Chitin receptor CERK1 links salt stress and chitin-triggered innate immunity in Arabidopsis

Catherine Espinoza, Yan Liang, Gary Stacey

Summary

In nature, plants need to respond to multiple environmental stresses that require involvement and fine-tuning of different stress signaling pathways. Cross-tolerance in which plants pre-treated with chitin (a fungal microbe-associated molecular pattern) have improved salt tolerance was observed in Arabidopsis but is not well understood. Here, we show a unique link between chitin and salt signaling mediated by the chitin receptor CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1). Transcriptome analysis revealed that salt stress-induced genes are highly correlated with chitin-induced genes, while this was not observed with other microbe-associated molecular patterns (MAMP) or with other abiotic stresses. The cerk1 mutant was more susceptible to NaCl than wild type. cerk1 plants had an irregular increase of cytosolic calcium ([Ca2+]cyt) after NaCl treatment. Bimolecular fluorescence complementation (BiFC) and co-immuno precipitation experiments indicated that CERK1 physically interacts with ANNEXIN 1 (ANN1), which was reported to form a calcium-permeable channel that contributes to the NaCl-induced [Ca2+]cyt signal. In turn, ann1 mutants showed elevated chitin-induced rapid responses. In short, molecular components previously shown to function in chitin or salt signaling physically interact and intimately link the downstream responses to fungal attack and salt stress.

Link to the journal article

Identification of Homogentisate Dioxygenase as a Target for Vitamin E Biofortification in Oilseeds (link to the full paper)

Minviluz G. Stacey*, Rebecca E. Cahoon , Hanh T. Nguyen, Yaya Cui, Shirley Sato, Cuong T. Nguyen, Nongnat Phoka, Kerry M. Clark, Yan Liang, Joe Forrester, Josef Batek, Phat Tien Do, David A. Sleper, Thomas E. Clemente, Edgar B. Cahoon, and Gary Stacey

Abstract

Soybean (Glycine max L.) is a major plant source of protein and oil and produces important secondary metabolites beneficial for human health. As a tool for gene function discovery and improvement of this important crop, a mutant population was generated using fast neutron irradiation. Visual screening of mutagenized seeds identified a mutant line, designated MO12, which produced brown seeds as opposed to the yellow seeds produced by the unmodified Williams 82 parental cultivar. Using forward genetic methods combined with comparative genome hybridization (CGH) analysis, we were able to establish that deletion of the GmHGO1 gene is the genetic basis of the brown seeded phenotype exhibited by the MO12 mutant line. GmHGO1 encodes a homogentisate dioxygenase (HGO) which catalyzes the committed enzymatic step in homogentisate catabolism. This report describes the first functional characterization of a plant HGO gene, defects of which are linked to the human genetic disease alkaptonuria. We show that reduced homogentisate catabolism in a soybean HGO mutant is an effective strategy for enhancing the production of lipid-soluble antioxidants such as vitamin E, as well as tolerance to herbicides that target pathways associated with homogentisate metabolism. Furthermore, this work demonstrates the utility of fast neutron mutagenesis in identifying novel genes that contribute to soybean agronomic traits.

Computational Analysis of the Ligand Binding Site of the Extracellular ATP Receptor, DORN1

Cuong The Nguyen, Kiwamu Tanaka, Yangrong Cao, Sung-Hwan Cho, Dong Xu, Gary Stacey

Abstract

DORN1 (also known as P2K1) is a plant receptor for extracellular ATP, which belongs to a large gene family of legume-type (L-type) lectin receptor kinases. Extracellular ATP binds to DORN1 with strong affinity through its lectin domain, and the binding triggers a variety of intracellular activities in response to biotic and abiotic stresses. However, information on the tertiary structure of the ligand binding site of DORN1is lacking, which hampers efforts to fully elucidate the mechanism of receptor action. Available data of the crystal structures from more than 50 L-type lectins enable us to perform an in silico study of molecular interaction between DORN1 and ATP. In this study, we employed a computational approach to develop a tertiary structure model of the DORN1 lectin domain. A blind docking analysis demonstrated that ATP binds to a cavity made by four loops (defined as loops A B, C and D) of the DORN1 lectin domain with high affinity. In silico target docking of ATP to the DORN1 binding site predicted interaction with 12 residues, located on the four loops, via hydrogen bonds and hydrophobic interactions. The ATP binding pocket is structurally similar in location to the carbohydrate binding pocket of the canonical L-type lectins. However, four of the residues predicted to interact with ATP are not conserved between DORN1 and the other carbohydrate-binding lectins, suggesting that diversifying selection acting on these key residues may have led to the ATP binding activity of DORN1. The in silico model was validated by in vitro ATP binding assays using the purified extracellular lectin domain of wild-type DORN1, as well as mutated DORN1 lacking key ATP binding residues.

Click here to access the full paper

The International Society for Molecular Plant-Microbe Interactions (IS-MPMI) has awarded Beverly Agtuca a travel award  to attend the IS-MPMI XVII Congress, July 17-21, 2016 in Portland, Oregon, USA.

Awards up to $750 were used to pay for her registration, travel, and/or lodging expenses.  Award selection was based on the quality of the applicant’s science reflected in the research abstract, impact statement, and curriculum vitae.

Congratulations Beverly!

IS-MPMI 2016 – Awards Brochure

The 5th Annual Soybean Precision Genomics and Mutant Finder Workshops

August 3-4, 2016

University of Missouri – Columbia

The 5th annual Soybean Precision Genomics and Mutant Finder Workshops will be held on August 3-4, 2016, at the University of Missouri, Columbia Missouri.

Jesse Hall from the Francis Quadrangle, Missouri University

The workshops will feature:

1) Presentations on soybean mutant resources

2) Tutorials on cutting edge technologies used for:

• Soybean targeted mutagenesis,

• Gene editing,

• Gene silencing

• Other functional genomics applications.

3) Field demonstrations of mutant populations and opportunity to order seeds from selected lines.

Sponsors:

• United Soybean Board

• National Science Foundation.

Funding support:

Funding is available to help defray travel and lodging costs for participants. Please contact Bing Stacey (staceym@missouri.edu) to learn more about the event and request for travel support. A strong background in molecular biology is recommended.

MU Alumna Receives National Distinguished Dissertation Award
Research will open a new field of plant research

Dec. 04, 2015

Link to original story

Story Contact(s):
Nathan Hurst, hurstn@missouri.edu, 573-882-6217

By Amanda Narverud

COLUMBIA, Mo. – Mizzou alumna Jeongmin Choi has received the Council of Graduate Schools/ProQuest Distinguished Dissertation Award for her innovative research in plant sciences. The prestigious national award is given to an individual whose doctoral dissertation makes unusually significant contributions to its discipline. When Choi wrote her dissertation, she was a doctoral candidate in plant sciences from the MU College of Agriculture, Food and Natural Resources.

From left: Suzanne T. Ortega, CGS; Jeongmin Choi, winner, 2015 ProQuest Distinguished Dissertation Award; Marlene Coles, ProQuest

For her dissertation, Choi identified the first extracellular ATP receptor in plants. Her successful identification of the receptor has opened a new field of plant research that explores the interconnections among plant stress, pathogen defense and development.

ATP (adenosine 5’- triphosphate) is the main energy source inside cells and is considered to drive many life processes in plants, animals and humans. ATP is found in high concentrations inside cells. It also can be found secreted outside cells, which is referred to as extracellular ATP. When the molecule is found outside of a cell, it acts as a signaling molecule. ATP receptors are proteins localized on the cell surface to bind ATP from outside the cells and deliver the information inside the cells. Therefore, the identification of ATP receptors is essential in understanding of the cells signaling pathway. Until now, ATP receptors had been characterized in mammals, but receptors in plants had not been identified.

“The interesting part is that the newly identified plant receptor is different from animal receptors,” Choi said. “Although they sense the same molecule, they are actually quite different. The molecule can be released in response to various stress responses and also during development. We believe that the function of this molecule might relate as a danger signal, so that the plant knows that it is in danger.”

Now that the first plant receptor for extracellular ATP is known, it is likely that this receptor exists in a wide range of plant species. According to Choi, extracellular ATP has a role in many plant functions, but especially in how they perceive environmental stresses such as drought and insect feeding. According the Choi’s dissertation advisor, Gary Stacey, Curators Professor of Plant Sciences, Choi was a valued member of her Mizzou laboratory.

“As is so often the case, Jeongmin excelled not only as a researcher, but in many other ways,” Stacey said. “As a lab citizen, as a mentor to undergraduates in the lab, as a leader among her other graduate students and as a teacher, she was a great addition to our laboratory. It was a great pleasure to have her in our laboratory and we fully expect great things from her in the future.”

Choi was recognized in 2014 by the MU Office of Graduate Studies for her outstanding doctoral dissertation research. As the recipient of the MU Graduate Studies Distinguished Doctoral Dissertation Award, she was the first student to be nominated by the University of Missouri for the national Council of Graduate Schools (CGS)/ProQuest award.

“Mizzou has incredibly innovative graduate students who will become the leaders of tomorrow,” Leona Rubin, associate vice chancellor for Graduate Studies said. “One goal of the Office of Graduate Studies is to provide support for students and their academic units in submitting nominations that showcase and promote students and their accomplishments. I think it is telling that in the first year we made a concentrated effort to showcase our students nationally, a Mizzou graduate wins the national Distinguished Dissertation of the Year Award from the Council of Graduate Schools.”

Choi is currently working as a post-doctoral research associate at the University of Cambridge in the U.K. as a European Molecular Biology Organization (EMBO) fellow. EMBO supports post-doctoral research visits to laboratories throughout Europe.

Catherine Espinoza (Cathy) received her bachelor degree in biological sciences from the University of Federico Villarreal, Lima-Peru in 2001. Before coming to MU in 2008, she worked as a research assistant at the Division of Conservation and Characterization of Plant Genetic Resources, International Potato Center (CIP), Lima-Peru (2003-2008), and as a biotechnology and biodiversity consultant at the Economic Commission for Latin America and the Caribbean (ECLAC) and Andean Development Corporation (CAF), Lima-Peru (2003). Cathy joined the Stacey lab in 2013 and her dissertation was entitled “Molecular mechanisms of stress tolerance in plants”. We congratulate Cathy on her successful Ph.D. dissertation defense and wish her all the best for a new chapter in her life.

Cathy shares her happy moment after the defense with her Committee and the Stacey lab members

It would not be hard to understand why Homecoming at the University of Missouri may have an extra special meaning to Hli, Yia and See Yang.

As first-generation Americans and college students they share a common bond not only through their Mizzou pride but also through the embedded core values of family, hard work and agriculture that helped lead their family to find a new home in America.

Their parents, Chao and Toua Yang, came to the United States in 1992 when their first child, See, was two years old and her little brother, Yeng, was only a couple months old. The Yangs, former refugees of the Vietnam War, left their family, friends and the farming life behind in Laos in pursuit of better opportunity for See, Yeng and the four children that would later be born in the United States.

“Growing up I always spent time with my siblings, and back then I really didn’t know what my parents were doing, but now I do — they were working so hard to save up so they could give us a better life,” Hli said.

Humble roots

The family originally moved to Wisconsin where they worked blue collar jobs. The Yangs dreamed of raising several children on a farm, and when they had saved up enough money, they purchased a poultry farm in Wheaton, Mo., where the parents returned to their agricultural roots and continued to show their children the true meaning of hard work.

“When they first came to America, they did not have anything,” Yia said. “They started off with jobs like picking strawberries that were way below minimum wage, and now we have a pretty large-scale farm operation. So I would say that they are really hard working.”

Hli recalled the story of her dad rationing his earnings when he first came to the states. Her father would split $20 in various ways to afford a week’s worth of gas, water and food. The sacrifices her parents made to pave the way for better opportunities for their children taught Hli and her siblings the kind of ambition necessary to succeed in life.

“Everything about them, like their struggles and their hard work, I think that’s had a big impact on my siblings and me,” Hli said. “We were raised to understand just how hard success is and how hard you have to work for it. You don’t just get things handed to you.”

The Yangs have six children: See, Yeng, Chee, Hli, Yia and Meng. All of their children, aside from the Meng, 17, who still attends high school, are in pursuit of their career goals. See, 25, is a CAFNR alumna and attends law school at the University of Arkansas. Hli, 20, and Yia, 19, are CAFNR undergraduate students. Hli is a junior studying science and agricultural journalism; Yia is a sophomore in plant sciences. Yeng, 23, is in the Air Force, and Chee, 22, attends nursing school at Missouri Southern State University in Joplin, Mo.

Life on the farm had a profound impact on three of their children, who decided to attend programs within the University of Missouri’s College of Agriculture, Food and Natural Resources. See, Hli and Yia became involved in the Future Farmers of America at their high school where all of them held officer positions at the district level. After becoming Mizzou Tigers, the siblings became involved in CAFNR student organizations and now pursue career goals in agriculture.

Leading by example

See received her bachelor’s degree in agribusiness and her master’s degree in agriculture economics from the University of Missouri. She now attends law school at the University of Arkansas and plans to use her degrees to work for a firm or for a food or agricultural business as an in-house council.

It was See, the oldest sibling, who first became involved in FFA and other high school organizations, and was the first to attend school at Mizzou. See is also a former member of the CAFNR Ambassadors, a student group promoting the College, where Hli is now co-director and Yia is a member. Hli said her sister’s example had a profound impact on the performance of her and her siblings.

“See is very driven. She is always wanting to better her life and the lives of others. She is a very big family person, too. She loves coming home and seeing all of us. I honestly think that if she wouldn’t have joined FFA, we wouldn’t have joined. We have followed each other’s footsteps, and she is the one who led the way… She set the bar really high for the rest of us.”

While visiting See in Columbia on various family visits over the years, Yia became exposed to Mizzou and the opportunities available. Although schools like the University of Arkansas and Oklahoma State University were closer to his home, Yia had developed a strong connection the programs available at CAFNR. Without this insider knowledge provided by See’s experience at Mizzou, Yia probably would not have made the decision to attend school at MU.

“See is the big reason why the rest of us are where we are today,” Yia said. “She’s the oldest, and the first one to go to college. Probably without her coming to University of Missouri and being so involved in CAFNR, I don’t think I would have made the decision to come here.”

A network of support

In addition to being co-director of CAFNR Ambassadors, Hli was involved in CAFNR Student Council during her first two years at Mizzou. She wants to become a voice for agriculture in the media after she graduates. She has worked at KOMU and interned for RFT-TV and Farm Journal Media.

See and Hli developed a closer relationship with one another while living together during See’s last year at Mizzou, despite their five-year age difference. See enjoyed playing the role as confidant for Hli and watching her grow.

“We have a very close relationship,” See said. “Hli is a very ambitious girl, and I see a lot of myself in her. I am so amazed at what she does in ag journalism. I’ve seen some of her video productions and I’m impressed by how well she’s mastered all the programs.”

For Yia, it comforts him to know that his sister always has his back here at the University.

“Hli is a very caring sister,” Yia said. “I lived with her for the first semester of college. And I know she would do anything for me. If I ever need anything, I just give her a call. She plays that big sister role since it’s only me and her here at the university.”

Yia plans to attend graduate school after he graduates and wants to pursue a Ph.D. in plant sciences. Yia is also a member of CAFNR Ambassadors and is a member of the Alpha Gamma Rho fraternity.

“I’m really happy that Yia’s found his own way and am impressed by the way he excels at everything he does,” See said. “It makes me happy to see him shine so bright.”

Although Hli and Yia often butt heads because they have similar and competitive personalities, they enjoy working with one another in CAFNR Ambassadors.

“Because we are in CAFNR Ambassadors together, I see him once a week, at least. And I think that’s a really good thing,” Hli said. “Being in an organization with him, I get to see him and catch up with him… We both get to see each other mature, which is really funny.”

‘He’s my family’

With her family more than four hours away in southern-most Missouri, Hli is relieved to have at least one sibling close throughout her time at Mizzou.

“It’s nice to have at least one close family member around here, especially because everyone else is four hours away,” Hli said. “Whenever I need things to be taken care of, I go to him. I rely on him, and I know he hates it, but he’s my family.”

The Mizzou experience has created a closer bond between the three Yang siblings. Whenever Yia and Hli struggle with homework or other issues, they are able to go to See or one another for help.

“The three of us having shared that same Mizzou experience and it has elevated our relationship,” See said. “I’ve already taken a lot of the same classes they are taking now and have been involved with the same organizations. They can come to me and I’m able to give them valuable advice because I’ve been in their shoes before.”

Written by Emily Brehe – October 14, 2015

Original story here

A MU sophomore Joined the Stacey Lab for a Summer Research Internship

(more…)

SoyKB: a powerful tool at the junction of plant biology and computer science

Click here to Original article with photos by Jan Wiese-Fales

Soybeans are big business in Missouri, which ranks in the nation’s top five soybean-producing states. In 2014, the tiny beans represented a $4.5 billion dollar industry for the Show-Me State.

The University of Missouri expanded its investment in soybean research in 1999 by hiring four faculty members with expertise in breeding, genetics, genomics and economics to fill endowed chair positions funded by the Missouri Soybean Merchandising Council (MSMC) with assets that came directly from the state’s soybean growers.

A national “checkoff” program initiated by U.S. soybean farmers in 1990 collects one-half percent of the market price per bushel from every soybean grower when crops are first sold. Half of the proceeds remain in state — with the Missouri Soybean Merchandising Council (MSMC) — and other half is forwarded to the United Soybean Board (USB) and managed by volunteer farmer-directors from around the nation.

Two of the MU hires, Endowed Professor of Genetics and Biotechnology Henry Nguyen and Gary Stacey, a Curators Professor in the Division of Plant Sciences, were named director and associate director, respectively of the university’s National Center for Soybean Biotechnology, launched in 2004. And one of the center’s first orders of business was to sequence the soybean genome.

“Plant science cannot be just biology anymore. You have to have the informatics,” Nguyen explained. “We had no bioinformatics capabilities, and [a campus taskforce] spent a year meeting about it. In the process, we recruitedDong Xu, who was familiar with the landscape.”

Xu, now the James C. Dowell Professor and chair of engineering’s Computer Science Department, came to MU with a background in protein structure prediction and high-throughput biological data analyses. He was accustomed to working with large data sets and biological modeling.

Trupti Joshi, an assistant computer science research professor, soon joined Xu’s research group to further support the center’s informatics goals. With a background in both biology and computer science, Joshi had a 180-degree view of plant biotechnology.

Joshi has had a passion for programming since 2000, when bioinformatics was a new field. “It was rapidly evolving field with cutting edge ideas. I found it so satisfying.”

In 2010, all four were members of an extended international team that successfully mapped soybean’s genome, a huge undertaking that generated a large amount of valuable genetic data. Making the data accessible to the larger science and agricultural communities was made possible by the National Science Foundation 2008 establishment of the iPlant Collaborative — cyberinfrastructure that anticipated the need for the supercomputing capabilities necessary for bioinformatic research — and the Obama Administration’s $200 million Big Data Initiative.

Xu and Joshi worked together initially to generate ideas for what they named the Soybean Knowledge Base (SoyKB). As lead designer and developer, it became Joshi’s dissertation project, and she has spearheaded the effort to build it into a comprehensive web resource featuring tools to functionalize integrated access to the original genomic data and a growing body of published genetic data that MU researchers and others from all over the world are generating.

“We have more than 400 registered users, including domestic and international, as well as [users from] academia and industry, who access both public and private data in SoyKB,” said Joshi. “Users can access the public data without any registration and login. We have more than 1,000 users who regularly visit SoyKB every month.”

According to Joshi, one of the problems with contemporary soybean varieties is that through selective breeding, natural variability has been reduced, and one of the project’s goals is to bring in data from regions with natural variations. The ongoing, USB-supported project to identify variations in 500-plus soybean lines through the academic and industry partnership among MU, Dow Agrosciences, Monsanto and Bayer will generate extremely valuable datasets in this regard.

“Users can utilize their own data, which is one of the biggest benefits,” said Joshi of SoyKB’s architecture, which includes database, genome browser, web interface and data integration modules. “They can look at visualizations of how gene expression might be different in different situations and are able to take all of the datasets and go in and make decisions by looking at regions of interest to design a crop computationally. It cuts down on the [traditional crossbreeding] time to make the combinations.”

Nguyen identified genetic traits of key interest to soybean researchers as drought tolerance, stress tolerance, increased yield and disease resistance, adding that those with interest in soy as biofuel would like to increase soybean oil content. Soybeans are also being examined for their potential role in the prevention of cancer and other human diseases. Scientists working with food grade soybeans would like to increase protein content and cooking oil quality, which is one of Nguyen’s interests.

“Researchers are able to use SoyKB to look at the gene structure and mutations to bring the right genetic combination of soybeans together,” Nguyen said. “Currently, soybean oil is 25 percent oleic acid, its most healthy component. We are working to make it 80 percent. It’s a game changer. Once in a while you get a breakthrough, and this is a breakthrough.

“Very soon, consumers in the U.S. can buy soybean oil that is healthier. It will revolutionize the use of oil in this country and the world,” he predicted.

Nguyen said the biotech research he is doing can be described as molecular breeding — using gene structure variation by changing a chemical base in a nucleotide sequence. Computational biology gives access to this marker-assisted selection, or breeding of natural variation traits, creating “better” genetics, not foreign genetics.

“Biotech [also] includes recombinant DNA technology [creating sequences that would not otherwise be found in biological organisms], which results in GMO crops, but not all biotech [results] are GMOs,” he explained in order to differentiate the work he is doing from genetic modification, which is viewed by some consumers as a controversial practice.

Joshi said their work has been supported by efforts from other computer scientists on the MU campus to expand the university’s cyberinfrastructure. National Science Foundation grants awarded to computer science Assistant Professor Prasad Calyam and Electrical and Computer Engineering Department Chair Chi-Ren Shyu were used to build a secure hybrid cloud networks, which support the high-volume data movement necessary for scientific research.

“It’s really exciting,” Joshi said. “It will give MU a high profile and gives us an opportunity to really make a difference. [At MU] there is the opportunity to work with so many groups. It’s interesting and rewarding.”

SoyKb also serves as an excellent tool and resource for training the next generation of plant breeders, computational biologists and computer scientists (see below).

Joshi recently has transitioned to the position of director of translational bioinformatics with the MU School of Medicine and will serve as assistant research professor in the Department of Molecular Microbiology and Immunology, but development of SoyKB will continue under her direction, through her many collaborations as a core faculty of MU Informatics Institute (MUII) and Interdisciplinary Plant Group (IPG).

“There is no way we could do this without the partnership between plant sciences and computer science,” Nguyen said of the collaboration. “SoyKB is a good bridging between CAFNR (College of Agriculture, Forestry and Natural Resources) and the College of Engineering.

“We have outstanding scientific recognition. It represents a lot of passion on the part of a lot of people.”