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Looking back on the sequencing of the soybean genome

JGI: https://jgi.doe.gov/jgi-at-25-strengthening-soybean/

Maximizing soybean yield is critical to energy independence in the U.S. Not only does it pair with maize, the dominant source of bioethanol, in crop rotation, but soybean (Glycine max) also has the advantage of reducing the need for nitrogen fertilizer. These impressive environmental and energy advantages explain why soybean is a flagship genome of the JGI’s Plant Program.

While soybean has desirable properties as a liquid transportation fuel, it simply doesn’t yield enough gallons of fuel per acre to compete with gasoline. Yet. 

In 2010, soybean became the first legume species with a published complete draft genome sequence. At the time, the vital global source of both protein and oil was also the largest plant project completed by the JGI. It has since been cited more than 5,400 times, including a number of projects that point to the potential of seed oils as biofuel.

After analyzing the original sequence, Gary Stacey of the University of Missouri said he and his colleagues had identified 1,110 genes involved in lipid metabolism. 

“There’s still a lot of thinking that truck fuel and airplane fuel and things like that are not going to be replaced by electricity anytime soon,” Stacey said when we caught up with him recently. “So, there’s going to be a need for these biofuels and that’s a good niche market for soybean.” 

Upon its initial release in 2009, the soybean genome sequence immediately spurred further research and additional discoveries. Stacey noted that even prior to the sequence being published in Nature, immediate progress had already been made positionally cloning genes involved in agronomic traits related to nutritional quality and disease resistance due to the sequence’s availability via Phytozome. In 2015, a new and revised version brought the soybean sequence up to date with current technology. 

In addition to supporting work on the soybean plant in order to maximize yields for biofuel, the JGI has also helped researchers understand a fungus that threatens these crops as they grow. Asian Soybean Rust is a major problem. Leaves grow discolored and rust pustules develop as the pathogen feeds on its soybean host, which is maintained alive. Once a crop is infected, ASR can decimate up to 60-90% of its yield. 

(Learn more about the soybean genome sequence and ASR in this JGIota, a Genome Insider podcast minisode.)

In 2016, the JGI accepted a proposal from Sebastien Duplessis of the French National Institute for Agricultural Research (INRAE) to sequence a reference genome for the fungus Phakopsora pachyrhizi, a major pathogen of soybean that causes ASR.

“I love working with these guys,” said Duplessis, who has collaborated with the JGI on multiple projects involving rust pathogens. “All along the way, it was just like rediscovering genetics, with the evolution of sequencing technologies and the evolution of bioinformatics.” 

P. pachyrhizi has a very large and complex genome with lots of repetitions, making it very difficult to sequence — roughly 1.25 billion Gb (gigabasepairs — most fungi are around 50 million Mb, or megabases, in size). So, the JGI helped a consortium of researchers from various institutions, including INRAE as well as the Sainsbury Institute, by annotating not just one but three genomes for P. pachyrhizi, which are available on MycoCosm

“We work on making good resistance traits against this disease for use in the field,” said Peter van Esse of the Sainsbury Institute, who works extensively on ASR. “Having the genomes of a crop like soybean ensures that what we bring to the grower is novel … We’re a long way there; we are developing traits with key partners, both Corteva and Bayer, and that’s going really well. And having the sequence data available for us to enable that research will have a great impact for growers.” 

#IAmScience: Mengran Yang

By Cara Penquite | Bond LSC

Mengran Yang sat perched on a stool too tall for the cart of lush green tobacco plants in front of her. Behind towering shelves of lab equipment, she hunched over the plants and steadily pricked each leaf with a syringe.

Yang works with Arabidopsis and tobacco plants to learn about plant immune systems as a postdoctoral fellow in the Gary Stacey lab. Her research focuses on signals plant cells send to coordinate a fight against pathogens.

“I think it’s very interesting to see how plants can defend against the pathogens,” Yang said.

Mengran Yang infiltrates the leaves of tobacco plants with a syringe. While her work mostly focuses on Arabidopsis plants, Yang also uses tobacco plants as a tool in her research since it is convenient to express the correct target proteins in their leaves. Photo by Cara Penquite | Bond LSC

Just like humans have immune cells that fight germs, plants have a network of cells and signals to deal with harmful microbes. This system is particularly important for plants since they are rooted in place and cannot avoid the attackers in their environment.

The plant immune system protects it both inside and outside its cells. Proteins inside the cell can recognize molecules from invaders and trigger an immune response, and the second — the part Yang’s research focuses on — uses receptors on the surface of the cells to recognize molecular patterns from microbes to signal for the plant to get rid of the pathogen.

“Our lab is focused on the extracellular ATP signaling pathway,” Yang said. “ATP, as maybe everyone knows, is an energy source, but we found it can also be a signal when it is released to the extracellular matrix, where it is referred to as extracellular ATP.”

Yang’s work with the lab started when she moved from China to Columbia for her postdoctoral research at Mizzou. Although originally drawn to the lab because of Stacey’s prominence in the field of plant immunity and signaling, Yang stays because of the community within the lab.

“Our lab is very international — some people are from China, Korea, Brazil, Vietnam and India,” Yang said. “A lot of the same-aged girls will go out for fun.”

This community stems from Stacey’s emphasis on the team’s collective success.

“You try to develop an esprit de corps in the lab where people care about each other’s success,” Stacey said. “They’re taking care of themselves, but at the same time, they care about other people’s success.”

Becoming a good researcher started with strong academics, and Yang remembers being the top of her class in biology, physics and math in middle school and high school. When she started her studies at the university level she followed her growing interest in biology.

Growing up with her twin sister in China, Yang recalls societal pressures to fill any spare time with more study. Her parents thought her teachers gave too much homework and pushed back on this expectation.

“My father thinks this kind of education is not good, he thinks you need to promote your efficiency and not just work hard,” Yang said. “You need to study smart, not just hard, and I think my dad influenced us a lot.”

Yang applies this mentality to her research and is supported by Stacey who encourages her to plan experiments and life goals.

“While I was a Ph.D. student, I spent the most time in the lab for fun,” Yang said. “But now I’m good at scheduling stuff, so I schedule my experiments at least a week ahead.”

Mengran Yang shows a dish with Arabidopsis plants. Yang’s work primarily focuses on studying extracellular ATP in Arabidopsis plants. Photo by Cara Penquite | Bond LSC

Stacey works with Yang to ensure her future impact as a researcher. When picking a project, Stacey guides his researchers towards projects with lots of potential.

“That’s the kind of discussion I have with people, what’s the best project for them where they have the chance to make an impact,” Stacey said.

With her lab mates and other research labs, Yang collaborates to strengthen each other’s weaknesses. If she does not have experience with an experiment, Yang asks other postdoc students with more experience for help with her project. When she publishes her research, she makes sure to give credit to the other students who helped her.

“In Chinese, ‘shuangying’ means ‘good to both sides,” Yang said. “That’s very common. You will read a paper, and you can also see most [papers] have a lot of authors there. That’s the cooperation.”

After finishing her research in the U.S., Yang plans to return to China to continue doing what she loves — research.

“I want to have my own lab in China,” Yang said. “It’s difficult, I know, but it’s my dream.”

Available at: https://decodingscience.missouri.edu/2022/04/29/iamscience-mengran-yang/

#IAmScience: Sam Yanders

By Cara Penquite | Bond LSC

When Samantha Yanders stepped to the front of Monsanto Auditorium, she followed presentations from two researchers with three degrees each.

Yanders only had three years of undergraduate research experience.

Nevertheless, she pinned the microphone to her tie, ran her fingers through her short curly hair, and explained her research with a calm certainty to her voice.

Having just finished her junior year as a plant science undergraduate, Yanders spent the first week of her summer sharing her passion for plants with fellow researchers during the 2022 Interdisciplinary Plant Group Symposium.

“I want to be inclusive in how I talk about my work to be able to educate people,” Yanders said. “Even if you’re talking to molecular biologists, they may have no idea about extracellular ATP.”

A clear communicator and advanced undergraduate researcher, Yanders was selected to present her research in Monsanto Auditorium during the symposium and often helps write and edit manuscripts for her lab.

Yanders began research in the Gary Stacey lab through Freshman Research in Plant Science, a program that places plant science freshmen in MU labs. Yanders’ research focuses on the signaling role of extracellular ATP when a plant experiences high-salt conditions.

Within a cell, ATP is a molecule used for energy. However, research shows that when a plant is in high stress or damaging conditions, ATP outside the cell signals for protective mechanisms.

“It’s really clever because instead of spending energy to make both a signaling molecule and a signal receptor, it already has something that’s really high concentrations in the cell and very low concentrations outside the cell,” Yanders said. “So it’s easy for the plant. It just has to make a signal receptor.”

Under normal conditions there is less ATP outside the cell and a high concentration of ATP inside the cell since it is used as energy. However, under high salt conditions there is an increase in ATP outside the cell, which binds to receptors on the cell surface that communicate with the cell to stunt plant growth. Yanders’ work explores the impact of high salt environments for plants — an increasingly relevant project as climate change raises sea levels and increases salt deposits in soil.

Although she now enthusiastically recounts her work to auditoriums of fellow scientists, biology was not originally Yanders’ first choice.

“In high school, I knew that I wanted to do something scientific because I’ve always liked science,” Yanders said, “But I didn’t think I wanted to go into biology, because I saw biology as mainly oriented towards animals.”

Sam Yanders shows the roots of arabidopsis plants. Yanders studies extracellular ATP in arabidopsis and tobacco plants. Photo by Cara Penquite | Bond LSC

With her geneticist grandfather piquing her interest from a young age and her enthusiasm for environmental science in high school, once she learned Mizzou had a plant science program she was ready to commit.

“So I was like, ‘Okay, I’ll go into biology and focus on plants.’ And then I’m looking on the Mizzou website and they [have] plant science. I didn’t even know that was a thing,” Yanders said. “So I switched to plant science.”

After enjoying high school chemistry labs, Yanders was ready to take the next step into research labs as soon as possible. Freshman Research in Plant Science allowed Yanders the opportunity to join a lab right away — fostering her interest in plant research.

“As humans, we move around. We can adapt to change by moving and changing what we do,” Yanders said. “But a plant has to do all of that management from a stationary position. . . It can’t change the circumstances that it’s in, so it has to adjust itself to be able to adapt.”

Tobacco plants grow under artificial light at Bond LSC. Photo by Cara Penquite | Bond LSC

Yanders’ love of plants extends beyond the walls of the lab, and she spends her free time in her herb garden where she learns more about plant and human interactions.

“The way that you interact with the plant fundamentally changes how the plant acts,” Yanders said. “So like with basil, if you just let a basil plant grow it just gets leggy and crazy, but if you do what you feel like is harming it by pinching the tops off, then it grows more compact and bushy, which is good for the plant.”

Yanders hopes to explore plant and human interactions in the future, potentially pursuing urban agriculture and ecology.

“I’m really interested in soil health, I feel like we’ve done a lot to deplete soils, and coming up with more renewable ways of doing things [and] producing things for human consumption,” Yanders said.

While uncertain which questions she will ask next, Yanders hopes to continue answering questions and explaining her research to others.

“[I like] being able to offer an explanation, and not just see it, but to create that explanation for other people,” Yanders said.

Full link: https://decodingscience.missouri.edu/2022/06/17/iamscience-sam-yanders/

Congratulations to Bruna Montes Luz, LSC Person of the Month for April!

Bruna Montes Luz, PhD student at the Stacey lab, has been chosen as the Bond Life Sciences Center Person of the Month for April. Here are some of the comments someone had to share about Bruna:

“Bruna is a constant in the LSC who welcomes everyone and built a community helping international students and other graduate students throughout the LSC. On top of being an excellent scientist, Bruna advocates for graduate students and is an active leader within the community. Individuals who have the capacity to excel in the strenuous work demanded by graduate school while still maintaining a connection to the community are few and far between, and fewer are those who care for the wellbeing of others enough to take action. Bruna is one of those few people.”

Congratulations, Bruna! This honor is well-deserved!

Another piece of the pathway: Stacey lab identifies enzyme key to regulating plant metabolism

Researcher Sung-Hwan Cho holds mutant Arabidopsis thalianas. The Gary Stacey lab used these mutant variations to study how plants react to external stressors. | Photo by Karly Balslew, Bond LSC

By: Karly Balslew | Bond LSC

When we get hurt, our body signals our brain to warn us about stress and damage. We acknowledge the damage and then initiate the proper steps to heal.

Plants may have different receptors that read these stress signals, but the process is similar.

“When someone crushes the plant tissue, this triggers their immune system like us,” said Sung-Hwan Cho a researcher in the Gary Stacey lab at Bond Life Sciences Center. “Our focus is how the plant responds to their stresses, especially wounding.”

In plants, Adenosine triphosphate (ATP) plays a crucial role in regulating this process.

Cho explains that this signal is especially important because unlike humans, plants cannot move away from their stressors so they must adapt. Therefore, signals travel down a certain pathway to ensure the plant reacts appropriately to the damage. But without ATP, the process is lost.

As part of the Stacey lab, Cho recently published a recent paper in Nature Communications that detailed a key metabolite pathway in the ATP plant signaling process.

“What’s exciting about the mevalonate pathway is that the pathway is involved in producing so many molecules that are critical for plant growth and development,” said Bond LSC principal investigator Gary Stacey. “Such as a variety of different hormones and various lipids that are required. It means that purinergic signaling has a profound effect on plant physiology.”

Purinergic signaling is named after the purine compounds that are found in ATP. This signal is important as it helps researchers understand how plants handle external factors from their surrounding environment.

Purinergic signaling underpins a multibillion-dollar pharmaceutical industry for humans and animals. Hence, the hope is that, just as in these cases, further exploration of purinergic in plants will lead to practical means to alleviate stress in plants, improving plant health and, ultimately, yield.

Stacey explains that mevalonate kinase (MVK) is one of the first enzymes in the mevalonate pathway and impacts the metabolites, or functioning, of the plant.

Just like in humans, plants have metabolic functions that keeps the organism alive. When we eat food, our body breaks the food down into an energy form that the body can utilize. Plants do the same. These metabolite compounds are synthesized by plants and used for essential functions like growth and development. This process gets turned on or off by ATP.

ATP is predominantly the energy molecule of the cell. All the food that we eat eventually turns into ATP and provides us energy to function.

“You can think about it [ATP] as money. You can’t go to the store and do anything without money so the cell can’t do anything without ATP,” principal investigator Gary Stacey said.

When the body experiences stress, ATP is transported outside of the cell and acts as a signal to the rest of the body. However, when this idea was proposed in the 1970s, it was highly controversial, and many rejected the notion entirely explains Stacey. Since ATP is crucial to human and plant functioning, the idea that ATP was traveling out of the cell as a signal was ridiculed.

However, in the early 1990s, researchers identified the first receptors in humans that utilized this extracellular ATP.  Researchers knew how important ATP is to the cell and realized how effective the molecule signal was. This is called purinergic signaling because it is triggered by nitrogen-based DNA building blocks named purines and compounds like ATP.

“If the cells make a receptor that’s recognizing extracellular ATP, then there must be extracellular ATP and it must act as a signal,” Stacey said.

Researchers turned to humans and studied their stress signals and the receptors.

However, the ATP receptors that were found in humans were not seen in plants. Researchers knew plants carried out these purinergic signals because plants reacted similarly to humans, but the receptor was unknown.

“Basically, what we do is we take the plant and then we screen for mutants that don’t recognize ATP. If the plant has a mutation in the receptor, then the plant will no longer recognize ATP. Once we identify the mutation, we can map the mutation and eventually identify the receptor,” Stacey said.

Stacey’s lab identified the first receptor, P2K1, back in 2014 through a genetic screening. Now the lab discovered another new receptor, P2K2. However, researchers also discovered that the enzyme mevalonate kinase (MVK) acts as a crucial component in the ATP signaling process.

“ATP can bind to the P2K1 and then the P2K1 interacts with the MVK. The MVK is then phosphorylated and activated to regulate diverse metabolites,” said researcher Daewon Kim, another author on the paper in the Stacey lab.

Yet even with new receptor and pathway discovery, more science is needed to fully understand this important signaling process. This research will move them closer to that understanding.

“Purinergic signaling is not just some side product but is really affecting a major pathway that is central to the way in which plants grow and develop,” Stacey said.

Read more about this work in the paper “Activation of the Plant Mevalonate Pathway by Extracellular ATP” published in January 2022 in the journal Nature Communications.

Sung-Hwan Cho is a Bond Life Sciences Center research scientist. Daewon Kim is a Bond Life Sciences Center research scientist. Gary Stacey is a curator’s professor of plant sciences and a Bond Life Sciences Center principal investigator.

New observation from Stacey lab could help advance plant engineering

By Lauren Hines | Bond LSC

Think about how a home alarm system alerts a person to a potential burglary with sensors detecting whether an intruder picked a lock, came through a window or came through a garage.

Plants are much like this, surviving with the help of their thousands of sensors that can send danger signals to the whole plant so it can react effectively.

“Plants have to have a whole variety of different mechanisms to respond to their environment because they’re stuck in one spot,” said Gary Stacey, principal investigator at Bond Life Sciences Center. “The way they do that is they have all these membrane-associated receptors, and they receive signals from the outside … so they can induce a defense response.”

Stacey’s lab recently made an observation that could lead to interesting future advancements in plant breeding and engineering. Its work was published May 12 in the journal Nature Communications.

The lab found when a lipid — a fatty molecule — is attached to a receptor, a cysteine amino acid within a protein is modified. This process, in turn, makes the receptor silent. The addition of the lipid is called acylation. The lab found that they could also reverse this process and reactivate the receptor.

In other words, this process can turn receptors on and off, which is what tells the plant that there’s danger.

In addition, the lab can use the acylation process to identify the binding protein and, therefore, identify the receptor that is binding to the protein.

“There’s a lot of receptors for which we don’t know the ligand,” said Stacey. “In other words, if you line up all the receptors, there are only a few of which we know what they’re binding to.”

Identifying these receptors’ functions and what these receptors bind to is a high priority in plant research and agriculture communities.

“If we knew all the receptors, say, that responded to drought or if we knew all the receptors that responded to high light or pathogens or whatever there might be in the ozone … then that would open up pathways for us to engineer plants that are more resistant to these stresses, which would make crop production more sustainable, especially in lieu of the changing climate that we have, and would really be a big step forward for agriculture,” Stacey said

According to Stacey, researchers have been able to identify the function of “a small fraction” of receptors out of 2,000 in the model plant, Arabidopsis. However, the Stacey lab is currently developing a way to find these receptors’ functions.

Developing this analysis has been technically difficult so far — needing more funding and manpower to do all the experiments — but the lab is currently in the proofing stage to verify what they know. So far, they can correctly identify the binding protein and the receptor it binds to for some receptors, but it’s less clear for other receptors. More experiments are needed to see if the analysis will work.

“There are 2,000 [receptors], and we only know the function of a handful,” Stacey said. “There’s a lot of stuff that remains to be discovered and a lot of potentials to do something useful.”’

More information about the study can be found in, “S-acylation of P2K1 mediates extracellular ATP-induced immune signaling in Arabidopsis.” Stacey’s lab collaborated with Dongqin Chen, Fengsheng Hao and Huiqi Mu of the State Key Laboratory of Agrobiotechnology in China, Nagib Ahsan of the University of Oklahoma and Jay Thelen at Bond Life Sciences Center.

Available at: https://decodingscience.missouri.edu/2021/05/25/new-observation-from-stacey-lab-could-help-advance-plant-engineering/

New publication in Nature Communications

Our latest publication, S-acylation of P2K1 mediates extracellular ATP-induced immune signaling in Arabidopsis, has just been published in Nature Communications. 

Abstract:

S-acylation is a reversible protein post-translational modification mediated by protein S-acyltransferases (PATs). How S-acylation regulates plant innate immunity is our main concern. Here, we show that the plant immune receptor P2K1 (DORN1, LecRK-I.9; extracellular ATP receptor) directly interacts with and phosphorylates Arabidopsis PAT5 and PAT9 to stimulate their S-acyltransferase activity. This leads, in a time-dependent manner, to greater S-acylation of P2K1, which dampens the immune response. pat5 and pat9 mutants have an elevated extracellular ATP-induced immune response, limited bacterial invasion, increased phosphorylation and decreased degradation of P2K1 during immune signaling. Mutation of S-acylated cysteine residues in P2K1 results in a similar phenotype. Our study reveals that S-acylation effects the temporal dynamics of P2K1 receptor activity, through autophosphorylation and protein degradation, suggesting an important role for this modification in regulating the ability of plants in respond to external stimuli.

Read the full article here.

 

#IAmScience Jordan Brungardt

By Becca Wolf | Bond LSC

When one hears of a magician, they think of a man that pulls a rabbit out of a top hat or ‘cuts’ people in half. Magicians have a lot of tricks up their sleeve.

People do not think of scientists as magicians, yet they still perform wonderous things.

“I heard a quote one time that says science and technology is kind of like magic,” Jordan Brungardt said. “For somebody that doesn’t know what is happening, experiments look like magic if they’re performed well. Think of cell phones allowing us to talk to people across the world. For somebody from a few decades ago, that would seem like magic.”

For Brungardt, a post-doctoral fellow in the Gary Stacey lab at Bond Life Sciences Center, this magic of sorts makes research exciting.

“When you get sequencing information back in the lab after going weeks without actually seeing something and it lines up with what you’re predicting, it’s like Christmas,” Brungardt said.

In the Stacey lab, Brungardt studies the genes involved in early nodule development in soybeans.

He looks at the interaction between rhizobia, a species of bacteria, and their plant hosts, legumes. His work aims to explore how the plants allow access to their inner roots through infection thread development.

“They undergo an intimate interaction that is really unique,” Brungardt said. “It’s pretty cool from that aspect, and the infection thread is an important part of the interaction.”

Brungardt currently works with Jaehyo Song, a postdoctoral student in the Stacey lab.

“He is a very careful person, and experimenting together helps prevent any mistakes,” Song said. “I can also see that the experiment is progressing step by step because we work very diligently.”

The two have been working together for a few months and have found their collaboration to be very beneficial.

“Even when a simple problem occurred in the experiment, he did not ignore it,” Song said. “He found the exact cause of the problem through previous research and eventually solved it. Through this, I could see that his problem-solving skills were very good.”

Brungardt is able to dodge problems that arise in his research easily.

“There’s a lot of different facets of my research,” Brungardt said. “If I get stuck somewhere, I can make headway somewhere else, which allows me to take my time on the process that I’m stuck on and come back to it later.”

Brungardt completed his undergraduate degree at Fort Hays State University in Kansas and his master’s degree at Wichita State University. That wasn’t his initial plan, though.

“I knew I wanted to do something with soybeans coming out of my undergrad and, to be honest, I actually interviewed with Dr. Stacy, who is my mentor right now, but it didn’t work out,” Brungardt said. “So, it was really nice coming back and getting a job here, because that’s what I initially wanted to do.”

Even though Brungardt did not initially come to Mizzou, he remained focused on it as the end goal. He ended up getting a job as a microbiologist where he produced Rhizobia for farmers to use to improve their crop production.

“My Ph.D. dealt with microbial interaction with plants, so it still had some loose application for what I’m doing now,” Brungardt said. “While my path wasn’t straight, it never strayed from what I wanted to do. I liked that I still did things that were relevant to what I wanted to do.

Brungardt arrived at Bond LSC last June and has adjusted nicely. His research is similar to what he has done previously, just in a new building in a new lab. He is happy to finally be able to completely focus on his research.

“I just graduated with my Ph.D. last year so there’s no more homework or classes for me. It’s a little bit of a change,” Brungardt said. “It’s simpler, I don’t have to break up my workday to go to class and then come back and work, and then switch up to something again. As a student I was doing several things at once and had other things in the back of my mind. Now I can just focus on my research.”

Since Brungardt can devote all of his time to his research now, he expects to see a lot more magical moments in the lab.

Available at: https://decodingscience.missouri.edu/2021/03/26/iamscience-jordan-brungardt/