Parallelised online biomass monitoring in shake flasks enables efficient strain and carbon source dependent growth characterisation of Saccharomyces cerevisiae

Microbial Cell Factories

Volumn 15, Issue 1, 2016, Pages

  Bruder, Stefan ^a   Reifenrath, Mara ^a   Thomik, Thomas ^a   Boles, Eckhard ^a   Herzog, Konrad ^b  

^a GOETHE UNIVERSITY   (Germany)

^b Aquila Biolabs GmbH   (Germany)

Author keywords

Backscattering; Biomass monitoring; Bioprocess automation; Diauxic effects; Metabolic shift; Online monitoring; Parallelisation; S. cerevisiae; Shake flask

Indexed keywords

ARTICLE; BIOMASS; CARBON SOURCE; CONTROLLED STUDY; CULTURE MEDIUM; FERMENTATION; FUNGAL STRAIN; FUNGUS CULTURE; FUNGUS GROWTH; GROWTH RATE; LIGHT INTENSITY; LIGHT SCATTERING; NONHUMAN; ONLINE MONITORING; SACCHAROMYCES CEREVISIAE; SHAKE FLASK CULTURE; AUTOMATION; BATCH CELL CULTURE; BIOREACTOR; EVALUATION STUDY; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIOLOGY; PROCEDURES;

ALCOHOL; CARBON; GLUCOSE; OXYGEN;

AUTOMATION; BATCH CELL CULTURE TECHNIQUES; BIOMASS; BIOREACTORS; CARBON; ETHANOL; FERMENTATION; GLUCOSE; OXYGEN; SACCHAROMYCES CEREVISIAE;

EID: 84979236393     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-016-0526-3     Document Type: Article

References (54)

1. Chao R, Yuan Y, Zhao H. Recent advances in DNA assembly technologies. FEMS Yeast Res. 2014. doi: 10.1111/1567-1364.12171.
2. David F, Siewers V. Advances in yeast genome engineering. FEMS Yeast Res. 2014. doi: 10.1111/1567-1364.12200.
3. Büchs J. Introduction to advantages and problems of shaken cultures. Biochem Eng J. 2001;7:91-8. doi: 10.1016/S1369-703X(00)00106-6.
4. Klöckner W, Büchs J. Advances in shaking technologies. Trends Biotechnol. 2012;30:307-14. doi: 10.1016/j.tibtech.2012.03.001.
5. 2 in shake-flasks. Biotechnol Lett. 2003;25:377-80. doi: 10.1023/A:1022402212537.
6. Anderlei T, Büchs J. Device for sterile online measurement of the oxygen transfer rate in shaking flasks. Biochem Eng J. 2001;7:157-62. doi: 10.1016/S1369-703X(00)00116-9.
7. Schneider K, Schütz V, John GT, Heinzle E. Optical device for parallel online measurement of dissolved oxygen and pH in shake flask cultures. Bioprocess Biosyst Eng. 2010;33:541-7. doi: 10.1007/s00449-009-0367-0.
8. Schmidt-Hager J, Ude C, Findeis M, John GT, Scheper T, Beutel S. Noninvasive online biomass detector system for cultivation in shake flasks. Eng Life Sci. 2014;14:467-76. doi: 10.1002/elsc.201400026.
9. Samorski M, Müller-Newen G, Büchs J. Quasi-continuous combined scattered light and fluorescence measurements: a novel measurement technique for shaken microtiter plates. Biotechnol Bioeng. 2005;92:61-8. doi: 10.1002/bit.20573.
10. Kensy F, Zang E, Faulhammer C, Tan R, Büchs J. Validation of a high-throughput fermentation system based on online monitoring of biomass and fluorescence in continuously shaken microtiter plates. Microb Cell Fact. 2009;8:31. doi: 10.1186/1475-2859-8-31.
11. Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast. 1998;14:115-32. doi: 10.1002/(SICI)1097-0061(19980130)14:2<115:AID-YEA204>3.0.CO;2-2.
12. Winzeler EA. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 1999;285:901-6. doi: 10.1126/science.285.5429.901.
13. Winston F, Dollard C, Ricupero-Hovasse SL. Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast. 1995;11:53-5. doi: 10.1002/yea.320110107.
14. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, et al. Life with 6000 genes. Science. 1996;274:546-67. doi: 10.1126/science.274.5287.546.
15. Ralser M, Kuhl H, Ralser M, Werber M, Lehrach H, Breitenbach M, Timmermann B. The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt. Open Biol. 2012;2:120093. doi: 10.1098/rsob.120093.
16. Mortimer RK, Johnston JR. Genealogy of principal strains of the yeast genetic stock center. Genetics. 1986;113:35-43.
17. Liu H, Styles CA, Fink GR. Saccharomyces cerevisiae S288c has a mutation in Flo8, a gene required for filamentous growth. Genetics. 1996;144:967-78.
18. Dimitrov LN, Brem RB, Kruglyak L, Gottschling DE. Polymorphisms in multiple genes contribute to the spontaneous mitochondrial genome instability of Saccharomyces cerevisiae S288C strains. Genetics. 2009;183:365-83. doi: 10.1534/genetics.109.104497.
19. Rogowska-Wrzesinska A, Larsen PM, Blomberg A, Görg A, Roepstorff P, Norbeck J, Fey SJ. Comparison of the proteomes of three yeast wild type strains: CEN.PK2, FY1679 and W303. Comp Funct Genom. 2001;2:207-25. doi: 10.1002/cfg.94.
20. Winzeler EA, Castillo-Davis CI, Oshiro G, Liang D, Richards DR, Zhou Y, Hartl DL. Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays. Genetics. 2003;163:79-89.
21. Petrezselyova S, Zahradka J, Sychrova H. Saccharomyces cerevisiae BY4741 and W303-1A laboratory strains differ in salt tolerance. Fungal Biol. 2010;114:144-50.
22. Zadrag-Tecza R, Kwolek-Mirek M, Bartosz G, Bilinski T. Cell volume as a factor limiting the replicative lifespan of the yeast Saccharomyces cerevisiae. Biogerontology. 2009;10:481-8. doi: 10.1007/s10522-008-9192-0.
23. Kokina A, Kibilds J, Liepins J. Adenine auxotrophy-be aware: some effects of adenine auxotrophy in Saccharomyces cerevisiae strain W303-1A. FEMS Yeast Res. 2014;14:697-707. doi: 10.1111/1567-1364.12154.
24. Veal EA, Ross SJ, Malakasi P, Peacock E, Morgan BA. Ybp1 is required for the hydrogen peroxide-induced oxidation of the Yap1 transcription factor. J Biol Chem. 2003;278:30896-904. doi: 10.1074/jbc.M303542200.
25. Voth WP, Olsen AE, Sbia M, Freedman KH, Stillman DJ. ACE2, CBK1, and BUD4 in budding and cell separation. Eukaryot Cell. 2005;4:1018-28. doi: 10.1128/EC.4.6.1018-1028.2005.
26. Sharma KG, Kaur R, Bachhawat AK. The glutathione-mediated detoxification pathway in yeast: an analysis using the red pigment that accumulates in certain adenine biosynthetic mutants of yeasts reveals the involvement of novel genes. Arch Microbiol. 2003;180:108-17. doi: 10.1007/s00203-003-0566-z.
27. Zimmermann FK. Procedures used in the induction of mitotic recombination and mutation in the yeast Saccharomyces cerevisiae. Mutat Res. 1975;31:71-86.
28. Weng YS, Nickoloff JA. Nonselective URA3 colony-color assay in yeast ade1 or ade2 mutants. Biotechniques. 1997;23:237-41.
29. Entian K, Kötter P. 23 yeast mutant and plasmid collections. In: Tuite MF, editor. Yeast gene analysis: yeast gene analysis. 1st ed. Amsterdam: Elsevier textbooks; 1998. p. 431-49. doi: 10.1016/S0580-9517(08)70344-1.
30. Entian K, Kötter P. 25 yeast genetic strain and plasmid collections. In: Yeast gene analysis. 2nd ed. Amsterdam: Elsevier; 2007. p. 629-66. doi: 10.1016/S0580-9517(06)36025-4.
31. Daran-Lapujade P, Daran J, Luttik MAH, Almering MJH, Pronk JT, Kotter P. An atypical PMR2 locus is responsible for hypersensitivity to sodium and lithium cations in the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D. FEMS Yeast Res. 2009;9:789-92. doi: 10.1111/j.1567-1364.2009.00530.x.
32. Vanhalewyn M, Dumortier F, Debast G, Colombo S, Ma P, Winderickx J, et al. A mutation in Saccharomyces cerevisiae adenylate cyclase, Cyr1K1876M, specifically affects glucose- and acidification-induced cAMP signalling and not the basal cAMP level. Mol Microbiol. 1999;33:363-76.
33. Dumortier F, Vanhalewyn M, Debast G, Colombo S, Ma P, Winderickx J, et al. A specific mutation in Saccharomyces cerevisiae adenylate cyclase, Cyr1K1876 M, eliminates glucose- and acidification-induced cAMP signalling and delays glucose-induced loss of stress resistance. Int J Food Microbiol. 2000;55:103-7. doi: 10.1016/S0168-1605(00)00184-7.
34. Daran-Lapujade P, Daran JM, Kotter P, Petit T, Piper MDW, Pronk JT. Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays. FEMS Yeast Res. 2003;4:259-69.
35. Schacherer J, Ruderfer DM, Gresham D, Dolinski K, Botstein D, Kruglyak L. Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS One. 2007;2:e322. doi: 10.1371/journal.pone.0000322.
36. Otero JM, Vongsangnak W, Asadollahi MA, Olivares-Hernandes R, Maury J, Farinelli L, et al. Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications. BMC Genom. 2010;11:723. doi: 10.1186/1471-2164-11-723.
37. Nijkamp JF, van den Broek M, Datema E, de Kok S, Bosman L, Luttik MA, et al. De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. Microb Cell Fact. 2012;11:36. doi: 10.1186/1475-2859-11-36.
38. Demeke MM, Dietz H, Li Y, Foulquié-Moreno MR, Mutturi S, Deprez S, et al. Development of a d-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering. Biotechnol Biofuels. 2013;6:89. doi: 10.1186/1754-6834-6-89.
39. Weber C, Farwick A, Benisch F, Brat D, Dietz H, Subtil T, Boles E. Trends and challenges in the microbial production of lignocellulosic bioalcohol fuels. Appl Microbiol Biotechnol. 2010;87:1303-15. doi: 10.1007/s00253-010-2707-z.
40. Wallace-Salinas V, Gorwa-Grauslund MF. Adaptive evolution of an industrial strain of Saccharomyces cerevisiae for combined tolerance to inhibitors and temperature. Biotechnol Biofuels. 2013;6:151. doi: 10.1186/1754-6834-6-151.
41. Jorgensen P, Nishikawa JL, Breitkreutz B, Tyers M. Systematic identification of pathways that couple cell growth and division in yeast. Science. 2002;297:395-400. doi: 10.1126/science.1070850.
42. Fraenkel DG. Yeast intermediary metabolism. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2011.
43. Taitec-online: OD-MonitorA&S. http://e-taitec.com/products/products-detail-en.php?machine_name=OD-MonitorA%26S. Accessed 20 June 2016.
44. TAITEC CORP. Method for contactless continuous measurement of proliferation of specimen during cultivation. 2012. Patent JP2012217426 (A). Espacenet. https://worldwide.espacenet.com. Accessed 20 June 2016.
45. Anderlei T, Zang W, Papaspyrou M, Büchs J. Online respiration activity measurement (OTR, CTR, RQ) in shake flasks. Biochem Eng J. 2004;17:187-94. doi: 10.1016/S1369-703X(03)00181-5.
46. Sherman F. Getting started with yeast. In: Guide to yeast genetics and molecular and cell biology-Part B. Amsterdam: Elsevier; 2002. p. 3-41. doi: 10.1016/S0076-6879(02)50954-X.
47. Swinnen S, Klein M, Carrillo M, McInnes J, Nguyen HTT, Nevoigt E. Re-evaluation of glycerol utilization in Saccharomyces cerevisiae: characterization of an isolate that grows on glycerol without supporting supplements. Biotechnol Biofuels. 2013;6:157. doi: 10.1186/1754-6834-6-157.
48. Verduyn C, Postma E, Scheffers WA, van Dijken JP. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast. 1992;8:501-17. doi: 10.1002/yea.320080703.
49. Funke M, Diederichs S, Kensy F, Müller C, Büchs J. The baffled microtiter plate: increased oxygen transfer and improved online monitoring in small scale fermentations. Biotechnol Bioeng. 2009;103:1118-28. doi: 10.1002/bit.22341.
50. Latimer P, Pyle BE. Light scattering at various angles. Biophys J. 1972;12:764-73. doi: 10.1016/S0006-3495(72)86120-4.
51. Canetta E, Adya AK, Walker GM. Atomic force microscopic study of the effects of ethanol on yeast cell surface morphology. FEMS Microbiol Lett. 2006;255:308-15. doi: 10.1111/j.1574-6968.2005.00089.x.
52. Aguilar-Uscanga B, Francois JM. A study of the yeast cell wall composition and structure in response to growth conditions and mode of cultivation. Lett Appl Microbiol. 2003;37:268-74. doi: 10.1046/j.1472-765X.2003.01394.x.
53. Madrid RE, Felice CJ. Microbial biomass estimation. Crit Rev Biotechnol. 2005;25:97-112. doi: 10.1080/07388550500248563.
54. Ude C, Schmidt-Hager J, Findeis M, John GT, Scheper T, Beutel S. Application of an online-biomass sensor in an optical multisensory platform prototype for growth monitoring of biotechnical relevant microorganism and cell lines in single-use shake flasks. Sensors (Basel). 2014;14:17390-405. doi: 10.3390/s140917390.