Construction of recombinant Saccharomyces cerevisiae strains for starch utilisation

Eksteen, Jeremy Michael (2002-12)

Thesis (MSc)--University of Stellenbosch, 2002.

Thesis

ENGLISH ABSTRACT: Starch-containing agricultural crops are widely available as feedstocks for the production of fuel ethanol, potable spirits or beer, single-cell protein (animal feed) and high-fructose corn syrups (sweeteners). Starch-rich crops, such as maize, rye, barley and wheat, are usually used for the production of whisky. One of the first steps in the production of whisky is to boil the raw starch at temperatures exceeding 100°C. This gelatinisation step is performed to disrupt and solubilise the starch granules to make them more accessible for enzymatic hydrolysis. After this cooking process, the starch is liquefied by a-amylase and then saccharified by glucoamylase and a debranching enzyme. Lipomyces kononenkoae and Saccharomycopsis fibuligera secrete highly effective a-amylases and glucoamylases, making them two of the most efficient raw-starchdegrading yeasts known. However, L. kononenkoae and S. fibuligera cannot be used in existing industrial fermentations because of their low ethanol tolerance, slow growth rate, catabolite repression, poorly characterised genetics and lack of GRAS (Generally Regarded As Safe) status. This study is divided into two sections. The aim of the first section was to clone a gene (LKA2) encoding a novel starch-degrading enzyme, a second a-amylase (Lka2p) from L. kononenkoae. LKA2 was cloned into a multicopy plasmid, the yeast episomal plasmid, YEp352, under the control of the phosphoglycerate kinase promoter (PGK1 p) and terminator (PGKh) expression cassette. This recombinant plasmid was designated pJUL3 and transformed into a laboratory strain of S. cerevisiae, I1278b. Plate and liquid assays revealed that the recombinant yeast secreted active a-amylase into the medium. The optimum pH for Lka2p was pH 3.5 and the optimum temperature 60°C. The aim of the second part of the study was to construct recombinant strains of S. cerevisiae secreting a-amylase and/or glucoamylase. The individual genes were cloned into a yeast-integrating plasmid, Ylp5, under the control of the PGK1p-PGK1.,-expression cassette. Two indigenous yeasts were selected on the basis of their ability to utilise raw starch, L. kononenkoae and S. fibuligera, as gene donors. Eight constructs containing the L. kononenkoae a-amylase genes, LKA 1 and LKA2, and the S. fibuligera a-amylase (SFA 1) and glucoamylase (SFG1) genes were prepared: four single-cassette plasmids expressing the individual coding sequences under the control of the PGK1 p-PGK1.,- expression cassette, resulting in plPLKA 1, pIPLKA2, plPSFA 1 and pIPSFG1, respectively; two double-cassette plasm ids (expressing both LKA 1 and LKA2 under the control of the PGK1p-PGK1 .,-expression cassette, and SFA 1 and SFG1 under their respective native promoters and terminators), resulting in pIPLKA1/2 and pIPSFAG, respectively, and two single-cassette plasmids expressing SFA 1 and SFG1 with their native promoters and terminators, resulting in pSFA 1 and pSFG1, respectively. The respective constructs were transformed into a laboratory strain of S. cere visiae , L1278b. By homologous recombination, each plasmid was integrated into the yeast genome at the ura3 locus. S. cerevisiae L:1278b that had been transformed with plPLKA 1/2, LKA 1 and LKA2 under the control of the PGK1 rrPGK1,expression cassette resulted in the highest levels of a-amylase activity when assayed for amylolytic activity in a liquid medium. This recombinant strain resulted in the most efficient starch utilisation in batch fermentations, consuming 80% of starch and producing 6 gIL of ethanol after 156 hours of fermentation. The strain expressing SFG1 under the control of the PGK1rrPGK1,expression cassette gave the highest levels of glucoamylase activity.' These results confirmed that co-expression of a-amylase and/or glucoamylase synergistically enhance starch degradation. This study paves the way for the development of efficient starch-degrading strains of S. cerevisiae for the production of whisky, beer and biofuel ethanol.

AFRIKAANSE OPSOMMING: Styselbevattende landbougewasse kom wydverspreid voor as die substraat vir die produksie van brandstofetanol, drinkbare spiritualië of bier, enkelselproteïen en hoëfruktose graanstroop. Styselbevattende gewasse, soos mielies, rog, gars en koring, word gewoonlik vir die produksie van whisky gebruik. Die eerste stap in die produksie van whisky is om die stysel by temperature bo 1DOOG te kook. Hierdie jelatinisasie stap word uitgevoer om die styselkorrels te versteur en vloeibaar te maak sodat hulle meer toeganklik vir ensimatiese hidrolise is. Na dié kookproses word die stysel deur o-arnilases vervloei en dan deur glukoamilases en 'n vertakkingsensiem versuiker. Lipomyces kononenkoae en Saccharomycopsis filuligera skei hoogs effektiewe a-amilases en glukoamilases uit, wat dit twee van die effektiefste rou-stysel-afbrekende giste bekend, maak. L. kononenkoae en S. fibuligera kan egter nie in reeds bestaande industriële fermentasies gebruik word nie, as gevolg van hulle lae etanoltoleransie, stadige groeitempo, katabolietonderdrukking, swak gekarakteriseerde genetika en gebrek aan ABAV (Algemeen Beskou As Veilig) status. Hierdie tesis is in twee afdelings verdeel. Die doel van die eerste deel was om 'n geen (LKA2) wat vir 'n nuwe, unieke styselafbrekende ensiem kodeer, te kloneer, 'n tweede a-amilase (Lka2p) van L. kononenkoae. LKA2 is in 'n multikopie plasmied, die gis episomale plasmied, YEp352, onder beheer van die fosfogliseraatkinasepromotor- en termineerder-kasset (PGK1 p-PGK1 r), gekloneer. Hierdie rekornbinante plasmied is pJUL3 genoem en in 'n laboratoriumras van Saccharomyces cerevisiae, L:1278b, getransformeer. Plaat- en vloeibare-ensiem toetse het getoon dat die rekombinante gis aktiewe a-amilase in die medium uitskei. Die optimum pH vir Lka2p is 3.5, is en die optimum temperatuur 60oG. Die doel van die tweede deel van die studie was om rekombinante rasse van S. cerevisiae te konstrueer wat a-amilases en/of glukoamilases uitskei. Die individuele gene is toe in 'n gis-integreringsplasmied, Ylp5, onder beheer van die PGK1p-PGK1,ekspressiekasset, gekloneer. Twee inheemse giste is op grond van hulle vermoë om stysel te benut geselekteer, L. kononenkoae en S. filuIigera, as geen donors. Agt konstrukte bevattende die L. kononenkoae se a-amilasegene, LKA 1 en LKA2, en S. filuligera se a-amilasegeen (SFA 1) en glukoamilasegeen (SFG1), moes gekonstrueer word: vier _enkel-kasset plasmiede wat die individuele koderende sekwense onder beheer van die PGK1 p-PGK1, ekspressiekasset uitdruk, wat onderskeidelik plPLKA 1, pIPLKA2, plPSFA 1 en plPSFG1 lewer; twee dubbel-kasset plasmiede (wat beide LKA 1 en LKA2 onder beheer van die PGK1 p-PGK1,ekspressiekasset, en SFA 1 en SFG1 met hulle onderskeie inheemse promotors en termineerders) uitdruk, wat onderskeidelik pIPLKA1/2 en plPSFAG lewer, en twee enkel-kasset plasmiede wat SFA 1 and SFG1 met hulonderskeie inheemse promotors en termineerders, en wat onderskeidelik pSFA 1 en pSFG1 lewer. Die onderskeie konstrukte is in 'n laboratoriumras van S. cerevisiae, L1278b, getransformeer. Deur middel van homoloë rekombinasie, is die onderskeie plasmiede in die ura3-lokus van die gisgenoom geïntegreer. S. cerevisiae L1278b, getransformeer met plPLKA 1/2, LKA 1 en LKA2 onder die beheer van die PGK1 ~PGK1 ïekspressiekasset, het die hoogste vlakke van a-amilase aktiwiteit gelewer toe dit vir amilolitiese aktiwiteit in vloeibare medium getoets is. Hierdie rekombinante ras het stysel die effektiefste benut, nl. 80% van die stysel en 'n opbrengs van 6 gIL etanol na 156 ure in lotfermentasies. Die ras wat SFG1 onder beheer van die PGK1~PGK1ïekspressiekasset uitdruk, het die hoogste vlakke van glukoamilase-aktiwiteit gelewer. Hierdie resultate bevestig dat die gesamentlike uitdrukking van a-amilase- en/of glukoamilase-ensieme styselafbreking sinergisties . bevorder. Hierdie studie baan die weg vir die ontwikkeling van 'n effektiewe styselfermenterende ras van S. cerevisiae wat moontlik gebruik kan word vir die produksie van whisky en biobrandstofalkohol.

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