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Xyleco's Redacted MCAN Submission Xyleco’s Redacted MCAN Submission T. reesei, strain 3CH-3 J-19-0001 January 24, 2020 145854099.4 i. Introduction Xyleco is seeking to use a modified T. reesei during its cellulase enzyme-production process using, e.g., corn stover or other inductant to induce the production of biomass-degrading cellulases. These cellulases are to be utilized for the manufacture of sugars such as xylose and glucose, or sugar-derived substances such as lactic acid. The EPA has previously determined that modified T. reesei is not likely to present an unreasonable risk, is not pathogenic to humans or animals, and has a long history of safe use for production of enzymes in a variety of industries, including sugar production, food and animal feed, pharmaceuticals, textiles, and paper processing.1 Xyleco’s enzyme preparations derived from strain 3CH-3, originating from Bio-Safety Level I RUT- C30 strain, is not likely to present an unreasonable risk. As required under 40 CFR § 725.155, Xyleco submits the following information regarding the organism, the enzyme’s safe attributes, as well as the Company’s benign production and disposal of the organism. Section I provides Submitter identification. Section II provides the microorganism information including the features and historical background of strain RUT-C30 from which the modified production strain 3CH-3 will be derived. Section III summarizes the purpose of using strain 3CH-3 for its enzyme production. Section IV details the genetic construction of the microorganism to enzyme production. Pursuant to § 14(c) of the Toxic Substances Control Act (TSCA), as amended by the Frank R. Lautenberg Chemical Safety for the 21st Century Act, the Company requests that the information be treated as Confidential Business Information (“CBI”) exempt from public disclosure. Xyleco believes this information does not require substantiation under 15 U.S.C. § 2613(c)(2). Section V describes Xyleco's proposed manufacturing process, including the fermentation process, recovery of the enzyme product, an inactivation step prior to saccharification, saccharification, disposal procedures and production volumes. Pursuant to § 14(c) of TSCA, the Company requests that the information be treated as CBI exempt from public disclosure. Xyleco believes this information does not require substantiation under 15 U.S.C. § 2613(c)(2). Section VI provides a description of the intended categories of use by function and application of the enzyme preparation and byproducts from the manufacturing of the organism. Section VII provides information on worker exposure and procedures to minimizes releases to the environment. 1 See TSCA Section 5(a)(3)(C) Determination for Microbial Commercial Activity Notice (MCAN) J-17-0022. 1 145854099.4 Section VIII includes the certification required under 15 U.S.C. § 2613(c)(5). Appendices A – I include information, details and data which might be helpful to reference about the topics discussed in this notice. 2 145854099.4 I. Submitter Identification (1) The name and headquarters of the submitter. Xyleco, Inc.2 360 Audubon Road Wakefield, MA 01880 (2) The name, address, and telephone number of the principal technical contacts representing the submitter. Xyleco, Inc. Attn.: Craig Masterman 360 Audubon Road Wakefield, MA 01880 (t) 781.557.5578 masterman@xyleco.com Perkins Coie LLP Attn: Jeffrey Hunter 1120 NW Couch Street, 10th Floor Portland, OR 97209 (t) 503.727.2265 JHunter@perkinscoie.com 2 A Delaware Corporation. 3 145854099.4 II. Microorganism Information A. Historical Overview and Phenotypic Traits T. reesei is believed to be an anamorph (asexual stage) of the fungus Hypocrea Jecorina. The T. reesei strain QM6a (wild type) was originally isolated from the Solomon Islands during World War II due to its degradation of canvas and garments of the US Army. It is commonly present on decaying plant matter. Trichoderma species exist within soils of all climates. All strains of T. reesei currently used in biotechnology and basic research are derived from this one isolate. In a 1970’s mutagenesis program at Rutgers University, a combination of UV light, electron beam radiation and chemical mutagenesis was used to generate QM6a mutant strains with higher cellulase production. One of the strains isolated was the hypersecreting RUT-C30, or T. reesei, modified.3 RUT-C30 is classified as Biosafety Level I (BSL1), meaning it is a well-characterized agent not known to present a risk to human health, while presenting minimal potential hazards to laboratory personnel and the environment. Many BSL1 organisms including T. reesei RUT-C30 have been utilized in food production processes.4 The EPA has previously determined that T. reesei RUT-C30 is not likely to present an unreasonable risk, is not pathogenic to humans or animals, and has a long history of safe use for production of enzymes.4 B. Taxonomic Designation Kingdom: Fungi Phylum: Ascomycota Class: Sordariomycetes Order: Hypocreales Family: Hypocreaceae Genus: Trichoderma Species: reesei Production strain: 3CH-3 Name of the Strain modified to produce Xyleco T. reesei 3CH-3: NRRL11460 (equivalent to ATCC 56765 or RUT-C30) C. Morphological and Physiological Features T. reesei is a mesophilic filamentous fungus. The hypersecreting feature of RUT-C30 was found to be associated with changes in ultrastructure of the strain, such as higher endoplasmic reticulum (ER) content.5 3 Peterson R. & Nevalainen H. (2012) Trichoderma reesei RUT-C30--thirty years of strain improvement. Microbiology. 2012 Jan;158(Pt 1):58-68. doi: 10.1099/mic.0.054031-0 4 See TSCA Section 5(a)(3)(C) Determination for Microbial Commercial Activity Notice (MCAN) J-17-0022. 5 Increased endoplasmic reticulum content of a mutant of Trichoderma reesei (RUT-C30) in relation to cellulase synthesis, Ghosh, Enzyme Microb Technol 4, 110–113. 4 145854099.4 RUT-C30 was also reported to lack the typical stacked appearance of the Golgi body which instead resembled individual ER-associated saccules.6 6 Subcellular fractionation of a hypercellulolytic mutant, Trichoderma reesei Rut-C30: localization of endoglucanase in microsomal fraction, Glenn, Appl Environ Microbiol 50, 1137–1143. 5 145854099.4 III. Purpose of Enzyme A. General RUT-C30, the hyper-secreting, hyper-producing mutant strain of T. reesei is a workhorse industrial strain and serves as the recipient strain for genetic modification, by introduction of β- glucosidase (cel3a). T. reesei RUT-C30 has an extensive history of safe use in industrial enzyme production in a variety of industries, including sugar production, food and animal feed, pharmaceuticals, textiles, and paper processing. See TSCA Section 5(a)(3)(C) Determination for Microbial Commercial Activity Notice (MCAN) J-19-0001. One well-known bottleneck in the RUT-C30 cellulolytic process is the relatively low expression of endogenous β-glucosidase (cel3a), resulting in low cellobiose hydrolysis and therefore lower monosaccharide yields. β-glucosidase has also been attributed to several other applications such as in food technology, the cosmetic industry, and various other commercial applications.7 The term cellulases broadly describes enzymes that catalyze the hydrolysis of the β-1,4- glycosidic bonds between individual glucose units within cellulose. The mechanism of cellulosic breakdown involves the synergistic action of endoglucanases, cellobiohydrolases, and β-glucosidases. Β-glucosidase (cel3a) is an extra-cellular enzyme which hydrolyzes cellobiose and cellooligosaccharides to release fermentable D-glucose. B. Common or Usual Name of Substance The enzyme preparation is a biological material containing secreted cellulases (the “Cocktail”), along with any organic and inorganic material derived from cultivation and fermentation processes. The over-expressed enzyme is β-glucosidase. Β-glucosidase is also commonly known as cellobiase or Bgl2, EC no. 3.2.1.21. Other designations include β-D-glucosidase and β-glucoside glucohydrolase, gentiobiase, emulsin, elaterase, aryl-β-glucosidase, β-glucoside glucohydrolase, arbutinase, amygdalinase, p- nitrophenyl β-glucosidase, primeverosidase, linamarase, salicilinase, and β-1,6-glucosidase. 7 Vaithanomsat, P., Songpim, M., Malapant, T., Kosugi, A., Thanapase, W., & Mori, Y. (2011). Production of β- Glucosidase from a Newly Isolated Aspergillus Species Using Response Surface Methodology. International Journal of Microbiology, 2011, 949252. doi: 10.1155/2011/949252 Juhasz T, Kozma K, Szengyel Z, Reczey K. (2003) Production of β-glucosidase in mixed culture of Aspergillus Niger BKMF 1305 and Trichoderma reesei RUT C30. Food Technol Biotechnol. 2003; 41:49–53 Karray R., Hamza M., Sayadi S. (2015) Evaluation of ultrasonic, acid, thermo-alkaline and enzymatic pre-treatments on anaerobic digestion of Ulva rigida for biogas production. Bioresour Technology 2015;187:205-213. doi: 10.1016/j.biortech.2015.03.108. 6 145854099.4 IV. Genetic Construction A. Recipient Organism The T. reesei RUT-C30 host strain was genetically engineered to overexpress modified endogenous β-glucosidase gene. 1. The name of the enzyme is β-glucosidase. See Section III B for other designations. 2. The name of the protein production strain is Trichoderma reesei 3CH-3. B. Donor Organism The homologous enzyme β-glucosidase gene described in this submission was selected in order to overcome bottleneck β-glucosidase activity of the parent strain, thus enhancing cellulosic degradation and bioconversion of lignocellulosic biomass to bioethanol and other biofuels. The native nucleotide sequence
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