Skip to main content

Biosensors of the Well-being of Cell Cultures

  • Living reference work entry
  • First Online:
Handbook of Cell Biosensors

Abstract

Genetically-encoded biosensors offer advantages over traditional analytical technologies in biological manufacturing. Various biosensor architectures can be employed based on activation of transcription, translation, or folding of a reporter. Such biosensors can be used in small volume, high throughput culture devices to provide a more complete picture of cellular physiology. In addition, because of their simple read out, genetically encoded biosensors can be employed for monitoring during production and offer the opportunity for increased measurement density. This chapter reviews current applications of biosensors to measure cellular health and well-being including designs for detecting the activation of cell stress responses as well as sensing of critical metabolites. Many of these designs have been demonstrated to be relevant to bioprocess engineering or cell line selection, but to date very few have been adopted by industry. In future, ensuring that biosensors function robustly under industrial conditions is a priority, as is designing systems that are compatible with industrial workflows. In the long term, engineering systems that move beyond sensing, to include the ability to adjust the environment of the culture based on signals, will allow biotechnology to fully capitalize on the advantages that genetically encoded biosensors can bring.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

References

  • Arias-Barreiro CR et al (2010) A bacterial biosensor for oxidative stress using the constitutively expressed redox-sensitive protein roGFP2. Sensors (Basel, Switzerland) 10:6290–6306. https://doi.org/10.3390/s100706290

    Article  CAS  Google Scholar 

  • Aw R, McKay PF, Shattock RJ, Polizzi KM (2018) A systematic analysis of the expression of the anti-HIV VRC01 antibody in Pichia pastoris through signal peptide optimization. Protein Expr Purif 149:43–50. https://doi.org/10.1016/j.pep.2018.03.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Banning C et al (2010) A flow cytometry-based FRET assay to identify and analyse protein-protein interactions in living cells. PLoS One 5:e9344. https://doi.org/10.1371/journal.pone.0009344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Behjousiar A, Kontoravdi C, Polizzi KM (2012) In situ monitoring of intracellular glucose and glutamine in CHO cell culture. PLoS One 7. https://doi.org/10.1371/journal.pone.0034512

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Belousov VV, Fradkov AF, Lukyanov KA, Staroverov DB, Shakhbazov KS, Terskikh AV, Lukyanov S (2006) Genetically encoded fluorescent indicator for intracellular hydrogen peroxide. Nat Methods 3:281

    Article  CAS  PubMed  Google Scholar 

  • Bermejo E et al (2018) Production of lutein, and polyunsaturated fatty acids by the acidophilic eukaryotic microalga Coccomyxa onubensis under abiotic stress by salt or ultraviolet light. J Biosci Bioeng 125:669–675. https://doi.org/10.1016/j.jbiosc.2017.12.025

    Article  CAS  PubMed  Google Scholar 

  • Bradley RW, Wang B (2015) Designer cell signal processing circuits for biotechnology. New Biotechnol 32:635–643

    Article  CAS  Google Scholar 

  • Brognaux A, Han SS, Sorensen SJ, Lebeau F, Thonart P, Delvigne F (2013a) A low-cost, multiplexable, automated flow cytometry procedure for the characterization of microbial stress dynamics in bioreactors. Microb Cell Factories 12. https://doi.org/10.1186/1475-2859-12-100

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Brognaux A, Thonart P, Delvigne F, Neubauer P, Twizere JC, Francis F, Gorret N (2013b) Direct and indirect use of GFP whole cell biosensors for the assessment of bioprocess performances: design of milliliter scale-down bioreactors. Biotechnol Prog 29:48–59

    Article  CAS  PubMed  Google Scholar 

  • Buschhaus JM, Humphries B, Luker KE, Luker GD (2018) A Caspase-3 reporter for fluorescence lifetime imaging of single-cell apoptosis. Cell 7:57

    Article  Google Scholar 

  • Cao H et al (2017) Systems-level understanding of ethanol-induced stresses and adaptation in E. coli. Sci Rep 7:44150

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carlquist M et al (2012) Physiological heterogeneities in microbial populations and implications for physical stress tolerance. Microb Cell Factories 11. https://doi.org/10.1186/1475-2859-11-94

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ceroni F, Algar R, Stan G-B, Ellis T (2015) Quantifying cellular capacity identifies gene expression designs with reduced burden. Nat Methods 12:415

    Article  CAS  PubMed  Google Scholar 

  • Chen A, Leith M, Tu R, Tahim G, Sudra A, Bhargava S (2017) Effects of diluents on cell culture viability measured by automated cell counter. PLoS One 12:e0173375

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chiang JJH, Truong K (2005) Using co-cultures expressing fluorescence resonance energy transfer based protein biosensors to simultaneously image caspase-3 and Ca2+ signaling. Biotechnol Lett 27:1219–1227

    Article  CAS  PubMed  Google Scholar 

  • Cilek MZ et al (2011) AHR, a novel acute hypoxia-response sequence, drives reporter gene expression under hypoxia in vitro and in vivo. Cell Biol Int 35:1–8

    Article  CAS  PubMed  Google Scholar 

  • Constantinou A, Polizzi KM (2013) Opportunities for bioprocess monitoring using FRET biosensors. Biochem Soc Trans 41:1146–1151

    Article  CAS  PubMed  Google Scholar 

  • Cost AL, Ringer P, Chrostek-Grashoff A, Grashoff C (2015) How to measure molecular forces in cells: a guide to evaluating genetically-encoded FRET-based tension sensors. Cell Mol Bioeng 8:96–105

    Article  CAS  PubMed  Google Scholar 

  • De Paepe B, Peters G, Coussement P, Maertens J, De Mey M (2017) Tailor-made transcriptional biosensors for optimizing microbial cell factories. J Ind Microbiol Biotechnol 44:623–645

    Article  PubMed  CAS  Google Scholar 

  • Dekker L, Polizzi KM (2017) Sense and sensitivity in bioprocessing – detecting cellular metabolites with biosensors. Curr Opin Chem Biol 40:31–36

    Article  CAS  PubMed  Google Scholar 

  • Delvigne F, Goffin P (2014) Microbial heterogeneity affects bioprocess robustness: dynamic single-cell analysis contributes to understanding of microbial populations. Biotechnol J 9:61–72

    Article  CAS  PubMed  Google Scholar 

  • Delvigne F, Boxus M, Ingels S, Thonart P (2009) Bioreactor mixing efficiency modulates the activity of a prpoS::GFP reporter gene in E. coli. Microb Cell Factories 8:15

    Article  CAS  Google Scholar 

  • Delvigne F et al (2011) Characterization of the response of GFP microbial biosensors sensitive to substrate limitation in scale-down bioreactors. Biochem Eng J 55:131–139

    Article  CAS  Google Scholar 

  • Demuth C, Varonier J, Jossen V, Eibl R, Eibl D (2016) Novel probes for pH and dissolved oxygen measurements in cultivations from millilitre to benchtop scale. Appl Microbiol Biotechnol 100:3853–3863

    Article  CAS  PubMed  Google Scholar 

  • Doucette J, Zhao Z, Geyer RJ, Barra MM, Balunas MJ, Zweifach A (2016) Flow cytometry enables multiplexed measurements of genetically encoded intramolecular FRET sensors suitable for screening. J Biomol Screen 21:535–547

    Article  CAS  PubMed  Google Scholar 

  • Du Z et al (2013) Non-invasive UPR monitoring system and its applications in CHO production cultures. Biotechnol Bioeng 110:2184–2194

    Article  CAS  PubMed  Google Scholar 

  • Dzyadevych SV, Arkhypova VN, Soldatkin AP, El’skaya AV, Martelet C, Jaffrezic-Renault N (2008) Amperometric enzyme biosensors: past, present and future. IRBM 29:171–180

    Article  Google Scholar 

  • Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818

    Article  CAS  PubMed  Google Scholar 

  • Ermakova YG et al (2014) Red fluorescent genetically encoded indicator for intracellular hydrogen peroxide. Nat Commun 5:5222

    Article  CAS  PubMed  Google Scholar 

  • Feng J et al (2015) A general strategy to construct small molecule biosensors in eukaryotes. elife 4:e10606

    Article  PubMed  PubMed Central  Google Scholar 

  • Fosbrink M, Aye-Han NN, Cheong R, Levchenko A, Zhang J (2010) Visualization of JNK activity dynamics with a genetically encoded fluorescent biosensor. Proc Natl Acad Sci U S A 107:5459–5464

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garcia JR, Cha HJ, Rao G, Marten MR, Bentley WE (2009) Microbial nar-GFP cell sensors reveal oxygen limitations in highly agitated and aerated laboratory-scale fermentors. Microb Cell Factories 8:15

    Article  CAS  Google Scholar 

  • Goers L, Kylilis N, Tomazou M, Wen KY, Freemont P, Polizzi K (2013) Engineering microbial biosensors. In: Harwood C, Wipat A (eds) Microbial synthetic biology. Methods in microbiology, vol 40. Academic, Oxford, pp 119–156

    Google Scholar 

  • Goers L, Ainsworth C, Goey CH, Kontoravdi C, Freemont PS, Polizzi KM (2017) Whole-cell Escherichia coli lactate biosensor for monitoring mammalian cell cultures during biopharmaceutical production. Biotechnol Bioeng 114:1290–1300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hanson GT, Aggeler R, Oglesbee D, Cannon M, Capaldi RA, Tsien RY, Remington SJ (2004) Investigating mitochondrial redox potential with redox-sensitive green fluorescent protein indicators. J Biol Chem 279:13044–13053

    Article  CAS  PubMed  Google Scholar 

  • Hendriks G et al (2012) The ToxTracker assay: novel GFP reporter systems that provide mechanistic insight into the genotoxic properties of chemicals. Toxicol Sci 125:285–298

    Article  CAS  PubMed  Google Scholar 

  • Hoynes-O’Connor A, Shopera T, Hinman K, Creamer JP, Moon TS (2017) Enabling complex genetic circuits to respond to extrinsic environmental signals. Biotechnol Bioeng 114:1626–1631

    Article  PubMed  CAS  Google Scholar 

  • Jang S, Jang S, Xiu Y, Kang TJ, Lee S-H, Koffas MAG, Jung GY (2017) Development of artificial riboswitches for monitoring of naringenin in vivo. ACS Synth Biol 6:2077–2085

    Article  CAS  PubMed  Google Scholar 

  • Jayaraman M, Radhika V, Bamne MN, Ramos R, Briggs R, Dhanasekaran DN (2005) Engineered Saccharomyces cerevisiae strain BioS-OS1/2, for the detection of oxidative stress. Biotechnol Prog 21:1373–1379

    Article  CAS  PubMed  Google Scholar 

  • Kober L, Zehe C, Bode J (2012) Development of a novel ER stress based selection system for the isolation of highly productive clones. Biotechnol Bioeng 109:2599–2611

    Article  CAS  PubMed  Google Scholar 

  • Kotova VY, Manukhov IV, Zavilgelskii GB (2010) Lux-biosensors for detection of SOS-response, heat shock, and oxidative stress. Appl Biochem Microbiol 46:781–788

    Article  CAS  Google Scholar 

  • Krampe B, Al-Rubeai M (2010) Cell death in mammalian cell culture: molecular mechanisms and cell line engineering strategies. Cytotechnology 62:175–188

    Article  PubMed  PubMed Central  Google Scholar 

  • Kuystermans D, Mohd A, Al-Rubeai M (2012) Automated flow cytometry for monitoring CHO cell cultures. Methods 56:358–365

    Article  CAS  PubMed  Google Scholar 

  • Kuystermans D, Avesh M, Al-Rubeai M (2016) Online flow cytometry for monitoring apoptosis in mammalian cell cultures as an application for process analytical technology. Cytotechnology 68:399–408

    Article  CAS  PubMed  Google Scholar 

  • Li CJ, Imanishi A, Komatsu N, Terai K, Amano M, Kaibuchi K, Matsuda M (2017a) A FRET biosensor for ROCK based on a consensus substrate sequence identified by KISS technology. Cell Struct Funct 42:1–13

    Article  CAS  PubMed  Google Scholar 

  • Li H, Liang C, Chen W, Jin J-M, Tang S-Y, Tao Y (2017b) Monitoring in vivo metabolic flux with a designed whole-cell metabolite biosensor of shikimic acid. Biosens Bioelectron 98:457–465

    Article  CAS  PubMed  Google Scholar 

  • Lim B, Gross CA (2011) Cellular response to heat shock and cold shock. In: Bacterial stress responses, 2nd edn. American Society of Microbiology, Washington, DC

    Google Scholar 

  • Lim CT, Zhou EH, Quek ST (2006) Mechanical models for living cells – a review. J Biomech 39:195–216

    Article  CAS  PubMed  Google Scholar 

  • Liu JY, Qu RJ, Ogura M, Shibata T, Harada H, Hiraoka M (2005) Real-time imaging of hypoxia-inducible factor-1 activity in tumor xenografts. J Radiat Res 46:93–102

    Article  CAS  PubMed  Google Scholar 

  • Liu D, Evans T, Zhang FZ (2015a) Applications and advances of metabolite biosensors for metabolic engineering. Metab Eng 31:35–43

    Article  PubMed  CAS  Google Scholar 

  • Liu YN et al (2015b) Developing a high-throughput screening method for threonine overproduction based on an artificial promoter. Microb Cell Factories 14:121

    Article  CAS  Google Scholar 

  • Ma YJ, Hendershot LM (2001) The unfolding tale of the unfolded protein response. Cell 107:827–830

    Article  CAS  PubMed  Google Scholar 

  • Ma TF, Chen YP, Guo JS, Wang W, Fang F (2018) Cellular analysis and detection using surface plasmon resonance imaging. TrAC Trends Anal Chem 103:102–109

    Article  CAS  Google Scholar 

  • Mahr R, Gatgens C, Gatgens J, Polen T, Kalinowski J, Frunzke J (2015) Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum. Metab Eng 32:184–194

    Article  CAS  PubMed  Google Scholar 

  • Mahr R, von Boeselager RF, Wiechert J, Frunzke J (2016) Screening of an Escherichia coli promoter library for a phenylalanine biosensor. Appl Microbiol Biotechnol 100:6739–6753

    Article  CAS  PubMed  Google Scholar 

  • McLamore ES, Porterfield DM (2011) Non-invasive tools for measuring metabolism and biophysical analyte transport: self-referencing physiological sensing. Chem Soc Rev 40:5308–5320

    Article  CAS  PubMed  Google Scholar 

  • Menolascina F et al (2014) In-vivo real-time control of protein expression from endogenous and synthetic gene networks. PLoS Comput Biol 10:e1003625–e1003625

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Merksamer PI, Trusina A, Papa FR (2008) Real-time redox measurements during endoplasmic reticulum stress reveal interlinked protein folding functions. Cell 135:933–947

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miesenbock G, De Angelis DA, Rothman JE (1998) Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins. Nature 394:192–195

    Article  CAS  PubMed  Google Scholar 

  • Milias-Argeitis A et al (2011) In silico feedback for in vivo regulation of a gene expression circuit. Nat Biotechnol 29:1114–1116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Millipore M (2018) 21CFR Part 11 Compliance Guidelines for Guava® ViaCount® Reagent Assay. https://www.merckmillipore.com/GB/en/life-science-research/cell-analysis-flow-cytometry/guava-easycyte-flow-cytometers/Flow-Cytometry-Applications/bioprocess/Yo.b.qB.dwoAAAFE5k1zAv6g,nav?ReferrerURL=https%3A%2F%2Fwww.google.co.uk%2F&bd=1

  • Pais DAM, Carrondo MJT, Alves PM, Teixeira AP (2014) Towards real-time monitoring of therapeutic protein quality in mammalian cell processes. Curr Opin Biotechnol 30:161–167

    Article  CAS  PubMed  Google Scholar 

  • Passoth V, Cohn M, Schafer B, Hahn-Hagerdal B, Klinner U (2003) Analysis of the hypoxia-induced ADH2 promoter of the respiratory yeast Pichia stipitis reveals a new mechanism for sensing of oxygen limitation in yeast. Yeast 20:39–51

    Article  CAS  PubMed  Google Scholar 

  • Pokhilko A (2017) Monitoring of nutrient limitation in growing E. coli: a mathematical model of a ppGpp-based biosensor. BMC Syst Biol 11:106

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Potzkei J, Kunze M, Drepper T, Gensch T, Jaeger K-E, Büchs J (2012) Real-time determination of intracellular oxygen in bacteria using a genetically encoded FRET-based biosensor. BMC Biol 10:28

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Randers-Eichhorn L, Albano CR, Sipior J, Bentley WE, Rao G (1997) Online green fluorescent protein sensor with LED excitation. Biotechnol Bioeng 55:921–926

    Article  CAS  PubMed  Google Scholar 

  • Rogers JK, Church GM (2016) Genetically encoded sensors enable real-time observation of metabolite production. Proc Natl Acad Sci U S A 113:2388–2393

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rugbjerg P, Gence HJ, Jensen K, Sarup-Lytzen K, Sommer MOA (2016) Molecular buffers permit sensitivity tuning and inversion of riboswitch signals. ACS Synth Biol 5:632–638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scognamiglio V, Antonacci A, Lambreva MD, Litescu SC, Rea G (2015) Synthetic biology and biomimetic chemistry as converging technologies fostering a new generation of smart biosensors. Biosens Bioelectron 74:1076–1086

    Article  CAS  PubMed  Google Scholar 

  • Seefried L et al (2010) A small scale cell culture system to analyze mechanobiology using reporter gene constructs and polyurethan dishes. Eur Cells Mater 20:344–355

    Article  CAS  Google Scholar 

  • Shi S, Ang EL, Zhao H (2018) In vivo biosensors: mechanisms, development, and applications. J Ind Microbiol Biotechnol 45:491–516

    Article  CAS  PubMed  Google Scholar 

  • Silberman M, Barac YD, Yahav H, Wolfovitz E, Einav S, Resnick N, Binah O (2009) Shear stress-induced transcriptional regulation via hybrid promoters as a potential tool for promoting angiogenesis. Angiogenesis 12:231–242

    Article  CAS  PubMed  Google Scholar 

  • Skjoedt ML et al (2016) Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast. Nat Chem Biol 12:951

    Article  CAS  PubMed  Google Scholar 

  • Slomovic S, Pardee K, Collins JJ (2015) Synthetic biology devices for in vitro and in vivo diagnostics. Proc Natl Acad Sci U S A 112:14429–14435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sonna LA, Fujita J, Gaffin SL, Lilly CM (2002) Invited review: effects of heat and cold stress on mammalian gene expression. J Appl Physiol 92:1725–1742

    Article  CAS  PubMed  Google Scholar 

  • Sou SN, Sellick C, Lee K, Mason A, Kyriakopoulos S, Polizzi KM, Kontoravdi C (2015) How does mild hypothermia affect monoclonal antibody glycosylation? Biotechnol Bioeng 112:1165–1176

    Article  CAS  PubMed  Google Scholar 

  • Tapsin S et al (2018) Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes. Nat Commun 9:1289

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tielker D, Eichhof I, Jaeger KE, Ernst JF (2009) Flavin mononucleotide-based fluorescent protein as an oxygen-independent reporter in Candida albicans and Saccharomyces cerevisiae. Eukaryot Cell 8:913–915

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505

    Article  CAS  PubMed  Google Scholar 

  • Varma S, Fendyur A, Box A, Voldman J (2017) Multiplexed cell-based sensors for assessing the impact of engineered systems and methods on cell health. Anal Chem 89:4663–4670

    Article  CAS  PubMed  Google Scholar 

  • Xiao Y, Jiang W, Zhang F (2017) Developing a genetically encoded, cross-species biosensor for detecting ammonium and regulating biosynthesis of cyanophycin. ACS Synth Biol 6:1807–1815

    Article  PubMed  CAS  Google Scholar 

  • Yang SJ, Yu HL, You YZ, Li XL, Jiang JX (2018a) Effective lactic acid production from waste paper using Streptococcus thermophilus at low enzyme loading assisted by Gleditsia saponin. Carbohydr Polym 200:122–127

    Article  CAS  PubMed  Google Scholar 

  • Yang T et al (2018b) A review of ratiometric electrochemical sensors: from design schemes to future prospects. Sensors Actuators B Chem 274:501–516

    Article  CAS  Google Scholar 

  • Yu LX, Amidon G, Khan MA, Hoag SW, Polli J, Raju GK, Woodcock J (2014) Understanding pharmaceutical quality by design. AAPS J 16:771–783

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang XD, Yang ST (2011) An online, non-invasive fluorescence probe for immobilized cell culture process development. Process Biochem 46:2030–2035

    Article  CAS  Google Scholar 

  • Zhang J et al (2013) Visualization of caspase-3-like activity in cells using a genetically encoded fluorescent biosensor activated by protein cleavage. Nat Commun 4:2157

    Article  PubMed  CAS  Google Scholar 

  • Zhao L, Fu HY, Zhou WC, Hu WS (2015) Advances in process monitoring tools for cell culture bioprocesses. Eng Life Sci 15:459–468

    Article  CAS  Google Scholar 

  • Zheng H, Bi J, Krendel M, Loh SN (2014) Converting a binding protein into a biosensing conformational switch using protein fragment exchange. Biochemistry 53:5505–5514

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Karen Marie Polizzi .

Editor information

Editors and Affiliations

Section Editor information

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this entry

Check for updates. Verify currency and authenticity via CrossMark

Cite this entry

Polizzi, K.M. (2019). Biosensors of the Well-being of Cell Cultures. In: Thouand, G. (eds) Handbook of Cell Biosensors. Springer, Cham. https://doi.org/10.1007/978-3-319-47405-2_119-1

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-47405-2_119-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-47405-2

  • Online ISBN: 978-3-319-47405-2

  • eBook Packages: Springer Reference Chemistry and Mat. ScienceReference Module Physical and Materials ScienceReference Module Chemistry, Materials and Physics

Publish with us

Policies and ethics