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  • richardmitnick 12:05 pm on July 28, 2014 Permalink | Reply
    Tags: , , Bioenergy, , , Joint BioEnergy Institute,   

    From Berkeley Lab: “How Sweet It Is: New Tool for Characterizing Plant Sugar Transporters Developed at Joint BioEnergy Institute” 


    Berkeley Lab

    July 28, 2014
    Lynn Yarris

    A powerful new tool that can help advance the genetic engineering of “fuel” crops for clean, green and renewable bioenergy, has been developed by researchers with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI), a multi-institutional partnership led by Lawrence Berkeley National Laboratory (Berkeley Lab). The JBEI researchers have developed an assay that enables scientists to identify and characterize the function of nucleotide sugar transporters, critical components in the biosynthesis of plant cell walls.

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    The Joint BioEnergy Institute (JBEI) is one of three Bioenergy Research Centers established by DOE’s Office of Science to accelerate the development of advanced, next-generation biofuels. (Photo by Roy Kaltschmidt)

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    A family of six nucleotide sugar transporters never before described have been characterized in Arabidopsis, a model plant for research in advanced biofuels. (Photo by Roy Kaltschmidt)

    “Our unique assay enabled us to analyze nucleotide sugar transporter activities in Arabidopsis and characterize a family of six nucleotide sugar transporters that has never before been described,” says Henrik Scheller, the leader of JBEI’s Feedstocks Division and a leading authority on cell wall biosynthesis. “Our method should enable rapid progress to be made in determining the functional role of nucleotide sugar transporters in plants and other organisms, which is very important for the metabolic engineering of cell walls.”

    Scheller is the corresponding author, along with Ariel Orellana at the Universidad Andrés Bello, Santiago, Chile, of a paper describing this research in the Proceedings of the National Academy of Sciences (PNAS). The paper is titled The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis. The lead authors are Carsten Rautengarten and Berit Ebert, both of whom hold appointments with JBEI, and both of whom, like Scheller, also hold appointments with Berkeley Lab’s Physical Biosciences Division. (See below for the full list of co-authors.)

    The sugars in plant biomass represent an enormous potential source of environmentally benign energy if they can be converted into transportation fuels – gasoline, diesel and jet fuel – in a manner that is economically competitive with petroleum-based fuels. One of the keys to success in this effort will be to engineer fuel crops whose cells walls have been optimized for sugar content.

    With the exception of cellulose and callose, the complex polysaccharide sugars in plant cell walls are synthesized in the Golgi apparatus by enzymes called glycosyltransferases. These polysaccharides are assembled from substrates of simple nucleotide sugars which are transported into the Golgi apparatus from the cytosol, the gel-like liquid that fills a plant cell’s cytoplasm. Despite their importance, few plant nucleotide sugar transporters have been functionally characterized at the molecular level. A big part of the holdup has been a lack of substrates that are necessary to carry out such characterizations.

    “Substrates of mammalian nucleotide sugar transporters are commercially available because of the medical interest but have not been available for plants, which made it difficult to study both nucleotide sugar transporters and glycosyltransferases,” Scheller says.

    For their assay, Scheller, Rautengarten, Ebert and their collaborators, created several artificial substrates for nucleotide sugar transporters, then reconstituted the transporters into liposomes for analysis with mass spectrometry. The researchers used this technique to characterize the functions of the six new nucleotide sugar transporters they identified in Arabidopsis, a relative of mustard that serves as a model plant for research in advanced biofuels.

    “We found that these six new nucleotide sugar transporters are bispecific, which is a surprise since the two substrates are not very similar from a physical standpoint to the human eye,” Scheller says. “We also found that limiting substrate availability has different effects on different polysaccharide products, which suggests that cell wall polysaccharide biosynthesis in the Golgi apparatus of plants is also regulated by substrate transport mechanisms.”

    In addition to these six nucleotide sugar transporters, the assay was used to characterize the functions of 20 other transporters, the details of which will soon be published.

    “Thanks largely to the efforts these past two years of Carsten Rautengarten and Berit Ebert, we now know the activity of three times more nucleotide sugar transporters than are known in humans, and we have determined the function of two-thirds of the plant transporters as compared to one-quarter of the human ones,” Scheller says. “This is a tremendous accomplishment and we are already using this information at JBEI to improve biomass sugar composition for biofuel production.”

    Other co-authors of the PNAS paper reporting this research were Ignacio Moreno, Henry Temple, Thomas Herter, Bruce Link, Daniela Doñas-Cofré, Adrián Moreno, Susana Saéz-Aguayo, Francisca Blanco, Jennifer Mortimer, Alex Schultink, Wolf-Dieter Reiter, Paul Dupre, Markus Pauly and Joshua Heazlewood.

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    (From left) Berit Ebert, Carsten Rautengarten and Henrik Scheller at JBEI have developed an assay for characterizing the functions of nucleotide sugar transporters in plant cell walls. (Photo by Irina Silva, JBEI)

    This research was supported by the DOE Office of Science.

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 10:19 pm on December 22, 2011 Permalink | Reply
    Tags: , , , Joint BioEnergy Institute,   

    From Berkeley Labs: “CAD for RNA” 


    Berkeley Lab

    Joint BioEnergy Institute Researchers Develop CAD-Type Tools for Engineering RNA Control Systems

    Lynn Yarris
    DECEMBER 22, 2011

    “The computer assisted design (CAD) tools that made it possible to fabricate integrated circuits with millions of transistors may soon be coming to the biological sciences. Researchers at the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) have developed CAD-type models and simulations for RNA molecules that make it possible to engineer biological components or “RNA devices” for controlling genetic expression in microbes. This holds enormous potential for microbial-based sustainable production of advanced biofuels, biodegradable plastics, therapeutic drugs and a host of other goods now derived from petrochemicals.

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    JBEI researchers have developed CAD-type tools for engineering RNA components that hold enormous potential for microbial-based production of advanced biofuels and other goods now derived from petrochemicals. (Image by Zosia Rostomian, Berkeley Lab)

    ‘Because biological systems exhibit functional complexity at multiple scales, a big question has been whether effective design tools can be created to increase the sizes and complexities of the microbial systems we engineer to meet specific needs,’ says Jay Keasling, director of JBEI and a world authority on synthetic biology and metabolic engineering. ‘Our work establishes a foundation for developing CAD platforms to engineer complex RNA-based control systems that can process cellular information and program the expression of very large numbers of genes. Perhaps even more importantly, we have provided a framework for studying RNA functions and demonstrated the potential of using biochemical and biophysical modeling to develop rigorous design-driven engineering strategies for biology.’

    Keasling, who also holds appointments with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkley, is the corresponding author of a paper in the journal Science that describes this work. The paper is titled Model-driven engineering of RNA devices to quantitatively-program gene expression. Other co-authors are James Carothers, Jonathan Goler and Darmawi Juminaga.”

    See the full article here.

    A US Department of Energy National Laboratory Operated by the University of California

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