Quantitative yeast physiology and nitrogen metabolism during heterologous protein production

Gorgens, Johann Ferdinand (Stellenbosch : University of Stellenbosch, 2003-04)

Thesis

ENGLISH ABSTRACT: QUANTITATIVE YEAST PHYSIOLOGY AND NITROGEN METABOLISM DURING HETEROLOGOUS PROTEIN PRODUCTION By Johann F. Görgens The physiology and nitrogen metabolism of the yeast, Saccharomyces cerevisiae, during heterologous xylanase production in a defined medium was quantified by the comparison of isogenic yeast strains, whereby several potential limitations in the production of the heterologous xylanase could be identified. The presence of global sensing and regulatory mechanisms, by which the yeast is able to actively regulate both heterologous gene expression and the physiological response to the process, was also investigated. The deleterious effects of heterologous xylanase production on the physiology of the recombinant host were disproportionately large with respect to the amount of foreign protein produced. The cellular processes involved in this response were identified by the transcriptional profiling of isogenic recombinant strains, in a novel analytical approach to investigating foreign protein production by S. cerevisiae. Heterologous gene expression affected a combination of cellular processes and induced the yeast stringent stress response. The corresponding loss of metabolic functionality resulted in the disproportionate physiological effects of foreign protein production, similar to previous observations in recombinant Escherichia coli, and a possible reduction in attainable production levels. Reducing the propensity of recombinant gene expression to introduce metabolic stress may therefore increase production levels of foreign proteins by yeast. The metabolic vitality of transformed strains was also reduced by the presence of multiple copies of active, plasmid-based PGK1-promoters in the cell without expression of the heterologous gene. The negative effect was caused by an increase in the biosynthetic and glycolytic capacity of the strain at the expense of other processes. Production levels of heterologous xylanase were influenced by expression vector selection and the presence of auxotrophic mutations in transformed strains of S. cerevisiae. The increased transcription levels obtained with the multicopy plasmidbased YEp-type expression system, compared to the integrative YIp-type expression system, resulted in higher levels of xylanase production. Heterologous xylanase production thus did not saturate the secretory capacity of the host strain. The genetic stability of the autoselective YEp-type expression system in long-term chemostat culture was also demonstrated. High levels of heterologous xylanase production by transformed S. cerevisiae strains containing auxotrophic markers required the stabilisation of nitrogen metabolism via saturation of yeast cells with an excess of imported amino acids. By the removal of excessive auxotrophic markers, high levels of xylanase production by a prototrophic transformant in defined medium without amino acid addition could be obtained. Heterologous xylanase production by the prototrophic transformant was further enhanced by increasing the availability of preferred amino acids or succinate in the defined medium, indicating an additional requirement for metabolic precursors and building blocks for foreign protein synthesis. Comparable levels of heterologous xylanase production were obtained in high cell density cultures of the alternative yeast, Pichia stipitis, by the proper induction of the native ADH2-promoter, the control of oxygenation, and addition of an amino acid mixture to the defined medium, indicating the presence of generic limitations in transcription, nutrient availability and the yeast biosynthetic capacity for foreign protein production by various yeasts. The presence of global sensing and regulatory mechanisms was confirmed by the physiological response of S. cerevisiae to heterologous protein production, which included the downregulation of biosynthesis and growth, and the induction of various processes involved in the stringent stress response. Additionally, heterologous xylanase production was actively regulated on a posttranscriptional level by the auxotrophic transformants in response to the level of amino acid availability. The biosynthetic capacity for foreign protein production by both recombinant S. cerevisiae and P. stiptis was also regulated in response to the physiological state of the yeast and the availability of nutrients. The presence of these regulatory mechanisms complicated the manipulation of cellular biosynthesis at will.

AFRIKAANSE OPSOMMING: KWANTITATIEWE GIS-FISIOLOGIE EN -STIKSTOF METABOLISME GEDURENDE HETEROLOË PROTEÏEN PRODUKSIE Deur Johann Ferdinand Görgens Die fisiologie en stikstof-metabolisme van die gis, Saccharomyces cerevisiae, gedurende heteroloë xilanase produksie in ‘n gedefiniëerde medium is gekarakteriseer deur isogeniese gis-rasse te vergelyk, waardeur verskeie moontlike beperkings in die produksie van die heteroloë xilanase uitgewys kon word. Die teenwoordigheid van globale sensoriese- en beheer-meganismes, wat die gis in staat stel om beide heteroloë geen uitdrukking en die fisiologiese respons op die proses aktief te reguleer, is ook ondersoek. Die nadelige effekte van heteroloë xilanase produksie op die fisiologie van die rekombinante gasheer-organisme was uitermatig groot in vergelyking met die hoeveelheid vreemde proteïen wat geproduseer is. Die sellulêre prosesse verantwoordelik vir hierdie respons is identifiseer deur die transkripsionele profiele van isogeniese rekombinante rasse te vergelyk, in ‘n nuwe analitiese benadering tot die bestudering van vreemde proteïen produksie deur S. cerevisiae. Heteroloë geen uitdrukking het ‘n kombinasie van sellulêre prosesse geaffekteer en die gis se algemene voedingstres-respons geaktiveer. Die gepaardgaande verlies aan metaboliese funksie het die uitermatige fisiologiese effek van vreemde proteïen produksie veroorsaak, soortgelyk aan vorige waarnemings met rekombinante Escherichia coli. Die haalbare produksie-vlakke is moontlik ook verlaag deur hierdie respons. ‘n Verlaging van die geneigdheid van rekombinante geen uitdrukking om metaboliese stres te veroorsaak, mag dus die produksievlakke van vreemde proteïene in gis verbeter. Die metaboliese groei-potensiaal van die getransformeerde rasse is ook verlaag deur die teenwoordigheid van etlike aktiewe kopieë van plasmied-gebaseerde PGK1-promotors in die sel, sonder uitdrukking van die heteroloë geen, deur ‘n toename in die biosintetiese en glikolitiese kapasiteit ten koste van die ander sellulêre prosesse. Die produksievlakke van heteroloë xilanase is deur die keuse van uitdrukkings-sisteem en die teenwoordigheid van autotrofiese mutasies in die getransformeerde rasse van S.cerevisiae beïnvloed. Die verhoogde transkripsie vlakke wat met die multi-kopie, plasmied-gebaseerde YEp-tipe uitdrukkingsisteem, eerder as die geïntegreerde YIp-tipe sisteem, verkry is, het tot verhoogde xilanase produksie gelei. Heteroloë xilanase produksie het dus nie die uitskeidingskapasiteit van die gasheer versadig nie. Die genetiese stabiliteit van die autoselektiewe, YEp-tipe uitdrukkingsisteem in langtermyn chemostaat-kulture is ook gedemonstreer. Hoë vlakke van xilanase produksie deur getransformeerde S. cerevisiae rasse met autotrofiese merkers het die stabilisering van die stikstof metabolisme, deur die versadiging van die sel met ingevoerde aminosure, vereis. Die verwydering van oormatige autotrofiese merkers het tot hoë vlakke van xilanase produksie deur die prototrofiese transformant in gedefinieerde medium sonder aminosuur byvoeging gelei. Heteroloë xilanase produksie deur die prototrofiese transformant kon verder verbeter word deur die byvoeging van voorkeur-aminosure of suksinaat tot die gedefinieerde medium, en ‘n addisionele behoefte aan metaboliese voorloper-molekules en bou-blokke vir vreemde proteïensintese het dus bestaan. Vergelykbare vlakke van heteroloë xilanase produksie is in kulture met hoë sel-digthede van die alternatiewe gis, Pichia stipitis, verkry deur die doeltreffende induksie van die eiesoortige ADH2-promotor en die byvoeging van ‘n aminosuur-mengsel tot die gedefinieerde medium, wat die teenwoordigheid van generiese beperkinge in transkripsie, voedingstof-beskikbaarheid en biosintetiese kapasiteit van die gis vir vreemde proteïen produksie deur verskeie giste uitgewys het. Die teenwoordigheid van globale sensoriese- en beheer-meganismes is bevestig deur die fisiologiese respons van S. cerevisiae tot heteroloë proteïen produksie, wat die afwaartse regulering van biosintese en groei, en die induksie van verskeie prosesse betrokke by die algemene voedingstres-respons, ingesluit het. Heteroloë xilanase produksie is ook op ‘n na-transkripsionele vlak aktief gereguleer deur die autotrofiese transformante in reaksie tot die vlak van aminosuur beskikbaarheid. Die biosintetiese kapasiteit vir vreemde proteïen-produksie van beide rekombinante S. cerevisiae en P. stipitis is ook in reaksie tot die fisiologiese toestand van die gis en die beskikbaarheid van voedingstowwe gereguleer. Die teenwoordigheid van hierdie regulatoriese meganismes het die willekeurige manipulasie van sellulêre proteïen-biosintese bemoeilik.

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