Engineering thermostable fungal cellobiohydrolases

Meeting the world's growing energy demands while protecting our fragile environment is a challenging issue. Second generation biofuels are liquid fuels like long-chain alcohols produced from lignocellulosic biomass. To reduce the cost of biofuel production, we engineered fungal family 6 cellobiohydrolases (Cel6A) for enhanced thermostability using random mutagenesis and recombination of beneficial mutations. During long-time hydrolysis, engineered thermostable cellulases hydrolyze more sugars than wild-type Cel6A as single enzymes and binary mixtures at their respective optimum temperatures. Engineered thermostable cellulases exhibit synergy in binary mixtures similar to wild-type cellulases, demonstrating the utility of engineering individual cellulases to produce novel thermostable mixtures. Crystal structures of the engineered thermostable cellulases indicate that the stabilization comes from improved hydrophobic interactions and restricted loop conformations by proline substitutions. At high temperature, free cysteines contribute to irreversible thermal inactivation in engineered thermostable Cel6A and wild-type Cel6A. The mechanism of thermal inactivation in this cellulase family is consistent with disulfide bond degradation and thiol-disulfide exchange. Enhancing the thermostability of Cel6A also increases tolerance to pretreatment chemicals, demonstrated by the strong correlation between thermostability and tolerance to 1-ethyl-3-methylimidazolium acetate. Several semi-rational protein engineering approaches – on the basis of consensus sequence analysis, proline stabilization, FoldX energy calculation, and high B-factors – were evaluated to further enhance the thermostability of Cel6A.

Progress towards the total synthesis of a spermine-conjugated dynemicin analog

Progress towards the synthesis of the spermine-conjugated Dynemicin analog 4 is described. The synthetic route starts with the Michael addition of menthyl acetoacetate to trans-ethyl crotonate followed by a Dieckman condensation to form the cyclohexanedione 14 which, through a series of chemical reactions, is transformed into the quinone imine 6. Key features in the route include the Suzuki coupling reaction of the aryl boronic acid 11 and the enol triflate 12, thermal deprotection/internal amidation of the biaryl 19, cis addition of the (Z)-enediyne 33 to the quinoline 25, intramolecular acetylide addition to a carbonyl within the ketone 29, and an addition/elimination of the cyanophthalide to the quinone imine 6 to form the anthraquinone 36 utilizing the Kraus and Sugimoto methodology.

Catechol 2,3-dioxygenase-assisted cleavage of aromatics by “anaerobic” termite gut spirochetes and genomic evidence of a complete meta-pathway

The termite hindgut microbial ecosystem functions like a miniature lignocellulose-metabolizing natural bioreactor, has significant implications to nutrient cycling in the terrestrial environment, and represents an array of microbial metabolic diversity. Deciphering the intricacies of this microbial community to obtain as complete a picture as possible of how it functions as a whole, requires a combination of various traditional and cutting-edge bioinformatic, molecular, physiological, and culturing approaches. Isolates from this ecosystem, including Treponema primitia str. ZAS-1 and ZAS-2 as well as T. azotonutricium str. ZAS-9, have been significant resources for better understanding the termite system. While not all functions predicted by the genomes of these three isolates are demonstrated in vitro, these isolates do have the capacity for several metabolisms unique to spirochetes and critical to the termite system’s reliance upon lignocellulose. In this thesis, work culturing, enriching for, and isolating diverse microorganisms from the termite hindgut is discussed. Additionally, strategies of members of the termite hindgut microbial community to defend against O₂-stress and to generate acetate, the “biofuel” of the termite system, are proposed. In particular, catechol 2,3-dioxygenase and other meta-cleavage catabolic pathway genes are described in the “anaerobic” termite hindgut spirochetes T. primitia str. ZAS-1 and ZAS-2, and the first evidence for aromatic ring cleavage in the phylum (division) Spirochetes is also presented. These results suggest that the potential for O₂-dependent, yet nonrespiratory, metabolisms of plant-derived aromatics should be re-evaluated in termite hindgut communities. Potential future work is also illustrated.

The isolation and partial biochemical analysis of Sindbis virus proteins

Recently, the amino acid sequences have been reported for several proteins, including the envelope glycoproteins of Sindbis virus, which all probably span the plasma membrane with a common topology: a large N-terminal, extracellular portion, a short region buried in the bilayer, and a short C-terminal intracellular segment. The regions of these proteins buried in the bilayer correspond to portions of the protein sequences which contain a stretch of hydrophobic amino acids and which have other common characteristics, as discussed. Reasons are also described for uncertainty, in some proteins more than others, as to the precise location of some parts of the sequence relative to the membrane.

The signal hypothesis for the transmembrane translocation of proteins is briefly described and its general applicability is reviewed. There are many proteins whose translocation is accurately described by this hypothesis, but some proteins are translocated in a different manner.

The transmembraneous glycoproteins E1 and E2 of Sindbis virus, as well as the only other virion protein, the capsid protein, were purified in amounts sufficient for biochemical analysis using sensitive techniques. The amino acid composition of each protein was determined, and extensive N-terminal sequences were obtained for E1 and E2. By these techniques E1 and E2 are indistinguishable from most water soluble proteins, as they do not contain an obvious excess of hydrophobic amino acids in their N-terminal regions or in the intact molecule.

The capsid protein was found to be blocked, and so its N-terminus could not be sequenced by the usual methods. However, with the use of a special labeling technique, it was possible to incorporate tritiated acetate into the N-terminus of the protein with good specificity, which was useful in the purification of peptides from which the first amino acids in the N-terminal sequence could be identified.

Nanomole amounts of PE2, the intracellular precursor of E2, were purified by an immuno-affinity technique, and its N-terminus was analyzed. Together with other work, these results showed that PE2 is not synthesized with an N-terminal extension, and the signal sequence for translocation is probably the N-terminal amino acid sequence of the protein. This N-terminus was found to be 80-90% blocked, also by Nacetylation, and this acetylation did not affect its function as a signal sequence. The putative signal sequence was also found to contain a glycosylated asparagine residue, but the inhibition of this glycosylation did not lead to the cleavage of the sequence.

Field and Laboratory Studies of Atmospheric Organic Aerosol

This thesis is the culmination of field and laboratory studies aimed at assessing processes that affect the composition and distribution of atmospheric organic aerosol. An emphasis is placed on measurements conducted using compact and high-resolution Aerodyne Aerosol Mass Spectrometers (AMS). The first three chapters summarize results from aircraft campaigns designed to evaluate anthropogenic and biogenic impacts on marine aerosol and clouds off the coast of California. Subsequent chapters describe laboratory studies intended to evaluate gas and particle-phase mechanisms of organic aerosol oxidation.

The 2013 Nucleation in California Experiment (NiCE) was a campaign designed to study environments impacted by nucleated and/or freshly formed aerosol particles. Terrestrial biogenic aerosol with > 85% organic mass was observed to reside in the free troposphere above marine stratocumulus. This biogenic organic aerosol (BOA) originated from the Northwestern United States and was transported to the marine atmosphere during periodic cloud-clearing events. Spectra recorded by a cloud condensation nuclei counter demonstrated that BOA is CCN active. BOA enhancements at latitudes north of San Francisco, CA coincided with enhanced cloud water concentrations of organic species such as acetate and formate.

Airborne measurements conducted during the 2011 Eastern Pacific Emitted Aerosol Cloud Experiment (E-PEACE) were aimed at evaluating the contribution of ship emissions to the properties of marine aerosol and clouds off the coast of central California. In one study, analysis of organic aerosol mass spectra during periods of enhanced shipping activity yielded unique tracers indicative of cloud-processed ship emissions (m/z 42 and 99). The variation of their organic fraction (f₄₂ and f₉₉) was found to coincide with periods of heavy (f₄₂ > 0.15; f₉₉ > 0.04), moderate (0.05 < f₄₂ < 0.15; 0.01 < f₉₉ < 0.04), and negligible (f₄₂ < 0.05; f₉₉ < 0.01) ship influence. Application of these conditions to all measurements conducted during E-PEACE demonstrated that a large fraction of cloud droplet (72%) and dry aerosol mass (12%) sampled in the California coastal study region was heavily or moderately influenced by ship emissions. Another study investigated the chemical and physical evolution of a controlled organic plume emitted from the R/V Point Sur. Under sunny conditions, nucleated particles composed of oxidized organic compounds contributed nearly an order of magnitude more cloud condensation nuclei (CCN) than less oxidized particles formed under cloudy conditions. The processing time necessary for particles to become CCN active was short ( < 1 hr) compared to the time needed for particles to become hygroscopic at sub-saturated humidity ( > 4 hr).

Laboratory chamber experiments were also conducted to evaluate particle-phase processes influencing aerosol phase and composition. In one study, ammonium sulfate seed was coated with a layer of secondary organic aerosol (SOA) from toluene oxidation followed by a layer of SOA from α-pinene oxidation. The system exhibited different evaporative properties than ammonium sulfate seed initially coated with α-pinene SOA followed by a layer of toluene SOA. This behavior is consistent with a shell-and-core model and suggests limited mixing among different SOA types. Another study investigated the reactive uptake of isoprene epoxy diols (IEPOX) onto non-acidified aerosol. It was demonstrated that particle acidity has limited influence on organic aerosol formation onto ammonium sulfate seed, and that the chemical system is limited by the availability of nucleophiles such as sulfate.

Flow tube experiments were conducted to examine the role of iron in the reactive uptake and chemical oxidation of glycolaldehyde. Aerosol particles doped with iron and hydrogen peroxide were mixed with gas-phase glycolaldehyde and photochemically aged in a custom-built flow reactor. Compared to particles free of iron, iron-doped aerosols significantly enhanced the oxygen to carbon (O/C) ratio of accumulated organic mass. The primary oxidation mechanism is suggested to be a combination of Fenton and photo-Fenton reactions which enhance particle-phase OH radical concentrations.