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Haemophilus influenzae, Restriction Enzymes, and Genome Sequencing


About the author: Frank Stearns is an Adjunct Professor teaching Genetics and a writing course on Science Communication. He is interested in adaptation and speciation genetics and in the history of biology. He recently finished a postdoc at Johns Hopkins University and he runs a Facebook page (Darwin’s Bulldog) that shares evolution news.




Haemophilus influenzae colonies growing on the chocolate agar (Author: Stefan Walkowski)

It may not be the first model organism that comes to mind, but Haemophilus influenzae (no relation*) is a modest little bacterium that has contributed significantly to the study of genetics. Two major breakthroughs in particular – restriction enzyme technology and genome sequencing – owe a great deal to H. influenzae and to the Nobel laureate that was involved with both: Dr. Hamilton “Ham” Smith. Coincidentally, 2020 marks the 50thand 25thanniversary of both of these landmark discoveries.

In 1970, Smith and Wilcox published the first description of a site-specific cleavage restriction enzyme, HindII. While other work had been previously done on restriction enzymes, this study paved the way for the specific use of restriction enzymes in biotechnology, and in 1978 Smith was awarded the Nobel Prize in Physiology and Medicine, along with Werner Arbner and Daniel Nathans, “for the discovery of restriction enzymes and their application to problems of molecular genetics.”

Smith did not set out to work with restriction enzymes, however.

Daniel Nathans (L) and Hamilton Smith (R) shortly after being awarded the Nobel Prize (Credit: Johns Hopkins Medicine)

“My discovery of HindII, the first site specific cleavage restriction enzyme was purely fortuitous,” he told me in a recent correspondence. “I was not working on restriction at the time.  I was studying DNA transformation in the bacterium Haemophilus influenzae.”

It had only been a few months since he began a position as an Assistant Professor at the Johns Hopkins Medical School when he assigned his first graduate student, Kevin Wilcox, to a project on the fate of phage DNA during transformation. Initial studies seemed to indicate that the DNA was degraded, and following a journal club meeting where Smith had presented a recent paper by Meselson (of Meselson-Stahl fame) and Yuan on (what became known as) type I restriction enzymes, Wilcox suggested that similar enzymes might be operating in his experiments. Although he was skeptical, Smith decided to take a look. And, that was how they discovered the first type II restriction enzyme.

As most students of genetics know, restriction enzymes cleave DNA based on particular nucleotide sequences called the recognition site. Type I restriction enzymes (like those from the Meselson and Yuan paper) cleave at positions that are found at a random distance from the recognition site. The type II restriction enzymes discovered by Smith and Wilcox are site specific and cut at the recognition site. Additionally, they do not require ATP for their action, typically only needing magnesium ions (Mg2+). These important differences allow for important biotech uses, including allowing geneticists to insert specific segments of DNA into bacteria in order to isolate and amplify genes for sequencing and/or functional studies.

Considering the importance of type II restriction enzymes for sequencing, it shouldn’t come as a surprise that Hamilton Smith was also involved in completing the first whole genome sequence of an organism– the same organism where he had made his Nobel Prize winning study 25 year before. Recent advances (particularly by Craig Venter) had made whole genome sequencing possible. A friend, Richard Moxon, suggested to Smith that they work on H. influenzae. As Smith puts it, “One thing led to another and Craig and I decided we would try his large-scale sequencing approaches with Haemophillus.”

With two big anniversaries for these major discoveries in one year, one might expect a celebration. But H. influenzae, discovered during a pandemic, was denied it’s recognition by another pandemic. As Smith said when I asked if they were doing anything to mark the occasion, “NO! We are afraid of Covid 19.”

*Haemophilus influenzae was discovered in association with an influenza pandemic in 1892 and was believed to be a cause of the flu until 1933. In actuality it causes various infections and the flu is (of course) caused by a virus.

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