The genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin

Jankowitsch F, Schwarz J, Rückert C, Gust B, Szczepanowski R, Blom J, Pelzer S, Kalinowski J, Mack M (2012)
Journal of bacteriology 194(24): 6818-6827.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Jankowitsch, Frank; Schwarz, Julia; Rückert, ChristianUniBi ; Gust, Bertolt; Szczepanowski, RafaelUniBi; Blom, JochenUniBi; Pelzer, Stefan; Kalinowski, JörnUniBi; Mack, Matthias
Abstract / Bemerkung
Streptoymces davawensis JCM 4913 synthesizes the antibiotic roseoflavin, a structural riboflavin (vitamin B(2)) analog. Here we report the 9,466,619 base pair linear chromosome of S. davawensis JCM 4913 and a 89,331 base pair linear plasmid. The sequence has an average G + C content of 70.58% and contains six rRNA operons (16S-23S-5S) and 69 tRNA genes. The 8,616 predicted protein-coding sequences include 32 clusters coding for secondary metabolites several of which are unique to S. davawensis. The chromosome contains long terminal inverted repeats of 33,255 bp each and atypical telomeres. Sequence analysis with regard to riboflavin biosynthesis revealed three different patterns of gene organization in Streptomyces species. Heterologous expression of a set of genes present on a subgenomic fragment of S. davawensis resulted in the production of roseoflavin by the host Streptomyces coelicolor M1152. Phylogenetic analysis revealed that S. davawensis is a close relative to Streptomyces cinnabarinus and, much to our surprise, we found that the latter bacterium is a roseoflavin producer as well.
Journal of bacteriology
Page URI


Jankowitsch F, Schwarz J, Rückert C, et al. The genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. Journal of bacteriology. 2012;194(24):6818-6827.
Jankowitsch, F., Schwarz, J., Rückert, C., Gust, B., Szczepanowski, R., Blom, J., Pelzer, S., et al. (2012). The genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. Journal of bacteriology, 194(24), 6818-6827. doi:10.1128/JB.01592-12
Jankowitsch, F., Schwarz, J., Rückert, C., Gust, B., Szczepanowski, R., Blom, J., Pelzer, S., Kalinowski, J., and Mack, M. (2012). The genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. Journal of bacteriology 194, 6818-6827.
Jankowitsch, F., et al., 2012. The genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. Journal of bacteriology, 194(24), p 6818-6827.
F. Jankowitsch, et al., “The genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin”, Journal of bacteriology, vol. 194, 2012, pp. 6818-6827.
Jankowitsch, F., Schwarz, J., Rückert, C., Gust, B., Szczepanowski, R., Blom, J., Pelzer, S., Kalinowski, J., Mack, M.: The genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. Journal of bacteriology. 194, 6818-6827 (2012).
Jankowitsch, Frank, Schwarz, Julia, Rückert, Christian, Gust, Bertolt, Szczepanowski, Rafael, Blom, Jochen, Pelzer, Stefan, Kalinowski, Jörn, and Mack, Matthias. “The genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin”. Journal of bacteriology 194.24 (2012): 6818-6827.

19 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov.
Landwehr W, Kämpfer P, Glaeser SP, Rückert C, Kalinowski J, Blom J, Goesmann A, Mack M, Schumann P, Atasayar E, Hahnke RL, Rohde M, Martin K, Stadler M, Wink J., Int J Syst Evol Microbiol 68(1), 2018
PMID: 29227220
Large inserts for big data: artificial chromosomes in the genomic era.
Tocchetti A, Donadio S, Sosio M., FEMS Microbiol Lett 365(9), 2018
PMID: 29718215
Characterization of the small flavin-binding dodecin in the roseoflavin producer Streptomyces davawensis.
Ludwig P, Sévin DC, Busche T, Kalinowski J, Bourdeaux F, Grininger M, Mack M., Microbiology 164(6), 2018
PMID: 29856311
Overlapping riboflavin supply pathways in bacteria.
García-Angulo VA., Crit Rev Microbiol 43(2), 2017
PMID: 27822970
The Crystal Structure of RosB: Insights into the Reaction Mechanism of the First Member of a Family of Flavodoxin-like Enzymes.
Konjik V, Brünle S, Demmer U, Vanselow A, Sandhoff R, Ermler U, Mack M., Angew Chem Int Ed Engl 56(4), 2017
PMID: 27981706
Identification of the Key Enzyme of Roseoflavin Biosynthesis.
Schwarz J, Konjik V, Jankowitsch F, Sandhoff R, Mack M., Angew Chem Int Ed Engl 55(20), 2016
PMID: 27062037
Uptake and Metabolism of Antibiotics Roseoflavin and 8-Demethyl-8-Aminoriboflavin in Riboflavin-Auxotrophic Listeria monocytogenes.
Matern A, Pedrolli D, Großhennig S, Johansson J, Mack M., J Bacteriol 198(23), 2016
PMID: 27672192
A Streptomyces coelicolor host for the heterologous expression of Type III polyketide synthase genes.
Thanapipatsiri A, Claesen J, Gomez-Escribano JP, Bibb M, Thamchaipenet A., Microb Cell Fact 14(), 2015
PMID: 26376792
African relapsing Fever borreliae genomospecies revealed by comparative genomics.
Elbir H, Abi-Rached L, Pontarotti P, Yoosuf N, Drancourt M., Front Public Health 2(), 2014
PMID: 25229054
Microbial exo-xylanases: a mini review.
Juturu V, Wu JC., Appl Biochem Biotechnol 174(1), 2014
PMID: 25080375
Recently published Streptomyces genome sequences.
Harrison J, Studholme DJ., Microb Biotechnol 7(5), 2014
PMID: 25100265
Complete genome sequence of the actinobacterium Amycolatopsis japonica MG417-CF17(T) (=DSM 44213T) producing (S,S)-N,N'-ethylenediaminedisuccinic acid.
Stegmann E, Albersmeier A, Spohn M, Gert H, Weber T, Wohlleben W, Kalinowski J, Rückert C., J Biotechnol 189(), 2014
PMID: 25193710
Flavoproteins are potential targets for the antibiotic roseoflavin in Escherichia coli.
Langer S, Hashimoto M, Hobl B, Mathes T, Mack M., J Bacteriol 195(18), 2013
PMID: 23836860

62 References

Daten bereitgestellt von Europe PubMed Central.

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
CRITICA: coding region identification tool invoking comparative analysis.
Badger JH, Olsen GJ, Woese CR., Mol. Biol. Evol. 16(4), 1999
PMID: 10331277
The ENZYME database in 2000.
Bairoch A., Nucleic Acids Res. 28(1), 2000
PMID: 10592255
The Universal Protein Resource (UniProt).
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS., Nucleic Acids Res. 33(Database issue), 2005
PMID: 15608167
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).
Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA., Nature 417(6885), 2002
PMID: 12000953
EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
Blom J, Albaum SP, Doppmeier D, Puhler A, Vorholter FJ, Zakrzewski M, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19457249
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.
Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA., Bioinformatics 28(4), 2011
PMID: 22199388
Enzyme-specific profiles for genome annotation: PRIAM.
Claudel-Renard C, Chevalet C, Faraut T, Kahn D., Nucleic Acids Res. 31(22), 2003
PMID: 14602924
High-performance searching of biosequence databases.
Coulson A., Trends Biotechnol. 12(3), 1994
PMID: 7764827
Improved microbial gene identification with GLIMMER.
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL., Nucleic Acids Res. 27(23), 1999
PMID: 10556321
Biosynthesis of 4'-O-methylpyridoxine (Ginkgotoxin) from primary precursors.
Fiehe K, Arenz A, Drewke C, Hemscheidt T, Williamson RT, Leistner E., J. Nat. Prod. 63(2), 2000
PMID: 10691705
Biosynthesis of flavocoenzymes.
Fischer M, Bacher A., Nat Prod Rep 22(3), 2005
PMID: 16010344
Rfam: updates to the RNA families database.
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18953034
A new bioinformatics analysis tools framework at EMBL-EBI.
Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R., Nucleic Acids Res. 38(Web Server issue), 2010
PMID: 20439314
Identification and characterization of two Streptomyces davawensis riboflavin biosynthesis gene clusters.
Grill S, Yamaguchi H, Wagner H, Zwahlen L, Kusch U, Mack M., Arch. Microbiol. 188(4), 2007
PMID: 17541777
Prodigal: prokaryotic gene recognition and translation initiation site identification.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ., BMC Bioinformatics 11(), 2010
PMID: 20211023
Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis.
Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S., Nat. Biotechnol. 21(5), 2003
PMID: 12692562
Structural elements of the Streptomyces oriC region and their interactions with the DnaA protein.
Jakimowicz D, Majka J, Messer W, Speck C, Fernandez M, Martin MC, Sanchez J, Schauwecker F, Keller U, Schrempf H, Zakrzewska-Czerwinska J., Microbiology (Reading, Engl.) 144 ( Pt 5)(), 1998
PMID: 9611803
A novel N,N-8-amino-8-demethyl-D-riboflavin Dimethyltransferase (RosA) catalyzing the two terminal steps of roseoflavin biosynthesis in Streptomyces davawensis.
Jankowitsch F, Kuhm C, Kellner R, Kalinowski J, Pelzer S, Macheroux P, Mack M., J. Biol. Chem. 286(44), 2011
PMID: 21911488
Formation of roseoflavin from 8-amino- and 8-methylamino-8-demethyl-D-riboflavin.
Juri N, Kubo Y, Kasai S, Otani S, Kusunose M, Matsui K., J. Biochem. 101(3), 1987
PMID: 3597348
KEGG: kyoto encyclopedia of genes and genomes.
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173
From genomics to chemical genomics: new developments in KEGG.
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381885
Practical streptomyces genetics
Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA., 2000
GISMO--gene identification using a support vector machine for ORF classification.
Krause L, McHardy AC, Nattkemper TW, Puhler A, Stoye J, Meyer F., Nucleic Acids Res. 35(2), 2006
PMID: 17175534
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
Krogh A, Larsson B, von Heijne G, Sonnhammer EL., J. Mol. Biol. 305(3), 2001
PMID: 11152613
RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW., Nucleic Acids Res. 35(9), 2007
PMID: 17452365
Clustal W and Clustal X version 2.0.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG., Bioinformatics 23(21), 2007
PMID: 17846036
REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes.
Linke B, McHardy AC, Neuweger H, Krause L, Meyer F., Appl. Bioinformatics 5(3), 2006
PMID: 16922601
CDD: specific functional annotation with the Conserved Domain Database.
Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18984618
CDD: a Conserved Domain Database for the functional annotation of proteins.
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH., Nucleic Acids Res. 39(Database issue), 2010
PMID: 21109532
Formation of roseoflavin from guanine through riboflavin.
Matsui K, Juri N, Kubo Y, Kasai S., J. Biochem. 86(1), 1979
PMID: 479119
Development of joint application strategies for two microbial gene finders.
McHardy AC, Goesmann A, Puhler A, Meyer F., Bioinformatics 20(10), 2004
PMID: 14988122
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.
Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R., Nucleic Acids Res. 39(Web Server issue), 2011
PMID: 21672958
The microbial pan-genome.
Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R., Curr. Opin. Genet. Dev. 15(6), 2005
PMID: 16185861
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
Infernal 1.0: inference of RNA alignments.
Nawrocki EP, Kolbe DL, Eddy SR., Bioinformatics 25(10), 2009
PMID: 19307242
Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350.
Ohnishi Y, Ishikawa J, Hara H, Suzuki H, Ikenoya M, Ikeda H, Yamashita A, Hattori M, Horinouchi S., J. Bacteriol. 190(11), 2008
PMID: 18375553
Letter: roseoflavin, a new antimicrobial pigment from
Otani S, Takatsu M, Nakano M, Kasai S, Miura R., 1974
A highly specialized flavin mononucleotide riboswitch responds differently to similar ligands and confers roseoflavin resistance to Streptomyces davawensis.
Pedrolli DB, Matern A, Wang J, Ester M, Siedler K, Breaker R, Mack M., Nucleic Acids Res. 40(17), 2012
PMID: 22740651
The antibiotics roseoflavin and 8-demethyl-8-amino-riboflavin from Streptomyces davawensis are metabolized by human flavokinase and human FAD synthetase.
Pedrolli DB, Nakanishi S, Barile M, Mansurova M, Carmona EC, Lux A, Gartner W, Mack M., Biochem. Pharmacol. 82(12), 2011
PMID: 21924249
The mechanism of action of bacimethrin, a naturally occurring thiamin antimetabolite.
Reddick JJ, Saha S, Lee J, Melnick JS, Perkins J, Begley TP., Bioorg. Med. Chem. Lett. 11(17), 2001
PMID: 11527707
Biosynthesis of riboflavin: characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis.
Richter G, Fischer M, Krieger C, Eberhardt S, Luttgen H, Gerstenschlager I, Bacher A., J. Bacteriol. 179(6), 1997
PMID: 9068650
Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology.
Schwientek P, Szczepanowski R, Ruckert C, Stoye J, Puhler A., J. Biotechnol. 155(1), 2011
PMID: 21536083
Spectral and reactivity studies of roseoflavin analogs: correlation between reactivity and spectral parameters
Shinkai S., 1986
nov. sp
Shinobu R., 1974
A hidden Markov model for predicting transmembrane helices in protein sequences.
Sonnhammer EL, von Heijne G, Krogh A., Proc Int Conf Intell Syst Mol Biol 6(), 1998
PMID: 9783223
Artificial chromosomes for antibiotic-producing actinomycetes.
Sosio M, Giusino F, Cappellano C, Bossi E, Puglia AM, Donadio S., Nat. Biotechnol. 18(3), 2000
PMID: 10700154
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
A genomic perspective on protein families.
Tatusov RL, Koonin EV, Lipman DJ., Science 278(5338), 1997
PMID: 9381173
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV., Nucleic Acids Res. 29(1), 2001
PMID: 11125040
Characterization of riboflavin (vitamin B2) transport proteins from Bacillus subtilis and Corynebacterium glutamicum.
Vogl C, Grill S, Schilling O, Stulke J, Mack M, Stolz J., J. Bacteriol. 189(20), 2007
PMID: 17693491
Chemical and enzymatic properties of riboflavin analogues.
Walsh C, Fisher J, Spencer R, Graham DW, Ashton WT, Brown JE, Brown RD, Rogers EF., Biochemistry 17(10), 1978
PMID: 207304
Genome sequence of the milbemycin-producing bacterium Streptomyces bingchenggensis.
Wang XJ, Yan YJ, Zhang B, An J, Wang JJ, Tian J, Jiang L, Chen YH, Huang SX, Yin M, Zhang J, Gao AL, Liu CX, Zhu ZX, Xiang WS., J. Bacteriol. 192(17), 2010
PMID: 20581206
Regulation of bacterial gene expression by riboswitches.
Winkler WC, Breaker RR., Annu. Rev. Microbiol. 59(), 2005
PMID: 16153177


Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®


PMID: 23043000
PubMed | Europe PMC

Suchen in

Google Scholar