Profile of Peter Walter

Germany to Tennessee

Walter, who currently chairs the Biochemistry and Biophysics Department at the University of California, San Francisco, was born in Berlin in 1954. “When I was 12, I was convinced that I wanted to become a scientist,” he says, “but I didn’t particularly enjoy biology then.” He recalls that it was a lot of cataloguing and memorization, not like the “science by inquiry that is taught now. Even chemistry was basically taught by watching,” he recalls. He owned a chemistry set that he liked to play with at home. “In retrospect, we played with things that I wouldn’t like my kids to play with. Society is much more safety-conscious these days,” he says. Walter fondly remembers his high school teacher Dr. Dietrich Warnatsch as “fantastic. He gave us a lot of freedom as students,” says Walter. He remembers that Warnatsch allowed the students to hang out in the preparation room, encouraged experimentation, and brought biological aspects to chemistry because he was trained as a biochemist.

Upon entering college in 1973, Walter chose to study chemistry. After two and a half years, he applied for a Fulbright fellowship to study in the United States, which he did not receive. But, he says, “I was stubborn, and I applied for direct exchange.” In 1976, Walter arrived at Vanderbilt University (Nashville, TN), and “it was a complete culture shock. It was so different in so many aspects. Scientifically, I was very much taken with it,” he says. Whereas in Germany Walter had been confined to classes and prescribed experiments, at Vanderbilt he was thrown into the middle of a project in the laboratory of Thomas M. Harris. Walter reveled in this “sheer independence,” as he describes it.

He studied the biosynthesis of an al kaloid isolated from red clover in Tennessee. The compound caused cows to “slobber,” says Walter, and “farmers didn’t like slobbering cows.” He studied the biosynthetic process of how the alkaloid, slaframine, was made (4). At the end of the exchange program, Walter planned to return to Berlin, but Stanford Moore, a biochemistry professor of The Rockefeller University (New York) and a trustee at Vanderbilt whom Walter had met, encouraged him to apply to the doctoral program at Rockefeller. Walter applied nowhere else and thinks that the admissions committee found this odd. Initially, he was not accepted, but “I slipped in on the waiting list,” he says. Walter recalls how in 1996, he delivered an annual Harvey Society lecture at Rockefeller, a black-tie affair, and his first slide was his initial rejection letter.

Walter spent 3 months “just talking to people” before choosing a laboratory, and ultimately he chose to work with Günter Blobel because of his exciting discussions with Blobel. “I liked his enthusiasm. It was the best decision I ever made,” says Walter. He liked how Blobel was able to communicate and how “he made everyone in his lab feel special,” says Walter. His first project focused on understanding how proteins move across membranes, by “dissecting the process biochemically. A competing hypothesis, called the membrane trigger hypothesis, suggested that a protein’s ability to move across a membrane was built into the structure of the protein rather than being controlled by proteins in the membrane,” explains Walter. He fractionated membranes, treated them with proteases, and showed that transport across the membrane ceased (5).

Walter then worked on identifying the protein involved in membrane transport. He used dog pancreatic microsomes, which he calls “an ideal system. The pancreas is stuffed with endoplasmic reticulum.” Walter found a protein complex that rescued membrane transport and named it signal recognition protein (SRP). SRP is made of six proteins that recognize signal sequences on nascent proteins and recruit ribosomes to the membrane (6). A year or so after publishing this finding, he had “the most wonderful moment of discovery” and serendipitously found that SRP also contained RNA (7). The name of the protein was changed to signal recognition particle.

After finishing his dissertation in 1981, Walter again planned to return to Germany, “but work was going so well,” he says. He remained in Blobel’s laboratory as a postdoctoral fellow for a year, and then, in 1982, he became an assistant professor at Rockefeller. Later that year, Walter was approached by the University of California, San Francisco, to join its biochemistry department. At the time, he says, “I was convinced I didn’t really want to go there but would go back to Germany, so I was perfectly relaxed during the job interview.” University of California, San Francisco, offered him a position, and the environment won him over. He joined the Department of Biochemistry and Biophysics as an assistant professor in 1983. “There were so many wonderful colleagues, and that has stayed true for the last 20 years. The opportunities for great interactions and collaborations have remained endless,” he says.

Across the States with SRP

Walter’s work on SRP traveled with him across the continent. “Günter [Blobel] was incredibly generous and allowed me to take the [SRP] project,” he says. The search for how SRP function continued with biochemical analyses of the complex in Walter’s laboratory. “We took [SRP] apart and showed that all of its components were essential,” says Walter (8). His group submitted SRP to functional assays, treated it with RNases, modified the structure, and mapped the relative position of its constituents to learn more about the complex (9–11). “We developed quite a sophisticated low-resolution structure–function relationship,” he says. As the field evolved, genetic techniques in yeast provided further insights. Throughout the 1990s, Walter and his group were able to “verify that the model suggested from the biochemistry applies to living cells,” he says.

Work in yeast opened his group to other things, as they found that protein movement across membranes can occur via two pathways. In addition to the SRP-mediated movement of ribosomes as they are recruited for protein translation, an SRP-independent pathway also exists (12). Walter’s next major step in learning about SRP came with biophysical methods like crystallography. Biophysically, “we gained incredible new insights,” he says, finding that SRP and its membrane receptor each contain a GTPase domain. These two GTPases form a unique GTPase subfamily and directly interact with one another, but they “do so in a very peculiar way,” says Walter. The 2′-hydroxyl group of one GTP bonds to the γ-phosphate of the other, and vice versa, to trigger hydrolysis symmetrically (13). Still to be understood is how the coupled GTP hydrolysis reactions serve to promote ribosome targeting to the membrane and to load and unload signal peptides from the SRP. Also, the role of SRP RNA has so far remained a challenging mystery.

Proteins Unfolded

In the 1990s, Walter began studying the unfolded protein response, in which misfolded proteins in the ER trigger transcriptional up-regulation. With two adventurous students in his laboratory, Carolyn Shamu and Jeff Cox, “we wanted to learn how information travels backwards from the ER to the nucleus,” says Walter. The unfolded protein response proliferates ER, up-regulates chaperones, and up-regulates degradation of unfolded proteins (14). It is “a gigantic transcriptional program that is being activated, comprising some 5% of the yeast genome,” Walter explains.

“We wanted to learn how information travels backwards from the endoplasmic reticulum to the nucleus.”

To study the genetics behind the unfolded protein response, Walter and his students started by examining which proteins map to the pathway in Saccharomyces cerevisiae yeast. They found a network of three genes: IRE1, HAC1, and RLG1 (15). Ire1 is a transmembrane kinase that regulates the unfolded protein response pathway. HAC1 encodes a transcriptional factor that regulates genes downstream in the pathway, but it is Hac1’s activation that is particularly unusual. Only upon removal of an intron is the transcription factor translated (16). Usually intron removal is mediated by spliceosomes, which are complex ribonucleoprotein machines that operate in the cell nucleus. In the case of Hac1, however, two enzymes are sufficient to mediate intron removal in the cytosol, and one of them is Ire1. Walter and colleagues were surprised to find that the transmembrane kinase phosphorylates itself, leading to a conformational change that activates an RNase activity in Ire1. Ire1 then cleaves the HAC1 mRNA as its only substrate by removing an unconventional intron (17). A tRNA ligase encoded by RLG1 next joins the two exons together. Walter and his laboratory were able to reconstitute this reaction by using purified components (18) and were amazed to find that many of the salient features of this unusual signal transduction pathway are conserved from yeast to mammalian cells (19). Around the same time, as Ire1’s secrets were being revealed, Walter was chosen as a Howard Hughes Medical Institute investigator.

Walter’s PNAS Inaugural Article (3) focuses on Ire1, which he coauthored with Stroud. Walter calls their work together “an incredibly easy-going, productive, and anxiety-free collaboration.” He continues, “Over the years, we’ve switched senior authorship back and forth in a semihazardous fashion.” Walter thinks their collaborations work well because Stroud is “local,” being only one floor away.

Walter’s and Stroud’s Inaugural Article (3) suggests how Ire1 can distinguish a misfolded protein from a correctly folded one. Walter explains that the previous model accepted by the field suggested that when protein translation is proceeding at the correct pace, many free chaperone proteins are present, and these free chaperones were thought to keep Ire1 in an inactive state (15). His findings showed however that the architecture of the luminal domain of Ire1, which senses unfolded proteins, resembles that of a major histocompatibility complex (MHC). “It was virtually screaming at us, ‘I have the properties to bind a polypeptide chain directly.’ The structure shows a big, deep groove, which is ideally predisposed to bind a polypeptide, and our structure-guided mutational analysis suggests that the residues lining the groove matter for Ire1 function,” says Walter. The next step will be to try to crystallize the luminal domain with polypeptides bound, in order to decipher the molecular details of the protein-recognition process.

Still SRP

Even today, SRP is a focus of Walter’s work. “We’re still playing with SRP,” he says. He wants to boil down the particle’s function to a precise molecular understanding of its constituent components. Walter also is interested in how cells fuse membranes with one another, an action important for events like fertilization. Another focus of Walter’s laboratory is the regulation of organelle synthesis. Too few organelles of one type can lead to bottlenecks, as in the case of ER, whereas too many organelles result in wasted space and energy. The work with Ire1 lends a partial understanding of how ER abundance is regulated according to need. Most recently, Walter and his colleagues have found a unique organelle in yeast, which they named eisosomes, derived from the Greek words “eis,” meaning “into” or “portal,” and “soma,” meaning “body.” “We think eisosomes define static sites that regulate where and when endocytosis occurs,” he says (20).

For Walter, though working his entire career with things invisible to the naked eye, it is important for him that people see his work. A member of the Public Library of Science Biology editorial board since 2003 and the PNAS editorial board since 2005, Walter is a firm believer in open access research articles, which are freely available to the public upon publication. “I think the work that we’re doing should be disseminated as widely as possible. The knowledge of whatever we learn belongs to everybody,” he says. “Everybody” includes nonscientists, to Walter, as he is also a strong supporter of science education and is proud of the work he and the University of California, San Francisco, do to connect scientists with teachers and to bring them into classrooms. Walter feels the education work gives students “a refreshing spark and enhances their ability to think rationally and communicate at all levels, not just in science class.”