Congratulations to Marlo! Marlo receives NSF graduate research fellowship to support their PhD and passes their qualifying exam! Marlo will pursue research on resistance to Pseudomonas syringae in tomato.
Jenn shared our tomato research at the International Society for Molecular Plant-Microbe Interactions Congress (IS-MPMI 2023) and the 37th Annual Tomato Disease Workshop.Â
Congratulations to Marlo, who received the Grace Kase award in recognition of academic and research excellence!
Nate's first-author paper is published in Plant Cell & Environment! Nate showed that the immune receptor ZAR1 is able to interact with multiple other ZED1-related kinases (ZRKs) while retaining specificity for certain kinases. Former postdoc Dr. Mael Baudin and research scientist Jana Hassan also contributed to the work, in collaboration with Dr. Chris Silva and Dr. Les Harden at the USDA. We showed that interaction strength between ZAR1 and a weakly interacting ZRK could be rationally engineered, which may expand the effector recognition profile for ZAR1.
Congratulations to Daniela Berman, who graduated with her B.Sc. in May! Dani majored in Microbial Biology and will be starting graduate school at UCSD.
Undergraduate student Dani Berman presented her honors research project. Dani screened cultivated and wild tomato accessions for resistance to Pseudomonas syringae. New sources of disease resistance will help protect plants from infection.Â
Undergraduate student Ivan Wang was nominated for an OSKI award for Outstanding Undergraduate Student Organization! Ivan founded the Vertical Farming at Berkeley club. In vertical farming, plants are grown in controlled conditions on vertically stacked racks, allowing for a smaller footprint. The club raised funds for the project, engineered the vertical farming system and characterized the biology of the plants.
Elan Tran and Marlo Hall rotated in the lab, and Marlo joins the lab! Elan did her B.Sc. at the University of Miami. Marlo did their B.Sc. at UC San Diego. Marlo will pursue research on the interaction between Pseudomonas syringae and tomato.
Ilea is now Dr. Ilea Chau-Ly! Ilea is the first Ph.D. graduate student in the Lewis Lab! Ilea characterized effector responses in wild tomato species and tomato immune responses, and demonstrated that CRISPR-Cas3 could make large deletions in Pseudomonas syringae. She will be joining a biotechnology company in Boston.
The Lewis Lab talked about and heard about exciting science at the first in-person Plant Biology meeting since San Jose in 2019! Ilea gave a talk on tomato immune responses to Pseudomonas syringae and Nate presented a poster on the interaction between ZAR1 and kinases. Jenn was a panelist for a workshop on mentoring.
Our collaborative paper using RB-TnSeq in Xanthomonas campestris is now published in New Phytologist! We developed a random barcoded transposon library in X. campestris that the groups of Alice Boulanger and Laurent Noel at INRA used to identify bacterial genes important in the colonization of hydathodes. X. campestris causes black rot in crucifers, which can severely affect yield. Identification of genes important for bacterial virulence will help protect plants from disease.
Jenn and colleagues' review on the phloem as a niche for plant pathogens is now published in Annual Review of Phytopathology! We discussed phloem development, physiology and phloem-infecting pathogens.Â
Congratulations to Kristi Yanigihara, who graduated with her B.Sc. in May! Kristi majored in Genetics & Plant Biology and will be starting work for a biotechnology company.
Nate receives an Outstanding GSI award for his work in the class "The Secret Life of Plants."
Jenn talked about the lab's research at Plant Biology 2021 and in IS-MPMI's eSymposia series. Both presentations featured work from former postdoc Dr. Karl Schreiber who identified susceptibility hubs in the host that are targeted by the pathogen to promote virulence.
Throughout the year, we have been conducting interviews with women plant pathologists to talk about their research, and their efforts to broaden science. Interviews are available here: Dr. Barbara Kunkel, Dr. Wenbo Ma, Dr. Valerie Williamson, and Dr. Kimberly Webb.
Congratulations to Ho Jung Jeong, Ani Chouldjian and Jinny Chung, who graduated with their B.Sc. degrees in May! Ho Jung and Ani majored in Microbial Biology, and Jinny majored in Molecular and Cell Biology.
Our former Amgen scholar Taylor Harris has co-authored an article on supporting black scientists in STEM. See article here.
Our invited review on the activities of type III secreted effectors is now published! This review was co-authored by Dr. Karl Schreiber and Ilea Chau-Ly. Understanding the virulence strategies of bacterial pathogens can help design approaches to protect plants from infection.
Nate successfully passed his qualifying exam! Nate's research will focus on the immune receptor ZAR1 and its broad recognition of effector proteins.
Karl's paper on a putative topoisomerase, ZIN1, that promotes bacterial virulence is now available in First Look at Molecular Plant-Microbe Interactions! Karl showed that ZIN1 is targeted by multiple type III secreted effectors. Plants lacking zin1 are more resistant to infection, suggesting that it is a susceptibility factor.
Karl's paper on a new susceptibility hub (ABR1) that is targeted by Pseudomonas syringae effector proteins is now available at Plant Journal! We showed that ABR1 can bind DNA and enable transcriptional activation. Mutants in abr1 do not have enhanced immunity, supporting that ABR1 is a susceptibility factor.
Our manuscript on natural diversity in HopZ1a recognition has been published in Plant, Cell & Environment! Using bioinformatic and genetic approaches, we showed the Arabidopsis ecotypes vary in their ability to recognize HopZ1a, primarily due to single nucleotide polymorphisms in the immune receptors ZAR1 and ZED1. These polymorphisms affect the interaction between ZAR1 and ZED1. This was the work of Dr. Mael Baudin, Jana Hassan, Dr. Claire Bendix, Rolin Sauceda and Nate Diplock from our lab, in collaboration with the groups of Dr. Chelsea Specht and Dr. Andrei-Jose Petrescu.
Ilea's collaborative project with Joe Bondy-Denomy's lab on genome engineering using CRISPR-Cas3 has been published in Nature Methods! The Cas3 system generates large deletions, which is particularly useful for virulence clusters. We showed that Cas3-generated mutants behave similarly to traditionally generated polymutants. This approach will expedite functional genomics in many bacterial species.
Jenn and Ilea presented the lab's research on plant-microbe interactions at the Plant Biology 2020 Worldwide Summit and Psyringae2020. Jenn discussed our work on natural diversity in effector recognition. Ilea discussed the CRISPR-Cas3 approach for functional genomics in bacteria.
As part of our ongoing commitment to broadening participation, the Lewis lab and members of the PGEC participated in an excellent workshop on implicit bias.
Jenn was invited to give a talk in MPMI's new remote talk series on Yuan and Claire's citrus greening work, which was MPMI's Editor's Pick for March. The talk is available at https://www.youtube.com/watch?v=atlFhMzvoUY. We identified peptides that elicited immune responses in citrus species and that could prevent plants from an unrelated pathogen.
Nathan Diplock has joined the Lewis Lab for his dissertation research. Nate will focus on ZAR1-mediated recognition of effectors through ZED1 and ZED1-related kinases.
Congratulations to Michelle Clarissa and Anushtha Sharma, who graduated with their B.Sc. degrees in May! Michelle and Anushtha majored in Microbial Biology.
Jamie Calma, an undergraduate student in the lab, has received a URAP summer award to continue her research. Congratulations Jamie!
Yuan and Claire's paper on microbe-associated peptides that trigger immunity in citrus is published in Molecular Plant-Microbe Interactions! We used comparative genomics and computational methods to identify potential microbe-associated peptides from the bacteria that causes citrus greening. Citrus greening is a devastating disease that is decimating citrus groves in Florida. We found that some peptides elicited basal immune responses in several species and one peptide bolstered the immune response against an unrelated pathogen. This paper was the Editor's Pick for March and was featured in several news articles.
The methods for Jana's seedling flood assay are published in the Journal of Visualized Experiments! We provided detailed protocols and videos to help other scientists use this high-throughput method for infecting tomato seedlings with Pseudomonas syringae. This method can expedite screens for new sources of disease resistance.
Our paper on structural aspects of ZAR1 that are critical for its function is now published in Plant Journal! This work was led by Dr. Mael Baudin with assistance from Dr. Karl Schreiber and our collaborators, Eliza Martin and Dr. Andrei-Jose Petrescu at the Institute of Biochemistry at the Romanian Academy. This work functionally validates the ZAR1 cryo-EM structure.
Nate Diplock is doing a rotation in the lab. Nate was an undergraduate student at Bates College and will be working on ZAR1-mediated recognition.
The Lewis Lab shared our research at the International Society of Molecular Plant-Microbe Interactions meeting in Glasgow, Scotland. Jenn discussed our work on peptides from Candidatus Liberibacter pathogens that can trigger immune responses in citrus. Mael presented our work on intramolecular and intermolecular interactions that regulate ZAR1. He also received a travel award to attend the meeting.
Congratulations to Lydia Zhang, who graduated with her B.Sc. in May! Lydia majored in Molecular and Cell Biology.
Jenn gave a talk on our tomato research at the Bay Area Meeting for Tomato Plant Pathology.
Our paper on protein acetylation during disease and defense is now published in Methods in Molecular Biology. This detailed protocol was co-authored by Dr. Karl Schreiber and Jenn.
Helen Liu from the University of Illinois at Urbana-Champaign, is a new rotating graduate student in the lab. She will be working on ZAR1-mediated recognition.
The Lewis Lab has received a Chau Hoi Shuen Foundation Women in Science research grant! The grant will focus on Pseudomonas syringae infection in Brachypodium.
Congratulations to Steven Yee and former lab member Taylor Harris, who graduated with their B.Sc. degrees in May! Steven majored in Microbial Biology. Taylor was an undergraduate student at Fisk University.
Ilea successfully passed her qualifying exam and has been awarded the prestigious NSF graduate research fellowship for her doctoral work! Ilea is working on bacterial effectors that elicit immune responses in tomato.
Our review on phloem-limited pathogens is now published in Molecular Plant Pathology! Postdoc Dr. Claire Bendix and Jenn discussed multiple types of phloem-limited pathogens, including bacteria, mollicutes and viruses, and commonalities in their infection strategies, to help design new approaches for understanding these pathogens and control disease.
Jana's paper is now available in Plant Direct! We found that some soil types could bolster plant resistance to aerial pathogens, in a salicylic acid-independent manner. This work also involved our collaborators, Dr. Roberto de la Torre-Roche and Dr. Jason White, at the Connecticut Agricultural Experiment Station.
Congratulations to Ilea, Taylor and Alice! Ilea Chau received the Grace Kase fellowship, in recognition of excellence for graduate coursework and rotations. Taylor Harris received a poster award at ABRCMS for the work she performed while in our lab. Dr. Alice Boulanger from the University of Toulouse and INRA, received a grant to visit our lab and discuss collaborative research.
Snigdha Chatterjee from Syracuse University, is a new rotating graduate student in the lab. Snigdha will be working on susceptibility genes in plants.
Our methods paper on a quantitative high-throughput yeast two-hybrid screen (QIS-Seq) is now out in Methods in Molecular Biology!
Mael, Jana and Karl's paper is now published in Plant Physiology! We showed that ZAR1-mediated recognition of HopZ1a is functionally conserved from the Brassicaceae to the Solanaceae and demonstrated that the coiled-coil domain of ZAR1 is sufficient for the hypersensitive response. Nicotiana benthamiana is a useful system for expediting functional analysis of ZAR1.
Ilea Chau is joining the Lewis Lab for her PhD studies. She will be examining the contribution of bacterial genes to immune elicitation in tomato.
Undergraduate students Taylor Harris, Zoe Caron and RJ Comandao will be joining us for the summer, to investigate plant-pathogen interactions. Taylor is a student at Fisk University. Zoe is a student at UC Berkeley and RJ is a student at Contra Costa Community College.
Jana's tomato paper is now out in Molecular Plant-Microbe Interactions! Jana developed a seedling-based assay for resistance, that recapitulates typical measures of disease and resistance. Using this assay, she identify multiple wild tomato species with resistance to an emerging strain of Pseudomonas syringae. Undergraduate student, Jane Zhou, also assisted with this project.
Congratulations to Amy Zhu and Juan Alcauter, who graduated with their B.Sc. degrees in May! Amy majored in Molecular Environmental Biology, and Environmental Economics and Policy. Juan majored in Microbial Biology.
Ilea Chau is a new rotating graduate student in the Lewis Lab. Ilea was an undergraduate student at Duke University. She will working on bacterial proteins that are recognized in tomato.
Congratulations to Tuong Pham and Rolin Sauceda, who graduated with their B.Sc. degrees in December! Tu majored in Molecular and Cell Biology, and Integrative Biology. Rolin majored in Genetics and Plant Biology.
Lily Gu is a new graduate student who is rotating in our lab. Lily received her B.Sc. from Emory University and her M.Sc. from Ball State University. Dr. Yuan Chen, formerly of the McCormick Lab has joined us to investigate plant immunity.
Lab members presented research at the IS-MPMI meeting in Portland, Oregon. Dr. Mael Baudin presented a biochemical approach to identify components of ZAR1 immune complexes. Dr. Karl Schreiber presented a high-throughput screen for identifying effector targets.
Our review on the molecular mechanisms of effector recognition in plants is now out in Seminars in Cell and Developmental Biology! The review was co-authored by Dr. Karl Schreiber, Dr. Mael Baudin, Jana Hassan and Jenn.Â
Four undergraduate students have joined the lab for summer research projects. Tuong Pham, Tanisha Muquit and Rolin Sauceda join us from UC Berkeley. Miguel Palermo joins us from Contra Costa Community College.
Congratulations to Juan Hernandez and Angela Ziqi Liu, who graduated from UC Berkeley with their B.Sc. degrees in May, and Ruben Rubalcava who graduated with his B.Sc. degree from UC Davis in June! Juan majored in Microbial Biology. Angela majored in Molecular and Cell Biology. Ruben majored in Biochemistry and Molecular Biology.
Dr. Karl Schreiber and Dr. Claire Bendix are two new postdocs in the Lewis Lab. Karl joins us with extensive expertise in molecular plant pathology. Claire joins us with experience in plant biology.
Ray Serafin, our Contra Costa College USDA Scholar, was profiled in The Advocate. See story here.
Congratulations to Dina Nazarchuk and Nolan Mori, who graduated from UC Berkeley with their B.Sc. degrees in May! Dina majored in Molecular Environmental Biology. Nolan majored in Genetics and Plant Biology.
Our manuscript on functions of the HopZ family of type III secreted effectors is published in PLOS One! We showed that the HopZ members have diverse means of suppressing plant immunity.
Dr. Mael Baudin is a new postdoc in the Lewis Lab! He joins us from INRA, where he studied symbiotic interactions. He will work on ZAR1-mediated recognition.
Recognition of effector proteins leads to robust immunity that prevents bacterial infection. We discuss ZED1 and ZED1-related kinases (ZRKs) that mediate the recognition of type III effector proteins through ZAR1.
Congratulations to Jane Zhou, who graduated from UC Berkeley with her B.A. degree in May! Jane majored in Integrative Biology.
Our manuscript on indirect recognition of HopZ1a through ZED1 and ZAR1 is now published in PNAS! Using a genetic approach, we showed that ZED1 is required for the recognition of Pseudomonas syringae effector HopZ1a. HopZ1a acetylates ZED1, which presumably affects the conformation of immune receptor ZAR1 to trigger resistance. ZED1 is a part of a small family of receptor-like cytoplasmic kinases, the ZRKs.