PXD017973

PXD017973 is an original dataset announced via ProteomeXchange.

Title	The expression of the acarbose biosynthetic gene cluster of Actinoplanes sp. SE50/110 is dependent on the growth phase
Description	Actinoplanes sp. SE50/110 produces the diabetes type II drug acarbose only during the growth phase and not in the stationary phase. This correlation between the course of the cell growth and the biosynthesis could be due to a decreasing expression of the acarbose biosynthesis genes until the stationary phase. Therefore, a genome wide transcriptome and proteome analysis in a high temporal resolution is well suited to study the acarbose biosynthesis and the transcriptional regulation thereof. In this study, RNA-seq data 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 the same transcription dynamics over the cultivation time. Typical indications for a metabolic switch from primary metabolism to secondary metabolism could be detected when the cells entered the stationary phase of growth. In this transition phase, a decreasing transcript abundance for all acarbose biosynthetic genes was observed, with the strongest decrease for the monocistronically transcribed genes acbA, acbB, acbD and acbE. The transcription of these genes shows the same pattern as the specific product formation rate of acarbose, indicating a correlation. However, the proteome dynamics does not follow the respective transcription for all genes. This suggests different protein stabilities of the Acb proteins, which in turn could be an indication for bottlenecks in the acarbose biosynthesis.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-08_23:49:32.250.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vera Ortseifen
SpeciesList	scientific name: Actinoplanes sp. SE50/110; NCBI TaxID: 134676;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-10 07:09:21	ID requested
⏵ 1	2021-09-08 23:49:32	announced

Droste J, Ortseifen V, Schaffert L, Persicke M, Schneiker-Bekel S, P, ü, hler A, Kalinowski J, The expression of the acarbose biosynthesis gene cluster in Actinoplanes sp. SE50/110 is dependent on the growth phase. BMC Genomics, 21(1):818(2020) [pubmed]

submitter keyword: Actinoplanes sp. SE50/110, acarbose, transcriptomics, proteomics, expression dynamics, co-regulation

Jörn Kalinowski
contact affiliation	Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
contact email	joern@cebitec.uni-bielefeld.de
lab head
Vera Ortseifen
contact affiliation	Bielefeld University / CeBiTec
contact email	vera@cebitec.uni-bielefeld.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD017973
     1. Label: PRIDE project
     2. Name: The expression of the acarbose biosynthetic gene cluster of Actinoplanes sp. SE50/110 is dependent on the growth phase