US2011294170A1PendingUtilityA1

Pentose Fermentation By a Recombinant Microorganism

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Assignee: SUBBIAN EZHILKANIPriority: May 28, 2010Filed: May 27, 2011Published: Dec 1, 2011
Est. expiryMay 28, 2030(~3.9 yrs left)· nominal 20-yr term from priority
Inventors:Ezhilkani SubbianXiyun ZhangBenjamin MijtsCatherine M. Cho
C12N 9/90C12Y 503/01005C12N 15/81Y02E50/10C12N 9/92C12P 2203/00C12P 7/04C12P 7/10C12P 19/02C12P 19/24
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Claims

Abstract

The present invention provides recombinant nucleic acid constructs comprising a xylose isomerase polynucleotide, a recombinant fungal host cell comprising a recombinant xylose isomerase polynucleotide, and related methods.

Claims

exact text as granted — not AI-modified
1 . A recombinant nucleic acid construct comprising a polynucleotide sequence that encodes a polypeptide which is capable of catalyzing the isomerization of D-xylose directly to D-xylulose, wherein the polynucleotide is a polynucleotide that encodes a polypeptide comprising an amino acid sequence having at least 70% identity to SEQ ID NO:2; or a polynucleotide that hybridizes under stringent hybridization conditions to the complement of a polynucleotide that encodes a polypeptide having the amino acid sequence of SEQ ID NO:2. 
     
     
         2 . The nucleic acid construct of  claim 1 , wherein the polynucleotide sequence encodes a polypeptide comprising an amino acid sequence at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO:2. 
     
     
         3 . The nucleic acid construct of  claim 2 , wherein the polynucleotide sequence encodes a polypeptide comprising the amino acid sequence of SEQ ID NO:2. 
     
     
         4 . The nucleic acid construct of  claim 2 , wherein the polynucleotide sequence encodes a polypeptide consisting of the amino acid sequence of SEQ ID NO:2. 
     
     
         5 . The nucleic acid construct of  claim 2 , wherein said polynucleotide sequence encodes a polypeptide having an amino acid sequence that comprises at least one substitution at position 2, 6, 13, 16, 18, 29, 62, 64, 67, 70, 71, 74, 75, 78, 81, 91, 106, 111, 116, 127, 128, 139, 156, 164, 182, 199, 201, 206, 211, 223, 237, 233, 236, 244, 248, 250, 274, 277, 281, 284, 325, 328, 329, 330, 339, 342, 356, 360, 371, 372, 373, 375, 378, 380, 382, 386, 389, 390, 391, 393, 397, 398, 399, 400, 404, 407, 414, 423, 424, 426, 427, 431, 433, 434, 435, and/or 436, wherein the positions are numbered by correspondence with the amino acid sequence set forth in SEQ ID NO:2. 
     
     
         6 . The nucleic acid construct of  claim 5 , wherein said polynucleotide sequence encodes a polypeptide having an amino acid sequence that comprises at least one substitution selected from E2, N6, Q13, K16, T18, E29, G62, T64, T67, Q70, S71, A74, A75, K78, V81, L91, S106, K111, Q116, K127, Q128, A139, 5156, A164, Y182, M199, K201, M206, K211, K223, K233, T236, K237, T244, V247, L248, F250, H274, Q277, R281, 8284, A325, F328, T329, N330, A339, G342, G356, F360, I371, E372, D373, R375, K378, V380, D382, 5386, T389, G390, I391, A393, A397, G398, K399, A400, S404, K407, E414, R423, Q424, M426, V431, N433, V434, L435, and/or F436, wherein the positions are numbered by correspondence with the amino acid sequence set forth in SEQ ID NO:2. 
     
     
         7 . The nucleic acid construct of  claim 6 , wherein said polynucleotide sequence encodes a polypeptide having an amino acid sequence that comprises at least one substitution selected from E2S, N6G, N6H, Q13K, K16E, T18C, T18K, T18L, T18M, E29N, G62F, T64Q, T67S, Q70E, S71L, A74G, A75T, K78R, V81I, L91M, S109D, K111A, K111L, Q116C, K1271, K127R, Q128A, A139G, S156T, A164V, Y182C, M199A, M199V, L201H, M206T, K211H, K223T, K233C, T236A, T236L, K237A, T244S, V247A, L248S, F250C, F250V, H274R, Q277R, R281L, R284H, A325R, A325S, F328H, T329S, N330G, N330H, N330L, N330W, N330Y, A339R, G342P, G342V, G356A, F360M, 1371G, I371L, 1371Q, 1371R, I371T, E372G, E372T, D373G, R375Q, R375T, R375V, K378A, K378D, V380W, D382G, D382N, S386K, T389H, G390M, 1391A, I391L, A393T, A397L, A397S, G398E, K399E, K399T, K399V, A400G, S404Y, K407E, K407L, K407R, E414A,R423G, Q424H, M426R, V431E, N433A, N433H, N433R, V434Q, V434S, L435S, and/or F436G, wherein the positions are numbered by correspondence with the amino acid sequence set forth in SEQ ID NO:2. 
     
     
         8 . The nucleic acid construct of  claim 6 , wherein said polynucleotide sequence encodes a polypeptide having an amino acid sequence that comprises at least one substitution set selected from N6G/E372G/F436G; K16E/K111A/E372G; K16E/K111A/E372G/K399T; E29N/E372G; T64Q/S71L/Q116C/M199A/F360M/E372G/K407R; T64Q/S71L/Q116C/K233C/F360M/E372G/K407L/Q424H; T64Q/S71L/M199A/K233C/E372G/I391L; T64Q/S71L/K233C/F360M/E372G; T64Q/L91M/A139G/A164V/K233C/E372G; T64Q/Q116C/M199A/F360M/E372G/K407L; T64Q/Q116C/K233C/E372G; T64Q/M199A/K233C/E372G; T64Q/M199A/K233C/E372G/K407L/Q424H; T64Q/K233C/F250C/E372G; T64Q/K233C/F360M/E372G/K407L/Q424H; T64Q/F360M/E372G; T67S/Q70E/A75T/E372G; T67S/Q70E/S109D/T236A/E372G/S386K; T67S/Q70E/S109D/T236L/E372G/I391L/G398E/V434S; T67S/Q70E/S109D/R281L/E372G; T67S/Q70E/S109D/R281L/E372G/S404Y; T67S/Q70E/S109D/E372G/S386K; T67S/Q70E/S109D/E372G/I391L/S404Y; T67S/Q70E/S109D/E372G/V431E; T67S/Q70E/S109D/E372GN434S; T67S/Q70E/T236A/E372G; T67S/Q70E/T236L/E372G/S386K; T67S/Q70E/T236L/E372G/V431E; T67S/Q70E/R281L/E372G; T67S/Q70E/R281L/E372G/S404Y; T67S/Q70E/A325 S/E372G; T67S/Q70E/E372G/S386K; T67S/Q70E/E372G/G390M; T67S/S109D/R281L/E372G; T67S/S109D/E372G/G398E/V434S; T67S/R281L/A325R/E372G; Q70E/S109D/T236A/E372G/I391L; Q70E/S109D/T236A/E372GN434S; Q70E/S109D/T236L/E372G/S386K/S404Y; Q70E/S109D/E372G; Q70E/S109D/E372G/G398E; Q70E/S109D/E372G/V431E; Q70E/T236A/E372G; Q70E/T236A/E372G/G398E; Q70E/T236A/R281L/A325S/E372G; Q70E/T236L/E372G/G398E; Q70E/E372GN434S; Q70E/E372G/G398E/V434S; S71L/M199A/K233C/E372G/K407L; S71L/E372G; K78R/Y182C/G356A/E372G; K78R/V247A/L248S/G356A/E372G; K78R/V247A/E372G; K78R/G356A/E372G; K78R/E372G/K399E/R423G; K78R/D373G; S109D/T236A/R281L/E372G; S109D/T236L/R281L/A325R/E372G; S109D/R281L/E372G; Q116C/M199A/K233C/E372G/K407L; Q116C/M199A/F360M/E372G; K127R/G356A/E372G; K127R/E372G/D373G; Y182C/V247A/G356A; L201H/E372G; M206T/L248S/H274R/K399E; M206T/L248S/E372G; K211H/E372G/K407E; K233C/F360M/E372GN380W/Q424H; K233C/E372G/V380W; K233C/E372G/K407L; K223T/K237A/E372G/K399T/K407E; V247A/L248S/G356A/E372G; R281L/A325S/E372G/A397S; R284H/E372G; T329S/N330H/E372G/R375V; N330Y/E372G/F436G; G356A/E372G; G356A/E372G/K399E/R423G; G356A/D373G; F360M/E372G/Q424H; 1371G/E372G/N433A; E372G/K378D; E372G/K378D/K399T/K407E; E372G/I391L/S404YN434S; E372G/K399T; E372G/K399T/K407E; E372G/K407E; E372G/K407R; and/or E372G/L435S, wherein the positions are numbered by correspondence with the amino acid sequence set forth in SEQ ID NO:2. 
     
     
         9 . The nucleic acid construct of  claim 2 , wherein the polynucleotide sequence comprises at least one mutation and/or mutation set selected from t9c/c12t/c15t/g123a/t132g/a135g/t492a/a606g/c612t; c15g/t132a/t249a/t252g/c927g/a930g/t1290c; a48g/c51t/a54g/t57c/t60g/a1209g; a48g/c108a/t882c; c51a/a54g/g1011a; a54g/t60a/t168c/t171c/c177t/a180t/c213a/c216t/a219c/g222a/a225c/t891a/c894t/a897c; a54g/g438a/c447t/t450g/c798t/t801c/c804t/c807a; t102c/c213a/c216t/a219g/g222t/a225c/a813g/a819g/c822t/a825g; t66a/c138g/t150g/a258g/t261c/t267c/t543g/t546c/c549t; t66c/c138g/g582a/a987g; a93t/c96t/t102c/a180g/g768a/t1008c/g1011t/a1014g/t1017g; a93t/c96t/t102g/a180t/a813g/a819g/a825t; c108g; c108t/c396t/t402c; t120c/t360a/c993a/c996g/g999a; g123a/a126g/c129t/t132a/a135c/t1164c/c1167t/t1170g; g123a/a333g/t403c/c423t/t426c/t429c/c435a/c549g/t552c/t981g/c984t/a987g/t990c/a1221g; a126g/t132c/a135c/g438a/c441t/c447t/t450c; c129t/a135g/c441t; c138a/c147t/t186c/g192t/c858t/t861g/a864g/a987t; c138a/t150a/c177t/g783a/t1143g/c1146t/c1155a/t1263a/a1269g; c138a/t150a/g783a/t1143g/c1146t/c1155a/t1263a; c138a/t150a/g783a/t1143g/c1146t/c1155a/t1263a/a1269g;c138a/t150a/c307t/g783a/t1143g/c1146t/c1155a/t1263a/a1269g; t150g/c1146t/t1152c/c1155g; t156c/t165c; t168a/c177t/a420g; t168c/a180g/a813g/a816c/a819g/c822t/a825g/g1011a/a1014g/t1017a/t1020c; t168g/a819g/c822t/a825g; a180t/c291t/c294t/a693g/c696t/a813g/a816t/c822t/a825g; t211a; c213t/a219g/c339a/a888g/t891g/c894t/a897g/g1011t/t1017a; c213g/a219g/a225g/c411g/t414c/t417g/g528a/g531a/c534g/a819g/a825g; g222t/a225g/a453t/t462g/t465g/g528a/g531a/c534g/t537g/c579g/a693g/c696t/a774g/c780t/g1134a/g1140a; a228g; t261a/t309g/t312g/t429c/c432t/c435t/a903g/a906g; t261a/t543g/t552c/a741c/t870g/t960c/t1026a/a1029t/c1032t/g1035c; c276t/t279c/c285t/a606g/c828t/a840g/t873a/t882g/c885t; c288t/c291t/c294t/t300c/a405g/t651c; c307t; a318g/t558a/t561a/a567g/t570g/t735g/c798g/t801c/c807g/a810g; g351t/c354t/t360g/c600g; t834c/a840g; c411t/t414g/t417g/a420g/t429c; t414g/t417g/a420g/a453c/t459a/t462c/c822t/a825t/t1008c/t1017g/t1020g; c441t/c447t/a810c/a1095g; c480t/c522g/t708g/c720t/c762tt960c/t1228c; a516g/t558g/a564g/c798g/c804t/a810c/a1209t/a1212c; g528a/t537a/c573t/c579g/g585c/c696a/t705g; t546c/c549t/c858t/t861g/a864c/t870a; t591g/c600g/a840g; g654a/t657g; t771c/a774g/c894t/a897g/t1128a/c1131t/t1185c; a816t/a819g/c822t/g1011t/a1014g; t1065c; a1086g/a1095g; a1125g; t1137c; and t1263a/t1266g, wherein the nucleotide position is determined by alignment with SEQ ID NO:1. 
     
     
         10 . The nucleic acid construct of  claim 2 , wherein said polynucleotide sequence is at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO:1 and/or SEQ ID NO:3. 
     
     
         11 . The nucleic acid construct of  claim 2 , wherein said construct comprises the nucleotide sequence of SEQ ID NO:1 and/or SEQ ID NO:3. 
     
     
         12 . The nucleic acid construct of  claim 2 , further comprising a genetic element that facilitates stable integration into a fungal host genome. 
     
     
         13 . The nucleic acid construct of  claim 12 , wherein the genetic element facilitates integration into a fungal host genome by homologous recombination. 
     
     
         14 . The nucleic acid construct of  claim 2 , further comprising a fungal origin of replication. 
     
     
         15 . The nucleic acid construct of  claim 14 , wherein the fungal origin of replication is a yeast origin of replication. 
     
     
         16 . The nucleic acid construct of  claim 2 , wherein the polynucleotide sequence is operatively linked to a promoter sequence that is functional in a fungal cell. 
     
     
         17 . The nucleic acid construct of  claim 16 , wherein the promoter sequence is a fungal promoter sequence. 
     
     
         18 . The nucleic acid construct of  claim 17 , wherein the fungal promoter sequence is a yeast promoter sequence. 
     
     
         19 . The nucleic acid construct of  claim 2 , wherein said polynucleotide sequence is operatively linked to a transcription termination sequence that is functional in a fungal cell. 
     
     
         20 . The nucleic acid construct of  claim 2 , wherein the polynucleotide sequence contains codons optimized for expression in a yeast cell. 
     
     
         21 . An isolated xylose isomerase variant, wherein said variant is a mature form having xylose isomerase activity and comprising a substitution at one or more positions selected from 2, 6, 13, 16, 18, 29, 62, 64, 67, 70, 71, 74, 75, 78, 81, 91, 106, 111, 116, 127, 128, 139, 156, 164, 182, 199, 201, 206, 211, 223, 237, 233, 236, 244, 248, 250, 274, 277, 281, 284, 325, 328, 329, 330, 339, 342, 356, 360, 371, 372, 373, 375, 378, 380, 382, 386, 389, 390, 391, 393, 397, 398, 399, 400, 404, 407, 414, 423, 424, 426, 427, 431, 433, 434, 435, and/or 436, wherein the positions are numbered by correspondence with the amino acid sequence of SEQ ID NO:2. 
     
     
         22 . The isolated xylose isomerase variant of  claim 21 , wherein said variant is a mature form having xylose isomerase activity and comprising a substitution at one or more positions selected from E2, N6, Q13, K16, T18, E29, G62, T64, T67, Q70, S71, A74, A75, K78, V81, L91, S106, K111, Q116, K127, Q128, A139, 5156, A164, Y182, M199, K201, M206, K211, K223, K233, T236, K237, T244, V247, L248, F250, H274, Q277, 8281, 8284, A325, F328, T329, N330, A339, G342, G356, F360, I371, E372, D373, R375, K378, V380, D382, 5386, T389, G390, I391, A393, A397, G398, K399, A400, S404, K407, E414, R423, Q424, M426, V431, N433, V434, L435, and/or F436, wherein the positions are numbered by correspondence with the amino acid sequence set forth in SEQ ID NO:2. 
     
     
         23 . An isolated xylose isomerase variant of  claim 22 , wherein said variant is a mature form having xylose isomerase activity and comprising a substitution at one or more positions selected from E2S, N6G, N6H, Q13K, K16E, T18C, T18K, T18L, T18M, E29N, G62F, T64Q, T67S, Q70E, S71L, A74G, A75T, K78R, V81I, L91M, S109D, K111A, K111L, Q116C, K127I, K127R, Q128A, A139G, S156T, A164V, Y182C, M199A, M199V, L201H, M206T, K211H, K223T, K233C, T236A, T236L, K237A, T244S, V247A, L248S, F250C, F250V, H274R, Q277R, R281L, R284H, A325R, A325S, F328H, T329S, N330G, N330H, N330L, N330W, N330Y, A339R, G342P, G342V, G356A, F360M, 1371G, I371L, 1371Q, 1371R, I371T, E372G, E372T, D373G, R375Q, R375T, R375V, K378A, K378D, V380W, D382G, D382N, S386K, T389H, G390M, 1391A, I391L, A393T, A397L, A397S, G398E, K399E, K399T, K399V, A400G, S404Y, K407E, K407L, K407R, E414A,R423G, Q424H, M426R, V431E, N433A, N433H, N433R, V434Q, V434S, L435S, and/or F436G, wherein the positions are numbered by correspondence with the amino acid sequence set forth in SEQ ID NO:2. 
     
     
         24 . An isolated xylose isomerase variant of  claim 21 , wherein said variant is a mature form having xylose isomerase activity and comprising at least one substitution set selected from N6G/E372G/F436G; K16E/K111A/E372G; K16E/K111A/E372G/K399T; E29N/E372G; T64Q/S71L/Q116C/M199A/F360M/E372G/K407R; T64Q/S71L/Q116C/K233C/F360M/E372G/K407L/Q424H; T64Q/S71L/M199A/K233C/E372G/I391L; T64Q/S71L/K233C/F360M/E372G; T64Q/L91M/A139G/A164V/K233C/E372G; T64Q/Q116C/M199A/F360M/E372G/K407L; T64Q/Q116C/K233C/E372G; T64Q/M199A/K233C/E372G; T64Q/M199A/K233C/E372G/K407L/Q424H; T64Q/K233C/F250C/E372G; T64Q/K233C/F360M/E372G/K407L/Q424H; T64Q/F360M/E372G; T67S/Q70E/A75T/E372G; T67S/Q70E/S109D/T236A/E372G/S386K; T67S/Q70E/S109D/T236L/E372G/I391L/G398E/V434S; T67S/Q70E/S109D/R281L/E372G; T67S/Q70E/S109D/R281L/E372G/S404Y; T67S/Q70E/S109D/E372G/S386K; T67S/Q70E/S109D/E372G/I391L/S404Y; T67S/Q70E/S109D/E372G/V431E; T67S/Q70E/S109D/E372GN434S; T67S/Q70E/T236A/E372G; T67S/Q70E/T236L/E372G/S386K; T67S/Q70E/T236L/E372G/V431E; T67S/Q70E/R281L/E372G; T67S/Q70E/R281L/E372G/S404Y; T67S/Q70E/A325 S/E372G; T67S/Q70E/E372G/S386K; T67S/Q70E/E372G/G390M; T67S/S109D/R281L/E372G; T67S/S109D/E372G/G398E/V434S; T67S/R281L/A325R/E372G; Q70E/S109D/T236A/E372G/I391L; Q70E/S109D/T236A/E372GN434S; Q70E/S109D/T236L/E372G/S386K/S404Y; Q70E/S109D/E372G; Q70E/S109D/E372G/G398E; Q70E/S109D/E372G/V431E; Q70E/T236A/E372G; Q70E/T236A/E372G/G398E; Q70E/T236A/R281L/A325S/E372G; Q70E/T236L/E372G/G398E; Q70E/E372GN434S; Q70E/E372G/G398E/V434S; S71L/M199A/K233C/E372G/K407L; S71L/E372G; K78R/Y182C/G356A/E372G; K78R/V247A/L248S/G356A/E372G; K78R/V247A/E372G; K78R/G356A/E372G; K78R/E372G/K399E/R423G; K78R/D373G; S109D/T236A/R281L/E372G; S109D/T236L/R281L/A325R/E372G; S109D/R281L/E372G; Q116C/M199A/K233C/E372G/K407L; Q116C/M199A/F360M/E372G; K127R/G356A/E372G; K127R/E372G/D373G; Y182C/V247A/G356A; L201H/E372G; M206T/L248S/H274R/K399E; M206T/L248S/E372G; K211H/E372G/K407E; K233C/F360M/E372GN380W/Q424H; K233C/E372G/V380W; K233C/E372G/K407L; K223T/K237A/E372G/K399T/K407E; V247A/L248S/G356A/E372G; R281L/A325S/E372G/A397S; R284H/E372G; T329S/N330H/E372G/R375V; N330Y/E372G/F436G; G356A/E372G; G356A/E372G/K399E/R423G; G356A/D373G; F360M/E372G/Q424H; 1371G/E372G/N433A; E372G/K378D; E372G/K378D/K399T/K407E; E372G/I391L/S404Y1V434S; E372G/K399T; E372G/K399T/K407E; E372G/K407E; E372G/K407R; and/or E372G/L435S, wherein the positions are numbered by correspondence with the amino acid sequence set forth in SEQ ID NO:2. 
     
     
         25 . A recombinant fungal host cell comprising a polynucleotide sequence that encodes a polypeptide that is capable of catalyzing the isomerization of D-xylose directly to D-xylulose, wherein the polynucleotide is a polynucleotide encoding a polypeptide comprising an amino acid sequence having at least 70% identity to SEQ ID NO:2, or a polynucleotide that hybridizes under stringent hybridization conditions to the complement of a polynucleotide that encodes a polypeptide having the amino acid sequence of SEQ ID NO:2. 
     
     
         26 . The host cell of  claim 25 , wherein said polynucleotide sequence is a polynucleotide sequence as provided in  claim 2 . 
     
     
         27 . The host cell of  claim 26 , wherein said polynucleotide sequence comprises a recombinant nucleic acid construct of  claim 2 . 
     
     
         28 . The host cell of  claim 25 , wherein the polynucleotide is integrated into the host cell genome. 
     
     
         29 . The host cell of  claim 25 , wherein the host cell is a yeast cell. 
     
     
         30 . The host cell of  claim 25 , wherein the host cell has had one or more native genes deleted from its genome. 
     
     
         31 . The host cell of  claim 30 , wherein the deletion results in one or more phenotypes including increased transport of xylose into the host cell, increased xylulose kinase activity, increased flux through the pentose phosphate pathway, decreased sensitivity to catabolite repression, increased tolerance to ethanol, increased tolerance to acetate, increased tolerance to increased osmolarity, increased tolerance to low pH, and/or reduced production of by products, wherein comparison is made with respect to the corresponding host cell without the deletion(s). 
     
     
         32 . The host cell of  claim 25 , wherein the host cell is altered to overexpress one or more polynucleotides. 
     
     
         33 . The host cell of  claim 32 , wherein overexpression results in one or more phenotypes, including increased transport of xylose into the host cell, increased xylulose kinase activity, increased flux through the pentose phosphate pathway, decreased sensitivity to catabolite repression, increased tolerance to ethanol, increased tolerance to acetate, increased tolerance to increased osmolarity, increased tolerance to low pH, and/or reduced product of by products, wherein comparison is made to the corresponding unaltered host cell. 
     
     
         34 . The host cell of  claim 25 , wherein the host cell is capable of growth in a xylose-based culture medium. 
     
     
         35 . The host cell of  claim 25 , wherein the host cell is capable of fermentation in a xylose-based culture medium. 
     
     
         36 . The host cell of  claim 25 , wherein the host cell is capable of faster growth in a xylose-based culture medium as compared to wild-type  Saccharomyces cerevisiae.    
     
     
         37 . The host cell of  claim 25 , wherein the xylose-based culture medium is a product from a cellulosic saccharification process and/or a hemicellulosic feedstock. 
     
     
         38 . A process for producing a fermentation product, wherein the method comprises:
 (a) providing the recombinant host cell of  claims 25 ;   (b) providing a fermentation medium comprising xylose; and   (c) contacting the fermentation medium with the recombinant fungal host cell under conditions suitable for generating the fermentation product.   
     
     
         39 . The process of  claim 38 , further comprising (d) recovering the fermentation product. 
     
     
         40 . The process of  claim 38 , wherein the fermenting step is carried out under microaerobic or aerobic conditions. 
     
     
         41 . The process of  claim 38 , wherein the fermenting step is carried out under anaerobic conditions. 
     
     
         42 . The process of  claim 38 , wherein the fermentation product is at least one alcohol, fatty alcohol, fatty acid, lactic acid, acetic acid, 3-hydroxypropionic acid, acrylic acid, succinic acid, citric acid, malic acid, fumaric acid, succinic acid, an amino acid, 1,3-propanediol, ethylene, glycerol, and/or a β-lactam. 
     
     
         43 . The process of  claim 42 , wherein the alcohol is ethanol, butanol, and/or a fatty alcohol. 
     
     
         44 . The process of  claim 43 , wherein the fermentation product is ethanol. 
     
     
         45 . The process of  claim 43 , wherein the fermentation product is a fatty alcohol that is a C8-C20 fatty alcohol. 
     
     
         46 . The process of  claim 38 , wherein the fermentation medium comprises product from a saccharification process.

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