2019 - Issue 4

​​​Please also visit the tribute to Dr. Jim Alfano in the MPMI journal​.

James “Jim” Robert Alfano, 56, Charles Bessey Professor of Plant Pathology at the University of Nebraska–Lincoln (UNL), died Nov. 21, 2019, following a battle with cancer. Jim served 17 years with UNL, joining the faculty in 2002. He was named director of the Department of Plant Pathology’s undergraduate Microbiology program in 2011. He also served as a member of the University’s Center for Plant Science Innovation. Jim’s research focused on how bacteria pathogens that cause plant diseases differ from those in animals. Studies in his lab were specifically directed at understanding type III secretion systems, a specialized protein apparatus present in gram-negative bacteria pathogens in plants and animals. An official obituary for Jim can be found on the University Of Nebraska–Lincoln’s website. 

Jim was a well-respected and well-liked member of the IS-MPMI community. Below is a tribute from Jim’s former mentor, Alan Collmer, and a subsequent article includes a compilation of homages from friends and colleagues on social media. Both tributes exemplify the enormous impact that Jim’s science and personality has had on our research community during his career.

Jim Alfano as a postdoc at Cornell in 1993.

Alan Collmer (Cornell University, U.S.A): Jim Alfano was a giant in our field who made paradigmatic discoveries involving the Pseudomonas syringae type III secretion system (T3SS), the effectors it injects into plant cells during pathogenesis, and the functions of those effectors in virulence. Jim was a postdoc in my lab in the mid-90’s and then a coPI on an NSF Plant Genome Research Program functional genomics project I led in the early 2000’s. Over the years, my working relationship with Jim evolved from mentor, to intellectual partner, to grateful reporter of joint NSF project progress, to ultimately, an admiring reader of his lab’s many, major discoveries. But it was my friendship with Jim that I will treasure above all else. 

In his postdoctoral research, Jim confronted the paradoxical activities of the P. syringae hrp gene cluster in eliciting the hypersensitive response (HR) and in trafficking different classes of proteins. Jim’s careful observations revealed that harpins, though known to be abundantly secreted in culture by the Hrp system and capable of eliciting the HR as isolated proteins, are actually “helpers” in the delivery into plant cells of another class of proteins that we now know of as effectors. This insight shifted our research focus to the effectors and their systematic identification. Jim consequently led an effort to sequence the hrp gene cluster and flanking sequences in three model strains of P. syringae – a massive effort that Jim brought to completion with his new lab in the Department of Biological Sciences at the University of Nevada, Las Vegas (UNLV). This work revealed that hrp genes are part of a tripartite pathogenicity island that includes an exchangeable effector locus and a conserved effector locus harboring core, ancestral effector genes (with many more effector genes somewhere else in the genome). Jim’s work was key to revealing the primary function of the Hrp T3SS and its centrality in the evolution of P. syringae virulence. 

As our excitement with these discoveries shifted from primary observations to broader implications, Jim took the lead in spreading the word of the many advances being made with plant pathogenic bacteria.  The two of us accordingly wrote a series of review articles for Plant Cell (1996), Journal of Bacteriology (1997), the textbook Principles of Bacterial Pathogenesis (2001), and Annual Review of Phytopathology (2004). In meshing with Jim’s thinking in this process, I developed a deep respect for his intellect and his gift for seeing and saying things clearly and directly. Indeed, when I found myself writing my sections with the thought of meeting his standards, I realized that I now had a great colleague and that our field had a rising new star. In 1997 Jim started his own lab at UNLV, and then in 2000 moved to the Plant Science Initiative and Department of Plant Pathology at the University of Nebraska-Lincoln (UNL). With his new lab, Jim began a career-long exploration of the environmental and genetic factors controlling the traffic of different classes of proteins through the T3SS and into plant cells. 

Jim’s pioneering work on the Hrp system was foundational to a 2000 multi-institutional award from NSF to sequence and study the genome of P. syringae pv. tomato (Pto) DC3000. As a coPI, Jim contributed to a remarkable 21 project-supported publications between 2002 and 2007. Three of the many publications that were led by his lab had particular impact. Petnicki-Ocwieja et al. (2002 PNAS) used an iterative approach involving experimental and computational methods to comprehensively identify effector genes in the DC3000 genome. Jamir et al. (2004 Plant Journal) revealed that several of the newly found effectors were suppressors of the HR. And, in work done entirely in Jim’s lab, Fu et al. (2007 Nature) discovered that one of the newly found effectors (HopU1) used ADP-ribosylation (an activity previously unknown for plant pathogens) to inhibit RNA-binding protein-dependent plant immunity. Jim’s lab also investigated host targets, biochemical activities, and subcellular localization of several other effectors. Finally, his group discovered important aspects of effector delivery by the T3SS, including the identification of chaperones for several effectors, the function of HrpK as a translocon component, and the dual activity of HrpJ, an extracellular T3SS component, in regulating substrate traffic and promoting virulence.

Jim was a scientist to his core, and he was fearless in using the best tools to get to the heart of hard problems. He also pulled

Image by Jim Alfano

​more than his weight for the larger scientific community— as a highly respected member of multiple editorial boards and grant review panels and as a teacher and mentor to a new generation of students and postdocs. He was deservedly an elected fellow of several scientific societies and a recipient of multiple honors. However, as much as Jim will be missed for his scientific prowess, he will be missed so much more as a person of many dimensions.

Jim arrived in my lab in March 1993 in a Jeep more suited for southern California than upstate New York. Tall and athletic, he came with a big dog named Jake and an open enthusiasm for life and science. He initiated an annual March Madness NCAA Basketball pool in the department and also got our lab hooked on listening to NPR and having lively discussions of politics, movies, writing styles, music, and endless other topics. Jim seemed like a spirited race horse, but he was also surprisingly aware and caring of others. At Cornell, he met Karin van Dijk, then a PhD student in the Graduate Field of Plant Pathology. They married and later had a daughter, Isabella (“Izzy”). Jim and Karin became collaborators as well as life partners, and she is now an Associate Professor of Biochemistry at UNL. As Jim’s former lab mate Amy Charkowski wrote me: “I remember how much he and Karin enjoyed running in Ithaca and how much he enjoyed spring in New York and the song birds. He had never lived someplace with so many song birds or with such dramatic springs and he could go on and on about this.” 

Two photos of Jim evoke particularly strong memories for me. The first is the official Plant Pathology Department photo of Jim as a new postdoc in 1993. In it I see the raw enthusiasm and promise that I was so lucky to experience. The second photo (below), from Gail Preston, is of Jim and Rob Jackson leading their respective “DC3000” and “1448A” soccer/football teams into battle at the 8th International Conference on Pseudomonas syringae Pathovars and Related Pathogens in Oxford in 2010. In it I see the wide-open sociability, sunny vitality, and love of fun for the whole group that Jim brought to the benefit of our lab and to so many scientific gatherings. Jim will be missed for so many reasons by so many people around the world. We have all lost a great scientist and a treasured friend. 

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