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Environmental remediation and biofuel production through nanoparticle stimulation of MASSACHUSETTS INSTITUTE yeast OF TECHNOLOGY 03 2019 by JUL Shalmalee Pandit LIBRARIES ARCHIVES B.S. Bioengineering The University of California, Berkeley (2015) Submitted to the Department of Biological Engineering in Partial Fulfillment of the Requirements for the Degree of Master of Science in Biological Engineering at the Massachusetts Institute of Technology June 2019 ©2019 Massachusetts Institute of Technology All rights reserved. redacted Signature of A uthor.........................&1............Signature .....--. ......... Department of Biological Engineering May 23, 2019 Certified.....Signature redacted Angela M. Belcher Professor, Department of Biological Engineering Thesis Supervisor Signature redacted Accepted by ........ ........................ Forest White Chair, Department Committee on Graduate Students 77 Massachusetts Avenue Cambridge, MA 02139 MITLibraries http'l'ibraries.mitedu/ask DISCLAIMER NOTICE Due to the condition of the original material, there are unavoidable flaws in this reproduction. We have made every effort possible to provide you with the best copy available. Thank you. The images contained In this document are of the best quality available. Environmental remediation and biofuel production through nanoparticle stimulation of yeast by Shalmalee Pandit Submitted to the Department of Biological Engineering On May 23, 2019 in Partial Fulfillment of the Requirements for the Degree of Master of Science in Biological Engineering Abstract Artificially photosynthetic systems aim to store solar energy and chemically reduce carbon dioxide. These systems have been developed in order to use light to drive processes for carbon fixation into biomass and/or liquid fuels. We have developed a hybrid-biological system that manages both genetically controlled generation of products along with the photoactivability of a semiconductor system. We show an increase in the production of ethanol, a common biofuel, through the electron transfer stimulated by biologically produced cadmium sulfide nanoparticles and light. This work provides a basis on which to improve the production of many metabolites and products through endogenously produced nanoparticles. Thesis Supervisor: Angela M. Belcher Title: Professor, Department of Biological Engineering 2 Contents 1 Chapter 1 Introduction ..................................................... .... ........... .... 7 1.1 Environmental and health effects due to cadmium ......................................... 7 1.1.1 Environmental cleanup of cadmiumc.a.............................. .................... 7 1.1.2 Current methods of cadmium ion removal............................................. 7 1.2 Current state of biofuel production ........................... .......................... 9 1.2.1 Drivers of biofuel production ................. ............................................. 9 1.2.2 Biofuel production to date... --..... ........... ....... 9 1.2.3 Key issues and considerations for biofuel production ......................... 10 2 Chapter 2 Characterization of yeast-hybrid system .................................... 11 2.1 Design of yeast-inorganic hybrid system .................. 11 2.2 Visual characterization of system........................................... 12 2.2.1 Transmission electron microscopy (TEM) images of system .............. 13 2.2.2 Elemental mapping analysis .--..... - .......-- ... ................. 14 2.3 Experimental design to use hybrid system ................. 17 2.4 Transcriptomic characterization of system................. 18 2.4.1 Principal component analysis of RNA sequencing data...................... 18 2.4.2 Gene expression fold change induced by cadmium treatment ..... 19 2.4.3 Gene expression fold change induced by light treatment....... 20 2.5 Experimental Methods........... ................. 21 2.5.1 Yeast strain and culture ... ................. ....... ........................ 21 2.5.2 Light experiments............................ 22 2.5.3 Transmission electron microscopy (TEM)................ 22 2.5.4 RNA sequencing and analysis .. .................... ................... 23 3 Chapter 3 Further characterization and effects of transcriptomic changes on metabolite production ......-............--...... ............... 24 3.1 Further characterization through gene set enrichment analysis (GSEA)... 24 3.2 Intracellular ATP levels in yeast strains ................................... 26 3.3 Intracellular glucose levels in yeast strains ........................ -................... 27 3 3.4 Intracellular NAD+ and NADH Concentration.......................................... 28 3.5 Discussion, conclusions, and future work ....................................................... 30 3.6 Experim ental M ethods.................. .............................................................. 31 3.6.1 Gene set enrichment analysis (GSEA) ...................... 31 3.6.2 Yeast lysate preparation ........................................................................ 31 3.6.3 Measuring intracellular ATP concentration .............. 31 3.6.4 Measuring intracellular glucose concentration .................................. 31 3.6.5 Measuring intracellular NAD+ and NADH ......................................... 31 4 Chapter 4 Producing biofuel using hybrid-biological system.......................... 32 4.1 Potential mechanistic explanation to produce biofuel (ethanol)............... 32 4.2 Measuring intracellular ethanol concentration......................................... 32 4.3 Implementing and characterizing the mutation in another yeast strain .... 33 4.3.1 Visual characterization of Y567 AMet17 ............................................. 33 4.3.2 Elemental m apping analysis .................................................................. 35 4.3.3 Measuring intracellular ATP concentration .................................... 38 4.3.4 Measuring the NAD+/NADH ratio ....................... 39 4.4 Intracellular ethanol concentration in Y567 AMet17 strain ............ 40 4.5 Discussion, conclusions, and future work ........ ........................................... 41 4.6 Experim ental M ethods............................................................................... 42 4.6.1 Yeast strain and culture methods......................... 42 4.6.2 Knocking out M et17 in Y567 ................................................................. 42 4.6.3 Measuring intracellular ethanol concentration................................... 42 B ibliography .................................................................................................................. 43 Acknowledgements ......................................... 48 4 List of Figures Figure 2-1 Yeast-hybrid biological system. a. Schematic of yeast-hybrid system. Knocking out a pathway in thiol production lead to an increase in hydrogen sulfide production. This hydrogen sulfide is shuttled out of the cell. b. When the yeast cells are treated with cadmium ions, cadmium sulfide nanoparticles are precipitated on the yeast's cell surface. The CdS nanoparticles excite at UV wavelengths........... 12 Figure 2-2 Wild-type yeast treated with cadmium ions display no CdS nanoparticles in the cell surface. ........................................................................................................... 13 Figure 2-3 Mutated yeast (AMet17) when treated with cadmium, precipitate CdS nanoparticles on the cell surface. ......................................................................... 14 Figure 2-4 CdS nanoparticles displayed on the yeast cell surface............... 15 Figure 2-5 Elemental mapping analysis of cadmium on TEM image.................... 15 Figure 2-6 Elemental mapping analysis of sulfur on TEM image. ........................ 16 Figure 2-7 Elemental analysis displaying both cadmium (red) and sulfur (blue) superim posed on the TEM im age. ..................... ................................................... 17 Figure 2-8 Experimental conditions for light and dark experiments. ................... 18 Figure 2-9 PCA plot displaying RNA Sequencing data........................................... 19 Figure 2-10 Log fold change volcano plot depicting the effects of the cadmium sulfide nanoparticles on the transcriptome of the yeast-hybrid system................ 20 Figure 2-11 Log fold change volcano plot depicting the effects of the light treatment on the transcriptome of the yeast-hybrid system. .................................................. 21 Figure 3-1 Gene set enrichment analysis of protein coding genes involved in ATP production and synthesis due to the presence of light. The p-value is less than 0.05. Random walk is displayed as well........................................................................... 25 Figure 3-2 Gene set enrichment analysis of genes involved in glycolysis due to the presence of cadmium sulfide nanoparticles on the yeast's cell surface. The p-value is less than 0.05. Random walk is also displayed. ....................................................... 26 Figure 3-3 ATP concentration in various yeast strains. ATP concentration was calculated per cell. Yellow plots indicate light treatment....................................... 27 Figure 3-4 Intracellular glucose concentration displayed in various yeast strains. Yellow bars indicate light treatm ent. ...................................................................... 28 Figure 3-5 Total NAD+ and NADH in