Friday, December 21, 2012

E. coli

o We’ve all heard the name: E. coli.  

Escherichia coli.

Victory is ours! The Nobel Laureated (L to R) Francois Jacob, Jacques Monod, and Andre Lwoff. Source:
All good stories should start with a bunch of dudes in
white lab coats. This one involve the Nobel laureates
(L to R) Francois Jacob, Jacques Monod, and Andre
Lwoff. Source:

Most of us only care about this bacterium after an outbreak of food-borne illnessa, causing us to shun leafy greens or hamburgers for a while. But E. coli has another, brighter story to tell that might change your perspective, and it starts with the advent of modern microbiology. During the mid-20th century, a man by the name of Jacques Monod and his research compadre Francois Jacob were trying to understand gene regulation. E. coli was already becoming a model organism in microbiology, with its nutrition and growth characteristics and some genetic features already well described. Using the regulation of lactose metabolism in E. coli as a model, Monod and his colleagues uncovered a novel way by which organisms can regulate gene expression so as to maximize cellular efficiency (1) (For those of you who are reminded of introductory biology and the negative feedback loop of the lac operon, that’s what I’m talking about). As it turns out, Monod and his colleagues identified a universal mechanism of gene regulation, which is used by many different species and on many different genes (i.e. Tryptophan, 2). This discovery won the posse of Frenchmen the Nobel Prize in Physiology/Medicine in 1965.

In case this esoteric example isn't enough, E. coli has also been responsible for the careers of many other influential scientists: visit the Nobel Laureates website and search for “E. coli”, for instance, and you’ll get 75 hitsb. Clearly this microbe has played a leading role in discovering much of what we know about modern microbiology and genetics, and that role continues to this day in thousands of labs all over the world (including many labs I have worked in over the years, for topics ranging from neuron physiology to genetic engineering).

Microscopic image of E. coli after Gram staining. Based on traditional
microbiological methods, E. coli is a gram-negative rod that typically
occurs as single cells or doublets. Phylogenetically, it belongs to the
gammaproteobacterial group. Source: G.Kaiser.

E. coli is also one of the fastest reproducing bacteria on the planet, with a generation time in the lab of less than 20 minutesc. That equates to 24 generations in a single 8-hour work day, something that would take about 480d years for humans to achieve!

A recently published article in the journal Nature (4) takes advantage of this fast growth rate to trace the evolution of mutations in laboratory strains of E. coli, in what must be the longest laboratory study of evolution ever. You see, when it comes to evolution, what really matters is the rate of mutations. To get mutations in a normal population, you need DNA replication, which means you need cell division. Each time a cell replicates its DNA, it is guaranteed to make mistakes (at an immeasurably small rate of about 10-9 mistakes per base pair. A cool new study suggests that this rate might be slowing in humans![3]).

Schematic of the development of aerobic citrate (cit) metabolism in E. coli, as depicted by Hendrickson and Rainey (doi:/10.1038/nature11487). Lineages that end in a dot went extinct due to competition. Cit+ lineages acquired the ability to metabolize citrate when oxygen was present, a clear advantage. 3 evolutionary steps were outlined (4) starting with "potentiation", or the development of mutations that provide the potential for aerobic citrate metabolism; followed by "actualization", or organization of the new genes to actually metabolize citrate, and eventually led to "refinement", or increased gene activity that increased growth on citrate. Interestingly, only 1 of the 3 citrate-metabolizing lineages made it to the "refinement" stage...

Most of these mistakes go unnoticed because they don’t change the physical appearance or function of the organism. But, after many generations (and we are talking about thousands of generations), a non-lethal, life-changing mistake can happen. The astonishing feature of this study is that these laboratory strains of E. coli have been growing for over 40,000 generations. The populations were grown under selective (low glucose, high citrate) conditions to test the ability of E. coli to adapt to growth on citrate, a compound that the original populations were unable to metabolize. Amazingly, after about 10,000 generations some select individuals ‘evolved’ the ability to transport citrate in the presence of oxygen, and again after another ~8,000 generations.

To put this into perspective, if the cells divided at a conservative rate of once every 30 minutes, then 10,000 generations will have past in just over 200 days. Humans, for their entire existence (assuming that we evolved ~1 million years ago and reproduce every 20 years) have undergone only about 50,000 generations, highlighting one of the great values in studying evolutionary processes in microbes. Thus, this study demonstrates that the accumulation of mutations over time can lead to truly revolutionary changes in a species. Amazing! From there, one could easily envision a species becoming so different from it’s original conception that it would be considered novel.
Schematic Venn diagram illustrating the gene overlap between
different strains of E. coli (not to scale). The outlined area in the
center highlights the amount of genetic code shared by all strains.
Pretty small, huh?

Most people will continue to associate E. coli with illness, and certain populations can pose a serious public health risk. But modern genomics has taught us that we cannot judge all strains based on the evil of a few. Most strains live harmoniously in our guts and do helpful things, like aiding in vitamin absorption (5). In fact, of 60 randomly sequenced E. coli isolates, only 20% of their genetic code is shared! This means that different E. coli isolates are less genetically related than we humans are to apes (~98%), and are only slightly more closely related than we are to dogs (we share about 5% of our genetic code with our "best friends", 7)

So, I hope that after reading this you now have a great deal more appreciation than apprehension when you hear the name E. coli, one of the powerhouses of modern microbiology.

Notes and References

a. For the record, most E. coli strains (serotypes) are completely harmless and reside within many people’s guts all of the time. There are a few pathogenic strains – such as O157:H7 – that do cause seriously disgusting illness in people. Yet another reason to avoid eating poop.
b For comparison, S. aureus has 10 hits, Bacillus subtilis has about 10 hits; Yeast has 179 hits! Go yeast!
c. They were strong contenders for the gold in the microbial Olympics sprinting event, “Most Progeny”, but sadly they were overcome by phage … (for an entertaining review, check out: Youle et al., Nature Reviews Microbiology, 2012, 583-588).
d. Assuming an average generation time of 20 years.

1. Jacob F, Monod J (1961). Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3: 318-356. PMID: 13718526.
2. Santillan M, Mackey MC (2001). Dynamic regulation of the tryptophan operonL A modeling study and comparison with experimental data. Proc. Natl. Acad. Sci. U.S.A. 80: 1364–9. doi:10.1073/pnas.98.4.1364.
3. Scally A, Durbin R (2012). Revising the human mutation rate: implications for understanding human evolution. Nature Reviews Genetics 13 (824). doi:10.1038/nrg3353
4. Blount ZD, Barrick JE, Davidson CJ, Lenski RE (2012). Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489: 513-520. doi: 10.1038/nature11514.
5. Bentley R, Meganathan R (1982). Biosynthesis of vitamin K in bacteria. Microbiol and Molecular Biol. Reviews 46: 241-280.
6. Lukjanenko O, Wassenaar TM, Ussery DW (2010). Comparison of 61 sequenced Escherichia coli genomes. Microbial Ecology 60: 708-720. doi:10.1007/s00248-010-9717-3.
7. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438: 803-819. doi 10.1038/nature04338.

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