E. coli: The Smallest Factories in the World

Macromoltek, Inc.
Jul 5 · 4 min read

Escherichia coli, more commonly known as E. coli, is a versatile tool in many biological labs. This gram-negative bacterium has a long history in medical, genetic, and biochemical research, and will continue to be used in groundbreaking research for years to come. These microscopic organisms have played a common role in all these fields — to produce genetic and biochemical products with their established cellular processes. By utilizing engineered strains of the bacterium and circular snippets of DNA (known as plasmids), E. coli can clone itself to turn one plasmid into millions. Thereby, it’s ideal for studying gene pathways and producing proteins — including human antibodies.

Petri dish containing E.coli colonies. PC Fernan Federici & Jim Haseloff. https://wellcomecollection.org/works/aqfr8nvc

History of E. coli in Science

The discovery of E. coli dates back to 1885, when Dr. Theodor Escherich isolated E. coli from the feces of his patients. He named his discovery Bacterium coli commune (1). This bacterium will later be named after Dr. Escherich as Escherichia coli to match the modern taxonomy nomenclature. Since its discovery, E. coli has been used as a model organism in microbiological research due to its capabilities to grow and adapt in vitro (outside of a living organism). Much like other model organisms, E. coli have been adapted to different capabilities in the lab — from being highly efficient at cloning to biochemical molecule production.

E. coli was one of the first model organisms to have its genome fully sequenced. In 1997. Dr. Blattner was the lead of the team to sequence the full 4,639,221-base pair sequence of the circular DNA genome of the E. coli K-12 strain (2). This discovery was one of the first of many complete genomic sequencing projects that were quick to follow. Another hallmark discovery regarding E. coli was the discovery and use of recombinant DNA plasmids in the 1970s. Using restriction enzymes, Dr. Stanley Cohen and Herbert Boyer utilized recombinant plasmids to engineer E. coli to produce human insulin (3). Using similar methods, E. coli have been engineered to produce a wide variety of products that are used in human medicine. This has opened the door into hundreds of different research endeavors including new ways to combat human diseases.

Use of E. coli Today

Within Macromoltek’s antibody production lab, E. coli cells are utilized in the production and testing of humanized, in silico designed antibodies. Two commonly used strains in protein production are the E. coli DH5-Alpha and BL21 strains, both having different uses in the protein production process. The DH5 strain has been engineered for efficient plasmid cloning. Three key mutations have been made in the genome of this strain: the lacZ Delta M15 mutation, the endA1 mutation, and the recA1 mutation (4). These mutations are helpful for screening of positive transformations, reducing endonuclease degradation, and reducing homologous recombination of the engineered plasmid which increasing the efficiency of the initial transformation process.

The BL21 strain, more specifically the BL21(DE3) strain, has been specialized for protein production. These cells have a T7 RNA polymerase gene that is controlled by the lacUV5 promoter that, when induced, will cause the cells to produce the protein encoded in the recombinant plasmid (5). These two strains, when used in conjunction, allow for the efficient and reliable process of antibody production.

Electron micrograph of E. coli, close-up. PC: David Gregory & Debbie Marshall. https://wellcomecollection.org/works/fqjs8eft

Appreciating E. coli

E. coli have a long, impactful history in laboratories, and this history is important to know in modern science. As scientists, it is beneficial to understand where our modern methods have come from so we may better understand expected behavior, recognize when things are amiss, and diagnose possible causes. E. coli have been a vital part of many amazing discoveries in medicine and biochemistry, and they deserve some more time in the spotlight.

Links and Citations:

  1. Escherich T (1885). “Die Darmbakterien des Neugeborenen und Säuglinge”. Fortschr. Med. 3: 515–522.
  2. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (September 1997). “The complete genome sequence of Escherichia coli K-12”. Science. 277 (5331): 1453–62.
  3. Cohen SN, Chang AC, Boyer HW, Helling RB (November 1973). “Construction of biologically functional bacterial plasmids in vitro”. Proc Natl Acad Sci USA. 70 (11): 3240–4.
  4. Taylor RG, Walker DC, McInnes RR. (1993). “E. coli host strains significantly affect the quality of small scale plasmid DNA preparations used for sequencing”. Nucleic acids research. 21 (7), 1677–78.
  5. Jeong H, Kim HJ, Lee SJ (March 2015). “Complete Genome Sequence of Escherichia coli Strain BL21”. Genome Announcment. 19;3 (2): e00134–15.

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Macromoltek, Inc.

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Welcome to the Macromoltek blog. We're an Austin-based biotech firm focused on using computers to further the discovery and design of antibodies.