Biology:Microbial cell factory

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Schematic workflow for microbial factory optimization

Microbial cell factory is an approach to bioengineering which considers microbial cells as a production facility in which the optimization process largely depends on metabolic engineering.[1] MCFs is a derivation of cell factories, which are engineered microbes and plant cells.[2] In 1980s and 1990s, MCFs were originally conceived to improve productivity of cellular systems and metabolite yields through strain engineering.[3] A MCF develops native and nonnative metabolites through targeted strain design.[4] In addition, MCFs can shorten the synthesis cycle while reducing the difficulty of product separation.

[5]

History

Prior to MCFs, scientists employed traditional engineering techniques to produce various commodities. These methodologies include modifying metabolic pathways, eliminating enzymes, or the balancing of ATP to drive metabolic flux.[6] However, when these approaches were applied for industrial productions, they could not withstand the industrial environments that consisted of toxins and fluctuating temperatures.[6] Ultimately, the techniques were never able to scale up and output bio-products that were obtained in the laboratory.[7]

Thus, MCFs were developed by using a heterogenous biosynthesis pathway in a microbial host.[8] As a host, MCFs take in various substrates and convert them into valuable compounds.[9] These products can range from fuels, chemical, food ingredients, to pharmaceuticals.[10]  

Structure

Cell Wall

In microbial cells, the cell walls are either Gram-positive or Gram-negative. These outcomes are based on the Gram Stain test. Gram-positive cell walls have thick peptidoglycan layer and no outer lipid membrane while Gram-negative bacteria have a thin peptidoglycan layer and an outer lipid membrane.[11] Although a thick Gram-positive cell wall is advantageous, it is easier to attack as the peptidoglycan layer absorbs antibiotics and cleaning products. A Gram-negative cell wall is more resistant to such attacks and more difficult to destroy.  

Membrane

The membrane of microbial cells are bilayers, composed of phospholipids.[12] The phospholipids may range in chain length to branching. Ultimately, the phospholipid will determine the membrane properties, such as fluidity and charge, that will regulate the interactions with nearby proteins. In addition, the membrane oversees the development of the cell's morphology and cell sizes.[13] Escherichia coli is often utilized a base line to differentiate and define the membrane of MCFs.[14]

Nucleoid

The nucleoid forms an irregular shaped region within a prokaryote cell, containing all or majority of the genetic material to reproduce.[15] The nucleoid controls the activity of the MCF and reproduction of itself and products.

Current Developments

Current methods of programming MCFs utilize strain engineering, which rely on random mutagenesis.[16] In addition, the conventional techniques are labor-intensive, timely, and difficult to analyze.[16] This has led many scientific trials to utilize genomic editing tools to improve MCFs, such as ZFNs, TALENs, and CRISPR. These approaches allow genetic manipulation and analysis, specifically creating double stranded breaks within a genome sequence.

ZFNs

Zinc-finger nucleases (ZFNs) were the first genomic editing tool to be able to target any genomic site. By inducing a double-stranded break, ZFNs can facilitate targeted editing. However, when employed to reinforce MCFs, ZFNs have an unusual low success rate. In various trials, the ZFNs were unable to obtain a three-finger array or the triplet was unable to be assembled into a new sequence.[16][17] Thus, incorporation of ZFNs into MCFs has remained strenuous and costly.

TALENs

Transcription activator-like effector nucleases (TALENs) work in a similar manner to ZFNs, but TALENs are based on fusion proteins. TALENs have been applied to numerous MCFs, such as yeast and zebrafish.[18] Many developments has explored fairyTALE, a liquid phase synthesis TALEN platform, to create nucleases, activators, and repressors for MCFs.[19] Although TALENs have fewer obstacles than ZFNs, they are still troublesome as assembling large quantities of repeats into an array remains a significant problem.[20]

CRISPR

Clustered regularly interspaced palindromic repeats (CRISPR) and its associated proteins (Cas) has become one of the most popular genome editing tools due to its efficiency and low cost. The CRISPR/CAS9 has been utilized to enhance MCFs to produce yeast, bacteria, and E.coli.[21] When optimizing yeast, CRISPR/CAS9 promoting S.pyogenes has been found to be the most influential strategy. For E.coli, studies have determined a strategy preventing genome instability to be the most robust metabolic engineering approach regardless of the specific methodology.[21]

Large-Scale Application

The most significant advantage of MCFs is the ability to be utilized in industrial environments with minimal limitations. Through metabolic engineering, MCFs rely on innovative strategic tools for the development and optimization of metabolic and gene regulatory networks for efficient production.[22] Going from lab to large scale development involves consideration of three factors: product yield, productivity, and the product titre.[22] A common dilemma however is the trade-off between product yield and productivity. If a company maximizes productivity, they will ultimately lower their product yield and vice versa.

To combat this issue, strategies have been developed to maximize all three factors. One of the most common techniques is utilizing fed-batch culture. Fed-batch culture is, in the broadest sense, defined as an operational technique in biotechnological processes where one or more nutrients (substrates) are fed (supplied) to the bioreactor during cultivation and in which the product(s) remain in the bioreactor until the end of the run.[23] Another method is utilizing continuous cultivation strategy. The premise behind continuous cultivation is to maintain a steady-state cell metabolism over long periods of times.[24] By having multiple approaches for MCF, companies may customize each process to their specific product(s).

Commercialization

The commercialization of MCFs has ranged from chemical to biofuels.

Table 1: Commercialization of MCFs[22]
Product Production Organism Status Feed Stock Companies Reference
Chemical
Acetone Clostridium acetobuylicum Commercialized Corn Green Biologics www.greenbiologics.com
Citric Acid Aspergillus niger Commercialized
Succinic Acid E. coli Commercialized Corn Sugars BioAmber www.bio-amber.com
E. coli Commercialized Sucrose Myriant www.myriant.com
S. cerevisiae Commercialized Starch, sugars Reverdia www.reverdia.com
B. succiniproducens Commercialized Glycerol, sugars Succinity www.succinity.com
Lactic Acid Commercialized Corn sugars and more NatureWorks www.natureworksllc.com
Itaconic Acid Aspergillus terreus Commercialized Biochemistry Qingdao Kehai www.kehai.info/en
1,3-PDO E. coli Commercialized Corn Sugars DuPont Tate & Lyle www.duponttateandlyle.com
1,3-BDO Demonstrated Genomatica and Versalis www.genomatica.com
1,4-BDO E.coli Commercialized Sugar Genomatica and DuPont Tate & Lyle www.genomatica.com
1,5-PDA Commercialized Sugar Cathay Industrial Biotech www.cathaybiotech.com
3-HP Commercialized Metabolix www.metabolix.com
Demonstration Novozymes and Cargill www.novozymes.com
Isoprene S. cerevisiae Preparing Sugar, cellulose Amyris, Braskem, Michelin www.amyris.com
Preparing DuPont, Goodyear www.biosciences.dupont.com
Isobutene E. coli Demonstration Glucose, sucrose Global Bioenergies www.global-bioenergies.com
Adipic acid Candida sp. Demonstration Plant oils Verdezyne www.verdezyne.com
Sebacic acid Candida sp. Demonstration Plant oils Verdezyne www.verdezyne.com
DDDA Candida sp. Under commercialization Plant oils Verdezyne www.verdezyne.com
Squalene S. cerevisiae Commercialized Sugarcane Amyris www.amyris.com
PHA E. coli Commercialized Metabolix www.metabolix.com
Fuels
Ethanol S. cerevisiae, Zymomonas mobilis, Kluyveromyces marxianus Commercialized Sugarcane, corn sugar, lignocellulose Many
Clostridium autoethanogenum Demonstration Flue gas Lanzatech www.lazatech.com
Farnesene S. cerevisiae Commercialized Amyris www.amyris.com
Butanol Clostridium acetobuylicum Commercialized Corn Green Biologics www.greenbiologics.com
Isobutanol Yeast Commercialized Sugars Gevo www.gevo.com

References

  1. ↑ Villaverde, Antonio (2010-07-05). "Nanotechnology, bionanotechnology and microbial cell factories". Microbial Cell Factories 9: 53. doi:10.1186/1475-2859-9-53. ISSN 1475-2859. PMID 20602780. 
  2. ↑ "Cell factory - benefits and potential of cell factories | VTT" (in en). https://www.vttresearch.com/en/ourservices/cell-factory. 
  3. ↑ Bailey, James E. (1991-06-21). "Toward a Science of Metabolic Engineering" (in en). Science 252 (5013): 1668–1675. doi:10.1126/science.2047876. ISSN 0036-8075. PMID 2047876. Bibcode: 1991Sci...252.1668B. https://www.science.org/doi/10.1126/science.2047876. 
  4. ↑ Gohil, Nisarg; Bhattacharjee, Gargi; Singh, Vijai (2021), "An introduction to microbial cell factories for production of biomolecules" (in en), Microbial Cell Factories Engineering for Production of Biomolecules (Elsevier): pp. 1–19, doi:10.1016/b978-0-12-821477-0.00021-0, ISBN 978-0-12-821477-0, https://linkinghub.elsevier.com/retrieve/pii/B9780128214770000210, retrieved 2022-04-18 
  5. ↑ Liu, Xiaonan; Ding, Wentao; Jiang, Huifeng (2017-07-19). "Engineering microbial cell factories for the production of plant natural products: from design principles to industrial-scale production". Microbial Cell Factories 16 (1): 125. doi:10.1186/s12934-017-0732-7. ISSN 1475-2859. PMID 28724386. 
  6. ↑ 6.0 6.1 Gong, Zhiwei; Nielsen, Jens; Zhou, Yongjin J. (October 2017). "Engineering Robustness of Microbial Cell Factories" (in en). Biotechnology Journal 12 (10): 1700014. doi:10.1002/biot.201700014. ISSN 1860-6768. PMID 28857502. https://onlinelibrary.wiley.com/doi/10.1002/biot.201700014. 
  7. ↑ Ling, Hua; Teo, Weisuong; Chen, Binbin; Leong, Susanna Su Jan; Chang, Matthew Wook (October 2014). "Microbial tolerance engineering toward biochemical production: from lignocellulose to products" (in en). Current Opinion in Biotechnology 29: 99–106. doi:10.1016/j.copbio.2014.03.005. PMID 24743028. https://linkinghub.elsevier.com/retrieve/pii/S0958166914000706. 
  8. ↑ Zhao, Liting; Ma, Zhongbao; Yin, Jian; Shi, Guiyang; Ding, Zhongyang (April 2021). "Biological strategies for oligo/polysaccharide synthesis: biocatalyst and microbial cell factory" (in en). Carbohydrate Polymers 258: 117695. doi:10.1016/j.carbpol.2021.117695. PMID 33593568. https://linkinghub.elsevier.com/retrieve/pii/S0144861721000825. 
  9. ↑ Navarrete, Clara; Jacobsen, Irene Hjorth; Martínez, José Luis; Procentese, Alessandra (July 2020). "Cell Factories for Industrial Production Processes: Current Issues and Emerging Solutions" (in en). Processes 8 (7): 768. doi:10.3390/pr8070768. ISSN 2227-9717. 
  10. ↑ Keasling, Jay D. (2010-12-03). "Manufacturing Molecules Through Metabolic Engineering" (in en). Science 330 (6009): 1355–1358. doi:10.1126/science.1193990. ISSN 0036-8075. PMID 21127247. Bibcode: 2010Sci...330.1355K. https://www.science.org/doi/10.1126/science.1193990. 
  11. ↑ Sizar, Omeed; Unakal, Chandrashekhar G. (2022), "Gram Positive Bacteria", StatPearls (Treasure Island (FL): StatPearls Publishing), PMID 29261915, http://www.ncbi.nlm.nih.gov/books/NBK470553/, retrieved 2022-04-18 
  12. ↑ Strahl, Henrik; Errington, Jeff (2017-09-08). "Bacterial Membranes: Structure, Domains, and Function" (in en). Annual Review of Microbiology 71 (1): 519–538. doi:10.1146/annurev-micro-102215-095630. ISSN 0066-4227. PMID 28697671. https://www.annualreviews.org/doi/10.1146/annurev-micro-102215-095630. 
  13. ↑ Guo, Liang; Diao, Wenwen; Gao, Cong; Hu, Guipeng; Ding, Qiang; Ye, Chao; Chen, Xiulai; Liu, Jia et al. (March 2020). "Engineering Escherichia coli lifespan for enhancing chemical production" (in en). Nature Catalysis 3 (3): 307–318. doi:10.1038/s41929-019-0411-7. ISSN 2520-1158. https://www.nature.com/articles/s41929-019-0411-7. 
  14. ↑ Wang, Jianli; Ma, Wenjian; Wang, Xiaoyuan (2021-03-20). "Insights into the structure of Escherichia coli outer membrane as the target for engineering microbial cell factories". Microbial Cell Factories 20 (1): 73. doi:10.1186/s12934-021-01565-8. ISSN 1475-2859. PMID 33743682. 
  15. ↑ Youssef, Noor; Budd, Aidan; Bielawski, Joseph P. (2019), Anisimova, Maria, ed., "Introduction to Genome Biology and Diversity" (in en), Evolutionary Genomics: Statistical and Computational Methods, Methods in Molecular Biology (New York, NY: Springer) 1910: pp. 3–31, doi:10.1007/978-1-4939-9074-0_1, ISBN 978-1-4939-9074-0, PMID 31278660 
  16. ↑ 16.0 16.1 16.2 Si, Tong; Xiao, Han; Zhao, Huimin (2015-11-15). "Rapid Prototyping of Microbial Cell Factories via Genome-scale Engineering". Biotechnology Advances 33 (7): 1420–1432. doi:10.1016/j.biotechadv.2014.11.007. ISSN 0734-9750. PMID 25450192. 
  17. ↑ Ramirez, Cherie L.; Foley, Jonathan E.; Wright, David A.; Müller-Lerch, Felix; Rahman, Shamim H.; Cornu, Tatjana I.; Winfrey, Ronnie J.; Sander, Jeffry D. et al. (May 2008). "Unexpected failure rates for modular assembly of engineered zinc fingers" (in en). Nature Methods 5 (5): 374–375. doi:10.1038/nmeth0508-374. ISSN 1548-7105. PMID 18446154. 
  18. ↑ Li, T.; Huang, S.; Zhao, X.; Wright, D. A.; Carpenter, S.; Spalding, M. H.; Weeks, D. P.; Yang, B. (2011). "Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes". Nucleic Acids Research 39 (14): 6315–6325. doi:10.1093/nar/gkr188. PMID 21459844. 
  19. ↑ Liang, Jing; Chao, Ran; Abil, Zhanar; Bao, Zehua; Zhao, Huimin (2014-02-21). "FairyTALE: A High-Throughput TAL Effector Synthesis Platform" (in en). ACS Synthetic Biology 3 (2): 67–73. doi:10.1021/sb400109p. ISSN 2161-5063. PMID 24237314. https://pubs.acs.org/doi/10.1021/sb400109p. 
  20. ↑ Briggs, A. W.; Rios, X.; Chari, R.; Yang, L.; Zhang, F.; Mali, P.; Church, G. M. (2012). "Iterative capped assembly: Rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers". Nucleic Acids Research 40 (15): e117. doi:10.1093/nar/gks624. PMID 22740649. PMC 3424587. https://academic.oup.com/nar/article/40/15/e117/1225035. Retrieved 2022-04-18. 
  21. ↑ 21.0 21.1 Jakočiūnas, Tadas; Jensen, Michael K.; Keasling, Jay D. (2016-03-01). "CRISPR/Cas9 advances engineering of microbial cell factories" (in en). Metabolic Engineering 34: 44–59. doi:10.1016/j.ymben.2015.12.003. ISSN 1096-7176. PMID 26707540. https://www.sciencedirect.com/science/article/pii/S1096717615001597. 
  22. ↑ 22.0 22.1 22.2 Gustavsson, Martin; Lee, Sang Yup (September 2016). "Prospects of microbial cell factories developed through systems metabolic engineering" (in en). Microbial Biotechnology 9 (5): 610–617. doi:10.1111/1751-7915.12385. ISSN 1751-7915. PMID 27435545. 
  23. ↑ Yamanè, Tsuneo; Shimizu, Shoichi (1984). "Fed-batch techniques in microbial processes" (in en). Bioprocess Parameter Control. Advances in Biochemical Engineering/Biotechnology (Berlin, Heidelberg: Springer) 30: 147–194. doi:10.1007/BFb0006382. ISBN 978-3-540-39004-6. https://link.springer.com/chapter/10.1007/BFb0006382. 
  24. ↑ Nieto-Taype, Miguel Angel; Garcia-Ortega, Xavier; Albiol, Joan; Montesinos-Seguí, José Luis; Valero, Francisco (2020-06-25). "Continuous Cultivation as a Tool Toward the Rational Bioprocess Development With Pichia Pastoris Cell Factory". Frontiers in Bioengineering and Biotechnology 8: 632. doi:10.3389/fbioe.2020.00632. ISSN 2296-4185. PMID 32671036. 



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