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(12) United States Patent (10) Patent No.: US 9.273,100 B2 Hallen-Adams Et Al

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(12) United States Patent (10) Patent No.: US 9.273,100 B2 Hallen-Adams Et Al US009273 100B2 (12) United States Patent (10) Patent No.: US 9.273,100 B2 Hallen-Adams et al. (45) Date of Patent: Mar. 1, 2016 (54) USE OF GALERINA MARGINATA GENES AND “U.S. Appl. No. 12/268,229, Final Office Action mailed Feb. 28, PROTEINS FOR PEPTIDE PRODUCTION 2013', 7 pgs. “U.S. Appl. No. 12/268,229. Final Office Action mailed Apr. 4. 2012”, 8 pgs. (75) Inventors: Heather E. Hallen-Adams, Lincoln, NE “U.S. Appl. No. 12/268,229. Non Final Office Action mailed Jul 16, (US); John S. Scott-Craig, East 2012', 9 pgs. Lansing, MI (US); Jonathan D. Walton, “U.S. Appl. No. 12/268,229. Non Final Office Action mailed Jul 22, East Lansing, MI (US); Hong Luo, 2011”, 13 pgs. Lansing, MI (US) “U.S. Appl. No. 12/268,229. Non Final Office Action mailed Dec. 21, 2010”, 13 pgs. (73) Assignee: Board of Trustees of Michigan State “U.S. Appl. No. 12/268,229. Preliminary Amendment filed Jun. 10, University, East Lansing, MI (US) 2009, 16 pgs. “U.S. Appl. No. 12/268,229, Response filed May 24, 2013 to Final Office Action mailed Feb. 28, 2013”, 6 pgs. (*) Notice: Subject to any disclaimer, the term of this “U.S. Appl. No. 12/268,229. Response filed May 27, 2011 to Supple patent is extended or adjusted under 35 mental Non-Final Office Action mailed Dec. 27, 2010”, 31 pgs. U.S.C. 154(b) by 105 days. “U.S. Appl. No. 12/268,229. Response filed Jun. 4, 2012 to Final Office Action mailed Apr. 4, 2012, 13 pgs. (21) Appl. No.: 13/362,561 “U.S. Appl. No. 12/268,229, Response filed Jun. 25, 2012 to Advi sory Action mailed Jun. 13, 2012 and to Final Office Action mailed (22) Filed: Jan. 31, 2012 Apr. 4, 2012, 15 pgs. “U.S. Appl. No. 12/268,229, Response filed Oct. 18, 2010 to Restric (65) Prior Publication Data tion Requirement mailed Sep. 16, 2010”. 1 pg. “U.S. Appl. No. 12/268,229, Response filed Nov. 16, 2012 to Non US 2012/O276588A1 Nov. 1, 2012 Final Office Action mailed Jul. 16, 2012', 12 pgs. “U.S. Appl. No. 12/268,229, Response filed Dec. 22, 2011 to Non Related U.S. Application Data Final Office Action mailed Jul. 22, 2011”, 13 pgs. “U.S. Appl. No. 12/268,229. Restriction Requirement mailed Sep. (63) Continuation-in-part of application No. 12/268,229. 16, 2010”, 7 pgs. filed on Nov. 10, 2008. “U.S. Appl. No. 12/268,229, Supplemental Non Final Office Action mailed Dec. 27, 2010”, 14pgs. (60) Provisional application No. 61/002,650, filed on Nov. “Machine Translation of CN1341362, obtained on Dec. 21, 2010’, 7 9, 2007. OgS. Ahn, J. H., et al., “An Extended Physical Map of the TOX2 Locus of (51) Int. Cl. Cochliobolus carbonum Required for Biosynthesis of HC-Toxin'. CI2N 9/48 (2006.01) Fungal Genet. Biol. 35(1), (2002), 31-38. CI2N L/20 (2006.01) Alves, A.M. C. R. et al., “Highly Efficient Production of Laccase by CI2O I/68 (2006.01) the Basidiomycete Pycnoportis cinnabarintis',s Appl. Environ. C07K L/00 (2006.01) Microbiol., 70(11). (2004), 6379-6384. C07K 7/64 (2006.01) Bamburg, J. R., “Proteins of the ADF/cofilin family: essential regu lators of actin dynamics.”. Annu. Rev. Cell. Dev. Biol. 15, (1999), C07K I4/375 (2006.01) 185-230. (52) U.S. Cl. Benedict, R. G., et al., "Fermentative Production of Amanita Toxins CPC ................. C07K 7/64 (2013.01); C07K 14/375 by a Strain of Galerina marginata", J. Bacteriol. 91(3), (1966), (2013.01) 1380-1381. (58) Field of Classification Search Beutler, J. A., et al., "Chemical Variation in Amanita', J. Nat. Prod, USPC .................. 536/23.2; 435/6, 212, 6.1, 252.31 44(4), (1981), 422-431. See application file for complete search history. Brandt, I., et al., “Suggested functions for prolyl oligopeptidase: A puzzling paradox”. Clin. Chim Acta, 377(1-2), (2007), 50-61. (56) References Cited (Continued) U.S. PATENT DOCUMENTS Primary Examiner — Maryam Monshipouri 4,683, 195 A 7, 1987 Mullis et al. (74) Attorney, Agent, or Firm — Schwegman Lundberg & 4,683.202 A 7, 1987 Mullis Woessner, P.A. 4,965,188 A 10, 1990 Mullis et al. 5,928,906 A 7, 1999 Koster et al. (57) ABSTRACT 2001 OO14445 A1 8, 2001 Urnovitz 2004/0081978 A1 4/2004 Ziman et al. The present invention relates to compositions and methods 2005/0255486 A1 11/2005 Behlke et al. comprising genes and peptides associated with cyclic pep 2006/0141495 A1 6, 2006 Wu 2008/0076677 A1 3/2008 Yershov et al. tides and cyclic peptide production in mushrooms. In particu 2009/0093620 A1 4/2009 Kovalic et al. lar, the present invention relates to using genes and proteins 2010/0267,019 A1 10/2010 Hallen et al. from Galerina species encoding peptides specifically relating to amatoxins in addition to proteins involved with processing FOREIGN PATENT DOCUMENTS cyclic peptide toxins. In a preferred embodiment, the present invention also relates to methods for making Small peptides CN 1341362 A 3, 2002 and Small cyclic peptides including peptides similar to aman OTHER PUBLICATIONS itin. Further, the present inventions relate to providing kits for making Small peptides. “U.S. Appl. No. 12/268,229, Advisory Action mailed Jun. 13, 2012”. 3 pgs. 16 Claims, 79 Drawing Sheets US 9.273,100 B2 Page 2 (56) References Cited Letschert, K., et al., “Molecular Characterization and Inhibition of Amanitin Uptake into Human Hepatocytes.”. Toxicol Sci., 91(1), OTHER PUBLICATIONS (2006), 140-149. Bulaj. G. et al., “Efficient oxidative folding of conotoxins and the Lindell, T.J., et al., “Specific Inhibition of Nuclear RNA Polymerase radiation of venomous cone snails'. Proc. Natl. Acad. Sci. USA, 100 II by O-Amanitin”, Science, 170(3959), (1970), 447-449. Lugones, L. G., et al., “Introns are necessary for mRNA accumula 2), (2003), 14562-14568. tion in Schizophyilurn commune', Mol. Microbiol. 32(4), (1999), Bushnell, D.A., et al., “Structural basis of transcription: O-Amanitin 681-700. RNA polymerase II cocrystal at 2.8 A resolution”, Proc. Natl. Acad. Malonek, S., et al., “Functional Characterization of Two Cytochrome Sci. USA,99(3), (2002), 1218-1222. P450 Monooxygenase Genes, P450-1 and P450-4, of the Gibberellic Butera, R., et al., “Diagnostic accuracy of urinary amanitin in Sus acid Gene Cluster in Fusarium proliferatum (Gibberellafiujikuroi pected mushroom poisoning: a pilot study’. Clinical Toxicology, MP-D)”, Appl. Environ. Microbiol. 71(3), (2005), 1462-1472. 42(6). (2004), 901-912. Maniatis, T., et al., “Regulation of Inducible and Tissue-Specific Craik. D. J., “Chemistry. Seamless Proteins Tie Up Their Loose Gene Expression”, Science, 236(4806), (1987), 1237-1245. Ends', Science, 311(5767), (2006), 1563-1564. Marqulies, M., et al., “Genome Sequencing in Microfabricated High Craik. D. J., et al., “The chemistry and biology of cyclotides'. Curr: Density Picolitre Reactors', Nature, 437(7057), (2005), 376-380. Opin. Drug Discov. Devel., 10(2), (2007), 176-184. May, J. P. et al., “Tryptathionine Bridges in Peptide Synthesis'. Crooks, G. E., et al., “WebLogo: A Sequence Logo Generator'. Biopolymers, 88(5), (2007), 714-724. Genome Res, 4(6), (2004), 1188-1190. Muraoka, S., et al., “Detection and Identification of Amanitins in the Cunningham, D. F., et al., “Proline specific peptidases”. Biochim Wood-Rotting Fungi Galerina fasciculata and Galerina Biophy's Acta, 1343(2), (1997), 160-186. helvoliceps, Appl. Environ. Microbiol. 65(9), (1999), 4207-4210. Duquesne, S., et al., “Two Enzymes Catalyze the Maturation of a Muraoka, S., et al., “Effective Production of Amanitins by Two-Step Lasso Peptide in Escherichia coli'', Chem. Biol., 14(7), (2007), 793 Cultivation of the Basidiomycete, Galerina fasciculata GF-060". J. 803. Biosci. Bioeng, 89(1), (2000), 73-76. Nikolskaya, A. N., et al., “Identification of peptide synthetase-encod Enjalbert. F., et al., “Treatment of Amatoxin Poisoning: 20-Year ing genes from filamentous fungi producing host-selective Retrospective Analysis, review of poisonings.”. J. Toxicol. Clin. phytotoxins or analogs”. Gene, 165(2), (1995), 207-211. Toxicol., 40(6), (2002), 715-757. Novick, R. P. et al., “Quorum Sensing in Staphylococci'. Annu. Rev. Escoubas, P. “Molecular diversification in spider venoms: A web of Genet., 42, (2008), 541-564. combinatorial peptide libraries.”. Mol. Divers., 10(4), (2006), 545 Olivera, B. M.. “Conus Peptides: Biodiversity-based Discovery and 554. Exogenomics”. J. Biol. Chern., 281, (2006), 31173-3 1177. Finking, R. et al., “Biosynthesis of Nonribosomal Peptides'. Annu. Panaccione, D. G., “Multiple families of peptide synthetase genes Rev. Microbiol. 58, (2004), 453-488 from ergopeptine-producing fungi'. Mycological Research, 100(4), Frohman, M. 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