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)
JOURNAL OF BIOTECHNOLOGY 251: 112-123.

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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.
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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.
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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

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