The Biotechnological Applications of E. coli

by Marianna Akritidou
Marianna is a biologist with over 4 years of experience in the fields of Cancer Immunology and Neuroimmunology

Type 1 diabetes (T1D) is a form of diabetes in which very little or no insulin is produced by the pancreas, which results in high blood sugar levels in the body. The cause of T1D is unknown, but it is believed to involve a combination of genetic and environmental factors.[1] Insulin is a hormone produced by the pancreas and is required from the body to use blood sugar. Treatment with insulin is required for T1D patients to survive.  

In order to have insulin massively produced, the technology of recombinant DNA is used. It is a technology that makes it possible to insert a human gene into the genetic material of a common bacterium. The bacterium normally used to produce insulin is Escherichia coli, and it is the most well-known microorganism with 340,000 research papers in PubMed database. Its value is shown just by its contribution to the fight against T1D, however it is used in many more cases, which are discussed below.

E.coli is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of endotherms.[2,3] E. coli stains Gram-negative because its cell wall is composed of a thin peptidoglycan layer and an outer membrane. The outer membrane provides a barrier to certain antibiotics, like penicillin.[4] Strains that possess flagella are motile.[5] E.coli attaches and effaces to the microvilli of the intestines via an adhesion molecule known as intimin.[6] Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in their hosts.[7] The harmless strains are part of the normal microbiota of the gut, and can benefit their hosts by producing vitamin K2,[8] and preventing colonization of the intestine with pathogenic bacteria, having a symbiotic relationship.[9] E. coli is expelled into the environment within fecal matter. The bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards.[10] E. coli and other facultative anaerobes constitute about 0.1% of gut microbiota.[11] Cells are normally able to survive outside the body for a limited amount of time,[12] although there are environmentally persistent E. coli which can survive for many days and grow outside a host.[13] The bacterium can be grown and cultured easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is a chemoheterotroph whose chemically defined medium must include a source of carbon and energy.[14] E. coli is the most widely studied prokaryotic model organism, and an important species in the fields of biotechnology and microbiology. Under favorable conditions, it takes around 20 minutes to reproduce.[15]

Plasmids are the most important tools not only for the manipulation of E. coli but also the foundation for the genetic engineering of many organisms, cloning and sequencing and generation of mutants. E. coli plasmids were the first ones to be extensively modified for such purposes,[16] for example ColE1, p15A and R6K for replication origin, Ampand Tetr as selection markers and LacZ, CcdB and Green Fluorescent protein (GFP) as additional elements required for positive clone selection and reporter protein fusions.

Genome modifications have occurred in order to better understand E. coli, thus several tools for genome modification have been developed. Some of the most important methods involve either the generation of deletion mutants by removing specific genes, one case being the use of the lambda Red system for inhibiting linear DNA degradation, and by homologous recombination the deletion of specific genes using PCR-derived selection marker cassettes with homologous sequences with target gene.[17, 18]

In biotechnology, biosensors are broadly defined as any device based on biological part, cell, tissue, or protein complex linked to a mechanical sensor or analytical receptor and providing a measurable signal proportional to the analyte in the reaction.[19,20] E. coli-based biosensors using plasmid or chromosomal constructs are useful for the detection of environmental traits or hazards or measuring cellular processes as any standard reporter system.[21] There are several reports where E. coli-based biosensors have been successful for detecting different traits: oxidants,[22,23] DNA-damaging compounds,[24] membrane-damaging compounds,[25] protein-damaging compounds,[26] aromatic compounds,[27] xenobiotics,[28] antibiotic panels using reporter strains without antibiotic selection,[29] etc.

The advancement of using E. coli for biotechnological applications based on synthetic approaches has led to the development of strains capable of synthesizing several novel compounds. E. coli is used in genetic engineering and synthetic biology, because it is a flexible platform for the efficient production of molecules for the pharmaceutical industry, metabolites and molecules relevant for food additives, pigments, and more recently complex aliphatic molecules.[30] Several aromatic compounds have been successfully synthesized in E. coli due to their biological activities (vitamins and antioxidants, for example), pigmentation (applied in different industrial processes), fragrance etc.[31]

Another direction is E. coli moving into biofuel production. There are several reports where E. coli has been successfully engineered for the synthesis of branched-chain fatty acids or short-chain fatty acids that can ultimately lead to the mass production of fuel precursors or useful materials derived from oil.[32, 33] Finally, an important field where E. coli is making an important contribution powered by synthetic biology is the antibiotic production. Recent efforts with known polyketides have started to give good production rates in E. coli, favoring the process of antibiotic production from different sources, eliminating the need for host growth standardization, and inducing conditions.[34]

Taken into consideration all the above, it is no wonder that E.coli is the most known prokaryotic organism, as it is well-studied, it is used in numerous biotechnological applications and will certainly be implemented in even more in the future.

We are grateful to Ms Akritidou for kindly providing the original article.


[1] “Diabetes Fact sheet N°312”. WHO. November 2016. Archived from the original on 26 August 2013

[2] Tenaillon O, Skurnik D, Picard B, Denamur E (March 2010). “The population genetics of commensal Escherichia coli”. Nature Reviews. Microbiology. 8 (3): 207–17. doi:10.1038/nrmicro2298. PMID 20157339

[3] Singleton P (1999). Bacteria in Biology, Biotechnology and Medicine (5th ed.). Wiley. pp. 444–454. ISBN 978-0-471-98880-9

[4] Tortora, Gerard (2010). Microbiology: An Introduction. San Francisco, CA: Benjamin Cummings. pp. 85–87, 161, 165. ISBN 978-0-321-55007-1

[5] Darnton NC, Turner L, Rojevsky S, Berg HC (March 2007). “On torque and tumbling in swimming Escherichia coli”. Journal of Bacteriology. 189 (5): 1756–64. doi:10.1128/JB.01501-06. PMC 1855780. PMID 17189361

[6] “E. Coli O157 in North America – microbewiki”

[7] Vogt RL, Dippold L (2005). “Escherichia coli O157:H7 outbreak associated with consumption of ground beef, June-July 2002”. Public Health Reports. 120 (2): 174–8. doi:10.1177/003335490512000211. PMC 1497708. PMID 15842119

[8] Bentley R, Meganathan R (September 1982). “Biosynthesis of vitamin K (menaquinone) in bacteria”. Microbiological Reviews. 46 (3): 241–80. doi:10.1128/MMBR.46.3.241-280.1982. PMC 281544. PMID 6127606

[9] Hudault S, Guignot J, Servin AL (July 2001). “Escherichia coli strains colonising the gastrointestinal tract protect germfree mice against Salmonella typhimurium infection”. Gut. 49 (1): 47–55. doi:10.1136/gut.49.1.47. PMC 1728375. PMID 11413110

[10] Russell JB, Jarvis GN (April 2001). “Practical mechanisms for interrupting the oral-fecal lifecycle of Escherichia coli”. Journal of Molecular Microbiology and Biotechnology. 3 (2): 265–72. PMID 11321582

[11] Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. (June 2005). “Diversity of the human intestinal microbial flora”. Science. 308 (5728): 1635–8. Bibcode:2005Sci…308.1635E. doi:10.1126/science.1110591. PMC 1395357. PMID 15831718

[12] Thompson A (4 June 2007). “E. coli Thrives in Beach Sands”. Live Science. Retrieved 3 December 2007.

[13] Montealegre MC, Roy S, Böni F, Hossain MI, Navab-Daneshmand T, Caduff L, et al. (December 2018). “Risk Factors for Detection, Survival, and Growth of Antibiotic-Resistant and Pathogenic Escherichia coli in Household Soils in Rural Bangladesh”. Applied and Environmental Microbiology. 84 (24): e01978–18. doi:10.1128/AEM.01978-18. PMC 6275341. PMID 30315075

[14] Tortora, Gerard (2010). Microbiology: An Introduction. San Francisco, CA: Benjamin Cummings. pp. 85–87, 161, 165. ISBN 978-0-321-55007-1.

[15] “Bacteria”. Microbiologyonline. Archived from the original on 27 February 2014. Retrieved 27 February 2014

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[17] Baba T, Ara T, Hasegawa M, et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006; 2:2006 0008

[18] Yamamoto N, Nakahigashi K, Nakamichi T, et al. Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol Syst Biol. 2009; 5:335

[19] Bhalla N, Jolly P, Formisano N, Estrela P. Introduction to biosensors. Essays Biochem. 2016; 60(1):1-8

[20] Daunert S, Barrett G, Feliciano JS, Shetty RS, Shrestha S, Smith-Spencer W. Genetically engineered whole-cell sensing systems: coupling biological recognition with reporter genes. Chem Rev. 2000; 100(7):2705-38

[21] Padilla-Martínez F, Carrizosa-Villegas LA, Rangel-Serrano Á, Paramo-Pérez I, Mondragón-Jaimes V, Anaya-Velázquez F, Padilla-Vaca F, Franco B. Cell damage detection using Escherichia coli reporter plasmids: fluorescent and colorimetric assays. Arch Microbiol. 2015; 197(6):815-21

[22] Belkin S, Smulski DR, Vollmer AC, Van Dyk TK, LaRossa RA. Oxidative stress detection with Escherichia coli harboring a katG’: lux fusion. Appl Environ Microbiol. 1996; 62:2252-6

[23] Lu C, Albano CR, Bentley WE, Rao G. Quantitative and kinetic study of oxidative stress regulons using green fluorescent protein. Biotechnol Bioeng. 2005; 89(5):574-87

[24] Vollmer AC, Belkin S, Smulski DR, Van Dyk TK, LaRossa RA. Detection of DNA damage by use of Escherichia coli carrying recA’: lux, uvrA’: lux, or alkA’: lux reporter plasmids. Appl Environ Microbiol. 1997; 63:2566-71

[25] Bechor O, Smulski DR, Van Dyk TK, LaRossa RA, Belkin S. Recombinant microorganisms as environmental biosensors: pollutants detection by Escherichia coli bearing fabA’: lux fusions. J Biotechnol. 2002; 94:125-32

[26] Van Dyk TK, Majarian WR, Konstantinov KB, Young RM, Dhurjati PS, LaRossa RA. Rapid and sensitive pollutant detection by induction of heat shock gene-bioluminescence gene fusions. Appl Environ Microbiol. 1994; 60(5):1414-20

[27] Anu Prathap MU, Chaurasia AK, Sawant SN, Apte SK. Polyaniline-based highly sensitive microbial biosensor for selective detection of lindane. Anal Chem. 2012; 84(15):6672-8

[28] Truffer F, Buffi N, Merulla D, Beggah S, van Lintel H, Renaud P, van der Meer JR, Geiser M. Compact portable biosensor for arsenic detection in aqueous samples with Escherichia coli bioreporter cells. Rev Sci Instrum. 2014; 85:015120

[29] Melamed S, Lalush C, Elad T, Yagur-Kroll S, Belkin S, Pedahzur R. A bacterial reporter panel for the detection and classification of antibiotic substances. Microb Biotechnol. 2012; 5(4):536-48. doi: 10.1111/j.1751-7915.2012.00333.x

[30] Becker J, Wittmann C. Systems metabolic engineering of Escherichia coli for the heterologous production of high value molecules-a veteran at new shores. Curr Opin Biotechnol. 2016; 42:178-88

[31] Tuli HS, Chaudhary P, Beniwal V, Sharma AK. Microbial pigments as natural color sources: current trends and future perspectives. J Food Sci Technol. 2015; 52:4669-78

[32] Koppolu V, Vasigala VK. Role of Escherichia coli in biofuel production. Microbiol Insights. 2016; 9:29-35

[33] Jawed K, Mattam AJ, Fatma Z, Wajid S, Abdin MZ, Yazdani SS. Engineered production of short chain fatty acid in Escherichia coli using fatty acid synthesis pathway. PLoS One. 2016; 11(7):e0160035

[34] Yang J, Xiong ZQ, Song SJ, Wang JF, Lv HJ, Wang Y. Improving heterologous polyketide production in Escherichia coli by transporter engineering. Appl Microbiol Biotechnol. 2015; 99(20):8691-700

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