Faculty | SIU

Research Interests:

The growing concerns of petroleum-based fuels and chemicals on global climate change and environmental pollution (e.g. plastics in the environment) combined with the revolution of synthetic and systems biology have bolstered worldwide attention into the biological production of commodity chemicals, fuels, polymers, and pharmaceuticals via renewable resources including lignocellulosic biomass. However, to compete with the well-established petrochemical industry, improving the yield, titer, and productivity of microbial processes is critical. Toxicity of substrate(s), intermediate metabolite(s), and end-product(s) on the microbial host is one of the fundamental limitations that must be overcome to create tailor-made cell factories for realistic commercialization of renewable fuels, chemicals, and polymer production. In this research landscape, my studies focus on identification and dissection of complex molecular mechanisms of microbial stress reponses via systems biology approaches (e.g. multi-omics/megavariate data modeling), exclusively targeted to identify the novel post-translational protein modifications events (PPMs) such as ubiquitination, sumoylation, and chaperone-cascade in stress resistance of microbes (model and non-model industrial microbial hosts). My studies contribute to understand cellular processes of both fundamental and industrial interests of tailoring biocatalysts, and enabled the development of novel PPMs-based synthetic biology tools and metabolic engineering approaches to craft efficient microbial cell factories for production of value-added fuels, chemicals, and polymers from renewable biomass, agricultural, and industrial waste substrates, and also enables plastic waste upcycling.

Currently, we are working in concert with yeast PPMs-based modern-synthetic biology tools for 1) understanding novel molecular mechanisms of repair and degradation of stress-induced abnormal proteins in yeast during fermentation process of highly toxic compounds 2) developing efficient commercial yeast chassis for novel-biopolymer production via substrates from biomass and unconventional substrates such as organic-rich heterogeneous waste streams including plastic waste.

Upcycle plastic biologically via synthetic yeast. Given the global environmental and energy concerns with plastics, there is a clear need for technologies in plastics “upcycling” (creation of a higher-value product from reclaimed plastic). Plastic upcycling will help to establish the Circular Materials Economy, reduce the environmental impacts, and provide market incentives for plastics reclamation. Synthetic yeast has been successfully developed to depolymerization and bioconversion of biomass into value-added products such as fuels and commodity chemicals. In the same vein, we are working on developing novel techno-economically feasible plastic upcycling processes to produce high-value chemicals and biodegradable polymers via yeast biological transformations. We are exploring the potential of an engineering yeast to selective degradation of recalcitrant plastic to monomers, and concurrent conversion into novel intermediates, such as muconic acid and ß-ketoadipate, which could be used to manufacture biodegradable plastic replacement material. Also, we are evolving plastic degradation enzyme system(s) in yeast for improving activity and detailed understanding of evolved enzymes for higher plastic turnover.

Book Chapters

• Jayakody LN, Hayashi N, Kitagaki H (2015). Breeding of bioethanol yeast by detoxification of glycolaldehyde, a novel fermentation inhibitor. Stress Biology of Yeasts and Fungi: Application for Industrial Brewing and Fermentation. Springer, Chapter1, pp: 3-23.
• Jayakody LN, Hayashi N, Kitagaki H (2014). Biotechnology and Bioinformatics- Currents trends and Future prospective, Identification of a novel fermentation inhibitor of bioethanol production, glycolaldehyde, and engineering of a resistant yeast strain toward it. Chapter 9, pp:232-246.
• Jayakody LN, Hayashi N, Kitagaki H (2013). Material and process for energy: communicating current research and technology development, A. Mendez-Vilas (Ed.), Molecular mechanisms for detoxification of major aldehyde inhibitors for production of bioethanol by Saccharomyces cerevisiae from hot-compressed water- treated lignocellulose, FORMATEX RESEARCH CENTER, Badajoz, Spain, pp: 302-311

Patents

• World patent application 2019, No. WO2019222396A1. Engineered microorganisms for the deconstruction of polymers.
• US patent application 2019, No. PCT/US19/32480. Engineered microorganisms for the deconstruction of polymers.
• US patent application 2018, No. 62/621,891. Biocatalysts for conversion of thermochemical waste streams.
• US patent application 2017, No. 62/535,074. Genetically engineered Pseudomonas strains capable of metabolizing ethylene glycol and its metabolic intermediates.
• International patent PCT/JP 2014/079090. Development of high tolerant yeast strain to the complex inhibitory stress of lignocelluloses hydrolysate through targeting SUMO–dependent ubiquitin system, manufacture the microbe and the method to produce ethanol using the microbes.

Publications:

• Turner TL, Lane S, Jayakody LN, Zhang GC, Kim H, Cho WY, Jin YS (2019). Deletion of JEN1 nd ADY2 reduces lactic acid yield from an engineered Saccharomyces cerevisiae, in xylose medium, expressing a heterologous lactate dehydrogenase. FEMS Yeast Research. Link
• Li WJ, Jayakody LN, Franden MA, Wehrmann M, Daun T, Hauer B, Blank LM, Gregg Beckham T, Klebensberger J, Wierckx N (2019). Genomic and metabolic basis of ethylene glycol metabolism by Pseudomonas putida KT2440. Environmental Microbiology. Link
• Jayakody LN, Liu JJ, Yun EU, Turner TL, Oh EJ, Jin YS (2018). Direct conversion of cellulose into ethanol and ethyl-β-D-glucoside via engineered Saccharomyces cerevisiae. Biotechnology and Bioengineering. 115(12):2859-2868. Link
• Jayakody LN, Turner TL, Liu JJ, Kong II, Jin YS. (2018). Gre2p expression in engineered xylose-fermenting Saccharomyces cerevisiae improved tolerance to glycolaldehyde during xylose metabolism. Applied Microbiology and Biotechnology. 102(18):8121-8133. Link
• Franden MA, Jayakody LN*, Li WJ, Seiler S, Hauer B, Blank L, Klebensberger J, Beckham GT, Wierckx N (2018). Engineering Pseudomonas putida KT2440 for efficient ethylene glycol utilization. Metabolic Engineering. 48:197-207. (* First author equal contributor) Link
• Jayakody LN, Johnson CW, Whitham JM, Giannone RJ, Black B, Cleveland NS, Klingeman DM, Michener WE, Olstad JL, Vardon DR, Brown RC, Brown SD, Hettich RL, Guss AM, Beckham GT (2018), Thermochemical wastewater valorization via enhanced microbial toxicity tolerance. Energy & Environmental Science, 11: 1625-1638 (*Selected as 2018 Energy and Environmental Science HOT Articles) Link
• Jayakody LN, Ferdouse J, Hayashi N, Kitagaki H (2017). Identification and detoxification of glycolaldehyde, an unattended bioethanol fermentation inhibitor. Critical Review in Biotechnology, 37(2):177-189. Link
• Liu JJ, Kong II, Zhang GC, Jayakody LN, Kim H, Xia PF, Kwak S, Sung BH, Sohn JH, Walukiewicz HE, Rao CV, Jin YS (2016). Metabolic Engineering of Probiotic Saccharomyces boulardii. Applied and Environment Microbiology, 82(8):2280-2287. Link
• Jayakody LN, Lane S, Kim H, Jin YS. (2016). Mitigating health risks associated with alcoholic beverages through metabolic engineering. Current Opinion in Biotechnology, 37:173-181. Link
• Xia PF, Turner TL, Jayakody LN* (2016). The Role of GroE chaperonins in developing biocatalysts for biofuel and chemical production. Enzyme Engineering, 5 (3), 153. (* corresponding author)
• Notonier S, Meyers A, Jayakody LN* (2016). An overview of P450 enzymes: opportunity and challenges in industrial applications, Enzyme Engineering, 5 (3), 152 (* corresponding author) Link
• Sawada K, Sato T, Hamajima H, Jayakody LN, Hirata M, Yamashiro M, Tajima M, Mitsutake S, Nagao K, Tsuge K, Abe F, Hanada K, Kitagaki H (2015). Glucosylceramide contained in mold-cultured cereal confers membrane and flavor modification and stress tolerance to yeast during co-culture fermentation. Applied and Environmental Microbiology, 81: 3688-3698. Link
• Jayakody LN, Kadowaki M, Tsuge K, Horie K, Suzuki A, Hayashi N, Kitagaki H (2015). SUMO expression shortens the lag phase of Saccharomyces cerevisiae yeast growth caused by complex interactive effects of major mixed fermentation inhibitors found in hot-compressed water-treated lignocelluloses hydrolysate. Applied Microbiology and Biotechnology, 99: 501-515. (Alltech young scientist award 2013, Renewable Energy Global Innovation, 2015) Link
• Shiroma S, Jayakody LN, Horie K, Okamoto K, Kitagaki H (2014). Enhancement of ethanol fermentation of Saccharomyces cerevisiae sake yeast strain by disrupting mitophagy function. Applied and Environmental Microbiology 80:1002-1012. Link
• Hiroshi K, Tan H, Jayakody LN (2013). Analysis of the role of mitochondria of sake yeast during sake brewing and its applications in fermentation technologies. AGri- Bioscience Monographs 3:1-12. Link
• Jayakody LN, Horie K, Hayashi N, Kitagaki H (2013). Engineering redox cofactor utilization for detoxification of glycolaldehyde, a key inhibitor of bioethanol production, in yeast Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 97: 6589-6600. Link
• Jayakody LN, Tsuge K, Suzuki A, Shimoi H, Kitagaki H (2013). Identification of sulphate ion as one of the key components of yeast spoilage of a sports drink through genome-wide expression analysis. Journal of General and Applied Microbiology 59: 227-238. Link
• Kitagaki H, Jayakody LN, Hayashi N (2013). Breeding of a yeast strain resistant to hot-compressed water-treated lignocelluloses by detoxification of a fermentation inhibitors, glycolaldehyde. Bioscience and Industry 71:155-156. Link
• Hirata H, Tsuge K, Jayakody LN, Urano Y, Sawada K, Inaba S, Nagao K, Kitagaki H (2012). Structural determination of glucosylceramides in the distillation remnants of shochu, the Japanese traditional liquor, and its production Aspergillus kawachii. Journal of Agricultural and Food Chemistry 60:11473-11482. Link
• Jayakody LN, Horie K, Hayashi N, Kitagaki H (2012). Improvement of Saccharamyces cerevisiae to hot-compressed water treated cellulose by expression of ADH1. Applied Microbiology and Biotechnology 94: 273-283. (Key scientific Article in Renewable Energy Global Innovation (REGI)2012). Link
• Jayakody LN, Hayashi N, Kitagaki H (2011). Identification of glycolaldehyde as the key inhibitor of bioethanol fermentation by yeast and genome-wide analysis of its toxicity. Biotechnology Letters 33: 285-292. Link