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Kim I.J.,Korea University | Ko H.-J.,Korea University | Kim T.-W.,Energy Biosciences Institute | Choi I.-G.,Korea University | Kim K.H.,Korea University
Biotechnology and Bioengineering | Year: 2013

Plant expansin proteins induce plant cell wall extension and have the ability to extend and disrupt cellulose. In addition, these proteins show synergistic activity with cellulases during cellulose hydrolysis. BsEXLX1 originating from Bacillus subtilis is a structural homolog of a β-expansin produced by Zea mays (ZmEXPB1). The Langmuir isotherm for binding of BsEXLX1 to microcrystalline cellulose (i.e., Avicel) revealed that the equilibrium binding constant of BsEXLX1 to Avicel was similar to those of other Type A surface-binding carbohydrate-binding modules (CBMs) to microcrystalline cellulose, and the maximum number of binding sites on Avicel for BsEXLX1 was also comparable to those on microcrystalline cellulose for other Type A CBMs. BsEXLX1 did not bind to cellooligosaccharides, which is consistent with the typical binding behavior of Type A CBMs. The preferential binding pattern of a plant expansin, ZmEXPB1, to xylan, compared to cellulose was not exhibited by BsEXLX1. In addition, the binding capacities of cellulose and xylan for BsEXLX1 were much lower than those for CtCBD3. © 2012 Wiley Periodicals, Inc. Source


Kim I.J.,Korea University | Ko H.-J.,Korea University | Kim T.-W.,Energy Biosciences Institute | Nam K.H.,Cornell University | And 2 more authors.
Applied Microbiology and Biotechnology | Year: 2013

BsEXLX1 from Bacillus subtilis is the first discovered bacterial expansin as a structural homolog of a plant expansin, and it exhibited synergism with cellulase on the cellulose hydrolysis in a previous study. In this study, binding characteristics of BsEXLX1 were investigated using pretreated and untreated Miscanthus x giganteus in comparison with those of CtCBD3, a cellulose-binding domain from Clostridium thermocellum. The amounts of BsEXLX1 bound to cellulose-rich substrates were significantly lower than those of CtCBD3. However, the amounts of BsEXLX1 bound to lignin-rich substrates were much higher than those of CtCBD3. A binding competition assay between BsEXLX1 and CtCBD3 revealed that binding of BsEXLX1 to alkali lignin was not affected by the presence of CtCBD3. This preferential binding of BsEXLX1 to lignin could be related to root colonization in plants by bacteria, and the bacterial expansin could be used as a lignin blocker in the enzymatic hydrolysis of lignocellulose. © 2012 Springer-Verlag Berlin Heidelberg. Source


News Article
Site: http://phys.org/biology-news/

"We evaluated germination and plant growth for prairie cordgrass accessions and switchgrass cultivars in a greenhouse study," says crop scientist D.K. Lee. In crop production, too much salt in the soil can interfere with the plant's ability to absorb water. Water moves into plant roots by osmosis, and when solutes inside root cells are more concentrated than in soil, water moves into the root. In salt-affected soil, the difference in solute concentration inside and outside of the root is not as great, meaning that water may not move in. So, even where soil is moist, plants experience drought-like conditions when too much salt is present. Certain mineral salts are also toxic to plants. When they are taken up along with soil water, plant tissue damage can occur. "Saline soils are characterized by high concentrations of soluble salts, such as sodium, chloride, calcium chloride, or magnesium sulfate, whereas sodic soils are solely characterized by their high sodium concentrations," Lee explains. "Many soils are both saline and sodic." The researchers subjected six prairie cordgrass accessions and three switchgrass cultivars to different levels of sodicity and salinity over two years of growth. The team conducted a similar experiment in an earlier study, but only looked at one cordgrass ('Red River') and one switchgrass ('Cave-In-Rock') cultivar, over only one growing season. "In that study, we found that 'Cave-In-Rock' switchgrass was not good at all in terms of salt tolerance. 'Red River' cordgrass was far superior," Lee recalls. The expanded study showed that prairie cordgrass had, on average, much higher germination rates than switchgrass in saline and sodic conditions. Dry biomass production was not as clearly split between the two species in salty conditions, however. Three prairie cordgrasses, pc17-102, pc17-109, and 'Red River', and one switchgrass, EG-1102, produced equivalent amounts of dry biomass when subjected to high-salt conditions. However, they produced approximately 70 to 80 percent less biomass in salty conditions than they did with no added salt. In contrast, the salt-susceptible switchgrass cultivar, EG-2012, produced approximately 99.5 percent less biomass in high-salt treatments than it did without added salt. The next step for the researchers is to bring this work out of the greenhouse, where climate is controlled and water is unlimited, to real-world scenarios. Preliminary field research has shown that prairie cordgrass is very successful in salt-affected areas in Illinois and South Dakota. "Even in highly saline soils, prairie cordgrass can do very well. Unlike switchgrass, it can take up salt dissolved in water without getting sick because it can excrete it out through specialized salt glands. Then, once the plants grow deep roots, they can access less salty water," Lee explains. More research and agronomic improvements are needed before prairie cordgrass can be recommended widely as a biomass crop, but Lee sees a lot of potential in this species. "Prairie cordgrass is an interesting species," he says. "As a warm season grass, I think it is unique in being able to handle low temperatures, and it is also well adapted to poorly drained soils and lands with frequent flooding. And even in high-salt conditions in the field, we're getting pretty good yields: up to 8 or 9 tons per acre." The article, "Determining effects of sodicity and salinity on switchgrass and prairie cordgrass germination and plant growth," is published in Industrial Crops and Products. Lee's co-authors, Eric Anderson, Tom Voigt, and Sumin Kim are also from the U of I. The project was funded by the Energy Biosciences Institute. More information: Eric K. Anderson et al. Determining effects of sodicity and salinity on switchgrass and prairie cordgrass germination and plant growth, Industrial Crops and Products (2015). DOI: 10.1016/j.indcrop.2014.11.016


Lee M.E.,University of California at Berkeley | Lee M.E.,Energy Biosciences Institute | Aswani A.,University of California at Berkeley | Han A.S.,University of California at Berkeley | And 3 more authors.
Nucleic Acids Research | Year: 2013

Engineered metabolic pathways often suffer from flux imbalances that can overburden the cell and accumulate intermediate metabolites, resulting in reduced product titers. One way to alleviate such imbalances is to adjust the expression levels of the constituent enzymes using a combinatorial expression library. Typically, this approach requires high-throughput assays, which are unfortunately unavailable for the vast majority of desirable target compounds. To address this, we applied regression modeling to enable expression optimization using only a small number of measurements. We characterized a set of constitutive promoters in Saccharomyces cerevisiae that spanned a wide range of expression and maintained their relative strengths irrespective of the coding sequence. We used a standardized assembly strategy to construct a combinatorial library and express for the first time in yeast the five-enzyme violacein biosynthetic pathway. We trained a regression model on a random sample comprising 3% of the total library, and then used that model to predict genotypes that would preferentially produce each of the products in this highly branched pathway. This generalizable method should prove useful in engineering new pathways for the sustainable production of small molecules. © 2013 The Author(s). Source


Crago C.L.,Energy Biosciences Institute | Khanna M.,301A Mumford Hall | Barton J.,University of British Columbia | Giuliani E.,Partners at Venture | Amaral W.,University of Sao Paulo
Energy Policy | Year: 2010

Corn ethanol produced in the US and sugarcane ethanol produced in Brazil are the world's leading sources of biofuel. Current US biofuel policies create both incentives and constraints for the import of ethanol from Brazil and together with the cost competitiveness and greenhouse gas intensity of sugarcane ethanol compared to corn ethanol will determine the extent of these imports. This study analyzes the supply-side determinants of cost competitiveness and compares the greenhouse gas intensity of corn ethanol and sugarcane ethanol delivered to US ports. We find that while the cost of sugarcane ethanol production in Brazil is lower than that of corn ethanol in the US, the inclusion of transportation costs for the former and co-product credits for the latter changes their relative competitiveness. We also find that the relative cost of ethanol in the US and Brazil is highly sensitive to the prevailing exchange rate and prices of feedstocks. At an exchange rate of US$1=R$2.15 the cost of corn ethanol is 15% lower than the delivered cost of sugarcane ethanol at a US port. Sugarcane ethanol has lower GHG emissions than corn ethanol but a price of over $113perton of CO2 is needed to affect competitiveness. © 2010 Elsevier Ltd. Source

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