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, Anne J, et al. (2018)

Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Busche, TobiasUniBi; Tsolis, Konstantinos C.; Koepff, Joachim; Rebets, Yuriy; Rückert, ChristianUniBi ; Hamed, Mohamed B.; Bleidt, Arne; Wiechert, Wolfgang; Lopatniuk, Mariia; Yousra, Ahmed; Anne, Jozef; Karamanou, Spyridoula
Abstract / Bemerkung
Gram-positive Streptomyces bacteria are profuse secretors of polypeptides using complex, yet unknown mechanisms. Many of their secretory proteins are proteases that play important roles in the acquisition of amino acids from the environment. Other proteases regulate cellular proteostasis. To begin dissecting the possible role of proteases in Streptomyces secretion, we applied a multi-omics approach. We probed the role of the 190 proteases of Streptomyces lividans strain TK24 in protein secretion in defined media at different stages of growth. Transcriptomics analysis revealed transcripts for 93% of these proteases and identified that 41 of them showed high abundance. Proteomics analysis identified 57 membrane-embedded or secreted proteases with variations in their abundance. We focused on 17 of these proteases and putative inhibitors and generated strains deleted of their genes. These were characterized in terms of their fitness, transcriptome and secretome changes. In addition, we performed a targeted analysis in deletion strains that also carried a secretion competent mRFP. One strain, carrying a deletion of the gene for the regulatory protease FtsH, showed significant global changes in overall transcription and enhanced secretome and secreted mRFP levels. These data provide a first multi-omics effort to characterize the complex regulatory mechanisms of protein secretion in Streptomyces lividans and lay the foundations for future rational manipulation of this process.
proteases; expression levels; mRFP; multi-omits; Streptomyces lividans; protein secretion; RNAseq; FtsH
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Busche T, Tsolis KC, Koepff J, et al. Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion. FRONTIERS IN MICROBIOLOGY. 2018;9: 12.
Busche, T., Tsolis, K. C., Koepff, J., Rebets, Y., Rückert, C., Hamed, M. B., Bleidt, A., et al. (2018). Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion. FRONTIERS IN MICROBIOLOGY, 9, 12. doi:10.3389/fmicb.2018.01174
Busche, T., Tsolis, K. C., Koepff, J., Rebets, Y., Rückert, C., Hamed, M. B., Bleidt, A., Wiechert, W., Lopatniuk, M., Yousra, A., et al. (2018). Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion. FRONTIERS IN MICROBIOLOGY 9:12.
Busche, T., et al., 2018. Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion. FRONTIERS IN MICROBIOLOGY, 9: 12.
T. Busche, et al., “Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion”, FRONTIERS IN MICROBIOLOGY, vol. 9, 2018, : 12.
Busche, T., Tsolis, K.C., Koepff, J., Rebets, Y., Rückert, C., Hamed, M.B., Bleidt, A., Wiechert, W., Lopatniuk, M., Yousra, A., Anne, J., Karamanou, S., Oldiges, M., Kalinowski, J., Luzhetskyy, A., Economou, A.: Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion. FRONTIERS IN MICROBIOLOGY. 9, : 12 (2018).
Busche, Tobias, Tsolis, Konstantinos C., Koepff, Joachim, Rebets, Yuriy, Rückert, Christian, Hamed, Mohamed B., Bleidt, Arne, Wiechert, Wolfgang, Lopatniuk, Mariia, Yousra, Ahmed, Anne, Jozef, Karamanou, Spyridoula, Oldiges, Marco, Kalinowski, Jörn, Luzhetskyy, Andriy, and Economou, Anastassios. “Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion”. FRONTIERS IN MICROBIOLOGY 9 (2018): 12.

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The metabolic switch can be activated in a recombinant strain of Streptomyces lividans by a low oxygen transfer rate in shake flasks.
Gamboa-Suasnavart RA, Valdez-Cruz NA, Gaytan-Ortega G, Reynoso-Cereceda GI, Cabrera-Santos D, López-Griego L, Klöckner W, Büchs J, Trujillo-Roldán MA., Microb Cell Fact 17(1), 2018
PMID: 30486842
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

52 References

Daten bereitgestellt von Europe PubMed Central.

Protein Secretion in Gram-Positive Bacteria: From Multiple Pathways to Biotechnology.
Anne J, Economou A, Bernaerts K., Curr. Top. Microbiol. Immunol. 404(), 2017
PMID: 27885530
Recombinant protein production and streptomycetes.
Anne J, Maldonado B, Van Impe J, Van Mellaert L, Bernaerts K., J. Biotechnol. 158(4), 2011
PMID: 21777629
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
Controlling the false discovery rate - a practical and powerful approach to multiple testing.
Benjamini Y., Hochberg Y.., 1995
The molecular architecture of the metalloprotease FtsH.
Bieniossek C, Schalch T, Bumann M, Meister M, Meier R, Baumann U., Proc. Natl. Acad. Sci. U.S.A. 103(9), 2006
PMID: 16484367
When, how and why? Regulated proteolysis by the essential FtsH protease in Escherichia coli.
Bittner LM, Arends J, Narberhaus F., Biol. Chem. 398(5-6), 2017
PMID: 28085670
Cloning and characterisation of an aminopeptidase P-encoding gene from Streptomyces lividans.
Butler MJ, Bergeron A, Soostmeyer G, Zimny T, Malek LT., Gene 123(1), 1993
PMID: 8422994
Recent advances in understanding Streptomyces.
Chater KF., F1000Res 5(), 2016
PMID: 27990276
Membrane proteases in the bacterial protein secretion and quality control pathway.
Dalbey RE, Wang P, van Dijl JM., Microbiol. Mol. Biol. Rev. 76(2), 2012
PMID: 22688815
Production and secretion of proteins by streptomycetes.
Gilbert M, Morosoli R, Shareck F, Kluepfel D., Crit. Rev. Biotechnol. 15(1), 1995
PMID: 7736599
Proteases and their targets in Escherichia coli.
Gottesman S., Annu. Rev. Genet. 30(), 1996
PMID: 8982462
Regulated proteolysis in Gram-negative bacteria--how and when?
Gur E, Biran D, Ron EZ., Nat. Rev. Microbiol. 9(12), 2011
PMID: 22020261
Lambda red-mediated genetic manipulation of antibiotic-producing Streptomyces.
Gust B, Chandra G, Jakimowicz D, Yuqing T, Bruton CJ, Chater KF., Adv. Appl. Microbiol. 54(), 2004
PMID: 15251278
Large-scale production of a thermostable Rhodothermus marinus cellulase by heterologous secretion from Streptomyces lividans.
Hamed MB, Karamanou S, Olafsdottir S, Basilio JSM, Simoens K, Tsolis KC, Van Mellaert L, Guðmundsdottir EE, Hreggvidsson GO, Anne J, Bernaerts K, Fridjonsson OH, Economou A., Microb. Cell Fact. 16(1), 2017
PMID: 29274637
Site-specific recombination strategies for engineering actinomycete genomes.
Herrmann S, Siegl T, Luzhetska M, Petzke L, Jilg C, Welle E, Erb A, Leadlay PF, Bechthold A, Luzhetskyy A., Appl. Environ. Microbiol. 78(6), 2012
PMID: 22247163
ReadXplorer 2-detailed read mapping analysis and visualization from one single source.
Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A., Bioinformatics 32(24), 2016
PMID: 27540267
Fluorescence thiol modification assay: oxidatively modified proteins in Bacillus subtilis.
Hochgrafe F, Mostertz J, Albrecht D, Hecker M., Mol. Microbiol. 58(2), 2005
PMID: 16194229

Hopwood D.., 2007

Kieser T., Bibb M., Buttner M., Chater K., Hopwood D.., 2000
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
Extracytoplasmic proteases determining the cleavage and release of secreted proteins, lipoproteins, and membrane proteins in Bacillus subtilis.
Krishnappa L, Dreisbach A, Otto A, Goosens VJ, Cranenburgh RM, Harwood CR, Becher D, van Dijl JM., J. Proteome Res. 12(9), 2013
PMID: 23937099
Degradation of extracytoplasmic catalysts for protein folding in Bacillus subtilis.
Krishnappa L, Monteferrante CG, Neef J, Dreisbach A, van Dijl JM., Appl. Environ. Microbiol. 80(4), 2013
PMID: 24362423
Structure and function of the bacterial AAA protease FtsH.
Langklotz S, Baumann U, Narberhaus F., Biochim. Biophys. Acta 1823(1), 2011
PMID: 21925212
A proteomic study of Corynebacterium glutamicum AAA+ protease FtsH.
Ludke A, Kramer R, Burkovski A, Schluesener D, Poetsch A., BMC Microbiol. 7(), 2007
PMID: 17254330
Iterative marker excision system.
Myronovskyi M, Rosenkranzer B, Luzhetskyy A., Appl. Microbiol. Biotechnol. 98(10), 2014
PMID: 24473925
Intramembrane protease RasP boosts protein production in Bacillus.
Neef J, Bongiorni C, Goosens VJ, Schmidt B, van Dijl JM., Microb. Cell Fact. 16(1), 2017
PMID: 28376795
Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins.
Pohl S, Bhavsar G, Hulme J, Bloor AE, Misirli G, Leckenby MW, Radford DS, Smith W, Wipat A, Williamson ED, Harwood CR, Cranenburgh RM., Proteomics 13(22), 2013
PMID: 24115457
Protein secretion biotechnology using Streptomyces lividans: large-scale production of functional trimeric tumor necrosis factor alpha.
Pozidis C, Lammertyn E, Politou AS, Anne J, Tsiftsoglou AS, Sianidis G, Economou A., Biotechnol. Bioeng. 72(6), 2001
PMID: 11460252
“An introduction to actinobacteria,” in
Ranjani A., Dhanasekaran D., Gopinath P.., 2016
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
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
Global quantification of mammalian gene expression control.
Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M., Nature 473(7347), 2011
PMID: 21593866
Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels.
Shevchenko A, Wilm M, Vorm O, Mann M., Anal. Chem. 68(5), 1996
PMID: 8779443
Functional large-scale production of a novel Jonesia sp. xyloglucanase by heterologous secretion from Streptomyces lividans.
Sianidis G, Pozidis C, Becker F, Vrancken K, Sjoeholm C, Karamanou S, Takamiya-Wik M, van Mellaert L, Schaefer T, Anne J, Economou A., J. Biotechnol. 121(4), 2005
PMID: 16168511
Use of red autofluorescence for monitoring prodiginine biosynthesis.
Tenconi E, Guichard P, Motte P, Matagne A, Rigali S., J. Microbiol. Methods 93(2), 2013
PMID: 23517679
Quantitative Proteomics of the E. coli Membranome.
Tsolis KC, Economou A., Meth. Enzymol. 586(), 2016
PMID: 28137561
Comprehensive subcellular topologies of polypeptides in Streptomyces.
Tsolis K., Tsare E., Orfanoudaki G., Busche T., Kanaki K., Ramakrishnan R.., 2018
Aspergillus as a host for heterologous protein production: the problem of proteases.
van den Hombergh JP, van de Vondervoort PJ, Fraissinet-Tachet L, Visser J., Trends Biotechnol. 15(7), 1997
PMID: 9237405
2016 update of the PRIDE database and its related tools.
Vizcaino JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H., Nucleic Acids Res. 44(D1), 2015
PMID: 26527722
The role of electrostatics in colicin nuclease domain translocation into bacterial cells.
Walker D, Mosbahi K, Vankemmelbeke M, James R, Kleanthous C., J. Biol. Chem. 282(43), 2007
PMID: 17720814


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