The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110

Schwientek P, Szczepanowski R, Rückert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Pühler A (2012)
BMC Genomics 13(1): 112.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
Background Actinoplanes sp. SE50/110 is known as the wild type producer of the alpha-glucosidase inhibitor acarbose, a potent drug used worldwide in the treatment of type-2 diabetes mellitus. As the incidence of diabetes is rapidly rising worldwide, an ever increasing demand for diabetes drugs, such as acarbose, needs to be anticipated. Consequently, derived Actinoplanes strains with increased acarbose yields are being used in large scale industrial batch fermentation since 1990 and were continuously optimized by conventional mutagenesis and screening experiments. This strategy reached its limits and is generally superseded by modern genetic engineering approaches. As a prerequisite for targeted genetic modifications, the complete genome sequence of the organism has to be known. Results Here, we present the complete genome sequence of Actinoplanes sp. SE50/110 [GenBank:CP003170], the first publicly available genome of the genus Actinoplanes, comprising various producers of pharmaceutically and economically important secondary metabolites. The genome features a high mean G + C content of 71.32% and consists of one circular chromosome with a size of 9,239,851 bp hosting 8,270 predicted protein coding sequences. Phylogenetic analysis of the core genome revealed a rather distant relation to other sequenced species of the family Micromonosporaceae whereas Actinoplanes utahensis was found to be the closest species based on 16S rRNA gene sequence comparison. Besides the already published acarbose biosynthetic gene cluster sequence, several new non-ribosomal peptide synthetase-, polyketide synthase- and hybrid-clusters were identified on the Actinoplanes genome. Another key feature of the genome represents the discovery of a functional actinomycete integrative and conjugative element. Conclusions The complete genome sequence of Actinoplanes sp. SE50/110 marks an important step towards the rational genetic optimization of the acarbose production. In this regard, the identified actinomycete integrative and conjugative element could play a central role by providing the basis for the development of a genetic transformation system for Actinoplanes sp. SE50/110 and other Actinoplanes spp. Furthermore, the identified non-ribosomal peptide synthetase- and polyketide synthase-clusters potentially encode new antibiotics and/or other bioactive compounds, which might be of pharmacologic interest.
Complete genome sequence; AICE; Actinomycetes; Actinoplanes; Acarbose; Genomics
BMC Genomics
Page URI


Schwientek P, Szczepanowski R, Rückert C, et al. The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics. 2012;13(1): 112.
Schwientek, P., Szczepanowski, R., Rückert, C., Kalinowski, J., Klein, A., Selber, K., Wehmeier, U. F., et al. (2012). The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics, 13(1), 112. doi:10.1186/1471-2164-13-112
Schwientek, P., Szczepanowski, R., Rückert, C., Kalinowski, J., Klein, A., Selber, K., Wehmeier, U. F., Stoye, J., and Pühler, A. (2012). The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics 13:112.
Schwientek, P., et al., 2012. The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics, 13(1): 112.
P. Schwientek, et al., “The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110”, BMC Genomics, vol. 13, 2012, : 112.
Schwientek, P., Szczepanowski, R., Rückert, C., Kalinowski, J., Klein, A., Selber, K., Wehmeier, U.F., Stoye, J., Pühler, A.: The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics. 13, : 112 (2012).
Schwientek, Patrick, Szczepanowski, Rafael, Rückert, Christian, Kalinowski, Jörn, Klein, Andreas, Selber, Klaus, Wehmeier, Udo F., Stoye, Jens, and Pühler, Alfred. “The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110”. BMC Genomics 13.1 (2012): 112.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Access Level
OA Open Access
Zuletzt Hochgeladen
MD5 Prüfsumme

Link(s) zu Volltext(en)
Access Level
Restricted Closed Access

40 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Coexistence of Anticoagulant and Anti-vascular Calcification Activities in Kribbella sp. UTMC 267 Metabolites.
Salimi F, Hamedi J, Motevaseli E, Mohammadipanah F., Iran J Pharm Res 18(1), 2019
PMID: 31089380
Comparative functional genomics of the acarbose producers reveals potential targets for metabolic engineering.
Xie H, Zhao Q, Zhang X, Kang Q, Bai L., Synth Syst Biotechnol 4(1), 2019
PMID: 30723817
Evaluation of vector systems and promoters for overexpression of the acarbose biosynthesis gene acbC in Actinoplanes sp. SE50/110.
Schaffert L, März C, Burkhardt L, Droste J, Brandt D, Busche T, Rosen W, Schneiker-Bekel S, Persicke M, Pühler A, Kalinowski J., Microb Cell Fact 18(1), 2019
PMID: 31253141
Genome improvement of the acarbose producer Actinoplanes sp. SE50/110 and annotation refinement based on RNA-seq analysis.
Wolf T, Schneiker-Bekel S, Neshat A, Ortseifen V, Wibberg D, Zemke T, Pühler A, Kalinowski J., J Biotechnol 251(), 2017
PMID: 28427920
Regulation of Sporangium Formation by BldD in the Rare Actinomycete Actinoplanes missouriensis.
Mouri Y, Konishi K, Fujita A, Tezuka T, Ohnishi Y., J Bacteriol 199(12), 2017
PMID: 28348024
Actinoplanes Swims into the Molecular Age.
Buttner MJ., J Bacteriol 199(12), 2017
PMID: 28348027
The MalR type regulator AcrC is a transcriptional repressor of acarbose biosynthetic genes in Actinoplanes sp. SE50/110.
Wolf T, Droste J, Gren T, Ortseifen V, Schneiker-Bekel S, Zemke T, Pühler A, Kalinowski J., BMC Genomics 18(1), 2017
PMID: 28743243
Comparative proteome analysis of Actinoplanes sp. SE50/110 grown with maltose or glucose shows minor differences for acarbose biosynthesis proteins but major differences for saccharide transporters.
Wendler S, Otto A, Ortseifen V, Bonn F, Neshat A, Schneiker-Bekel S, Wolf T, Zemke T, Wehmeier UF, Hecker M, Kalinowski J, Becher D, Pühler A., J Proteomics 131(), 2016
PMID: 26597626
Metabolic differences of industrial acarbose-producing Actinoplanes sp. A56 under various osmolality levels.
Li KT, Peng WF, Xia W, Huang L, Cheng X., World J Microbiol Biotechnol 32(1), 2016
PMID: 26712618
Metabolic differences of industrial acarbose-producing Actinoplanes sp. A56 under various osmolality levels
Li Kt, Peng Wf, Xia W, Huang L, Cheng X., World J Microbiol Biotechnol 32(1), 2016
PMID: IND604775110
Complete mitochondrial genome of the scleractinian coral Porites rus.
Celis JS, Wibberg D, Winkler A, Wilke T, Kalinowski J., Mitochondrial DNA A DNA Mapp Seq Anal 27(5), 2016
PMID: 27158873
Draft Genome Sequence of an Endophytic Actinoplanes Species, Encoding Uncommon trans-Acyltransferase Polyketide Synthases.
Centeno-Leija S, Vinuesa P, Rodríguez-Peña K, Trenado-Uribe M, Cárdenas-Conejo Y, Serrano-Posada H, Rodríguez-Sanoja R, Sánchez S., Genome Announc 4(2), 2016
PMID: 27013046
Integration event induced changes in recombinant protein productivity in Pichia pastoris discovered by whole genome sequencing and derived vector optimization.
Schwarzhans JP, Wibberg D, Winkler A, Luttermann T, Kalinowski J, Friehs K., Microb Cell Fact 15(), 2016
PMID: 27206580
Targeted genome editing in the rare actinomycete Actinoplanes sp. SE50/110 by using the CRISPR/Cas9 System.
Wolf T, Gren T, Thieme E, Wibberg D, Zemke T, Pühler A, Kalinowski J., J Biotechnol 231(), 2016
PMID: 27262504
Genetic and Transcriptional Analyses of the Flagellar Gene Cluster in Actinoplanes missouriensis.
Jang MS, Mouri Y, Uchida K, Aizawa S, Hayakawa M, Fujita N, Tezuka T, Ohnishi Y., J Bacteriol 198(16), 2016
PMID: 27274031
An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH.
Nguyen TV, Wibberg D, Battenberg K, Blom J, Vanden Heuvel B, Berry AM, Kalinowski J, Pawlowski K., BMC Genomics 17(1), 2016
PMID: 27729005
Complete genome sequence of the actinobacterium Streptomyces glaucescens GLA.O (DSM 40922) consisting of a linear chromosome and one linear plasmid.
Ortseifen V, Winkler A, Albersmeier A, Wendler S, Pühler A, Kalinowski J, Rückert C., J Biotechnol 194(), 2015
PMID: 25499805
Genome Sequence of the Urethral Catheter Isolate Pseudomonas aeruginosa MH19.
Vorhölter FJ, Tielen P, Wibberg D, Narten M, Schobert M, Tüpker R, Blom J, Schatschneider S, Winkler A, Albersmeier A, Goesmann A, Pühler A, Jahn D., Genome Announc 3(2), 2015
PMID: 25767242
Comprehensive proteome analysis of Actinoplanes sp. SE50/110 highlighting the location of proteins encoded by the acarbose and the pyochelin biosynthesis gene cluster.
Wendler S, Otto A, Ortseifen V, Bonn F, Neshat A, Schneiker-Bekel S, Walter F, Wolf T, Zemke T, Wehmeier UF, Hecker M, Kalinowski J, Becher D, Pühler A., J Proteomics 125(), 2015
PMID: 25896738
The adpA-like regulatory gene from Actinoplanes teichomyceticus: in silico analysis and heterologous expression.
Ostash B, Yushchuk O, Tistechok S, Mutenko H, Horbal L, Muryn A, Dacyuk Y, Kalinowski J, Luzhetskyy A, Fedorenko V., World J Microbiol Biotechnol 31(8), 2015
PMID: 26041369
The Sinorhizobium fredii HH103 Genome: A Comparative Analysis With S. fredii Strains Differing in Their Symbiotic Behavior With Soybean.
Vinardell JM, Acosta-Jurado S, Zehner S, Göttfert M, Becker A, Baena I, Blom J, Crespo-Rivas JC, Goesmann A, Jaenicke S, Krol E, McIntosh M, Margaret I, Pérez-Montaño F, Schneiker-Bekel S, Serranía J, Szczepanowski R, Buendía AM, Lloret J, Bonilla I, Pühler A, Ruiz-Sainz JE, Weidner S., Mol Plant Microbe Interact 28(7), 2015
PMID: 25675256
Draft Genome Sequence of Pseudomonas aeruginosa Strain WS136, a Highly Cytotoxic ExoS-Positive Wound Isolate Recovered from Pyoderma Gangrenosum.
Arnold M, Wibberg D, Blom J, Schatschneider S, Winkler A, Kutter Y, Rückert C, Albersmeier A, Albaum S, Goesmann A, Zange S, Heesemann J, Pühler A, Hogardt M, Vorhölter FJ., Genome Announc 3(4), 2015
PMID: 26139712
Genome Sequence of the Urethral Isolate Pseudomonas aeruginosa RN21.
Wibberg D, Tielen P, Narten M, Schobert M, Blom J, Schatschneider S, Meyer AK, Neubauer R, Albersmeier A, Albaum S, Jahn M, Goesmann A, Vorhölter FJ, Pühler A, Jahn D., Genome Announc 3(4), 2015
PMID: 26184943
The adpA-like regulatory gene from Actinoplanes teichomyceticus: in silico analysis and heterologous expression
Ostash B, Yushchuk O, Tistechok S, Mutenko H, Horbal L, Muryn A, Dacyuk Y, Kalinowski J, Luzhetskyy A, Fedorenko V., World J Microbiol Biotechnol 31(8), 2015
PMID: IND604401124
A novel teichuronic acid, the major polymer from the cell wall of Actinoplanes lobatus VKM Ac-676(T.).
Shashkov AS, Streshinskaya GM, Tul'skaya EM, Kozlova YI, Senchenkova SN, Evtushenko LI., Carbohydr Res 387(), 2014
PMID: 24531391
MbtH homology codes to identify gifted microbes for genome mining.
Baltz RH., J Ind Microbiol Biotechnol 41(2), 2014
PMID: 24197465
Genome Sequence of the Acute Urethral Catheter Isolate Pseudomonas aeruginosa MH38.
Wibberg D, Tielen P, Blom J, Rosin N, Schobert M, Tüpker R, Schatschneider S, Spilker D, Albersmeier A, Goesmann A, Vorhölter FJ, Pühler A, Jahn D., Genome Announc 2(2), 2014
PMID: 24625869
Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts.
Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A., J Biotechnol 190(), 2014
PMID: 24642337
Genomics of sponge-associated Streptomyces spp. closely related to Streptomyces albus J1074: insights into marine adaptation and secondary metabolite biosynthesis potential.
Ian E, Malko DB, Sekurova ON, Bredholt H, Rückert C, Borisova ME, Albersmeier A, Kalinowski J, Gelfand MS, Zotchev SB., PLoS One 9(5), 2014
PMID: 24819608
Carbon source dependent biosynthesis of acarviose metabolites in Actinoplanes sp. SE50/110.
Wendler S, Ortseifen V, Persicke M, Klein A, Neshat A, Niehaus K, Schneiker-Bekel S, Walter F, Wehmeier UF, Kalinowski J, Pühler A., J Biotechnol 191(), 2014
PMID: 25169663
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
Draft Genome Sequence of Pseudomonas aeruginosa Strain WS394, a Multidrug-Resistant and Highly Cytotoxic Wound Isolate from Chronic Ulcus Cruris.
Vorhölter FJ, Arnold M, Wibberg D, Blom J, Winkler A, Viehoever P, Albersmeier A, Goesmann A, Zange S, Heesemann J, Pühler A, Hogardt M., Genome Announc 2(6), 2014
PMID: 25523779
Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media.
Schwientek P, Wendler S, Neshat A, Eirich C, Rückert C, Klein A, Wehmeier UF, Kalinowski J, Stoye J, Pühler A., J Biotechnol 167(2), 2013
PMID: 23142701
Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14.
Wibberg D, Jelonek L, Rupp O, Hennig M, Eikmeyer F, Goesmann A, Hartmann A, Borriss R, Grosch R, Pühler A, Schlüter A., J Biotechnol 167(2), 2013
PMID: 23280342
The noncanonical type III secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection.
Wichmann F, Vorhölter FJ, Hersemann L, Widmer F, Blom J, Niehaus K, Reinhard S, Conradin C, Kölliker R., Mol Plant Pathol 14(6), 2013
PMID: 23578314
Complete genome sequence of the motile actinomycete Actinoplanes missouriensis 431(T) (= NBRC 102363(T)).
Yamamura H, Ohnishi Y, Ishikawa J, Ichikawa N, Ikeda H, Sekine M, Harada T, Horinouchi S, Otoguro M, Tamura T, Suzuki K, Hoshino Y, Arisawa A, Nakagawa Y, Fujita N, Hayakawa M., Stand Genomic Sci 7(2), 2012
PMID: 23407331

120 References

Daten bereitgestellt von Europe PubMed Central.

Actinoplane, A New Genus of the Actinomycetales
Some New Genera and Species of the Actinoplanaceae

Members of the genus Actinoplanes and their antibiotics.
Parenti F, Coronelli C., Annu. Rev. Microbiol. 33(), 1979
PMID: 386928
Actaplanin, new glycopeptide antibiotics produced by Actinoplanes missouriensis. The isolation and preliminary chemical characterization of actaplanin.
Debono M, Merkel KE, Molloy RM, Barnhart M, Presti E, Hunt AH, Hamill RL., J. Antibiot. 37(2), 1984
PMID: 6706856
Sch 42137, a novel antifungal antibiotic from an Actinoplanes sp. Fermentation, isolation, structure and biological properties.
Cooper R, Truumees I, Gunnarsson I, Loebenberg D, Horan A, Marquez J, Patel M, Gullo V, Puar M, Das P., J. Antibiot. 45(4), 1992
PMID: 1592676
Biosynthesis, biotechnological production, and application of teicoplanin: current state and perspectives.
Jung HM, Jeya M, Kim SY, Moon HJ, Kumar Singh R, Zhang YW, Lee JK., Appl. Microbiol. Biotechnol. 84(3), 2009
PMID: 19609520
Glycoside-hydrolase enzyme inhibitors
Amino sugar derivatives
Process for the production of a saccharase inhibitor
[New enzyme inhibitors from microorganisms (author's transl)]
Frommer W, Junge B, Muller L, Schmidt D, Truscheit E., Planta Med. 35(3), 1979
PMID: 432298

Biotechnology and molecular biology of the alpha-glucosidase inhibitor acarbose.
Wehmeier UF, Piepersberg W., Appl. Microbiol. Biotechnol. 63(6), 2003
PMID: 14669056
Weiße Biotechnologie bei Bayer HealthCare Product Supply: Mehr als 30 Jahre Erfahrung
Strain improvement in actinomycetes in the postgenomic era.
Baltz RH., J. Ind. Microbiol. Biotechnol. 38(6), 2011
PMID: 21253811
Acarbose (acb) Cluster from Actinoplanes sp. SE 50/110
Crystal structures of the bacterial solute receptor AcbH displaying an exclusive substrate preference for β-D-galactopyranose.
Licht A, Bulut H, Scheffel F, Daumke O, Wehmeier UF, Saenger W, Schneider E, Vahedi-Faridi A., J. Mol. Biol. 406(1), 2010
PMID: 21168419
Verfahren zur Isolierung von (O{4,6-Dideoxy-4[[1S-(1,4,6/5)-4,5,6-trihydroxy-3-hydroxymethyl-2-cyclohexen-1-yl]-amino]-α-D-glucopyranosyl}-(1 → 4)-O-α-D-glucopyranosyl-(1 → 4)-D-glucopyranose) aus Kulturbrühen
Identification, cloning, expression, and characterization of the extracellular acarbose-modifying glycosyltransferase, AcbD, from Actinoplanes sp. strain SE50.
Hemker M, Stratmann A, Goeke K, Schroder W, Lenz J, Piepersberg W, Pape H., J. Bacteriol. 183(15), 2001
PMID: 11443082
Biosynthesis of the C(7)-cyclitol moiety of acarbose in Actinoplanes species SE50/110. 7-O-phosphorylation of the initial cyclitol precursor leads to proposal of a new biosynthetic pathway.
Zhang CS, Stratmann A, Block O, Bruckner R, Podeschwa M, Altenbach HJ, Wehmeier UF, Piepersberg W., J. Biol. Chem. 277(25), 2002
PMID: 11937512
The acarbose-biosynthetic enzyme AcbO from Actinoplanes sp. SE 50/110 is a 2-epi-5-epi-valiolone-7-phosphate 2-epimerase.
Zhang CS, Podeschwa M, Altenbach HJ, Piepersberg W, Wehmeier UF., FEBS Lett. 540(1-3), 2003
PMID: 12681481
The acbH gene of Actinoplanes sp. encodes a solute receptor with binding activities for acarbose and longer homologs.
Brunkhorst C, Wehmeier UF, Piepersberg W, Schneider E., Res. Microbiol. 156(3), 2004
PMID: 15808935
The Biosynthesis and Metabolism of Acarbose in Actinoplane sp. SE 50/110: A Progress Report
Enzymology of aminoglycoside biosynthesis-deduction from gene clusters.
Wehmeier UF, Piepersberg W., Meth. Enzymol. 459(), 2009
PMID: 19362651
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
The composite genome of the legume symbiont Sinorhizobium meliloti.
Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J., Science 293(5530), 2001
PMID: 11474104
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
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
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensi
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
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
Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.
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., Nat. Biotechnol. 24(11), 2006
PMID: 17057704
Complete genome sequence of the myxobacterium Sorangium cellulosum.
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, 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., Nat. Biotechnol. 25(11), 2007
PMID: 17965706
The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity.
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., J. Bacteriol. 190(6), 2008
PMID: 18192381
The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
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., J. Biotechnol. 134(1-2), 2008
PMID: 18304669
Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
Genomics. Genome project standards in a new era of sequencing.
Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A; Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter JC., Science 326(5950), 2009
PMID: 19815760
Prodigal: prokaryotic gene recognition and translation initiation site identification
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
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 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

Architecture of bacterial replication initiation complexes: orisomes from four unrelated bacteria.
Zawilak-Pawlik A, Kois A, Majka J, Jakimowicz D, Smulczyk-Krawczyszyn A, Messer W, Zakrzewska-Czerwinska J., Biochem. J. 389(Pt 2), 2005
PMID: 15790315
Nucleotide sequences of streptomycete 16S ribosomal DNA: towards a specific identification system for streptomycetes using PCR
A genomic perspective on protein families.
Tatusov RL, Koonin EV, Lipman DJ., Science 278(5338), 1997
PMID: 9381173
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
Hexacyclinic acid, a Polyketide from Streptomyce with a Novel Carbon Skeleton
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM., Nucleic Acids Res. 37(Database issue), 2008
PMID: 19004872
Confidence limits on phylogenies: an approach using the bootstrap
Evolution of protein molecules
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Tamura K, Dudley J, Nei M, Kumar S., Mol. Biol. Evol. 24(8), 2007
PMID: 17488738
EDGAR: a software framework for the comparative analysis of prokaryotic genomes
Genome sequence of the abyssomicin- and proximicin-producing marine actinomycete Verrucosispora maris AB-18-032.
Roh H, Uguru GC, Ko HJ, Kim S, Kim BY, Goodfellow M, Bull AT, Kim KH, Bibb MJ, Choi IG, Stach JE., J. Bacteriol. 193(13), 2011
PMID: 21551311
New genetic methods to improve secondary metabolite production in Streptomyce
Improving production of bioactive secondary metabolites in actinomycetes by metabolic engineering.
Olano C, Lombo F, Mendez C, Salas JA., Metab. Eng. 10(5), 2008
PMID: 18674632
rmlB and rmlC genes are essential for growth of mycobacteria.
Li W, Xin Y, McNeil MR, Ma Y., Biochem. Biophys. Res. Commun. 342(1), 2006
PMID: 16472764
Developments in the Biosynthesis and Regulation of Aminoglycosides
Actinomycete integrative and conjugative elements.
te Poele EM, Bolhuis H, Dijkhuizen L., Antonie Van Leeuwenhoek 94(1), 2008
PMID: 18523858
Shaping bacterial genomes with integrative and conjugative elements.
Burrus V, Waldor MK., Res. Microbiol. 155(5), 2004
PMID: 15207870
Characterization of the att site of the integrative element pSAM2 from Streptomyces ambofacien
Conjugative plasmid transfer in gram-positive bacteria.
Grohmann E, Muth G, Espinosa M., Microbiol. Mol. Biol. Rev. 67(2), 2003
PMID: 12794193
Characterization of pra, a gene for replication control in pSAM2, the integrating element of Streptomyces ambofaciens.
Sezonov G, Hagege J, Pernodet JL, Friedmann A, Guerineau M., Mol. Microbiol. 17(3), 1995
PMID: 8559072
The chemical biology of modular biosynthetic enzymes.
Meier JL, Burkart MD., Chem Soc Rev 38(7), 2009
PMID: 19551180
Nonribosomal peptide synthetases involved in the production of medically relevant natural products.
Felnagle EA, Jackson EE, Chan YA, Podevels AM, Berti AD, McMahon MD, Thomas MG., Mol. Pharm. 5(2), 2008
PMID: 18217713
PKS and NRPS release mechanisms.
Du L, Lou L., Nat Prod Rep 27(2), 2009
PMID: 20111804
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 sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways.
Medema MH, Trefzer A, Kovalchuk A, van den Berg M, Muller U, Heijne W, Wu L, Alam MT, Ronning CM, Nierman WC, Bovenberg RA, Breitling R, Takano E., Genome Biol Evol 2(), 2010
PMID: 20624727
SBSPKS: structure based sequence analysis of polyketide synthases.
Anand S, Prasad MV, Yadav G, Kumar N, Shehara J, Ansari MZ, Mohanty D., Nucleic Acids Res. 38(Web Server issue), 2010
PMID: 20444870
Type II thioesterase from Streptomyces coelicolor A3(2).
Kotowska M, Pawlik K, Butler AR, Cundliffe E, Takano E, Kuczek K., Microbiology (Reading, Engl.) 148(Pt 6), 2002
PMID: 12055297
Identification of unique type II polyketide synthase genes in soil.
Wawrik B, Kerkhof L, Zylstra GJ, Kukor JJ., Appl. Environ. Microbiol. 71(5), 2005
PMID: 15870305
Characterization of the 'pristinamycin supercluster' of Streptomyces pristinaespiralis.
Mast Y, Weber T, Golz M, Ort-Winklbauer R, Gondran A, Wohlleben W, Schinko E., Microb Biotechnol 4(2), 2010
PMID: 21342465
Discovery and molecular engineering of sugar-containing natural product biosynthetic pathways in actinomycetes.
Oh TJ, Mo SJ, Yoon YJ, Sohng JK., J. Microbiol. Biotechnol. 17(12), 2007
PMID: 18167436
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
Ewing B, Hillier L, Wendl MC, Green P., Genome Res. 8(3), 1998
PMID: 9521921
Automated finishing with autofinish.
Gordon D, Desmarais C, Green P., Genome Res. 11(4), 2001
PMID: 11282977
Development of joint application strategies for two microbial gene finders.
McHardy AC, Goesmann A, Puhler A, Meyer F., Bioinformatics 20(10), 2004
PMID: 14988122
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
Improved microbial gene identification with GLIMMER.
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL., Nucleic Acids Res. 27(23), 1999
PMID: 10556321
CRITICA: coding region identification tool invoking comparative analysis.
Badger JH, Olsen GJ, Woese CR., Mol. Biol. Evol. 16(4), 1999
PMID: 10331277
High-performance searching of biosequence databases.
Coulson A., Trends Biotechnol. 12(3), 1994
PMID: 7764827
CDD: a database of conserved domain alignments with links to domain three-dimensional structure.
Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH., Nucleic Acids Res. 30(1), 2002
PMID: 11752315
The ENZYME database in 2000.
Bairoch A., Nucleic Acids Res. 28(1), 2000
PMID: 10592255
Enzyme-specific profiles for genome annotation: PRIAM.
Claudel-Renard C, Chevalet C, Faraut T, Kahn D., Nucleic Acids Res. 31(22), 2003
PMID: 14602924
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
The COG database: an updated version includes eukaryotes
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
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
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
Nielsen H, Engelbrecht J, Brunak S, von Heijne G., Protein Eng. 10(1), 1997
PMID: 9051728
Prediction of signal peptides and signal anchors by a hidden Markov model.
Nielsen H, Krogh A., Proc Int Conf Intell Syst Mol Biol 6(), 1998
PMID: 9783217
Improved prediction of signal peptides: SignalP 3.0.
Bendtsen JD, Nielsen H, von Heijne G, Brunak S., J. Mol. Biol. 340(4), 2004
PMID: 15223320
Non-classical protein secretion in bacteria.
Bendtsen JD, Kiemer L, Fausboll A, Brunak S., BMC Microbiol. 5(), 2005
PMID: 16212653
Operons in Escherichia coli: genomic analyses and predictions.
Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J., Proc. Natl. Acad. Sci. U.S.A. 97(12), 2000
PMID: 10823905
MUSCLE: a multiple sequence alignment method with reduced time and space complexity


Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®


PMID: 22443545
PubMed | Europe PMC

Suchen in

Google Scholar