PROFILE PROFILE Profile of Graham C. Walker

Jennifer Viegas Science Writer

When biologist Graham Walker was intro- DNA, however, changed those plans. “Iknew duced to DNA during a biology course at just enough about the state of quantum Carleton University in Canada, it was fasci- mechanics in 1966 to realize that it wasn’t nation at first sight. “IthoughtDNAwasthe quite ready to deal with a molecule as big as coolest molecule in the world and decided I DNA, so I decided to become an organic wanted to work on it,” says the recently elec- chemist instead so that I could synthesize ted National Academy of Sciences member. it,” he says. Since then, Walker’s research has helped ex- plicate the structure and function of proteins Focus on Nucleic Acids involved in DNA repair and mutagenesis, Carleton chemistry professor Robert Wight- with potential applications for cancer treat- man was an early, influential mentor. As “ ments and antibiotics. His work has also Walker says, He not only ignited the fire in contributed to our understanding of how my belly for experimentation by letting me bacteria infect plants and mammals. synthesize a methylated nucleoside in his lab Fornearlyfourdecades Walker has taught for my honors thesis, but tolerated with good at the Massachusetts Institute of Technology humor the large explosion that occurred (MIT), where he is in charge of the biology when my reaction generating diazomethane undergraduate program. “I am proud of hav- got out of control.” ing been able to make my research contri- Wightman arranged for Walker to work in butions at the same time that I was devoting the laboratory of molecular biologist Saran considerable time and effort towards im- Narang at the National Research Council in Graham C. Walker. Image credit: Jan Walker. proving education and helping undergradu- Ottawa. Narang’sgroupatthetimecom- ate students,” he says. Since 2002, Walker peted with another group, led by Walker’s led Walker to the laboratory of microbial has been a Howard Hughes Medical Institute future MIT colleague H. Gobind Khorana, geneticist and biochemist Bruce Ames at the Professor and used his funding to establish to synthesize the first gene. Walker was ex- a science education group with meetings cited by the prospects and decided to go to University of California at Berkeley. Walker ’ modeled on those of his research laboratory. graduate school in chemistry to study admired Ames understanding of bacterial The group’s accomplishments include con- nucleic acids. Wightman introduced Walker physiology that allowed him to “think like tributing to the internationally used biology to the work of organic chemist Nelson acell,” as Walker puts it. education software programs StarBiochem Leonard at the University of Illinois. Leo- From 1974 to 1976, Walker’s postdoctoral and StarGenetics. nard became Walker’s doctorate mentor, as work with Ames led to findings concerning “ did biochemist Olke Uhlenbeck. Isoon chemical and radiation mutagenesis. For ex- Science vs. Classics found myself running back and forth excit- ample, Walker used his budding skills as Walker’s interest in science blossomed when edly between their two labs, developing a bacterial geneticist to identify the muta- he was a child, spending summers in the a half-chemical, half-enzymatic way of syn- ’ genesis-enhancing genes on pKM101, a de- Canadian woods at his family srusticcabin thesizing short oligoribonucleotides [frag- on the shore of the Gatineau River, north of ments of RNA] that had previously been rivative of a naturally occurring drug-resistant “ ’ “ Ottawa, Canada. There were so many things unattainable,” Walker recalls. He later used plasmid. Ames group created the Ames I could see and understand about biology by the enzyme T4 RNA ligase, which he had test,” still used today, to test whether a given just keeping my eyes open as I wandered purified, to carry out the intermolecular chemical is likely to cause cancer. The pres- through the forest and along the edge of the joining of two RNA oligonucleotides. ence of the plasmid pKM101 in the bacterial ” water, he says. The chemistry set given to tester strains increases error-prone repair of him by his biochemist mother as well as Isaac “Think Like a Cell” DNA damage. Walker says, “I learned ways to Asimov’s Building Blocks of the Universe in- By the end of his graduate work, Walker think about bacterial physiology from Bruce spired Walker to conduct scientific experi- realized that he did not wish to focus ex- ments at home. clusively on nucleic acid chemistry or bio- and was struck by his ability to connect su- As a young student, Walker excelled in chemistry. “Rather, I wanted to be able to perficially unrelated concepts from different Latin and the classics, but decided to focus on pursue interesting biological problems using fields to gain new insights.” science. In 1966, Walker went to Carleton whatever experimental approach was re- University in his hometown of Ottawa, hop- quired,” he says. “With that in mind, I de- This is a Profile of a recently elected member of the National ingtostudyquantummechanicsasachem- cided I needed to gain experience with living Academy of Sciences to accompany the member’s Inaugural Article istry major. The introductory biology class on cells and genetics.” Those considerations on page 3217.

www.pnas.org/cgi/doi/10.1073/pnas.1400519111 PNAS | March 4, 2014 | vol. 111 | no. 9 | 3201–3202 Downloaded by guest on September 24, 2021 DNA Damage and the SOS System One Bacterium, Many Research (14) is published with the accompanying In 1976, Walker was offered an assistant Applications article, “Host plant peptides elicit a transcrip- professorship in the MIT Department of Bi- AnotherprimaryfocusofWalker’s research tional response to control the Sinorhizobium ology that he eagerly accepted. He credits concerns Rhizobium-legume symbiosis. Dur- meliloti cell cycle during symbiosis” (15). Boris Magasanik, Gene Brown, Salvador ing Walker’s postdoctoral years, recombinant Together, these reports shed light on plant- Luria, Maury Fox, David Botstein, Mary-Lou DNA technology was developed and trans- bacterium symbiosis. Walker and his team Pardue, Lisa Steiner, Tom RajBhandary, and posons, which are DNA sequences that can carried out the first analysis of the S. meliloti Harvey Lodish as his early mentors at MIT. change position within the genome, routinely cell cycle and showed that a particular plant- Walker’s prior research on the mutagene- began to be used in bacterial genetics. “Ire- encoded peptide, NCR247, affects cell cycle sis-enhancing function of pKM101 led to the alized these advances made it possible, in regulation, cell division, chromosome segre- ’ “ ” analysis of Escherichia coli s SOS system, principle, to develop an E. coli-style genetic gation genes, and certain signaling pathways a set of physiological responses induced by system for any bacterium and began to study important for symbiosis. The discovery sheds DNA damage. By screening E. coli derivatives Sinorhizobium meliloti,whichformsanitro- light on the molecular strategies underlying ” carrying random fusions, Walker and his gen-fixing symbiosis with its legume hosts, certain chronic intracellular pathogens of graduate student Cynthia Kenyon were able Walker says. plants and animals. The findings, along with to identify DNA damage-inducible genes that When teaching an undergraduate research ’ other research on symbiosis, could lead to are regulated as part of E. coli s SOS response laboratory, Walker unexpectedly discovered a new class of broad-spectrum antibiotics to (1). Many of the genes encode functions in- that the microbially produced polysaccharide treat infectious diseases. volved in DNA repair or mutagenesis. “These succinoglycan is critical for legume nodule For his contributions, Walker was awarded results constituted the first direct evidence, in invasion (10). The way that S. meliloti infects fellowship in the American Academy of Arts any organism, that DNA damage induces the cells turned out to have commonalities with and Sciences in 2004. He has also received expression of a set of genes,” Walker says. how the cattle disease-causing Brucella abortus the Environmental Mutagen Society Award, Walker later showed that the mutagenesis- establishes chronic infection (11). Studies of along with many other honors. In future, enhancing genes on pKM101 were orthologs symbiotically defective S. meliloti mutants Walker says, “I plan to continue studying of the chromosomal umuDC genes, required additionally led to the discovery of the long- how cells respond to DNA damage and the for most UV and chemical mutagenesis in sought “missing step” in vitamin B12 bio- E. coli and cloned by his graduate student molecular mechanisms underlying the Rhi- synthesis (12) and of a previously unrecog- – Stephen Elledge (2). Additional studies shed nized ribonuclease enzyme, YbeY (13), which zobium legume symbiosis, but hope that the further light on proteins associated with these has a central role in RNA metabolism. discovery-based component of my research genes and the SOS system (3, 4). More recent stylewillcontinuetoleadtoexcitingun- work identified the biological role of one of Paving the Way for a New Class of anticipated insights into fundamental cellu- themostcommonDNA-damageresponse Antibiotics lar processes. I also hope that some of our enzymes, DinB (5), and suggested an addi- Walker’s Inaugural Article, “Global anal- work may impact human health by im- tional mechanism by which antibiotics can ysis of cell cycle gene expression of the proving chemotherapy and by helping us to become toxic to bacterial cells (6). legume symbiont Sinorhizobium meliloti” address the impending antibiotic crisis.” Formulating Cancer Treatment

Strategies 1 Kenyon CJ, Walker GC (1980) DNA-damaging agents stimulate 9 Xu X, et al. (2013) Enhancing tumor cell response to After being named an American Cancer So- gene expression at specific loci in Escherichia coli. Proc Natl Acad Sci chemotherapy through nanoparticle-mediated codelivery of siRNA USA – 77(5):2819 2823. and cisplatin prodrug. Proc Natl Acad Sci USA 110(46): ciety Research Professor in 2002, Walker 2 Elledge SJ, Walker GC (1983) Proteins required for ultraviolet light 18638–18643. collaborated with MIT colleague Michael and chemical mutagenesis. Identification of the products of the 10 Leigh JA, Signer ER, Walker GC (1985) Exopolysaccharide- umuC locus of Escherichia coli. J Mol Biol 164(2):175–192. Hemann. Together, they showed that dimin- Rhizobium meliloti 3 Perry KL, Elledge SJ, Mitchell BB, Marsh L, Walker GC (1985) deficient mutants of that form ineffective ishing the activity of a DNA repair pathway umuDC and mucAB operons whose products are required for UV nodules. Proc Natl Acad Sci USA 82(18):6231–6235. by reducing the activity of the specialized en- light- and chemical-induced mutagenesis: UmuD, MucA, and LexA 11 LeVier K, Phillips RW, Grippe VK, Roop RM, 2nd, Walker GC zyme Rev1 dramatically reduced the frequency proteins share homology. Proc Natl Acad Sci USA 82(13):4331–4335. (2000) Similar requirements of a plant symbiont and a mammalian 4 Nohmi T, Battista JR, Dodson LA, Walker GC (1988) RecA- pathogen for prolonged intracellular survival. Science 287(5462): of acquired drug resistance when tumors re- mediated cleavage activates UmuD for mutagenesis: Mechanistic 2492–2493. relationship between transcriptional derepression and lapse after chemotherapy (7). Interfering with 12 Taga ME, Larsen NA, Howard-Jones AR, Walsh CT, Walker GC posttranslational activation. Proc Natl Acad Sci USA 85(6): (2007) BluB cannibalizes flavin to form the lower ligand of vitamin B . the same pathway by reducing the level of the 1816–1820. 12. Nature – protein Rev3 made resistant lung cancers 5 Jarosz DF, Godoy VG, Delaney JC, Essigmann JM, Walker GC 446(7134):449 453. sensitive to the chemotherapy drug cisplatin (2006) A single amino acid governs enhanced activity of DinB DNA 13 Jacob AI, Köhrer C, Davies BW, RajBhandary UL, Walker GC polymerases on damaged templates. Nature 439(7073):225–228. (2013) Conserved bacterial RNase YbeY plays key roles in 70S (8). Walker and his colleagues suggested that 6 Foti JJ, Devadoss B, Winkler JA, Collins JJ, Walker GC (2012) ribosome quality control and 16S rRNA maturation. Mol Cell 49(3): interfering with the pathway might improve Oxidation of the guanine nucleotide pool underlies cell death by 427–438. Science – bactericidal antibiotics. 336(6079):315 319. 14 Walker GC (2014) Global analysis of cell cycle gene expression of the effects of chemotherapy. Recently, he and 7 Xie K, Doles J, Hemann MT, Walker GC (2010) Error-prone the legume symbiont Sinorhizobium meliloti. Proc Natl Acad Sci USA his collaborators used those insights to make translesion synthesis mediates acquired chemoresistance. Proc Natl – nanoparticles that prevented tumor growth in Acad Sci USA 107(48):20792–20797. 111:3217 3224. 8 Doles J, et al. (2010) Suppression of Rev3, the catalytic subunit of 15 Penterman J, et al. (2014) Host plant peptides elicit a human lymph node carcinoma of the Pol{zeta}, sensitizes drug-resistant lung tumors to chemotherapy. Proc a transcriptional response to control the Sinorhizobium meliloti cell prostate gland in a mouse model (9). Natl Acad Sci USA 107(48):20786–20791. cycle during symbiosis. Proc Natl Acad Sci USA 111:3561–3566.

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