Goesmann A

References (53)

Title : A reference genome of the Chinese hamster based on a hybrid assembly strategy - Rupp_2018_Biotechnol.Bioeng_115_2087
Author(s) : Rupp O , MacDonald ML , Li S , Dhiman H , Polson S , Griep S , Heffner K , Hernandez I , Brinkrolf K , Jadhav V , Samoudi M , Hao H , Kingham B , Goesmann A , Betenbaugh MJ , Lewis NE , Borth N , Lee KH
Ref : Biotechnol Bioeng , 115 :2087 , 2018
Abstract : Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read-based assemblies. Here, we completely resequenced C. griseus using single molecule real time sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up- and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important Chinese hamster ovary cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.
ESTHER : Rupp_2018_Biotechnol.Bioeng_115_2087
PubMedSearch : Rupp_2018_Biotechnol.Bioeng_115_2087
PubMedID: 29704459
Gene_locus related to this paper: crigr-g3h083 , crigr-a0a3l7ib08 , crigr-g3ifk5 , crigr-g3h7k6

Title : The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract - Wegmann_2015_BMC.Genomics_16_1023
Author(s) : Wegmann U , Mackenzie DA , Zheng J , Goesmann A , Roos S , Swarbreck D , Walter J , Crossman LC , Juge N
Ref : BMC Genomics , 16 :1023 , 2015
Abstract : BACKGROUND: Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown.
RESULTS: To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity.
CONCLUSIONS: This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations.
ESTHER : Wegmann_2015_BMC.Genomics_16_1023
PubMedSearch : Wegmann_2015_BMC.Genomics_16_1023
PubMedID: 26626322
Gene_locus related to this paper: lacre-a0a0s4nmr3

Title : Genome Sequence of the Acute Urethral Catheter Isolate Pseudomonas aeruginosa MH38 - Wibberg_2014_Genome.Announc_2_e00161
Author(s) : Wibberg D , Tielen P , Blom J , Rosin N , Schobert M , Tupker R , Schatschneider S , Spilker D , Albersmeier A , Goesmann A , Vorholter FJ , Puhler A , Jahn D
Ref : Genome Announc , 2 : , 2014
Abstract : Pseudomonas aeruginosa is a major nosocomial bacterial pathogen causing complicated catheter-associated urinary tract infections (CAUTIs). Here, we present the 6.9-Mb draft genome sequence of P. aeruginosa MH38 isolated from an acute nosocomial CAUTI. It exhibits resistance to several antibiotics but revealed low-level production of virulence factors.
ESTHER : Wibberg_2014_Genome.Announc_2_e00161
PubMedSearch : Wibberg_2014_Genome.Announc_2_e00161
PubMedID: 24625869
Gene_locus related to this paper: pseae-PA3695 , pseae-q9i252

Title : Complete genome sequence of the actinobacterium Actinoplanes friuliensis HAG 010964, producer of the lipopeptide antibiotic friulimycin - Ruckert_2014_J.Biotechnol_178_41
Author(s) : Ruckert C , Szczepanowski R , Albersmeier A , Goesmann A , Fischer N , Steinkamper A , Puhler A , Biener R , Schwartz D , Kalinowski J
Ref : J Biotechnol , 178 :41 , 2014
Abstract : Actinoplanes friuliensis HAG 010964 (DSM 7358) was isolated from a soil sample from the Friuli region in Italy and characterized as a producer of the antibiotic friulimycin. The complete genome sequence includes genomic information of secondary metabolite biosynthesis and of its lifestyle. Genbank/EMBL/DDBJ Accession Nr: CP006272 (chromosome).
ESTHER : Ruckert_2014_J.Biotechnol_178_41
PubMedSearch : Ruckert_2014_J.Biotechnol_178_41
PubMedID: 24637369
Gene_locus related to this paper: 9actn-u5w1i4 , 9actn-u5w1j2 , 9actn-u5w2q0 , 9actn-u5wd34 , 9actn-u5w1u3 , 9actn-u5w019 , 9actn-u5w4l0

Title : The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) - Dohm_2014_Nature_505_546
Author(s) : Dohm JC , Minoche AE , Holtgrawe D , Capella-Gutierrez S , Zakrzewski F , Tafer H , Rupp O , Sorensen TR , Stracke R , Reinhardt R , Goesmann A , Kraft T , Schulz B , Stadler PF , Schmidt T , Gabaldon T , Lehrach H , Weisshaar B , Himmelbauer H
Ref : Nature , 505 :546 , 2014
Abstract : Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.
ESTHER : Dohm_2014_Nature_505_546
PubMedSearch : Dohm_2014_Nature_505_546
PubMedID: 24352233
Gene_locus related to this paper: betvu-a0a0j8bcg5 , betvu-a0a0j8fqe7 , spiol-a0a0k9r9x3 , spiol-a0a0k9rit5 , spiol-a0a0k9riw3 , spiol-a0a0k9rub8 , spiol-a0a0k9rxl0 , spiol-a0a0k9qau1 , spiol-a0a0k9rrd8 , spiol-a0a0k9qe58 , spiol-a0a0k9r322 , betvv-a0a0j8b442 , spiol-a0a0k9qnw2 , spiol-a0a0k9ri52 , spiol-a0a0k9r6e9

Title : Chinese hamster genome sequenced from sorted chromosomes -
Author(s) : Brinkrolf K , Rupp O , Laux H , Kollin F , Ernst W , Linke B , Kofler R , Romand S , Hesse F , Budach WE , Galosy S , Muller D , Noll T , Wienberg J , Jostock T , Leonard M , Grillari J , Tauch A , Goesmann A , Helk B , Mott JE , Puhler A , Borth N
Ref : Nat Biotechnol , 31 :694 , 2013
PubMedID: 23929341
Gene_locus related to this paper: crigr-a0a061igd5 , crigr-g3grm1 , crigr-g3i1j5 , crigr-a0a061ika1 , crigr-a0a061ijg4 , crigr-a0a061ihy9

Title : Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production - Bogen_2013_BMC.Genomics_14_926
Author(s) : Bogen C , Al-Dilaimi A , Albersmeier A , Wichmann J , Grundmann M , Rupp O , Lauersen KJ , Blifernez-Klassen O , Kalinowski J , Goesmann A , Mussgnug JH , Kruse O
Ref : BMC Genomics , 14 :926 , 2013
Abstract : BACKGROUND: Microalgae are gaining importance as sustainable production hosts in the fields of biotechnology and bioenergy. A robust biomass accumulating strain of the genus Monoraphidium (SAG 48.87) was investigated in this work as a potential feedstock for biofuel production. The genome was sequenced, annotated, and key enzymes for triacylglycerol formation were elucidated.
RESULTS: Monoraphidium neglectum was identified as an oleaginous species with favourable growth characteristics as well as a high potential for crude oil production, based on neutral lipid contents of approximately 21% (dry weight) under nitrogen starvation, composed of predominantly C18:1 and C16:0 fatty acids. Further characterization revealed growth in a relatively wide pH range and salt concentrations of up to 1.0% NaCl, in which the cells exhibited larger structures. This first full genome sequencing of a member of the Selenastraceae revealed a diploid, approximately 68 Mbp genome with a G + C content of 64.7%. The circular chloroplast genome was assembled to a 135,362 bp single contig, containing 67 protein-coding genes. The assembly of the mitochondrial genome resulted in two contigs with an approximate total size of 94 kb, the largest known mitochondrial genome within algae. 16,761 protein-coding genes were assigned to the nuclear genome. Comparison of gene sets with respect to functional categories revealed a higher gene number assigned to the category "carbohydrate metabolic process" and in "fatty acid biosynthetic process" in M. neglectum when compared to Chlamydomonas reinhardtii and Nannochloropsis gaditana, indicating a higher metabolic diversity for applications in carbohydrate conversions of biotechnological relevance.
CONCLUSIONS: The genome of M. neglectum, as well as the metabolic reconstruction of crucial lipid pathways, provides new insights into the diversity of the lipid metabolism in microalgae. The results of this work provide a platform to encourage the development of this strain for biotechnological applications and production concepts.
ESTHER : Bogen_2013_BMC.Genomics_14_926
PubMedSearch : Bogen_2013_BMC.Genomics_14_926
PubMedID: 24373495
Gene_locus related to this paper: 9chlo-a0a0d2mui5

Title : Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics - Smits_2013_Syst.Appl.Microbiol_36_449
Author(s) : Smits TH , Rezzonico F , Lopez MM , Blom J , Goesmann A , Frey JE , Duffy B
Ref : Syst Appl Microbiol , 36 :449 , 2013
Abstract : Erwinia piriflorinigrans is a necrotrophic pathogen of pear reported from Spain that destroys flowers but does not progress further into the host. We sequenced the complete genome of the type strain CFBP 5888(T) clarifying its phylogenetic position within the genus Erwinia, and indicating a position between its closest relative, the epiphyte Erwinia tasmaniensis and other plant pathogenic Erwinia spp. (i.e., the fire blight pathogen E. amylovora and the Asian pear pathogen E. pyrifoliae). Common features are the type III and type VI secretion systems, amylovoran biosynthesis and desferrioxamine production. The E. piriflorinigrans genome also provided the first evidence for production of the siderophore chrysobactin within the genus Erwinia sensu stricto, which up to now was mostly associated with phytopathogenic, soft-rot Dickeya and Pectobacterium species. Plasmid pEPIR37, reported in this strain, is closely related to small plasmids found in the fire blight pathogen E. amylovora and E. pyrifoliae. The genome of E. piriflorinigrans also gives detailed insights in evolutionary genomics of pathoadapted Erwinia.
ESTHER : Smits_2013_Syst.Appl.Microbiol_36_449
PubMedSearch : Smits_2013_Syst.Appl.Microbiol_36_449
PubMedID: 23726521
Gene_locus related to this paper: 9entr-v5z3f3 , 9entr-v5z7i6 , 9gamm-v5z8v7

Title : Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7\/3\/14 - Wibberg_2013_J.Biotechnol_167_142
Author(s) : Wibberg D , Jelonek L , Rupp O , Hennig M , Eikmeyer F , Goesmann A , Hartmann A , Borriss R , Grosch R , Puhler A , Schluter A
Ref : J Biotechnol , 167 :142 , 2013
Abstract : Anastomosis group AG1-IB isolates of the anamorphic basidiomycetous fungus Rhizoctonia solani Kuhn affect various agricultural and horticultural important crops including bean, rice, soybean, figs, hortensia, cabbage and lettuce. To gain insights into the genome structure and content, the first draft genome sequence of R. solani AG1-IB isolate 7/3/14 was established. Four complete runs on the Genome Sequencer (GS) FLX platform (Roche Applied Science) yielding approx. a 25-fold coverage of the R. solani genome were accomplished. Assembly of the sequence reads by means of the gsAssembler software version 2.6 applying the heterozygotic mode resulted in numerous contigs and scaffolds and a predicted size of 87.1 Mb for the diploid status of the genome. 'Contig-length vs. read-count' analysis revealed that the assembled contigs can be classified into five different groups. Detailed BLAST-analysis revealed that most contigs of group II feature high-scoring matches to other contigs of the same group suggesting that distinguishable allelic variants exist for many genes. Due to the supposed diploid and heterokaryotic nature of R. solani AG1-IB 7/3/14, this result has been anticipated. However, the heterokaryotic character of the isolate is not really supported by sequencing data obtained for the isolate R. solani AG1-IB 7/3/14. Coverage of group III contigs is twice as high as for group II contigs which can also be explained by the diploid status of the genome and indistinguishable alleles on homologous chromosomes. Assembly of sequence data led to the identification of the rRNA unit (group V contigs) and the mitochondrial (mt) genome (group IV contigs) which is a circular molecule of 162,751 bp in size featuring a GC-content of 36.4%. The R. solani 7/3/14 mt-genome is one of the largest fungal mitochondrial genomes known to date. Its large size essentially is due to the presence of numerous non-conserved hypothetical ORFs and introns. Gene prediction for the R. solani AG1-IB 7/3/14 genome was conducted by the Augustus Gene Prediction Software for Eukaryotes (version 2.6.) applying the parameter set for the fungus Coprinopsis cinerea okayama 7 130. Gene prediction and annotation provided first insights into the R. solani AG1-IB 7/3/14 gene structure and content. In total, 12,422 genes were predicted. The average number of exons per gene is five. Exons have a mean length of 214 bp, whereas introns on average are 66 bp in length. Annotation of the genome revealed that 4169 of 12,422 genes could be assigned to KOG functional categories.
ESTHER : Wibberg_2013_J.Biotechnol_167_142
PubMedSearch : Wibberg_2013_J.Biotechnol_167_142
PubMedID: 23280342
Gene_locus related to this paper: thacb-m5c801 , thacb-m5blb1 , thacb-m5bzl7 , thacb-m5c2d3

Title : Complete genome sequence of the kirromycin producer Streptomyces collinus Tu 365 consisting of a linear chromosome and two linear plasmids - Ruckert_2013_J.Biotechnol_168_739
Author(s) : Ruckert C , Szczepanowski R , Albersmeier A , Goesmann A , Iftime D , Musiol EM , Blin K , Wohlleben W , Puhler A , Kalinowski J , Weber T
Ref : J Biotechnol , 168 :739 , 2013
Abstract : Streptomyces collinus Tu 365 (DSMZ 40733), isolated from Kouroussa (Guinea), is the producer of the elfamycin family antibiotic kirromycin, which inhibits bacterial protein biosynthesis by interfering with elongation factor EF-Tu. Here, we report on the Streptomyces collinus Tu 365 complete genome sequence of the 8.27 MB chromosome and the two plasmids SCO1 and SCO2.
ESTHER : Ruckert_2013_J.Biotechnol_168_739
PubMedSearch : Ruckert_2013_J.Biotechnol_168_739
PubMedID: 24140291
Gene_locus related to this paper: strc3-s5v3l4 , strc3-s5vff6 , strc3-s5va60

Title : Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage - Heinl_2012_J.Biotechnol_161_153
Author(s) : Heinl S , Wibberg D , Eikmeyer F , Szczepanowski R , Blom J , Linke B , Goesmann A , Grabherr R , Schwab H , Puhler A , Schluter A
Ref : J Biotechnol , 161 :153 , 2012
Abstract : Lactobacillus buchneri belongs to the group of heterofermentative lactic acid bacteria and is a common member of the silage microbiome. Here we report the completely annotated genomic sequence of L. buchneri CD034, a strain isolated from stable grass silage. The whole genome of L. buchneri CD034 was sequenced on the Roche Genome Sequencer FLX platform. It was found to consist of four replicons, a circular chromosome, and three plasmids. The circular chromosome was predicted to encode 2319 proteins and contains a genomic island and two prophages which significantly differ in G+C-content from the remaining chromosome. It possesses all genes for enzymes of a complete phosphoketolase pathway, whereas two enzymes necessary for glycolysis are lacking. This confirms the classification of L. buchneri CD034 as an obligate heterofermentative lactic acid bacterium. A set of genes considered to be involved in the lactate degradation pathway and genes putatively involved in the breakdown of plant cell wall polymers were identified. Moreover, several genes encoding putative S-layer proteins and two CRISPR systems, belonging to the subclasses I-E and II-A, are located on the chromosome. The largest plasmid pCD034-3 was predicted to encode 57 genes, including a putative polysaccharide synthesis gene cluster, whereas the functions of the two smaller plasmids, pCD034-1 and pCD034-2, remain cryptic. Phylogenetic analysis based on sequence comparison of the conserved marker gene rpoA reveals that L. buchneri CD034 is more closely related to Lactobacillus hilgardii strains than to Lactobacillus brevis and Lactobacillus plantarum strains. Comparison of the L. buchneri CD034 core genome to other fully sequenced and closely related members of the genus Lactobacillus disclosed a high degree of conservation between L. buchneri CD034 and the recently sequenced L. buchneri strain NRRL B-30929 and a more distant relationship to L. buchneri ATCC 11577 and L. brevis ssp. gravesensis ATCC 27305, which cluster together with L. hilgardii type strain ATCC 8290. L. buchneri CD034 genome information will certainly provide the basis for further postgenome studies with the objective to optimize application of the strain in silage production.
ESTHER : Heinl_2012_J.Biotechnol_161_153
PubMedSearch : Heinl_2012_J.Biotechnol_161_153
PubMedID: 22465289
Gene_locus related to this paper: lacbn-f4fwx4

Title : Draft genome sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10 - Schneider_2012_Eukaryot.Cell_11_1582
Author(s) : Schneider J , Andrea H , Blom J , Jaenicke S , Ruckert C , Schorsch C , Szczepanowski R , Farwick M , Goesmann A , Puhler A , Schaffer S , Tauch A , Kohler T , Brinkrolf K
Ref : Eukaryot Cell , 11 :1582 , 2012
Abstract : Wickerhamomyces ciferrii is a microorganism characterized by the production and secretion of large amounts of acetylated sphingoid bases, in particular tetraacetyl phytosphingosine. Here, we present the 15.90-Mbp draft genome sequence of W. ciferrii NRRL Y-1031 F-60-10 generated by pyrosequencing and de novo assembly. The draft genome sequence comprising 364 contigs in 150 scaffolds was annotated and covered 6,702 protein-coding sequences. This information will contribute to the metabolic engineering of this yeast to improve the yield and spectrum of acetylated sphingoid bases in biotechnological production.
ESTHER : Schneider_2012_Eukaryot.Cell_11_1582
PubMedSearch : Schneider_2012_Eukaryot.Cell_11_1582
PubMedID: 23193139
Gene_locus related to this paper: wiccf-k0k780 , wiccf-k0kcu3 , wiccf-k0kir4 , wiccf-k0kmk9 , wiccf-k0kn23 , wiccf-k0krq2 , wiccf-k0ksx2 , wiccf-k0kpv8 , wiccf-k0ksn3 , wiccf-k0kqu5

Title : Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities - Schneider_2012_FEMS.Yeast.Res_12_382
Author(s) : Schneider J , Rupp O , Trost E , Jaenicke S , Passoth V , Goesmann A , Tauch A , Brinkrolf K
Ref : FEMS Yeast Res , 12 :382 , 2012
Abstract : The ascomycetous yeast Wickerhamomyces anomalus (formerly Pichia anomala and Hansenula anomala) exhibits antimicrobial activities and flavoring features that are responsible for its frequent association with food, beverage and feed products. However, limited information on the genetic background of this yeast and its multiple capabilities are currently available. Here, we present the draft genome sequence of the neotype strain W. anomalus DSM 6766. On the basis of pyrosequencing, a de novo assembly of this strain resulted in a draft genome sequence with a total size of 25.47 Mbp. An automatic annotation using RAPYD generated 11 512 protein-coding sequences. This annotation provided the basis to analyse metabolic capabilities, phylogenetic relationships, as well as biotechnologically important features and yielded novel candidate genes of W. anomalus DSM 6766 coding for proteins participating in antimicrobial activities.
ESTHER : Schneider_2012_FEMS.Yeast.Res_12_382
PubMedSearch : Schneider_2012_FEMS.Yeast.Res_12_382
PubMedID: 22292503
Gene_locus related to this paper: hanan-h6uwn2 , hanan-h6uwn4 , hanan-h6uwn6 , hanan-h6uwn8

Title : Complete genome sequence of clinical isolate Pantoea ananatis LMG 5342 - De Maayer_2012_J.Bacteriol_194_1615
Author(s) : De Maayer P , Chan WY , Rezzonico F , Buhlmann A , Venter SN , Blom J , Goesmann A , Frey JE , Smits TH , Duffy B , Coutinho TA
Ref : Journal of Bacteriology , 194 :1615 , 2012
Abstract : The enterobacterium Pantoea ananatis is an ecologically versatile species. It has been found in the environment, as plant epiphyte and endophyte, as an emerging phytopathogen, and as a presumptive, opportunistic human pathogen. Here, we report the complete genome sequence of P. ananatis LMG 5342, isolated from a human wound.
ESTHER : De Maayer_2012_J.Bacteriol_194_1615
PubMedSearch : De Maayer_2012_J.Bacteriol_194_1615
PubMedID: 22374951
Gene_locus related to this paper: panam-d4gf31 , panam-d4gn21 , panan-g7uev1 , panan-u4w979

Title : Genome sequence of a Neisseria meningitidis capsule null locus strain from the clonal complex of sequence type 198 - Schork_2012_J.Bacteriol_194_5144
Author(s) : Schork S , Schluter A , Blom J , Schneiker-Bekel S , Puhler A , Goesmann A , Frosch M , Schoen C
Ref : Journal of Bacteriology , 194 :5144 , 2012
Abstract : Neisseria meningitidis is a commensal and accidental pathogen exclusively of humans. Although the production of polysaccharide capsules is considered to be essential for meningococcal virulence, there have been reports of constitutively unencapsulated strains causing invasive meningococcal disease (IMD). Here we report the genome sequence of a capsule null locus (cnl) strain of sequence type 198 (ST-198), which is found in half of the reported cases of IMD caused by cnl meningococcal strains.
ESTHER : Schork_2012_J.Bacteriol_194_5144
PubMedSearch : Schork_2012_J.Bacteriol_194_5144
PubMedID: 22933768

Title : Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes - Hain_2012_BMC.Genomics_13_144
Author(s) : Hain T , Ghai R , Billion A , Kuenne CT , Steinweg C , Izar B , Mohamed W , Mraheil MA , Domann E , Schaffrath S , Karst U , Goesmann A , Oehm S , Puhler A , Merkl R , Vorwerk S , Glaser P , Garrido P , Rusniok C , Buchrieser C , Goebel W , Chakraborty T
Ref : BMC Genomics , 13 :144 , 2012
Abstract : BACKGROUND: Listeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for two L. monocytogenes strains belonging to serotype 4a (L99) and 4b (CLIP80459), and transcriptomes of representative strains from lineages I, II, and III, thereby permitting in-depth comparison of genome- and transcriptome -based data from three lineages of L. monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans.
RESULTS: The genome analysis of the weakly pathogenic L99 serotype 4a provides extensive evidence of virulence gene decay, including loss of several important surface proteins. The 4b CLIP80459 genome, unlike the previously sequenced 4b F2365 genome harbours an intact inlB invasion gene. These lineage I strains are characterized by the lack of prophage genes, as they share only a single prophage locus with other L. monocytogenes genomes 1/2a EGD-e and 4a L99. Comparative transcriptome analysis during intracellular growth uncovered adaptive expression level differences in lineages I, II and III of Listeria, notable amongst which was a strong intracellular induction of flagellar genes in strain 4a L99 compared to the other lineages. Furthermore, extensive differences between strains are manifest at levels of metabolic flux control and phosphorylated sugar uptake. Intriguingly, prophage gene expression was found to be a hallmark of intracellular gene expression. Deletion mutants in the single shared prophage locus of lineage II strain EGD-e 1/2a, the lma operon, revealed severe attenuation of virulence in a murine infection model. CONCLUSION: Comparative genomics and transcriptome analysis of L. monocytogenes strains from three lineages implicate prophage genes in intracellular adaptation and indicate that gene loss and decay may have led to the emergence of attenuated lineages.
ESTHER : Hain_2012_BMC.Genomics_13_144
PubMedSearch : Hain_2012_BMC.Genomics_13_144
PubMedID: 22530965
Gene_locus related to this paper: lismo-LMO0110 , lismo-LMO0493 , lismo-LMO0580 , lismo-LMO0950 , lismo-LMO0951 , lismo-LMO1128 , lismo-LMO1258 , lismo-LMO2089 , lismo-LMO2433 , lismo-LMO2578 , lismo-LMO2755 , lismo-metx

Title : Complete genome sequence of the porcine isolate Enterococcus faecalis D32 - Zischka_2012_J.Bacteriol_194_5490
Author(s) : Zischka M , Kuenne C , Blom J , Dabrowski PW , Linke B , Hain T , Nitsche A , Goesmann A , Larsen J , Jensen LB , Witte W , Werner G
Ref : Journal of Bacteriology , 194 :5490 , 2012
Abstract : The complete and annotated genome sequence of Enterococcus faecalis D32, a commensal strain isolated from a Danish pig, suggests putative adaptation to the porcine host and absence of distinct virulence-associated traits.
ESTHER : Zischka_2012_J.Bacteriol_194_5490
PubMedSearch : Zischka_2012_J.Bacteriol_194_5490
PubMedID: 22965105

Title : Genome sequence of Fibrella aestuarina BUZ 2(T), a filamentous marine bacterium - Filippini_2012_J.Bacteriol_194_3555
Author(s) : Filippini M , Qi W , Blom J , Goesmann A , Smits TH , Bagheri HC
Ref : Journal of Bacteriology , 194 :3555 , 2012
Abstract : Fibrella aestuarina BUZ 2(T) is the type strain of the recently characterized genus Fibrella. Here we report the draft genome sequence of this strain, which consists of a single scaffold representing the chromosome (with 11 gaps) and a 161-kb circular plasmid.
ESTHER : Filippini_2012_J.Bacteriol_194_3555
PubMedSearch : Filippini_2012_J.Bacteriol_194_3555
PubMedID: 22689241
Gene_locus related to this paper: 9bact-i0k5k6 , 9bact-i0k9r5 , 9bact-i0k566 , 9bact-i0kex0 , 9bact-i0kei5 , 9bact-i0k9r6 , 9bact-i0kc75 , 9bact-i0k9s0 , 9bact-i0k9c8

Title : Genome sequence of the filamentous bacterium Fibrisoma limi BUZ 3T - Filippini_2012_J.Bacteriol_194_4445
Author(s) : Filippini M , Qi W , Jaenicke S , Goesmann A , Smits TH , Bagheri HC
Ref : Journal of Bacteriology , 194 :4445 , 2012
Abstract : Fibrisoma limi strain BUZ 3(T), a Gram-negative bacterium, was isolated from coastal mud from the North Sea (Fedderwardersiel, Germany) and characterized using a polyphasic approach in 2011. The genome consists of a chromosome of about 7.5 Mb and three plasmids.
ESTHER : Filippini_2012_J.Bacteriol_194_4445
PubMedSearch : Filippini_2012_J.Bacteriol_194_4445
PubMedID: 22843583
Gene_locus related to this paper: 9bact-i2ght8 , 9bact-i2gt16 , 9bact-i2gds2 , 9bact-i2gjh9

Title : Genome of a European fresh-vegetable food safety outbreak strain of Salmonella enterica subsp. enterica serovar weltevreden - Brankatschk_2011_J.Bacteriol_193_2066
Author(s) : Brankatschk K , Blom J , Goesmann A , Smits TH , Duffy B
Ref : Journal of Bacteriology , 193 :2066 , 2011
Abstract : The genome of Salmonella enterica subsp. enterica serovar Weltevreden strain 2007-60-3289-1 was sequenced. The genome sequence of this fresh-vegetable isolate from Scandinavia will be useful for the elucidation of plant host factors in comparison to other serovars of S. enterica subsp. enterica.
ESTHER : Brankatschk_2011_J.Bacteriol_193_2066
PubMedSearch : Brankatschk_2011_J.Bacteriol_193_2066
PubMedID: 21296964
Gene_locus related to this paper: salen-OPDB , salti-q8z717 , salty-AES , salty-DLHH , salty-ENTF , salty-FES , salty-IROD , salty-IROE , salty-PLDB , salty-STY1441 , salty-STY3846 , salty-yafa , salty-YBFF , salty-ycfp , salty-YHET

Title : Whole-genome sequence of the transformable Neisseria meningitidis serogroup A strain WUE2594 - Schoen_2011_J.Bacteriol_193_2064
Author(s) : Schoen C , Weber-Lehmann J , Blom J , Joseph B , Goesmann A , Strittmatter A , Frosch M
Ref : Journal of Bacteriology , 193 :2064 , 2011
Abstract : Serogroup A meningococci are a leading cause of bacterial meningitis in children and young adults worldwide. However, the genetic basis of serogroup A strains' virulence and their epidemiological properties remain poorly understood. Therefore, we sequenced the complete genome of the transformable Neisseria meningitidis serogroup A strain WUE2594.
ESTHER : Schoen_2011_J.Bacteriol_193_2064
PubMedSearch : Schoen_2011_J.Bacteriol_193_2064
PubMedID: 21296965
Gene_locus related to this paper: neigo-pip , neima-metx , neime-ESD , neime-NMB0276 , neime-NMB1877 , neime-r0tza2

Title : Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid - Wibberg_2011_J.Biotechnol_155_50
Author(s) : Wibberg D , Blom J , Jaenicke S , Kollin F , Rupp O , Scharf B , Schneiker-Bekel S , Sczcepanowski R , Goesmann A , Setubal JC , Schmitt R , Puhler A , Schluter A
Ref : J Biotechnol , 155 :50 , 2011
Abstract : Agrobacterium sp. H13-3, formerly known as Rhizobium lupini H13-3, is a soil bacterium that was isolated from the rhizosphere of Lupinus luteus. The isolate has been established as a model system for studying novel features of flagellum structure, motility and chemotaxis within the family Rhizobiaceae. The complete genome sequence of Agrobacterium sp. H13-3 has been established and the genome structure and phylogenetic assignment of the organism was analysed. For de novo sequencing of the Agrobacterium sp. H13-3 genome, a combined strategy comprising 454-pyrosequencing on the Genome Sequencer FLX platform and PCR-based amplicon sequencing for gap closure was applied. The finished genome consists of three replicons and comprises 5,573,770 bases. Based on phylogenetic analyses, the isolate could be assigned to the genus Agrobacterium biovar I and represents a genomic species G1 strain within this biovariety. The highly conserved circular chromosome (2.82 Mb) of Agrobacterium sp. H13-3 mainly encodes housekeeping functions characteristic for an aerobic, heterotrophic bacterium. Agrobacterium sp. H13-3 is a motile bacterium driven by the rotation of several complex flagella. Its behaviour towards external stimuli is regulated by a large chemotaxis regulon and a total of 17 chemoreceptors. Comparable to the genome of Agrobacterium tumefaciens C58, Agrobacterium sp. H13-3 possesses a linear chromosome (2.15 Mb) that is related to its reference replicon and features chromosomal and plasmid-like properties. The accessory plasmid pAspH13-3a (0.6 Mb) is only distantly related to the plasmid pAtC58 of A. tumefaciens C58 and shows a mosaic structure. A tumor-inducing Ti-plasmid is missing in the sequenced strain H13-3 indicating that it is a non-virulent isolate.
ESTHER : Wibberg_2011_J.Biotechnol_155_50
PubMedSearch : Wibberg_2011_J.Biotechnol_155_50
PubMedID: 21329740
Gene_locus related to this paper: agrsh-f0l326 , agrsh-f0lb16 , agrsh-f0lfg1 , agrsh-f0lgt6 , agrt5-a9cfs8 , agrt5-q7d1j0 , agrt5-q7d1j3 , agrtu-ATU2126 , agrtu-ATU2481 , agrsh-f0lfk1

Title : The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome - Schneiker-Bekel_2011_J.Biotechnol_155_20
Author(s) : Schneiker-Bekel S , Wibberg D , Bekel T , Blom J , Linke B , Neuweger H , Stiens M , Vorholter FJ , Weidner S , Goesmann A , Puhler A , Schluter A
Ref : J Biotechnol , 155 :20 , 2011
Abstract : Isolates of the symbiotic nitrogen-fixing species Sinorhizobium meliloti usually contain a chromosome and two large megaplasmids encoding functions that are absolutely required for the specific interaction of the microsymbiont with corresponding host plants leading to an effective symbiosis. The complete genome sequence, including the megaplasmids pSmeSM11c (related to pSymA) and pSmeSM11d (related to pSymB), was established for the dominant, indigenous S. meliloti strain SM11 that had been isolated during a long-term field release experiment with genetically modified S. meliloti strains. The chromosome, the largest replicon of S. meliloti SM11, is 3,908,022bp in size and codes for 3785 predicted protein coding sequences. The size of megaplasmid pSmeSM11c is 1,633,319bp and it contains 1760 predicted protein coding sequences whereas megaplasmid pSmeSM11d is 1,632,395bp in size and comprises 1548 predicted coding sequences. The gene content of the SM11 chromosome is quite similar to that of the reference strain S. meliloti Rm1021. Comparison of pSmeSM11c to pSymA of the reference strain revealed that many gene regions of these replicons are variable, supporting the assessment that pSymA is a major hot-spot for intra-specific differentiation. Plasmids pSymA and pSmeSM11c both encode unique genes. Large gene regions of pSmeSM11c are closely related to corresponding parts of Sinorhizobium medicae WSM419 plasmids. Moreover, pSmeSM11c encodes further novel gene regions, e.g. additional plasmid survival genes (partition, mobilisation and conjugative transfer genes), acdS encoding 1-aminocyclopropane-1-carboxylate deaminase involved in modulation of the phytohormone ethylene level and genes having predicted functions in degradative capabilities, stress response, amino acid metabolism and associated pathways. In contrast to Rm1021 pSymA and pSmeSM11c, megaplasmid pSymB of strain Rm1021 and pSmeSM11d are highly conserved showing extensive synteny with only few rearrangements. Most remarkably, pSmeSM11b contains a new gene cluster predicted to be involved in polysaccharide biosynthesis. Compilation of the S. meliloti SM11 genome sequence contributes to an extension of the S. meliloti pan-genome.
ESTHER : Schneiker-Bekel_2011_J.Biotechnol_155_20
PubMedSearch : Schneiker-Bekel_2011_J.Biotechnol_155_20
PubMedID: 21396969
Gene_locus related to this paper: rhime-PCAD , rhime-RB1395

Title : High-quality genome sequence of Pichia pastoris CBS7435 - Kuberl_2011_J.Biotechnol_154_312
Author(s) : Kuberl A , Schneider J , Thallinger GG , Anderl I , Wibberg D , Hajek T , Jaenicke S , Brinkrolf K , Goesmann A , Szczepanowski R , Puhler A , Schwab H , Glieder A , Pichler H
Ref : J Biotechnol , 154 :312 , 2011
Abstract : The methylotrophic yeast Pichia pastoris (Komagataella phaffii) CBS7435 is the parental strain of commonly used P. pastoris recombinant protein production hosts making it well suited for improving the understanding of associated genomic features. Here, we present a 9.35 Mbp high-quality genome sequence of P. pastoris CBS7435 established by a combination of 454 and Illumina sequencing. An automatic annotation of the genome sequence yielded 5007 protein-coding genes, 124 tRNAs and 29 rRNAs. Moreover, we report the complete DNA sequence of the first mitochondrial genome of a methylotrophic yeast. Fifteen genes encoding proteins, 2 rRNA and 25 tRNA loci were identified on the 35.7 kbp circular, mitochondrial DNA. Furthermore, the architecture of the putative alpha mating factor protein of P. pastoris CBS7435 turned out to be more complex than the corresponding protein of Saccharomyces cerevisiae.
ESTHER : Kuberl_2011_J.Biotechnol_154_312
PubMedSearch : Kuberl_2011_J.Biotechnol_154_312
PubMedID: 21575661
Gene_locus related to this paper: picp7-f2qwe3 , picpa-cbpy , picpa-KEX1 , picpg-c4qw07 , picpg-c4r0k6 , picpg-c4r5w7 , picpg-c4r6t8 , picpg-c4r272 , picpg-c4r403 , picpg-c4r663 , picpg-c4r788 , picpa-a0a1b2jh35

Title : Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp - Smits_2010_Mol.Plant.Microbe.Interact_23_384
Author(s) : Smits TH , Rezzonico F , Kamber T , Blom J , Goesmann A , Frey JE , Duffy B
Ref : Mol Plant Microbe Interact , 23 :384 , 2010
Abstract : Fire blight, caused by the enterobacterium Erwinia amylovora, is a devastating disease of rosaceous plants that has global economic importance for apple and pear production and trade. The complete genome of E. amylovora CFBP 1430 was sequenced, annotated, and compared with the genomes of other Erwinia spp. Several singleton and shared features of the E. amylovora CFBP 1430 genome were identified that offer a first view into evolutionary aspects within the genus Erwinia. Comparative genomics identified or clarified virulence and fitness determinants and secretion systems. Novel insights revealed in the genome of E. amylovora CFBP 1430 hold potential for exploitation to improve the design of more effective fire blight control strategies.
ESTHER : Smits_2010_Mol.Plant.Microbe.Interact_23_384
PubMedSearch : Smits_2010_Mol.Plant.Microbe.Interact_23_384
PubMedID: 20192826
Gene_locus related to this paper: erwac-d4hwt0 , erwac-d4hxs4 , erwac-d4i2q5 , erwac-d4i3s4 , erwac-d4i259 , erwac-d4i301 , erwae-d4idw0 , erwse-e3dex4

Title : Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity - Smits_2010_BMC.Genomics_11_2
Author(s) : Smits TH , Jaenicke S , Rezzonico F , Kamber T , Goesmann A , Frey JE , Duffy B
Ref : BMC Genomics , 11 :2 , 2010
Abstract : BACKGROUND: Erwinia pyrifoliae is a newly described necrotrophic pathogen, which causes fire blight on Asian (Nashi) pear and is geographically restricted to Eastern Asia. Relatively little is known about its genetics compared to the closely related main fire blight pathogen E. amylovora.
RESULTS: The genome of the type strain of E. pyrifoliae strain DSM 12163T, was sequenced using both 454 and Solexa pyrosequencing and annotated. The genome contains a circular chromosome of 4.026 Mb and four small plasmids. Based on their respective role in virulence in E. amylovora or related organisms, we identified several putative virulence factors, including type III and type VI secretion systems and their effectors, flagellar genes, sorbitol metabolism, iron uptake determinants, and quorum-sensing components. A deletion in the rpoS gene covering the most conserved region of the protein was identified which may contribute to the difference in virulence/host-range compared to E. amylovora. Comparative genomics with the pome fruit epiphyte Erwinia tasmaniensis Et1/99 showed that both species are overall highly similar, although specific differences were identified, for example the presence of some phage gene-containing regions and a high number of putative genomic islands containing transposases in the E. pyrifoliae DSM 12163T genome.
CONCLUSIONS: The E. pyrifoliae genome is an important addition to the published genome of E. tasmaniensis and the unfinished genome of E. amylovora providing a foundation for re-sequencing additional strains that may shed light on the evolution of the host-range and virulence/pathogenicity of this important group of plant-associated bacteria.
ESTHER : Smits_2010_BMC.Genomics_11_2
PubMedSearch : Smits_2010_BMC.Genomics_11_2
PubMedID: 20047678
Gene_locus related to this paper: erwac-d4i3s4 , erwp6-d2tb51 , erwpe-d0fv08 , erwpe-d0fwy1 , erwpe-d0fx20 , erwpy-d0fr69 , erwse-e3dex4

Title : Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8 - Farnbacher_2010_BMC.Genomics_11_335
Author(s) : Farnbacher M , Jahns T , Willrodt D , Daniel R , Haas R , Goesmann A , Kurtz S , Rieder G
Ref : BMC Genomics , 11 :335 , 2010
Abstract : BACKGROUND: The Mongolian gerbils are a good model to mimic the Helicobacter pylori-associated pathogenesis of the human stomach. In the current study the gerbil-adapted strain B8 was completely sequenced, annotated and compared to previous genomes, including the 73 supercontigs of the parental strain B128.
RESULTS: The complete genome of H. pylori B8 was manually curated gene by gene, to assign as much function as possible. It consists of a circular chromosome of 1,673,997 bp and of a small plasmid of 6,032 bp carrying nine putative genes. The chromosome contains 1,711 coding sequences, 293 of which are strain-specific, coding mainly for hypothetical proteins, and a large plasticity zone containing a putative type-IV-secretion system and coding sequences with unknown function. The cag-pathogenicity island is rearranged such that the cagA-gene is located 13,730 bp downstream of the inverted gene cluster cagB-cag1. Directly adjacent to the cagA-gene, there are four hypothetical genes and one variable gene with a different codon usage compared to the rest of the H. pylori B8-genome. This indicates that these coding sequences might be acquired via horizontal gene transfer.The genome comparison of strain B8 to its parental strain B128 delivers 425 unique B8-proteins. Due to the fact that strain B128 was not fully sequenced and only automatically annotated, only 12 of these proteins are definitive singletons that might have been acquired during the gerbil-adaptation process of strain B128. CONCLUSION: Our sequence data and its analysis provide new insight into the high genetic diversity of H. pylori-strains. We have shown that the gerbil-adapted strain B8 has the potential to build, possibly by a high rate of mutation and recombination, a dynamic pool of genetic variants (e.g. fragmented genes and repetitive regions) required for the adaptation-processes. We hypothesize that these variants are essential for the colonization and persistence of strain B8 in the gerbil stomach during in ammation.
ESTHER : Farnbacher_2010_BMC.Genomics_11_335
PubMedSearch : Farnbacher_2010_BMC.Genomics_11_335
PubMedID: 20507619
Gene_locus related to this paper: helpy-o25061

Title : Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion - Trost_2010_BMC.Genomics_11_91
Author(s) : Trost E , Gotker S , Schneider J , Schneiker-Bekel S , Szczepanowski R , Tilker A , Viehoever P , Arnold W , Bekel T , Blom J , Gartemann KH , Linke B , Goesmann A , Puhler A , Shukla SK , Tauch A
Ref : BMC Genomics , 11 :91 , 2010
Abstract : BACKGROUND: Corynebacterium aurimucosum is a slightly yellowish, non-lipophilic, facultative anaerobic member of the genus Corynebacterium and predominantly isolated from human clinical specimens. Unusual black-pigmented variants of C. aurimucosum (originally named as C. nigricans) continue to be recovered from the female urogenital tract and they are associated with complications during pregnancy. C. aurimucosum ATCC 700975 (C. nigricans CN-1) was originally isolated from a vaginal swab of a 34-year-old woman who experienced a spontaneous abortion during month six of pregnancy. For a better understanding of the physiology and lifestyle of this potential urogenital pathogen, the complete genome sequence of C. aurimucosum ATCC 700975 was determined.
RESULTS: Sequencing and assembly of the C. aurimucosum ATCC 700975 genome yielded a circular chromosome of 2,790,189 bp in size and the 29,037-bp plasmid pET44827. Specific gene sets associated with the central metabolism of C. aurimucosum apparently provide enhanced metabolic flexibility and adaptability in aerobic, anaerobic and low-pH environments, including gene clusters for the uptake and degradation of aromatic amines, L-histidine and L-tartrate as well as a gene region for the formation of selenocysteine and its incorporation into formate dehydrogenase. Plasmid pET44827 codes for a non-ribosomal peptide synthetase that plays the pivotal role in the synthesis of the characteristic black pigment of C. aurimucosum ATCC 700975.
CONCLUSIONS: The data obtained by the genome project suggest that C. aurimucosum could be both a resident of the human gut and possibly a pathogen in the female genital tract causing complications during pregnancy. Since hitherto all black-pigmented C. aurimucosum strains have been recovered from female genital source, biosynthesis of the pigment is apparently required for colonization by protecting the bacterial cells against the high hydrogen peroxide concentration in the vaginal environment. The location of the corresponding genes on plasmid pET44827 explains why black-pigmented (formerly C. nigricans) and non-pigmented C. aurimucosum strains were isolated from clinical specimens.
ESTHER : Trost_2010_BMC.Genomics_11_91
PubMedSearch : Trost_2010_BMC.Genomics_11_91
PubMedID: 20137072
Gene_locus related to this paper: cora7-c3peg4 , cora7-c3pft2 , cora7-c3pgf2 , cora7-c3ph31 , cora7-c3phx8 , cora7-c3piw1 , cora7-c3pix7 , cora7-c3pj13 , cora7-c3pjc9 , cora7-c3pjm1 , cora7-c3pju4 , cora7-c3pjx9 , cora7-c3pjy0 , cora7-c3pk62 , cora7-c3pk63 , cora7-c3pk94 , cora7-c3pk60 , cora7-c3phz6 , cora7-c3phz5 , cora7-c3pim5 , cora7-c3pjw4

Title : Complete genome sequence of Listeria seeligeri, a nonpathogenic member of the genus Listeria - Steinweg_2010_J.Bacteriol_192_1473
Author(s) : Steinweg C , Kuenne CT , Billion A , Mraheil MA , Domann E , Ghai R , Barbuddhe SB , Karst U , Goesmann A , Puhler A , Weisshaar B , Wehland J , Lampidis R , Kreft J , Goebel W , Chakraborty T , Hain T
Ref : Journal of Bacteriology , 192 :1473 , 2010
Abstract : We report the complete and annotated genome sequence of the nonpathogenic Listeria seeligeri SLCC3954 serovar 1/2b type strain harboring the smallest completely sequenced genome of the genus Listeria.
ESTHER : Steinweg_2010_J.Bacteriol_192_1473
PubMedSearch : Steinweg_2010_J.Bacteriol_192_1473
PubMedID: 20061480
Gene_locus related to this paper: lisin-LIN0976 , lismo-LMO2452 , lismo-metx , lisss-d3ulc5 , lisss-d3unw0 , lisss-d3urb3 , lisss-d3urc9

Title : Genome sequence of the biocontrol agent Pantoea vagans strain C9-1 - Smits_2010_J.Bacteriol_192_6486
Author(s) : Smits TH , Rezzonico F , Kamber T , Goesmann A , Ishimaru CA , Stockwell VO , Frey JE , Duffy B
Ref : Journal of Bacteriology , 192 :6486 , 2010
Abstract : Pantoea vagans is a Gram-negative enterobacterial plant epiphyte of a broad range of plants. Here we report the 4.89-Mb genome sequence of P. vagans strain C9-1 (formerly Pantoea agglomerans), which is commercially registered for biological control of fire blight, a disease of pear and apple trees caused by Erwinia amylovora.
ESTHER : Smits_2010_J.Bacteriol_192_6486
PubMedSearch : Smits_2010_J.Bacteriol_192_6486
PubMedID: 20952567
Gene_locus related to this paper: panvc-e1se23 , panvc-e1sek2 , panvc-e1sgb2 , 9entr-h8dpn5 , panvc-e1sjq6

Title : Genomic and phenotypic characterization of a nonpigmented variant of Pantoea vagans biocontrol strain C9-1 lacking the 530-kb megaplasmid pPag3 - Smits_2010_FEMS.Microbiol.Lett_308_48
Author(s) : Smits TH , Rezzonico F , Pelludat C , Goesmann A , Frey JE , Duffy B
Ref : FEMS Microbiology Letters , 308 :48 , 2010
Abstract : A 530-kb megaplasmid pPag3 contributing 10.8% of the total genome of Pantoea vagans biocontrol strain C9-1 was sequenced. A rare nonpigmented variant C9-1W was obtained and shown to have lost pPag3, but retained all other plasmids (pPag1, pPag2). Phenotypic characterization of the variant confirmed the function of several annotated genes that may influence ecological fitness and efficacy. Metabolic profiling revealed important plasmid-based carbon utilization phenotypes. Plasmid loss resulted in thiamine auxotrophy, absence of carotenoid pigmentation, desferrioxamine diffusible siderophore biosynthesis, inherent ampicillin resistance and expression of AI-1 quorum-sensing signaling. This confirmed the functional expression of the corresponding genes located on pPag3 in P. vagans.
ESTHER : Smits_2010_FEMS.Microbiol.Lett_308_48
PubMedSearch : Smits_2010_FEMS.Microbiol.Lett_308_48
PubMedID: 20487014

Title : Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence - Joseph_2010_J.Bacteriol_192_5363
Author(s) : Joseph B , Schneiker-Bekel S , Schramm-Gluck A , Blom J , Claus H , Linke B , Schwarz RF , Becker A , Goesmann A , Frosch M , Schoen C
Ref : Journal of Bacteriology , 192 :5363 , 2010
Abstract : Neisseria meningitidis serogroup B strains are responsible for most meningococcal cases in the industrialized countries, and strains belonging to the clonal complex ST-41/44 are among the most prevalent serogroup B strains in carriage and disease. Here, we report the first genome and transcriptome comparison of a serogroup B carriage strain from the clonal complex ST-41/44 to the serogroup B disease strain MC58 from the clonal complex ST-32. Both genomes are highly colinear, with only three major genome rearrangements that are associated with the integration of mobile genetic elements. They further differ in about 10% of their gene content, with the highest variability in gene presence as well as gene sequence found for proteins involved in host cell interactions, including Opc, NadA, TonB-dependent receptors, RTX toxin, and two-partner secretion system proteins. Whereas housekeeping genes coding for metabolic functions were highly conserved, there were considerable differences in their expression pattern upon adhesion to human nasopharyngeal cells between both strains, including differences in energy metabolism and stress response. In line with these genomic and transcriptomic differences, both strains also showed marked differences in their in vitro infectivity and in serum resistance. Taken together, these data support the concept of a polygenic nature of meningococcal virulence comprising differences in the repertoire of adhesins as well as in the regulation of metabolic genes and suggest a prominent role for immune selection and genetic drift in shaping the meningococcal genome.
ESTHER : Joseph_2010_J.Bacteriol_192_5363
PubMedSearch : Joseph_2010_J.Bacteriol_192_5363
PubMedID: 20709895
Gene_locus related to this paper: neigo-pip , neima-metx , neime-ESD , neime-NMB0276 , neime-NMB1877

Title : The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence - Trost_2010_BMC.Genomics_11_728
Author(s) : Trost E , Ott L , Schneider J , Schroder J , Jaenicke S , Goesmann A , Husemann P , Stoye J , Dorella FA , Rocha FS , Soares Sde C , D'Afonseca V , Miyoshi A , Ruiz J , Silva A , Azevedo V , Burkovski A , Guiso N , Join-Lambert OF , Kayal S , Tauch A
Ref : BMC Genomics , 11 :728 , 2010
Abstract : BACKGROUND: Corynebacterium pseudotuberculosis is generally regarded as an important animal pathogen that rarely infects humans. Clinical strains are occasionally recovered from human cases of lymphadenitis, such as C. pseudotuberculosis FRC41 that was isolated from the inguinal lymph node of a 12-year-old girl with necrotizing lymphadenitis. To detect potential virulence factors and corresponding gene-regulatory networks in this human isolate, the genome sequence of C. pseudotuberculosis FCR41 was determined by pyrosequencing and functionally annotated.
RESULTS: Sequencing and assembly of the C. pseudotuberculosis FRC41 genome yielded a circular chromosome with a size of 2,337,913 bp and a mean G+C content of 52.2%. Specific gene sets associated with iron and zinc homeostasis were detected among the 2,110 predicted protein-coding regions and integrated into a gene-regulatory network that is linked with both the central metabolism and the oxidative stress response of FRC41. Two gene clusters encode proteins involved in the sortase-mediated polymerization of adhesive pili that can probably mediate the adherence to host tissue to facilitate additional ligand-receptor interactions and the delivery of virulence factors. The prominent virulence factors phospholipase D (Pld) and corynebacterial protease CP40 are encoded in the genome of this human isolate. The genome annotation revealed additional serine proteases, neuraminidase H, nitric oxide reductase, an invasion-associated protein, and acyl-CoA carboxylase subunits involved in mycolic acid biosynthesis as potential virulence factors. The cAMP-sensing transcription regulator GlxR plays a key role in controlling the expression of several genes contributing to virulence. CONCLUSION: The functional data deduced from the genome sequencing and the extended knowledge of virulence factors indicate that the human isolate C. pseudotuberculosis FRC41 is equipped with a distinct gene set promoting its survival under unfavorable environmental conditions encountered in the mammalian host.
ESTHER : Trost_2010_BMC.Genomics_11_728
PubMedSearch : Trost_2010_BMC.Genomics_11_728
PubMedID: 21192786
Gene_locus related to this paper: corpf-d8knc3 , corpf-d8kpq1 , corpf-d8kps5 , corpf-d8kq17 , corps-h8lrl6 , corps-i0as85 , corpf-d8klm2 , corpf-d8kp39

Title : The Waddlia genome: a window into chlamydial biology - Bertelli_2010_PLoS.One_5_e10890
Author(s) : Bertelli C , Collyn F , Croxatto A , Ruckert C , Polkinghorne A , Kebbi-Beghdadi C , Goesmann A , Vaughan L , Greub G
Ref : PLoS ONE , 5 :e10890 , 2010
Abstract : Growing evidence suggests that a novel member of the Chlamydiales order, Waddlia chondrophila, is a potential agent of miscarriage in humans and abortion in ruminants. Due to the lack of genetic tools to manipulate chlamydia, genomic analysis is proving to be the most incisive tool in stimulating investigations into the biology of these obligate intracellular bacteria. 454/Roche and Solexa/Illumina technologies were thus used to sequence and assemble de novo the full genome of the first representative of the Waddliaceae family, W. chondrophila. The bacteria possesses a 2'116'312 bp chromosome and a 15'593 bp low-copy number plasmid that might integrate into the bacterial chromosome. The Waddlia genome displays numerous repeated sequences indicating different genome dynamics from classical chlamydia which almost completely lack repetitive elements. Moreover, W. chondrophila exhibits many virulence factors also present in classical chlamydia, including a functional type III secretion system, but also a large complement of specific factors for resistance to host or environmental stresses. Large families of outer membrane proteins were identified indicating that these highly immunogenic proteins are not Chlamydiaceae specific and might have been present in their last common ancestor. Enhanced metabolic capability for the synthesis of nucleotides, amino acids, lipids and other co-factors suggests that the common ancestor of the modern Chlamydiales may have been less dependent on their eukaryotic host. The fine-detailed analysis of biosynthetic pathways brings us closer to possibly developing a synthetic medium to grow W. chondrophila, a critical step in the development of genetic tools. As a whole, the availability of the W. chondrophila genome opens new possibilities in Chlamydiales research, providing new insights into the evolution of members of the order Chlamydiales and the biology of the Waddliaceae.
ESTHER : Bertelli_2010_PLoS.One_5_e10890
PubMedSearch : Bertelli_2010_PLoS.One_5_e10890
PubMedID: 20531937
Gene_locus related to this paper: wadcw-d6ywc6

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 : Complete genome sequence of Lactobacillus johnsonii FI9785, a competitive exclusion agent against pathogens in poultry - Wegmann_2009_J.Bacteriol_191_7142
Author(s) : Wegmann U , Overweg K , Horn N , Goesmann A , Narbad A , Gasson MJ , Shearman C
Ref : Journal of Bacteriology , 191 :7142 , 2009
Abstract : Lactobacillus johnsonii is a member of the acidophilus group of lactobacilli. Because of their probiotic properties, including attachment to epithelial cells, immunomodulation, and competitive exclusion of pathogens, representatives of this group are being intensively studied. Here we report the complete annotated genome sequence of Lactobacillus johnsonii FI9785, a strain which prevents the colonization of specific-pathogen-free chicks by Clostridium perfringens.
ESTHER : Wegmann_2009_J.Bacteriol_191_7142
PubMedSearch : Wegmann_2009_J.Bacteriol_191_7142
PubMedID: 19767436
Gene_locus related to this paper: lacga-q043a3 , lacga-q047a5 , lacjf-d0r6b0 , lacjo-q74hh0 , lacjo-q74hz2 , lacjo-q74ii3 , lacjo-q74k55 , lacjo-q74kk4 , lacjo-q74lt6

Title : The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity - Gartemann_2008_J.Bacteriol_190_2138
Author(s) : Gartemann KH , Abt B , Bekel T , Burger A , Engemann J , Flugel M , Gaigalat L , Goesmann A , Grafen I , Kalinowski J , Kaup O , Kirchner O , Krause L , Linke B , McHardy A , Meyer F , Pohle S , Ruckert C , Schneiker S , Zellermann EM , Puhler A , Eichenlaub R , Kaiser O , Bartels D
Ref : Journal of Bacteriology , 190 :2138 , 2008
Abstract : Clavibacter michiganensis subsp. michiganensis is a plant-pathogenic actinomycete that causes bacterial wilt and canker of tomato. The nucleotide sequence of the genome of strain NCPPB382 was determined. The chromosome is circular, consists of 3.298 Mb, and has a high G+C content (72.6%). Annotation revealed 3,080 putative protein-encoding sequences; only 26 pseudogenes were detected. Two rrn operons, 45 tRNAs, and three small stable RNA genes were found. The two circular plasmids, pCM1 (27.4 kbp) and pCM2 (70.0 kbp), which carry pathogenicity genes and thus are essential for virulence, have lower G+C contents (66.5 and 67.6%, respectively). In contrast to the genome of the closely related organism Clavibacter michiganensis subsp. sepedonicus, the genome of C. michiganensis subsp. michiganensis lacks complete insertion elements and transposons. The 129-kb chp/tomA region with a low G+C content near the chromosomal origin of replication was shown to be necessary for pathogenicity. This region contains numerous genes encoding proteins involved in uptake and metabolism of sugars and several serine proteases. There is evidence that single genes located in this region, especially genes encoding serine proteases, are required for efficient colonization of the host. Although C. michiganensis subsp. michiganensis grows mainly in the xylem of tomato plants, no evidence for pronounced genome reduction was found. C. michiganensis subsp. michiganensis seems to have as many transporters and regulators as typical soil-inhabiting bacteria. However, the apparent lack of a sulfate reduction pathway, which makes C. michiganensis subsp. michiganensis dependent on reduced sulfur compounds for growth, is probably the reason for the poor survival of C. michiganensis subsp. michiganensis in soil.
ESTHER : Gartemann_2008_J.Bacteriol_190_2138
PubMedSearch : Gartemann_2008_J.Bacteriol_190_2138
PubMedID: 18192381
Gene_locus related to this paper: clam3-a5cln9 , clam3-a5clw2 , clam3-a5cm48 , clam3-a5cmg3 , clam3-a5cmk0 , clam3-a5cn86 , clam3-a5cr52 , clam3-a5cr57 , clam3-a5crq6 , clam3-a5csc5 , clam3-metx , clams-b0rcr0 , clams-b0rdd6 , clams-b0rde2 , clams-b0rga8 , clams-b0riv5 , clam3-a5cui5 , clam3-a5cp43 , clam3-a5cp56

Title : Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis - Schoen_2008_Proc.Natl.Acad.Sci.U.S.A_105_3473
Author(s) : Schoen C , Blom J , Claus H , Schramm-Gluck A , Brandt P , Muller T , Goesmann A , Joseph B , Konietzny S , Kurzai O , Schmitt C , Friedrich T , Linke B , Vogel U , Frosch M
Ref : Proc Natl Acad Sci U S A , 105 :3473 , 2008
Abstract : Neisseria meningitidis is a leading cause of infectious childhood mortality worldwide. Most research efforts have hitherto focused on disease isolates belonging to only a few hypervirulent clonal lineages. However, up to 10% of the healthy human population is temporarily colonized by genetically diverse strains mostly with little or no pathogenic potential. Currently, little is known about the biology of carriage strains and their evolutionary relationship with disease isolates. The expression of a polysaccharide capsule is the only trait that has been convincingly linked to the pathogenic potential of N. meningitidis. To gain insight into the evolution of virulence traits in this species, whole-genome sequences of three meningococcal carriage isolates were obtained. Gene content comparisons with the available genome sequences from three disease isolates indicate that there is no core pathogenome in N. meningitidis. A comparison of the chromosome structure suggests that a filamentous prophage has mediated large chromosomal rearrangements and the translocation of some candidate virulence genes. Interspecific comparison of the available Neisseria genome sequences and dot blot hybridizations further indicate that the insertion sequence IS1655 is restricted only to N. meningitidis; its low sequence diversity is an indicator of an evolutionarily recent population bottleneck. A genome-based phylogenetic reconstruction provides evidence that N. meningitidis has emerged as an unencapsulated human commensal from a common ancestor with Neisseria gonorrhoeae and Neisseria lactamica and consecutively acquired the genes responsible for capsule synthesis via horizontal gene transfer.
ESTHER : Schoen_2008_Proc.Natl.Acad.Sci.U.S.A_105_3473
PubMedSearch : Schoen_2008_Proc.Natl.Acad.Sci.U.S.A_105_3473
PubMedID: 18305155
Gene_locus related to this paper: neigo-pip , neima-metx , neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB1828 , neime-NMB1877

Title : The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing - Tauch_2008_J.Biotechnol_136_11
Author(s) : Tauch A , Trost E , Tilker A , Ludewig U , Schneiker S , Goesmann A , Arnold W , Bekel T , Brinkrolf K , Brune I , Gotker S , Kalinowski J , Kamp PB , Lobo FP , Viehoever P , Weisshaar B , Soriano F , Droge M , Puhler A
Ref : J Biotechnol , 136 :11 , 2008
Abstract : Corynebacterium urealyticum is a lipid-requiring, urealytic bacterium of the human skin flora that has been recognized as causative agent of urinary tract infections. We report the analysis of the complete genome sequence of C. urealyticum DSM7109, which was initially recovered from a patient with alkaline-encrusted cystitis. The genome sequence was determined by a combination of pyrosequencing and Sanger technology. The chromosome of C. urealyticum DSM7109 has a size of 2,369,219bp and contains 2024 predicted coding sequences, of which 78% were considered as orthologous with genes in the Corynebacterium jeikeium K411 genome. Metabolic analysis of the lipid-requiring phenotype revealed the absence of a fatty acid synthase gene and the presence of a beta-oxidation pathway along with a large repertoire of auxillary genes for the degradation of exogenous fatty acids. A urease locus with the gene order ureABCEFGD may play a pivotal role in virulence of C. urealyticum by the alkalinization of human urine and the formation of struvite stones. Multidrug resistance of C. urealyticum DSM7109 is mediated by transposable elements, conferring resistances to macrolides, lincosamides, ketolides, aminoglycosides, chloramphenicol, and tetracycline. The complete genome sequence of C. urealyticum revealed a detailed picture of the lifestyle of this opportunistic human pathogen.
ESTHER : Tauch_2008_J.Biotechnol_136_11
PubMedSearch : Tauch_2008_J.Biotechnol_136_11
PubMedID: 18367281
Gene_locus related to this paper: corjk-q4jta2 , coru7-b1vdx7 , coru7-b1vec6 , coru7-b1vec7 , coru7-b1vgb2 , coru7-b1vhj3 , coru7-b1vhm7 , coru7-b1vhw7 , coru7-b1vi01 , coru7-b1vi11 , coru7-b1vi21 , coru7-b1vig1 , coru7-b1vik9 , coru7-metx , coru7-b1vec9 , coru7-b1vix1

Title : Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids - Tauch_2008_J.Biotechnol_136_22
Author(s) : Tauch A , Schneider J , Szczepanowski R , Tilker A , Viehoever P , Gartemann KH , Arnold W , Blom J , Brinkrolf K , Brune I , Gotker S , Weisshaar B , Goesmann A , Droge M , Puhler A
Ref : J Biotechnol , 136 :22 , 2008
Abstract : Corynebacterium kroppenstedtii is a lipophilic corynebacterial species that lacks in the cell envelope the characteristic alpha-alkyl-beta-hydroxy long-chain fatty acids, designated mycolic acids. We report here the bioinformatic analysis of genome data obtained by pyrosequencing of the type strain C. kroppenstedtii DSM44385 that was initially isolated from human sputum. A single run with the Genome Sequencer FLX system revealed 560,248 shotgun reads with 110,018,974 detected bases that were assembled into a contiguous genomic sequence with a total size of 2,446,804bp. Automatic annotation of the complete genome sequence resulted in the prediction of 2122 coding sequences, of which 29% were considered as specific for C. kroppenstedtii when compared with predicted proteins from hitherto sequenced pathogenic corynebacteria. This comparative content analysis of the genome data revealed a large repertoire of genes involved in sugar uptake and central carbohydrate metabolism and the presence of the mevalonate route for isoprenoid biosynthesis. The lack of mycolic acids and the lipophilic lifestyle of C. kroppenstedtii are apparently caused by gene loss, including a condensase gene cluster, a mycolate reductase gene, and a microbial type I fatty acid synthase gene. A complete beta-oxidation pathway involved in the degradation of fatty acids is present in the genome. Evaluation of the genomic data indicated that lipophilism is the dominant feature involved in pathogenicity of C. kroppenstedtii.
ESTHER : Tauch_2008_J.Biotechnol_136_22
PubMedSearch : Tauch_2008_J.Biotechnol_136_22
PubMedID: 18430482
Gene_locus related to this paper: cork4-c4lgq2 , cork4-c4lgs3 , cork4-c4lgs4 , cork4-c4lgw6 , cork4-c4lh42 , cork4-c4lhh1 , cork4-c4lhj6 , cork4-c4lic3 , cork4-c4ljb8 , cork4-c4llg6 , cork4-c4llg7 , cork4-c4lli9 , cork4-c4llk3 , cork4-c4lgs6 , cork4-c4lhk4

Title : The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis - Vorholter_2008_J.Biotechnol_134_33
Author(s) : Vorholter FJ , Schneiker S , Goesmann A , Krause L , Bekel T , Kaiser O , Linke B , Patschkowski T , Ruckert C , Schmid J , Sidhu VK , Sieber V , Tauch A , Watt SA , Weisshaar B , Becker A , Niehaus K , Puhler A
Ref : J Biotechnol , 134 :33 , 2008
Abstract : The complete genome sequence of the Xanthomonas campestris pv. campestris strain B100 was established. It consisted of a chromosome of 5,079,003bp, with 4471 protein-coding genes and 62 RNA genes. Comparative genomics showed that the genes required for the synthesis of xanthan and xanthan precursors were highly conserved among three sequenced X. campestris pv. campestris genomes, but differed noticeably when compared to the remaining four Xanthomonas genomes available. For the xanthan biosynthesis genes gumB and gumK earlier translational starts were proposed, while gumI and gumL turned out to be unique with no homologues beyond the Xanthomonas genomes sequenced. From the genomic data the biosynthesis pathways for the production of the exopolysaccharide xanthan could be elucidated. The first step of this process is the uptake of sugars serving as carbon and energy sources wherefore genes for 15 carbohydrate import systems could be identified. Metabolic pathways playing a role for xanthan biosynthesis could be deduced from the annotated genome. These reconstructed pathways concerned the storage and metabolization of the imported sugars. The recognized sugar utilization pathways included the Entner-Doudoroff and the pentose phosphate pathway as well as the Embden-Meyerhof pathway (glycolysis). The reconstruction indicated that the nucleotide sugar precursors for xanthan can be converted from intermediates of the pentose phosphate pathway, some of which are also intermediates of glycolysis or the Entner-Doudoroff pathway. Xanthan biosynthesis requires in particular the nucleotide sugars UDP-glucose, UDP-glucuronate, and GDP-mannose, from which xanthan repeat units are built under the control of the gum genes. The updated genome annotation data allowed reconsidering and refining the mechanistic model for xanthan biosynthesis.
ESTHER : Vorholter_2008_J.Biotechnol_134_33
PubMedSearch : Vorholter_2008_J.Biotechnol_134_33
PubMedID: 18304669
Gene_locus related to this paper: xanax-ENTF2 , xanax-GAA , xanax-PTRB , xanax-XAC0515 , xanax-XAC0628 , xanax-XAC0736 , xanax-XAC0753 , xanax-XAC1713 , xanca-acvB , xanca-BIOH , xanca-CATD , xanca-CPO , xanca-estA1 , xanca-impep , xanca-METX , xanca-XCC0080 , xanca-XCC0180 , xanca-XCC0266 , xanca-XCC0843 , xanca-XCC1105 , xanca-XCC1734 , xanca-XCC2285 , xanca-XCC2374 , xanca-XCC2397 , xanca-XCC2405 , xanca-XCC2566 , xanca-XCC2722 , xanca-XCC2817 , xanca-XCC3028 , xanca-XCC3164 , xanca-XCC3219 , xanca-XCC3514 , xanca-XCC3548 , xanca-XCC3555 , xanca-XCC3961 , xanca-XCC3970 , xanca-XCC4016 , xanca-XCC4180 , xanca-XYNB2 , xancb-b0rna3 , xancb-b0rq23

Title : The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae - Gross_2008_BMC.Genomics_9_449
Author(s) : Gross R , Guzman CA , Sebaihia M , dos Santos VA , Pieper DH , Koebnik R , Lechner M , Bartels D , Buhrmester J , Choudhuri JV , Ebensen T , Gaigalat L , Herrmann S , Khachane AN , Larisch C , Link S , Linke B , Meyer F , Mormann S , Nakunst D , Ruckert C , Schneiker-Bekel S , Schulze K , Vorholter FJ , Yevsa T , Engle JT , Goldman WE , Puhler A , Gobel UB , Goesmann A , Blocker H , Kaiser O , Martinez-Arias R
Ref : BMC Genomics , 9 :449 , 2008
Abstract : BACKGROUND: Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described. RESULTS: In this manuscript we present the results of the analysis of the completely annotated genome sequence of the B. petrii strain DSMZ12804. B. petrii has a mosaic genome of 5,287,950 bp harboring numerous mobile genetic elements, including seven large genomic islands. Four of them are highly related to the clc element of Pseudomonas knackmussii B13, which encodes genes involved in the degradation of aromatics. Though being an environmental isolate, the sequenced B. petrii strain also encodes proteins related to virulence factors of the pathogenic Bordetellae, including the filamentous hemagglutinin, which is a major colonization factor of B. pertussis, and the master virulence regulator BvgAS. However, it lacks all known toxins of the pathogenic Bordetellae. CONCLUSION: The genomic analysis suggests that B. petrii represents an evolutionary link between free-living environmental bacteria and the host-restricted obligate pathogenic Bordetellae. Its remarkable metabolic versatility may enable B. petrii to thrive in very different ecological niches.
ESTHER : Gross_2008_BMC.Genomics_9_449
PubMedSearch : Gross_2008_BMC.Genomics_9_449
PubMedID: 18826580
Gene_locus related to this paper: alceu-CBNC , borpd-a9hwh7 , borpd-a9hxw5 , borpd-a9hyr5 , borpd-a9hzm8 , borpd-a9i1l8 , borpd-a9i4f4 , borpd-a9i8i7 , borpd-a9icj9 , borpd-a9iec4 , borpd-a9iep7 , borpd-a9ih03 , borpd-a9iu09 , borpd-metx , bursp-tecF , borpd-a9i1v7

Title : Complete genome sequence of the myxobacterium Sorangium cellulosum - Schneiker_2007_Nat.Biotechnol_25_1281
Author(s) : Schneiker S , Perlova O , Kaiser O , Gerth K , Alici A , Altmeyer MO , Bartels D , Bekel T , Beyer S , Bode E , Bode HB , Bolten CJ , Choudhuri JV , Doss S , Elnakady YA , Frank B , Gaigalat L , Goesmann A , Groeger C , Gross F , Jelsbak L , Kalinowski J , Kegler C , Knauber T , Konietzny S , Kopp M , Krause L , Krug D , Linke B , Mahmud T , Martinez-Arias R , McHardy AC , Merai M , Meyer F , Mormann S , Munoz-Dorado J , Perez J , Pradella S , Rachid S , Raddatz G , Rosenau F , Ruckert C , Sasse F , Scharfe M , Schuster SC , Suen G , Treuner-Lange A , Velicer GJ , Vorholter FJ , Weissman KJ , Welch RD , Wenzel SC , Whitworth DE , Wilhelm S , Wittmann C , Blocker H , Puhler A , Muller R
Ref : Nat Biotechnol , 25 :1281 , 2007
Abstract : The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum So ce56, which produces several natural products and has morphological and physiological properties typical of the genus. The circular genome, comprising 13,033,779 base pairs, is the largest bacterial genome sequenced to date. No global synteny with the genome of Myxococcus xanthus is apparent, revealing an unanticipated level of divergence between these myxobacteria. A large percentage of the genome is devoted to regulation, particularly post-translational phosphorylation, which probably supports the strain's complex, social lifestyle. This regulatory network includes the highest number of eukaryotic protein kinase-like kinases discovered in any organism. Seventeen secondary metabolite loci are encoded in the genome, as well as many enzymes with potential utility in industry.
ESTHER : Schneiker_2007_Nat.Biotechnol_25_1281
PubMedSearch : Schneiker_2007_Nat.Biotechnol_25_1281
PubMedID: 17965706
Gene_locus related to this paper: sorc5-a9en84 , sorc5-a9enf0 , sorc5-a9eu04 , sorc5-a9eur8 , sorc5-a9ev31 , sorc5-a9ewe7 , sorc5-a9f2w6 , sorc5-a9fd82 , sorc5-a9fec8 , sorc5-a9fg26 , sorc5-a9fjh7 , sorc5-a9fpe7 , sorc5-a9fvz2 , sorc5-a9fw17 , sorc5-a9fw70 , sorc5-a9fwe6 , sorc5-a9fya1 , sorc5-a9g9n9 , sorc5-a9g651 , sorc5-a9gj93 , sorc5-a9glc5 , sorc5-a9glv5 , sorc5-a9gqy4 , sorc5-a9grj0 , sorc5-a9grk3 , sorc5-a9grp4 , sorc5-a9grt6 , sorc5-a9guw3 , sorc5-a9gy73 , sorce-q2n3s7 , sorc5-a9fsu5 , sorc5-a9gq11 , sorc5-a9ev65 , sorc5-a9fcj4 , sorc5-a9gut3 , sorc5-a9env4 , sorc5-a9fai0 , sorc5-a9g908 , sorc5-a9gmg6 , sorc5-ce1

Title : Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara - Meisinger-Henschel_2007_J.Gen.Virol_88_3249
Author(s) : Meisinger-Henschel C , Schmidt M , Lukassen S , Linke B , Krause L , Konietzny S , Goesmann A , Howley P , Chaplin P , Suter M , Hausmann J
Ref : Journal of General Virology , 88 :3249 , 2007
Abstract : Chorioallantois vaccinia virus Ankara (CVA) is the parental virus of modified vaccinia virus Ankara (MVA), which was derived from CVA by more than 570 passages in chicken embryo fibroblasts (CEF). MVA became severely host-cell-restricted to avian cells and has strongly diminished virulence in mammalian hosts, while maintaining good immunogenicity. We determined the complete coding sequence of the parental CVA and mapped the exact positions of the six major deletions that emerged in the MVA genome. All six major deletions occurred in regions of the CVA genome where one or more truncated or fragmented open reading frames (ORFs) pre-existed. The CVA genome contains 229 ORFs of which 51 are fragments of full-length orthopoxvirus (OPV) genes, including fragmented orthologues of C9L and M1L (encoding two well-conserved ankyrin-like proteins), A39R (encoding a semaphorin-like protein) and A55R (encoding a kelch-like protein). Phylogenetic analysis demonstrated that MVA was most closely related to CVA, followed by the vaccinia virus (VACV) strain DUKE, a patient-derived isolate of the Dryvax vaccine virus. Loss or mutation of genes outside the six major deletions are assumed to contribute to the restricted host range phenotype of MVA. In support of this notion, deletions, insertions and non-synonymous mutations were found in 122 of the 195 ORFs remaining in MVA when compared with their CVA counterparts. Thus, detailed knowledge of the CVA genomic sequence is a prerequisite to further dissect the genetic basis of the MVA host range phenotype as well as the particular immunological properties of MVA.
ESTHER : Meisinger-Henschel_2007_J.Gen.Virol_88_3249
PubMedSearch : Meisinger-Henschel_2007_J.Gen.Virol_88_3249
PubMedID: 18024893
Gene_locus related to this paper: cowvi-M5L

Title : Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363 - Wegmann_2007_J.Bacteriol_189_3256
Author(s) : Wegmann U , O'Connell-Motherway M , Zomer A , Buist G , Shearman C , Canchaya C , Ventura M , Goesmann A , Gasson MJ , Kuipers OP , van Sinderen D , Kok J
Ref : Journal of Bacteriology , 189 :3256 , 2007
Abstract : Lactococcus lactis is of great importance for the nutrition of hundreds of millions of people worldwide. This paper describes the genome sequence of Lactococcus lactis subsp. cremoris MG1363, the lactococcal strain most intensively studied throughout the world. The 2,529,478-bp genome contains 81 pseudogenes and encodes 2,436 proteins. Of the 530 unique proteins, 47 belong to the COG (clusters of orthologous groups) functional category "carbohydrate metabolism and transport," by far the largest category of novel proteins in comparison with L. lactis subsp. lactis IL1403. Nearly one-fifth of the 71 insertion elements are concentrated in a specific 56-kb region. This integration hot-spot region carries genes that are typically associated with lactococcal plasmids and a repeat sequence specifically found on plasmids and in the "lateral gene transfer hot spot" in the genome of Streptococcus thermophilus. Although the parent of L. lactis MG1363 was used to demonstrate lysogeny in Lactococcus, L. lactis MG1363 carries four remnant/satellite phages and two apparently complete prophages. The availability of the L. lactis MG1363 genome sequence will reinforce its status as the prototype among lactic acid bacteria through facilitation of further applied and fundamental research.
ESTHER : Wegmann_2007_J.Bacteriol_189_3256
PubMedSearch : Wegmann_2007_J.Bacteriol_189_3256
PubMedID: 17307855
Gene_locus related to this paper: lacla-cpo , lacla-pepx , laclk-d2bl62 , lacls-q02y15 , lacls-q030p2

Title : Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes - Hain_2006_J.Bacteriol_188_7405
Author(s) : Hain T , Steinweg C , Kuenne CT , Billion A , Ghai R , Chatterjee SS , Domann E , Karst U , Goesmann A , Bekel T , Bartels D , Kaiser O , Meyer F , Puhler A , Weisshaar B , Wehland J , Liang C , Dandekar T , Lampidis R , Kreft J , Goebel W , Chakraborty T
Ref : Journal of Bacteriology , 188 :7405 , 2006
Abstract : We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the genus Listeria. Listeria welshimeri harbors a circular chromosome of 2,814,130 bp with 2,780 open reading frames. Comparative genomic analysis of chromosomal regions between L. welshimeri, Listeria innocua, and Listeria monocytogenes shows strong overall conservation of synteny, with the exception of the translocation of an F(o)F(1) ATP synthase. The smaller size of the L. welshimeri genome is the result of deletions in all of the genes involved in virulence and of "fitness" genes required for intracellular survival, transcription factors, and LPXTG- and LRR-containing proteins as well as 55 genes involved in carbohydrate transport and metabolism. In total, 482 genes are absent from L. welshimeri relative to L. monocytogenes. Of these, 249 deletions are commonly absent in both L. welshimeri and L. innocua, suggesting similar genome evolutionary paths from an ancestor. We also identified 311 genes specific to L. welshimeri that are absent in the other two species, indicating gene expansion in L. welshimeri, including horizontal gene transfer. The species L. welshimeri appears to have been derived from early evolutionary events and an ancestor more compact than L. monocytogenes that led to the emergence of nonpathogenic Listeria spp.
ESTHER : Hain_2006_J.Bacteriol_188_7405
PubMedSearch : Hain_2006_J.Bacteriol_188_7405
PubMedID: 16936040
Gene_locus related to this paper: lisin-LIN0976 , lisin-LIN2544 , lismo-LMO2089 , lismo-LMO2452 , lismo-LMO2453 , lismo-metx , lisss-d3urb3 , lisw6-a0agy6 , lisw6-a0ajc8 , lisw6-a0am12

Title : Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72 - Krause_2006_Nat.Biotechnol_24_1385
Author(s) : Krause A , Ramakumar A , Bartels D , Battistoni F , Bekel T , Boch J , Bohm M , Friedrich F , Hurek T , Krause L , Linke B , McHardy AC , Sarkar A , Schneiker S , Syed AA , Thauer R , Vorholter FJ , Weidner S , Puhler A , Reinhold-Hurek B , Kaiser O , Goesmann A
Ref : Nat Biotechnol , 24 :1385 , 2006
Abstract : Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium strain EbN1 revealed a surprisingly low degree of synteny. Coding sequences involved in the synthesis of surface components potentially important for plant-microbe interactions were more closely related to those of plant-associated bacteria. Strain BH72 appears to be 'disarmed' compared to plant pathogens, having only a few enzymes that degrade plant cell walls; it lacks type III and IV secretion systems, related toxins and an N-acyl homoserine lactones-based communication system. The genome contains remarkably few mobile elements, indicating a low rate of recent gene transfer that is presumably due to adaptation to a stable, low-stress microenvironment.
ESTHER : Krause_2006_Nat.Biotechnol_24_1385
PubMedSearch : Krause_2006_Nat.Biotechnol_24_1385
PubMedID: 17057704
Gene_locus related to this paper: azosb-a1k1f9 , azosb-a1k1w3 , azosb-a1k2q2 , azosb-a1k4p7 , azosb-a1k5d3 , azosb-a1k5m5 , azosb-a1k5s0 , azosb-a1k6q2 , azosb-a1k6w9 , azosb-a1k6y0 , azosb-a1k7c8 , azosb-a1k9j2 , azosb-a1k9v9 , azosb-a1k696 , azosb-a1k988 , azosb-a1kbn4 , azosb-metx , azosb-a1kal1 , azosb-a1kal0 , azosb-a1k3c3 , azosb-hboh , azosb-a1kb81

Title : Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis - Schneiker_2006_Nat.Biotechnol_24_997
Author(s) : Schneiker S , Martins dos Santos VA , Bartels D , Bekel T , Brecht M , Buhrmester J , Chernikova TN , Denaro R , Ferrer M , Gertler C , Goesmann A , Golyshina OV , Kaminski F , Khachane AN , Lang S , Linke B , McHardy AC , Meyer F , Nechitaylo T , Puhler A , Regenhardt D , Rupp O , Sabirova JS , Selbitschka W , Yakimov MM , Timmis KN , Vorholter FJ , Weidner S , Kaiser O , Golyshin PN
Ref : Nat Biotechnol , 24 :997 , 2006
Abstract : Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. Although barely detectable in unpolluted environments, A. borkumensis becomes the dominant microbe in oil-polluted waters. A. borkumensis SK2 has a streamlined genome with a paucity of mobile genetic elements and energy generation-related genes, but with a plethora of genes accounting for its wide hydrocarbon substrate range and efficient oil-degradation capabilities. The genome further specifies systems for scavenging of nutrients, particularly organic and inorganic nitrogen and oligo-elements, biofilm formation at the oil-water interface, biosurfactant production and niche-specific stress responses. The unique combination of these features provides A. borkumensis SK2 with a competitive edge in oil-polluted environments. This genome sequence provides the basis for the future design of strategies to mitigate the ecological damage caused by oil spills.
ESTHER : Schneiker_2006_Nat.Biotechnol_24_997
PubMedSearch : Schneiker_2006_Nat.Biotechnol_24_997
PubMedID: 16878126
Gene_locus related to this paper: alcbo-Q9F9H0 , alcbs-q0vl04 , alcbs-q0vl36 , alcbs-q0vl92 , alcbs-q0vlp5 , alcbs-q0vlq1 , alcbs-q0vlt9 , alcbs-q0vm92 , alcbs-q0vmd2 , alcbs-q0vmd6 , alcbs-q0vmn9 , alcbs-q0vnu3 , alcbs-q0vp43 , alcbs-q0vpa9 , alcbs-q0vpc7 , alcbs-q0vpg7 , alcbs-q0vpn2 , alcbs-q0vps0 , alcbs-q0vq49 , alcbs-q0vsg4 , alcbs-q0vth9 , marav-a1u5n0 , alcbs-q0vp59 , alcbs-q0vlk5

Title : Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence - Thieme_2005_J.Bacteriol_187_7254
Author(s) : Thieme F , Koebnik R , Bekel T , Berger C , Boch J , Buttner D , Caldana C , Gaigalat L , Goesmann A , Kay S , Kirchner O , Lanz C , Linke B , McHardy AC , Meyer F , Mittenhuber G , Nies DH , Niesbach-Klosgen U , Patschkowski T , Ruckert C , Rupp O , Schneiker S , Schuster SC , Vorholter FJ , Weber E , Puhler A , Bonas U , Bartels D , Kaiser O
Ref : Journal of Bacteriology , 187 :7254 , 2005
Abstract : The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. This pathosystem has become a well-established model for studying bacterial infection strategies. Here, we present the whole-genome sequence of the pepper-pathogenic Xanthomonas campestris pv. vesicatoria strain 85-10, which comprises a 5.17-Mb circular chromosome and four plasmids. The genome has a high G+C content (64.75%) and signatures of extensive genome plasticity. Whole-genome comparisons revealed a gene order similar to both Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris and a structure completely different from Xanthomonas oryzae pv. oryzae. A total of 548 coding sequences (12.2%) are unique to X. campestris pv. vesicatoria. In addition to a type III secretion system, which is essential for pathogenicity, the genome of strain 85-10 encodes all other types of protein secretion systems described so far in gram-negative bacteria. Remarkably, one of the putative type IV secretion systems encoded on the largest plasmid is similar to the Icm/Dot systems of the human pathogens Legionella pneumophila and Coxiella burnetii. Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides.
ESTHER : Thieme_2005_J.Bacteriol_187_7254
PubMedSearch : Thieme_2005_J.Bacteriol_187_7254
PubMedID: 16237009
Gene_locus related to this paper: xanac-q8pmm6 , xanax-ACVB , xanax-BIOH , xanax-CATD , xanax-CPO , xanax-DHAA , xanax-ENTF2 , xanax-GAA , xanax-META , xanax-METX , xanax-PCAD , xanax-PHBC , xanax-PTRB , xanax-Q8PMQ8 , xanax-XAC0198 , xanax-XAC0262 , xanax-XAC0319 , xanax-XAC0372 , xanax-XAC0375 , xanax-XAC0515 , xanax-XAC0574 , xanax-XAC0591 , xanax-XAC0619 , xanax-XAC0628 , xanax-XAC0736 , xanax-XAC0753 , xanax-XAC0805 , xanax-XAC0874 , xanax-XAC1200 , xanax-XAC1213 , xanax-XAC1713 , xanax-XAC2532 , xanax-XAC2541 , xanax-XAC2907 , xanax-XAC2981 , xanax-XAC2990 , xanax-XAC3037 , xanax-XAC3053 , xanax-XAC3152 , xanax-XAC3770 , xanax-XAC3999 , xanax-XAC4046 , xanax-XAC4055 , xanax-XAC4106 , xanax-XAC4221 , xanax-XAC4316 , xanax-XYNB , xanc5-q3bqi2 , xanc5-q3bst4 , xanc5-q3btn4 , xanc5-q3bup9 , xanc5-q3byx0 , xanca-estA1 , xanca-impep , xanca-XCC1105 , xanca-XCC2285 , xanca-XCC2566 , xanca-XCC2722 , xanca-XCC3164 , xanca-XCC3555 , xanor-q5h3e8

Title : Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora - Tauch_2005_J.Bacteriol_187_4671
Author(s) : Tauch A , Kaiser O , Hain T , Goesmann A , Weisshaar B , Albersmeier A , Bekel T , Bischoff N , Brune I , Chakraborty T , Kalinowski J , Meyer F , Rupp O , Schneiker S , Viehoever P , Puhler A
Ref : Journal of Bacteriology , 187 :4671 , 2005
Abstract : Corynebacterium jeikeium is a "lipophilic" and multidrug-resistant bacterial species of the human skin flora that has been recognized with increasing frequency as a serious nosocomial pathogen. Here we report the genome sequence of the clinical isolate C. jeikeium K411, which was initially recovered from the axilla of a bone marrow transplant patient. The genome of C. jeikeium K411 consists of a circular chromosome of 2,462,499 bp and the 14,323-bp bacteriocin-producing plasmid pKW4. The chromosome of C. jeikeium K411 contains 2,104 predicted coding sequences, 52% of which were considered to be orthologous with genes in the Corynebacterium glutamicum, Corynebacterium efficiens, and Corynebacterium diphtheriae genomes. These genes apparently represent the chromosomal backbone that is conserved between the four corynebacteria. Among the genes that lack an ortholog in the known corynebacterial genomes, many are located close to transposable elements or revealed an atypical G+C content, indicating that horizontal gene transfer played an important role in the acquisition of genes involved in iron and manganese homeostasis, in multidrug resistance, in bacterium-host interaction, and in virulence. Metabolic analyses of the genome sequence indicated that the "lipophilic" phenotype of C. jeikeium most likely originates from the absence of fatty acid synthase and thus represents a fatty acid auxotrophy. Accordingly, both the complete gene repertoire and the deduced lifestyle of C. jeikeium K411 largely reflect the strict dependence of growth on the presence of exogenous fatty acids. The predicted virulence factors of C. jeikeium K411 are apparently involved in ensuring the availability of exogenous fatty acids by damaging the host tissue.
ESTHER : Tauch_2005_J.Bacteriol_187_4671
PubMedSearch : Tauch_2005_J.Bacteriol_187_4671
PubMedID: 15968079
Gene_locus related to this paper: corjk-q4jsq8 , corjk-q4jst9 , corjk-q4jt28 , corjk-q4jt69 , corjk-q4jta2 , corjk-q4jth4 , corjk-q4jti5 , corjk-q4ju26 , corjk-q4jug4 , corjk-q4juz4 , corjk-q4jv41 , corjk-q4jvr2 , corjk-q4jwi5 , corjk-q4jwq5 , corjk-q4jwu9 , corjk-q4jx57 , corjk-q4jx58 , corjk-q4jxf4 , corjk-q4jxg1 , corjk-q4jxi0 , corjk-q4jxk5 , corjk-q4jxw6 , corjk-q4jxx7 , corjk-q4jy17 , corjk-q4jy19 , corjk-q4jy21 , corjk-q4jy22 , corjk-q4jyd0 , corjk-q4jyf2

Title : A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective - Rendulic_2004_Science_303_689
Author(s) : Rendulic S , Jagtap P , Rosinus A , Eppinger M , Baar C , Lanz C , Keller H , Lambert C , Evans KJ , Goesmann A , Meyer F , Sockett RE , Schuster SC
Ref : Science , 303 :689 , 2004
Abstract : Predatory bacteria remain molecularly enigmatic, despite their presence in many microbial communities. Here we report the complete genome of Bdellovibrio bacteriovorus HD100, a predatory Gram-negative bacterium that invades and consumes other Gram-negative bacteria. Its surprisingly large genome shows no evidence of recent gene transfer from its prey. A plethora of paralogous gene families coding for enzymes, such as hydrolases and transporters, are used throughout the life cycle of B. bacteriovorus for prey entry, prey killing, and the uptake of complex molecules.
ESTHER : Rendulic_2004_Science_303_689
PubMedSearch : Rendulic_2004_Science_303_689
PubMedID: 14752164
Gene_locus related to this paper: bdeba-Bd2632 , bdeba-q6mgv6 , bdeba-q6mhk8 , bdeba-q6mhq7 , bdeba-q6mhr0 , bdeba-q6mhs4 , bdeba-q6mhs7 , bdeba-q6mi80 , bdeba-q6mif3 , bdeba-q6mii2 , bdeba-q6mik4 , bdeba-q6mim6 , bdeba-q6miz5 , bdeba-q6mk90 , bdeba-q6mlg1 , bdeba-q6mlj2 , bdeba-q6mmk6 , bdeba-q6mnq0 , bdeba-q6mnv9 , bdeba-q6mp35 , bdeba-q6mp81 , bdeba-q6mpe5 , bdeba-q6mpf6 , bdeba-q6mpi1 , bdeba-q6mpv3 , bdeba-q6mq23 , bdeba-q6mq81 , bdeba-q6mr18 , bdeba-q6mr19 , bdeba-q6mrp5 , bdeba-q6mh49

Title : The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP) - Westberg_2004_Genome.Res_14_221
Author(s) : Westberg J , Persson A , Holmberg A , Goesmann A , Lundeberg J , Johansson KE , Pettersson B , Uhlen M
Ref : Genome Res , 14 :221 , 2004
Abstract : Mycoplasma mycoides subsp. mycoidesSC (MmymySC)is the etiological agent of contagious bovine pleuropneumonia (CBPP), a highly contagious respiratory disease in cattle. The genome of Mmymy SC type strain PG1(T) has been sequenced to map all the genes and to facilitate further studies regarding the cell function of the organism and CBPP. The genome is characterized by a single circular chromosome of 1211703 bp with the lowest G+C content (24 mole%)and the highest density of insertion sequences (13% of the genome size)of all sequenced bacterial genomes. The genome contains 985 putative genes, of which 72 are part of insertion sequences and encode transposases. Anomalies in the GC-skew pattern and the presence of large repetitive sequences indicate a high genomic plasticity. A variety of potential virulence factors was identified, including genes encoding putative variable surface proteins and enzymes and transport proteins responsible for the production of hydrogen peroxide and the capsule, which is believed to have toxic effects on the animal.
ESTHER : Westberg_2004_Genome.Res_14_221
PubMedSearch : Westberg_2004_Genome.Res_14_221
PubMedID: 14762060
Gene_locus related to this paper: mycms-q6msd9 , mycms-q6mt27 , mycms-q6mt79 , mycms-q6mt80 , mycms-q6mtn3

Title : The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins - Kalinowski_2003_J.Biotechnol_104_5
Author(s) : Kalinowski J , Bathe B , Bartels D , Bischoff N , Bott M , Burkovski A , Dusch N , Eggeling L , Eikmanns BJ , Gaigalat L , Goesmann A , Hartmann M , Huthmacher K , Kramer R , Linke B , McHardy AC , Meyer F , Mockel B , Pfefferle W , Puhler A , Rey DA , Ruckert C , Rupp O , Sahm H , Wendisch VF , Wiegrabe I , Tauch A
Ref : J Biotechnol , 104 :5 , 2003
Abstract : The complete genomic sequence of Corynebacterium glutamicum ATCC 13032, well-known in industry for the production of amino acids, e.g. of L-glutamate and L-lysine was determined. The C. glutamicum genome was found to consist of a single circular chromosome comprising 3282708 base pairs. Several DNA regions of unusual composition were identified that were potentially acquired by horizontal gene transfer, e.g. a segment of DNA from C. diphtheriae and a prophage-containing region. After automated and manual annotation, 3002 protein-coding genes have been identified, and to 2489 of these, functions were assigned by homologies to known proteins. These analyses confirm the taxonomic position of C. glutamicum as related to Mycobacteria and show a broad metabolic diversity as expected for a bacterium living in the soil. As an example for biotechnological application the complete genome sequence was used to reconstruct the metabolic flow of carbon into a number of industrially important products derived from the amino acid L-aspartate.
ESTHER : Kalinowski_2003_J.Biotechnol_104_5
PubMedSearch : Kalinowski_2003_J.Biotechnol_104_5
PubMedID: 12948626
Gene_locus related to this paper: corgl-CGL0007 , corgl-CGL0081 , corgl-CGL0091 , corgl-CGL0118 , corgl-CGL0151 , corgl-CGL0340 , corgl-CGL0343 , corgl-CGL0587 , corgl-CGL0591 , corgl-CGL0839 , corgl-CGL0922 , corgl-CGL1031 , corgl-Cgl1133 , corgl-CGL1144 , corgl-CGL1178 , corgl-CGL1439 , corgl-CGL1481 , corgl-CGL2002 , corgl-CGL2067 , corgl-CGL2181 , corgl-Cgl2249 , corgl-CGL2254 , corgl-CGL2393 , corgl-CGL2474 , corgl-CGL2568 , corgl-CGL2596 , corgl-CGL2618 , corgl-CGL2871 , corgl-CGL2878 , corgl-CMT3 , corgl-csp1 , corgl-q8nlm9 , corgl-q8nlr5 , corgl-q8nlz1 , corgl-y967 , corgt-g6wsn6