Skip to main content

Microbial Production of Industrial Proteins and Enzymes Using Metabolic Engineering

  • Chapter
  • First Online:
Engineering of Microbial Biosynthetic Pathways

Abstract

Metabolic engineering is a field of science, which takes advantage of previously gathered information about a particular pathway in a living organism and utilizes this for the improvement of product that could be either metabolite, enzyme, or any protein. Advances in various field of science specifically r-DNA technology, bioinformatics, synthetic biology, molecular genetics as well as other protein engineering technologies had given wings to metabolic engineering. Metabolic engineering has the capacity to mold the flux of a completely enzymatic pathway to a very newly designed pathway. It allows the modulation and production of either previously working metabolite or the production of a new novel enzyme in a different microbial strain. In the present era, there is huge demand of microbial enzymes and proteins for various purposes such as medication, oil and gas industry, dairy industry, baking industry, etc. Microbial strains are utilized as micro factories for the production of microbial enzymes and proteins via metabolic engineering. Therefore, in this book chapter we are dealing with the various criteria that are utilized for the selection of the strains, various approaches that are routinely utilized for the higher expression of genes, as well as various metabolic engineering strategies.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Apte AA, Senger RS, Fong SS (2014) Designing novel cellulase systems through agent-based modeling and global sensitivity analysis. Bioengineered 5:1–11

    Google Scholar 

  • Bartual SG, Garcia-Doval C, Alonso J, Schoehn G, van Raaij MJ (2010) Two-chaperone assisted soluble expression and purification of the bacteriophage T4 long tail fibre protein gp37. Protein Expr Purif 70:116–121

    PubMed  Google Scholar 

  • Bernal V, Castaño-Cerezo S, Gallego-Jara J, Écija-Conesa A, de Diego T et al (2014) Regulation of bacterial physiology by lysine acetylation of proteins. New Biotechnol 31:586–595

    CAS  Google Scholar 

  • Brinkworth AJ, Malcolm DS, Pedrosa AT, Roguska K, Shahbazian S, Graham JE et al (2011) Chlamydia trachomatis Slc1 is a type III secretion chaperone that enhances the translocation of its invasion effector substrate TARP. Mol Microbiol 82:131–144

    CAS  PubMed  PubMed Central  Google Scholar 

  • Buchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T et al (2013) Path 2 models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol 7:116

    PubMed  PubMed Central  Google Scholar 

  • Burgess-Brown NA, Sharma S, Sobott F, Loenarz C, Oppermann U, Gileadi O (2008) Codon optimization can improve expression of human genes in Escherichia coli: a multi-gene study. Protein Expr Purif 59:94–102

    CAS  PubMed  Google Scholar 

  • Calderone TL, Stevens RD, Oas TG (1996) High-level misincorporation of lysine for arginine at AGA codons in a fusion protein expressed in Escherichia coli. J Mol Biol 262:407–412

    CAS  PubMed  Google Scholar 

  • Chao YP, Wen CS, Wang JY (2004) A facile and efficient method to achieve LacZ overproduction by the expression vector carrying the thermoregulated promoter and plasmid copy number. Biotechnol Prog 20:420–425

    CAS  PubMed  Google Scholar 

  • Emruzi Z, Aminzadeh S, Karkhane AA, Alikhajeh J, Haghbeen K, Gholami D (2018) Improving the thermostability of Serratia marcescens B4A chitinase via G191V site-directed mutagenesis. Int J Biol Macromol 116:64–70

    CAS  PubMed  Google Scholar 

  • Ferrer-Miralles N, Villaverde A (2013a) Bacterial cell factories for recombinant protein production; expanding the catalogue. Microb Cell Factories 12:113

    Google Scholar 

  • Ferrer-Miralles N, Villaverde A (2013b) Bacterial cell factories for recombinant protein production; expanding the catalogue. Microb Cell Fact 12:113

    PubMed  PubMed Central  Google Scholar 

  • Fisher AK, Freedman BG, Bevan DR, Senger RS (2014) A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories. Comput Struct Biotechnol J 11(18):91–99

    PubMed  PubMed Central  Google Scholar 

  • Fong SS, Palsson BO (2004) Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 36:1056–1058

    CAS  PubMed  Google Scholar 

  • Guazzaroni ME, Silva-Rocha R, Ward RJ (2015) Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening. Microb Biotechnol 8(1):52–64

    CAS  PubMed  Google Scholar 

  • Gustafsson C, Govindarajan S, Minshull J (2004) Codon bias and heterologous protein expression. Trends Biotechnol 22:346–353

    CAS  PubMed  Google Scholar 

  • Hartl FU (1996) Molecular chaperones in cellular protein folding. Nature 381:571–579

    CAS  PubMed  Google Scholar 

  • Hartl FU, Bracher A, Hayer-Hartl M (2011) Molecular chaperones in protein folding and proteostasis. Nature 475:324–332

    CAS  Google Scholar 

  • Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B et al (2010) High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 28:977–982

    CAS  PubMed  Google Scholar 

  • Hsieh PC, Vaisvila R (2013) Protein engineering: single or multiple site-directed mutagenesis. Methods Mol Biol 978:173–186

    CAS  PubMed  Google Scholar 

  • Hutterer KM, Zhang Z, Michaels ML, Belouski E, Hong RW, Shah B et al (2012) Targeted codon optimization improves translational fidelity for an Fc fusion protein. Biotechnol Bioeng 109:2770–2777

    CAS  PubMed  Google Scholar 

  • Irfan M, Gonzalez CF, Raza S, Rafiq M, Hasan F, Khan S, Shah AA (2018) Improvement in thermostability of xylanase from Geobacillus thermodenitrificans C5 by site directed mutagenesis. Enzym Microb Technol 111:38–47

    CAS  Google Scholar 

  • Ismail NF, Hamdan S, Mahadi NM, Murad AMA, Rabu A, Bakar FDA et al (2011) A mutant L-asparaginase II signal peptide improves the secretion of recombinant cyclodextrin glucanotransferase and the viability of Escherichia coli. Biotechnol Lett 33:999–1005

    CAS  PubMed  Google Scholar 

  • Kim S, Lee SB (2006) Rare codon clusters at 5′-end influence heterologous expression of archaeal gene in Escherichia coli. Protein Expr Purif 50:49–57

    CAS  PubMed  Google Scholar 

  • Kim YM, Shimizu R, Nakai H, Mori H, Okuyama M, Kang MS et al (2011) Truncation of N- and C-terminal regions of Streptococcus mutans dextranase enhances catalytic activity. Appl Microbiol Biotechnol 91:329–339

    CAS  PubMed  Google Scholar 

  • Kleber-Janke T, Becker WM (2000) Use of modified BL21 (DE3) Escherichia coli cells for high-level expression of recombinant peanut allergens affected by poor codon usage. Protein Expr Purif 19:419–424

    CAS  PubMed  Google Scholar 

  • Liu S-L, Du K, Chen W-Z, Liu G, Xing M (2012) Effective approach to greatly enhancing selective secretion and expression of three cytoplasmic enzymes in Escherichia coli through synergistic effect of EDTA and lysozyme. J Ind Microbiol Biotechnol 39:1301–1307

    PubMed  Google Scholar 

  • Lu Z, Wang Q, Jiang S, Zhang G, Ma Y (2016) Truncation of the unique N-terminal domain improved the thermos-stability and specific activity of alkaline α-amylase Amy703. Sci Rep 6:22465

    CAS  PubMed  PubMed Central  Google Scholar 

  • Makoff A, Parry N, Dicken L (1989) Translational fusions with fragments of the trpE gene improve the expression of a poorly expressed heterologous gene in Escherichia coli. J Gen Microbiol 135:11–24

    CAS  PubMed  Google Scholar 

  • Mattanovich D, Branduardi P, Dato L, Gasser B, Sauer M et al (2012) Recombinant protein production in yeasts. Methods Mol Biol 824:329–358

    CAS  PubMed  Google Scholar 

  • Mendez-Perez D, Gunasekaran S, Orler VJ, Pfleger BF (2012) A translation-coupling DNA cassette for monitoring protein translation in Escherichia coli. Metab Eng 14:298–305

    CAS  PubMed  Google Scholar 

  • Newbury SF, Smith NH, Robinson EC, Hiles ID, Higgins CF (1987) Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell 48:297–310

    CAS  PubMed  Google Scholar 

  • Okesli A, Cooper LE, Fogle EJ, van der Donk WA (2011) Nine post-translational modifications during the biosynthesis of cinnamycin. J Am Chem Soc 133:13753–13760

    CAS  PubMed  PubMed Central  Google Scholar 

  • Olins PO, Rangwala S (1989) A novel sequence element derived from bacteriophage T7 mRNA acts as an enhancer of translation of the lacZ gene in Escherichia coli. J Biol Chem 264:16973–16976

    CAS  PubMed  Google Scholar 

  • Osterlehner A, Simmeth S, Göpfert U (2011) Promoter methylation and transgene copy numbers predict unstable protein production in recombinant Chinese hamster ovary cell lines. Biotechnol Bioeng 108:2670–2681

    CAS  PubMed  Google Scholar 

  • Pandhal J, Woodruff LBA, Jaffe S, Desai P, Ow SY et al (2013) Inverse metabolic engineering to improve Escherichia coli as an N-glycosylation host. Biotechnol Bioeng 110:2482–2493

    CAS  PubMed  Google Scholar 

  • Pérez-Pérez J, Márquez G, Barbero JL, Gutiérrez J (1994) Increasing the efficiency of protein export in Escherichia coli. Nat Biotechnol 12:178–180

    Google Scholar 

  • Ringquist S, Shinedling S, Barrick D, Green L, Binkley J, Stormo GD et al (1992) Translation initiation in Escherichia coli: sequences within the ribosome-binding site. Mol Microbiol 6:1219–1229

    CAS  PubMed  Google Scholar 

  • Rosano GL, Ceccarelli EA (2014) Recombinant protein expression in Escherichia coli: advances and challenges. Front Microbiol 5:172

    PubMed  PubMed Central  Google Scholar 

  • Sprengart ML, Fuchs E, Porter A (1996) The downstream box: an efficient and independent translation initiation signal in Escherichia coli. EMBO J 15:665

    CAS  PubMed  PubMed Central  Google Scholar 

  • Steffens DL, Williams JG (2007) Efficient site-directed saturation mutagenesis using degenerate oligonucleotides. J Biomol Tech 18(3):147

    PubMed  PubMed Central  Google Scholar 

  • Tokunaga H, Arakawa T, Tokunaga M (2010) Novel soluble expression technologies derived from unique properties of halophilic proteins. Appl Microbiol Biotechnol 88:1223–1231

    CAS  PubMed  Google Scholar 

  • Urvoas A, Valerio-Lepiniec M, Minard P (2012) Artificial proteins from combinatorial approaches. Trends Biotechnol 30(10):512–520

    CAS  PubMed  Google Scholar 

  • Uthandi S, Prunetti L, De Vera IMS, Fanucci GE, Angerhofer A, Maupin-Furlow JA (2012) Enhanced archaeal laccase production in recombinant Escherichia coli by modification of N-terminal propeptide and twin arginine translocation motifs. J Ind Microbiol Biotechnol 39:1523–1532

    Google Scholar 

  • Wang Y, San KY, Bennett GN (2013) Cofactor engineering for advancing chemical biotechnology. Curr Opin Biotechnol 24:994–999

    CAS  PubMed  Google Scholar 

  • Ward OP (2012) Production of recombinant proteins by filamentous fungi. Biotechnol Adv 30(5):1119–1139

    CAS  PubMed  Google Scholar 

  • Yang H, Li J, Du G, Liu L (2017) Microbial production and molecular engineering of industrial enzymes: challenges and strategies. In: Biotechnology of microbial enzymes. Academic, Cambridge, pp 151–165

    Google Scholar 

  • Zhan J, Stayton P, Press OW (1998) Modification of ricin A chain, by addition of endoplasmic reticulum (KDEL) or Golgi (YQRL) retention sequences, enhances its cytotoxicity and translocation. Cancer Immunol Immunother 46:55–60

    CAS  PubMed  Google Scholar 

  • Zhang YB, Greenberg B, Lacks SA (1997) Analysis of a Streptococcus pneumoniae gene encoding signal peptidase I and overproduction of the enzyme. Gene 194:249–255

    CAS  PubMed  Google Scholar 

  • Zhang F, Carothers JM, Keasling JD (2012) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30:354–359

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Madhvi Joshi .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Doshi, P., Shri, M., Bhargava, P., Joshi, C.G., Joshi, M. (2020). Microbial Production of Industrial Proteins and Enzymes Using Metabolic Engineering. In: Singh, V., Singh, A., Bhargava, P., Joshi, M., Joshi, C. (eds) Engineering of Microbial Biosynthetic Pathways. Springer, Singapore. https://doi.org/10.1007/978-981-15-2604-6_12

Download citation

Publish with us

Policies and ethics