Matching Items (25)
Description
Synechocystis sp. PCC 6803 is a readily transformable cyanobacteria used to study cyanobacterial genetics, as well as production of biofuels, polyesters, and other industrial chemicals. Free fatty acids are precursors to biofuels which are used by Synechocystis cells as a means of energy storage. By genetically modifying the cyanobacteria to expel these chemicals, costs associated with retrieving the products will be reduced; concurrently, the bacteria will be able to produce the products at a higher concentration. This is achieved by adding genes encoding components of the Escherichia coli AcrAB-TolC efflux system, part of the resistance-nodulation-division (RND) transporter family, to Synechocystis sp. PCC 6803. AcrAB-TolC is a relatively promiscuous multidrug efflux pump that is noted for expelling a wide range of substrates including dyes, organic solvents, antibiotics, and free fatty acids. Adding components of the AcrAB-TolC multidrug efflux pump to a previously created high free fatty acid producing strain, SD277, allowed cells to move more free fatty acids to the extracellular environment than did the parent strain. Some of these modifications also improved tolerance to antibiotics and a dye, rhodamine 6G. To confirm the function of this exogenous efflux pump, the genes encoding components of the AcrAB-TolC efflux pump were also added to Synechocystis sp. PCC 6803 and shown to grow on a greater concentration of various antibiotics and rhodamine 6G. Various endogenous efflux systems have been elucidated, but their usefulness in expelling products currently generated in Synechocystis is limited. Most of the elucidated pumps in the cyanobacteria are part of the ATP-binding cassette superfamily. The knowledge of the resistance-nodulation-division (RND) family transporters is limited. Two genes in Synechocystis sp. PCC 6803, slr2131 and sll0180 encoding homologs to the genes that encode acrB and acrA, respectively, were removed and the modifications resulted in changes in resistance to various antibiotics and a dye and also had an impact on free fatty acid secretion. Both of these deletions were complemented independently with the homologous E. coli gene and the resulting cyanobacteria strains had some of the inherent resistance restored to chloramphenicol and free fatty acid secretion was modified when compared to the wild-type and a high free fatty acid producing strain.
ContributorsBellefleur, Matthew Paul Allen (Author) / Curtiss, III, Roy (Thesis advisor) / Nielsen, David R (Committee member) / Wang, Xuan (Committee member) / Rittmann, Bruce E. (Committee member) / Arizona State University (Publisher)
Created2018
Description
The aims of this project are to demonstrate the design and implementation of separations modalities for 1) in situ product recovery and 2) upstream pretreatment of toxic feedstocks. Many value-added bioproducts such as alcohols (ethanol and butanol) developed for the transportation sector are known to be integral to a sustainable future. Likewise, bioproduced aromatic building blocks for sustainable manufacturing such as phenol will be equally important. The production of these compounds is often limited by product toxicity at 2- 20 g/L, whereas it may desirable to produce 20-200 g/L for economically feasible scale up. While low-cost feedstocks are desirable for economical production, they contain highly cytotoxic value-added byproducts such as furfural. It is therefore desirable to design facile detoxification methods for lignocellulose-derived feedstocks to isolate and recover furfural preceding ethanol fermentation by Escherichia coli. Correspondingly it is desirable to design efficient facile in situ recovery modalities for bioalcohols and phenolic bioproducts. Accordingly, in-situ removal modalities were designed for simultaneous acetone, butanol, and ethanol recovery. Additionally, a furfural removal modality from lignocellulosic hydrolysates was designed for upstream pretreatment. Solid-liquid adsorption was found to serve well each of the recovery modalities characterized here. More hydrophobic compounds such as butanol and furfural are readily recovered from aqueous solutions via adsorption. The primary operational drawback to adsorption is adsorbent recovery and subsequent desorption of the product. Novel magnetically separable mesoporous carbon powders (MMCPs) were characterized and found to be rapidly separable from solutions at 91% recovery by mass. Thermal desorption of value added products was found efficient for recovery of butanol and furfural. Fufural was desorbed from the MMCPs up to 57% by mass with repeated adsorption/thermal desorption cycles. Butanol was recovered from MMCPs up to an average 93% by mass via thermal desorption. As another valuable renewable fermentation product, phenol was also collected via in-situ adsorption onto Dowex Optipore L-493 resin. Phenol recovery from the resins was efficiently accomplished with tert-butyl methyl ether up to 77% after 3 washes.
ContributorsStaggs, Kyle William (Author) / Nielsen, David R (Thesis advisor) / Lin, Jerry S (Committee member) / Torres, César I (Committee member) / Lind, Mary Laura (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2017
Description
The engineering of microbial cell factories capable of synthesizing industrially relevant chemical building blocks is an attractive alternative to conventional petrochemical-based production methods. This work focuses on the novel and enhanced biosynthesis of phenol, catechol, and muconic acid (MA). Although the complete biosynthesis from glucose has been previously demonstrated for all three compounds, established production routes suffer from notable inherent limitations. Here, multiple pathways to the same three products were engineered, each incorporating unique enzyme chemistries and/or stemming from different endogenous precursors. In the case of phenol, two novel pathways were constructed and comparatively evaluated, with titers reaching as high as 377 ± 14 mg/L at a glucose yield of 35.7 ± 0.8 mg/g. In the case of catechol, three novel pathways were engineered with titers reaching 100 ± 2 mg/L. Finally, in the case of MA, four novel pathways were engineered with maximal titers reaching 819 ± 44 mg/L at a glucose yield of 40.9 ± 2.2 mg/g. Furthermore, the unique flexibility with respect to engineering multiple pathways to the same product arises in part because these compounds are common intermediates in aromatic degradation pathways. Expanding on the novel pathway engineering efforts, a synthetic ‘metabolic funnel’ was subsequently constructed for phenol and MA, wherein multiple pathways were expressed in parallel to maximize carbon flux toward the final product. Using this novel ‘funneling’ strategy, maximal phenol and MA titers exceeding 0.5 and 3 g/L, respectively, were achieved, representing the highest achievable production metrics products reported to date.
ContributorsThompson, Brian (Author) / Nielsen, David R (Thesis advisor) / Nannenga, Brent (Committee member) / Green, Matthew (Committee member) / Wang, Xuan (Committee member) / Moon, Tae Seok (Committee member) / Arizona State University (Publisher)
Created2017
Description
The project aims at utilization of hydrothermal liquefaction (HTL) byproducts like biochar to grow microalgae. HTL is a promising method to convert wet algal biomasses into biofuels. The initial microalgae liquefaction at a temperature of 300 °C for 30 minute, converted 31.22 % of the Galdieria sulphuraria and 41.00 % of the Kirchneriella cornutum into biocrude. Upon changing the reactor from a 100 ml to a 250 ml reactor, the yield in biocrude increased to 31.48 % for G. sulphuraria and dropped to 38.05 % for K. cornutum. Further, energy recoveries based on calorific values of HTL products were seen to drop by about 5 % of the 100 ml calculated values in the larger reactor.
Biochar from HTL of G. sulphuraria at 300 °C showed 15.98 and 5.27 % of phosphorous and nitrogen, respectively. HTL products from the biomass were analyzed for major elements through ICP-OES and CHNS/O. N and P are macronutrients that can be utilized in growing microalgae. This could reduce the operational demands in growing algae like, phosphorous mined to meet annual national demand for aviation fuel. Acidic leaching of these elements as phosphates and ammoniacal nitrogen was studied. Improved leaching of 49.49 % phosphorous and 95.71 % nitrogen was observed at 40 °C and pH 2.5 over a period of 7 days into the growth media. These conditions being ideal for growth of G. sulphuraria, leaching can be done in-situ to reduce overhead cost.
Growth potential of G. sulphuraria in leached media was compared to a standard cyanidium media produced from inorganic chemicals. Initial inhibition studies were done in the leached media at 40 °C and 2-3 vol. % CO2 to observe a positive growth rate of 0.273 g L-1 day-1. Further, growth was compared to standard media with similar composition in a 96 well plate 50 μL microplate assay for 5 days. The growth rates in both media were comparable. Additionally, growth was confirmed in a 240 times larger tubular reactor in a Tissue Culture Roller drum apparatus. A better growth was observed in the leached cyanidium media as compared to the standard variant.
Biochar from HTL of G. sulphuraria at 300 °C showed 15.98 and 5.27 % of phosphorous and nitrogen, respectively. HTL products from the biomass were analyzed for major elements through ICP-OES and CHNS/O. N and P are macronutrients that can be utilized in growing microalgae. This could reduce the operational demands in growing algae like, phosphorous mined to meet annual national demand for aviation fuel. Acidic leaching of these elements as phosphates and ammoniacal nitrogen was studied. Improved leaching of 49.49 % phosphorous and 95.71 % nitrogen was observed at 40 °C and pH 2.5 over a period of 7 days into the growth media. These conditions being ideal for growth of G. sulphuraria, leaching can be done in-situ to reduce overhead cost.
Growth potential of G. sulphuraria in leached media was compared to a standard cyanidium media produced from inorganic chemicals. Initial inhibition studies were done in the leached media at 40 °C and 2-3 vol. % CO2 to observe a positive growth rate of 0.273 g L-1 day-1. Further, growth was compared to standard media with similar composition in a 96 well plate 50 μL microplate assay for 5 days. The growth rates in both media were comparable. Additionally, growth was confirmed in a 240 times larger tubular reactor in a Tissue Culture Roller drum apparatus. A better growth was observed in the leached cyanidium media as compared to the standard variant.
ContributorsMathew, Melvin (Author) / Deng, Shuguang (Thesis advisor) / Lammers, Peter J. (Committee member) / Nielsen, David R (Committee member) / Arizona State University (Publisher)
Created2017
Description
The release of organophosphorus compounds (OPs) and subsequent exposure to these compounds is of concern to humans and the environment. The goal of this work was to control the concentrations of gaseous OPs through interaction with sorbent oxides. Experimental and computational methods were employed to assess the interactions of dimethyl phosphite (DMHP), dimethyl methylphosphonate (DMMP), dimethyl ethylphosphonate (DMEP), diethyl ethylphosphonate (DEEP), and triethyl phosphate (TEP) with amorphous silica (a-silica), ã-alumina, and monoclinic zirconia (m-zirconia) for applications in air pollution control. Interactions of the selected OPs with a-silica were chosen as a baseline to determine the applicability of the computational predictions. Based on the a-silica results, computational methods were deemed valid for predicting the trends among materials with comparable interactions (e.g. -OH functionality of a-silica interacting with the phosphonyl O atoms of the OPs). Computational evaluations of the interactions with the OPs were extended to the oxide material, m-zirconia, and compared with the results for ã-alumina. It was hypothesized that m-zirconia had the potential to provide for the effective sorption of OPs in a manner superior to that of the a-silica and the ã-alumina surfaces due to the surface charges of the zirconium Lewis acid sites when coordinated in the oxidized form. Based on the computational study, the predicted heats of adsorption for the selected OPs onto m-zirconia were more favorable than those that were predicted for ã-alumina and a-silica. Experimental studies were carried out to confirm these computational results. M-zirconia nanoparticles were synthesized to determine if the materials could be utilized for the adsorption of the selected OPs. M-zirconia was shown to adsorb the OPs, and the heats of adsorption were stronger than those determined for commercial samples of a-silica. However, water interfered with the adsorption of the OPs onto m-zirconia, thus leading to heats of adsorption that were much weaker than those predicted computationally. Nevertheless, this work provides a first investigation of m-zirconia as a viable sorbent material for the ambient control of the selected gaseous OPs. Additionally, this work represents the first comparative study between computational predictions and experimental determination of thermodynamic properties for the interactions of the selected OPs and oxide surfaces.
ContributorsSiu, Eulalia Yuen-Yi (Author) / Andino, Jean M (Thesis advisor) / Forzani, Erica S (Committee member) / Hristovski, Kiril (Committee member) / Nielsen, David R (Committee member) / Pfeffer, Robert (Committee member) / Arizona State University (Publisher)
Created2011
Description
Amino acids and related targets are typically produced by well-characterized heterotrophs including Corynebacterium glutamicum and Escherichia coli. Recent efforts have sought to supplant these sugar-intensive processes through the metabolic engineering of cyanobacteria, which instead can directly utilize atmospheric carbon dioxide (CO2) and sunlight. One of the most promising among recently discovered photoautotrophic strains is Synechococcus elongatus UTEX 2973 (hereafter UTEX 2973), which has been reported to have doubling times as low as 1.5 hours. While encouraging, there are still major challenges preventing the widespread industrial acceptance of engineered cyanobacteria, chief among them is the scarcity of genetic tools and parts with which to engineer production strains. Here, UTEX 2973 was engineered to overproduce L-lysine through the heterologous expression of feedback-resistant copies of aspartokinase lysC and the L-lysine exporter ybjE from Escherichia coli, as aided by the characterization of novel combinations of genetic parts and expression sites. At maximum, using a plasmid-based expression system, a L-lysine titer of 556 ± 62.3 mg/L was attained after 120 hours, surpassing a prior report of photoautotrophic L-lysine bioproduction. Modular extension of the pathway then led to the novel photosynthetic production of the corresponding diamine cadaverine (55.3 ± 6.7 mg/L by 96 hours) and dicarboxylate glutarate (67.5 ± 2.2 mg/L by 96 hours). Lastly, mass transfer experiments were carried out to determine if the solubility of CO2 in and its rate of mass transfer to BG-11 media could be improved by supplementing it with various amines, including cadaverine. Ultimately, however, cyanobacteria grown in the presence of all tested amines was worse than in BG-11 alone, demonstrating the need for additional tolerance engineering to successfully implement this strategy.
ContributorsDookeran, Zachary Anthony (Author) / Nielsen, David R (Thesis advisor) / Wang, Xuan (Committee member) / Nannenga, Brent L (Committee member) / Varman, Arul M (Committee member) / Peebles, Christie AM (Committee member) / Arizona State University (Publisher)
Created2022
Description
Alkanolamines are useful as building blocks for a variety of applications, ranging from medical applications such as drug and gene delivery. In this work, Escherichia coli was investigated as a viable candidate for the production of 5-amino-1-pentanol (5-AP). Taking advantage of the existing L-lysine degradation pathway, a novel route to 5-AP was constructed by co-expressing the genes cadA (encoding lysine decarboxylase, responsible for the conversion of L-lysine to cadaverine) and patA (encoding putrescine aminotransferase, responsible for the conversion of cadaverine to 5-amino-1-pentanal), followed by the endogenous reduction of 5-amino-pentanal (5-APL) to 5-AP. To avoid the competing conversion of 5-APL to 5-amino-1-pentanoate and avoid accumulation of byproduct 1-Δ-piperideine, further host engineering was performed to delete the gene patD also known as prr (encoding 5-amino-pentanal dehydrogenase). Flask scale fermentation experiments in minimal medium of the newly constructed pathway was conducted where 62.6 mg/L 5-AP was observed to be produced. It was hypothesized that 5-AP production could be boosted by optimizing production medium to M10 media. However, change in the culture medium resulted in the production of just 51 mg/L 5-AP. Shifts observed in HPLC chromatogram peaks made it difficult to conclude exact titers of 5-AP and can be further improved by exploring different analysis methods and optimization of the method currently in place.
ContributorsBrookhouser, Brendan (Author) / Nielsen, David R (Thesis advisor) / Tonkovich, Anna L (Committee member) / Varman, Arul M (Committee member) / Arizona State University (Publisher)
Created2022
Description
In this work, secretion of free fatty acids (FFAs) and ω-hydroxy FFAs wasachieved in the model cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis), and
FFAs were detected by a novel fluorescence assay. Current methods of detecting FFA
concentrations, including HPLC-based and GC-based methods or enzyme-based kits,
have hindered research advancement due to their laborious and/or expensive nature. The
work herein establishes a novel, rapid, fluorescence-based assay for detecting total FFA
concentrations secreted by Synechocystis FFA secretion strains. The novel FFA-detection
assay demonstrates the efficacy of using Nile Red as a fluorescent reporter for laurate or
palmitate at concentrations up to 500 µM in the presence of cationic surfactants. Total
FFA concentrations in Synechocystis supernatants quantified by the novel, Nile Red fluorescence-based assay are demonstrated herein to be highly correlative to total FFA
concentrations quantified by LC-MS; this correlation was seen in supernatant samples of
wild type Synechocystis and Synechocystis FFA secretion strains, both in 96-well plates
and 30-mL, aerated culture tubes.
This work also establishes the expression of a cytochrome P450 fusion enzyme,
CYP153A-CPRmut, or a monooxygenase system from Pseudomonas putida GPo1,
AlkBGT, in FFA secretion strains of Synechocystis for the generation of ω-hydroxy
laurate from laurate. After finding greatly increased ω-hydroxylation activity of
CYP153A-CPRmut with concurrent superoxide dismutase and catalase overexpression, 55
or 1.5 µM of ω-hydroxy laurate were produced over five days by Synechocystis strains
expressing CYP153A-CPRmut or AlkBGT, respectively. As further indication of the
presence of reactive oxygen species affecting ω-hydroxy laurate production with
Synechocystis strains expressing CYP153A-CPRmut, concentrations of ω-hydroxy laurate
in the supernatant increased over two-fold in the presence of 250 µM of the anti-oxidant,
methionine, in bench-scale cultures and in 96-well plate cultures. Additionally, a
mutation at the 55th amino acid position in AlkB (tryptophan to cysteine; AlkBW55C),
resulted in a more than two-fold shift in AlkB’s substrate preference from decanoate
towards the desired substrate, laurate. As a result, Synechocystis expressing AlkBW55C
could produce 5.9 µM ω-hydroxy laurate and 2.0 µM dodecanedioic acid over five days
of growth.
ContributorsAshe, Christopher (Author) / Vermaas, Willem Fj (Thesis advisor, Committee member) / Wang, Xuan (Committee member) / Nielsen, David R (Committee member) / Misra, Rajeev (Committee member) / Arizona State University (Publisher)
Created2023
Description
Lignocellulose, the major structural component of plant biomass, represents arenewable substrate of enormous biotechnological value. Microbial production of
chemicals from lignocellulosic biomass is an attractive alternative to chemical synthesis.
However, to create industrially competitive strains to efficiently convert lignocellulose to
high-value chemicals, current challenges must be addressed. Redox constraints, allosteric
regulation, and transport-related limitations are important bottlenecks limiting the
commercial production of renewable chemicals from lignocellulose. Advances in
metabolic engineering techniques have enabled researchers to engineer microbial strains
that overcome some of these challenges but new approaches that facilitate the
commercial viability of lignocellulose valorization are needed. Biological systems are
complex with a plethora of regulatory systems that must be carefully modulated to
efficiently produce and excrete the desired metabolites. In this work, I explore metabolic
engineering strategies to address some of the biological constraints limiting
bioproduction such as redox, allosteric, and transport constraints to facilitate cost-effective
lignocellulose bioconversion.
ContributorsOnyeabor, Moses Ekenedilichukwu (Author) / Wang, Xuan (Thesis advisor) / Varman, Arul M (Committee member) / Nannenga, Brent (Committee member) / Nielsen, David R (Committee member) / Geiler-Samerotte, Kerry (Committee member) / Arizona State University (Publisher)
Created2023
Description
Clustered regularly interspace short palindromic repeats (CRISPR) and CRISPR associated (Cas) technologies have become integral to genome editing. Canonical CRISPR-Cas9 systems function as a ribonucleic acid (RNA)-guided nucleases. Single guide RNAs (sgRNA) can be easily designed to target Cas9’s nuclease activity towards protospacer deoxyribonucleic acid (DNA) sequences. The relatively ease and efficiency of CRISPR-Cas9 systems has enabled numerous technologies and DNA manipulations. Genome engineering in human cell lines is centered around the study of genetic contribution to disease phenotypes. However, canonical CRISPR-Cas9 systems are largely reliant on double stranded DNA breaks (DSBs). DSBs can induce unintended genomic changes including deletions and complex rearrangements. Likewise, DSBs can induce apoptosis and cell cycle arrest confounding applications of Cas9-based systems for disease modeling. Base editors are a novel class of nicking Cas9 engineered with a cytidine or adenosine deaminase. Base editors can install single letter DNA edits without DSBs. However, detecting single letter DNA edits is cumbersome, requiring onerous DNA isolation and sequencing, hampering experimental throughput. This document describes the creation of a fluorescent reporter system to detect Cytosine-to-Thymine (C-to-T) base editing. The fluorescent reporter utilizes an engineered blue fluorescent protein (BFP) that is converted to green fluorescent protein (GFP) upon targeted C-to-T conversion. The BFP-to-GFP conversion enables the creation of a strategy to isolate edited cell populations, termed Transient Reporter for Editing Enrichment (TREE). TREE increases the ease of optimizing base editor designs and assists in editing cell types recalcitrant to DNA editing. More recently, Prime editing has been demonstrated to introduce user defined DNA edits without the need for DSBs and donor DNA. Prime editing requires specialized prime editing guide RNAs (pegRNAs). pegRNAs are however difficult to manually design. This document describes the creation of a software tool: Prime Induced Nucleotide Engineering Creator of New Edits (PINE-CONE). PINE-CONE rapidly designs pegRNAs based off basic edit information and will assist with synthetic biology and biomedical research.
ContributorsStandage-Beier, Kylie S (Author) / Wang, Xiao (Thesis advisor) / Brafman, David A (Committee member) / Tian, Xiao-jun (Committee member) / Nielsen, David R (Committee member) / Arizona State University (Publisher)
Created2023