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Discovery may someday allow farmers to grow crops in climates where they currently won't grow and allows scientists to make a subtle, targeted mutation to a specific native plant protein Findings of a new study solve a key mystery about the chemistry of how plants tell time so they can flower and metabolize nutrients. The process -- a subtle chemical event -- takes place in the cells of every plant every second of every day. The new understanding means farmers may someday grow crops under conditions or in climates where they currently can't grow, said chemist Brian D. Zoltowski, Southern Methodist University, Dallas, who led the study. "We now understand the chemistry allowing plants to maintain a natural 24-hour rhythm in sync with their environment. This allows us to tune the chemistry, like turning a dimmer switch up or down, to alter the organism's ability to keep time," Zoltowski said. "So we can either make the plant's clock run faster, or make it run slower. By altering these subtle chemical events we might be able to rationally redesign a plant's photochemistry to allow it to adapt to a new climate." Specifically, the researchers figured out the chemical nuts and bolts of how a chemical bond in the protein Zeitlupe forms and breaks in reaction to sunlight, and the rate at which it does so, to understand how proteins in a plant's cells signal the plant when to bloom, metabolize, store energy and perform other functions. Zoltowski's team, with collaborators at the University of Washington and Ohio State University, have made plant strains with specific changes to the way they are able to respond to blue-light. "With these plants we demonstrate that indeed we can tune how the organisms respond to their environment in an intelligible manner," Zoltowski said. Zoltowski and his colleagues made the discovery by mapping the crystal structure of a plant protein whose function is to measure the intensity of sunlight. The protein is able to translate light intensity to a bond formation event that allows the plant to track the time of day and tell the plant when to bloom or metabolize nutrients. A plant uses visual cues to constantly read every aspect of its environment and retune its physiological functions to adapt accordingly. Some of these cues are monitored by plant proteins that absorb and transmit light signals -- called photoreceptors. The research team specifically studied two key photoreceptors, Zeitlupe (Zite-LOO-puh) and FKF-1. "Plants have a very complex array of photoreceptors absorbing all different wavelengths of light to recognize every aspect of their environment and adapt accordingly," said Zoltowski, an assistant professor in the SMU Department of Chemistry. "All their cells and tissue types are working in concert with each other." The finding was reported in the article "Kinetics of the LOV domain of Zeitlupe determine its circadian function in Arabidopsis" in the journal eLIFE online in advance of print publication. Co-author and lead author is Ashutosh Pudasaini, a doctoral graduate from the SMU Department of Chemistry who is now a postdoctoral fellow at the University of Texas Southwestern Medical School, Dallas. Other co-authors are Jae Sung Shim, Young Hun Song and Takato Imaizumi, University of Washington, Seattle; Hua Shi and David E. Somers, Ohio State University; and Takatoshi Kiba, RIKEN Center for Sustainable Resource Science, Japan. The research is funded through a grant from the National Institute of General Medical Sciences of the National Institutes of Health awarded to Zoltowski's lab. Nighttime is the right time for plants to grow "If you live in the Midwest, people say you hear the corn growing at night," said Zoltowski, who grew up in rural Wisconsin. "During the day, a plant is storing as much energy as it can by absorbing photons of sunlight, so that during the evening it can do all its metabolism and growth and development. So there's this separation between day and night." Plants measure these day and night oscillations as well as seasonal changes. Knowledge already existed of the initial chemistry, biology and physiology of that process. In addition, Zoltowski and colleagues published in 2013 the discovery that the amino acids in Zeitlupe -- working like a dimmer switch -- gradually get more active as daytime turns to evening, thereby managing the 24-hour Circadian rhythm. Additionally, they found that FKF-1 is very different from Zeitlupe. FKF-1 switches on with morning light and measures seasonal changes, otherwise called photoperiodism. But a knowledge gap remained. It was a mystery how the information is integrated by the organism. "Ultimately that has to be related to some kind of chemical event occurring, some kind of chemical timekeeper," Zoltowski said. "So by following that trail we figured out how the chemistry works." The problem required a two-pronged approach: Solving the structure of the protein to understand how forming and breaking bonds changes how the organism perceives its environment; and solving the chemistry, specifically the crystal structures of the protein's dark and light states. That process yielded a snapshot of the protein in the dark state and a snapshot of the protein in the light state, so the researchers could watch changes in protein structure in response to the bond-forming event. From there, the researchers made mathematical models 1) that explain how the chemistry of the bond breaking and bond forming event, and the rate at which it occurs, should affect the organism; and 2) that design mutations to the protein that affect how it goes from the dark state to the light state to block that process. The team used a few standard techniques. To get at the chemistry, they deployed ultra-violet visible spectroscopy to measure how efficiently proteins absorb light. They followed differences in the absorption spectrum, seeing what wavelengths are absorbed, to track chemical changes between the dark and the light states. On the structure side, they crystallized the proteins and collected data at synchrotron sources at Cornell University, then mapped out like a puzzle where all the electrons are located in the crystal. From there they could fit and build -- amino acid by amino acid -- the protein, yielding a three-dimensional image of where every atom in the protein is located. "This gives us pictures and snapshots of all those discrete events, where then we can look at how the atoms are moving and changing from one to the other," Zoltowski said. "That allows us to see the bonds forming, the bonds breaking, and how the rest of the protein changes in response to that." Why didn't we think of that? The question has been an important one in the field, but challenging technical hurdles thwarted solutions, said Zoltowski. The key for his team was persistence and years of experience. "This is not an easy protein to work with -- it's difficult to get crystals of these proteins. It requires a protein that is stable enough and will interact in a way that it yields a perfectly ordered crystal. So it's difficult to do the chemistry and the structures. Researchers have struggled with getting adequate amounts of protein to be able to do these types of characterizations," he said. Think of it like a diamond, Zoltowski said, which is a perfectly ordered crystal that is just carbon atoms arranged in a specific way. "Zeitlupe and FKF-1 have thousands of atoms in each protein, and in order to get a crystal, each molecule of the protein needs to arrange itself with the same type of accuracy and precision as carbon atoms in a diamond. Getting that to occur, where they pack nicely together, is non trivial. And some proteins just are really challenging to work with." Zoltowski and his colleagues have been fortunate in having years of experience working with these families of proteins, called the Light-oxygen-voltage-sensing domains, or LOV domains, for short. "So we've developed a lot of skills and techniques over the years that can get over some of the technical hurdles," he said. "So just from gaining experience over time, we've gotten better with working with some very difficult proteins. It makes something that is challenging, much more tractable for our lab." Does this apply to all LOV proteins in every plant? Zeitlupe is a German word that means slow motion. The protein was dubbed Zeitlupe because scientists discovered when they found mutations of this protein previously that it made the Circadian clock run slower. It naturally altered the way the organism perceived time. "We wanted to understand the proteins well enough that we could selectively alter the chemistry, or selectively alter the structure, to create mutations that would be testable in the organism," Zoltowski said. "We wanted a predictive model that would tell us that these mutations that affect the kinetics -- the rate at which this bond breaks -- should do 'X' in the organism." The team's new discovery results in hybrid plants -- something nature already does and has done for millions of years through the process of evolution so that plants adapt to survive. "We're not putting anything into the plant or changing its genetics," Zoltowski said. "We're making a very subtle, targeted mutation to a specific protein that already is a native plant protein -- and one that we've shown in this paper has evolved considerably throughout various different agricultural crops to already do this." The discovery gives scientists the ability to rationally interpret environmental information affecting a plant in order to introduce mutations, instead of relying on selective breeding to achieve a targeted mutation to generate phenotypes that potentially allow the plant to grow in a different environment. The research opens a lot of new doors, including new questions about how these proteins are changing their configuration and how other variables, like oxidative stress, couple with the plant's global sensory networks to also alter proteins and send multiple signals from the environment. "What we've learned is that you need to pay careful attention to specific parts of the protein because they're modulating activity selectively in different categories of this family," Zoltowski said. "If we look at the whole family of these proteins, there are key amino acids that are evolutionarily selected, so they evolve specific modulations of this activity for their own independent niche in the environment. One of the take-homes is there are areas in the protein we need to look at to see how the amino acids are now different." Besides the NIH grant, the lab operates with $250,000 from the American Chemical Society's Herman Frasch Foundation for Chemical Research Grants in Agricultural Chemistry.


News Article | May 16, 2017
Site: www.sciencedaily.com

Findings of a new study solve a key mystery about the chemistry of how plants tell time so they can flower and metabolize nutrients. The process -- a subtle chemical event -- takes place in the cells of every plant every second of every day. The new understanding means farmers may someday grow crops under conditions or in climates where they currently can't grow, said chemist Brian D. Zoltowski, Southern Methodist University, Dallas, who led the study. "We now understand the chemistry allowing plants to maintain a natural 24-hour rhythm in sync with their environment. This allows us to tune the chemistry, like turning a dimmer switch up or down, to alter the organism's ability to keep time," Zoltowski said. "So we can either make the plant's clock run faster, or make it run slower. By altering these subtle chemical events we might be able to rationally redesign a plant's photochemistry to allow it to adapt to a new climate." Specifically, the researchers figured out the chemical nuts and bolts of how a chemical bond in the protein Zeitlupe forms and breaks in reaction to sunlight, and the rate at which it does so, to understand how proteins in a plant's cells signal the plant when to bloom, metabolize, store energy and perform other functions. Zoltowski's team, with collaborators at the University of Washington and Ohio State University, have made plant strains with specific changes to the way they are able to respond to blue-light. "With these plants we demonstrate that indeed we can tune how the organisms respond to their environment in an intelligible manner," Zoltowski said. Zoltowski and his colleagues made the discovery by mapping the crystal structure of a plant protein whose function is to measure the intensity of sunlight. The protein is able to translate light intensity to a bond formation event that allows the plant to track the time of day and tell the plant when to bloom or metabolize nutrients. A plant uses visual cues to constantly read every aspect of its environment and retune its physiological functions to adapt accordingly. Some of these cues are monitored by plant proteins that absorb and transmit light signals -- called photoreceptors. The research team specifically studied two key photoreceptors, Zeitlupe (Zite-LOO-puh) and FKF-1. "Plants have a very complex array of photoreceptors absorbing all different wavelengths of light to recognize every aspect of their environment and adapt accordingly," said Zoltowski, an assistant professor in the SMU Department of Chemistry. "All their cells and tissue types are working in concert with each other." The finding was reported in the article "Kinetics of the LOV domain of Zeitlupe determine its circadian function in Arabidopsis" in the journal eLIFE online in advance of print publication. Co-author and lead author is Ashutosh Pudasaini, a doctoral graduate from the SMU Department of Chemistry who is now a postdoctoral fellow at the University of Texas Southwestern Medical School, Dallas. Other co-authors are Jae Sung Shim, Young Hun Song and Takato Imaizumi, University of Washington, Seattle; Hua Shi and David E. Somers, Ohio State University; and Takatoshi Kiba, RIKEN Center for Sustainable Resource Science, Japan. The research is funded through a grant from the National Institute of General Medical Sciences of the National Institutes of Health awarded to Zoltowski's lab. Nighttime is the right time for plants to grow "If you live in the Midwest, people say you hear the corn growing at night," said Zoltowski, who grew up in rural Wisconsin. "During the day, a plant is storing as much energy as it can by absorbing photons of sunlight, so that during the evening it can do all its metabolism and growth and development. So there's this separation between day and night." Plants measure these day and night oscillations as well as seasonal changes. Knowledge already existed of the initial chemistry, biology and physiology of that process. In addition, Zoltowski and colleagues published in 2013 the discovery that the amino acids in Zeitlupe -- working like a dimmer switch -- gradually get more active as daytime turns to evening, thereby managing the 24-hour Circadian rhythm. Additionally, they found that FKF-1 is very different from Zeitlupe. FKF-1 switches on with morning light and measures seasonal changes, otherwise called photoperiodism. But a knowledge gap remained. It was a mystery how the information is integrated by the organism. "Ultimately that has to be related to some kind of chemical event occurring, some kind of chemical timekeeper," Zoltowski said. "So by following that trail we figured out how the chemistry works." The problem required a two-pronged approach: Solving the structure of the protein to understand how forming and breaking bonds changes how the organism perceives its environment; and solving the chemistry, specifically the crystal structures of the protein's dark and light states. That process yielded a snapshot of the protein in the dark state and a snapshot of the protein in the light state, so the researchers could watch changes in protein structure in response to the bond-forming event. From there, the researchers made mathematical models 1) that explain how the chemistry of the bond breaking and bond forming event, and the rate at which it occurs, should affect the organism; and 2) that design mutations to the protein that affect how it goes from the dark state to the light state to block that process. The team used a few standard techniques. To get at the chemistry, they deployed ultra-violet visible spectroscopy to measure how efficiently proteins absorb light. They followed differences in the absorption spectrum, seeing what wavelengths are absorbed, to track chemical changes between the dark and the light states. On the structure side, they crystallized the proteins and collected data at synchrotron sources at Cornell University, then mapped out like a puzzle where all the electrons are located in the crystal. From there they could fit and build -- amino acid by amino acid -- the protein, yielding a three-dimensional image of where every atom in the protein is located. "This gives us pictures and snapshots of all those discrete events, where then we can look at how the atoms are moving and changing from one to the other," Zoltowski said. "That allows us to see the bonds forming, the bonds breaking, and how the rest of the protein changes in response to that." Why didn't we think of that? The question has been an important one in the field, but challenging technical hurdles thwarted solutions, said Zoltowski. The key for his team was persistence and years of experience. "This is not an easy protein to work with -- it's difficult to get crystals of these proteins. It requires a protein that is stable enough and will interact in a way that it yields a perfectly ordered crystal. So it's difficult to do the chemistry and the structures. Researchers have struggled with getting adequate amounts of protein to be able to do these types of characterizations," he said. Think of it like a diamond, Zoltowski said, which is a perfectly ordered crystal that is just carbon atoms arranged in a specific way. "Zeitlupe and FKF-1 have thousands of atoms in each protein, and in order to get a crystal, each molecule of the protein needs to arrange itself with the same type of accuracy and precision as carbon atoms in a diamond. Getting that to occur, where they pack nicely together, is non trivial. And some proteins just are really challenging to work with." Zoltowski and his colleagues have been fortunate in having years of experience working with these families of proteins, called the Light-oxygen-voltage-sensing domains, or LOV domains, for short. "So we've developed a lot of skills and techniques over the years that can get over some of the technical hurdles," he said. "So just from gaining experience over time, we've gotten better with working with some very difficult proteins. It makes something that is challenging, much more tractable for our lab." Does this apply to all LOV proteins in every plant? Zeitlupe is a German word that means slow motion. The protein was dubbed Zeitlupe because scientists discovered when they found mutations of this protein previously that it made the Circadian clock run slower. It naturally altered the way the organism perceived time. "We wanted to understand the proteins well enough that we could selectively alter the chemistry, or selectively alter the structure, to create mutations that would be testable in the organism," Zoltowski said. "We wanted a predictive model that would tell us that these mutations that affect the kinetics -- the rate at which this bond breaks -- should do 'X' in the organism." The team's new discovery results in hybrid plants -- something nature already does and has done for millions of years through the process of evolution so that plants adapt to survive. "We're not putting anything into the plant or changing its genetics," Zoltowski said. "We're making a very subtle, targeted mutation to a specific protein that already is a native plant protein -- and one that we've shown in this paper has evolved considerably throughout various different agricultural crops to already do this." The discovery gives scientists the ability to rationally interpret environmental information affecting a plant in order to introduce mutations, instead of relying on selective breeding to achieve a targeted mutation to generate phenotypes that potentially allow the plant to grow in a different environment. The research opens a lot of new doors, including new questions about how these proteins are changing their configuration and how other variables, like oxidative stress, couple with the plant's global sensory networks to also alter proteins and send multiple signals from the environment. "What we've learned is that you need to pay careful attention to specific parts of the protein because they're modulating activity selectively in different categories of this family," Zoltowski said. "If we look at the whole family of these proteins, there are key amino acids that are evolutionarily selected, so they evolve specific modulations of this activity for their own independent niche in the environment. One of the take-homes is there are areas in the protein we need to look at to see how the amino acids are now different." Besides the NIH grant, the lab operates with $250,000 from the American Chemical Society's Herman Frasch Foundation for Chemical Research Grants in Agricultural Chemistry.


News Article | November 4, 2016
Site: www.eurekalert.org

In research published in The Plant Journal, a group of scientists led by researchers from the RIKEN Center for Sustainable Resource Science in Japan have decoded the genome of Glycyrrhiza uralensis, or Chinese licorice, a plant that is important for its use in Chinese medicine and as a natural sweetener. Chinese licorice, which is closely related to the plant--Glycyrrhiza glabra--used for licorice candy, is an important component of Chinese traditional medicine. According to Kazuki Saito of CSRS, who led the team, "It is incorporated in approximately 70 percent of the 200 major formulations used in traditional Kampo medicine in Japan. Considering that 90 percent of Japanese physicians prescribe Kampo medicine in their practices, it is easy to see the importance of this plant." The team chose to examine the genome of Chinese licorice rather than other related species partly because it is known to contain the highest concentration of glycyrrhizin, a compound that is associated with the medical properties of the plant, which include anti-inflammatory, anti-cancer, anti-allergic, and anti-viral activities. To conduct the screening, they chose a strain of G. uralensis kept at the Takeda Garden for Medicinal Plant Conservation in Kyoto. Using a combination of long read and short read sequencing, and by comparing the genome to published sequences of other legume species, they predicted that the plant's genome coded just over 34,000 proteins, a number somewhat higher than the 20,000 in the human genome. They focused in particular on two genetic regions--one coding saponins, which are important plant compounds including glycyrrhizin, and the other producing isoflavonoids, which are also known as medicinal components. Through the research, the group demonstrated that there is a close conservation of genes between licorice and other related plants such as barrelclover (s species close to alfalfa) and chickpea, showing that legumes use a small number of genes to create "scaffolds" that allow for the production of an enormous diversity of compounds. Keiichi Mochida, the first author of the paper, says, "Chinese licorice is an important and heavily consumed medicinal plant, and we hope that our work will make it possible to carry out molecular breeding to create strains that will grow sustainably in Japan, and which produce large concentrations of useful compounds such as glycyrrhizin." According to Saito, "We very much hope that our draft genome sequence will facilitate the identification, isolation, and editing of useful genes to improve the agronomic and medicinal traits of licorice through molecular breeding. There remains much to learn about the immense diversity of plant metabolism, and this research will contribute to further progress in that direction." The group plans to do further work to examines differences between the genome of G. uralensis and other licorice species, to further deepen their understanding of the production of useful compounds. The work was carried out by RIKEN CSRS in collaboration with a group including Chiba University, Kochi University, and Osaka University.


News Article | November 4, 2016
Site: www.sciencedaily.com

In research published in The Plant Journal, a group of scientists led by researchers from the RIKEN Center for Sustainable Resource Science in Japan have decoded the genome of Glycyrrhiza uralensis, or Chinese licorice, a plant that is important for its use in Chinese medicine and as a natural sweetener. Chinese licorice, which is closely related to the plant -- Glycyrrhiza glabra -- used for licorice candy, is an important component of Chinese traditional medicine. According to Kazuki Saito of CSRS, who led the team, "It is incorporated in approximately 70 percent of the 200 major formulations used in traditional Kampo medicine in Japan. Considering that 90 percent of Japanese physicians prescribe Kampo medicine in their practices, it is easy to see the importance of this plant." The team chose to examine the genome of Chinese licorice rather than other related species partly because it is known to contain the highest concentration of glycyrrhizin, a compound that is associated with the medical properties of the plant, which include anti-inflammatory, anti-cancer, anti-allergic, and anti-viral activities. To conduct the screening, they chose a strain of G. uralensis kept at the Takeda Garden for Medicinal Plant Conservation in Kyoto. Using a combination of long read and short read sequencing, and by comparing the genome to published sequences of other legume species, they predicted that the plant's genome coded just over 34,000 proteins, a number somewhat higher than the 20,000 in the human genome. They focused in particular on two genetic regions -- one coding saponins, which are important plant compounds including glycyrrhizin, and the other producing isoflavonoids, which are also known as medicinal components. Through the research, the group demonstrated that there is a close conservation of genes between licorice and other related plants such as barrelclover (s species close to alfalfa) and chickpea, showing that legumes use a small number of genes to create "scaffolds" that allow for the production of an enormous diversity of compounds. Keiichi Mochida, the first author of the paper, says, "Chinese licorice is an important and heavily consumed medicinal plant, and we hope that our work will make it possible to carry out molecular breeding to create strains that will grow sustainably in Japan, and which produce large concentrations of useful compounds such as glycyrrhizin." According to Saito, "We very much hope that our draft genome sequence will facilitate the identification, isolation, and editing of useful genes to improve the agronomic and medicinal traits of licorice through molecular breeding. There remains much to learn about the immense diversity of plant metabolism, and this research will contribute to further progress in that direction." The group plans to do further work to examines differences between the genome of G. uralensis and other licorice species, to further deepen their understanding of the production of useful compounds. The work was carried out by RIKEN CSRS in collaboration with a group including Chiba University, Kochi University, and Osaka University.


PubMed | University of Michigan, Max Planck Institute for Evolutionary Anthropology, Tokyo Electron, Azabu University and 6 more.
Type: Journal Article | Journal: Cell | Year: 2015

Intestinal Th17 cells are induced and accumulate in response to colonization with a subgroup of intestinal microbes such as segmented filamentous bacteria (SFB) and certain extracellular pathogens. Here, we show that adhesion of microbes to intestinal epithelial cells (ECs) is a critical cue for Th17 induction. Upon monocolonization of germ-free mice or rats with SFB indigenous to mice (M-SFB) or rats (R-SFB), M-SFB and R-SFB showed host-specific adhesion to small intestinal ECs, accompanied by host-specific induction of Th17 cells. Citrobacter rodentium and Escherichia coli O157 triggered similar Th17 responses, whereas adhesion-defective mutants of these microbes failed to do so. Moreover, a mixture of 20 bacterial strains, which were selected and isolated from fecal samples of a patient with ulcerative colitis on the basis of their ability to cause a robust induction of Th17 cells in the mouse colon, also exhibited EC-adhesive characteristics.


Atarashi K.,RIKEN | Atarashi K.,Keio University | Tanoue T.,RIKEN | Ando M.,Yakult Central Institute | And 34 more authors.
Cell | Year: 2015

Intestinal Th17 cells are induced and accumulate in response to colonization with a subgroup of intestinal microbes such as segmented filamentous bacteria (SFB) and certain extracellular pathogens. Here, we show that adhesion of microbes to intestinal epithelial cells (ECs) is a critical cue for Th17 induction. Upon monocolonization of germ-free mice or rats with SFB indigenous to mice (M-SFB) or rats (R-SFB), M-SFB and R-SFB showed host-specific adhesion to small intestinal ECs, accompanied by host-specific induction of Th17 cells. Citrobacter rodentium and Escherichia coli O157 triggered similar Th17 responses, whereas adhesion-defective mutants of these microbes failed to do so. Moreover, a mixture of 20 bacterial strains, which were selected and isolated from fecal samples of a patient with ulcerative colitis on the basis of their ability to cause a robust induction of Th17 cells in the mouse colon, also exhibited EC-adhesive characteristics. © 2015 Elsevier Inc.


PubMed | Kobe University, Niigata University, Center for Sustainable Resource Science, Watanabe Seed Co. and 2 more.
Type: | Journal: BMC plant biology | Year: 2016

Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior performance compared to their parental inbred lines. Most commercial Chinese cabbage cultivars are F1 hybrids and their level of hybrid vigour is of critical importance and is a key selection criterion in the breeding system.We have characterized the heterotic phenotype of one F1 hybrid cultivar of Chinese cabbage and its parental lines from early- to late-developmental stages of the plants. Hybrid cotyledons are larger than those of the parents at 4 days after sowing and biomass in the hybrid, determined by the fresh weight of leaves, is greater than that of the larger parent line by approximately 20% at 14 days after sowing. The final yield of the hybrid harvested at 63 days after sowing is 25% greater than the yield of the better parent. The larger leaves of the hybrid are a consequence of increased cell size and number of the photosynthetic palisade mesophyll cells and other leaf cells. The accumulation of plant hormones in the F1 was within the range of the parental levels at both 2 and 10 days after sowing. Two days after sowing, the expression levels of chloroplast-targeted genes in the cotyledon cells were upregulated in the F1 hybrid relative to their mid parent values. Shutdown of chlorophyll biosynthesis in the cotyledon by norflurazon prevented the increased leaf area in the F1 hybrid.In the cotyledons of F1 hybrids, chloroplast-targeted genes were upregulated at 2 days after sowing. The increased activity levels of this group of genes suggested that their differential transcription levels could be important for establishing early heterosis but the increased transcription levels were transient. Inhibition of the photosynthetic process in the cotyledon reduced heterosis in later seedling stages. These observations suggest early developmental events in the germinating seedling of the hybrid may be important for later developmental vigour and yield advantage.


PubMed | Kanto Gakuin University, Yokohama City University, Center for Sustainable Resource science and University of Tokyo
Type: Journal Article | Journal: PloS one | Year: 2017

Profiling elemental contents in wheat grains and clarifying the underlying genetic systems are important for the breeding of biofortified crops. Our objective was to evaluate the genetic potential of 269 Afghan wheat landraces for increasing elemental contents in wheat cultivars. The contents of three major (Mg, K, and P) and three minor (Mn, Fe, and Zn) elements in wheat grains were measured by energy dispersive X-ray fluorescence spectrometry. Large variations in elemental contents were observed among landraces. Marker-based heritability estimates were low to moderate, suggesting that the elemental contents are complex quantitative traits. Genetic correlations between two locations (Japan and Afghanistan) and among the six elements were estimated using a multi-response Bayesian linear mixed model. Low-to-moderate genetic correlations were observed among major elements and among minor elements respectively, but not between major and minor elements. A single-response genome-wide association study detected only one significant marker, which was associated with Zn, suggesting it will be difficult to increase the elemental contents of wheat by conventional marker-assisted selection. Genomic predictions for major elemental contents were moderately or highly accurate, whereas those for minor elements were mostly low or moderate. Our results indicate genomic selection may be useful for the genetic improvement of elemental contents in wheat.


News Article | December 16, 2015
Site: phys.org

Researchers at the RIKEN Center for Sustainable Resource Science and the University of Tokyo have demonstrated that the bacterium Acidithiobacillus ferrooxidans can take electrons needed for growth directly from an electrode power source when iron—its already known source of energy—is absent. The study, published in Frontiers in Microbiology, shows that A. ferrooxidans can use direct uptake of electrons from an electrode to fuel the same metabolic pathway that is activated by the oxidation of diffusible iron ions. Just as plants with chlorophyll use photosynthesis to convert energy from light into sugars needed for growth, other organisms—like animals—gain energy for the manufacture of sugars by taking electrons from substances in their surrounding environments—a process called chemosynthesis. Organisms that gain their energy this way are called chemotrophs, and those that get their electrons through oxidation of inorganic substances are called chemolithoautotrophs. Phototrophs and chemotrophs make up two interconnected ecosystems. "We are investigating the possibility of a third type of ecosystem," explains group leader Ryuhei Nakamura. "We call it the electro-ecosystem because microbial activity is sustained primarily by direct electrical current." Recently, his team has discovered geo-electric currents across the walls of black-smoker chimneys formed by hydrothermanl vents, suggesting that some deep-sea microbes might double as a electrolithoautotrophs, organisms that can use electrical potential—meaning that they simply eat electrons—as an energy source instead of light or surrounding inorganic substances. Because access to microbes in this environment is not easy, and to verify their hypothesis that being able to switch energy sources from inorganic substances to electricity is not unique in the microbial world, the team experimented with A. ferrooxidans, a chemolithoautotrophic bacterium known to oxidize iron ions (Fe2+). The team cultured A. ferrooxidans in an Fe2+-free environment and supplied an electrode with an electrical potential of +0.4 V, carbon-dioxide as a carbon source, and oxygen as an electron acceptor. They found that these conditions created a current that originated from the electrode, and that the strength of the current depended on how many cells were attached to the electrode. Killing the cells with UV light immediately suppressed the current. To determine how this current was being generated, they used an artificial photochemical reaction. Normally, carbon monoxide attaches to heme proteins in A. ferrooxidans outer membranes and prevents oxidation. But, when exposed to light, this bond is broken and oxidation continues as usual. When tested, carbon-monoxide also prevented the current formed between the electrode and A. ferrooxidans cells and exposure to light reversed this block and allowed the current to flow. This suggested that a heme protein is needed for the electrosynthesis exhibited by A. ferrooxidans. Further analysis showed that the responsible heme protein is the aa3 complex which is known to play a role in down-hill electron transfer in A. ferrooxidans that generates ATP and the proton-motive-force that allows uphill electron transfer and carbon fixation—the hallmarks of sugar production. Inhibition of a protein complex that is part of the uphill-transfer process suppressed the current, showing that the proton-motive-forces being generated were indeed used for up-hill electron transport. Additionally, the optical density of cells cultured with the electrode for eight days increased over time, indicating growth and that the current generated by electrons flowing from the electrode to the cells was being used for carbon fixation. "Now that we have identified the metabolic pathway for electrolithoautotrophs in A. ferrooxidans, we will be able to apply this knowledge to bacteria we find in the deep sea vent," says Nakamura. "The next step is to prove the existence of electro-ecosystems in on-site deep-sea experiments." Understanding electro-ecosystems and how electrical currents can support life could lead to a blueprint for sustainable human ecosystems, using technology such as fuel cells, batteries, and thermoelectric converters." Explore further: Scientists trick iron-eating bacteria into breathing electrons instead More information: Takumi Ishii et al. From chemolithoautotrophs to electrolithoautotrophs: CO2 fixation by Fe(II)-oxidizing bacteria coupled with direct uptake of electrons from solid electron sources, Frontiers in Microbiology (2015). DOI: 10.3389/fmicb.2015.00994

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