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 (2017)

Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Wolf, TimoUniBi; Schneiker-Bekel, Susanne; Neshat, ArminUniBi; Ortseifen, Vera; Wibberg, Daniel; Zemke, Till; Pühler, AlfredUniBi ; Kalinowski, JörnUniBi
Abstract / Bemerkung
Actinoplanes sp. SE50/110 is the natural producer of acarbose, which is used in the treatment of diabetes mellitus type II. However, until now the transcriptional organization and regulation of the acarbose biosynthesis are only understood rudimentarily. The genome sequence of Actinoplanes sp. SE50/110 was known before, but was resequenced in this study to remove assembly artifacts and incorrect base callings. The annotation of the genome was refined in a multi-step approach, including modern bioinformatic pipelines, transcriptome and proteome data. A whole transcriptome RNA-seq library as well as an RNA-seq library enriched for primary 5 '-ends were used for the detection of transcription start sites, to correct tRNA predictions, to identify novel transcripts like small RNAs and to improve the annotation through the correction of falsely annotated translation start sites. The transcriptome data sets were also applied to identify 31 cis-regulatory RNA structures, such as riboswitches or RNA thermometers as well as three leaderless transcribed short peptides found in putative attenuators upstream of genes for amino acid biosynthesis. The transcriptional organization of the acarbose biosynthetic gene cluster was elucidated in detail and fourteen novel biosynthetic gene clusters were suggested. The accurate genome sequence and precise annotation of the Actinoplanes sp. SE50/110 genome will be the foundation for future genetic engineering and systems biology studies.
Actinoplanes; Acarbose; RNA-seq; Cis-regulatory elements; Attenuation; Secondary metabolite gene clusters
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Wolf T, Schneiker-Bekel S, Neshat A, et al. Genome improvement of the acarbose producer Actinoplanes sp SE50/110 and annotation refinement based on RNA-seq analysis. JOURNAL OF BIOTECHNOLOGY. 2017;251:112-123.
Wolf, T., Schneiker-Bekel, S., Neshat, A., Ortseifen, V., Wibberg, D., Zemke, T., Pühler, A., et al. (2017). Genome improvement of the acarbose producer Actinoplanes sp SE50/110 and annotation refinement based on RNA-seq analysis. JOURNAL OF BIOTECHNOLOGY, 251, 112-123. doi:10.1016/j.jbiotec.2017.04.013
Wolf, T., Schneiker-Bekel, S., Neshat, A., Ortseifen, V., Wibberg, D., Zemke, T., Pühler, A., and Kalinowski, J. (2017). Genome improvement of the acarbose producer Actinoplanes sp SE50/110 and annotation refinement based on RNA-seq analysis. JOURNAL OF BIOTECHNOLOGY 251, 112-123.
Wolf, T., et al., 2017. Genome improvement of the acarbose producer Actinoplanes sp SE50/110 and annotation refinement based on RNA-seq analysis. JOURNAL OF BIOTECHNOLOGY, 251, p 112-123.
T. Wolf, et al., “Genome improvement of the acarbose producer Actinoplanes sp SE50/110 and annotation refinement based on RNA-seq analysis”, JOURNAL OF BIOTECHNOLOGY, vol. 251, 2017, pp. 112-123.
Wolf, T., Schneiker-Bekel, S., Neshat, A., Ortseifen, V., Wibberg, D., Zemke, T., Pühler, A., Kalinowski, J.: Genome improvement of the acarbose producer Actinoplanes sp SE50/110 and annotation refinement based on RNA-seq analysis. JOURNAL OF BIOTECHNOLOGY. 251, 112-123 (2017).
Wolf, Timo, Schneiker-Bekel, Susanne, Neshat, Armin, Ortseifen, Vera, Wibberg, Daniel, Zemke, Till, Pühler, Alfred, and Kalinowski, Jörn. “Genome improvement of the acarbose producer Actinoplanes sp SE50/110 and annotation refinement based on RNA-seq analysis”. JOURNAL OF BIOTECHNOLOGY 251 (2017): 112-123.

2 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

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
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

98 References

Daten bereitgestellt von Europe PubMed Central.

Discovering motifs that induce sequencing errors.
Allhoff M, Schonhuth A, Martin M, Costa IG, Rahmann S, Marschall T., BMC Bioinformatics 14 Suppl 5(), 2013
PMID: 23735080
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
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control.
Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR., Proc. Natl. Acad. Sci. U.S.A. 101(17), 2004
PMID: 15096624
Pharmacology of alpha-glucosidase inhibition.
Bischoff H., Eur. J. Clin. Invest. 24 Suppl 3(), 1994
PMID: 8001624
Evidence for widespread gene control function by the ydaO riboswitch candidate.
Block KF, Hammond MC, Breaker RR., J. Bacteriol. 192(15), 2010
PMID: 20511502
EDGAR 2.0: an enhanced software platform for comparative gene content analyses.
Blom J, Kreis J, Spanig S, Juhre T, Bertelli C, Ernst C, Goesmann A., Nucleic Acids Res. 44(W1), 2016
PMID: 27098043
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B., Bioinformatics 30(15), 2014
PMID: 24695404
Coenzyme B12 controls transcription of the Streptomyces class Ia ribonucleotide reductase nrdABS operon via a riboswitch mechanism.
Borovok I, Gorovitz B, Schreiber R, Aharonowitz Y, Cohen G., J. Bacteriol. 188(7), 2006
PMID: 16547038
Ramoplanin (A-16686), a new glycolipodepsipeptide antibiotic. III. Structure elucidation.
Ciabatti R, Kettenring JK, Winters G, Tuan G, Zerilli L, Cavalleri B., J. Antibiot. 42(2), 1989
PMID: 2597278


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
The riboswitch-mediated control of sulfur metabolism in bacteria.
Epshtein V, Mironov AS, Nudler E., Proc. Natl. Acad. Sci. U.S.A. 100(9), 2003
PMID: 12702767
Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity.
Filiatrault MJ, Stodghill PV, Bronstein PA, Moll S, Lindeberg M, Grills G, Schweitzer P, Wang W, Schroth GP, Luo S, Khrebtukova I, Yang Y, Thannhauser T, Butcher BG, Cartinhour S, Schneider DJ., J. Bacteriol. 192(9), 2010
PMID: 20190049
PCR-amplification of GC-rich regions: 'slowdown PCR'.
Frey UH, Bachmann HS, Peters J, Siffert W., Nat Protoc 3(8), 2008
PMID: 18714299
Structural insights into recognition of c-di-AMP by the ydaO riboswitch.
Gao A, Serganov A., Nat. Chem. Biol. 10(9), 2014
PMID: 25086507
The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA.
Giuliodori AM, Di Pietro F, Marzi S, Masquida B, Wagner R, Romby P, Gualerzi CO, Pon CL., Mol. Cell 37(1), 2010
PMID: 20129052
Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
Transcriptome complexity in a genome-reduced bacterium.
Guell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kuhner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L., Science 326(5957), 2009
PMID: 19965477
Metabolic engineering for the microbial production of carotenoids and related products with a focus on the rare C50 carotenoids.
Heider SA, Peters-Wendisch P, Wendisch VF, Beekwilder J, Brautaset T., Appl. Microbiol. Biotechnol. 98(10), 2014
PMID: 24687754
The biosynthetic logic of polyketide diversity.
Hertweck C., Angew. Chem. Int. Ed. Engl. 48(26), 2009
PMID: 19514004
ReadXplorer--visualization and analysis of mapped sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
PMID: 24790157
r2cat: synteny plots and comparative assembly.
Husemann P, Stoye J., Bioinformatics 26(4), 2009
PMID: 20015948
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
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A., Bioinformatics 28(12), 2012
PMID: 22543367
Functional analysis of genes from Streptomyces griseus involved in the synthesis of isorenieratene, a carotenoid with aromatic end groups, revealed a novel type of carotenoid desaturase
Krügel, Biochim. Biophys. Acta (BBA) Mol. Cell Biol. Lipids 1439(1), 1999
Histidine biosynthesis, its regulation and biotechnological application in Corynebacterium glutamicum.
Kulis-Horn RK, Persicke M, Kalinowski J., Microb Biotechnol 7(1), 2013
PMID: 23617600
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.
Laslett D, Canback B., Nucleic Acids Res. 32(1), 2004
PMID: 14704338
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
Taxonomic outline of the phylum Actinobacteria
Ludwig, 2012
Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.
Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT., PLoS ONE 7(2), 2012
PMID: 22347999
A glycine-dependent riboswitch that uses cooperative binding to control gene expression.
Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR., Science 306(5694), 2004
PMID: 15472076
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032.
Mentz A, Neshat A, Pfeifer-Sancar K, Puhler A, Ruckert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24138339
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
Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes.
Nahvi A, Barrick JE, Breaker RR., Nucleic Acids Res. 32(1), 2004
PMID: 14704351
Transcription attenuation in bacteria: theme and variations.
Naville M, Gautheret D., Brief Funct Genomics 9(2), 2010
PMID: 20352660
ARNold: a web tool for the prediction of Rho-independent transcription terminators.
Naville M, Ghuillot-Gaudeffroy A, Marchais A, Gautheret D., RNA Biol 8(1), 2011
PMID: 21282983
Infernal 1.1: 100-fold faster RNA homology searches.
Nawrocki EP, Eddy SR., Bioinformatics 29(22), 2013
PMID: 24008419
Rfam 12.0: updates to the RNA families database.
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD., Nucleic Acids Res. 43(Database issue), 2014
PMID: 25392425
Riboswitches in eubacteria sense the second messenger c-di-AMP.
Nelson JW, Sudarsan N, Furukawa K, Weinberg Z, Wang JX, Breaker RR., Nat. Chem. Biol. 9(12), 2013
PMID: 24141192
The riboswitch control of bacterial metabolism.
Nudler E, Mironov AS., Trends Biochem. Sci. 29(1), 2004
PMID: 14729327
Search and discovery of new antibiotics
Okami, 1988
c-di-AMP reports DNA integrity during sporulation in Bacillus subtilis.
Oppenheimer-Shaanan Y, Wexselblatt E, Katzhendler J, Yavin E, Ben-Yehuda S., EMBO Rep. 12(6), 2011
PMID: 21566650
Branched-chain amino acids
Pátek, 2007
Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique.
Pfeifer-Sancar K, Mentz A, Ruckert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24341750
Sioxanthin, a novel glycosylated carotenoid, reveals an unusual subclustered biosynthetic pathway.
Richter TK, Hughes CC, Moore BS., Environ. Microbiol. 17(6), 2014
PMID: 25329237
Riboswitch discovery by combining RNA-seq and genome-wide identification of transcriptional start sites.
Rosinski-Chupin I, Soutourina O, Martin-Verstraete I., Meth. Enzymol. 549(), 2014
PMID: 25432742
Discovery of microbial natural products by activation of silent biosynthetic gene clusters.
Rutledge PJ, Challis GL., Nat. Rev. Microbiol. 13(8), 2015
PMID: 26119570
Carotenoids of biotechnological importance.
Sandmann G., Adv. Biochem. Eng. Biotechnol. 148(), 2015
PMID: 25326165
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs.
Schattner P, Brooks AN, Lowe TM., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980563
Triggering cryptic natural product biosynthesis in microorganisms.
Scherlach K, Hertweck C., Org. Biomol. Chem. 7(9), 2009
PMID: 19590766
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 complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110.
Schwientek P, Szczepanowski R, Ruckert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Puhler A., BMC Genomics 13(), 2012
PMID: 22443545
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, Ruckert C, Schneiker-Bekel S, Wendler S, Stoye J, Puhler A., J. Biotechnol. 190(), 2014
PMID: 24642337
Prokka: rapid prokaryotic genome annotation.
Seemann T., Bioinformatics 30(14), 2014
PMID: 24642063
Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria.
Seliverstov AV, Putzer H, Gelfand MS, Lyubetsky VA., BMC Microbiol. 5(), 2005
PMID: 16202131
Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch.
Serganov A, Huang L, Patel DJ., Nature 458(7235), 2009
PMID: 19169240
The primary transcriptome of the major human pathogen Helicobacter pylori.
Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermuller J, Reinhardt R, Stadler PF, Vogel J., Nature 464(7286), 2010
PMID: 20164839
Chemistry and biochemistry of microbialα-glucosidase inhibitors
Truscheit, Angew. Chem. Int. Ed. Engl. 20(9), 1981
Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis.
Vitreschak AG, Lyubetskaya EV, Shirshin MA, Gelfand MS, Lyubetsky VA., FEMS Microbiol. Lett. 234(2), 2004
PMID: 15135544
Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS., Nucleic Acids Res. 30(14), 2002
PMID: 12136096
Vobis, 2012
The genus Actinoplanes and related genera
Vobis, 2006
Regulatory RNAs in bacteria.
Waters LS, Storz G., Cell 136(4), 2009
PMID: 19239884
The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis.
Watson PY, Fedor MJ., Nat. Chem. Biol. 8(12), 2012
PMID: 23086297
antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.
Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Muller R, Wohlleben W, Breitling R, Takano E, Medema MH., Nucleic Acids Res. 43(W1), 2015
PMID: 25948579
In silico tools for the analysis of antibiotic biosynthetic pathways.
Weber T., Int. J. Med. Microbiol. 304(3-4), 2014
PMID: 24631213
Biotechnology and molecular biology of the alpha-glucosidase inhibitor acarbose.
Wehmeier UF, Piepersberg W., Appl. Microbiol. Biotechnol. 63(6), 2003
PMID: 14669056
The biosynthesis and metabolism of acarbose in Actinoplanes sp. SE 50/110: a progress report
Wehmeier, Biocatal. Biotransform. 21(4–5), 2003
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.
Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR., Genome Biol. 11(3), 2010
PMID: 20230605
The cytosolic and extracellular proteomes of Actinoplanes sp. SE50/110 led to the identification of gene products involved in acarbose metabolism.
Wendler S, Hurtgen D, Kalinowski J, Klein A, Niehaus K, Schulte F, Schwientek P, Wehlmann H, Wehmeier UF, Puhler A., J. Biotechnol. 167(2), 2012
PMID: 22944206
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, Puhler A., J. Biotechnol. 191(), 2014
PMID: 25169663
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, Puhler A., J Proteomics 125(), 2015
PMID: 25896738
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, Puhler A., J Proteomics 131(), 2015
PMID: 26597626
Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes.
Wibberg D, Andersson L, Tzelepis G, Rupp O, Blom J, Jelonek L, Puhler A, Fogelqvist J, Varrelmann M, Schluter A, Dixelius C., BMC Genomics 17(), 2016
PMID: 26988094
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.
Winkler W, Nahvi A, Breaker RR., Nature 419(6910), 2002
PMID: 12410317
An mRNA structure that controls gene expression by binding S-adenosylmethionine.
Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR., Nat. Struct. Biol. 10(9), 2003
PMID: 12910260
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, Puhler A, Kalinowski J., J. Biotechnol. 231(), 2016
PMID: 27262504
A single-base resolution map of an archaeal transcriptome.
Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons BA, Sorek R., Genome Res. 20(1), 2009
PMID: 19884261
The complete nucleotide sequence of the tryptophan operon of Escherichia coli.
Yanofsky C, Platt T, Crawford IP, Nichols BP, Christie GE, Horowitz H, VanCleemput M, Wu AM., Nucleic Acids Res. 9(24), 1981
PMID: 7038627


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