Analysis of culture media screening data by projection to latent pathways: The case of Pichia pastoris X-33.
Cell culture media formulations contain hundreds of individual components in water solutions which have complex interactions with metabolic pathways. The currently used statistical design methods are empirical and very limited to explore such a large design space. In a previous work we developed a computational method called projection to latent pathways (PLP), which was conceived to maximize covariance between envirome and fluxome data under the constraint of metabolic network elementary flux modes (EFM). More specifically, PLP identifies a minimal set of EFMs (i.e., pathways) with the highest possible correlation with envirome and fluxome measurements. In this paper we extend the concept for the analysis of culture media screening data to investigate how culture medium components up-regulate or down-regulate key metabolic pathways. A Pichia pastoris X-33 strain was cultivated in 26 shake flask experiments with variations in trace elements concentrations and basal medium dilution, based on the standard BSM+PTM1 medium. PLP identified 3 EFMs (growth, maintenance and by-product formation) describing 98.8% of the variance in observed fluxes. Furthermore, PLP presented an overall predictive power comparable to that of PLS regression. Our results show iron and manganese at concentrations close to the PTM1 standard inhibit overall metabolic activity, while the main salts concentration (BSM) affected mainly energy expenditures for cellular maintenance.
Faculty of Sciences and Technology, Universidade NOVA de Lisboa, P-2829-516 Caparica, Portugal; Instituto de Biologia Experimental e Tecnológica (IBET), Av. da República, EAN, P-2780-157 Oeiras, Portugal.
Inês A
IA
Isidro
Faculty of Sciences and Technology, Universidade NOVA de Lisboa, P-2829-516 Caparica, Portugal; Instituto de Biologia Experimental e Tecnológica (IBET), Av. da República, EAN, P-2780-157 Oeiras, Portugal; Functional Enviromics Technologies S.A., Campus da Caparica, Faculty of Sciences and Technology, Universidade NOVA de Lisboa, P-2829-516 Caparica, Portugal.
Ana R
AR
Ferreira
Instituto de Biologia Experimental e Tecnológica (IBET), Av. da República, EAN, P-2780-157 Oeiras, Portugal.
João J
JJ
Clemente
Instituto de Biologia Experimental e Tecnológica (IBET), Av. da República, EAN, P-2780-157 Oeiras, Portugal.
António E
AE
Cunha
Faculty of Sciences and Technology, Universidade NOVA de Lisboa, P-2829-516 Caparica, Portugal; Instituto de Biologia Experimental e Tecnológica (IBET), Av. da República, EAN, P-2780-157 Oeiras, Portugal; Functional Enviromics Technologies S.A., Campus da Caparica, Faculty of Sciences and Technology, Universidade NOVA de Lisboa, P-2829-516 Caparica, Portugal. Electronic address: rmo@fct.unl.pt.
Rui
R
Oliveira
D003470:Culture Media / Q000032:analysis*; D015536:Down-Regulation; D005990:Glycerol / Q000378:metabolism; D007501:Iron / Q000378:metabolism; D008345:Manganese / Q000378:metabolism; D064688:Metabolic Flux Analysis / Q000379:methods; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D010843:Pichia / Q000737:chemistry / Q000254:growth & development / Q000378:metabolism*; D049490:Systems Biology; D014131:Trace Elements / Q000378:metabolism; D015854:Up-Regulation
D003470:Culture Media; D014131:Trace Elements; D008345:Manganese; D007501:Iron; D005990:Glycerol
Culture media design; Elementary flux modes; Pichia pastoris X-33; Projection to latent pathways