Implementing industrial-academic partnerships to advance bioenergy research: the Energy Biosciences Institute.

The Energy Bioscience Institute (EBI) is an example of an ambitious academic-industry collaboration. We present a summary of how the EBI was organized during the first eight years and examples of several major research thrusts within the Institute to develop renewable biodiesel, jet fuel and lubricants from carbohydrates. In particular, we describe how the multidisciplinary nature and management structure of the organization led to hybrid approaches in which bioconversions and chemical synthesis were combined to develop new products.

Development of feedstocks for cellulosic biofuels.

The inclusion of cellulosic ethanol in the Energy Independence and Security Act (EISA) of 2007 and the revised Renewable Fuel Standard (RFS2) has spurred development of the first commercial scale cellulosic ethanol biorefineries. These efforts have also revived interest in the development of dedicated energy crops selected for biomass productivity and for properties that facilitate conversion of biomass to liquid fuels. While many aspects of developing these feedstocks are compatible with current agricultural activities, improving biomass productivity may provide opportunities to expand the potential for biofuel production beyond the classical research objectives associated with improving traditional food and feed crops.

Feedstocks for lignocellulosic biofuels.

In 2008, the world produced approximately 87 gigaliters of liquid biofuels, which is roughly equal to the volume of liquid fuel consumed by Germany that year. Essentially, all of this biofuel was produced from crops developed for food production, raising concerns about the net energy and greenhouse gas effects and potential competition between use of land for production of fuels, food, animal feed, fiber, and ecosystem services. The pending implementation of improved technologies to more effectively convert the nonedible parts of plants (lignocellulose) to liquid fuels opens diverse options to use biofuel feedstocks that reach beyond current crops and the land currently used for food and feed. However, there has been relatively little discussion of what types of plants may be useful as bioenergy crops.

High-resolution crystal structure of manganese peroxidase: substrate and inhibitor complexes.

Manganese peroxidase (MnP) is an extracellular heme enzyme that catalyzes the peroxide-dependent oxidation of Mn(II) to Mn(III). The Mn(III) is released from the enzyme in complex with oxalate. One heme propionate and the side chains of Glu35, Glu39, and Asp179 were identified as Mn(II) ligands in the 2.0 A resolution crystal structure. The new 1.45 A crystal structure of MnP complexed with Mn(II) provides a more accurate view of the Mn-binding site. New features include possible partial protonation of Glu39 in the Mn-binding site and glycosylation at Ser336. This is also the first report of MnP-inhibitor complex structures. At the Mn-binding site, divalent Cd(II) exhibits octahedral, hexacoordinate ligation geometry similar to that of Mn(II). Cd(II) also binds to a putative second weak metal-binding site with tetrahedral geometry at the C-terminus of the protein. Unlike that for Mn(II) and Cd(II), coordination of trivalent Sm(III) at the Mn-binding site is octacoordinate. Sm(III) was removed from a MnP-Sm(III) crystal by soaking the crystal in oxalate and then reintroduced into the binding site. Thus, direct comparisons of Sm(III)-bound and metal-free structures were made using the same crystal. No ternary complex was observed upon incubation with oxalate. The reversible binding of Sm(III) may be a useful model for the reversible binding of Mn(III) to the enzyme, which is too unstable to allow similar examination.

Toward a systems approach to understanding plant cell walls.

One of the defining features of plants is a body plan based on the physical properties of cell walls. Structural analyses of the polysaccharide components, combined with high-resolution imaging, have provided the basis for much of the current understanding of cell walls. The application of genetic methods has begun to provide new insights into how walls are made, how they are controlled, and how they function. However, progress in integrating biophysical, developmental, and genetic information into a useful model will require a system-based approach.

The PEN1 syntaxin defines a novel cellular compartment upon fungal attack and is required for the timely assembly of papillae.

Attack by the host powdery mildew Erysiphe cichoracearum usually results in successful penetration and rapid proliferation of the fungus on Arabidopsis. By contrast, the nonhost barley powdery mildew Blumeria graminis f. sp. hordei (Bgh) typically fails to penetrate Arabidopsis epidermal cells. In both instances the plant secretes cell wall appositions or papillae beneath the penetration peg of the fungus. Genetic screens for mutations that result in increased penetration of Bgh on Arabidopsis have recently identified the PEN1 syntaxin. Here we examine the role of PEN1 and of its closest homologue, SYP122, identified as a syntaxin whose expression is responsive to infection. pen1 syp122 double mutants are both dwarfed and necrotic, suggesting that the two syntaxins have overlapping functions. Although syp122-1 and the cell wall mur mutants have considerably more pronounced primary cell wall defects than pen1 mutants, these have relatively subtle or no effects on penetration resistance. Upon fungal attack, PEN1 appears to be actively recruited to papillae, and there is a 2-h delay in papillae formation in the pen1-1 mutant. We conclude that SYP122 may have a general function in secretion, including a role in cell wall deposition. By contrast, PEN1 appears to have a basal function in secretion and a specialized defense-related function, being required for the polarized secretion events that give rise to papilla formation.