Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans

Koepff J, Morschett H, Busche T, Winkler A, Kalinowski J, Wiechert W, Oldiges M (2018)
BIOTECHNOLOGY PROGRESS 34(1): 287-292.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Koepff, Joachim; Morschett, Holger; Busche, TobiasUniBi; Winkler, AnikaUniBi; Kalinowski, JörnUniBi; Wiechert, Wolfgang; Oldiges, Marco
Abstract / Bemerkung
Recently, a comprehensive screening workflow for the filamentous bacterium Streptomyces lividans, a highly performant source for pharmaceutically active agents was introduced. This framework used parallelized cultivation in microtiter plates to efficiently accelerate early upstream process development. Focusing on growth performance, cultivation was successfully scaled-up to 1 L stirred tank reactors. However, metabolic adaptation was observed on the transcriptomic level as among others, several genes incorporated in light response were upregulated during bioreactor cultivation. Despite it was assumed that this was attributed to the fact that reactor cultivations were performed in glass vessels exposed to daylight and artificial room light, this setup did not allow distinguishing exclusively between light and other effects. Upon that, the present study directly investigates the influence of light by defined illumination of microtiter plate cultures. Almost identical growth performance was observed for cultures grown in the dark or with illumination. Transcriptomics revealed the upregulation of seven genes of which 6 have previously been described to be relevant for carotenoid synthesis and its regulation. These pigments are effective quenchers of reactive oxygen species. The seventh transcript coded for a photo-lyase incorporated in UV-damage repair of DNA further confirming induced light response. However, this was fully compensated by metabolic adaptation on the transcriptomic level and overall process performance was maintained. Consequently, environmental conditions need extremely careful control and evaluation during in-depth omics analysis of bioprocesses. Otherwise metabolic adaptation induced by such issues can easily be misinterpreted, especially during studies addressing cultivation system comparisons. (c) 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:287-292, 2018
Stichworte
Streptomyces lividans; miniaturized cultivation; parallelized; cultivation; light response; transcriptomic analysis; high-throughput; bioprocess development; Photo BioLector
Erscheinungsjahr
2018
Zeitschriftentitel
BIOTECHNOLOGY PROGRESS
Band
34
Ausgabe
1
Seite(n)
287-292
ISSN
8756-7938
eISSN
1520-6033
Page URI
https://pub.uni-bielefeld.de/record/2918672

Zitieren

Koepff J, Morschett H, Busche T, et al. Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans. BIOTECHNOLOGY PROGRESS. 2018;34(1):287-292.
Koepff, J., Morschett, H., Busche, T., Winkler, A., Kalinowski, J., Wiechert, W., & Oldiges, M. (2018). Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans. BIOTECHNOLOGY PROGRESS, 34(1), 287-292. doi:10.1002/btpr.2566
Koepff, Joachim, Morschett, Holger, Busche, Tobias, Winkler, Anika, Kalinowski, Jörn, Wiechert, Wolfgang, and Oldiges, Marco. 2018. “Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans”. BIOTECHNOLOGY PROGRESS 34 (1): 287-292.
Koepff, J., Morschett, H., Busche, T., Winkler, A., Kalinowski, J., Wiechert, W., and Oldiges, M. (2018). Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans. BIOTECHNOLOGY PROGRESS 34, 287-292.
Koepff, J., et al., 2018. Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans. BIOTECHNOLOGY PROGRESS, 34(1), p 287-292.
J. Koepff, et al., “Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans”, BIOTECHNOLOGY PROGRESS, vol. 34, 2018, pp. 287-292.
Koepff, J., Morschett, H., Busche, T., Winkler, A., Kalinowski, J., Wiechert, W., Oldiges, M.: Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans. BIOTECHNOLOGY PROGRESS. 34, 287-292 (2018).
Koepff, Joachim, Morschett, Holger, Busche, Tobias, Winkler, Anika, Kalinowski, Jörn, Wiechert, Wolfgang, and Oldiges, Marco. “Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans”. BIOTECHNOLOGY PROGRESS 34.1 (2018): 287-292.

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28 References

Daten bereitgestellt von Europe PubMed Central.

Taxonomy, Physiology, and Natural Products of Actinobacteria.
Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk HP, Clement C, Ouhdouch Y, van Wezel GP., Microbiol. Mol. Biol. Rev. 80(1), 2015
PMID: 26609051

Hopwood, 2007
Production and secretion of proteins by streptomycetes.
Gilbert M, Morosoli R, Shareck F, Kluepfel D., Crit. Rev. Biotechnol. 15(1), 1995
PMID: 7736599
Unlocking Streptomyces spp. for use as sustainable industrial production platforms by morphological engineering.
van Wezel GP, Krabben P, Traag BA, Keijser BJ, Kerste R, Vijgenboom E, Heijnen JJ, Kraal B., Appl. Environ. Microbiol. 72(8), 2006
PMID: 16885277
Robust, small-scale cultivation platform for Streptomyces coelicolor.
Sohoni SV, Bapat PM, Lantz AE., Microb. Cell Fact. 11(), 2012
PMID: 22252012
Morphogenesis of Streptomyces in submerged cultures.
van Dissel D, Claessen D, van Wezel GP., Adv. Appl. Microbiol. 89(), 2014
PMID: 25131399
Reducing the variability of antibiotic production in Streptomyces by cultivation in 24-square deepwell plates.
Siebenberg S, Bapat PM, Lantz AE, Gust B, Heide L., J. Biosci. Bioeng. 109(3), 2009
PMID: 20159569
Fast and reliable strain characterization of Streptomyces lividans through micro-scale cultivation.
Koepff J, Keller M, Tsolis KC, Busche T, Ruckert C, Hamed MB, Anne J, Kalinowski J, Wiechert W, Economou A, Oldiges M., Biotechnol. Bioeng. 114(9), 2017
PMID: 28436005
Design and validation of a parallelized micro-photobioreactor enabling phototrophic bioprocess development at elevated throughput.
Morschett H, Schiprowski D, Muller C, Mertens K, Felden P, Meyer J, Wiechert W, Oldiges M., Biotechnol. Bioeng. 114(1), 2016
PMID: 27424867
The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island.
Cruz-Morales P, Vijgenboom E, Iruegas-Bocardo F, Girard G, Yanez-Guerra LA, Ramos-Aboites HE, Pernodet JL, Anne J, van Wezel GP, Barona-Gomez F., Genome Biol Evol 5(6), 2013
PMID: 23709624
Amino acid uptake profiling of wild type and recombinant Streptomyces lividans TK24 batch fermentations.
D'Huys PJ, Lule I, Van Hove S, Vercammen D, Wouters C, Bernaerts K, Anne J, Van Impe JF., J. Biotechnol. 152(4), 2010
PMID: 20797416
Bioprocess automation on a Mini Pilot Plant enables fast quantitative microbial phenotyping.
Unthan S, Radek A, Wiechert W, Oldiges M, Noack S., Microb. Cell Fact. 14(), 2015
PMID: 25888907
Complete genome sequence of Streptomyces lividans TK24.
Ruckert C, Albersmeier A, Busche T, Jaenicke S, Winkler A, Friðjonsson OH, Hreggviðsson GO, Lambert C, Badcock D, Bernaerts K, Anne J, Economou A, Kalinowski J., J. Biotechnol. 199(), 2015
PMID: 25680930
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
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
Differential expression analysis for sequence count data.
Anders S, Huber W., Genome Biol. 11(10), 2010
PMID: 20979621
Carotenoid-related alteration of cell membrane fluidity impacts Staphylococcus aureus susceptibility to host defense peptides.
Mishra NN, Liu GY, Yeaman MR, Nast CC, Proctor RA, McKinnell J, Bayer AS., Antimicrob. Agents Chemother. 55(2), 2010
PMID: 21115796
The singlet oxygen and carotenoid interaction.
Conn PF, Schalch W, Truscott TG., J. Photochem. Photobiol. B, Biol. 11(1), 1991
PMID: 1791493
Chemical quenching of singlet oxygen by carotenoids in plants.
Ramel F, Birtic S, Cuine S, Triantaphylides C, Ravanat JL, Havaux M., Plant Physiol. 158(3), 2012
PMID: 22234998
Lycopene as the most efficient biological carotenoid singlet oxygen quencher.
Di Mascio P, Kaiser S, Sies H., Arch. Biochem. Biophys. 274(2), 1989
PMID: 2802626
Involvement of CarA/LitR and CRP/FNR family transcriptional regulators in light-induced carotenoid production in Thermus thermophilus.
Takano H, Kondo M, Usui N, Usui T, Ohzeki H, Yamazaki R, Washioka M, Nakamura A, Hoshino T, Hakamata W, Beppu T, Ueda K., J. Bacteriol. 193(10), 2011
PMID: 21421762

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