title: Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts.
abstract: Actinoplanes sp. SE50/110 is the producer of the alpha-glucosidase inhibitor acarbose, which is an economically relevant and potent drug in the treatment of type-2 diabetes mellitus. In this study, we present the detection of transcription start sites on this genome by sequencing enriched 5'-ends of primary transcripts. Altogether, 1427 putative transcription start sites were initially identified. With help of the annotated genome sequence, 661 transcription start sites were found to belong to the leader region of protein-coding genes with the surprising result that roughly 20% of these genes rank among the class of leaderless transcripts. Next, conserved promoter motifs were identified for protein-coding genes with and without leader sequences. The mapped transcription start sites were finally used to improve the annotation of the Actinoplanes sp. SE50/110 genome sequence. Concerning protein-coding genes, 41 translation start sites were corrected and 9 novel protein-coding genes could be identified. In addition to this, 122 previously undetermined non-coding RNA (ncRNA) genes of Actinoplanes sp. SE50/110 were defined. Focusing on antisense transcription start sites located within coding genes or their leader sequences, it was discovered that 96 of those ncRNA genes belong to the class of antisense RNA (asRNA) genes. The remaining 26 ncRNA genes were found outside of known protein-coding genes. Four chosen examples of prominent ncRNA genes, namely the transfer messenger RNA gene ssrA, the ribonuclease P class A RNA gene rnpB, the cobalamin riboswitch RNA gene cobRS, and the selenocysteine-specific tRNA gene selC, are presented in more detail. This study demonstrates that sequencing of enriched 5'-ends of primary transcripts and the identification of transcription start sites are valuable tools for advanced genome annotation of Actinoplanes sp. SE50/110 and most probably also for other bacteria.
authors.affiliation: Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; Genome Informatics Research Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
authors.forename: Patrick
authors.initials: P
authors.lastname: Schwientek
authors.affiliation: Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Armin
authors.initials: A
authors.lastname: Neshat
authors.affiliation: Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Jörn
authors.initials: J
authors.lastname: Kalinowski
authors.affiliation: Bayer HealthCare AG, Friedrich-Ebert-Str. 475, 42117 Wuppertal, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Klein
authors.affiliation: Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Rückert
authors.affiliation: Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Susanne
authors.initials: S
authors.lastname: Schneiker-Bekel
authors.affiliation: Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Sergej
authors.initials: S
authors.lastname: Wendler
authors.affiliation: Genome Informatics Research Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Stoye
authors.affiliation: Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany. Electronic address: Puehler@CeBiTec.Uni-Bielefeld.de.
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
mesh_terms: D020909:Acarbose / Q000378:metabolism*; D016680:Genome, Bacterial; D065089:Glycoside Hydrolase Inhibitors; D008848:Micromonosporaceae / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D012333:RNA, Messenger / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000235:genetics; D043262:Ribonuclease P / Q000235:genetics; D017279:Selenocysteine / Q000235:genetics; D017423:Sequence Analysis, RNA; D014805:Vitamin B 12 / Q000235:genetics
chemical_list: D065089:Glycoside Hydrolase Inhibitors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; C430328:small protein B; D017279:Selenocysteine; D043262:Ribonuclease P; D014805:Vitamin B 12; D020909:Acarbose
keywords: Acarbose production; Actinoplanes; Genome annotation improvement; Sequencing of 5′-ends of primary transcripts; Transcriptomics