Publications

Frontiers in Bioengineering and Biotechnology

Mahtre, Apurv M.; Shinde, Somnath S.; Jha, Amit K.; Rodriquez, Alberto R.; Wardak, Zohal W.; Jansen, Abigail J.; Gladden, John M.; George, Anthe G.; Varman, Arul M.; Davis, Ryan W.

Corynebacterium glutamicum has been successfully employed for the industrial production of amino acids and other bioproducts, partially due to its native ability to utilize a wide range of carbon substrates. We demonstrated C. glutamicum as an efficient microbial host for utilizing diverse carbon substrates present in biomass hydrolysates, such as glucose, arabinose, and xylose, in addition to its natural ability to assimilate lignin-derived aromatics. As a case study to demonstrate its bioproduction capabilities, L-lactate was chosen as the primary fermentation end product along with acetate and succinate. C. glutamicum was found to grow well in different aromatics (benzoic acid, cinnamic acid, vanillic acid, and p-coumaric acid) up to a concentration of 40 mM. Besides, ¹³ C-fingerprinting confirmed that carbon from aromatics enter the primary metabolism via TCA cycle confirming the presence of β-ketoadipate pathway in C. glutamicum . ¹³ C-fingerprinting in the presence of both glucose and aromatics also revealed coumarate to be the most preferred aromatic by C. glutamicum contributing 74 and 59% of its carbon for the synthesis of glutamate and aspartate respectively. ¹³ C-fingerprinting also confirmed the activity of ortho-cleavage pathway, anaplerotic pathway, and cataplerotic pathways. Finally, the engineered C. glutamicum strain grew well in biomass hydrolysate containing pentose and hexose sugars and produced L-lactate at a concentration of 47.9 g/L and a yield of 0.639 g/g from sugars with simultaneous utilization of aromatics. Succinate and acetate co-products were produced at concentrations of 8.9 g/L and 3.2 g/L, respectively. Our findings open the door to valorize all the major carbon components of biomass hydrolysate by using C. glutamicum as a microbial host for biomanufacturing.

Quiroz-Arita, Carlos E.; Davis, Ryan W.

Abstract not provided.

Kim, Sungwhan K.; Quiroz-Arita, Carlos E.; Monroe, Eric A.; Siccardi, Anthony J.; Mitchell, Jacqueline M.; Huysman, Nathan D.; Davis, Ryan W.

Abstract not provided.

Kim, Sungwhan K.; Quiroz-Arita, Carlos E.; Monroe, Eric M.; Siccardi, Anthony J.; Mitchell, Jacqueline M.; Huysman, Nathan D.; Davis, Ryan W.

Abstract not provided.

PLoS ONE

Sarnaik, Aditya; Mhatre, Apurv; Faisal, Muhammad; Smith, Dylan; Davis, Ryan W.; Varman, Arul M.

Ultra-low temperature (ULT) storage of microbial biomass is routinely practiced in biological laboratories. However, there is very little insight regarding the effects of biomass storage at ULT and the structure of the cell envelope, on cell viability. Eventually, these aspects influence bacterial cell lysis which is one of the critical steps for biomolecular extraction, especially protein extraction. Therefore, we studied the effects of ULT-storage (-80°C) on three different bacterial platforms: Escherichia coli, Bacillus subtilis and the cyanobacterium Synechocystis sp. PCC 6803. By using a propidium iodide assay and a modified MTT assay we determined the impact of ULT storage on cellular viability. Subsequently, the protein extraction efficiency was determined by analyzing the amount of protein released following the storage. The results successfully established that longer the ULT-storage time lower is the cell viability and larger is the protein extraction efficiency. Interestingly, E. coli and B. subtilis exhibited significant reduction in cell viability over Synechocystis 6803. This indicates that the cell membrane structure and composition may play a major role on cell viability in ULT storage. Interestingly, E. coli exhibited concomitant increase in cell lysis efficiency resulting in a 4.5-fold increase (from 109 μg/ml of protein on day 0 to 464 μg/ml of protein on day 2) in the extracted protein titer following ULT storage. Furthermore, our investigations confirmed that the protein function, tested through the extraction of fluorescent proteins from cells stored at ULT, remained unaltered. These results established the plausibility of using ULT storage to improve protein extraction efficiency. Towards this, the impact of shorter ULT storage time was investigated to make the strategy more time efficient to be adopted into protocols. Interestingly, E. coli transformants expressing mCherry yielded 2.7-fold increase (93 μg/mL to 254 μg/mL) after 10 mins, while 4-fold increase (380 μg/mL) after 120 mins of ULT storage in the extracted soluble protein. We thereby substantiate that: (1) the storage time of bacterial cells in-80°C affect cell viability and can alter protein extraction efficiency; and (2) exercising a simple ULT-storage prior to bacterial cell lysis can improve the desired protein yield without impacting its function.

Shinde, Somnath D.; Davis, Ryan W.; George, Anthe G.

Abstract not provided.

Shinde, Somnath D.; Sarnaik, Aditya S.; Nguyen, Mark N.; Jansen, Abigail J.; Smith, Dylan S.; Sarwar, Mysha S.; George, Anthe G.; Varman, Arul M.; Davis, Ryan W.

Abstract not provided.

Landera, Alexander L.; Davis, Ryan W.; George, Anthe G.

Abstract not provided.

Shinde, Somnath D.; Carlson, Joseph S.; Monroe, Eric M.; Jha, Amit K.; George, Anthe G.; Davis, Ryan W.

Abstract not provided.

Quiroz-Arita, Carlos E.; Shinde, Somnath D.; Kim, Sungwhan K.; Monroe, Eric M.; Pienkos, Philip P.; Laurens, Lieve L.; Quinn, Jason Q.; Nagle, Nick N.; Knoshaug, Eric K.; Kruger, Jacob K.; Dong, Tao, D.; Davis, Ryan W.

Abstract not provided.

Quiroz-Arita, Carlos E.; Monroe, Eric M.; Blaylock, Myra L.; Smernoff, David S.; Mancinelli, Rocco M.; Davis, Ryan W.

Abstract not provided.

Davis, Ryan W.; Monroe, Eric M.; Carlson, Joseph S.; George, Anthe G.

Abstract not provided.

Shinde, Somnath D.; Monroe, Eric M.; Jha, Amit K.; Landera, Alexander L.; Sarwar, Mysha S.; Carlson, Joseph S.; George, Anthe G.; Davis, Ryan W.

Abstract not provided.

Shinde, Somnath D.; Monroe, Eric M.; Jha, Amit K.; Liu, Fang L.; Varman, Arul M.; George, Anthe G.; Davis, Ryan W.

Abstract not provided.

Fuel

Monroe, Eric M.; Shinde, Somnath D.; Carlson, Joseph S.; Eckles, Tyler P.; Liu, Fang L.; Varman, Arul M.; George, Anthe G.; Davis, Ryan W.

We demonstrated production of a superior performance biodiesel referred to here as fatty acid fusel alcohol esters (FAFE) – by reacting fusel alcohols (isobutanol, 3-methyl-1-butanol, and (S)-(-)-2-methyl-1-butanol) with oil (glyceryl trioleate) using lipase from Aspergillus oryzae. Reaction conditions corresponding to a molar ratio of 5:1 (fusel alcohols to oil), enzyme loading of 2% w/w, reaction temperature of 35 °C, shaking speed of 250 rpm, and reaction time of 24 h achieved >97% conversion to FAFE. Further, FAFE obtained from reacting a fusel alcohol mixture with corn oil were evaluated for use as a fuel for diesel engines. FAFE mixtures showed superior combustion and cold-flow properties, with the derived cetane numbers up to 4.8 points higher, cloud points up to -6 °C lower, and the heat of combustion up to 2.1% higher than the corresponding FAME samples, depending on the fusel mixture used. This represents a significant improvement for all three metrics, which are typically anti-correlated. Finally, FAFE provides a new opportunity for expanded usage of biodiesel by addressing feedstock limitations, fuel performance, and low temperature tolerance.

Shinde, Somnath D.; Jha, Amit K.; Mhatre, Apurv M.; Rodriguez, Alberto R.; Gladden, John M.; Varman, Arul M.; George, Anthe G.; Davis, Ryan W.

Abstract not provided.

Shinde, Somnath D.; Monroe, Eric M.; Liu, Fang L.; Varman, Arul M.; George, Anthe G.; Davis, Ryan W.

Abstract not provided.

Davis, Ryan W.

Abstract not provided.

Environmental Science and Technology

Derose, Katherine; Liu, Fang; Davis, Ryan W.; Simmons, Blake A.; Quinn, Jason C.

Distiller's grains are a byproduct of corn ethanol production and provide an opportunity for increasing the economic viability and sustainability of the overall grain-to-fuels process. Typically, these grains are dried and sold as a ruminant feed adjunct. This study considers utilization of the residuals in a novel supplementary fermentation process to produce two products, enriched protein and fusel alcohols. The value-added proposition and environmental impact of this second fermentation step for distiller's grains are evaluated by considering three different processing scenarios. Techno-economic results show the minimum protein selling price, assuming fusel alcohol products are valued at $0.79 per liter gasoline equivalent, ranges between $1.65-$2.48 kg protein-1 for the different cases. Environmental impacts of the systems were evaluated through life cycle assessment. Results show a baseline emission results of 17 g CO2-eq (MJ fuel)-1 for the fuel product and 10.3 kg CO2-eq kg protein-1 for the protein product. Sensitivity to allocation methods show a dramatic impact with results ranging between -8 to 140 g CO2-eq (MJ fuel)-1 for the fuel product and -0.3 to 6.4 kg CO2-eq kg protein-1 for the protein product. The discussion is focused on the potential impact of the technology on corn ethanol production economics and sustainability.

Kim, Sungwhan K.; Poorey, Kunal N.; Monroe, Eric M.; Davis, Ryan W.; Siccardi, Anthony J.

Abstract not provided.

Behnke, Lily C.; Monroe, Eric M.; George, Anthe G.; Davis, Ryan W.

Abstract not provided.

Kim, Sungwhan K.; Davis, Ryan W.; Monroe, Eric M.; Eckles, Tyler P.; Lucero, Janette L.; Siccardi, Anthony J.

Abstract not provided.

Monroe, Eric M.; Liu, Fang L.; Wu, Weihua W.; Jaryenneh, James D.; Varman, Arul M.; Shinde, Somnath D.; Davis, Ryan W.

Abstract not provided.

Shinde, Somnath D.; Jha, Amit K.; Varman, Arul M.; George, Anthe G.; Davis, Ryan W.

Abstract not provided.

Microbial Cell Factories

Zhuang, Xun; Kilian, Oliver K.; Monroe, Eric M.; Ito, Masakazu; Tran-Gyamfi, Mary B.; Liu, Fang L.; Davis, Ryan W.; Mirsiaghi, Mona; Sundstrom, Eric; Pray, Todd; Skerker, Jeffrey M.; George, Anthe G.; Gladden, John M.

Background: Due to their high energy density and compatible physical properties, several monoterpenes have been investigated as potential renewable transportation fuels, either as blendstocks with petroleum or as drop-in replacements for use in vehicles (both heavy and light-weight) or in aviation. Sustainable microbial production of these biofuels requires the ability to utilize cheap and readily available feedstocks such as lignocellulosic biomass, which can be depolymerized into fermentable carbon sources such as glucose and xylose. However, common microbial production platforms such as the yeast Saccharomyces cerevisiae are not naturally capable of utilizing xylose, hence requiring extensive strain engineering and optimization to efficiently utilize lignocellulosic feedstocks. In contrast, the oleaginous red yeast Rhodosporidium toruloides is capable of efficiently metabolizing both xylose and glucose, suggesting that it may be a suitable host for the production of lignocellulosic bioproducts. In addition, R. toruloides naturally produces several carotenoids (C40 terpenoids), indicating that it may have a naturally high carbon flux through its mevalonate (MVA) pathway, providing pools of intermediates for the production of a wide range of heterologous terpene-based biofuels and bioproducts from lignocellulose. Results: Sixteen terpene synthases (TS) originating from plants, bacteria and fungi were evaluated for their ability to produce a total of nine different monoterpenes in R. toruloides. Eight of these TS were functional and produced several different monoterpenes, either as individual compounds or as mixtures, with 1,8-cineole, sabinene, ocimene, pinene, limonene, and carene being produced at the highest levels. The 1,8-cineole synthase HYP3 from Hypoxylon sp. E74060B produced the highest titer of 14.94 ± 1.84 mg/L 1,8-cineole in YPD medium and was selected for further optimization and fuel properties study. Production of 1,8-cineole from lignocellulose was also demonstrated in a 2L batch fermentation, and cineole production titers reached 34.6 mg/L in DMR-EH (Deacetylated, Mechanically Refined, Enzymatically Hydorlized) hydrolysate. Finally, the fuel properties of 1,8-cineole were examined, and indicate that it may be a suitable petroleum blend stock or drop-in replacement fuel for spark ignition engines. Conclusion: Our results demonstrate that Rhodosporidium toruloides is a suitable microbial platform for the production of non-native monoterpenes with biofuel applications from lignocellulosic biomass.