Summary of CMS Seminar Club presentation on Saturday, February 25, 2022.
Title: The Path to the Nobel Prize
Speaker: Sir Richard John Roberts, Nobel laureate, Prof., Ph.D., Chief Scientific Officer, New England Biolabs, Ipswich, Massachusetts, USA
On Saturday, February 25, Sir Richard J. Roberts (Sir Richard from here) gave a presentation at Fujita Health University. He told us about his scientific career and how he won the Nobel Prize, hereby giving us inspirational and valuable lessons on how to choose a career path.
Recording: For members of Fujita University, a recording of the meeting (without the discussion part) will be available at our Manabi system. Unfortunately, we cannot open the recording for a wider audience.
There were 67 participants who enjoyed the meeting. His presentation was very personal and, including its scientific part, remarkably easy to follow.
The meeting was chaired by Prof. Akila Mayeda of FHU, who first shortly introduced Sir Richard. Prof. Mayeda told us how in 1990 he had worked for a few months as a postdoctoral fellow in Sir Richard’s lab at Cold Spring Harbor, with Dr. Adrian R. Krainer as his direct advisor (Fig. 1). Sir Richard and Prof. Mayeda have remained friends since then, and Fig. 2 shows a picture of their recent meeting in Tokyo.
From the audience, I only heard very positive reactions and so were two chat messages during the meeting. One chat mentioned Sir Richard’s obvious enthusiasm and love for science, and, more or less, asked if the freedom to follow one’s instinct is important for good science. Sir Richard agreed with that idea, but cautioned that he typically also lets his staff members dedicate part of their efforts to more common/predictable “bread and butter” research, to improve their chances of professional survival.
What struck me most, personally, was Sir Richard’s sensitive and friendly, while also firm and robust attitude for interacting with people throughout his scientific career. He described life-long loyalties towards a diverse set of people, and when mentioning conflicts with his previous boss, the Director of the Cold Spring Harbor Laboratory, Nobel laureate James D. Watson (who threatened to fire him on several occasions for not listening), he was just factual and did not add negative emotion to the story. It was also amazing that this gentle person, who organized his scientific career very logically and co-initiated the growth of—and is one of the leaders of—the big molecular biology company New England Biolabs, appeared to advocate some level of rebellion against leadership if that disagrees with what one believes in.
Contents of the seminar
I will not describe all topics discussed by Sir Richard, but just summarize those that captivated me the most.
Luck: He was born during World War II in 1943 in Derby, UK, and the street he lived on was in the direct flight path of the German airplanes on their way to bomb the Rolls Royce factory in the same city that made airplane engines. Whereas the other side of the street was hit by several bombs, his side of the street was spared. Sir Richard rode his luck again when in 2001 he was booked for one of the 9/11 flights, his appointment only to be canceled at the last moment. He also gave other examples of his luck and believes that luck happens to everyone, but that we need to learn how to make use of it.
Good at Puzzles: The headmaster of his primary school in Bath, UK, very often gave him a—usually mathematical—puzzle at the end of the day on his way home. Sir Richard did these puzzles with great enthusiasm and assumed that all children got them, but later found out that he was the only one. The headmaster must have seen something unique in him, and luckily was still alive when Sir Richard got the Nobel Prize in 1993.
Connection with Japan: Sir Richard studied chemistry at Sheffield University, UK, and did his graduate work with Prof. W.D. Ollis, who was a very good teacher who made chemistry fun. However, the person whom Sir Richard remembers as his most influential teacher—ever—was a Japanese postdoc, Dr. Kazu Kurosawa, who in Sheffield taught the young Sir Richard how to do experiments and always made him first realize the why of an experiment. He also taught him the board games Go (which is from China) and Shogi (Japanese chess), and they kept playing by mail for many years.
(i) Following his own path, (ii) Restriction enzymes, and (iii) Disobedience: Sir Richard developed a passion for biochemistry, and when working at Harvard University for Prof. Jack L. Strominger (by the way, also an ex-mentor of our previous speaker Prof. Jim Kaufman) he became one of the few people at the time who became good in the sequencing of RNA, which led to a job offer at Cold Spring Harbor by its Director, Nobel laureate James D. Watson who wanted to know the sequence of the genome of SV40 virus. Arriving there, however, Sir Richard discovered that two other groups were already working on the same question by the usual method of the time, which was by first converting DNA into RNA and subsequently sequencing that RNA. To Sir Richard, it did not seem like a useful investment of his time and effort to do the same, so he approached a route involving restriction enzymes. Restriction enzymes, found in bacteria, cut DNA at defined small sequence motifs and were only getting known at the time, and Sir Richard figured that if he would have more different restriction enzymes, he could conveniently cut the SV40 genome into pieces small enough for being sequenced. So, he and his group set out to discover more different restriction enzymes, and pretty soon they had already found 30 different ones. It is these restriction enzymes—and methylases, many of which form a partner system with restriction enzymes to prohibit bacteria from cutting their own DNA—that arguably became the major focus of his scientific career. During the 1970s and early 1980s, about 75 of the most useful (Type II) restriction enzymes known at the time were discovered by Sir Richard’s group. Many people came to the lab and asked for the use of the enzymes or the bacteria that made them, and Sir Richard provided their requests. He realized there was a possible business model, but the Director James Watson was not very interested in this or restriction enzymes. Instead, Director James Watson would get displeased with Sir Richard because he did not want to sequence SV40, to the point that on a number of occasions he threatened to fire Sir Richard. Only the intervention of a mutual friend, Prof. Norton D. Zinder (Rockefeller University), prohibited that.
Maybe ironically, until not so long ago, restriction enzyme mapping was the common way to identify virus strains, and restriction enzymes were also a major tool for the genetic manipulation of viral genomes. Therefore, Sir Richard’s work on restriction enzymes made an immense contribution to the field of virology, arguably more than the sequencing of SV40 would have done.
The work for the Nobel Prize, Step 1 (Gelinas and Roberts 1977): While Sir Richard’s lab was mainly dedicated to restriction enzymes, besides working on that topic, all members also had a unique project. In 1974, he and his new post-doc Dr. Richard Gelinas decided that the latter would work on adenovirus (adenovirus 2, Ad2), asking the question of whether the gene promotors in prokaryotic systems (just having been revealed at the time) and eukaryotic systems are similar. To answer this question, first, the 5’ ends of transcripts needed to be determined. An advantage of using a virus is that especially at later stages of viral infection the viral mRNAs in a cell tend to be very abundant—while largely shutting down host cell mRNA synthesis—, which was experimentally important in that era in which the currently available sequence-specific amplification techniques did not exist yet. Dr. Gelinas initially focused on the adenovirus “early” transcripts E1A and E4 (E for “early”) because they are initiated close to the virus genome ends —of which sequences were already known at the time—but found that these transcripts were not abundant enough for analysis and therefore switched his focus to the more abundant “late” transcripts expressed later during virus infection (see Fig. 3 for modern detailed knowledge of adenovirus transcripts). It was already known that the adenovirus had multiple late RNAs among which, for example, L3 (hexon), L4 (100K), and L5 (fiber) (Fig. 3). Dr. Gelinas first cut (using RNAse T1) the viral RNAs (which could be isolated by hybridizing them to adenovirus genomic DNA) into fragments that were small enough to be analyzed by the techniques available at the time. Then, he isolated those of the fragments that were derived from the mRNA 5’ ends based on them—as is characteristic for mRNAs—being “capped” (with 7-methylguanosine via a 5’,5’-triphosphate bridge with the 5’ terminal residue of the RNA chain), for which he used dihydroxyboryl cellulose columns that bound the 2’,3’-cis diol bonds of the caps. Against expectations, using this method, Dr. Gelinas and Sir Richard only found single-length 5’ capped fragments of 11 residues with the sequence G5’ppp5’AmCmUCCCCUUUG. When analyzing different late mRNAs, which they could separate based on hybridization to different parts of the adenovirus genome, Dr. Gelinas and Sir Richard showed that this single 11 nt fragment was found at the 5’ end of different viral transcripts indeed. This ultimately would be explained by the different late transcripts all being transcribed from a single promoter, after which intra-transcript cutting followed by ligation of the new strand ends generated the different transcripts, a process nowadays known as “pre-mRNA splicing.” However, at the time, other possible biological or technical explanations could not be excluded. It testifies to the brilliance of Sir Richard that within the complexity of the generated biochemical data, he could deeply understand their experimental solidity, distil the relevant puzzle, and solve that puzzle by providing evidence for pre-mRNA splicing using a different line of experimental evidence.
The work for the Nobel Prize, Step 2 (Chow et al. 1977): That different line of evidence involved electron microscopy (EM). For that, a relevant finding was that in hybrids of adenovirus transcripts with adenovirus genomic DNA not only the poly(A)-tails at the 3’ end were not well protected from RNase activity (revealing their single-strandedness) but also the 5’ ends (Top image in Fig. 4) (Gelinas and Roberts 1977; Klessig 1977). At that time, Sir Richard already suspected that the adenovirus late transcripts started upstream of the VA region (Fig. 3), and he thought of an experiment to visualize how in an adenovirus late transcript several separated parts of the adenovirus genome are connected (middle image in Fig. 4). For that, he asked members of a neighboring lab at Cold Spring Harbor, Dr. Louise T. Chow and Dr. Thomas R. Broker, to use electron microscopy for showing the combined hybridization patterns of adenovirus late transcripts with the adenovirus genome and different (restriction enzyme cut, nick translation labeled, denatured) single-strand DNA fragments from the adenovirus genome. The experiment worked out as hoped for, and besides the “RNA-displacement loops (R-loops)” in which the matching protein-coding part of the adenovirus genome the two DNA strands were separated by DNA-RNA hybridization (which is more stable than DNA-DNA hybridization), the 5’ ends of the RNA transcripts could simultaneously be labeled with a single-strand DNA probe derived from upstream of the VA region. The hybridization pattern was even more exciting than expected, with the 5’ end common to most late transcripts being divided into three parts (1, 2, and 3 in Fig. 3), resulting in looped hybridization patterns (schematic example in the bottom image of Fig. 4) of which the (intron-exon) organization could be understood by using DNA probes from different genomic regions. Nowadays, separated parts of the genome that are connected in transcripts are known as “exons.” Convinced of how amazing the finding was, Sir Richard used this word against convention in the article title “An Amazing Sequence Arrangement at the 5’ Ends of Adenovirus 2 Messenger RNA,” which after some convincing was accepted by Cell, a very young journal at the time. In 1993, Sir Richard would get the Nobel prize for this amazing work, because the two above studies (Gelinas and Roberts 1977; Chow et al. 1977) together with studies by Prof. Phillip Allen Sharp, who independently came to similar conclusions, were deemed the critical steps in the finding that in the biological process from converting DNA information to mRNA, genes are split.
New England Biolabs: Another big success story of Sir Richard is how he joined New England Biolabs (NEB) in 1992, after being an advisor to the company since 1975, and helped to make it one of the biggest worldwide players in molecular biology. He is still the Chief Scientific Officer of NEB to date. At the time of their first contact, NEB was only a small company working from the basement of the owner Dr. Donald Comb and his first wife Marilyn, and they only had one technician. However, the production of restriction enzymes introduced by Sir Richard helped to make NEB the big company it is nowadays. One of the reasons that Sir Richard joined NEB was their very positive policy of investing a large part of their profits into new research, which they are still doing to date. NEB is also involved in charity, and overall has some very innovative and positive policies (see their Wikipedia page). Recent profits have been high, because as a high-quality player in the molecular biology field, NEB is making some of the enzymes used for COVID-19 vaccine production by Pfizer and Moderna.
Apart from the above, Sir Richard told us many more things about his amazing life, including his involvement in charity and the early development of bioinformatics. There was also plenty of time for hobbies, and as a youngster, he even was West England junior champion in billiards. I strongly recommend all the members of Fujita Health University to watch the recording of his presentation. It is quite humbling, while also very inspirational, to see how much a single person can achieve, while remaining so kind and well-grounded.
