Clyde A. Hutchison III: Genome Sequencer and Synthetic Biologist

From sequencing bacteriophages to synthesizing bacterial genomes to defining a minimal genome

By | August 1, 2016

CLYDE A. HUTCHISON III
Distinguished Professor, Synthetic Biology Group,
J. Craig Venter Institute, San Diego, CA
Professor Emeritus, University of North Carolina, Chapel Hill
COURTESY OF CLYDE HUTCHISON
As an undergraduate at Yale University, Clyde Hutchison III was required by his financial-assistance package to have a part-time job. Planning to major in physics, he had lined up a sophomore-year job with an astrophysicist. But Hutchison returned to school to find that the professor had given the job to someone else. “I was pretty upset, because the people assigning jobs wanted me to work in an accounting office, and I was not interested in that. I pleaded with them to find me a science job.” Hutchison got his wish: he was assigned to work in Harold Morowitz’s biophysics lab, a placement Hutchison says has directed his career trajectory up to the present day. He worked with Morowitz’s postdoc, Carl Woese, who went on to discover Archaea as the third domain of life. “I went from working in the dining hall freshman year to working with Carl Woese, one of the most influential people in biology.” With Woese, Hutchison studied chemicals, including L-alanine, that could trigger bacterial spore germination, publishing his first paper in 1958.

While Hutchison always knew that he would major in science and, emulating his chemist father, that he would pursue a PhD and a career as a researcher, it was the influence of the Morowitz lab that pulled him from physics to biology.  In 1960, he moved on to Caltech to do PhD in biology.

Here, Hutchison traces his path from studying genomes to synthesizing them, explains why he likes to “think small,” and reveals why he still finds himself at the lab bench after all these years.

HUTCHISON HATCHES

Late bloomer. Hutchison was born in 1938 in New York City, where his father, Clyde A. Hutchison Jr., a physical chemist, was a postdoc at Columbia and later returned there to participate in the Manhattan Project, working on isotope separation. Hutchison attended first grade at the Horace Mann School (then a part of Teachers College, Columbia University), where he refused to learn to read. “It was fashionable at the time to not learn phonics, but full words. The teacher would hold up a sign that said ‘cat,’ but didn’t mention the letters, nor that the written language was linked to the spoken one, or that the letters stood for sounds,” says Hutchison. The school was permissive, so Hutchison opted to spend reading lessons hiding in forts that he built out of blocks. In 1945, when he moved with his mother and sister to a small town in Ohio following the end of World War II (his father had gone ahead to the University of Chicago to set up his laboratory), his second-grade teacher was shocked to learn that the young Hutchison couldn’t read. “That’s when the teachers told me about the letters, and I quickly learned how to read.”

“One of the themes that runs through my work is that I like to think small. . . . The smaller the thing you are studying, the more chance you have of trying to understand the whole thing.”

Drawn to genetics. At Caltech, Hutchison joined the lab of biophysicist Robert Sinsheimer, who was studying the ΦX174 bacteriophage. Hutchison was drawn to the gene mapping that faculty members Robert Edgar and Max Delbrück were doing with mutants of other phages. “I wanted to apply the same approach to ΦX174, which had a relatively small genome, to get a detailed picture of its genes.” In Sinsheimer’s lab, Hutchison used the genetic techniques he was learning in other labs within the department to help characterize how the phage infects bacteria and to identify and map genes on ΦX174’s 5,000-base-pair genome.

“One of the themes that runs through my work is that I like to think small. . . . The smaller the thing you are studying, the more chance you have of trying to understand the whole thing.”

Time of his life. Hutchison stayed at Caltech for eight years. “Graduate school is a perfect existence; I wish I was still there! You can work a lot in the lab and you can focus, because you don’t have much money so you don’t have to waste time spending it.” During his time at Caltech, Hutchison collaborated with Marshall Edgell, a Sinsheimer lab postdoc. Sinsheimer recommended both scientists to the University of North Carolina at Chapel Hill, which was recruiting new faculty members. Both Hutchison and Edgell became assistant professors there in 1968 and ran their labs jointly for about 25 years. They had seen a publication by Hamilton Smith on type II restriction enzymes (which would later earn Smith a Nobel Prize) and became early adopters of the enzymes as a tool to study DNA. Along with Edgell, Hutchison’s lab showed that the ΦX174 genome could be cut up into specific DNA pieces. His student June Middleton did the first screen for novel restriction enzymes from Haemophilus aegyptius, identifying a number of new enzymes including endonuclease Z, now called HaeIII.

HUTCHISON HARVESTS

Maternal heredity. Hutchison next decided to apply restriction enzymes to analyze more-complex mammalian genomes. But to keep things simple, his lab focused on the 16-kilobase mammalian mitochondrial genome. Prior studies had demonstrated that amphibian mitochondrial DNA is inherited from the mother, and Edgell and Hutchison wanted to test whether the same was true in mammals.
Isolating mitochondrial DNA from the livers of horses, donkeys, mules (a hybrid with a horse mother and a donkey father), and hinnies (a donkey-mother, horse-father hybrid) they showed that the hybrid had the same mitochondrial DNA pattern as the mother. The work, published in 1974, demonstrated the maternal nature of mitochondrial inheritance in mammals.

Sequencing points the way. In 1975, Hutchison spent a yearlong sabbatical in Fred Sanger’s lab in Cambridge, England. There, Hutchison learned how to sequence DNA using the method Sanger had recently developed and helped to sequence the genome of ΦX174, the first DNA molecule to be completely sequenced. “At the time, other researchers would say to me, ‘Why would you want to sequence DNA?’ Some people didn’t perceive the DNA sequence thing as interesting.” But ΦX174 turned out to have interesting features: a compact genome with overlapping genes. “The protein sizes hadn’t added up correctly according to the DNA sizes. I think we never would have figured out the virus’s genes using mutational genetics. I think this helped to stimulate the rapid development of sequencing. But maybe that’s just an egocentric view of the history.”

Ahead of the pack. While in Sanger’s lab, Hutchison met Michael Smith, a University of British Columbia researcher also there on sabbatical. Smith had been working on methods to enzymatically link nucleotides together to form oligonucleotides before automated machines began to churn out DNA oligos. Hutchison and Smith collaborated to develop site-directed mutagenesis of the ΦX174 genome using small oligonucleotide primers synthesized in Smith’s lab that could introduce base pair substitutions. Smith shared the 1993 Nobel Prize in chemistry for helping to develop the method. Hutchison also began to sequence murine hemoglobin genes, again, because the task was “relatively small and approachable,” says Hutchison. “Coming back from Sanger’s lab, we were in a unique position. Our lab was initially the first in the U.S. to use Sanger’s sequencing method, and then it quickly caught on and everyone was doing it.” Within the beta globin cluster, Hutchison and Edgell’s lab discovered a transposable, repetitive element in the mammalian genome called long interspersed repetitive element one (L1). L1—the most abundant transposable element in the mammalian genome—encoded a gene that looked like reverse transcriptase, which synthesizes a DNA molecule from RNA. The repeated element was later established as a retrotransposon.

Minimal genome. Focusing on small genomes led Hutchison, in 1990, to begin work with Mycoplasma genitalium, which has the smallest known genome for an independently replicating cell. With graduate student Scott Peterson, Hutchison and colleagues used a random sequencing approach, which placed markers on the physical map of the M. genitalium genome akin to shotgun whole-genome sequencing. “We didn’t have the wherewithal to get the whole sequence, but we got a few short sequences, and this meant we could identify genes by comparing sequences with other genes and make estimates of the fraction of the genome that coded for proteins.” The paper caught the eye of Hamilton Smith, who was then collaborating with Craig Venter to sequence the Haemophilus influenzae genome. The H. influenzae sequence was published in 1995, the first full cellular genomic sequence to be determined. Smith called Hutchison, and thus began the initial collaboration among the three scientists. That same year, the trio published the complete sequence of M. genitalium using whole-genome random sequencing and assembly. Hutchison then took a sabbatical year at Venter’s Institute for Genomic Research (TIGR) in Rockville, Maryland. At TIGR, Hutchison developed a global transposon mutagenesis method to see whether disruption of each of M. genitalium’s genes could still result in a viable organism. The study, published in 1999, suggested that as many as 350 of the organisms’ 480 protein-coding genes are essential.

What retirement? Since 1996, Hutchison has collaborated with TIGR, spending part of his time doing bench work there. “As I was approaching a normal retirement age, I thought it would be interesting to work at TIGR since I had been at UNC for a long time.” Hutchison moved to TIGR in 2005; the following year it was merged with several other organizations to form the J. Craig Venter Institute (JCVI), headquartered in Rockville. In 2007, Hutchison moved to a new JCVI campus in La Jolla, California.  

Synthetic biology beginnings. “It was during those experiments identifying nonessential genes in mycoplasma that Craig, Ham, and I started thinking about synthesizing genomes and about synthesizing the 5,000-base-pair ΦX174 genome as a test case,” says Hutchison. They reported the construction of that synthetic genome in 2003. “Those experiments took a while because the mutation rates in the chemically synthesized DNA pieces were too high, so we kept getting inaccurate assembly.” Their synthetic viral genome, however, was not the first: Eckard Wimmer’s lab, in 2002, had made a synthetic poliovirus. Hutchison and his colleagues subsequently synthesized the much larger (half a million base pairs) genome of M. genitalium in 2008. “For that, it was key that Gwynedd Benders figured out how to clone these genomes as extra chromosomes in a yeast cell.”

Putting it all together. In 2010, Hutchison, along with Daniel Gibson and others, synthesized the 1.1 million–base-pair genome of the bacterium M. mycoides from scratch, assembled it inside a yeast cell, and then transplanted the genome into a related bacterium, M. capricolum. Called JCVI-syn1.0, it was the first cell controlled by a synthetic genome and the culmination of the team’s work since 1995. “What was key, besides cloning these genomes as yeast extra chromosomes, was that one of the postdocs, Carol Lartigue, had learned how to transplant the genome of one mycoplasma species into another. We switched to M. mycoides because we couldn’t figure out how to transplant the M. genitalium genome.”

Down to the basics. This year, Hutchison and his colleagues built on this JCVI-syn1.0 cell using global transposon mutagenesis to create an M. genitalium cell with a minimal genome. They worked with eight overlapping DNA segments, delineating which genes were essential, nonessential, or what the team called quasi-essential (the organism could live without them, but their absence significantly slowed its growth). “It took three cycles and many years. The genome we ended up with is about 100 genes bigger than the number of known essential genes, and we don’t have a clue as to what 149 of these genes do, which is surprising.”

End goal. “To me, a minimal genome is less important than having one where we know what all of the parts do. If we have that, we can make a computer model of how the cell works. Having a computer model based on a living cell will be a satisfactory explanation of how gene function predicts cell behavior and what happens if you add or take away genes or change the environment,” Hutchison says.

HUTCHISON HERE AND NOW

Music spurts. Hutchison took piano lessons in elementary school but quit after five years. In his forties, he began to take jazz piano lessons and now plays once a week at a bar restaurant in La Jolla as “Clyde and Mac.” “Mac is a MacBook Air that plays bass and drums.”

Predictions. It’s been 17 years since Hutchison’s 1999 work on the minimal mycoplasma genome. “In the 1999 paper, we had discussed the building of a synthetic genome, and it was Craig’s encouragement to put the sentence at the end of the paper that synthesizing a genome from scratch was the way to test this. It seemed a bit out there to me at the time, but it’s happened! To me, 17 years seems like a short time.”  

Think small. “One of the themes that runs through my work is that I like to think small. The reason is that the smaller the thing you are studying, the more chance you have of trying to understand the whole thing.”

Hands-on. “I’ve always thought it was important to keep doing laboratory experiments. It is hard to make time for it between writing grants and mentoring and other obligations, but I’ve always thought it was important because, first, I do like doing it, and second, you can easily lose touch with what is reasonable to do in the lab and what is reasonable to expect from someone else if you aren’t doing it yourself.” 

Greatest Hits

  • Along with Marshall Edgell, developed a marker rescue assay for specific fragments of the ΦX174 phage genome
  • With colleagues, provided the first evidence of the maternal inheritance of mitochondrial DNA in mammals
  • Took part in sequencing the first DNA molecule, the genome of the ΦX174 phage
  • Codeveloped site-directed mutagenesis with Michael Smith
  • Codiscovered L1, the most abundant transposable element in the mammalian genome
  • Took part in creating the first synthetic minimal genome

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