Granted Patent
B2
US 12,460,195 · App. 18/503,542 · Granted Nov 4, 2025
Engineered deoxyribose-phosphate aldolases
Inventors:
Da Duan (Foster City, CA); Oscar Alvizo (Fremont, CA); Jovana Nazor (Milpitas, CA); Harvinder Chagger Maniar (Hayward, CA); James Nicholas Riggins (San Francisco, CA); Jonathan Vroom (South San Francisco, CA); Santhosh Sivaramakrishnan (Redwood City, CA); Hao Yang (Rahway, NJ); Anna Fryszkowska (New York, NY); Mark A. Huffman (Rahway, NJ); Joshua N. Kolev (Rahway, NJ); Iman Farasat (Rahway, NJ); Agustina Rodriguez-Granillo (Rahway, NJ); Deeptak Verma (Rahway, NJ)
Assignee:
Codexis, Inc.
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Abstract
The present invention provides engineered deoxyribose-phosphate aldolase polypeptides useful under industrial process conditions for the production of pharmaceutical and fine chemical compounds.
Claims (11)
1 . An engineered deoxyribose-phosphate aldolase comprising a polypeptide sequence having at least 95% sequence identity to SEQ ID NO: 2, or a functional fragment thereof, wherein said engineered deoxyribose-phosphate aldolase comprises a substitution in said polypeptide sequence of a methionine residue at position 47 relative to SEQ ID NO: 2, wherein said engineered deoxyribose-phosphate aldolase exhibits at least one improved property compared to the wild-type deoxyribose-phosphate aldolase of SEQ ID NO:2.
2 . The engineered deoxyribose-phosphate aldolase of claim 1 , wherein said polypeptide sequence further comprises at least one substitution or substitution set in said polypeptide sequence at one or more positions relative to SEQ ID NO: 2 selected from 10/66/141/145/156, 2, 6, 9, 10/88/156, 13, 31, 46, 134/141/212, 66, 66/88/112/134/141/143/145/212, 71, 72, 88, 94, 102, 104, 112, 116, 133, 133/173/204/235/236, 134, 147, 173, 184, 189, 197, 203, 204, 207, 226, 235, 235/236, and 236.
3 . The engineered deoxyribose-phosphate aldolase of claim 1 , wherein said polypeptide sequence further comprises at least one substitution or substitution set in said polypeptide sequence at one or more positions relative to SEQ ID NO: 2 selected from 2, 2/6/10/66/88/102/184/235/236, 2/6/102/141/203/235, 2/10/102/235/236, 2/66/71/141/184/203/235/236, 2/71/88/203/235/236, 2/71/141/197/235/236, 2/88/141/235/236, 2/203/235/236, 5, 6/203/235/236, 9, 10/66/184/197/236, 10/66/235/236, 10/71/184/203/235/236, 13, 13/46, 13/46/66/94, 13/46/66/94/184/204, 13/46/66/133/134/184, 13/46/66/184, 13/46/112/134/184, 13/46/133/184, 13/66/94, 13/66/94/184, 13/66/112/133/134/184/204, 13/66/112/133/134/204, 13/66/112/184, 13/66/133/134/184/204, 13/66/184/204, 13/94/133/184, 13/94/184, 13/94/184/204, 13/133/134/184, 13/133/134/204, 13/134/204, 13/184, 27, 40, 46/66/94/112, 46/66/112/133/134/184, 46/66/133/134, 46/66/133/184/197, 46/66/133/197, 46/66/134/184/197/204, 46/66/184, 46/112/133, 46/112/133/134/204, 46/133/204, 46/197/204, 66/71/88/203/235/236, 66/71/141/184, 66/88/184/235, 66/88/203/235/236, 66/141/235/236, 66/184/197/203/235/236, 66/184/197/236, 71/88/184/203/235, 71/88/184/203/236, 71/141/184/203/235, 71/184, 71/184/197/236, 71/184/235, 71/184/236, 88/102/141/235/236, 88/203/235/236, 88/235/236, 102/184/197/235/236, 102/203/235/236, 141/184, 141/184/236, 184/236, 203/235, 203/235/236, 203/236, 235/236, 62, 66, 66/88/102/184/197/203/235/236, 66/88/197, 66/88/235, 66/88/235/236, 66/94, 66/94/112/133/184, 66/94/112/184/204, 66/102/184/235/236, 66/112/133/134/197, 66/112/133/197, 66/112/134/197, 66/112/184, 66/133/184, 66/133/197, 66/184, 66/197/203/235, 84, 88, 88/102/141/184/235/236, 88/184, 88/184/197/203/235/236, 88/184/197/235/236, 88/184/203/235, 88/184/236, 88/197/235/236, 88/236, 94/112/184/197, 94/133/184, 96, 102/141/203, 102/184/203/236, 102/184/236, 102/197/235, 112, 112/133/134, 112/133/184/204, 112/134/197, 114, 115, 120, 127, 132, 133, 133/134/184, 141/184/203/235/236, 141/184/235, 141/197, 141/203/235/236, 141/236, 146, 148, 184, 184/203, 184/203/235, 184/203/236, 184/235/236, 184/236, 197/235, 203/235/236, 203/236, 204, 218, 235, 235/236, and 236.
4 . The engineered deoxyribose-phosphate aldolase of claim 1 , wherein said polypeptide sequence further comprises at least one substitution or substitution set in said polypeptide sequence relative to SEQ ID NO: 2 at one or more positions selected from 71/88/94/133, 71/133, and 133.
5 . The engineered deoxyribose-phosphate aldolase of claim 1 , wherein said engineered deoxyribose-phosphate aldolase comprises a polypeptide sequence that is at least 95% identical to the sequence of at least one engineered deoxyribose-phosphate aldolase variant set forth in the even numbered sequences of SEQ ID NOS: 4-478.
6 . The engineered deoxyribose-phosphate aldolase of claim 1 , wherein said engineered deoxyribose-phosphate aldolase comprises a polypeptide sequence forth in the even numbered sequences of SEQ ID NOS: 4, 6, 8, 124, and 140-326, 334, 338, 342, 344, 348-352, 356, 358, 362, 374, 376, 386, 388, 392-396, 400, 402, 406-410, 418, 420-424, 428, 430, 434-440, 448, 450, 454, 456, 460-464, 470, and 472.
7 . The engineered deoxyribose-phosphate aldolase of claim 1 , wherein said improved property comprises improved activity on a substrate.
8 . The engineered deoxyribose-phosphate aldolase of claim 7 , wherein said substrate comprises R-2-ethynyl-glyceraldehyde.
9 . The engineered deoxyribose-phosphate aldolase of claim 1 , wherein said improved property comprises improved thermostability.
10 . The engineered deoxyribose-phosphate aldolase of claim 1 , wherein said engineered deoxyribose-phosphate aldolase is purified.
11 . A composition comprising at least one engineered deoxyribose-phosphate aldolase provided in claim 1 .
Assignments (1)
SECURITY INTEREST
Recorded Feb 15, 2024
From: CODEXIS, INC.
To: INNOVATUS LIFE SCIENCES LENDING FUND I, LP, AS COLLATERAL AGENT
Reel/Frame 066600/0650 →
Continuity (5)
Provisional Application
62822273
· Mar 22, 2019
Provisional Application
62695520
· Jul 9, 2018
References Cited (239)
US 5308854A
· Hoffman, Jr. et al.
· 1994
[cited by applicant]
US 5527819A
· Williams et al.
· 1996
[cited by applicant]
US 5605793A
· Stemmer
· 1997
[cited by applicant]
US 5811238A
· Stemmer et al.
· 1998
[cited by applicant]
US 5830721A
· Stemmer et al.
· 1998
[cited by applicant]
US 5834252A
· Stemmer et al.
· 1998
[cited by applicant]
US 5837458A
· Minshull et al.
· 1998
[cited by applicant]
US 5928905A
· Stemmer et al.
· 1999
[cited by applicant]
US 6096548A
· Stemmer
· 2000
[cited by applicant]
US 6117679A
· Stemmer
· 2000
[cited by applicant]
US 6132970A
· Stemmer
· 2000
[cited by applicant]
US 6165793A
· Stemmer
· 2000
[cited by applicant]
US 6180406B1
· Stemmer
· 2001
[cited by applicant]
US 6251674B1
· Tobin et al.
· 2001
[cited by applicant]
US 6265201B1
· Wackett et al.
· 2001
[cited by applicant]
US 6277638B1
· Stemmer
· 2001
[cited by applicant]
US 6287861B1
· Stemmer et al.
· 2001
[cited by applicant]
US 6287862B1
· delCardayre et al.
· 2001
[cited by applicant]
US 6291242B1
· Stemmer
· 2001
[cited by applicant]
US 6297053B1
· Stemmer
· 2001
[cited by applicant]
US 6303344B1
· Patten et al.
· 2001
[cited by applicant]
US 6309883B1
· Minshull et al.
· 2001
[cited by applicant]
US 6319713B1
· Patten et al.
· 2001
[cited by applicant]
US 6319714B1
· Crameri et al.
· 2001
[cited by applicant]
US 6323030B1
· Stemmer
· 2001
[cited by applicant]
US 6326204B1
· delCardayre et al.
· 2001
[cited by applicant]
US 6335160B1
· Patten et al.
· 2002
[cited by applicant]
US 6335198B1
· delCardayre et al.
· 2002
[cited by applicant]
US 6337186B1
· Krebber
· 2002
[cited by applicant]
US 6344356B1
· Stemmer
· 2002
[cited by applicant]
US 6352859B1
· delCardayre et al.
· 2002
[cited by applicant]
US 6355484B1
· Patten et al.
· 2002
[cited by applicant]
US 6358740B1
· Patten et al.
· 2002
[cited by applicant]
US 6358742B1
· Stemmer
· 2002
[cited by applicant]
US 6365377B1
· Patten et al.
· 2002
[cited by applicant]
US 6365408B1
· Stemmer
· 2002
[cited by applicant]
US 6368861B1
· Crameri et al.
· 2002
[cited by applicant]
US 6372497B1
· Stemmer
· 2002
[cited by applicant]
US 6376246B1
· Crameri et al.
· 2002
[cited by applicant]
US 6379964B1
· delCardayre et al.
· 2002
[cited by applicant]
US 6387702B1
· Stemmer
· 2002
[cited by applicant]
US 6391552B2
· Stemmer
· 2002
[cited by applicant]
US 6391640B1
· Minshull et al.
· 2002
[cited by applicant]
US 6395547B1
· Stemmer
· 2002
[cited by applicant]
US 6406855B1
· Patten et al.
· 2002
[cited by applicant]
US 6406910B1
· Patten et al.
· 2002
[cited by applicant]
US 6413745B1
· Patten et al.
· 2002
[cited by applicant]
US 6413774B1
· Stemmer
· 2002
[cited by applicant]
US 6420175B1
· Stemmer
· 2002
[cited by applicant]
US 6423542B1
· Crameri et al.
· 2002
[cited by applicant]
US 6426224B1
· Crameri et al.
· 2002
[cited by applicant]
US 6436675B1
· Welch et al.
· 2002
[cited by applicant]
US 6444468B1
· Stemmer et al.
· 2002
[cited by applicant]
US 6455253B1
· Patten et al.
· 2002
[cited by applicant]
US 6479652B1
· Crameri et al.
· 2002
[cited by applicant]
US 6482647B1
· Stemmer
· 2002
[cited by applicant]
US 6483011B1
· Stemmer et al.
· 2002
[cited by applicant]
US 6484105B2
· Zhang
· 2002
[cited by applicant]
US 6489146B2
· Stemmer et al.
· 2002
[cited by applicant]
US 6500617B1
· Stemmer et al.
· 2002
[cited by applicant]
US 6500639B2
· Subramanian
· 2002
[cited by applicant]
US 6506602B1
· Stemmer
· 2003
[cited by applicant]
US 6506603B1
· Stemmer
· 2003
[cited by applicant]
US 6518065B1
· Stemmer
· 2003
[cited by applicant]
US 6519065B1
· Colbourne et al.
· 2003
[cited by applicant]
US 6521453B1
· Crameri et al.
· 2003
[cited by applicant]
US 6528311B1
· delCardayre et al.
· 2003
[cited by applicant]
US 6537746B2
· Arnold et al.
· 2003
[cited by applicant]
US 6573098B1
· Stemmer
· 2003
[cited by applicant]
US 6576467B1
· Stemmer
· 2003
[cited by applicant]
US 6579678B1
· Patten et al.
· 2003
[cited by applicant]
US 6586182B1
· Patten et al.
· 2003
[cited by applicant]
US 6602986B1
· Stemmer et al.
· 2003
[cited by applicant]
US 6605430B1
· Affholter et al.
· 2003
[cited by applicant]
US 6613514B2
· Patten et al.
· 2003
[cited by applicant]
US 6653072B1
· Patten et al.
· 2003
[cited by applicant]
US 6686515B1
· Lassner et al.
· 2004
[cited by applicant]
US 6703240B1
· Stemmer et al.
· 2004
[cited by applicant]
US 6716631B1
· delCardayre et al.
· 2004
[cited by applicant]
US 6825001B2
· Wackett et al.
· 2004
[cited by applicant]
US 6902922B2
· Ness et al.
· 2005
[cited by applicant]
US 6917882B2
· Selifonov et al.
· 2005
[cited by applicant]
US 6946296B2
· Patten et al.
· 2005
[cited by applicant]
US 6961664B2
· Selifonov et al.
· 2005
[cited by applicant]
US 6995017B1
· Stemmer
· 2006
[cited by applicant]
US 7024312B1
· Selifonov et al.
· 2006
[cited by applicant]
US 7058515B1
· Selifonov et al.
· 2006
[cited by applicant]
US 7105297B2
· Minshull et al.
· 2006
[cited by applicant]
US 7148054B2
· delCardayre et al.
· 2006
[cited by applicant]
US 7220566B2
· Ness et al.
· 2007
[cited by applicant]
US 7270992B2
· Shimizu et al.
· 2007
[cited by applicant]
US 7288375B2
· Stemmer et al.
· 2007
[cited by applicant]
US 7384387B1
· Raillard et al.
· 2008
[cited by applicant]
US 7399627B2
· Emalfarb et al.
· 2008
[cited by applicant]
US 7421347B2
· Selifonov et al.
· 2008
[cited by applicant]
US 7430477B2
· Selifonov et al.
· 2008
[cited by applicant]
US 7462469B2
· Bass et al.
· 2008
[cited by applicant]
US 7534564B2
· Patten et al.
· 2009
[cited by applicant]
US 7620500B2
· Mundorff et al.
· 2009
[cited by applicant]
US 7620502B2
· Selifonov et al.
· 2009
[cited by applicant]
US 7629157B2
· Davis et al.
· 2009
[cited by applicant]
US 7629170B2
· delCardayre et al.
· 2009
[cited by applicant]
US 7702464B1
· Emig et al.
· 2010
[cited by applicant]
US 7747391B2
· Gustafsson et al.
· 2010
[cited by applicant]
US 7747393B2
· Fox
· 2010
[cited by applicant]
US 7751986B2
· Gustafsson et al.
· 2010
[cited by applicant]
US 7776598B2
· Patten et al.
· 2010
[cited by applicant]
US 7783428B2
· Gustafsson et al.
· 2010
[cited by applicant]
US 7795030B2
· Minshull et al.
· 2010
[cited by applicant]
US 7853410B2
· Selifonov et al.
· 2010
[cited by applicant]
US 7868138B2
· Stemmer et al.
· 2011
[cited by applicant]
US 7873477B1
· Gustafsson et al.
· 2011
[cited by applicant]
US 7873499B2
· Selifonov et al.
· 2011
[cited by applicant]
US 7904249B2
· Selifonov et al.
· 2011
[cited by applicant]
US 7927842B2
· Shimizu et al.
· 2011
[cited by applicant]
US 7927843B2
· Shimizu et al.
· 2011
[cited by applicant]
US 7957912B2
· Selifonov et al.
· 2011
[cited by applicant]
US 7981614B2
· Stemmer et al.
· 2011
[cited by applicant]
US 8014961B2
· Bass et al.
· 2011
[cited by applicant]
US 8029988B2
· Crameri et al.
· 2011
[cited by applicant]
US 8048674B2
· Minshull et al.
· 2011
[cited by applicant]
US 8058001B2
· Crameri et al.
· 2011
[cited by applicant]
US 8076138B2
· delCardayre et al.
· 2011
[cited by applicant]
US 8108150B2
· Mundorff et al.
· 2012
[cited by applicant]
US 8170806B2
· Selifonov et al.
· 2012
[cited by applicant]
US 8224580B2
· Mundorff et al.
· 2012
[cited by applicant]
US 8377681B2
· delCardayre et al.
· 2013
[cited by applicant]
US 8383346B2
· Colbeck et al.
· 2013
[cited by applicant]
US 8457903B1
· Emig et al.
· 2013
[cited by applicant]
US 8504498B2
· Fox
· 2013
[cited by applicant]
US 8589085B2
· Selifonov et al.
· 2013
[cited by applicant]
US 8762066B2
· Fox
· 2014
[cited by applicant]
US 8768871B2
· Fox
· 2014
[cited by applicant]
US 9593326B2
· Clark et al.
· 2017
[cited by applicant]
US 20050153407A1
· Greenberg et al.
· 2005
[cited by applicant]
US 20080220990A1
· Fox
· 2008
[cited by applicant]
US 20090209001A1
· Schuermann et al.
· 2009
[cited by applicant]
US 20090312196A1
· Colbeck et al.
· 2009
[cited by applicant]
US 20110296543A1
· Chang et al.
· 2011
[cited by applicant]
US 20130332133A1
· Horn et al.
· 2013
[cited by applicant]
US 20160244787A1
· Chan et al.
· 2016
[cited by applicant]
US 20170191095A1
· Marliere
· 2017
[cited by applicant]
EP 0137280B1
· 1992
[cited by applicant]
WO 9522625A1
· 1995
[cited by applicant]
WO 9533836A1
· 1995
[cited by applicant]
WO 9600787A1
· 1996
[cited by applicant]
WO 970078A1
· 1997
[cited by applicant]
WO 9735966A1
· 1997
[cited by applicant]
WO 9827230A1
· 1998
[cited by applicant]
WO 0042651A1
· 2000
[cited by applicant]
WO 0175767A2
· 2001
[cited by applicant]
WO 2009008908A2
· 2009
[cited by applicant]
WO 2009152336A1
· 2009
[cited by applicant]
WO 2012177527A1
· 2012
[cited by applicant]
WO 2015181074A1
· 2015
[cited by applicant]
Huffman. Design of an in vitro biocatalytic cascade for the manufacture of islatravir. Science. Dec. 6, 2019;366(6470): 1255-1259.
[cited by examiner]
Altschul, S., et al., “Basic local alignment search tool,” J. Mol. Biol., 215: 403-410 (1990).
[cited by applicant]
Altschul, S.F., et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Res., 25(17):3389-3402 (1997).
[cited by applicant]
Barbas, III, C.F., et al., “Deoxyribose-5-phosphate Aldolase as a Synthetic Catalyst,” J. Am. Chem. Soc., 112:2013- 2014 [1990].
[cited by applicant]
Beaucage, S.L., et al., “Deoxynucleoside phosphoamidites—A new class of key intermediates for deoxypolynucleotide synthesis,” Tetrahedron Letters, 22(20):1859-62 (1981).
[cited by applicant]
Blaiseau, P-L., et al., “Primary structure of a chitinase-encoding gene (chi1) from the filamentous fungus
[cited by applicant]
Boel, E., et al., “Two different types of intervening sequences in the glucoamylase gene from Aspergillus niger,” EMBO J., 3:1581-85 [1984].
[cited by applicant]
Botstein, D., et al., “Strategies and applications of in vitro mutagenesis,” Science, 229(4719):1193-1201, 1985.
[cited by applicant]
Carter, P., “Site-directed mutagenesis,” Biochem. J., 237:1-7 (1986).
[cited by applicant]
Chaveroche, M., et al., “A rapid method for efficient gene replacement in the filamentous fungus
[cited by applicant]
Cho, Y., et al., “A high throughput targeted gene disruption method for Alternaria brassicicola functional genomics using linear minimal element (LME) constructs,” Mol Plant Microbe Interact, 19(1):7-15 [2006].
[cited by applicant]
Christians, F.C., et al., “Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling,” Nat. Biotechnol., 17:259-264 (1999).
[cited by applicant]
Combier, J.-P., et al., “Agrobacterium tumefaciens-mediated transformation as a tool for insertional mutagenesis in the symbiotic ectomycorrhizal fungus
[cited by applicant]
Crameri, A., et al., “DNA shuffling of a family of genes from diverse species accelerates directed evolution”, Nature, 391:288-291 (1998).
[cited by applicant]
Crameri, A., et al., “Improved green fluorescent protein by molecular evolution using DNA shuffling, ”Nat. Biotechnol., 14(3):315-319 (1996).
[cited by applicant]
Crameri, A., et al., “Molecular evolution of an arsenate detoxification pathway by DNA shuffling,” Nat. Biotechnol., 15(5):436-438 (1997).
[cited by applicant]
Dale, S.J., et al., “Oligonucleotide-directed random mutagenesis using the phosphorothioate method,” Methods Mol. Biol., 57:369-74 (1996).
[cited by applicant]
De Boer, H.A., et al., “The tac promoter: A functional hybrid derived from the trp and lac promoters,” Proc. Natl Acad. Sci. USA, 80: 21-25 (1983).
[cited by applicant]
Dean, S.M., et al., “Recent Advances in Aldolase-Catalyzed Asymmetric Synthesis,” Adv. Synth. Catal., 349(8-9): 1308-1320 [2007].
[cited by applicant]
Ehrlich, S.D.,“DNA cloning in Bacillus subtilis,” Proc. Natl. Acad. Sci. USA, 75(3):1433-1436 [1978].
[cited by applicant]
Eisenberg, D., et al., “Analysis of Membrane and Surface Protein Sequences with the Hydrophobic Moment Plot,” J. Mol. Biol., 179:125-142 [1984].
[cited by applicant]
Firon, A., et al., “Identification of Essential Genes in the Human Fungal Pathogen Aspergillus fumigatus by Transposon Mutagenesis,” Eukaryot. Cell, 2(2):247-55 [2003].
[cited by applicant]
Guo, Z., et al., “3'-End-Forming Signals of Yeast mRNA,” Mol. Cell. Biol., 15(11):5983-5990 [1995].
[cited by applicant]
Henaut and Danchin in Neidhardt et al. [eds.],
[cited by applicant]
Henikoff, S., et al., “Amino acid substitution matrices from protein blocks,” Proc. Natl. Acad. Sci. USA, 89:10915-10919 [1992].
[cited by applicant]
Hong, J., et al., “Cloning and functional expression of thermostable beta-glucosidase gene from Thermoascus aurantiacus,” Appl. Microbiol. Biotechnol, 73:1331-1339 [2007].
[cited by applicant]
Koszelewski, D., et al., “Immobilization of omega-transaminases by encapsulation in a sol-gel/celite matrix,” Journal of Molecular Catalysis B: Enzymatic, 63: 39-44 (2010).
[cited by applicant]
Kramer, B., et al., “Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of
[cited by applicant]
Lathe, R., et al., “Plasmid and bacteriolphage vecotrs for excision of intact inserts,” Gene, 57:193-201 [1987].
[cited by applicant]
Limon, C., et al., “Primary structure and expression pattern of the 33-kDa chitinase gene from the nucoparasitic fungus Trichocherma harzianum,” Curr. Genet., 28:478-83 [1995].
[cited by applicant]
Ling, M.M., et al., “Approaches to DNA Mutagenesis: An Overview,” Anal. Biochem., 254(2):157-78 [1997].
[cited by applicant]
Martin, A.R., et al., “Characterization of free and immobilized (S)-aminotransferase for acetophenone production,” Applied Microbiology and Biotechnology, 76(4): 843-851 (2007).
[cited by applicant]
Maruyama, J., “Multiple gene disruptions by marker recycling with highly efficient gene-targeting background (delta-ligD) in Aspergillus oryzae,” Biotechnol Lett., 30:1811-1817 [2008].
[cited by applicant]
Mateo, C., et al., “Epoxy sepabeads: a novel epoxy support for stabilization of industrial enzymes via very intense multipoint covalent attachment,” Biotechnology Progress 18(3):629-34 (2002).
[cited by applicant]
Matthes, H.W.D., et al., “Simultaneous rapid chemical synthesis of over one hundred oligonucleotides on a microscale,” EMBO J., 3(4):801-05 (1984).
[cited by applicant]
McInerney, J.O., “GCUA: general codon usage analysis,” Bioinformatics, 14(4):372-73 [1998].
[cited by applicant]
Minshull, J., et al., “Protein evolution by molecular breeding,” Curr. Op. Chem. Biol., 3(3):284-290 (1999).
[cited by applicant]
Nakamura, Y., et al., “Codon usage tabulated from international DNA sequence databases: status for the year 2000,” Nucl. Acids Res., 28:292 [2000].
[cited by applicant]
Needleman, S., et al., “A general method applicable to the search for similarities in the amino acid sequence of two proteins,” J. Mol. Biol. 48:443-453 (1970).
[cited by applicant]
Nunberg, J.H., et al., “Molecular Cloning and Characterization of the Glucoamylase Gene of Aspergillus awamori,” Mol. Cell Biol., 4(11):2306-2315 [1984].
[cited by applicant]
Parry, N.J., et al., “Biochemical characterization and mechanism of action of a thermostablebeta-glucosidase purified from Thermoascus aurantiacus,” Biochem. J., 353:117-127 [2001].
[cited by applicant]
Pearson, W.R., “Improved tools for biological sequence comparison,” Proc. Nat'l. Acad. Sci. USA, 85:2444-2448 (1988).
[cited by applicant]
Porath, J., “Immobilized metal ion affinity chromatography,” Protein Expression and Purification, 3:263-281 (1992).
[cited by applicant]
Racker, E., “Enzymatic Synthesis and Breakdown of Desoxyribose Phosphate,” J. Biol. Chem., 196:347-365 [1952].
[cited by applicant]
Romanos, M.A., et al., “Foreign gene expression in yeast: a review,” Yeast 8:423-488 [1992].
[cited by applicant]
Simonen, M., et al., “Protein Secretion in Bacillus Species,” Microbiological Reviews, 57:109-137 (1993).
[cited by applicant]
Smith, M., “In vitro mutagenesis,” Ann. Rev. Genet., 19:423-462 (1985).
[cited by applicant]
Smith, T., et al., “Comparison of Biosequences,” Adv. Appl. Math, 2:482-489 (1981).
[cited by applicant]
Stemmer, W., “DNA Shuffling by Random Fragmentation and Reassembly: In vitro Recombination for Molecular Evolution,” Proc. Natl. Acad. Sci. USA, 91:10747-10751 (1994).
[cited by applicant]
Stemmer, W.P.C., “Rapid evolution of a protein in vitro by DNA shuffling”, Nature, 370:389-391 (1994).
[cited by applicant]
Stenico, M., et al., “Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases,” Nucl. Acids Res. 22(13):2437-46 [1994].
[cited by applicant]
Takahashi, T., et al., “Efficient gene disruption in the koji-mold
[cited by applicant]
Tiwari, S., et al., “Prediction of probable genes by Fourier analysis of genomic sequences,” Comput. Appl. Biosci. 13 (3):263-270 [1997].
[cited by applicant]
Truppo, M.D., et al., “Development of an Improved Immobilized CAL-B for the Enzymatic Resolution of a Key Intermediate to Odanacatib,” Organic Process Research & Development, 15:1033-1035 (2011).
[cited by applicant]
Uberbacher, E.C., et al., “Discovering and Understanding Genes in Human DNA Sequence Using GRAIL,” Methods Enzymol., 266:259-281 [1996].
[cited by applicant]
Villa-Komaroff, L., et al., “A bacterial clone synthesizing proinsulin,” Proc. Natl Acad. Sci. USA, 75:3727-3731 (1978).
[cited by applicant]
Wada, K., et al., “Codon usage tabulated from the GenBank genetic sequence data,” Nucl. Acids Res., 20:2111-2118 [1992].
[cited by applicant]
Wells, J.A., et al., “Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites,” Gene, 34:315-323 (1985).
[cited by applicant]
Wilson, I.A., et al., “The structure of antigenic determinant in a protein,” Cell, 37:767-778 [1984].
[cited by applicant]
Wright, F., “The ‘effective number of codons’ used in a gene,” Gene 87:23-29 [1990].
[cited by applicant]
Yi, S., et al., “Covalent immobilization of omega-transaminase from Vibrio fluvialis JS17 on chitosan beads,” Process Biochemistry 42(5): 895-898 (2007).
[cited by applicant]
You, B., et al., “Gene-specifc disruption in the fillamentous fungus
[cited by applicant]
Zhang, J-H., et al., “Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening,”Proc. Nat. Acad. Sci., U.S.A., 94:4504-4509 (1997).
[cited by applicant]
Hoffee, P., et al., “The Mechanism of Action of Aldolases: VI. Crystallization of Deoxyribose 5-Phosphate Aldolase and the Number of Active Sites,” J. Biological Chemistry, 240(4):1512-1516 [1965].
[cited by applicant]
Bramski, J., et al., “Probing the acetaldehyde-sensitivity of 2-deoxy-ribose-5-phosphate aldolase (DERA) leads to resistant variants,” J. Biotechnology, 258:56-58 [2017].
[cited by applicant]
PubChem CID 45934311, Deoxyribose 5-phosphate, from https://pubchem.ncbi.nlm.nih.gov downloaded Apr. 25, 2018.
[cited by applicant]
Dick, M., et al., “Trading off stability against activity in extremophilic aldolases,” Nature Specific Reports, 6(17908):1-6 [2016].
[cited by applicant]
UniPROT Sequence A0A210DN74_9GAMM dated Feb. 28, 2018.
[cited by applicant]
Studer, R.A., et al., “Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes,” Biochem J., 449:581-594 [2013].
[cited by applicant]
UniProt/KB Database Accession No. A0A1E5ISV3 dated Jan. 18, 2017.
[cited by applicant]
UniProt/KB Database Accession No. DEOC_SHEHH dated Jun. 7, 2017.
[cited by applicant]
UniProt/KB Database Accession No. A0A1S2TZ70_9GAMM dated Jul. 5, 2017.
[cited by applicant]
Jennewein, S., et al., “Directed evolution of an industrial biocatalyst: 2-deoxy-D-ribose 5-phosphate aldolase,” Biotechnology Journal, 1(5): 537-548 [2006].
[cited by applicant]
Dick, M., et al., “Supplementary Information Trading off stability against activity in extremophilic adolases,” retrieved from https://static-content.springer.com/esm/art%3A10.1038%2Fsrep17908/MediaObjects/41598_2016_BF…
[cited by applicant]
Nov,Y., “When Second Best Is Good Enough: Another Probabilistic Look at Saturation Mutagenesis,” Applied and Environmental Microbiology, 78(1):258-262 [2012].
[cited by applicant]
Windle, C.L., et al., “Engineering aldolases as biocatalysts,” Current Opinion in Chemical Biology, 19:25-33 [2014].
[cited by applicant]
Desantis, G., et al., “Structure-Based mutagenesis approaches toward expanding the substrate specificity of d-2-Deoxyribose-5-phosphate aldolase,” Biooganic, 11(1):43-52 [2003].
[cited by applicant]
GenBank Accession No. PJBM01000265.1 dated Dec. 12, 2017.
[cited by applicant]
GenBank Accession No. MCBT01000041.1 dated Sep. 19, 2016.
[cited by applicant]
GenBank Accession No. CP000931.1 dated Jan. 28, 2014.
[cited by applicant]
Multispecies: deoxyribose-phosphate aldolase [Shewanella], NCBI Reference Sequence: WP_028769128.1 dated May 13, 2018.
[cited by applicant]
Jennewein et al., “Directed evolution of an industrial biocatalyst: 2-deoxy-D-ribose 5-phosphate aldolase,” Biotechnology Journal., 1(5),537-548 [2006].
[cited by applicant]