Category Archives: Agriculture

New Gene To Make Plants Heat-tolerant in Rising Temperatures (Agriculture)

With temperatures rising globally, agricultural crops are feeling the stress. Warmer weather can cause a large reduction in crop yield. The Kendal Hirschi Lab at Baylor College of Medicine recently had a patent approved for a gene to make plants more tolerant to higher temperatures.

Drs. Kendal Hirschi and Ninghui Cheng discuss the importance of the patent and its environmental impact.

Helping crops beat the heat
Dr. Ninghui Cheng © BCM
Dr. Kendal Hirschi © BCM

“In commercial agriculture, we want high yield and nutritious foods. In hot temperatures, the yield can be low, which is a problem. With this new gene, we’re protecting plants when the temperatures rise so they can grow better,” said Cheng, assistant professor of pediatrics-nutrition at Baylor and Texas Children’s Hospital.

The yield of crops is falling due to increased temperatures, as crops were not bred to withstand this kind of heat.

When this plant gene is expressed in crops, it gives them a booster shot that enables them to grow at temperatures that are not permissive for growth of traditional crops.

“When it gets hot, plants grows less. For instance, raising the temperature two degrees can cause a 50% reduction in crop yield. Two degrees doesn’t sound like much, but the effect is that the crop will be lost,” said Hirschi, professor of pediatrics-nutrition at Baylor and Texas Children’s.

Hirschi said, “With this technology, the two-degree temperature shift will cost no yield penalty. Crop yield will remain at 100 bushels, whereas without the gene, yield would come down to 50 bushels.”

As the world environment gets warmer, it becomes important to develop crop varieties that are responsive to environmental changes. Traditional breeding approaches have been effective but take decades to produce heat-tolerant crops.

With this technology, scientists can develop better crops over the course of a few years, including rice, corn wheat and soybeans.

Heat Tolerance of Genetically Modified Tomatoes. Control plants on the left and modified plants on the right were subjected to several days of high temperatures and then returned to normal growth conditions. Note that the modified plants retain their vigor. They will go on to produce fruit whereas the wild-type will not. Image courtesy of the Hirschi lab.
How the new gene works

“We’re speculating that high temperatures affect plants because they trigger an inflammatory response similar to what we see in our bodies. Inflammation is associated with reactive oxygen species, compounds made by cells to serve as signaling molecules for normal biologic processes. However, reactive oxygen species also can be detrimental to cells, ultimately disrupting biological processes. We think this gene reduces the reactive oxygen species that are generated during heat – it distresses the plant,” Hirschi said.

The Hirschi Lab is part of the Children’s Nutrition Research Center, which houses laboratories of varied disciplines, a vast array of state-of-the-art equipment, a greenhouse, observation labs and accommodations for research volunteers, a metabolic kitchen, and an elite group of scientists conducting groundbreaking research.

Other collaborators include Dr. Sunghun Park, professor of crop functional genomics at Kansas State University.

  • For more information about this patent, “PLANTS WITH ENHANCED TOLERANCE TO MULTIPLE ABIOTIC STRESSES,” click here.
  • Are you interested in learning more about the Hirschi lab, its projects, publications, lab members and what they do for fun? Visit its website .
  • Learn more in Plant integration in the Kendal Hirschi Lab.

Featured image: A sustained two degree increase in temperature can cause a 50% reduction in the yield of this wheat crop field. Pixabay


Provided by BCM

Biofertiliser For Better Farms (Agriculture)

While agricultural production around the world struggles with declining soil health, Australian researchers are investigating production of a sustainable organic nitrogen fertiliser made from aquatic cyanobacterial biomass – ideally suited for badly degraded areas reliant on chemical fertilisers.

Large-scale agricultural production is often reliant on synthetic fertiliser. Photo: Pixabay

“Many soils are degraded and becoming less fertile. This challenges agriculture to produce sufficient high-quality food to feed the continuously growing population, which is further exacerbated by climatic instability threatening crop production,” says Flinders University researcher Associate Professor Kirsten Heimann.

Scientists in Australia, US and Europe are testing a new biofertiliser made from a fast-growing freshwater cyanobacterium Tolypothrix, which can fix nitrogen from the atmosphere without the need for additional nitrogen fertilisation, making the biomass inexpensive to produce compared to alternative microalgal and macroalgal biofertilisers.

This form of non-toxic blue-green algae can be cultivated in freshwater, and even slightly saline or industrial wastewater such as from coal-fired power stations, the research team has found. Capturing biofuel may also be used to offset production costs.

Schematic diagram of ATS-cultivation of Tolypothrix sp. biofilms, pretreatment and anaerobic digestion.

Energy inputs for the production of Tolypothrix biomass can be offset by producing biogas, essentially a methane-rich gas for either drying the biomass to extract high-value health supplement phycocyanin or to produce carbon and nitrogen-rich liquid and solid biofertilisers to remediate soil infertility.

In a recent paper in Chemosphere, Dr Heimann and colleagues in Australia, the US and Spain investigate Tolypothrix production as a sustainable solution for biological soil improvement, which when combined with biogas or the spirulina-like nutritional powder promises “strong economic returns for regional and remote farming communities”.

Associate Professor Kirsten Heimann, from the Centre for Marine Bioproducts Development at Flinders University.

“Australian soils, in particular in the marginal wheat belt in Western Australia, are structurally degraded, which cannot be overcome by applications of synthetic fertilisers,” says Associate Professor Heimann, from the Flinders University Centre for Marine Bioproducts Development in South Australia.

“To improve soil structure, organic carbon applications are required to return the soils’ capacity to sustain a healthy soil microbiome and to improve the soils’ cation exchange of nutrients and water-holding capacity.”

Researchers say conversion of pond-produced cyanobacterial biomass produced on farming land would provide a major in-situ source of renewable nitrogen-rich fertiliser, also helping to reduce carbon emissions from chemical fertiliser production and transport.

Higher energy and food demands are forecast as a consequence of expected global population growth, predicted by the UN to reach 8.5 billion in 2030, 9.7 billion by 2050 and 10.9 billion in 2100.

These projections encourage research into biofertilizer and biogas production through sustainable energy generation using waste organic material of controlled production of biomass such as microalgae and multicellular cyanobacteria.

Researchers have previously reported photosynthetic fixation of CO2 by cyanobacteria of 100 to >200 tons CO2 ha−1 y−1 under outdoor cultivation conditions in open ponds, raceway ponds, photo-bioreactors and attached growth bioreactors.

Unlike many cyanobacterial species, Tolypothrix sp., a freshwater cyanobacterium, is filamentous and forms aggregates that self-flocculate, making it very easy to harvest from suspension cultures, reducing dewatering costs by up to 90%, studies suggest.

The article, Biomass pre-treatments of the N2-fixing cyanobacterium Tolypothrix for co-production of methane (2021) by C Velu, OP Karthikeyan, DL Brinkman, S Cirés and K Heimann has been published in Chemosphere (Elsevier) DOI: 10.1016/j.chemosphere.2021.131246

Acknowledgements: This research received funding from the Advanced Manufacturing Cooperative Research Centre (AMCRC) and associated Universities.

Featured image credit: Pixabay, rest images credit: Flinders University


Provided by Flinders University

Returning Nitrogen To Soils Without Chemicals (Agriculture)

While agricultural production around the world struggles with declining soil health, Australian researchers are investigating production of a sustainable organic nitrogen fertilizer made from aquatic cyanobacterial biomass—ideally suited for badly degraded areas reliant on chemical fertilizers.

“Many soils are degraded and becoming less fertile. This challenges agriculture to produce sufficient high-quality food to feed the continuously growing population, which is further exacerbated by climatic instability threatening crop production,” says Flinders University researcher Associate Professor Kirsten Heimann.

Scientists in Australia, US and Europe are testing a new biofertiliser made from a fast-growing freshwater cyanobacterium Tolypothrix, which can fix nitrogen from the atmosphere without the need for additional nitrogen fertilization, making the biomass inexpensive to produce compared to alternative microalgal and macroalgal biofertilisers.

This form of non-toxic blue-green algae can be cultivated in freshwater, and even slightly saline or industrial wastewater such as from coal-fired power stations, the research team has found. Capturing biofuel may also be used to offset production costs.

Energy inputs for the production of Tolypothrix biomass can be offset by producing biogas, essentially a methane-rich gas for either drying the biomass to extract high-value health supplement phycocyanin or to produce carbon and nitrogen-rich liquid and solid biofertilisers to remediate soil infertility.

In a recent paper in Chemosphere, Dr. Heimann and colleagues in Australia, the US and Spain investigate Tolypothrix production as a sustainable solution for biological soil improvement, which when combined with biogas or the spirulina-like nutritional powder promises “strong economic returns for regional and remote farming communities.”

“Australian soils, in particular in the marginal wheat belt in Western Australia, are structurally degraded, which cannot be overcome by applications of synthetic fertilizers,” says Associate Professor Heimann, from the Flinders University Centre for Marine Bioproducts Development in South Australia.

“To improve soil structure, organic carbon applications are required to return the soils’ capacity to sustain a healthy soil microbiome and to improve the soils’ cation exchange of nutrients and water-holding capacity.”

Researchers say conversion of pond-produced cyanobacterial biomass produced on farming land would provide a major in-situ source of renewable nitrogen-rich fertilizer, also helping to reduce carbon emissions from chemical fertilizer production and transport.

Higher energy and food demands are forecast as a consequence of expected global population growth, predicted by the UN to reach 8.5 billion in 2030, 9.7 billion by 2050 and 10.9 billion in 2100.

These projections encourage research into biofertilizer and biogas production through sustainable energy generation using waste organic material of controlled production of biomass such as microalgae and multicellular cyanobacteria.

Researchers have previously reported photosynthetic fixation of CO2by cyanobacteria of 100 to >200 tons CO2ha−1y−1under outdoor cultivation conditions in open ponds, raceway ponds, photobioreactors and attached growthbioreactors.

Unlike many cyanobacterial species,Tolypothrixsp., a freshwater cyanobacterium, is filamentous and forms aggregates that self-flocculate, making it very easy to harvest from suspension cultures, reducing dewatering costs by up to 90%, studies suggest.

The article, “Biomass pre-treatments of the N2-fixing cyanobacterium Tolypothrix for co-production of methane,” by C Velu, OP Karthikeyan, DL Brinkman, S Cirés and K Heimann, has been published in Chemosphere.

Featured image credit: Flinders University


Reference: Chinnathambi Velu et al, Biomass pre-treatments of the N2-fixing cyanobacterium Tolypothrix for co-production of methane, Chemosphere (2021). DOI: 10.1016/j.chemosphere.2021.131246


Provided by Flinders University

RNA Breakthrough Creates Crops That Can Grow 50% More Potatoes, Rice (Agriculture)

Manipulating RNA can allow plants to yield dramatically more crops, as well as increasing drought tolerance, announced a group of scientists from the University of Chicago, Peking University and Guizhou University.

In initial tests, adding a gene encoding for a protein called FTO to both rice and potato plants increased their yield by 50% in field tests. The plants grew significantly larger, produced longer root systems and were better able to tolerate drought stress. Analysis also showed that the plants had increased their rate of photosynthesis.

“The change really is dramatic,” said University of Chicago Prof. Chuan He, who together with Prof. Guifang Jia at Peking University, led the research. “What’s more, it worked with almost every type of plant we tried it with so far, and it’s a very simple modification to make.”

The researchers are hopeful about the potential of this breakthrough, especially in the face of climate change and other pressures on crop systems worldwide.

“This really provides the possibility of engineering plants to potentially improve the ecosystem as global warming proceeds,” said He, who is the John T. Wilson Distinguished Service Professor of Chemistry, Biochemistry and Molecular Biology. “We rely on plants for many, many things—everything from wood, food, and medicine, to flowers and oil—and this potentially offers a way to increase the stock material we can get from most plants.”

Rice nudged along

For decades, scientists have been working to boost crop production in the face of an increasingly unstable climate and a growing global population. But such processes are usually complicated, and often result only in incremental changes.

The way this discovery came about was quite different.

Many of us remember RNA from high school biology, where we were taught that the RNA molecule reads DNA, then makes proteins to carry out tasks. But in 2011, He’s lab opened an entire new field of research by discovering the keys to a different way that genes are expressed in mammals. It turns out that RNA doesn’t simply read the DNA blueprint and carry it out blindly; the cell itself can also regulate which parts of the blueprint get expressed. It does so by placing chemical markers onto RNA to modulate which proteins are made and how many.

He and his colleagues immediately realized that this had major implications for biology. Since then, his team and others around the world have been trying to flesh out our understanding of the process and what it affects in animals, plants and different human diseases; for example, He is a co-founder of a biotech company now developing new anti-cancer medicines based on targeting RNA modification proteins.

He and Guifang Jia, a former UChicago postdoctoral researcher who is now an associate professor at Peking University, began to wonder how it affected plant biology.

They focused on a protein called FTO, the first known protein that erases chemical marks on RNA, which Jia found as a postdoctoral researcher in He’s group at UChicago. The scientists knew it worked on RNA to affect cell growth in humans and other animals, so they tried inserting the gene for it into rice plants—and then watched in amazement as the plants took off.

“I think right then was when all of us realized we were doing something special,” He said.

The rice plants grew three times more rice under laboratory conditions. When they tried it out in real field tests, the plants grew 50% more mass and yielded 50% more rice. They grew longer roots, photosynthesized more efficiently, and could better withstand stress from drought.

The scientists repeated the experiments with potato plants, which are part of a completely different family. The results were the same.

“That suggested a degree of universality that was extremely exciting,” He said.

It took the scientists longer to begin to understand how this was happening. Further experiments showed that FTO started working early in the plant’s development, boosting the total amount of biomass it produced.

The scientists think that FTO controls a process known as m6A, which is a key modification of RNA. In this scenario, FTO works by erasing m6A RNA to muffle some of the signals that tell plants to slow down and reduce growth. Imagine a road with lots of stoplights; if scientists cover up the red lights and leave the green, more and more cars can move along the road.

Overall, the modified plants produced significantly more RNA than control plants.

Modifying the process

The process described in this paper involves using an animal FTO gene in a plant. But once scientists fully understand this growth mechanism, He thinks there could be alternate ways to get the same effect.

“It seems that plants already have this layer of regulation, and all we did is tap into it,” He said. “So the next step would be to discover how to do it using the plant’s existing genetics.”

He can imagine all sorts of uses down the road—and he’s working with the university and the Polsky Center for Entrepreneurship and Innovation to explore the possibilities.

“Even beyond food, there are other consequences of climate change,” said He. “Perhaps we could engineer grasses in threatened areas that can withstand drought. Perhaps we could teach a tree in the Midwest to grow longer roots, so that it’s less likely to be toppled during strong storms. There are so many potential applications.”

The study is published in Nature Biotechnology.

Featured image: Ripening heads of rice (Oryza sativa).© apisitwilaijit29/stock.adobe.com


Reference: Yu, Q., Liu, S., Yu, L. et al. RNA demethylation increases the yield and biomass of rice and potato plants in field trials. Nat Biotechnol (2021). https://doi.org/10.1038/s41587-021-00982-9


Provided by University of Chicago

New Technique Reduces Nicotine Levels, Harmful Compounds Simultaneously in Tobacco (Agriculture)

North Carolina State University researchers have developed a new technique that can alter plant metabolism. Tested in tobacco plants, the technique showed that it could reduce harmful chemical compounds, including some that are carcinogenic. The findings could be used to improve the health benefits of crops.

“A number of techniques can be used to successfully reduce specific chemical compounds, or alkaloids, in plants such as tobacco, but research has shown that some of these techniques can increase other harmful chemical compounds while reducing the target compound,” said De-Yu Xie, professor of plant and microbial biology at NC State and the corresponding author of a paper describing the research. “Our technology reduced a number of harmful compounds – including the addictive nicotine, the carcinogenic N-nitrosonornicotine (NNN), and other tobacco-specific nitrosamines (TSNAs) – simultaneously without detrimental effects to the plant.”

The technique uses transcription factors and regulatory elements as molecular tools for new regulation designs. Regulatory elements are short, non-coding DNA fragments that control the transcription of nearby coding genes. Transcription factors are proteins that help turn certain genes on or off by binding to regulatory elements. Xie hypothesized that these could be useful molecular tools to design new regulations for engineering new plant traits. Two Arabidopsis transcription factors in particular, PAP1 and TT8, are known to regulate the biosynthesis of anthocyanins, or classes of nutraceutical compounds with antioxidant properties. Xie further hypothesized that these proteins could be used as molecular tools to help repress a number of harmful chemical compound levels, such as nicotine.

“PAP1 regulates pigmentation, so tobacco plants with our overexpressed PAP1 genes are red,” Xie said. “We screened plant DNAs and found that tobacco has PAP1- and TT8-favored regulatory elements near JAZ genes, which repress nicotine biosynthesis. We then proposed that these elements were appropriate tools for a test. In all, we found four JAZ genes activated in red tobacco plants with a designed PAP1 and TT8 cassette overexpressed.”

Xie and his colleagues tested the hypothesis by examining tobacco plants in the greenhouse and in the field and showed the reductions of harmful chemical compounds and nicotine in both types of experiments. NNN levels were reduced from 63 to 79% in leaves from tobacco plants that had PAP1 and TT8 overexpressed, for example. Overall, four carcinogenic TSNAs were significantly reduced by the technique.

Xie believes that the technique holds the potential to be used in other crop plants to promote other beneficial traits and make some foods healthier.

The paper appears in Journal of Advanced Research. Research associate Mingzhu Li is a first author of the paper. Former postdoctoral fellows Xianzhi He and Christophe La Hovary are co-first authors. The research was supported by the R.J. Reynolds Tobacco Co.

Featured image: Overexpressed PAP1 and TT8 genes turn tobacco plants red, but also help reduce carcinogenic chemical compounds. Photo courtesy of De-Yu Xie


Reference:

  • Title: “A De Novo regulation design shows an effectiveness in altering plant secondary metabolism”
  • Authors: Mingzhuo Li, Xianzhi He, Christophe La Hovary, Yue Zhu, Yilun Dong, Shibiao Liu, Hucheng Xing, Yajun Liu, Yucheng Jie, Dongming Ma, Seyit Yuzuak and De-Yu Xie, NC State University
  • Published: June 20, 2021 in Journal of Advanced Research
  • DOI: 10.1016/j.jare.2021.06.017

Provided by NC State

Continuous Activation of Immune Response Mediated by Gene Ne2 Results in Hybrid Necrosis in Wheat (Agriculture)

Wheat is one of the most important food crops in the world. Hybrid necrosis often occurs in the process of wheat improvement, which seriously hinders the combination of superior traits among different genotypes of wheat. In the 1960s, scientists demonstrated that the hybrid necrosis in wheat was controlled by a pair of complementary genes, Ne1 and Ne2. However, the formation mechanism of hybrid necrosis in wheat has still not been uncovered. 

Recently, the research group led by Prof. LING Hongqing from the Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences performed a series of experiments to isolate the responsible genes and illustrate the formation mechanism of wheat hybrid necrosis. 

The researchers carried out the preliminary map of Ne1 and Ne2 by genome-wide association analysis. Then, they cloned Ne2 by map-based cloning approach using residual heterozygous lines of Ne2 locus (carrying Ne1Ne1Ne2ne2 genotype) from the recombination inbred line population derived from common wheat varieties “Zhengnong 17” (ne1ne1Ne2Ne2) and “Yangbaimai” (Ne1Ne1ne2ne2). Ne2 encodes a coiled coil-nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR) domain protein. 

Furthermore, they demonstrated that Ne2 was the gene responded for wheat hybrid necrosis via knocking out of Ne2. Homozygous frameshift mutations of Ne2 generated by CRISPR/Cas9 in the genetic background of necrotic lines NIL-Ne2 and RIL-66 resulted in normal leaf growth.

Frameshift mutations of Ne2 generated by CRISPR/Cas9 in the genetic background of necrotic lines NIL-Ne2 and RIL-66 restored normal leaf growth (Image IGDB)

qPCR analysis and histological staining revealed that the immune response in the necrotic plants was continuously activated. Therefore, they concluded that up-regulated expression of Ne2 induced by Ne1 and excessive accumulation of hydrogen peroxide (H2O2) were closely related to the formation of hybrid necrosis in wheat. 

Combined with previous reports, they speculated that Ne2 and leaf rust resistance gene LrLC10/Lr13 might be the same gene according to analysis results of genetics, collinearity of the Ne2 candidate interval and sequence alignment. 

Using the developed diagnostic marker for Ne2 allele, they tested 501 common wheat materials (including 301 cultivars, 200 landraces) from different countries of the world and found that the frequency of Ne2 allele in landrace (2.0%) was much lower than that in modern cultivars (13.6%). The result showed that Ne2/LrLC10/Lr13 had been partially used during wheat genetic improvement, and its utilization was limited by the existence of Ne1 gene. 

This work provides an opportunity to further investigate the molecular mechanism of hybrid necrosis, to select Lr13 by molecular marker-assisted selection, and to avoid hybrid necrosis simultaneously. 

This study entitled “Ne2, a typical CC-NBS-LRR-type gene, is responsible for hybrid necrosis in wheat” was published online in New Phytologist on June 23. 

This research was supported by the National Natural Science Foundation of China, the Major Basic Research Program of Shandong Natural Science Foundation, and the Research Program of Hebei Science and Technology.


Reference: Si, Y., Zheng, S., Niu, J., Tian, S., Gu, M., Lu, Q., He, Y., Zhang, J., Shi, X., Li, Y. and Ling, H.-Q. (2021), Ne2, a typical CC-NBS-LRR-type gene, is responsible for hybrid necrosis in wheat. New Phytologist. Accepted Author Manuscript. https://doi.org/10.1111/nph.17575


Provided by Chinese Academy of Sciences

Protein Crop’s Potential Unlocked By Deciphering Anti-nutrient Biosynthesis (Agriculture)

Faba beans are an excellent source of food protein, but about 4% of the world’s population are afflicted by favism, which renders them sensitive to the faba bean anti-nutrients vicine and convicine. Now, an international research team has identified the VC1 gene as responsible for the production of these compounds.

Faba beans have actually been a source of food protein since pre-historic times, but a fraction of the population, mostly from warm southern regions, cannot tolerate them. Pythagoras and his followers avoided them, and Roman priests of Jupiter associated them with death. Today, we know that faba beans produce the anti-nutrients vicine and convicine, which cause a risk for favism – a condition arising from damage to red blood cells – for susceptible individuals.

Among legumes – the pod-producing family of plants to which pea, chickpea and soybean also belong – faba beans have the second-highest yield globally. They also have the highest seed protein content of the starch-containing legumes and out-perform soybean in cool climates. Faba beans are consequently a prime protein source for facilitating a global switch to a plant-based diet, considered necessary for significant reductions in carbon emissions.

The VC1 gene is responsible for vicine-convicine content

However, when people deficient in a specific enzyme eat a large portion of uncooked faba beans, vicine and convicine can induce abnormal breakdown of red blood cells. The resultant hemolytic anemia, known as favism, has inevitably limited the potential use of faba beans. Although there are a number of faba bean varieties with low levels of vicine and convicine, the gene responsible for this trait was previously unknown.

Now, the scientists have identified the gene responsible for vicine-convicine content. What is more, they have identified the specific mutation within this gene that causes the reduction in synthesis. They found that all faba bean varieties with a low vicine-convicine content, descended from a single accession found in a genebank, had two nucleotides – the “letters” that make up DNA – inserted within the VC1 gene. This insertion disrupts the VC1 function and is the only known genetic source of low vicine and convicine content.

Stig U. Andersen, one of project leaders, says, “Working across disciplines to integrate biochemical and molecular genetic data was key to finally unveiling the genetic source of low vicine and convicine.”

The work has been published in Nature Plants, and it paves the way for the complete description of the biosynthetic pathway of vicine and convicine, and ultimately for breeding, production and commercial use of faba bean varieties totally free from these anti-nutritional compounds.

The team, comprising leading scientists from Denmark, Finland, Germany, the UK and Canada, are already looking to the future. Fernando Geu-Flores, who led the work, says “Now that we understand where these anti-nutrients come from, we can attempt to breed them out completely, thus contributing to food safety and sustainability.“


Additional information

We strive to ensure that all our articles live up to the Danish universities’ principles for good research communication (scroll down to find the English version on the website). Because of this, the following information will be given:

Funding: The studies have received financial support from Innovation Fund Denmark, the Academy of Finland, the UK Biotechnology and Biological Science Research Council, the VILLUM Foundation, the Danish National Research Foundation, Guangzhou Elite and the German Federal Ministry of Food and Agriculture

Read more:

Link to the article in Nature Plants:

VC1 catalyses a key step in the biosynthesis of vicine in faba bean Emilie Björnsdotter, Marcin Nadzieja, Wei Chang, Leandro Escobar-Herrera, Davide Mancinotti, Deepti Angra, Xinxing Xia, Rebecca Tacke, Hamid Khazaei, Christoph Crocoll, Albert Vandenberg, Wolfgang Link, Frederick L. Stoddard, Donal M. O’Sullivan, Jens Stougaard, Alan H. Schulman, Stig U. Andersen, and Fernando Geu-Flores, DOI: https://doi.org/10.1038/s41477-021-00950-w

Featured image: Researchers have identified the VC1 gene as responsible for the production of anti-nutrients vicine and convicine that make people sensitive to the faba bean (photo: Frederick Stoddard, University of Helsinki)


Provided by University of Aarhus

How Seeds Know It’s A Good Time To Germinate (Agriculture)

Dehydrated plant seeds can lay dormant for long periods—over 1,000 years in some species—before the availability of water can trigger germination. This protects the embryonic plant inside from a variety of environmental stresses until conditions are favorable for growth and survival. However, the mechanism by which the baby plant senses water and reactivates cellular activity has remained a mystery until now.

New work jointly led by Carnegie’s Yanniv Dorone and Sue Rhee and Stanford University’s Steven Boeynaems and Aaron Gitler discovered a protein that plays a critical “go, or no-go” role in this process—halting germination if the soil’s hydrological conditions are less than ideal or allowing it to proceed if the chances of survival are good. Their findings have major implications for understanding plant ecology in a warming world and for the possibility of designing drought-resistant crops that can survive climate change and fight world hunger.

Their work is published in Cell.

Dorone, Rhee, Boeynaems, Gitler, and their colleagues—including Carnegie’s Benjamin Jin, Shannon Hateley, Flavia Bossi, Elena Lazarus, and Moises Exposito-Alonso—used molecular, physiological, and ecological research techniques to reveal a previously uncharacterized protein that they named FLOE1.

“Despite the extraordinary toughness of many seeds, plants are still at their most vulnerable during this stage of their lives, because germination must be precisely timed to ensure the greatest chance of survival. Once germination starts, the plant cannot go back into its hibernation state—the genie can’t be put back in the bottle,” Dorone explained. “So, a protein like FLOE1 is crucial to a plant’s ability to walk the tightrope between too soon and too late.”

The key to FLOE1’s capabilities is a recently discovered biophysical phenomenon that’s a hot research topic right now called phase separation. This mechanism allows cells to dynamically compartmentalize biomolecules into membrane-less assemblies, rather than cordoning them off in a cellular organelle surrounded by a membrane.

Caption: Electron tomographic reconstruction and segmentation of membrane-bound organelles (in blue) of an Arabidopsis embryo cell. Video is courtesy of Jannice G. Pennington and Marisa S. Otegui.

“Think of an organelle as an office building where components of the cell are assigned to complete their physiological jobs; whereas, these phase-separation-enabled assemblies are more like a maker faire or hackathon, where proteins can come together to accomplish a task and then disburse when it’s complete,” Rhee said.  “We found that FLOE1’s ability to very quickly initiate this type of temporary gathering is crucial to its functionality.”

When a dormant seed senses moisture in its proximity, FLOE1 almost instantaneously assembles in the cell to test the waters, so to speak, and determine whether the conditions are good for the seed to reactivate and start growing. Because the FLOE1 aggregation is temporary and reversible, it can act as a go or no-go signal, halting germination if water availability is determined to be less than optimal, or allowing it to proceed if the environment has enough water to support successful growth.

“We believe that this is the first study that provides information on how seeds can directly perceive their hydration state and act upon it,” Rhee added.

The authors say that their discovery could lay the groundwork for engineering crops that are able to harness FLOE1’s abilities in order to withstand the detrimental effects of climate change.  This type of enhancement will be increasingly important to combat hunger around the world.

Caption: FLOE1 proteins tagged to Green Fluorescent Protein (GFP) streaming through the cytoplasm in tobacco cells. Video is courtesy of Yanniv Dorone.

Although their work was conducted using the experimental mustard green Arabidopsis thaliana, Dorone, Rhee, Boeynaems, and Gitler found found that FLOE1 is present throughout the plant kingdom, even in plants that precede the evolution of seeds, meaning it could play many additional roles in plant cellular physiology, which could have additional bioengineering potential.

“What’s more, FLOE1 is the first known protein to reversibly phase separate over hydration-dehydration cycles, but it’s likely that similar processes occur in other organisms that have desiccated periods of dormancy, including human pathogens,” Dorone concluded.

Other collaborators on the research team were: Eduardo Flores and Shahar Sukenik of University of California Merced; Janice G. Pennington and Marisa S. Otegui of University of Wisconsin Madison; Emiel Michiels, Mathias De Decker, Katlijn Vints, and Pieter Baatsen of KU Leuven; George W. Bassel of University of Warwick; and Alex S. Holehouse of Washington University in St. Louis.

This work was funded by the U.S. Department of Energy, U.S. National Science Foundation, a Stanford Graduate Fellowship in Science and Engineering, the Carnegie Institution for Science, Brigitte Berthelemot, EMBO, and the U.S. National Institutes of Health.

Featured image: A 3D reconstruction of an Arabidopsis embryo. Different colors are used to annotate different cells. Image is courtesy of George W. Bassel


Provided by Carnegie Science

A Specific Protein Complex From Plant Stem Cells Regulates Their Division And Response To Stress (Agriculture)

A multidisciplinary research team led by the CSIC biologist at CRAG Ana I. Caño Delgado and the physicist from the University of Barcelona Marta Ibañes, found that two plant stem cell proteins, known for their role in the proper development of the root, interact physically and regulate each other to avoid cellular division. The study, which results from fifteen years of research conducted by both researchers, reveals these two proteins, called BRAVO and WOX5, act in a certain manner on a small group of stem cells, and their interaction is key for the survival of the plant regarding genomic and environmental stress factors, such as extreme heat or cold, or floods. A recently published article in the journal Molecular Systems Biology gathers these results, obtained with the model plant Arabidopsis thaliana.

The findings would have been possible without joining the knowledge and academic disciplines of the teams of both scientists: on the one hand, biochemistry, genetics, and cellular biology, and on the other, mathematical modelling.

“Previous studies by our team and others from other teams had shown that the loss of one of these proteins (BRAVO or WOX) generates the division of the root’s stem cells. However, the molecular relation was not understood yet”, notes Ana I. Caño Delgado.

“In general, genic regulations involve a complexity that is not very intuitive most of the times, and which is only understood by means of mathematical models and computing simulations. The mathematical models we created could provide a sense to the great amount of gathered data by the CRAG team”, notes Marta Ibañes.

Ana I. Caño-Delgado (CSIC-CRAG) i Marta Ibañes (UB).

These mathematical models will allow researchers to experiment virtually, creating hypothetical situations that could occur in the root’s stem cells, such as the effect of applying hormones or the response in stress situations.

The quiescent centre: a stem cell insurance policy

Plants have a set of stem cells at the tip of the taproot that give the taproot the ability to grow indefinitely. Most of these cells divide rapidly, giving rise to other stem cells and the various cells that make up the root tissues, such as the epidermis or vascular tissue. However, at one end of this niche are a few stem cells that divide much more slowly, which is why the area they occupy has been called the quiescent centre.

Every time a cell duplicates its genetic material in order to divide itself, it runs the risk of incorporating errors, mutations that can have negative consequences for the organism. To deal with this, the stem cells in the quiescent centre build a safeguard, a reservoir of genetically safe cells. If necessary, these cells can “wake up” and divide to fill the stem cell niche.

It is precisely in these few cells in the quiescent centre that the BRAVO and WOX5 proteins use their important function by repressing cell division. Isabel Betegón-Putze, first author of the article, explains the experiments she carried out during her doctoral thesis to reach this conclusion: “We created Arabidopsis plants with the BRAVO and WOX5 genes mutated simultaneously and observed that they had less capacity to regenerate roots, which were shorter and less abundant”.

Under situations of severe or prolonged stress, two types of response occur in the stem cell niche: the death of fast-dividing cells and the activation of quiescent centre cells. Thus, for example, the cells of the quiescent centre are activated after a cut in the root cap, or after freezing or lead poisoning of the root. When doing so, it is possible to replace the dead stem cells and still ensure the growth and proper development of the root, which in turn ensures the nutrition and support of the plant.

Understanding the molecular mechanisms that regulate these processes is key to obtain more resilient crops, especially in the current situation, when climate is getting more extreme every time.

An extraordinary source of youth

Plants, unlike animals, can create new organs, (leaves, flowers, etc.) at an adult age, and they keep growing during their whole life, which can last more than 2,000 years. Animal and plant stem cells seem to use similar strategies to solve similar biological problems. However, molecular processes that regulate these seem to be different. Understanding these differences can be useful to design strategies in medicine and cosmetics that slow down ageing and promote the regeneration of the damaged tissue. This study and others will shed light on advancing in this direction.

The study, “Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots”, Mol Syst Biol. (2021) e9864. https://doi.org/10.15252/msb.20209864

Featured image: Arabidopsis roots stained and visualized under a confocal microscope. The root cells contour is shown in pink. In yellow, the stem cells from the quiescent centre. In the left, a wild-type root, and in the right, a root with mutated BRAVO and WOX5 genes. These mutation produces the division of the cells of the quiescent centre, which are more abundant in the right image. (Credit: CRAG).


Provided by University of Barcelona