Liesegang H

References (31)

Title : How to kill the honey bee larva: genomic potential and virulence mechanisms of Paenibacillus larvae - Djukic_2014_PLoS.One_9_e90914
Author(s) : Djukic M , Brzuszkiewicz E , Funfhaus A , Voss J , Gollnow K , Poppinga L , Liesegang H , Garcia-Gonzalez E , Genersch E , Daniel R
Ref : PLoS ONE , 9 :e90914 , 2014
Abstract : Paenibacillus larvae, a Gram positive bacterial pathogen, causes American Foulbrood (AFB), which is the most serious infectious disease of honey bees. In order to investigate the genomic potential of P. larvae, two strains belonging to two different genotypes were sequenced and used for comparative genome analysis. The complete genome sequence of P. larvae strain DSM 25430 (genotype ERIC II) consisted of 4,056,006 bp and harbored 3,928 predicted protein-encoding genes. The draft genome sequence of P. larvae strain DSM 25719 (genotype ERIC I) comprised 4,579,589 bp and contained 4,868 protein-encoding genes. Both strains harbored a 9.7 kb plasmid and encoded a large number of virulence-associated proteins such as toxins and collagenases. In addition, genes encoding large multimodular enzymes producing nonribosomally peptides or polyketides were identified. In the genome of strain DSM 25719 seven toxin associated loci were identified and analyzed. Five of them encoded putatively functional toxins. The genome of strain DSM 25430 harbored several toxin loci that showed similarity to corresponding loci in the genome of strain DSM 25719, but were non-functional due to point mutations or disruption by transposases. Although both strains cause AFB, significant differences between the genomes were observed including genome size, number and composition of transposases, insertion elements, predicted phage regions, and strain-specific island-like regions. Transposases, integrases and recombinases are important drivers for genome plasticity. A total of 390 and 273 mobile elements were found in strain DSM 25430 and strain DSM 25719, respectively. Comparative genomics of both strains revealed acquisition of virulence factors by horizontal gene transfer and provided insights into evolution and pathogenicity.
ESTHER : Djukic_2014_PLoS.One_9_e90914
PubMedSearch : Djukic_2014_PLoS.One_9_e90914
PubMedID: 24599066
Gene_locus related to this paper: 9bacl-v9wcv0

Title : First Insights into the Completely Annotated Genome Sequence of Bacillus licheniformis Strain 9945A - Rachinger_2013_Genome.Announc_1_e00525
Author(s) : Rachinger M , Volland S , Meinhardt F , Daniel R , Liesegang H
Ref : Genome Announc , 1 : , 2013
Abstract : Strains of the species Bacillus licheniformis are widely used in biotechnology for the production of enzymes and antibiotics (M. Schallmey, A. Singh, and O. P. Ward, Can. J. Microbiol. 50:1-17, 2004). However, research and application of B. licheniformis strains are adversely affected by poor genetic accessibility. Thus, for a closer inspection of natural competence in B. licheniformis, the genome of strain 9945A, of which derivatives are known to be naturally competent (C. B. Thorne and H. B. Stull, J. Bacteriol. 91:1012-1020, 1966), was completely sequenced and manually annotated.
ESTHER : Rachinger_2013_Genome.Announc_1_e00525
PubMedSearch : Rachinger_2013_Genome.Announc_1_e00525
PubMedID: 23908277
Gene_locus related to this paper: bacld-q65eq1 , bacld-q65my7 , bacld-q65n63

Title : Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium - Wiegand_2013_Genome.Announc_1_e0009213
Author(s) : Wiegand S , Rabausch U , Chow J , Daniel R , Streit WR , Liesegang H
Ref : Genome Announc , 1 :e0009213 , 2013
Abstract : Geobacillus sp. strain GHH01 was isolated during a screening for producers of extracellular thermostable lipases. The completely sequenced and annotated 3.6-Mb genome encodes 3,478 proteins. The strain is genetically equipped to utilize a broad range of different substrates and might develop natural competence.
ESTHER : Wiegand_2013_Genome.Announc_1_e0009213
PubMedSearch : Wiegand_2013_Genome.Announc_1_e0009213
PubMedID: 23618712
Gene_locus related to this paper: geoka-q5l3h0 , geosc-d7d055 , geotn-a4isp0 , geos2-a0a0e0tby6

Title : Complete Genome Sequence of Bacillus thuringiensis Strain 407 Cry - Sheppard_2013_Genome.Announc_1_e00158
Author(s) : Sheppard AE , Poehlein A , Rosenstiel P , Liesegang H , Schulenburg H
Ref : Genome Announc , 1 :e00158 , 2013
Abstract : Bacillus thuringiensis is an insect pathogen that has been used widely as a biopesticide. Here, we report the genome sequence of strain 407 Cry-, which is used to study the genetic determinants of pathogenicity. The genome consists of a 5.5-Mb chromosome and nine plasmids, including a novel 502-kb megaplasmid.
ESTHER : Sheppard_2013_Genome.Announc_1_e00158
PubMedSearch : Sheppard_2013_Genome.Announc_1_e00158
PubMedID: 23405326

Title : Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics - Gardebrecht_2012_ISME.J_6_766
Author(s) : Gardebrecht A , Markert S , Sievert SM , Felbeck H , Thurmer A , Albrecht D , Wollherr A , Kabisch J , Le Bris N , Lehmann R , Daniel R , Liesegang H , Hecker M , Schweder T
Ref : Isme J , 6 :766 , 2012
Abstract : The two closely related deep-sea tubeworms Riftia pachyptila and Tevnia jerichonana both rely exclusively on a single species of sulfide-oxidizing endosymbiotic bacteria for their nutrition. They do, however, thrive in markedly different geochemical conditions. A detailed proteogenomic comparison of the endosymbionts coupled with an in situ characterization of the geochemical environment was performed to investigate their roles and expression profiles in the two respective hosts. The metagenomes indicated that the endosymbionts are genotypically highly homogeneous. Gene sequences coding for enzymes of selected key metabolic functions were found to be 99.9% identical. On the proteomic level, the symbionts showed very consistent metabolic profiles, despite distinctly different geochemical conditions at the plume level of the respective hosts. Only a few minor variations were observed in the expression of symbiont enzymes involved in sulfur metabolism, carbon fixation and in the response to oxidative stress. Although these changes correspond to the prevailing environmental situation experienced by each host, our data strongly suggest that the two tubeworm species are able to effectively attenuate differences in habitat conditions, and thus to provide their symbionts with similar micro-environments.
ESTHER : Gardebrecht_2012_ISME.J_6_766
PubMedSearch : Gardebrecht_2012_ISME.J_6_766
PubMedID: 22011719
Gene_locus related to this paper: 9gamm-g2d8y1

Title : Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life - Thole_2012_ISME.J_6_2229
Author(s) : Thole S , Kalhoefer D , Voget S , Berger M , Engelhardt T , Liesegang H , Wollherr A , Kjelleberg S , Daniel R , Simon M , Thomas T , Brinkhoff T
Ref : Isme J , 6 :2229 , 2012
Abstract : Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts.
ESTHER : Thole_2012_ISME.J_6_2229
PubMedSearch : Thole_2012_ISME.J_6_2229
PubMedID: 22717884

Title : ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer - Michael_2012_J.Antimicrob.Chemother_67_91
Author(s) : Michael GB , Kadlec K , Sweeney MT , Brzuszkiewicz E , Liesegang H , Daniel R , Murray RW , Watts JL , Schwarz S
Ref : J Antimicrob Chemother , 67 :91 , 2012
Abstract : BACKGROUND: Integrative and conjugative elements (ICEs) have not been detected in Pasteurella multocida. In this study the multiresistance ICEPmu1 from bovine P. multocida was analysed for its core genes and its ability to conjugatively transfer into strains of the same and different genera.
METHODS: ICEPmu1 was identified during whole genome sequencing. Coding sequences were predicted by bioinformatic tools and manually curated using the annotation software ERGO. Conjugation into P. multocida, Mannheimia haemolytica and Escherichia coli recipients was performed by mating assays. The presence of ICEPmu1 and its circular intermediate in the recipient strains was confirmed by PCR and sequence analysis. Integration sites were sequenced. Susceptibility testing of the ICEPmu1-carrying recipients was conducted by broth microdilution.
RESULTS: The 82 214 bp ICEPmu1 harbours 88 genes. The core genes of ICEPmu1, which are involved in excision/integration and conjugative transfer, resemble those found in a 66 641 bp ICE from Histophilus somni. ICEPmu1 integrates into a tRNA(Leu) and is flanked by 13 bp direct repeats. It is able to conjugatively transfer to P. multocida, M. haemolytica and E. coli, where it also uses a tRNA(Leu) for integration and produces closely related 13 bp direct repeats. PCR assays and susceptibility testing confirmed the presence and the functional activity of the ICEPmu1-associated resistance genes in the recipient strains.
CONCLUSIONS: The observation that the multiresistance ICEPmu1 is present in a bovine P. multocida and can easily spread across strain and genus boundaries underlines the risk of a rapid dissemination of multiple resistance genes, which will distinctly decrease the therapeutic options.
ESTHER : Michael_2012_J.Antimicrob.Chemother_67_91
PubMedSearch : Michael_2012_J.Antimicrob.Chemother_67_91
PubMedID: 22001176
Gene_locus related to this paper: pasmu-PM0055

Title : Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs - Vogel_2011_Microb.Cell.Fact_10 Suppl 1_S6
Author(s) : Vogel RF , Pavlovic M , Ehrmann MA , Wiezer A , Liesegang H , Offschanka S , Voget S , Angelov A , Bocker G , Liebl W
Ref : Microb Cell Fact , 10 Suppl 1 :S6 , 2011
Abstract : Sourdough has played a significant role in human nutrition and culture for thousands of years and is still of eminent importance for human diet and the bakery industry. Lactobacillus sanfranciscensis is the predominant key bacterium in traditionally fermented sourdoughs.The genome of L. sanfranciscensis TMW 1.1304 isolated from an industrial sourdough fermentation was sequenced with a combined Sanger/454-pyrosequencing approach followed by gap closing by walking on fosmids. The sequencing data revealed a circular chromosomal sequence of 1,298,316 bp and two additional plasmids, pLS1 and pLS2, with sizes of 58,739 bp and 18,715 bp, which are predicted to encode 1,437, 63 and 19 orfs, respectively. The overall GC content of the chromosome is 34.71%. Several specific features appear to contribute to the ability of L. sanfranciscensis to outcompete other bacteria in the fermentation. L. sanfranciscensis contains the smallest genome within the lactobacilli and the highest density of ribosomal RNA operons per Mbp genome among all known genomes of free-living bacteria, which is important for the rapid growth characteristics of the organism. A high frequency of gene inactivation and elimination indicates a process of reductive evolution. The biosynthetic capacity for amino acids scarcely availably in cereals and exopolysaccharides reveal the molecular basis for an autochtonous sourdough organism with potential for further exploitation in functional foods. The presence of two CRISPR/cas loci versus a high number of transposable elements suggests recalcitrance to gene intrusion and high intrinsic genome plasticity.
ESTHER : Vogel_2011_Microb.Cell.Fact_10 Suppl 1_S6
PubMedSearch : Vogel_2011_Microb.Cell.Fact_10 Suppl 1_S6
PubMedID: 21995419

Title : Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis - Kalhoefer_2011_BMC.Genomics_12_324
Author(s) : Kalhoefer D , Thole S , Voget S , Lehmann R , Liesegang H , Wollher A , Daniel R , Simon M , Brinkhoff T
Ref : BMC Genomics , 12 :324 , 2011
Abstract : BACKGROUND: Roseobacter litoralis OCh149, the type species of the genus, and Roseobacter denitrificans OCh114 were the first described organisms of the Roseobacter clade, an ecologically important group of marine bacteria. Both species were isolated from seaweed and are able to perform aerobic anoxygenic photosynthesis.
RESULTS: The genome of R. litoralis OCh149 contains one circular chromosome of 4,505,211 bp and three plasmids of 93,578 bp (pRLO149_94), 83,129 bp (pRLO149_83) and 63,532 bp (pRLO149_63). Of the 4537 genes predicted for R. litoralis, 1122 (24.7%) are not present in the genome of R. denitrificans. Many of the unique genes of R. litoralis are located in genomic islands and on plasmids. On pRLO149_83 several potential heavy metal resistance genes are encoded which are not present in the genome of R. denitrificans. The comparison of the heavy metal tolerance of the two organisms showed an increased zinc tolerance of R. litoralis. In contrast to R. denitrificans, the photosynthesis genes of R. litoralis are plasmid encoded. The activity of the photosynthetic apparatus was confirmed by respiration rate measurements, indicating a growth-phase dependent response to light. Comparative genomics with other members of the Roseobacter clade revealed several genomic regions that were only conserved in the two Roseobacter species. One of those regions encodes a variety of genes that might play a role in host association of the organisms. The catabolism of different carbon and nitrogen sources was predicted from the genome and combined with experimental data. In several cases, e.g. the degradation of some algal osmolytes and sugars, the genome-derived predictions of the metabolic pathways in R. litoralis differed from the phenotype.
CONCLUSIONS: The genomic differences between the two Roseobacter species are mainly due to lateral gene transfer and genomic rearrangements. Plasmid pRLO149_83 contains predominantly recently acquired genetic material whereas pRLO149_94 was probably translocated from the chromosome. Plasmid pRLO149_63 and one plasmid of R. denitrifcans (pTB2) seem to have a common ancestor and are important for cell envelope biosynthesis. Several new mechanisms of substrate degradation were indicated from the combination of experimental and genomic data. The photosynthetic activity of R. litoralis is probably regulated by nutrient availability.
ESTHER : Kalhoefer_2011_BMC.Genomics_12_324
PubMedSearch : Kalhoefer_2011_BMC.Genomics_12_324
PubMedID: 21693016
Gene_locus related to this paper: rosdo-q161f4 , roslo-f7zm11 , roslo-f7zjk8

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 : The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea - Wagner-Dobler_2010_Isme.J_4_61
Author(s) : Wagner-Dobler I , Ballhausen B , Berger M , Brinkhoff T , Buchholz I , Bunk B , Cypionka H , Daniel R , Drepper T , Gerdts G , Hahnke S , Han C , Jahn D , Kalhoefer D , Kiss H , Klenk HP , Kyrpides N , Liebl W , Liesegang H , Meincke L , Pati A , Petersen J , Piekarski T , Pommerenke C , Pradella S , Pukall R , Rabus R , Stackebrandt E , Thole S , Thompson L , Tielen P , Tomasch J , von Jan M , Wanphrut N , Wichels A , Zech H , Simon M
Ref : Isme J , 4 :61 , 2010
Abstract : Dinoroseobacter shibae DFL12(T), a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates. Its annotated 4 417 868 bp genome sequence revealed a possible advantage of this symbiosis for the algal host. D. shibae DFL12(T) is able to synthesize the vitamins B(1) and B(12) for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B(12) are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B(12) was confirmed to be functional, and D. shibae DFL12(T) was shown to provide the growth-limiting vitamins B(1) and B(12) to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12(T) is able to grow anaerobically using the alternative electron acceptors nitrate and dimethylsulfoxide; it has the arginine deiminase survival fermentation pathway and a complex oxygen-dependent Fnr (fumarate and nitrate reduction) regulon. Many of these traits are shared with other members of the Roseobacter clade. D. shibae DFL12(T) has five plasmids, showing examples for vertical recruitment of chromosomal genes (thiC) and horizontal gene transfer (cox genes, gene cluster of 47 kb) possibly by conjugation (vir gene cluster). The long-range (80%) synteny between two sister plasmids provides insights into the emergence of novel plasmids. D. shibae DFL12(T) shows the most complex viral defense system of all Rhodobacterales sequenced to date.
ESTHER : Wagner-Dobler_2010_Isme.J_4_61
PubMedSearch : Wagner-Dobler_2010_Isme.J_4_61
PubMedID: 19741735
Gene_locus related to this paper: dinsh-a8lqy2 , dinsh-a8luk0 , dinsh-a8lpz7

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 : Genome sequence of the polysaccharide-degrading, thermophilic anaerobe Spirochaeta thermophila DSM 6192 - Angelov_2010_J.Bacteriol_192_6492
Author(s) : Angelov A , Liebl S , Ballschmiter M , Bomeke M , Lehmann R , Liesegang H , Daniel R , Liebl W
Ref : Journal of Bacteriology , 192 :6492 , 2010
Abstract : Spirochaeta thermophila is a thermophilic, free-living anaerobe that is able to degrade various alpha- and beta-linked sugar polymers, including cellulose. We report here the complete genome sequence of S. thermophila DSM 6192, which is the first genome sequence of a thermophilic, free-living member of the Spirochaetes phylum. The genome data reveal a high density of genes encoding enzymes from more than 30 glycoside hydrolase families, a noncellulosomal enzyme system for (hemi)cellulose degradation, and indicate the presence of a novel carbohydrate-binding module.
ESTHER : Angelov_2010_J.Bacteriol_192_6492
PubMedSearch : Angelov_2010_J.Bacteriol_192_6492
PubMedID: 20935097
Gene_locus related to this paper: spitd-e0rq60 , spitd-e0rrc2 , spitd-e0rsy8

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 : 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 : 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 : Structural and functional characterization of gene clusters directing nonribosomal synthesis of bioactive cyclic lipopeptides in Bacillus amyloliquefaciens strain FZB42 - Koumoutsi_2004_J.Bacteriol_186_1084
Author(s) : Koumoutsi A , Chen XH , Henne A , Liesegang H , Hitzeroth G , Franke P , Vater J , Borriss R
Ref : Journal of Bacteriology , 186 :1084 , 2004
Abstract : The environmental strain Bacillus amyloliquefaciens FZB42 promotes plant growth and suppresses plant pathogenic organisms present in the rhizosphere. We sampled sequenced the genome of FZB42 and identified 2,947 genes with >50% identity on the amino acid level to the corresponding genes of Bacillus subtilis 168. Six large gene clusters encoding nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) occupied 7.5% of the whole genome. Two of the PKS and one of the NRPS encoding gene clusters were unique insertions in the FZB42 genome and are not present in B. subtilis 168. Matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis revealed expression of the antibiotic lipopeptide products surfactin, fengycin, and bacillomycin D. The fengycin (fen) and the surfactin (srf) operons were organized and located as in B. subtilis 168. A large 37.2-kb antibiotic DNA island containing the bmy gene cluster was attributed to the biosynthesis of bacillomycin D. The bmy island was found inserted close to the fen operon. The responsibility of the bmy, fen, and srf gene clusters for the production of the corresponding secondary metabolites was demonstrated by cassette mutagenesis, which led to the loss of the ability to produce these peptides. Although these single mutants still largely retained their ability to control fungal spread, a double mutant lacking both bacillomycin D and fengycin was heavily impaired in its ability to inhibit growth of phytopathogenic fungi, suggesting that both lipopeptides act in a synergistic manner.
ESTHER : Koumoutsi_2004_J.Bacteriol_186_1084
PubMedSearch : Koumoutsi_2004_J.Bacteriol_186_1084
PubMedID: 14762003
Gene_locus related to this paper: bacam-q70jx5 , bacam-q70k06 , bacsu-q6yk39 , bacsu-SRFC , bacsu-SRFD

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 : An evolutionary hot spot: the pNGR234b replicon of Rhizobium sp. strain NGR234 - Streit_2004_J.Bacteriol_186_535
Author(s) : Streit WR , Schmitz RA , Perret X , Staehelin C , Deakin WJ , Raasch C , Liesegang H , Broughton WJ
Ref : Journal of Bacteriology , 186 :535 , 2004
Abstract : Rhizobium sp. strain NGR234 has an exceptionally broad host range and is able to nodulate more than 112 genera of legumes. Since the overall organization of the NGR234 genome is strikingly similar to that of the narrow-host-range symbiont Rhizobium meliloti strain 1021 (also known as Sinorhizobium meliloti), the obvious question is why are the spectra of hosts so different? Study of the early symbiotic genes of both bacteria (carried by the SymA plasmids) did not provide obvious answers. Yet, both rhizobia also possess second megaplasmids that bear, among many other genes, those that are involved in the synthesis of extracellular polysaccharides (EPSs). EPSs are involved in fine-tuning symbiotic interactions and thus may help answer the broad- versus narrow-host-range question. Accordingly, we sequenced two fragments (total, 594 kb) that encode 575 open reading frames (ORFs). Comparisons revealed 19 conserved gene clusters with high similarity to R. meliloti, suggesting that a minimum of 28% (158 ORFs) of the genetic information may have been acquired from a common ancestor. The largest conserved cluster carried the exo and exs genes and contained 31 ORFs. In addition, nine highly conserved regions with high similarity to Agrobacterium tumefaciens C58, Bradyrhizobium japonicum USDA110, and Mesorhizobium loti strain MAFF303099, as well as two conserved clusters that are highly homologous to similar regions in the plant pathogen Erwinia carotovora, were identified. Altogether, these findings suggest that >/==" BORDER="0">40% of the pNGR234b genes are not strain specific and were probably acquired from a wide variety of other microbes. The presence of 26 ORFs coding for transposases and site-specific integrases supports this contention. Surprisingly, several genes involved in the degradation of aromatic carbon sources and genes coding for a type IV pilus were also found.
ESTHER : Streit_2004_J.Bacteriol_186_535
PubMedSearch : Streit_2004_J.Bacteriol_186_535
PubMedID: 14702322
Gene_locus related to this paper: rhime-R01391 , rhisn-c3kku8 , rhisn-c3kl46 , rhisn-c3kly5 , rhisn-c3klz9 , rhisn-c3kmf4 , rhisn-c3kmp5 , rhisn-c3knq1 , rhisn-c3krv5 , rhisn-q6w1e1 , rhisn-q6w231 , rhisn-q6w256 , sinmw-a6ugj8 , rhisn-c3km61

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 : Metagenome survey of biofilms in drinking-water networks - Schmeisser_2003_Appl.Environ.Microbiol_69_7298
Author(s) : Schmeisser C , Stockigt C , Raasch C , Wingender J , Timmis KN , Wenderoth DF , Flemming HC , Liesegang H , Schmitz RA , Jaeger KE , Streit WR
Ref : Applied Environmental Microbiology , 69 :7298 , 2003
Abstract : Most naturally occurring biofilms contain a vast majority of microorganisms which have not yet been cultured, and therefore we have little information on the genetic information content of these communities. Therefore, we initiated work to characterize the complex metagenome of model drinking water biofilms grown on rubber-coated valves by employing three different strategies. First, a sequence analysis of 650 16S rRNA clones indicated a high diversity within the biofilm communities, with the majority of the microbes being closely related to the Proteobacteria: Only a small fraction of the 16S rRNA sequences were highly similar to rRNA sequences from Actinobacteria, low-G+C gram-positives and the Cytophaga-Flavobacterium-Bacteroides group. Our second strategy included a snapshot genome sequencing approach. Homology searches in public databases with 5,000 random sequence clones from a small insert library resulted in the identification of 2,200 putative protein-coding sequences, of which 1,026 could be classified into functional groups. Similarity analyses indicated that significant fractions of the genes and proteins identified were highly similar to known proteins observed in the genera Rhizobium, Pseudomonas, and Escherichia: Finally, we report 144 kb of DNA sequence information from four selected cosmid clones, of which two formed a 75-kb overlapping contig. The majority of the proteins identified by whole-cosmid sequencing probably originated from microbes closely related to the alpha-, beta-, and gamma-Proteobacteria: The sequence information was used to set up a database containing the phylogenetic and genomic information on this model microbial community. Concerning the potential health risk of the microbial community studied, no DNA or protein sequences directly linked to pathogenic traits were identified.
ESTHER : Schmeisser_2003_Appl.Environ.Microbiol_69_7298
PubMedSearch : Schmeisser_2003_Appl.Environ.Microbiol_69_7298
PubMedID: 14660379
Gene_locus related to this paper: 9bact-q6wlc7

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