Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids
Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehöver P, Gartemann K-H, Arnold W, Blom J, Brinkrolf K, Brune I, Goetker S, et al. (2008)
Journal of Biotechnology 136(1-2): 22-30.
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Autor*in
Einrichtung
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Arbeitsgruppe B. Weisshaar
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Tauch
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Fakultät für Biologie > Genetik und Genomik der Pflanzen
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Arbeitsgruppe B. Weisshaar
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Tauch
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Fakultät für Biologie > Genetik und Genomik der Pflanzen
Abstract / Bemerkung
Corynebacterium kroppenstedtii is a lipophilic corynebacterial species that lacks in the cell envelope the characteristic alpha-alkyl-beta-hyclroxy 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 2,446,804 bp. 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. (C) 2008 Elsevier B.V. All rights reserved.
Stichworte
isoprenoid biosynthesis;
beta-oxidation;
mycolic acid biosynthesis;
lipophilism;
mevalonate pathway;
Corynebacterium kroppenstentii;
biotin biosynthesis;
pyrosequencing
Erscheinungsjahr
2008
Zeitschriftentitel
Journal of Biotechnology
Band
136
Ausgabe
1-2
Seite(n)
22-30
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/1585939
Zitieren
Tauch A, Schneider J, Szczepanowski R, et al. Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Journal of Biotechnology. 2008;136(1-2):22-30.
Tauch, A., Schneider, J., Szczepanowski, R., Tilker, A., Viehöver, P., Gartemann, K. - H., Arnold, W., et al. (2008). Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Journal of Biotechnology, 136(1-2), 22-30. https://doi.org/10.1016/j.jbiotec.2008.03.004
Tauch, Andreas, Schneider, Jessica, Szczepanowski, Rafael, Tilker, Alexandra, Viehöver, Prisca, Gartemann, Karl-Heinz, Arnold, Walter, et al. 2008. “Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids”. Journal of Biotechnology 136 (1-2): 22-30.
Tauch, A., Schneider, J., Szczepanowski, R., Tilker, A., Viehöver, P., Gartemann, K. - H., Arnold, W., Blom, J., Brinkrolf, K., Brune, I., et al. (2008). Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Journal of Biotechnology 136, 22-30.
Tauch, A., et al., 2008. Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Journal of Biotechnology, 136(1-2), p 22-30.
A. Tauch, et al., “Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids”, Journal of Biotechnology, vol. 136, 2008, pp. 22-30.
Tauch, A., Schneider, J., Szczepanowski, R., Tilker, A., Viehöver, P., Gartemann, K.-H., Arnold, W., Blom, J., Brinkrolf, K., Brune, I., Goetker, S., Weisshaar, B., Goesmann, A., Droege, M., Pühler, A.: Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Journal of Biotechnology. 136, 22-30 (2008).
Tauch, Andreas, Schneider, Jessica, Szczepanowski, Rafael, Tilker, Alexandra, Viehöver, Prisca, Gartemann, Karl-Heinz, Arnold, Walter, Blom, Jochen, Brinkrolf, Karina, Brune, Iris, Goetker, Susanne, Weisshaar, Bernd, Goesmann, Alexander, Droege, Marcus, and Pühler, Alfred. “Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids”. Journal of Biotechnology 136.1-2 (2008): 22-30.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
EMBL
1 Eintrag gefunden, die diesen Artikel zitieren
Corynebacterium kroppenstedtii DSM 44385, complete genome. (EMBL: CP001620)
Sequence length: 2446804
Download in FASTA format
Sequence length: 2446804
Download in FASTA format
UNIPROT
2018 Einträge gefunden, die diesen Artikel zitieren von denen 10 angezeigt werden
Protein translocase subunit SecA (UNIPROT: C4LK74)
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Ribosomal RNA small subunit methyltransferase G (UNIPROT: C4LGJ3)
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Peptide chain release factor 1 (UNIPROT: C4LJM5)
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Putative helicase (UNIPROT: C4LJ23)
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Pyrazinamidase / nicotinamidase (UNIPROT: C4LHN6)
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Putative dipeptidase (UNIPROT: C4LIK4)
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Mannopyranosyltransferase (UNIPROT: C4LIQ2)
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Putative secreted protein (UNIPROT: C4LKH0)
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Putative substrate-binding protein (UNIPROT: C4LHH5)
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Methionine aminopeptidase (UNIPROT: C4LJ99)
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
Organism: Corynebacterium kroppenstedtii (strain DSM 44385 / CCUG 35717)
Download in FASTA format
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Corynebacterium amycolatum sp. nov. a new mycolic acid-less Corynebacterium species from human skin
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Corynebacterium kroppenstedtii sp. nov., a novel corynebacterium that does not contain mycolic acids.
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Cordwell SJ., Arch. Microbiol. 172(5), 1999
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The cell envelope of corynebacteria
Daffé, 2005
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Evidence for symmetric chromosomal inversions around the replication origin in bacteria.
Eisen JA, Heidelberg JF, White O, Salzberg SL., Genome Biol. 1(6), 2000
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Eisen JA, Heidelberg JF, White O, Salzberg SL., Genome Biol. 1(6), 2000
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Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A., Nucleic Acids Res. 36(Database issue), 2007
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Funahashi A, Jouraku A, Matsuoka Y, Kitano H., In Silico Biol. (Gedrukt) 7(2 Suppl), 2007
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Funahashi A, Jouraku A, Matsuoka Y, Kitano H., In Silico Biol. (Gedrukt) 7(2 Suppl), 2007
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Acyl-CoA carboxylases (accD2 and accD3), together with a unique polyketide synthase (Cg-pks), are key to mycolic acid biosynthesis in Corynebacterianeae such as Corynebacterium glutamicum and Mycobacterium tuberculosis.
Gande R, Gibson KJ, Brown AK, Krumbach K, Dover LG, Sahm H, Shioyama S, Oikawa T, Besra GS, Eggeling L., J. Biol. Chem. 279(43), 2004
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The structures of transcription factor CGL2947 from Corynebacterium glutamicum in two crystal forms: a novel homodimer assembling and the implication for effector-binding mode.
Gao YG, Yao M, Itou H, Zhou Y, Tanaka I., Protein Sci. 16(9), 2007
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Corynebacterium atypicum sp. nov., from a human clinical source, does not contain corynomycolic acids.
Hall V, Collins MD, Hutson RA, Lawson PA, Falsen E, Duerden BI., Int. J. Syst. Evol. Microbiol. 53(Pt 4), 2003
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Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module.
Hebbeln P, Rodionov DA, Alfandega A, Eitinger T., Proc. Natl. Acad. Sci. U.S.A. 104(8), 2007
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Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites.
Hendrickson H, Lawrence JG., Mol. Microbiol. 64(1), 2007
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The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
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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., J. Biotechnol. 104(1-3), 2003
PMID: 12948626
[A young woman with granulomatous mastitis: a corynebacteria may be involved in the pathogenesis of these disease].
Kieffer P, Dukic R, Hueber M, Kieffer C, Bouhala M, Riegel P, Wilhelm JM., Rev Med Interne 27(7), 2006
PMID: 16750284
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Mevalonate and nonmevalonate pathways for the biosynthesis of isoprene units.
Kuzuyama T., Biosci. Biotechnol. Biochem. 66(8), 2002
PMID: 12353619
Kuzuyama T., Biosci. Biotechnol. Biochem. 66(8), 2002
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The reductase that catalyzes mycolic motif synthesis is required for efficient attachment of mycolic acids to arabinogalactan.
Lea-Smith DJ, Pyke JS, Tull D, McConville MJ, Coppel RL, Crellin PK., J. Biol. Chem. 282(15), 2007
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Analysis of cellular components, biochemical reactions, and habitat of human cutaneous lipophilic diphtheroids.
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GenDB--an open source genome annotation system for prokaryote genomes.
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The genome stability in Corynebacterium species due to lack of the recombinational repair system.
Nakamura Y, Nishio Y, Ikeo K, Gojobori T., Gene 317(1-2), 2003
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Nakamura Y, Nishio Y, Ikeo K, Gojobori T., Gene 317(1-2), 2003
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Transport and metabolism of glycerophosphodiesters produced through phospholipid deacylation.
Patton-Vogt J., Biochim. Biophys. Acta 1771(3), 2006
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Patton-Vogt J., Biochim. Biophys. Acta 1771(3), 2006
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Paviour S, Musaad S, Roberts S, Taylor G, Taylor S, Shore K, Lang S, Holland D., Clin. Infect. Dis. 35(11), 2002
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Paviour S, Musaad S, Roberts S, Taylor G, Taylor S, Shore K, Lang S, Holland D., Clin. Infect. Dis. 35(11), 2002
PMID: 12439810
A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms.
Portevin D, De Sousa-D'Auria C, Houssin C, Grimaldi C, Chami M, Daffe M, Guilhot C., Proc. Natl. Acad. Sci. U.S.A. 101(1), 2003
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Isolations of Corynebacterium kroppenstedtii from a breast abscess.
Riegel P, Liegeois P, Chenard MP, Mathelin C, Monteil H., Int. J. Med. Microbiol. 294(6), 2004
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Riegel P, Liegeois P, Chenard MP, Mathelin C, Monteil H., Int. J. Med. Microbiol. 294(6), 2004
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Microbial type I fatty acid synthases (FAS): major players in a network of cellular FAS systems.
Schweizer E, Hofmann J., Microbiol. Mol. Biol. Rev. 68(3), 2004
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Schweizer E, Hofmann J., Microbiol. Mol. Biol. Rev. 68(3), 2004
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The effect of antibiotic treatment of inflammatory breast disease associated with the isolation of lipophilic corynebacteria
Skinner, ANZ J. Surg. 77(), 2007
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Biotin in microbes, the genes involved in its biosynthesis, its biochemical role and perspectives for biotechnological production.
Streit WR, Entcheva P., Appl. Microbiol. Biotechnol. 61(1), 2002
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Streit WR, Entcheva P., Appl. Microbiol. Biotechnol. 61(1), 2002
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The COG database: a tool for genome-scale analysis of protein functions and evolution.
Tatusov RL, Galperin MY, Natale DA, Koonin EV., Nucleic Acids Res. 28(1), 2000
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Tatusov RL, Galperin MY, Natale DA, Koonin EV., Nucleic Acids Res. 28(1), 2000
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Comparative genomics identified two conserved DNA modules in a corynebacterial plasmid family present in clinical isolates of the opportunistic human pathogen Corynebacterium jeikeium.
Tauch A, Bischoff N, Puhler A, Kalinowski J., Plasmid 52(2), 2004
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Tauch A, Bischoff N, Puhler A, Kalinowski J., Plasmid 52(2), 2004
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Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
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., J. Bacteriol. 187(13), 2005
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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., J. Bacteriol. 187(13), 2005
PMID: 15968079
Ultrafast de novo sequencing of Corynebacterium urealyticum using the Genome Sequencer 20 System
Tauch, Biochemica 4(), 2006
Tauch, Biochemica 4(), 2006
The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing.
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., J. Biotechnol. 136(1-2), 2008
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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., J. Biotechnol. 136(1-2), 2008
PMID: 18367281
A clinicopathological review of 34 cases of inflammatory breast disease showing an association between corynebacteria infection and granulomatous mastitis.
Taylor GB, Paviour SD, Musaad S, Jones WO, Holland DJ., Pathology 35(2), 2003
PMID: 12745457
Taylor GB, Paviour SD, Musaad S, Jones WO, Holland DJ., Pathology 35(2), 2003
PMID: 12745457
To sialylate, or not to sialylate: that is the question.
Vimr E, Lichtensteiger C., Trends Microbiol. 10(6), 2002
PMID: 12088651
Vimr E, Lichtensteiger C., Trends Microbiol. 10(6), 2002
PMID: 12088651
Nitrogen metabolism and nitrogen control in corynebacteria: variations of a common theme.
Walter B, Hanssler E, Kalinowski J, Burkovski A., J. Mol. Microbiol. Biotechnol. 12(1-2), 2007
PMID: 17183220
Walter B, Hanssler E, Kalinowski J, Burkovski A., J. Mol. Microbiol. Biotechnol. 12(1-2), 2007
PMID: 17183220
Facile recovery of individual high-molecular-weight, low-copy-number natural plasmids for genomic sequencing.
Williams LE, Detter C, Barry K, Lapidus A, Summers AO., Appl. Environ. Microbiol. 72(7), 2006
PMID: 16820486
Williams LE, Detter C, Barry K, Lapidus A, Summers AO., Appl. Environ. Microbiol. 72(7), 2006
PMID: 16820486
Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R.
Yukawa H, Omumasaba CA, Nonaka H, Kos P, Okai N, Suzuki N, Suda M, Tsuge Y, Watanabe J, Ikeda Y, Vertes AA, Inui M., Microbiology (Reading, Engl.) 153(Pt 4), 2007
PMID: 17379713
Yukawa H, Omumasaba CA, Nonaka H, Kos P, Okai N, Suzuki N, Suda M, Tsuge Y, Watanabe J, Ikeda Y, Vertes AA, Inui M., Microbiology (Reading, Engl.) 153(Pt 4), 2007
PMID: 17379713
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