Fast and reliable strain characterization of Streptomyces lividans through micro-scale cultivation.

Koepff J, Keller M, Tsolis CK, Busche T, Rückert C, Hamed MB, Anné J, Kalinowski J, Wiechert W, Economou A, Oldiges M (2017)
Biotechnol Bioeng 114(9): 2011-2022.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Koepff, J; Keller, M; Tsolis, CK; Busche, TobiasUniBi; Rückert, ChristianUniBi ; Hamed, MB; Anné, J; Kalinowski, JörnUniBi; Wiechert, W; Economou, A; Oldiges, M
Abstract / Bemerkung
Filamentous organisms of the genus Streptomyces play an important role in industrial production processes, due to their extensive secondary metabolism variability, as well as their ability to secrete efficiently large amounts of (heterologous) proteins. While genetic engineering tools are available to rapidly build up large strain libraries, the subsequent strain screening and bioprocess development still constitutes a bottleneck. This is due to the lack of reliable parallelized and accelerated cultivation techniques for morphologically challenging organisms. To address this challenge, we developed an integrated cultivation workflow for Streptomyces lividans based on a parallelized shaken 48-well microtiter-plate (MTP) cultivation device. In a first step, a feasible pre-culture method was identified and validated, revealing high comparability in subsequent main cultivations (coefficient of variation of 1.1% for in-plate replicates and 3.2% between different pre-cultures). When validating the growth performance in 1 mL MTP cultivation against an established 1000 mL lab-scale cultivation system, highly comparable cultivation patterns were found for online (pH, dissolved oxygen), as well as for offline derived parameters (glucose uptake, cell-dry-weight and pellet size). Additionally, the two cultivation regimes were compared with respect to transcriptional and protein secretion activity of Streptomyces, showing overall good comparability with minor, but well explainable discrepancies, most probably caused by different energy dissipation (shaking vs. stirring) and adaption effects due to different illumination conditions. Embedded within the presented cultivation workflow, the 1 mL MTP-based parallelized cultivation system seems to be a suitable screening tool for filamentous and industrial relevant organisms like Streptomyces. This can contribute to widen the field of application for these organisms and facilitate screening and early-stage bioprocess development.
Biotechnol Bioeng
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Koepff J, Keller M, Tsolis CK, et al. Fast and reliable strain characterization of Streptomyces lividans through micro-scale cultivation. Biotechnol Bioeng. 2017;114(9):2011-2022.
Koepff, J., Keller, M., Tsolis, C. K., Busche, T., Rückert, C., Hamed, M. B., Anné, J., et al. (2017). Fast and reliable strain characterization of Streptomyces lividans through micro-scale cultivation. Biotechnol Bioeng, 114(9), 2011-2022. doi:10.1002/bit.26321
Koepff, J, Keller, M, Tsolis, CK, Busche, Tobias, Rückert, Christian, Hamed, MB, Anné, J, et al. 2017. “Fast and reliable strain characterization of Streptomyces lividans through micro-scale cultivation.”. Biotechnol Bioeng 114 (9): 2011-2022.
Koepff, J., Keller, M., Tsolis, C. K., Busche, T., Rückert, C., Hamed, M. B., Anné, J., Kalinowski, J., Wiechert, W., Economou, A., et al. (2017). Fast and reliable strain characterization of Streptomyces lividans through micro-scale cultivation. Biotechnol Bioeng 114, 2011-2022.
Koepff, J., et al., 2017. Fast and reliable strain characterization of Streptomyces lividans through micro-scale cultivation. Biotechnol Bioeng, 114(9), p 2011-2022.
J. Koepff, et al., “Fast and reliable strain characterization of Streptomyces lividans through micro-scale cultivation.”, Biotechnol Bioeng, vol. 114, 2017, pp. 2011-2022.
Koepff, J., Keller, M., Tsolis, C.K., Busche, T., Rückert, C., Hamed, M.B., Anné, J., Kalinowski, J., Wiechert, W., Economou, A., Oldiges, M.: Fast and reliable strain characterization of Streptomyces lividans through micro-scale cultivation. Biotechnol Bioeng. 114, 2011-2022 (2017).
Koepff, J, Keller, M, Tsolis, CK, Busche, Tobias, Rückert, Christian, Hamed, MB, Anné, J, Kalinowski, Jörn, Wiechert, W, Economou, A, and Oldiges, M. “Fast and reliable strain characterization of Streptomyces lividans through micro-scale cultivation.”. Biotechnol Bioeng 114.9 (2017): 2011-2022.

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A closer look at Aspergillus: online monitoring via scattered light enables reproducible phenotyping.
Jansen RP, Beuck C, Moch M, Klein B, Küsters K, Morschett H, Wiechert W, Oldiges M., Fungal Biol Biotechnol 6(), 2019
PMID: 31396392
Morphology-driven downscaling of Streptomyces lividans to micro-cultivation.
van Dissel D, van Wezel GP., Antonie Van Leeuwenhoek 111(3), 2018
PMID: 29094245
Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans.
Koepff J, Morschett H, Busche T, Winkler A, Kalinowski J, Wiechert W, Oldiges M., Biotechnol Prog 34(1), 2018
PMID: 28960883
Microbioreactor Systems for Accelerated Bioprocess Development.
Hemmerich J, Noack S, Wiechert W, Oldiges M., Biotechnol J 13(4), 2018
PMID: 29283217
Comprehensive subcellular topologies of polypeptides in Streptomyces.
Tsolis KC, Tsare EP, Orfanoudaki G, Busche T, Kanaki K, Ramakrishnan R, Rousseau F, Schymkowitz J, Rückert C, Kalinowski J, Anné J, Karamanou S, Klapa MI, Economou A., Microb Cell Fact 17(1), 2018
PMID: 29544487
Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion.
Busche T, Tsolis KC, Koepff J, Rebets Y, Rückert C, Hamed MB, Bleidt A, Wiechert W, Lopatniuk M, Yousra A, Anné J, Karamanou S, Oldiges M, Kalinowski J, Luzhetskyy A, Economou A., Front Microbiol 9(), 2018
PMID: 29915569
Germination and Growth Analysis of Streptomyces lividans at the Single-Cell Level Under Varying Medium Compositions.
Koepff J, Sachs CC, Wiechert W, Kohlheyer D, Nöh K, Oldiges M, Grünberger A., Front Microbiol 9(), 2018
PMID: 30524383
Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions.
Rebets Y, Tsolis KC, Guðmundsdóttir EE, Koepff J, Wawiernia B, Busche T, Bleidt A, Horbal L, Myronovskyi M, Ahmed Y, Wiechert W, Rückert C, Hamed MB, Bilyk B, Anné J, Friðjónsson Ó, Kalinowski J, Oldiges M, Economou A, Luzhetskyy A., Front Microbiol 9(), 2018
PMID: 30619125
Automated growth rate determination in high-throughput microbioreactor systems.
Hemmerich J, Wiechert W, Oldiges M., BMC Res Notes 10(1), 2017
PMID: 29178966
Large-scale production of a thermostable Rhodothermus marinus cellulase by heterologous secretion from Streptomyces lividans.
Hamed MB, Karamanou S, Ólafsdottir S, Basílio JSM, Simoens K, Tsolis KC, Van Mellaert L, Guðmundsdóttir EE, Hreggvidsson GO, Anné J, Bernaerts K, Fridjonsson OH, Economou A., Microb Cell Fact 16(1), 2017
PMID: 29274637

55 References

Daten bereitgestellt von Europe PubMed Central.

Protein secretion biotechnology in Gram-positive bacteria with special emphasis on Streptomyces lividans.
Anne J, Vrancken K, Van Mellaert L, Van Impe J, Bernaerts K., Biochim. Biophys. Acta 1843(8), 2014
PMID: 24412306
Characterization of microtiterplates with integrated optical sensors for oxygen and pH, and their applications to enzyme activity screening, respirometry, and toxicological assays
Arain, Sens Actuators B Chem 113(2), 2006

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
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).
Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA., Nature 417(6885), 2002
PMID: 12000953
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
Use of an inducible promoter for antibiotic production in a heterologous host.
Dangel V, Westrich L, Smith MC, Heide L, Gust B., Appl. Microbiol. Biotechnol. 87(1), 2010
PMID: 20127238
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
Methods for intense aeration, growth, storage, and replication of bacterial strains in microtiter plates.
Duetz WA, Ruedi L, Hermann R, O'Connor K, Buchs J, Witholt B., Appl. Environ. Microbiol. 66(6), 2000
PMID: 10831450
Mixing at the microscale: Power input in shaken microtiter plates.
Durauer A, Hobiger S, Walther C, Jungbauer A., Biotechnol J 11(12), 2016
PMID: 27367149

Evans, 1996
Streptomyces morphogenetics: dissecting differentiation in a filamentous bacterium.
Flardh K, Buttner MJ., Nat. Rev. Microbiol. 7(1), 2009
PMID: 19079351
Framework for Kriging-based iterative experimental analysis and design: Optimization of secretory protein production in Corynebacterium glutamicum
Freier, Eng Live Sci 16(6), 2016
The baffled microtiter plate: increased oxygen transfer and improved online monitoring in small scale fermentations.
Funke M, Diederichs S, Kensy F, Muller C, Buchs J., Biotechnol. Bioeng. 103(6), 2009
PMID: 19449392
Production and secretion of proteins by streptomycetes.
Gilbert M, Morosoli R, Shareck F, Kluepfel D., Crit. Rev. Biotechnol. 15(1), 1995
PMID: 7736599
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
Dispersed growth of Streptomyces in liquid culture
Hobbs, Appl Microbiol Biotechnol 31(3), 1989

Hopwood, 2007
Novel and tightly regulated resorcinol and cumate-inducible expression systems for Streptomyces and other actinobacteria.
Horbal L, Fedorenko V, Luzhetskyy A., Appl. Microbiol. Biotechnol. 98(20), 2014
PMID: 25012786
New milliliter-scale stirred tank bioreactors for the cultivation of mycelium forming microorganisms.
Hortsch R, Stratmann A, Weuster-Botz D., Biotechnol. Bioeng. 106(3), 2010
PMID: 20198653
Milliliter-scale stirred tank reactors for the cultivation of microorganisms.
Hortsch R, Weuster-Botz D., Adv. Appl. Microbiol. 73(), 2010
PMID: 20800759
Robo-Lector - a novel platform for automated high-throughput cultivations in microtiter plates with high information content.
Huber R, Ritter D, Hering T, Hillmer AK, Kensy F, Muller C, Wang L, Buchs J., Microb. Cell Fact. 8(), 2009
PMID: 19646274

Kieser, 2000

Korn, 1978

Krull, 2015
Pitfalls in optical on-line monitoring for high-throughput screening of microbial systems.
Kunze M, Roth S, Gartz E, Buchs J., Microb. Cell Fact. 13(), 2014
PMID: 24725602
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
Microscale and miniscale fermentation and screening.
Lattermann C, Buchs J., Curr. Opin. Biotechnol. 35(), 2014
PMID: 25544012
Effect of volumetric power input by aeration and agitation on pellet morphology and product formation of Aspergillus niger
Lin, Biochem Eng J 49(2), 2010
The development and application of high throughput cultivation technology in bioprocess development.
Long Q, Liu X, Yang Y, Li L, Harvey L, McNeil B, Bai Z., J. Biotechnol. 192 Pt B(), 2014
PMID: 24698846
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Love MI, Huber W, Anders S., Genome Biol. 15(12), 2014
PMID: 25516281
The role of volumetric power input in the growth, morphology, and production of a recombinant glycoprotein by Streptomyces lividans in shake flasks
Marín-Palacio, Biochem Eng J 90(), 2014

Méchin, 2007
Consistent development of bioprocesses from microliter cultures to the industrial scale
Neubauer, Eng Life Sci 13(3), 2013
Development of a minimal defined medium for recombinant human interleukin-3 production by Streptomyces lividans 66.
Nowruzi K, Elkamel A, Scharer JM, Cossar D, Moo-Young M., Biotechnol. Bioeng. 99(1), 2008
PMID: 17615562
Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Subsequent Fermentation for Optimized Production.
Rebets Y, Kormanec J, Luzhetskyy A, Bernaerts K, Anne J., Methods Mol. Biol. 1539(), 2017
PMID: 27900687
An automated workflow for enhancing microbial bioprocess optimization on a novel microbioreactor platform.
Rohe P, Venkanna D, Kleine B, Freudl R, Oldiges M., Microb. Cell Fact. 11(), 2012
PMID: 23113930
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
New approaches to achieve high level enzyme production in Streptomyces lividans.
Sevillano L, Vijgenboom E, van Wezel GP, Diaz M, Santamaria RI., Microb. Cell Fact. 15(), 2016
PMID: 26846788
Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels.
Shevchenko A, Wilm M, Vorm O, Mann M., Anal. Chem. 68(5), 1996
PMID: 8779443
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
Robust, small-scale cultivation platform for Streptomyces coelicolor.
Sohoni SV, Bapat PM, Lantz AE., Microb. Cell Fact. 11(), 2012
PMID: 22252012
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
Morphogenesis of Streptomyces in submerged cultures.
van Dissel D, Claessen D, van Wezel GP., Adv. Appl. Microbiol. 89(), 2014
PMID: 25131399
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
Prediction of inclusion body solubilization from shaken to stirred reactors.
Walther C, Mayer S, Trefilov A, Sekot G, Hahn R, Jungbauer A, Durauer A., Biotechnol. Bioeng. 111(1), 2013
PMID: 23860724

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