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Institute of Biological Chemistry

The Institute of Biological Chemistry (IBC) was established at Washington State University in 1980 to pursue fundamental research in the molecular biology and biochemistry of plants. Work at the IBC focuses on basic plant science with an emphasis on plant derived products synthesis, determinants of plant architecture, bioenergetics, and plant-microbe interacts. The research outcomes have potential applications in agricultural biotechnology, bioenergy, and medicine.

For more information about specific research programs in the IBC, please call us at (509) 335-8382, fax to (509) 335-7643 or email us at instbiolchem@wsu.edu.

IBC News and Updates

New leadership for prestigious WSU protein biotech training program

A unique partnership between WSU and the National Institutes of Health (NIH) will have new leadership, starting in January.

John Peters, director of WSU’s Institute of Biological Chemistry (IBC), will take the reins of WSU’s NIH Protein Biotechnology Training Program from Michael Kahn, who has led the program since 2017.

The graduate student training program is associated with an NIH training grant, a prestigious type of federal grant funding, according to Kahn. WSU is the only institution that has maintained continuous funding in the Biotechnology Training Grant program since NIH started it in 1989.

“The NIH is basically saying that our graduate student training in this area is first-class, and they have said that several times,” said Kahn, an original faculty member in the program. “That has helped us be more competitive in recruiting top graduate students and new faculty.”

Peters, who came to WSU in 2016, didn’t know about the program before his arrival, but was quickly recruited to be a faculty member. Now he’s taking over Kahn as the director. (Full Article)

 

Dr. Florence Mus is the Principle Investigator on a new grant by the Washington Research Foundation titled “Tailored associations to transfer ammonia from a model associative diazotroph to crop plants”.
We propose to edit the carbon acquisition pathway of ammonia-excreting strains to force their dependence on root exudates, thereby promoting the colonization of roots and reducing the persistence of bacteria in the environment after the growing season. These strains will be specifically engineered to metabolize dedicated plant-derived carbon sources present in the rhizosphere that can energize nitrogen fixation. We propose to use two wheat varieties (Soft White and Hard Red) primary grown in Washington. Successful completion of this project will result in creating strains as superior candidates for biofertilizers that may result in the reduction of chemical nitrogen fertilizers leading to increase crop production. This project will provide a unique new approach to lead to the development and commercialization of efficacious microbial inoculants for crops.

 

Dr. Laura Bartley is the Principle Investigator on a new grant by the National Science Foundation Plant Genome Research Program entitled, “Genome-Enabled Characterization of Orphan Receptor-Like Kinases in Plants”. Receptor-like kinases (RLKs) act as cellular sentries, perceiving molecular signals from other organisms or neighboring cells and then passing signals along to intracellular protein clients to initiate responses such as defense induction or growth cessation. Though RLKs are one of the most abundant plant gene families, they have proven difficult to study. This research will utilize new knowledge and technologies to characterize the functions and clients of RLKs of Arabidopsis, rice, and soybean. The work at WSU will focus on RLKs that halt growth of the stems (culms) of rice under drought and that induce rice root architecture changes in response to endogenous small secreted peptides. Improvements in knowledge of kinases will open new avenues for promoting plant production for food, feed, fiber, and energy. In addition, the project includes a multi-tiered outreach program including professional development of high school teachers and research workshops and longer experiences for high school and undergraduate students that meld plant and data science. The $2M, 3-year project is a collaboration with Drs. Gary Stacey, Dong Xu, and Jay Thelen from the University of Missouri, and Dr. Ljiliana Pasa-Tolic from Pacific Northwest National Labs.

 

Dr. Philip Bates has been awarded a new grant by the United States Department of Agriculture, Agriculture and Food Research Initiative titled, “Characterization of a novel triacylglycerol remodeling pathway for accumulation of industrially valuable fatty acids in Physaria fendleri”.

Hydroxylated fatty acids (HFA) are natural bioproducts that have important industrial uses as feedstocks to produce resins, lubricants, plastics, biodegradable polyesters, coatings, any many more. HFA also have various uses in the cosmetic and pharmaceutical industries. For many applications, HFA are a renewable replacement to petroleum-based feedstocks. The major source of HFA is castor seeds, which due to toxicity is limited for production in the US. Castor oil is mostly imported into the US from India, and has a market value of $993 million (2017). Physaria fendleri native to the southwest US produces oil with >60% HFA. Physaria is nontoxic, grows on marginal lands, can be used as winter rotation/cover crop, and is an emerging domestic source of HFA. However, enhancement of domestic HFA sources through Physaria breeding or engineering of other oilseeds is hampered by the lack of molecular knowledge on HFA accumulation in seed oils. Our recent metabolic flux analysis of Physaria oil biosynthesis indicated a novel triacylglycerol (TAG) remodeling pathway for HFA accumulation. When combined with transcriptomic resources, we identified gene candidates that may control this novel pathway. In this project, we will characterize the biochemical features and in planta roles of Physaria candidate genes in TAG remodeling, and engineer TAG remodeling into the industrial platform crop Camelina sativa for accumulation novel oil compositions. This work in collaboration with Grace Chen (USDA-ARS, Albany, CA) will support the goal of producing valuable plant oil-based bioproducts through the continued development of new crops, Physaria and/or engineered Camelina.

 

 

Dr. Mark Lange has been awarded a new grant by the Department of Energy entitled “Understanding Selectivity in Terpene Synthases – Unique Mechanisms to Generate Precursors for Biocrude and Specialty Chemicals”.  Terpenoid oils and resins accumulated in plants (and sometimes microbes) are characterized by a high volumetric energy density and high degree of reduction, and are thus viable “biocrude” feedstocks for fuels in the diesel and kerosene range.  Furthermore, many specialty chemicals are also based on terpenoid backbones, including polymers (e.g., rubber), solvents (e.g., limonene), and diverse small molecules (e.g., menthol).  The newly funded work aims to unravel the mechanistic basis for selectivity in the sophisticated enzymes, termed monoterpene synthases, that catalyze the formation of cyclic hydrocarbons as the first committed step in monoterpene biosynthesis.  Such knowledge will allow us to infer the mechanistic underpinnings of how plants produce highly complex, reduced chemical scaffolds.  The proposed activities will be performed in collaboration with IBC Adjunct Faculty Dr. Simone Raugei, a computational scientist at the Pacific Northwest National Laboratory.

 

Dr. Helmut Kirchhoff has received a new NSF-funded project: High-resolution mapping of the protein landscape in plant photosynthetic membranes.

In plants, photosynthetic energy conversion is realized by pigment-protein complexes that are harbored in highly specialized thylakoid membranes inside the chloroplasts. The new project will map light-induced protein landscape dynamics in thylakoid membranes with molecular resolution as a basis for understanding key photosynthetic functions. It defines an innovative pipeline of methods, ranging from state-of the art electron microscopy to coarse grain computer simulations, which will provide a quantitative understanding of photosynthetic light harvesting and electron transport. This pipeline will lead to urgently needed insights into dynamic structure-function relationships in thylakoid membranes. This an interdisciplinary NSF- BSF project with groups from WSU (lead), Southern Methodist University, Weizmann Institute (Israel), and the University of Goettingen (Germany) and support by a total of over $1,1 million over three years.

 

Helen Miller, IBC Administrative Manager, has been selected as the 2019-2020 Administrative Professional Staff Excellence Award Winner! This award recognizes contributions to a productive workplace through leadership and collegial activities, as well as professional and ethical behavior. These awards recognize the quality and quantity of the recipient’s work and contributions to the college’s mission, image, and goals. As one of the best in our college, Helen will receive a personalized framed certificate and is invited to the Faculty Staff Awards Banquet on April 15 in Ensminger Pavilion. Award winners will have their photo taken with Dean Wright to be posted on the CAHNRS Award Website.

 

Dr. Helmut Kirchhoff’s lab in collaboration with the University of California recently published a journal article in the The Journal of Biological Chemistry that was an editor’s pick in JBC and now picked by Science editor. From the Science editor’s choice article (https://science.sciencemag.org/content/367/6482/twil): “Bulky lipids for light-harvesting control Lipid membranes are extraordinarily complex, with many different acyl chains, head groups, and proteins contributing to their shape, curvature, and fluidity. In membranes with specialized functions, such as the thylakoid membranes within chloroplasts, these properties can influence the function of the embedded membrane proteins. Tietz et al. measured changes in the behavior of proteoliposome-reconstituted light harvesting complex II, a protein that normally gathers light for photosystem II, in the presence or absence of the non–bilayer forming lipid monogalactosyldiacylglycerol. In this assay, the lipid stimulated energy quenching, which would divert light energy into heat and be photoprotective in high-intensity light. The authors suggest that changes in lateral membrane pressure caused by the bulky lipids may influence pigment conformations within the protein and thus alter the amount of light energy moving through the system.”

 

Dr. Philip Bates has been granted tenured and promoted to Associate Professor.  The granting of tenure and promotion is indeed the strongest possible statement that can be made of the confidence of colleagues and the College and University administration have in the potential to contribute and advance professionally as a faculty member at Washington State University.  Phil will be recognized at the Showcase 2020 banquet in March.  

 

Dr. Laura Bartley will be joining the faculty of the IBC in July 2020.  Bartley currently holds positions as a Visiting Associate Professor at Kyoto University in Japan and as an Associate Professor in the Department of Microbiology and Plant Biology at the University of Oklahoma.  Her research focuses on plant cell walls, including their biosynthesis, regulation, and roles in plant physiological processes. She is particularly interested in phenylpropanoids, as these molecules have promise for use as non-fossil sourced biochemicals but also reduce efficiency of biomass conversion to biofuels.  Her goal is to improve properties of biomass, especially from cereals and other grasses, toward enhancing sustainable bio-refining, crop agronomic properties, and ecosystem services.

 

Natasha Pence, a graduate student in John Peters’ lab was elected as the next Co-Chair for the 2022 Bioinorganic Chemistry Gordon Research Seminar (GRS). The Bioinorganic Chemistry GRS is an annual event associated with the Metals in Biology Gordon Research Conference. In its 24th year, the Bioinorganic Chemistry GRS is an opportunity for graduate students, postdoctoral researchers, and early career scientists to showcase their work in a diverse, multidisciplinary setting. It attracts participants from U.S. and international research institutions who are studying topics related to the diverse role of metals in biology. Natasha’s dissertation work is on mechanisms of gating nucleotide-driven electron transfer to nitrogenase.

 

In collaboration with Tony Brave, the outreach coordination of the Native American Programs, we organized the EXploring Emerging College Leaders (EXCEL) program held on November 1-3, 2019. A total of 39 students from Native American Communities in Washington, Oregon, and Idaho attended the event. Students conducted a mini-project on microscopy, DNA electrophoresis, and making simple drinking water filters and testing their efficiency. During the brakes, students froze marshmallows in liquid nitrogen. The activities were designed and conducted by Dr. Andrei Smertenko, Dr. Phil Bates, Dr. John Browse, Dr. Tom Okita, Dr. John Peters, Dr. Paul Hwang and Dr. Florence Mus and also Dr. Indrnil Chowdhury from the Department of Engineering. Besides faculty, graduate students Sharol Schmidt and Alyssa Parish (Smertenko’s lab), Brandon Johnson and David Sliman (Bates’ Lab), Alex Alleman (Peters’ lab), Iftay Alam (Chowdhury’s lab), and post-doctoral scientists Taras Nazarov and Tetyana Smertenko (Smertenko’s lab) also participated in the organization and running the activities.

 

Dr. Phil Bates’ lab in collaboration with CSIRO Agriculture & Food in Australia and USDA Donald Danforth Plant Science Center published a paper in Plant Physiology.   A recent trend in the plant oil field is to engineer plants to accumulate oils in vegetative tissues rather than just seed tissues. Vegetative oil crops have the potential to produce vastly more oil per unit of land than common temperate oilseed crops. However, oil biosynthesis is part of a complicated metabolic network involving essential membrane lipid biosynthesis. It is unclear how enhancing oil biosynthesis in a leaf tissue effects the control of fatty acid flux into various membrane systems. Therefore, to understand the metabolic plasticity of leaf lipid metabolism to adapt to new metabolic sinks induced by engineering, we analyzed the lipid metabolic flux in both wild-type and oil accumulating tobacco leaves using in vivo isotopic labeling. The results reveal unexpected changes within the lipid metabolic network that allow both membrane lipids and oil to accumulate, as well has provide insights into future leaf oil engineering.

 

Nitrogen-fixing genes could help grow more food using fewer resources

Scientists have transferred a collection of genes into plant-colonizing bacteria that let them draw nitrogen from the air and turn it into ammonia, a natural fertilizer.

The work could help farmers around the world use less man-made fertilizers to grow important food crops like wheat, corn, and soybeans.

The group of scientists, including two from Washington State University, published the study “Control of nitrogen fixation in bacteria that associate with cereals” late last month in Nature Microbiology.

“There’s a growing interest in reducing the amount of fertilizer used in agriculture because it’s expensive, has negative environmental impacts, and takes a lot of energy to make,” said John Peters, Director of WSU’s Institute of Biological Chemistry and a co-author on the paper. “There’s a huge benefit to developing ways to increase the contributions of biological nitrogen fixation for crop production around the world.” (Full Article)

 

Dr. Phil Bates’ lab published a paper in The Plant Cell. Its long been known that lipid substrates are trafficked between the chloroplast and endoplasmic reticulum (ER) and are essential to leaf development, however the mechanisms of lipid trafficking between the two compartments has been unclear. Through the combined use of Arabidopsis mutants and in vivo lipid flux analysis we demonstrate that LPCAT1 and LPCAT2 enzymes are associated with chloroplast and are responsible for the incorporation of newly synthesized fatty acids directly into the ER membrane lipid phosphatidylcholine (PC). In addition, we demonstrate that there are at least three different pools of PC involved in different aspects of acyl trafficking between the ER and the chloroplast and produce a new model for leaf lipid flux.

This work was also recently recommended as a significant update on the understanding leaf lipid metabolism by F1000 (Feussner I and Zienkiewicz A: F1000Prime Recommendation of [Karki N et al., Plant Cell 2019 31(11):2768-2788]. In F1000Prime, 15 Jan 2020; https://doi.org/10.3410/f.736596500.793569434).

 

At the IBC Holiday Party in December 2019, the following graduate students received awards:

Sharol Schmidt in Dr. Andrei Smertenko’s Lab received a 2019-2020 Helen and Loyal H. Davis Fellowship. This Research Fellowship consists of a stipend for calendar year 2020 and a cash award of $3,000 to spend for travel to a professional conference and/or research supplies.
Alex Alleman in Dr. John Peters’ Lab received a 2019-2020 John & Maggie McDougall Scholarship.  The Scholarship carries a cash award of $3,000 to spend for travel to a professional conference and/or research supplies.

 

Sajina Bandari in Dr. Phil Bates’ Lab, Joshua Polito in Dr. Mark Lange’s Lab, and Hsin-Hua (Joelle) Wu in Dr. John Peters’ Lab received the Clarence “Bud” Ryan Institute of Biological Chemistry Travel Scholarship for the 2019-2020 academic year in the amount of $1500.  The travel scholarships were made possible through a endowment gift by Pat Ryan (wife of the late Bud Ryan).

 

The following faculty and staff received service awards:

5 years:  Daniel Tejeda Lunn
10 Years:  Ruifeng He and Helmut Kirchhoff.  Not pictured Anna Berim and David Gang.
15 Years:  Iris Lange
40 Years:  Mike Kahn

 

Professor John Peters in collaboration with Montana State University received a DOE-BES Physical Biosciences Grant “Novel microbial based enzymatic CO2 fixation mechanisms: Conformational control of enzymatic reactivity”, for $1,472,456 for three years.  The collaborative project is providing an understanding of the mechanisms of unique carboxylation and electron transfer reactions. An integrated approach is used combining mechanistic enzymology, spectroscopy, and structural work to link mechanistic steps with defined conformational changes that promote high fidelity catalysis of difficult reactions having unstable intermediates. Within the context of the mission of the Department of Energy and the core activities of the Energy Biosciences, the results obtained in the study will reveal new insights into these novel carboxylation reactions and will provide the basis for the comparison of the mechanisms of these interesting enzymes to other well-characterized CO2 fixing and carboxylating enzymes.

 

Thomas W. OkitaDr. Tom Okita has been named a Fellow of the American Association for the Advancement of Science (AAAS).

Election as an AAAS Fellow is a distinction bestowed upon AAAS members by their peers, in recognition of scientifically or socially distinguished efforts to advance science and its applications. AAAS is the world’s largest general scientific society and publisher of the journal Science (www.sciencemag.org).

 

An international group of scientists, including Dr. Mark Lange at the Institute of Biological Chemistry, received a $4 million grant from the National Center for Complementary and Integrative Health, part of the National Institutes of Health, to work on developing novel approaches for the production of taxol, one of the best-selling anti-cancer drugs on the market (for details see full article).

 

Washington State University researchers have for the first time grown the bacteria in a laboratory that causes Citrus Greening Disease, considered the world’s most harmful citrus disease.

Being able to grow the elusive and poorly understood bacterium, Candidatus Liberibacter asiaticus (CLas), will make it easier for researchers to find treatments for the disease that has destroyed millions of acres of orange, grapefruit and lemon groves around the world and has devastated the citrus industry in Florida.

The researchers, including Phuc Ha, postdoctoral research associate, Haluk Beyenal, Paul Hohenschuh Professor in the Gene and Linda Voiland School of Chemical Engineering and Bioengineering, David Gang and Ruifeng He, from WSU’s Institute of Biological Chemistry, Anders Omsland, from the Paul G. Allen School for Global Animal Health, and researchers from the University of Florida and University of Arizona, report on their work in the journal, Biofilm (Full Article).

 

The WSU-NIH Biotechnology Predoctoral Training Grant in Protein Biotechnology, led by PI Michael Kahn, was successfully renewed for the sixth time for 2019-2024. It will now have been continuously funded for 35 years and is the only Program that has had uninterrupted funding since the NIH started to fund Biotechnology Training Grants in 1989. The only other Biotechnology Training Grants in the west are at Stanford, Berkeley, Caltech, UCLA, and UCSD. The award for this renewal includes NIH slots for ten PhD students with a total award of approximately $2.3 Million. Over 150 PhD students have been associated with WSU’s program, which involves four colleges and five graduate units (currently Immunology and Infectious Disease, Molecular Biosciences, Molecular Plant Sciences, Chemistry, and Chemical Engineering).

 

The Lange laboratory at the Institute of Biological Chemistry published a breakthrough study demonstrating a link between the formation of cannabinoids and aroma-related terpenoids in marijuana and hemp strains of cannabis.  The paper also suggests new approaches for the broader analysis of these metabolites, thus contributing to an improved quality control in the industry.  This work, which appeared in the August issue of the journal Plant Physiology, was featured in news articles in Forbes Magazine, National Geographic, The Spokesman Review, Science Daily, The Columbian, and is currently ranked among the most discussed (99th percentile) science articles in social media, according to Altmetric, a data science company that tracks where published research is mentioned online.

 

Alex Alleman (graduate student in Peters Lab) won best poster presentation and Rachel DeTar (graduate student in Kirchhoff Lab) won best student oral presentation at the international Cluster of Excellence on Plant Sciences (CEPLAS) Transatlantic Summer School – Frontiers in Plant Sciences, May 27-31, 2019. They are pictured with Stan Kopriva, head of CEPLAS. The international CEPLAS Summer School offers an opportunity to learn about current topics, to delve into state-of-the-art plant science and to network with fellow early career scientists and well-known experts in the field.

 

WSU scientists measuring how plants convert light to energy

Plants take sunlight and turn it into energy, but scientists are still figuring out exactly how they do this complex conversion.

“Photosynthesis can be dangerous,” said Helmut Kirchhoff, an associate professor in WSU’s Institute of Biological Chemistry. “At the point where light is collected, the energy is there. That energy has to be deactivated right away and transferred to different parts of the plant or it can damage the plant.”

Because sunlight fluctuates—with clouds or as the sun travels and shadows are cast—plants react to different light environments to stay safe and not make more energy than they can process, Kirchhoff said.

Now Kirchhoff and his colleagues have developed a way to monitor how plants adjust these photosynthetic functions.

“We developed a way to measure the components of this energy converting machinery,” he said. “To understand the process, you have to know the exact ratio of components. And now we can measure that.”

Kirchhoff’s results are available in the February 2019 issue of The Plant Journal. His article, “The structural and functional domains of plant thylakoid membranes,” is featured on the cover. The journal also highlighted the research with this story. (Full Article)

 

WSU researchers tease out genetic differences between cannabis strains

Research from Washington State University could provide government regulators with powerful new tools for addressing a bevy of commercial claims and other concerns as non-medical marijuana, hemp and CBD products become more commonplace. The new analysis of the genetic and chemical characteristics of cannabis is believed to be the first thorough examination of its kind.

The current method is inadequate, says Mark Lange, a professor in WSU’s Institute for Biological Chemistry. Regulators focus on levels of the psychoactive compound THC and just a handful of the more than 90 other cannabinoids. The industry makes various claims about different strains, from sedating indicas to invigorating sativas, Acapulco Gold to Zkittlez, but they defy objective analysis.

“There is a reason why all these strains have different names – because a lot of them are very different,” said Lange. “But some strains with different names are actually very similar. The bottom line is there is a lot of confusion.”

Until now. (Full article)

 

Two undergraduates from Andrei Smertenko’s Lab, Jessica Fisher and Austin Lenssen (both standing next to Andrei to the far right), won a Novice award at the 2019 Showcase for Undergraduate Research and Creative Activities (SURCA) showcase. Washington State University undergraduates are conducting research, pursuing scholarship, and/or involved in creative activities in partnership with a mentor. The students’ efforts make original intellectual or creative contributions to a discipline. SURCA invites undergraduate presenters who are in the early stages of their research as well as those who are more experienced. The Novice, Early Career, Crimson, and Gray awards provide students with all levels of experience an opportunity to compete for awards. Awards are made in eight categories of disciplines.

 

Ronald Nugen was awarded the Administrative Professional Technical Staff Excellence Award for 2018 at the CAHNRS Faculty & Staff Award Recognition Night.  This award recognizes contributions to a productive workplace through leadership and collegial activities, as well as professional and ethical behavior. This award recognizes the quality and quantity of the recipient’s work and contributions to the College’s mission, image, and goals.

 

At the IBC Holiday Party in December 2018, the following graduate students received awards:

Kaan Koper in Dr. Tom Okita’s Lab received a 2018-2019 Helen and Loyal H. Davis Fellowship. This Research Fellowship consists of a stipend for calendar year 2019 and a cash award of $3,000 to spend for travel to a professional conference and/or research supplies.

 

Jesse Bengtsson in Dr. John Browse’s Lab received a 2018-2019 John & Maggie McDougall Scholarship.  The Scholarship carries a cash award of $3,000 to spend for travel to a professional conference and/or research supplies.

 

Alex Alleman in Dr. John Peters’ Lab and Olivia Oung in Dr. Helmut Kirchhoff’s Lab received the Clarence “Bud” Ryan Institute of Biological Chemistry Travel Scholarship for the 2019-2020 academic year in the amount of $1000.  The travel scholarships were made possible through a endowment gift by Pat Ryan (wife of the late Bud Ryan – pictured left with the award recipients).

 

 

Dr. John W. Peters
Professor and Director
jw.peters@wsu.edu

Jeff Bowman
Administrative Manager
jeff.bowman@wsu.edu

Teresa Beckvold
Principal Assistant
teresa.beckvold@wsu.edu

Julie Thayer
Greenhouse Manager
jthayer@wsu.edu

Past IBC News and Updates