remarkable capacity of C. tetani: The organism can rely on an extensive sodium ion bioenergetics. Additional candidate genes involved in the establishment and maintenance of a pathogenic lifestyle of C. tetani are presented.
ESTHER : Bruggemann_2003_Proc.Natl.Acad.Sci.U.S.A_100_1316
PubMedSearch : Bruggemann_2003_Proc.Natl.Acad.Sci.U.S.A_100_1316
PubMedID: 12552129
Gene_locus related to this paper: clote-CTC00812 , clote-CTC00947 , clote-CTC01150 , clote-CTC01505 , clote-CTC02183 , clote-CTC02480