Gottschalk G

References (33)

Title : First Insights into the Genome of the Gram-Negative, Endospore-Forming Organism Sporomusa ovata Strain H1 DSM 2662 - Poehlein_2013_Genome.Announc_1_e00734
Author(s) : Poehlein A , Gottschalk G , Daniel R
Ref : Genome Announc , 1 : , 2013
Abstract : The genome of Sporomusa ovata strain H1 DSM 2662, an anaerobic, Gram-negative endospore-forming bacterium, was sequenced. S. ovata uses N-methyl compounds, primary alcohols, fatty acids, and H2 and CO2 as energy and carbon sources to produce acetate. The genome harbors one chromosome, which encodes proteins typical for sporulation.
ESTHER : Poehlein_2013_Genome.Announc_1_e00734
PubMedSearch : Poehlein_2013_Genome.Announc_1_e00734
PubMedID: 24029766
Gene_locus related to this paper: 9firm-t0iev1 , 9firm-t0ikb0

Title : DNA sequence analysis of the composite plasmid pTC conferring virulence and antimicrobial resistance for porcine enterotoxigenic Escherichia coli - Fekete_2012_Int.J.Med.Microbiol_302_4
Author(s) : Fekete PZ , Brzuszkiewicz E , Blum-Oehler G , Olasz F , Szabo M , Gottschalk G , Hacker J , Nagy B
Ref : Int J Med Microbiol , 302 :4 , 2012
Abstract : In this study the plasmid pTC, a 90 kb self-conjugative virulence plasmid of the porcine enterotoxigenic Escherichia coli (ETEC) strain EC2173 encoding the STa and STb heat-stable enterotoxins and tetracycline resistance, has been sequenced in two steps. As a result we identified five main distinct regions of pTC: (i) the maintenance region responsible for the extreme stability of the plasmid, (ii) the TSL (toxin-specific locus comprising the estA and estB genes) which is unique and characteristic for pTC, (iii) a Tn10 transposon, encoding tetracycline resistance, (iv) the tra (plasmid transfer) region, and (v) the colE1-like origin of replication. It is concluded that pTC is a self-transmissible composite plasmid harbouring antibiotic resistance and virulence genes. pTC belongs to a group of large conjugative E. coli plasmids represented by NR1 with a widespread tra backbone which might have evolved from a common ancestor. This is the first report of a completely sequenced animal ETEC virulence plasmid containing an antimicrobial resistance locus, thereby representing a selection advantage for spread of pathogenicity in the presence of antimicrobials leading to increased disease potential.
ESTHER : Fekete_2012_Int.J.Med.Microbiol_302_4
PubMedSearch : Fekete_2012_Int.J.Med.Microbiol_302_4
PubMedID: 22000740
Gene_locus related to this paper: ecoli-ypt1

Title : Genome sequence of Staphylococcus aureus VC40, a vancomycin- and daptomycin-resistant strain, to study the genetics of development of resistance to currently applied last-resort antibiotics - Sass_2012_J.Bacteriol_194_2107
Author(s) : Sass P , Berscheid A , Jansen A , Oedenkoven M , Szekat C , Strittmatter A , Gottschalk G , Bierbaum G
Ref : Journal of Bacteriology , 194 :2107 , 2012
Abstract : The increasing emergence of multidrug-resistant Staphylococcus aureus is a problem of global importance. Here, we report the genome of S. aureus VC40, which is resistant to the last-resort antibiotics vancomycin and daptomycin. Its genome sequence will allow insights into the mechanisms that convey full resistance to these compounds.
ESTHER : Sass_2012_J.Bacteriol_194_2107
PubMedSearch : Sass_2012_J.Bacteriol_194_2107
PubMedID: 22461548
Gene_locus related to this paper: staau-SA0897 , staau-SA2240

Title : Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5 - Volland_2011_J.Bacteriol_193_5043
Author(s) : Volland S , Rachinger M , Strittmatter A , Daniel R , Gottschalk G , Meyer O
Ref : Journal of Bacteriology , 193 :5043 , 2011
Abstract : We report on genome sequencing of Oligotropha carboxidovorans strain OM4 and resequencing of strain OM5. The genomes of both are composed of one chromosome and two plasmids. The presence of two plasmids in the OM5 genome is inconsistent with the previously published sequence, for which only one plasmid was described (D. Paul, S. Bridges, S. Burgess, Y. Dandass, and M. Lawrence, BMC Genomics 11:511, 2010).
ESTHER : Volland_2011_J.Bacteriol_193_5043
PubMedSearch : Volland_2011_J.Bacteriol_193_5043
PubMedID: 21742883
Gene_locus related to this paper: olico-b6jb07 , olico-b6jhe6

Title : Comparative genomics and transcriptomics of Propionibacterium acnes - Brzuszkiewicz_2011_PLoS.One_6_e21581
Author(s) : Brzuszkiewicz E , Weiner J , Wollherr A , Thurmer A , Hupeden J , Lomholt HB , Kilian M , Gottschalk G , Daniel R , Mollenkopf HJ , Meyer TF , Bruggemann H
Ref : PLoS ONE , 6 :e21581 , 2011
Abstract : The anaerobic gram-positive bacterium Propionibacterium acnes is a human skin commensal that is occasionally associated with inflammatory diseases. Recent work has indicated that evolutionary distinct lineages of P. acnes play etiologic roles in disease while others are associated with maintenance of skin homeostasis. To shed light on the molecular basis for differential strain properties, we carried out genomic and transcriptomic analysis of distinct P. acnes strains. We sequenced the genome of the P. acnes strain 266, a type I-1a strain. Comparative genome analysis of strain 266 and four other P. acnes strains revealed that overall genome plasticity is relatively low; however, a number of island-like genomic regions, encoding a variety of putative virulence-associated and fitness traits differ between phylotypes, as judged from PCR analysis of a collection of P. acnes strains. Comparative transcriptome analysis of strains KPA171202 (type I-2) and 266 during exponential growth revealed inter-strain differences in gene expression of transport systems and metabolic pathways. In addition, transcript levels of genes encoding possible virulence factors such as dermatan-sulphate adhesin, polyunsaturated fatty acid isomerase, iron acquisition protein HtaA and lipase GehA were upregulated in strain 266. We investigated differential gene expression during exponential and stationary growth phases. Genes encoding components of the energy-conserving respiratory chain as well as secreted and virulence-associated factors were transcribed during the exponential phase, while the stationary growth phase was characterized by upregulation of genes involved in stress responses and amino acid metabolism. Our data highlight the genomic basis for strain diversity and identify, for the first time, the actively transcribed part of the genome, underlining the important role growth status plays in the inflammation-inducing activity of P. acnes. We argue that the disease-causing potential of different P. acnes strains is not only determined by the phylotype-specific genome content but also by variable gene expression.
ESTHER : Brzuszkiewicz_2011_PLoS.One_6_e21581
PubMedSearch : Brzuszkiewicz_2011_PLoS.One_6_e21581
PubMedID: 21738717
Gene_locus related to this paper: proac-q6a5t3 , proac-q6a5w7 , proac-q6a981

Title : Genomic features and insights into the biology of Mycoplasma fermentans - Rechnitzer_2011_Microbiology_157_760
Author(s) : Rechnitzer H , Brzuszkiewicz E , Strittmatter A , Liesegang H , Lysnyansky I , Daniel R , Gottschalk G , Rottem S
Ref : Microbiology , 157 :760 , 2011
Abstract : We present the complete genomic sequence of Mycoplasma fermentans, an organism suggested to be associated with the pathogenesis of rheumatoid arthritis in humans. The genome is composed of 977,524 bp and has a mean G+C content of 26.95 mol%. There are 835 predicted protein-coding sequences and a mean coding density of 87.6 %. Functions have been assigned to 58.8 % of the predicted protein-coding sequences, while 18.4 % of the proteins are conserved hypothetical proteins and 22.8 % are hypothetical proteins. In addition, there are two complete rRNA operons and 36 tRNA coding sequences. The largest gene families are the ABC transporter family (42 members), and the functionally heterogeneous group of lipoproteins (28 members), which encode the characteristic prokaryotic cysteine 'lipobox'. Protein secretion occurs through a pathway consisting of SecA, SecD, SecE, SecG, SecY and YidC. Some highly conserved eubacterial proteins, such as GroEL and GroES, are notably absent. The genes encoding DnaK-DnaJ-GrpE and Tig, forming the putative complex of chaperones, are intact, providing the only known control over protein folding. Eighteen nucleases and 17 proteases and peptidases were detected as well as three genes for the thioredoxin-thioreductase system. Overall, this study presents insights into the physiology of M. fermentans, and provides several examples of the genetic basis of systems that might function as virulence factors in this organism.
ESTHER : Rechnitzer_2011_Microbiology_157_760
PubMedSearch : Rechnitzer_2011_Microbiology_157_760
PubMedID: 21109561
Gene_locus related to this paper: mycfe-c4xfu4 , mycfp-c4xfg3

Title : The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis virulence plasmids - Klee_2010_PLoS.One_5_e10986
Author(s) : Klee SR , Brzuszkiewicz EB , Nattermann H , Bruggemann H , Dupke S , Wollherr A , Franz T , Pauli G , Appel B , Liebl W , Couacy-Hymann E , Boesch C , Meyer FD , Leendertz FH , Ellerbrok H , Gottschalk G , Grunow R , Liesegang H
Ref : PLoS ONE , 5 :e10986 , 2010
Abstract : Anthrax is a fatal disease caused by strains of Bacillus anthracis. Members of this monophyletic species are non motile and are all characterized by the presence of four prophages and a nonsense mutation in the plcR regulator gene. Here we report the complete genome sequence of a Bacillus strain isolated from a chimpanzee that had died with clinical symptoms of anthrax. Unlike classic B. anthracis, this strain was motile and lacked the four prohages and the nonsense mutation. Four replicons were identified, a chromosome and three plasmids. Comparative genome analysis revealed that the chromosome resembles those of non-B. anthracis members of the Bacillus cereus group, whereas two plasmids were identical to the anthrax virulence plasmids pXO1 and pXO2. The function of the newly discovered third plasmid with a length of 14 kbp is unknown. A detailed comparison of genomic loci encoding key features confirmed a higher similarity to B. thuringiensis serovar konkukian strain 97-27 and B. cereus E33L than to B. anthracis strains. For the first time we describe the sequence of an anthrax causing bacterium possessing both anthrax plasmids that apparently does not belong to the monophyletic group of all so far known B. anthracis strains and that differs in important diagnostic features. The data suggest that this bacterium has evolved from a B. cereus strain independently from the classic B. anthracis strains and established a B. anthracis lifestyle. Therefore we suggest to designate this isolate as "B. cereus variety (var.) anthracis".
ESTHER : Klee_2010_PLoS.One_5_e10986
PubMedSearch : Klee_2010_PLoS.One_5_e10986
PubMedID: 20634886
Gene_locus related to this paper: bacan-BA1866 , bacan-BA2392 , bacan-BA4324 , bacan-BA5009 , bacan-BA5110 , bacce-BC2171 , bacce-BC5130

Title : Host imprints on bacterial genomes--rapid, divergent evolution in individual patients - Zdziarski_2010_PLoS.Pathog_6_e1001078
Author(s) : Zdziarski J , Brzuszkiewicz E , Wullt B , Liesegang H , Biran D , Voigt B , Gronberg-Hernandez J , Ragnarsdottir B , Hecker M , Ron EZ , Daniel R , Gottschalk G , Hacker J , Svanborg C , Dobrindt U
Ref : PLoS Pathog , 6 :e1001078 , 2010
Abstract : Bacteria lose or gain genetic material and through selection, new variants become fixed in the population. Here we provide the first, genome-wide example of a single bacterial strain's evolution in different deliberately colonized patients and the surprising insight that hosts appear to personalize their microflora. By first obtaining the complete genome sequence of the prototype asymptomatic bacteriuria strain E. coli 83972 and then resequencing its descendants after therapeutic bladder colonization of different patients, we identified 34 mutations, which affected metabolic and virulence-related genes. Further transcriptome and proteome analysis proved that these genome changes altered bacterial gene expression resulting in unique adaptation patterns in each patient. Our results provide evidence that, in addition to stochastic events, adaptive bacterial evolution is driven by individual host environments. Ongoing loss of gene function supports the hypothesis that evolution towards commensalism rather than virulence is favored during asymptomatic bladder colonization.
ESTHER : Zdziarski_2010_PLoS.Pathog_6_e1001078
PubMedSearch : Zdziarski_2010_PLoS.Pathog_6_e1001078
PubMedID: 20865122
Gene_locus related to this paper: ecoli-rutD , ecoli-bioh , ecoli-yafa , ecoli-ybff , ecoli-ycfp , ecoli-YFBB , ecoli-yqia , ecoli-YfhR

Title : Clostridium ljungdahlii represents a microbial production platform based on syngas - Kopke_2010_Proc.Natl.Acad.Sci.U.S.A_107_13087
Author(s) : Kopke M , Held C , Hujer S , Liesegang H , Wiezer A , Wollherr A , Ehrenreich A , Liebl W , Gottschalk G , Durre P
Ref : Proc Natl Acad Sci U S A , 107 :13087 , 2010
Abstract : Clostridium ljungdahlii is an anaerobic homoacetogen, able to ferment sugars, other organic compounds, or CO(2)/H(2) and synthesis gas (CO/H(2)). The latter feature makes it an interesting microbe for the biotech industry, as important bulk chemicals and proteins can be produced at the expense of CO(2), thus combining industrial needs with sustained reduction of CO and CO(2) in the atmosphere. Sequencing the complete genome of C. ljungdahlii revealed that it comprises 4,630,065 bp and is one of the largest clostridial genomes known to date. Experimental data and in silico comparisons revealed a third mode of anaerobic homoacetogenic metabolism. Unlike other organisms such as Moorella thermoacetica or Acetobacterium woodii, neither cytochromes nor sodium ions are involved in energy generation. Instead, an Rnf system is present, by which proton translocation can be performed. An electroporation procedure has been developed to transform the organism with plasmids bearing heterologous genes for butanol production. Successful expression of these genes could be demonstrated, leading to formation of the biofuel. Thus, C. ljungdahlii can be used as a unique microbial production platform based on synthesis gas and carbon dioxide/hydrogen mixtures.
ESTHER : Kopke_2010_Proc.Natl.Acad.Sci.U.S.A_107_13087
PubMedSearch : Kopke_2010_Proc.Natl.Acad.Sci.U.S.A_107_13087
PubMedID: 20616070
Gene_locus related to this paper: clold-d8gi04 , clold-d8gqb1 , clold-d8gsx2 , clold-d8gue9

Title : Complete genome sequence of Methanothermobacter marburgensis, a methanoarchaeon model organism - Liesegang_2010_J.Bacteriol_192_5850
Author(s) : Liesegang H , Kaster AK , Wiezer A , Goenrich M , Wollherr A , Seedorf H , Gottschalk G , Thauer RK
Ref : Journal of Bacteriology , 192 :5850 , 2010
Abstract : The circular genome sequence of the chemolithoautotrophic euryarchaeon Methanothermobacter marburgensis, with 1,639,135 bp, was determined and compared with that of Methanothermobacter thermautotrophicus. The genomes of the two model methanogens differ substantially in protein coding sequences, in insertion sequence (IS)-like elements, and in clustered regularly interspaced short palindromic repeats (CRISPR) loci.
ESTHER : Liesegang_2010_J.Bacteriol_192_5850
PubMedSearch : Liesegang_2010_J.Bacteriol_192_5850
PubMedID: 20802048

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 : Rhizobium sp. strain NGR234 possesses a remarkable number of secretion systems - Schmeisser_2009_Appl.Environ.Microbiol_75_4035
Author(s) : Schmeisser C , Liesegang H , Krysciak D , Bakkou N , Le Quere A , Wollherr A , Heinemeyer I , Morgenstern B , Pommerening-Roser A , Flores M , Palacios R , Brenner S , Gottschalk G , Schmitz RA , Broughton WJ , Perret X , Strittmatter AW , Streit WR
Ref : Applied Environmental Microbiology , 75 :4035 , 2009
Abstract : Rhizobium sp. strain NGR234 is a unique alphaproteobacterium (order Rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. We report here that the 3.93-Mbp chromosome (cNGR234) encodes most functions required for cellular growth. Few essential functions are encoded on the 2.43-Mbp megaplasmid (pNGR234b), and none are present on the second 0.54-Mbp symbiotic plasmid (pNGR234a). Among many striking features, the 6.9-Mbp genome encodes more different secretion systems than any other known rhizobia and probably most known bacteria. Altogether, 132 genes and proteins are linked to secretory processes. Secretion systems identified include general and export pathways, a twin arginine translocase secretion system, six type I transporter genes, one functional and one putative type III system, three type IV attachment systems, and two putative type IV conjugation pili. Type V and VI transporters were not identified, however. NGR234 also carries genes and regulatory networks linked to the metabolism of a wide range of aromatic and nonaromatic compounds. In this way, NGR234 can quickly adapt to changing environmental stimuli in soils, rhizospheres, and plants. Finally, NGR234 carries at least six loci linked to the quenching of quorum-sensing signals, as well as one gene (ngrI) that possibly encodes a novel type of autoinducer I molecule.
ESTHER : Schmeisser_2009_Appl.Environ.Microbiol_75_4035
PubMedSearch : Schmeisser_2009_Appl.Environ.Microbiol_75_4035
PubMedID: 19376903
Gene_locus related to this paper: rhime-R01391 , rhime-R02260 , rhime-R02478 , rhisn-c3kku8 , rhisn-c3kl46 , rhisn-c3kly5 , rhisn-c3klz9 , rhisn-c3kmf4 , rhisn-c3kmp5 , rhisn-c3knq1 , rhisn-c3krv5 , rhisn-c3mdb6 , rhisn-c3mee2 , rhisn-c3meq6 , rhisn-c3mev4 , rhisn-c3mgd2 , rhisn-c3mil7 , rhisn-c3miq5 , rhisn-q6w1e1 , sinmw-a6ugj8 , rhisn-c3km61 , rhisn-c3m991 , sinfn-c3m9f4 , sinfn-y4kf

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 : Complete nucleotide sequence of the 113-kilobase linear catabolic plasmid pAL1 of Arthrobacter nitroguajacolicus Ru61a and transcriptional analysis of genes involved in quinaldine degradation - Parschat_2007_J.Bacteriol_189_3855
Author(s) : Parschat K , Overhage J , Strittmatter AW , Henne A , Gottschalk G , Fetzner S
Ref : Journal of Bacteriology , 189 :3855 , 2007
Abstract : The nucleotide sequence of the linear catabolic plasmid pAL1 from the 2-methylquinoline (quinaldine)-degrading strain Arthrobacter nitroguajacolicus Ru61a comprises 112,992 bp. A total of 103 open reading frames (ORFs) were identified on pAL1, 49 of which had no annotatable function. The ORFs were assigned to the following functional groups: (i) catabolism of quinaldine and anthranilate, (ii) conjugation, and (iii) plasmid maintenance and DNA replication and repair. The genes for conversion of quinaldine to anthranilate are organized in two operons that include ORFs presumed to code for proteins involved in assembly of the quinaldine-4-oxidase holoenzyme, namely, a MobA-like putative molybdopterin cytosine dinucleotide synthase and an XdhC-like protein that could be required for insertion of the molybdenum cofactor. Genes possibly coding for enzymes involved in anthranilate degradation via 2-aminobenzoyl coenzyme A form another operon. These operons were expressed when cells were grown on quinaldine or on aromatic compounds downstream in the catabolic pathway. Single-stranded 3' overhangs of putative replication intermediates of pAL1 were predicted to form elaborate secondary structures due to palindromic and superpalindromic terminal sequences; however, the two telomeres appear to form different structures. Sequence analysis of ORFs 101 to 103 suggested that pAL1 codes for one or two putative terminal proteins, presumed to be covalently bound to the 5' termini, and a multidomain telomere-associated protein (Tap) comprising 1,707 amino acids. Even if the putative proteins encoded by ORFs 101 to 103 share motifs with the Tap and terminal proteins involved in telomere patching of Streptomyces linear replicons, their overall sequences and domain structures differ significantly.
ESTHER : Parschat_2007_J.Bacteriol_189_3855
PubMedSearch : Parschat_2007_J.Bacteriol_189_3855
PubMedID: 17337569
Gene_locus related to this paper: artsp-hod

Title : Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42 - Chen_2007_Nat.Biotechnol_25_1007
Author(s) : Chen XH , Koumoutsi A , Scholz R , Eisenreich A , Schneider K , Heinemeyer I , Morgenstern B , Voss B , Hess WR , Reva O , Junge H , Voigt B , Jungblut PR , Vater J , Sussmuth R , Liesegang H , Strittmatter A , Gottschalk G , Borriss R
Ref : Nat Biotechnol , 25 :1007 , 2007
Abstract : Bacillus amyloliquefaciens FZB42 is a Gram-positive, plant-associated bacterium, which stimulates plant growth and produces secondary metabolites that suppress soil-borne plant pathogens. Its 3,918-kb genome, containing an estimated 3,693 protein-coding sequences, lacks extended phage insertions, which occur ubiquitously in the closely related Bacillus subtilis 168 genome. The B. amyloliquefaciens FZB42 genome reveals an unexpected potential to produce secondary metabolites, including the polyketides bacillaene and difficidin. More than 8.5% of the genome is devoted to synthesizing antibiotics and siderophores by pathways not involving ribosomes. Besides five gene clusters, known from B. subtilis to mediate nonribosomal synthesis of secondary metabolites, we identified four giant gene clusters absent in B. subtilis 168. The pks2 gene cluster encodes the components to synthesize the macrolactin core skeleton.
ESTHER : Chen_2007_Nat.Biotechnol_25_1007
PubMedSearch : Chen_2007_Nat.Biotechnol_25_1007
PubMedID: 17704766
Gene_locus related to this paper: baca2-a7z1n9 , baca2-a7z2m6 , baca2-a7z3i0 , baca2-a7z7y5 , baca2-a7z8b1 , baca2-a7z811 , baca2-a7z924 , bacam-q1rs52 , bacam-q1rs69 , bacam-q70jx5 , bacas-e1ukt2 , bacsu-SRFC , bacsu-SRFD , bacsu-YVAK , baca2-a7z0n6

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 : Structural and functional characterization of three polyketide synthase gene clusters in Bacillus amyloliquefaciens FZB 42 - Chen_2006_J.Bacteriol_188_4024
Author(s) : Chen XH , Vater J , Piel J , Franke P , Scholz R , Schneider K , Koumoutsi A , Hitzeroth G , Grammel N , Strittmatter AW , Gottschalk G , Sussmuth RD , Borriss R
Ref : Journal of Bacteriology , 188 :4024 , 2006
Abstract : Although bacterial polyketides are of considerable biomedical interest, the molecular biology of polyketide biosynthesis in Bacillus spp., one of the richest bacterial sources of bioactive natural products, remains largely unexplored. Here we assign for the first time complete polyketide synthase (PKS) gene clusters to Bacillus antibiotics. Three giant modular PKS systems of the trans-acyltransferase type were identified in Bacillus amyloliquefaciens FZB 42. One of them, pks1, is an ortholog of the pksX operon with a previously unknown function in the sequenced model strain Bacillus subtilis 168, while the pks2 and pks3 clusters are novel gene clusters. Cassette mutagenesis combined with advanced mass spectrometric techniques such as matrix-assisted laser desorption ionization-time of flight mass spectrometry and liquid chromatography-electrospray ionization mass spectrometry revealed that the pks1 (bae) and pks3 (dif) gene clusters encode the biosynthesis of the polyene antibiotics bacillaene and difficidin or oxydifficidin, respectively. In addition, B. subtilis OKB105 (pheA sfp(0)), a transformant of the B. subtilis 168 derivative JH642, was shown to produce bacillaene, demonstrating that the pksX gene cluster directs the synthesis of that polyketide. The GenBank accession numbers for gene clusters pks1(bae), pks2, and pks3(dif) are AJ 634060.2, AJ 6340601.2, and AJ 6340602.2, respectively.
ESTHER : Chen_2006_J.Bacteriol_188_4024
PubMedSearch : Chen_2006_J.Bacteriol_188_4024
PubMedID: 16707694
Gene_locus related to this paper: bacam-q1rs52 , bacam-q1rs60 , bacam-q1rs69

Title : Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536 - Hochhut_2006_Mol.Microbiol_61_584
Author(s) : Hochhut B , Wilde C , Balling G , Middendorf B , Dobrindt U , Brzuszkiewicz E , Gottschalk G , Carniel E , Hacker J
Ref : Molecular Microbiology , 61 :584 , 2006
Abstract : The genome of uropathogenic Escherichia coli isolate 536 contains five well-characterized pathogenicity islands (PAIs) encoding key virulence factors of this strain. Except PAI IV(536), the four other PAIs of strain 536 are flanked by direct repeats (DRs), carry intact integrase genes and are able to excise site-specifically from the chromosome. Genome screening of strain 536 identified a sixth putative asnW-associated PAI. Despite the presence of DRs and an intact integrase gene, excision of this island was not detected. To investigate the role of PAI-encoded integrases for the recombination process the int genes of each unstable island of strain 536 were inactivated. For PAI I(536) and PAI II(536), their respective P4-like integrase was required for their excision. PAI III(536) carries two integrase genes, intA, encoding an SfX-like integrase, and intB, coding for an integrase with weak similarity to P4-like integrases. Only intB was required for site-specific excision of this island. For PAI V(536), excision could not be abolished after deleting its P4-like integrase gene but additional deletion of the PAI II(536)-specific integrase gene was required. Therefore, although all mediated by P4-like integrases, the activity of the PAI excision machinery is most often restricted to its cognate island. This work also demonstrates for the first time the existence of a cross-talk between integrases of different PAIs and shows that this cross-talk is unidirectional.
ESTHER : Hochhut_2006_Mol.Microbiol_61_584
PubMedSearch : Hochhut_2006_Mol.Microbiol_61_584
PubMedID: 16879640
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C0410 , ecoli-C2429 , ecoli-C2451 , ecoli-C4836 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-IROD , ecoli-IROE , 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-yqia , ecoli-YfhR , ecolx-q707d7 , yerpe-YBTT

Title : Escherichia coli induces DNA double-strand breaks in eukaryotic cells - Nougayrede_2006_Science_313_848
Author(s) : Nougayrede JP , Homburg S , Taieb F , Boury M , Brzuszkiewicz E , Gottschalk G , Buchrieser C , Hacker J , Dobrindt U , Oswald E
Ref : Science , 313 :848 , 2006
Abstract : Transient infection of eukaryotic cells with commensal and extraintestinal pathogenic Escherichia coli of phylogenetic group B2 blocks mitosis and induces megalocytosis. This trait is linked to a widely spread genomic island that encodes giant modular nonribosomal peptide and polyketide synthases. Contact with E. coli expressing this gene cluster causes DNA double-strand breaks and activation of the DNA damage checkpoint pathway, leading to cell cycle arrest and eventually to cell death. Discovery of hybrid peptide-polyketide genotoxins in E. coli will change our view on pathogenesis and commensalism and open new biotechnological applications.
ESTHER : Nougayrede_2006_Science_313_848
PubMedSearch : Nougayrede_2006_Science_313_848
PubMedID: 16902142
Gene_locus related to this paper: ecoli-C2451

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 pathogenicity island-associated K15 capsule determinant exhibits a novel genetic structure and correlates with virulence in uropathogenic Escherichia coli strain 536 - Schneider_2004_Infect.Immun_72_5993
Author(s) : Schneider G , Dobrindt U , Bruggemann H , Nagy G , Janke B , Blum-Oehler G , Buchrieser C , Gottschalk G , Emody L , Hacker J
Ref : Infect Immun , 72 :5993 , 2004
Abstract : The K15 capsule determinant of uropathogenic Escherichia coli strain 536 (O6:K15:H31) is part of a novel 79.6-kb pathogenicity island (PAI) designated PAI V536 that is absent from the genome of nonpathogenic E. coli K-12 strain MG1655. PAI V536 shows typical characteristics of a composite PAI that is associated with the pheV tRNA gene and contains the pix fimbriae determinant as well as genes coding for a putative phosphoglycerate transport system, an autotransporter protein, and hypothetical open reading frames. A gene cluster coding for a putative general secretion pathway system, together with a kps(K15) determinant, is localized downstream of a truncated pheV gene ('pheV) also present in this chromosomal region. The distribution of genes present on PAI V536 was studied by PCR in different pathogenic and nonpathogenic E. coli isolates of various sources. Analysis of the 20-kb kps locus revealed a so far unknown genetic organization. Generally, the kps(K15) gene cluster resembles that of group 2 and 3 capsules, where two conserved regions (regions 1 and 3) are located up- or downstream of a highly variable serotype-specific region (region 2). Interestingly, recombination of a group 2 and 3 determinant may have been involved in the evolution of the K15 capsule-encoding gene cluster. Expression of the K15 capsule is important for virulence in a murine model of ascending urinary tract infection but not for serum resistance of E. coli strain 536.
ESTHER : Schneider_2004_Infect.Immun_72_5993
PubMedSearch : Schneider_2004_Infect.Immun_72_5993
PubMedID: 15385503
Gene_locus related to this paper: ecolx-q707d7

Title : Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917 - Grozdanov_2004_J.Bacteriol_186_5432
Author(s) : Grozdanov L , Raasch C , Schulze J , Sonnenborn U , Gottschalk G , Hacker J , Dobrindt U
Ref : Journal of Bacteriology , 186 :5432 , 2004
Abstract : Nonpathogenic Escherichia coli strain Nissle 1917 (O6:K5:H1) is used as a probiotic agent in medicine, mainly for the treatment of various gastroenterological diseases. To gain insight on the genetic level into its properties of colonization and commensalism, this strain's genome structure has been analyzed by three approaches: (i) sequence context screening of tRNA genes as a potential indication of chromosomal integration of horizontally acquired DNA, (ii) sequence analysis of 280 kb of genomic islands (GEIs) coding for important fitness factors, and (iii) comparison of Nissle 1917 genome content with that of other E. coli strains by DNA-DNA hybridization. PCR-based screening of 324 nonpathogenic and pathogenic E. coli isolates of different origins revealed that some chromosomal regions are frequently detectable in nonpathogenic E. coli and also among extraintestinal and intestinal pathogenic strains. Many known fitness factor determinants of strain Nissle 1917 are localized on four GEIs which have been partially sequenced and analyzed. Comparison of these data with the available knowledge of the genome structure of E. coli K-12 strain MG1655 and of uropathogenic E. coli O6 strains CFT073 and 536 revealed structural similarities on the genomic level, especially between the E. coli O6 strains. The lack of defined virulence factors (i.e., alpha-hemolysin, P-fimbrial adhesins, and the semirough lipopolysaccharide phenotype) combined with the expression of fitness factors such as microcins, different iron uptake systems, adhesins, and proteases, which may support its survival and successful colonization of the human gut, most likely contributes to the probiotic character of E. coli strain Nissle 1917.
ESTHER : Grozdanov_2004_J.Bacteriol_186_5432
PubMedSearch : Grozdanov_2004_J.Bacteriol_186_5432
PubMedID: 15292145
Gene_locus related to this paper: ecoli-C3633 , ecoli-C3636 , ecoli-IROD , ecoli-IROE

Title : The complete genome sequence of Propionibacterium acnes, a commensal of human skin - Bruggemann_2004_Science_305_671
Author(s) : Bruggemann H , Henne A , Hoster F , Liesegang H , Wiezer A , Strittmatter A , Hujer S , Durre P , Gottschalk G
Ref : Science , 305 :671 , 2004
Abstract : Propionibacterium acnes is a major inhabitant of adult human skin, where it resides within sebaceous follicles, usually as a harmless commensal although it has been implicated in acne vulgaris formation. The entire genome sequence of this Gram-positive bacterium encodes 2333 putative genes and revealed numerous gene products involved in degrading host molecules, including sialidases, neuraminidases, endoglycoceramidases, lipases, and pore-forming factors. Surface-associated and other immunogenic factors have been identified, which might be involved in triggering acne inflammation and other P. acnes-associated diseases.
ESTHER : Bruggemann_2004_Science_305_671
PubMedSearch : Bruggemann_2004_Science_305_671
PubMedID: 15286373
Gene_locus related to this paper: proac-q6a5e5 , proac-q6a5t3 , proac-q6a5w4 , proac-q6a5w7 , proac-q6a6d0 , proac-q6a6l8 , proac-q6a6t8 , proac-q6a7a8 , proac-q6a7s1 , proac-q6a7u0 , proac-q6a8r8 , proac-q6a8x9 , proac-q6a9s4 , proac-q6a879 , proac-q6a897 , proac-q6a981 , proac-q6aa67 , proac-q6ab58

Title : The genome sequence of the extreme thermophile Thermus thermophilus - Henne_2004_Nat.Biotechnol_22_547
Author(s) : Henne A , Bruggemann H , Raasch C , Wiezer A , Hartsch T , Liesegang H , Johann A , Lienard T , Gohl O , Martinez-Arias R , Jacobi C , Starkuviene V , Schlenczeck S , Dencker S , Huber R , Klenk HP , Kramer W , Merkl R , Gottschalk G , Fritz HJ
Ref : Nat Biotechnol , 22 :547 , 2004
Abstract : Thermus thermophilus HB27 is an extremely thermophilic, halotolerant bacterium, which was originally isolated from a natural thermal environment in Japan. This organism has considerable biotechnological potential; many thermostable proteins isolated from members of the genus Thermus are indispensable in research and in industrial applications. We present here the complete genome sequence of T. thermophilus HB27, the first for the genus Thermus. The genome consists of a 1,894,877 base pair chromosome and a 232,605 base pair megaplasmid, designated pTT27. The 2,218 identified putative genes were compared to those of the closest relative sequenced so far, the mesophilic bacterium Deinococcus radiodurans. Both organisms share a similar set of proteins, although their genomes lack extensive synteny. Many new genes of potential interest for biotechnological applications were found in T. thermophilus HB27. Candidates include various proteases and key enzymes of other fundamental biological processes such as DNA replication, DNA repair and RNA maturation.
ESTHER : Henne_2004_Nat.Biotechnol_22_547
PubMedSearch : Henne_2004_Nat.Biotechnol_22_547
PubMedID: 15064768
Gene_locus related to this paper: thet2-q72hm9 , thet2-q72hv6 , thet2-q72hz1 , thet2-q72i91 , thet2-q72j75 , thet2-q72jk9 , thet2-q72jm3 , thet2-q72kf4 , thet2-q72kp8 , thet2-q746k7 , theth-metx , theth-TT1662 , theth-TTC1787

Title : The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential - Veith_2004_J.Mol.Microbiol.Biotechnol_7_204
Author(s) : Veith B , Herzberg C , Steckel S , Feesche J , Maurer KH , Ehrenreich P , Baumer S , Henne A , Liesegang H , Merkl R , Ehrenreich A , Gottschalk G
Ref : J Molecular Microbiology Biotechnol , 7 :204 , 2004
Abstract : The genome of Bacillus licheniformis DSM13 consists of a single chromosome that has a size of 4,222,748 base pairs. The average G+C ratio is 46.2%. 4,286 open reading frames, 72 tRNA genes, 7 rRNA operons and 20 transposase genes were identified. The genome shows a marked co-linearity with Bacillus subtilis but contains defined inserted regions that can be identified at the sequence as well as at the functional level. B. licheniformis DSM13 has a well-conserved secretory system, no polyketide biosynthesis, but is able to form the lipopeptide lichenysin. From the further analysis of the genome sequence, we identified conserved regulatory DNA motives, the occurrence of the glyoxylate bypass and the presence of anaerobic ribonucleotide reductase explaining that B. licheniformis is able to grow on acetate and 2,3-butanediol as well as anaerobically on glucose. Many new genes of potential interest for biotechnological applications were found in B. licheniformis; candidates include proteases, pectate lyases, lipases and various polysaccharide degrading enzymes.
ESTHER : Veith_2004_J.Mol.Microbiol.Biotechnol_7_204
PubMedSearch : Veith_2004_J.Mol.Microbiol.Biotechnol_7_204
PubMedID: 15383718
Gene_locus related to this paper: bacld-q62u01 , bacld-q62yz9 , bacld-q65dz7 , bacld-q65e02 , bacld-q65eq1 , bacld-q65fc5 , bacld-q65fg2 , bacld-q65fg3 , bacld-q65fk9 , bacld-q65ft3 , bacld-q65fw3 , bacld-q65fy2 , bacld-q65gx2 , bacld-q65hn8 , bacld-q65hr4 , bacld-q65if8 , bacld-q65iy4 , bacld-q65j72 , bacld-q65le0 , bacld-q65ly2 , bacld-q65m29 , bacld-q65mg8 , bacld-q65my7 , bacld-q65n63 , bacld-q65nk2 , bacld-q65nm7 , bacli-LICC

Title : Genome sequence of Picrophilus torridus and its implications for life around pH 0 - Futterer_2004_Proc.Natl.Acad.Sci.U.S.A_101_9091
Author(s) : Futterer O , Angelov A , Liesegang H , Gottschalk G , Schleper C , Schepers B , Dock C , Antranikian G , Liebl W
Ref : Proc Natl Acad Sci U S A , 101 :9091 , 2004
Abstract : The euryarchaea Picrophilus torridus and Picrophilus oshimae are able to grow around pH 0 at up to 65 degrees C, thus they represent the most thermoacidophilic organisms known. Several features that may contribute to the thermoacidophilic survival strategy of P. torridus were deduced from analysis of its 1.55-megabase genome. P. torridus has the smallest genome among nonparasitic aerobic microorganisms growing on organic substrates and simultaneously the highest coding density among thermoacidophiles. An exceptionally high ratio of secondary over ATP-consuming primary transport systems demonstrates that the high proton concentration in the surrounding medium is extensively used for transport processes. Certain genes that may be particularly supportive for the extreme lifestyle of P. torridus appear to have been internalized into the genome of the Picrophilus lineage by horizontal gene transfer from crenarchaea and bacteria. Finally, it is noteworthy that the thermoacidophiles from phylogenetically distant branches of the Archaea apparently share an unexpectedly large pool of genes.
ESTHER : Futterer_2004_Proc.Natl.Acad.Sci.U.S.A_101_9091
PubMedSearch : Futterer_2004_Proc.Natl.Acad.Sci.U.S.A_101_9091
PubMedID: 15184674
Gene_locus related to this paper: picto-q6kyx8 , picto-q6kz86 , picto-q6kzp3 , picto-q6kzx6 , picto-q6kzy9 , picto-q6l0c9 , picto-q6l018 , picto-q6l189 , picto-q6l217

Title : Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis - Schwartz_2003_J.Mol.Biol_332_369
Author(s) : Schwartz E , Henne A , Cramm R , Eitinger T , Friedrich B , Gottschalk G
Ref : Journal of Molecular Biology , 332 :369 , 2003
Abstract : The self-transmissible megaplasmid pHG1 carries essential genetic information for the facultatively lithoautotrophic and facultatively anaerobic lifestyles of its host, the Gram-negative soil bacterium Ralstonia eutropha H16. We have determined the complete nucleotide sequence of pHG1. This megaplasmid is 452,156 bp in size and carries 429 potential genes. Groups of functionally related genes form loose clusters flanked by mobile elements. The largest functional group consists of lithoautotrophy-related genes. These include a set of 41 genes for the biosynthesis of the three previously identified hydrogenases and of a fourth, novel hydrogenase. Another large cluster carries the genetic information for denitrification. In addition to a dissimilatory nitrate reductase, both specific and global regulators were identified. Also located in the denitrification region is a set of genes for cytochrome c biosynthesis. Determinants for several enzymes involved in the mineralization of aromatic compounds were found. The genes for conjugative plasmid transfer predict that R.eutropha forms two types of pili. One of them is related to the type IV pili of pathogenic enterobacteria. pHG1 also carries an extensive "junkyard" region encompassing 17 remnants of mobile elements and 22 partial or intact genes for phage-type integrase. Among the mobile elements is a novel member of the IS5 family, in which the transposase gene is interrupted by a group II intron.
ESTHER : Schwartz_2003_J.Mol.Biol_332_369
PubMedSearch : Schwartz_2003_J.Mol.Biol_332_369
PubMedID: 12948488

Title : Complete nucleotide sequence and genetic organization of the 210-kilobase linear plasmid of Rhodococcus erythropolis BD2 - Stecker_2003_J.Bacteriol_185_5269
Author(s) : Stecker C , Johann A , Herzberg C , Averhoff B , Gottschalk G
Ref : Journal of Bacteriology , 185 :5269 , 2003
Abstract : The complete nucleotide sequence of the linear plasmid pBD2 from Rhodococcus erythropolis BD2 comprises 210,205 bp. Sequence analyses of pBD2 revealed 212 putative open reading frames (ORFs), 97 of which had an annotatable function. These ORFs could be assigned to six functional groups: plasmid replication and maintenance, transport and metalloresistance, catabolism, transposition, regulation, and protein modification. Many of the transposon-related sequences were found to flank the isopropylbenzene pathway genes. This finding together with the significant sequence similarities of the ipb genes to genes of the linear plasmid-encoded biphenyl pathway in other rhodococci suggests that the ipb genes were acquired via transposition events and subsequently distributed among the rhodococci via horizontal transfer.
ESTHER : Stecker_2003_J.Bacteriol_185_5269
PubMedSearch : Stecker_2003_J.Bacteriol_185_5269
PubMedID: 12923100
Gene_locus related to this paper: rhoer-q6xn97 , rhosp-EtbD1

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

Title : Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536 - Dobrindt_2002_Infect.Immun_70_6365
Author(s) : Dobrindt U , Blum-Oehler G , Nagy G , Schneider G , Johann A , Gottschalk G , Hacker J
Ref : Infect Immun , 70 :6365 , 2002
Abstract : For the uropathogenic Escherichia coli strain 536 (O6:K15:H31), the DNA sequences of three pathogenicity islands (PAIs) (PAI I(536) to PAI III(536)) and their flanking regions (about 270 kb) were determined to further characterize the virulence potential of this strain. PAI I(536) to PAI III(536) exhibit features typical of PAIs, such as (i) association with tRNA-encoding genes; (ii) G+C content differing from that of the host genome; (iii) flanking repeat structures; (iv) a mosaic-like structure comprising a multitude of functional, truncated, and nonfunctional putative open reading frames (ORFs) with known or unknown functions; and (v) the presence of many fragments of mobile genetic elements. PAI I(536) to PAI III(536) range between 68 and 102 kb in size. Although these islands contain several ORFs and known virulence determinants described for PAIs of other extraintestinal pathogenic E. coli (ExPEC) isolates, they also consist of as-yet-unidentified ORFs encoding putative virulence factors. The genetic structure of PAI IV(536), which represents the core element of the so-called high-pathogenicity island encoding a siderophore system initially identified in pathogenic yersiniae, was further characterized by sample sequencing. For the first time, multiple PAI sequences (PAI I(536) to PAI IV(536)) in uropathogenic E. coli were studied and their presence in several wild-type E. coli isolates was extensively investigated. The results obtained suggest that these PAIs or at least large fragments thereof are detectable in other pathogenic E. coli isolates. These results support our view that the acquisition of large DNA regions, such as PAIs, by horizontal gene transfer is an important factor for the evolution of bacterial pathogens.
ESTHER : Dobrindt_2002_Infect.Immun_70_6365
PubMedSearch : Dobrindt_2002_Infect.Immun_70_6365
PubMedID: 12379716
Gene_locus related to this paper: ecoli-IROD

Title : S-Fimbria-encoding determinant sfa(I) is located on pathogenicity island III(536) of uropathogenic Escherichia coli strain 536 - Dobrindt_2001_Infect.Immun_69_4248
Author(s) : Dobrindt U , Blum-Oehler G , Hartsch T , Gottschalk G , Ron EZ , Funfstuck R , Hacker J
Ref : Infect Immun , 69 :4248 , 2001
Abstract : The sfa(I) determinant encoding the S-fimbrial adhesin of uropathogenic Escherichia coli strains was found to be located on a pathogenicity island of uropathogenic E. coli strain 536. This pathogenicity island, designated PAI III(536), is located at 5.6 min of the E. coli chromosome and covers a region of at least 37 kb between the tRNA locus thrW and yagU. As far as it has been determined, PAI III(536) also contains genes which code for components of a putative enterochelin siderophore system of E. coli and Salmonella spp. as well as for colicin V immunity. Several intact or nonfunctional mobility genes of bacteriophages and insertion sequence elements such as transposases and integrases are present on PAI III(536). The presence of known PAI III(536) sequences has been investigated in several wild-type E. coli isolates. The results demonstrate that the determinants of the members of the S-family of fimbrial adhesins may be located on a common pathogenicity island which, in E. coli strain 536, replaces a 40-kb DNA region which represents an E. coli K-12-specific genomic island.
ESTHER : Dobrindt_2001_Infect.Immun_69_4248
PubMedSearch : Dobrindt_2001_Infect.Immun_69_4248
PubMedID: 11401961
Gene_locus related to this paper: ecoli-IROD , ecoli-IROE

Title : Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli - Henne_2000_Appl.Environ.Microbiol_66_3113
Author(s) : Henne A , Schmitz RA , Bomeke M , Gottschalk G , Daniel R
Ref : Applied Environmental Microbiology , 66 :3113 , 2000
Abstract : Environmental DNA libraries prepared from three different soil samples were screened for genes conferring lipolytic activity on Escherichia coli clones. Screening on triolein agar revealed 1 positive clone out of 730,000 clones, and screening on tributyrin agar revealed 3 positive clones out of 286,000 E. coli clones. Substrate specificity analysis revealed that one recombinant strain harbored a lipase and the other three contained esterases. The genes responsible for the lipolytic activity were identified and characterized.
ESTHER : Henne_2000_Appl.Environ.Microbiol_66_3113
PubMedSearch : Henne_2000_Appl.Environ.Microbiol_66_3113
PubMedID: 10877816
Gene_locus related to this paper: bacte-ester , gamho-LIPA , uncba-Q9KIU0 , uncba-Q9KIU2