Abstract
The emergence of natural products and industrial microbiology nearly eight decades ago propelled an era of bioprocess innovation. Half a century later, recombinant protein technology spurred the tremendous growth of biologics and added mammalian cells to the forefront of industrial producing cells in terms of the value of products generated. This review highlights the process technology of natural products and protein biologics. Despite the separation in time, there is a remarkable similarity in their progression. As the new generation of therapeutics for gene and cell therapy emerges, its process technology development can take inspiration from that of natural products and biologics.
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(1999) Discovery and development of penicillin. http://www.acs.org/content/acs/en/education/whatischemistry/landmarks/flemingpenicillin.html
Abu-Absi SF, Yang L, Thompson P, Jiang C, Kandula S, Schilling B, Shukla AA (2010) Defining process design space for monoclonal antibody cell culture. Biotechnol Bioeng 106:894–905. doi:10.1002/bit.22764
Adrio JL, Demain AL (2006) Genetic improvement of processes yielding microbial products. FEMS Microbiol Rev 30:187–214. doi:10.1111/j.1574-6976.2005.00009.x
Agarabi CD, Chavez BK, Lute SC, Read EK, Rogstad S, Awotwe-Otoo D, Brown MR, Boyne MT 2nd, Brorson KA (2016) Exploring the linkage between cell culture process parameters and downstream processing utilizing a plackett-burman design for a model monoclonal antibody. Biotechnol Prog. doi:10.1002/btpr.2402
Aigle B, Corre C (2012) Waking up Streptomyces secondary metabolism by constitutive expression of activators or genetic disruption of repressors. Methods Enzymol 517:343–366. doi:10.1016/B978-0-12-404634-4.00017-6
Aigle B, Lautru S, Spiteller D, Dickschat JS, Challis GL, Leblond P, Pernodet JL (2014) Genome mining of Streptomyces ambofaciens. J Ind Microbiol Biotechnol 41:251–263. doi:10.1007/s10295-013-1379-y
Amano SI, Sakurai T, Endo K, Takano H, Beppu T, Furihata K, Sakuda S, Ueda K (2011) A cryptic antibiotic triggered by monensin. J Antibiot (Tokyo) 64:703. doi:10.1038/ja.2011.69
Anderson EW, Lau EF (1955) Commercial extraction of unfiltered fermentation broth in the podbielniak contactor. Chem Eng Prog 51:7
Baltz RH (2011) Strain improvement in actinomycetes in the postgenomic era. J Ind Microbiol Biotechnol 38:657–666
Baltz RH (2010) Streptomyces and Saccharopolyspora hosts for heterologous expression of secondary metabolite gene clusters. J Ind Microbiol Biotechnol 37:759–772. doi:10.1007/s10295-010-0730-9
Carlage T, Hincapie M, Zang L, Lyubarskaya Y, Madden H, Mhatre R, Hancock WS (2009) Proteomic profiling of a high-producing Chinese hamster ovary cell culture. Anal Chem 81:7357–7362. doi:10.1021/ac900792z
Challis GL (2014) Exploitation of the Streptomyces coelicolor A3(2) genome sequence for discovery of new natural products and biosynthetic pathways. J Ind Microbiol Biotechnol 41:219–232. doi:10.1007/s10295-013-1383-2
Chandra S, Groener A, Feldman F (2002) Effectiveness of alternative treatments for reducing potential viral contaminants from plasma-derived products. Thromb Res 105:391–400
Chen J, Bergevin J, Kiss R, Walker G, Battistoni T, Lufburrow P, Lam H, Vinther A (2012) Case study: a novel bacterial contamination in cell culture production-leptospira licerasiae. PDA J Pharm Sci Technol 66:580–591. doi:10.5731/pdajpst.2012.00892
Chen Y, Wendt-Pienkowski E, Shen B (2008) Identification and utility of FdmR1 as a Streptomyces antibiotic regulatory protein activator for fredericamycin production in Streptomyces griseus ATCC 49344 and heterologous hosts. J Bacteriol 190:5587–5596. doi:10.1128/JB.00592-08
Choi SS, Rhee WJ, Kim EJ, Park TH (2006) Enhancement of recombinant protein production in Chinese hamster ovary cells through anti-apoptosis engineering using 30Kc6 gene. Biotechnol Bioeng 95:459–467. doi:10.1002/bit.21023
Chong WP, Reddy SG, Yusufi FN, Lee DY, Wong NS, Heng CK, Yap MG, Ho YS (2010) Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth: overexpression of malate dehydrogenase II. J Biotechnol 147:116–121. doi:10.1016/j.jbiotec.2010.03.018
Cipriano D, Burnham M, Hughes JV (2012) Effectiveness of various processing steps for viral clearance of therapeutic proteins: database analyses of commonly used steps. In: Voynov V, Caravella AJ (eds) Therapeutic proteins: methods and protocols. Humana Press, Totowa, NJ, pp 277–292
Cobb RE, Wang Y, Zhao H (2015) High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 4:723–728. doi:10.1021/sb500351f
Cohen SN, Chang AC, Boyer HW, Helling RB (1973) Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci USA 70:3240–3244
Cruz AJG, Silva AS, Araujo MLGC, Giordano RC, Hokka CO (1999) Modelling and optimization of the cephalosporin C production bioprocess in a fed-batch bioreactor with invert sugar as substrate. Chem Eng Sci 54:3137–3142. doi:10.1016/S0009-2509(98)00364-9
Demain AL (1989) Carbon source regulation of idiolite biosynthesis in actinomycetes. CRC Press, Boca Raton
Demain AL (2014) Importance of microbial natural products and the need to revitalize their discovery. J Ind Microbiol Biotechnol 41:185–201. doi:10.1007/s10295-013-1325-z
Demain AL, Adrio JL (2008) Strain improvement for production of pharmaceuticals and other microbial metabolites by fermentation. Progress in drug research Fortschritte der Arzneimittelforschung Progrès des recherches pharmaceutiques 65:89. doi:10.1007/978-3-7643-8117-2_7
Dorai H, Kyung YS, Ellis D, Kinney C, Lin C, Jan D, Moore G, Betenbaugh MJ (2009) Expression of anti-apoptosis genes alters lactate metabolism of Chinese Hamster Ovary cells in culture. Biotechnol Bioeng 103:592–608. doi:10.1002/bit.22269
Elander RP (2003) Industrial production of beta-lactam antibiotics. Appl Microbiol Biotechnol 61:385–392. doi:10.1007/s00253-003-1274-y
Gallo G, Renzone G, Alduina R, Stegmann E, Weber T, Lantz AE, Thykaer J, Sangiorgi F, Scaloni A, Puglia AM (2010) Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina. Proteomics 10:1336–1358. doi:10.1002/pmic.200900175
Geistlich M, Losick R, Turner JR, Rao RN (1992) Characterization of a novel regulatory gene governing the expression of a polyketide synthase gene in Streptomyces ambofaciens. Mol Microbiol 6:2019–2029
Gomez-Escribano JP, Bibb MJ (2012) Streptomyces coelicolor as an expression host for heterologous gene clusters. Methods Enzymol 517:279–300. doi:10.1016/B978-0-12-404634-4.00014-0
Hartman TE, Sar N, Genereux K, Barritt DS, He Y, Burky JE, Wesson MC, Tso JY, Tsurushita N, Zhou W et al (2007) Derivation and characterization of cholesterol-independent non-GS NS0 cell lines for production of recombinant antibodies. Biotechnol Bioeng 96:294–306. doi:10.1002/bit.21099
Hauser H (2015) Cell line development. In: Al-Rubeai M (ed) Animal cell culture. Springer International Publishing, Cham, pp 1–25
Hopwood DA, Malpartida F, Kieser HM, Ikeda H, Duncan J, Fujii I, Rudd BAM, Floss HG, Omura S (1985) Production of hybrid antibiotics by genetic-engineering. Nature 314:642–644
Hossler P, Mulukutla BC, Hu WS (2007) Systems analysis of N-glycan processing in mammalian cells. PLoS One 2:e713. doi:10.1371/journal.pone.0000713
Huang H, Zheng G, Jiang W, Hu H, Lu Y (2015) One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces. Acta Biochim Biophys Sin (Shanghai) 47:231–243. doi:10.1093/abbs/gmv007
Hwang YS, Kim ES, Biro S, Choi CY (2003) Cloning and analysis of a DNA fragment stimulating avermectin production in various Streptomyces avermitilis strains. Appl Environ Microbiol 69:1263–1269
Irani N, Wirth M, van Den Heuvel J, Wagner R (1999) Improvement of the primary metabolism of cell cultures by introducing a new cytoplasmic pyruvate carboxylase reaction. Biotechnol Bioeng 66:238–246
Jefferis R (2009) Recombinant antibody therapeutics: the impact of glycosylation on mechanisms of action. Trends Pharmacol Sci 30:356–362. doi:10.1016/j.tips.2009.04.007
Ju KS, Gao J, Doroghazi JR, Wang KK, Thibodeaux CJ, Li S, Metzger E, Fudala J, Su J, Zhang JK et al (2015) Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes. Proc Natl Acad Sci USA 112:12175–12180. doi:10.1073/pnas.1500873112
Kennedy J, Auclair K, Kendrew SG, Park C, Vederas JC, Hutchinson CR (1999) Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis. Science 284:1368–1372
Khetan A, Huang YM, Dolnikova J, Pederson NE, Wen DY, Yusuf-Makagiansar H, Chen P, Ryll T (2010) Control of misincorporation of serine for asparagine during antibody production using CHO cells. Biotechnol Bioeng 107:116–123
Kim M, Yi JS, Lakshmanan M, Lee DY, Kim BG (2016) Transcriptomics-based strain optimization tool for designing secondary metabolite overproducing strains of Streptomyces coelicolor. Biotechnol Bioeng 113:651–660. doi:10.1002/bit.25830
Kim SH, Lee GM (2007) Down-regulation of lactate dehydrogenase-A by siRNAs for reduced lactic acid formation of Chinese hamster ovary cells producing thrombopoietin. Appl Microbiol Biotechnol 74:152–159. doi:10.1007/s00253-006-0654-5
Kim SH, Lee GM (2007) Functional expression of human pyruvate carboxylase for reduced lactic acid formation of Chinese hamster ovary cells (DG44). Appl Microbiol Biotechnol 76:659–665. doi:10.1007/s00253-007-1041-6
Komatsu M, Uchiyama T, Omura S, Cane DE, Ikeda H (2010) Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proc Natl Acad Sci USA 107:2646–2651. doi:10.1073/pnas.0914833107
Krampe B, Al-Rubeai M (2010) Cell death in mammalian cell culture: molecular mechanisms and cell line engineering strategies. Cytotechnology 62:175–188. doi:10.1007/s10616-010-9274-0
Kyung YS, Peshwa MV, Gryte DM, Hu WS (1994) High density culture of mammalian cells with dynamic perfusion based on on-line oxygen uptake rate measurements. Cytotechnology 14:183–190
Lee J, Hwang Y, Kim S, Kim E, Choi C (2000) Effect of a global regulatory gene, afsR2, from Streptomyces lividans on avermectin production in Streptomyces avermitilis. J Biosci Bioeng 89:606–608
Lombo F, Brana AF, Mendez C, Salas JA (1999) The mithramycin gene cluster of Streptomyces argillaceus contains a positive regulatory gene and two repeated DNA sequences that are located at both ends of the cluster. J Bacteriol 181:642–647
Malmberg LH, Hu WS, Sherman DH (1995) Effects of enhanced lysine epsilon-aminotransferase activity on cephamycin biosynthesis in Streptomyces clavuligerus. Appl Microbiol Biotechnol 44:198–205
Marks L (2012) The birth pangs of monoclonal antibody therapeutics: the failure and legacy of Centoxin. MAbs 4:403–412. doi:10.4161/mabs.19909
Moore JM, Bradshaw E, Seipke RF, Hutchings MI, McArthur M (2012) Use and discovery of chemical elicitors that stimulate biosynthetic gene clusters in Streptomyces bacteria. Methods Enzymol 517:367–385. doi:10.1016/B978-0-12-404634-4.00018-8
Mori K, Kuni-Kamochi R, Yamane-Ohnuki N, Wakitani M, Yamano K, Imai H, Kanda Y, Niwa R, Iida S, Uchida K et al (2004) Engineering Chinese hamster ovary cells to maximize effector function of produced antibodies using FUT8 siRNA. Biotechnol Bioeng 88:901–908. doi:10.1002/bit.20326
Mou DG, Cooney CL (1983) Growth monitoring and control through computer-aided on-line mass balancing in a fed-batch penicillin fermentation. Biotechnol Bioeng 25:225–255. doi:10.1002/bit.260250118
Murphy M, Quesada GM, Chen DY (2011) Effectiveness of mouse minute virus inactivation by high temperature short time treatment technology: a statistical assessment. Biologicals 39:438–443
Neves AA, Pereira DA, Vieira LM, Menezes JC (2000) Real time monitoring biomass concentration in Streptomyces clavuligerus cultivations with industrial media using a capacitance probe. J Biotechnol 84:45–52
Ochi K, Tanaka Y, Tojo S (2014) Activating the expression of bacterial cryptic genes by rpoB mutations in RNA polymerase or by rare earth elements. J Ind Microbiol Biotechnol 41:403–414. doi:10.1007/s10295-013-1349-4
Parekh S, Vinci VA, Strobel RJ (2000) Improvement of microbial strains and fermentation processes. Appl Microbiol Biotechnol. doi:10.1007/s002530000403
Patridge E, Gareiss P, Kinch MS, Hoyer D (2016) An analysis of FDA-approved drugs: natural products and their derivatives. Drug Discov Today 21:204–207
Quan C, Alcala E, Petkovska I, Matthews D, Canova-Davis E, Taticek R, Ma S (2008) A study in glycation of a therapeutic recombinant humanized monoclonal antibody: where it is, how it got there, and how it affects charge-based behavior. Anal Biochem 373:179–191. doi:10.1016/j.ab.2007.09.027
Rathore AS, Winkle H (2009) Quality by design for biopharmaceuticals. Nat Biotechnol 27:26–34. doi:10.1038/nbt0109-26
Reeves CD (2003) The enzymology of combinatorial biosynthesis. Crit Rev Biotechnol 23:95–147. doi:10.1080/713609311
Rix U, Fischer C, Remsing LL, Rohr J (2002) Modification of post-PKS tailoring steps through combinatorial biosynthesis. Nat Prod Rep 19:542–580
Ryu YG, Butler MJ, Chater KF, Lee KJ (2006) Engineering of primary carbohydrate metabolism for increased production of actinorhodin in Streptomyces coelicolor. Appl Environ Microbiol 72:7132–7139. doi:10.1128/AEM.01308-06
Sanfeliu A, Paredes C, Cairo JJ, Godia F (1997) Identification of key patterns in the metabolism of hybridoma cells in culture. Enzyme Microb Technol 21:421–428
Schlatter S, Stansfield SH, Dinnis DM, Racher AJ, Birch JR, James DC (2005) On the optimal ratio of heavy to light chain genes for efficient recombinant antibody production by CHO cells. Biotechnol Prog 21:122–133. doi:10.1021/bp049780w
Schleh M, Romanowski P, Bhebe P, Zhang L, Chinniah S, Lawrence B, Bashiri H, Gaduh A, Rajurs V, Rasmussen B et al (2009) Susceptibility of mouse minute virus to inactivation by heat in two cell culture media types. Biotechnol Prog 25:854–860. doi:10.1002/btpr.181
Seth G, Charaniya S, Wiaschin KF, Hu WS (2007) In pursuit of a super producer—alternative paths to high producing recombinant mammalian cells. Curr Opin Biotechnol 18:557–564
Seth G, Hossler P, Yee JC, Hu WS (2006) Engineering cells for cell culture bioprocessing—physiological fundamentals. Adv Biochem Eng Biotechnol 101:119–164
Shields RL, Lai J, Keck R, O’Connell LY, Hong K, Meng YG, Weikert SH, Presta LG (2002) Lack of fucose on human IgG1 N-linked oligosaccharide improves binding to human Fcgamma RIII and antibody-dependent cellular toxicity. J Biol Chem 277:26733–26740. doi:10.1074/jbc.M202069200
Shwab EK, Bok JW, Tribus M, Galehr J, Graessle S, Keller NP (2007) Histone deacetylase activity regulates chemical diversity in Aspergillus. Eukaryot Cell 6:1656–1664. doi:10.1128/EC.00186-07
Singh V (1999) Disposable bioreactor for cell culture using wave-induced agitation. Cytotechnology 30:149–158. doi:10.1023/A:1008025016272
Skatrud PL, Tietz AJ, Ingolia TD, Cantwell CA, Fisher DL, Chapman JL, Queener SW (1989) Use of recombinant DNA to improve production of cephalosporin C by Cephalosporium acremonium. Nat Biotech 7:477–485
Smanski MJ, Peterson RM, Rajski SR, Shen B (2009) Engineered Streptomyces platensis strains that overproduce antibiotics platensimycin and platencin. Antimicrob Agents Chemother 53:1299–1304. doi:10.1128/AAC.01358-08
Spencer S, Gugliotta A, Koenitzer J, Hauser H, Wirth D (2015) Stability of single copy transgene expression in CHOK1 cells is affected by histone modifications but not by DNA methylation. J Biotechnol 195:15–29. doi:10.1016/j.jbiotec.2014.12.009
Staunton J, Wilkinson B (2001) Combinatorial biosynthesis of polyketides and nonribosomal peptides. Curr Opin Chem Biol 5:159–164
Stratigopoulos G, Bate N, Cundliffe E (2004) Positive control of tylosin biosynthesis: pivotal role of TylR. Mol Microbiol 54:1326–1334. doi:10.1111/j.1365-2958.2004.04347.x
Sung BH, Lee JH, Kim SC (2009) Escherichia coli genome engineering and minimization for the construction of a bioengine. In: Lee SY (ed) Systems biology and biotechnology of Escherichia coli. Springer, Netherlands, City, pp 19–40
Tong Y, Charusanti P, Zhang L, Weber T, Lee SY (2015) CRISPR-Cas9 based engineering of actinomycetal genomes. ACS Synth Biol 4:1020–1029. doi:10.1021/acssynbio.5b00038
Vishwanathan N, Le H, Jacob NM, Tsao YS, Ng SW, Loo B, Liu Z, Kantardjieff A, Hu WS (2014) Transcriptome dynamics of transgene amplification in Chinese hamster ovary cells. Biotechnol Bioeng 111:518–528. doi:10.1002/bit.25117
Volokhan O, Sletta H, Sekurova ON, Ellingsen TE, Zotchev SB (2005) An unexpected role for the putative 4′-phosphopantetheinyl transferase-encoding gene nysF in the regulation of nystatin biosynthesis in Streptomyces noursei ATCC 11455. FEMS Microbiol Lett 249:57–64. doi:10.1016/j.femsle.2005.05.052
von Horsten HH, Ogorek C, Blanchard V, Demmler C, Giese C, Winkler K, Kaup M, Berger M, Jordan I, Sandig V (2010) Production of non-fucosylated antibodies by co-expression of heterologous GDP-6-deoxy-D-lyxo-4-hexulose reductase. Glycobiology 20:1607–1618. doi:10.1093/glycob/cwq109
Wang X, Sena Filho JG, Hoover AR, King JB, Ellis TK, Powell DR, Cichewicz RH (2010) Chemical epigenetics alters the secondary metabolite composition of guttate excreted by an atlantic-forest-soil-derived Penicillium citreonigrum. J Nat Prod 73:942–948. doi:10.1021/np100142h
Warikoo V, Godawat R, Brower K, Jain S, Cummings D, Simons E, Johnson T, Walther J, Yu M, Wright B et al (2012) Integrated continuous production of recombinant therapeutic proteins. Biotechnol Bioeng 109:3018–3029. doi:10.1002/bit.24584
Wen DY, Vecchi MM, Gu S, Su LH, Dolnikova J, Huang YM, Foley SF, Garber E, Pederson N, Meier W (2009) Discovery and investigation of misincorporation of serine at asparagine positions in recombinant proteins expressed in chinese hamster ovary cells. J Biol Chem 284:32686–32694
Wilkens CA, Altamirano C, Gerdtzen ZP (2011) Comparative metabolic analysis of lactate for CHO cells in glucose and galactose. Biotechnol Bioproc E 16:714–724
Wu C, Du C, Gubbens J, Choi YH, van Wezel GP (2015) Metabolomics-driven discovery of a prenylated isatin antibiotic produced by Streptomyces species MBT28. J Nat Prod 78:2355–2363. doi:10.1021/acs.jnatprod.5b00276
Yamane-Ohnuki N, Kinoshita S, Inoue-Urakubo M, Kusunoki M, Iida S, Nakano R, Wakitani M, Niwa R, Sakurada M, Uchida K et al (2004) Establishment of FUT8 knockout Chinese hamster ovary cells: an ideal host cell line for producing completely defucosylated antibodies with enhanced antibody-dependent cellular cytotoxicity. Biotechnol Bioeng 87:614–622. doi:10.1002/bit.20151
Yanai K, Murakami T, Bibb M (2006) Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Proc Natl Acad Sci USA 103:9661–9666. doi:10.1073/pnas.0603251103
Yongky A, Lee J, Le T, Mulukutla BC, Daoutidis P, Hu WS (2015) Mechanism for multiplicity of steady states with distinct cell concentration in continuous culture of mammalian cells. Biotechnol Bioeng 112:1437–1445. doi:10.1002/bit.25566
Yoo YJ, Hwang JY, Shin HL, Cui H, Lee J, Yoon YJ (2015) Characterization of negative regulatory genes for the biosynthesis of rapamycin in Streptomyces rapamycinicus and its application for improved production. J Ind Microbiol Biotechnol 42:125–135. doi:10.1007/s10295-014-1546-9
Zabala D, Brana AF, Florez AB, Salas JA, Mendez C (2013) Engineering precursor metabolite pools for increasing production of antitumor mithramycins in Streptomyces argillaceus. Metab Eng 20:187–197. doi:10.1016/j.ymben.2013.10.002
Zha W, Rubin-Pitel SB, Shao Z, Zhao H (2009) Improving cellular malonyl-CoA level in Escherichia coli via metabolic engineering. Metab Eng 11:192–198. doi:10.1016/j.ymben.2009.01.005
Zhang L, Inniss MC, Han S, Moffat M, Jones H, Zhang B, Cox WL, Rance JR, Young RJ (2015) Recombinase-mediated cassette exchange (RMCE) for monoclonal antibody expression in the commercially relevant CHOK1SV cell line. Biotechnol Prog 31:1645–1656. doi:10.1002/btpr.2175
Zhang XQ, Lok SHL, Kon OL (1998) Stable expression of human alpha-2,6-sialyltransferase in Chinese hamster ovary cells: functional consequences for human erythropoietin expression and bioactivity. BBA Gen Subj 1425:441–452
Zhou M, Crawford Y, Ng D, Tung J, Pynn AF, Meier A, Yuk IH, Vijayasankaran N, Leach K, Joly J et al (2011) Decreasing lactate level and increasing antibody production in Chinese Hamster Ovary cells (CHO) by reducing the expression of lactate dehydrogenase and pyruvate dehydrogenase kinases. J Biotechnol 153:27–34. doi:10.1016/j.jbiotec.2011.03.003
Zhou W, Rehm J, Hu WS (1995) High viable cell concentration fed-batch cultures of hybridoma cells through on-line nutrient feeding. Biotechnol Bioeng 46:579–587. doi:10.1002/bit.260460611
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Bandyopadhyay, A.A., Khetan, A., Malmberg, LH. et al. Advancement in bioprocess technology: parallels between microbial natural products and cell culture biologics. J Ind Microbiol Biotechnol 44, 785–797 (2017). https://doi.org/10.1007/s10295-017-1913-4
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DOI: https://doi.org/10.1007/s10295-017-1913-4