The expression of the acarbose biosynthesis gene cluster in Actinoplanes sp. SE50/110 is dependent on the growth phase

Abstract

Background: Actinoplanes sp. SE50/110 is the natural producer of the diabetes mellitus drug acarbose, which is highly produced during the growth phase and ceases during the stationary phase. In previous works, the growth-dependency of acarbose formation was assumed to be caused by a decreasing transcription of the acarbose biosynthesis genes during transition and stationary growth phase.Results: In this study, transcriptomic data using RNA-seq and state-of-the-art proteomic data from seven time points of controlled bioreactor cultivations were used to analyze expression dynamics during growth of Actinoplanes sp. SE50/110. A hierarchical cluster analysis revealed co-regulated genes, which display similar transcription dynamics over the cultivation time. Aside from the expected metabolic switch from primary to secondary metabolism during transition phase, we observed a significantly decreasing transcript abundance of all acarbose biosynthetic genes, with the strongest decrease for the monocistronically transcribed genes acbA, acbB, acbD and acbE. Our data confirm a similar trend for acb gene transcription and acarbose formation rate.Surprisingly, the proteome dynamics does not follow the respective transcription for all acb genes. This suggests different protein stabilities or post-transcriptional regulation of the Acb proteins, which in turn could indicate bottlenecks in the acarbose biosynthesis. Furthermore, several genes are co-expressed with the acb gene cluster over the course of the cultivation, including eleven transcriptional regulators (e.g. ACSP50_0424), two sigma factors (ACSP50_0644, ACSP50_6006) and further genes, which have not previously been in focus of acarbose research in Actinoplanes sp. SE50/110.Conclusion: In conclusion, we have demonstrated, that a genome wide transcriptome and proteome analysis in a high temporal resolution is well suited to study the acarbose biosynthesis and the transcriptional and post-transcriptional regulation thereof.

A maltose-regulated large genomic region is activated by the transcriptional regulator MalT in Actinoplanes sp. SE50/110

“…A large genomic region of 51 genes (ACSP50_3900 to ACSP50_3950) was found to be transcribed coordinately during growth. For 41 of the 51 genes, a highly similar continuously increasing transcript amount over the course of the cultivation was determined by hierarchical cluster analysis (Droste et al 2020). Interestingly, we also identified this genomic region by comparative transcriptome analysis of Actinoplanes sp.…”

“…In recent studies, several co-expressed genes were identified by transcriptome and proteome analyses during growth of Actinoplanes sp. SE50/110 (Droste et al 2020). These genes might belong to the same regulons.…”

“…Therefore, binding sites for transcription factors or alternative sigma factors might be conserved upstream of the transcription start sites (TSS) of these genes. Since many genes are organized in operons, a TSS was not identified upstream of every gene (Droste et al 2020). Therefore, the transcription is initiated at the same sequence position for several genes.…”

“…Recent studies analyzed expression dynamics of all genes and operons during growth (Droste et al 2020). Many co-regulated genes were identified by hierarchical cluster analyses, such as the acb gene cluster responsible for acarbose biosynthesis.…”

“…Many co-regulated genes were identified by hierarchical cluster analyses, such as the acb gene cluster responsible for acarbose biosynthesis. A total of 71 genes were found to be transcribed coordinately, showing an increasing transcript amount during growth (Cluster 36, Droste et al 2020). Interestingly, 41 genes were found to be located in close proximity in a region comprised of 51 genes (ACSP50_3900 to ACSP50_3950).…”