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.

Journal Article | Published | English

No fulltext has been uploaded

Abstract
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.
Publishing Year
ISSN
PUB-ID

Cite this

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.
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.
This data publication is cited in the following publications:
This publication cites the following data publications:

23 Citations in Europe PMC

Data provided by Europe PubMed Central.

Antimicrobial Treatment Options for Granulomatous Mastitis Caused by Corynebacterium Species.
Dobinson HC, Anderson TP, Chambers ST, Doogue MP, Seaward L, Werno AM., J. Clin. Microbiol. 53(9), 2015
PMID: 26135858
Draft Genome Sequences of Corynebacterium kroppenstedtii CNM633/14 and CNM632/14, Multidrug-Resistant and Antibiotic-Sensitive Isolates from Nodules of Granulomatous Mastitis Patients.
Fernandez-Natal MI, Soriano F, Ariza-Miguel J, Marrodan-Ciordia T, Acedo A, Hernandez M, Tauch A, Rodriguez-Lazaro D., Genome Announc 3(3), 2015
PMID: 25999560
Complete Genome Sequence of Corynebacterium ureicelerivorans DSM 45051, a Lipophilic and Urea-Splitting Isolate from the Blood Culture of a Septicemia Patient.
Tippelt A, Albersmeier A, Brinkrolf K, Ruckert C, Fernandez-Natal I, Soriano F, Tauch A., Genome Announc 2(6), 2014
PMID: 25414509
Mycolic Acid Biosynthesis Genes in the Genome Sequence of Corynebacterium atypicum DSM 44849.
Tippelt A, Mollmann S, Albersmeier A, Jaenicke S, Ruckert C, Tauch A., Genome Announc 2(4), 2014
PMID: 25146145
Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: biodeterioration risk and contamination of the indoor air.
Pinar G, Piombino-Mascali D, Maixner F, Zink A, Sterflinger K., FEMS Microbiol. Ecol. 86(2), 2013
PMID: 23772650
The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains.
Soares SC, Silva A, Trost E, Blom J, Ramos R, Carneiro A, Ali A, Santos AR, Pinto AC, Diniz C, Barbosa EG, Dorella FA, Aburjaile F, Rocha FS, Nascimento KK, Guimaraes LC, Almeida S, Hassan SS, Bakhtiar SM, Pereira UP, Abreu VA, Schneider MP, Miyoshi A, Tauch A, Azevedo V., PLoS ONE 8(1), 2013
PMID: 23342011
Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient.
Schroder J, Maus I, Meyer K, Wordemann S, Blom J, Jaenicke S, Schneider J, Trost E, Tauch A., BMC Genomics 13(), 2012
PMID: 22524407
Attenuation of virulence in an apicomplexan hemoparasite results in reduced genome diversity at the population level.
Lau AO, Kalyanaraman A, Echaide I, Palmer GH, Bock R, Pedroni MJ, Rameshkumar M, Ferreira MB, Fletcher TI, McElwain TF., BMC Genomics 12(), 2011
PMID: 21838895
Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island.
van Schaik W, Top J, Riley DR, Boekhorst J, Vrijenhoek JE, Schapendonk CM, Hendrickx AP, Nijman IJ, Bonten MJ, Tettelin H, Willems RJ., BMC Genomics 11(), 2010
PMID: 20398277
Common patterns - unique features: nitrogen metabolism and regulation in Gram-positive bacteria.
Amon J, Titgemeyer F, Burkovski A., FEMS Microbiol. Rev. 34(4), 2010
PMID: 20337720
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 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., BMC Genomics 11(), 2010
PMID: 20137072
Genome update: the 1000th genome--a cautionary tale.
Lagesen K, Ussery DW, Wassenaar TM., Microbiology (Reading, Engl.) 156(Pt 3), 2010
PMID: 20093288
The Zur regulon of Corynebacterium glutamicum ATCC 13032.
Schroder J, Jochmann N, Rodionov DA, Tauch A., BMC Genomics 11(), 2010
PMID: 20055984
Phylogenetic comparative assembly.
Husemann P, Stoye J., Algorithms Mol Biol 5(), 2010
PMID: 20047659
Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays.
Jochmann N, Kurze AK, Czaja LF, Brinkrolf K, Brune I, Huser AT, Hansmeier N, Puhler A, Borovok I, Tauch A., Microbiology (Reading, Engl.) 155(Pt 5), 2009
PMID: 19372162

48 References

Data provided by Europe PubMed Central.

Mevalonate and nonmevalonate pathways for the biosynthesis of isoprene units.
Kuzuyama T., Biosci. Biotechnol. Biochem. 66(8), 2002
PMID: 12353619
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
PMID: 17308303
Analysis of cellular components, biochemical reactions, and habitat of human cutaneous lipophilic diphtheroids.
McGinley KJ, Labows JN, Zechman JM, Nordstrom KM, Webster GF, Leyden JJ., J. Invest. Dermatol. 85(4), 1985
PMID: 3930617
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
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
PMID: 14604803
Corynebacterium species isolated from patients with mastitis.
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), 2004
PMID: 14695899
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
PMID: 15595392
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
PMID: 15353567
The effect of antibiotic treatment of inflammatory breast disease associated with the isolation of lipophilic corynebacteria
Skinner, ANZ J. Surg. 77(), 2007
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
PMID: 10592175
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
PMID: 15968079
Ultrafast de novo sequencing of Corynebacterium urealyticum using the Genome Sequencer 20 System
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
PMID: 18367281
To sialylate, or not to sialylate: that is the question.
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
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
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

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 18430482
PubMed | Europe PMC

Search this title in

Google Scholar