Macromolecular and elemental composition analysis and extracellular metabolite balances of Pichia pastoris growing at different oxygen levels

Background: Analysis of the cell operation at the metabolic level requires collecting data of different types and to determine their confidence level. In addition, the acquired information has to be combined in order to obtain a consistent operational view. In the case of Pichia pastoris, information of its biomass composition at macromolecular and elemental level is scarce particularly when different environmental conditions, such as oxygen availability or, genetic backgrounds (e.g. recombinant protein production vs. non production conditions) are compared. Results: P. pastoris cells growing in carbon-limited chemostat cultures under different oxygenation conditions (% O2 in the bioreactor inlet gas: 21%, 11% and 8%, corresponding to normoxic, oxygen-limiting and hypoxic conditions, respectively), as well as under recombinant protein (antibody fragment, Fab) producing and non-producing conditions, were analyzed from different points of view. On the one hand, the macromolecular and elemental composition of the biomass was measured using different techniques at the different experimental conditions and proper reconciliation techniques were applied for gross error detection of the measured substrates and products conversion rates. On the other hand, fermentation data was analyzed applying elemental mass balances. This allowed detecting a previously missed by-product secreted under hypoxic conditions, identified as arabinitol (aka. arabitol). After identification of this C5 sugar alcohol as a fermentation by-product, the mass balances of the fermentation experiments were validated. Conclusions: After application of a range of analytical and statistical techniques, a consistent view of growth parameters and compositional data of P. pastoris cells growing under different oxygenation conditions was obtained. The obtained data provides a first view of the effects of oxygen limitation on the physiology of this microorganism, while recombinant Fab production seems to have little or no impact at this level of analysis. Furthermore, the results will be highly useful in other complementary quantitative studies of P. pastoris physiology, such as metabolic flux analysis

Quantitative Metabolomics and Instationary 13C-Metabolic Flux Analysis Reveals Impact of Recombinant Protein Production on Trehalose and Energy Metabolism in Pichia pastoris

Pichia pastoris has been recognized as an effective host for recombinant protein production. In this work, we combine metabolomics and instationary 13C metabolic flux analysis (INST 13C-MFA) using GC-MS and LC-MS/MS to evaluate the potential impact of the production of a Rhizopus oryzae lipase (Rol) on P. pastoris central carbon metabolism. Higher oxygen uptake and CO2 production rates and slightly reduced biomass yield suggest an increased energy demand for the producing strain. This observation is further confirmed by 13C-based metabolic flux analysis. In particular, the flux through the methanol oxidation pathway and the TCA cycle was increased in the Rol-producing strain compared to the reference strain. Next to changes in the flux distribution, significant variations in intracellular metabolite concentrations were observed. Most notably, the pools of trehalose, which is related to cellular stress response, and xylose, which is linked to methanol assimilation, were significantly increased in the recombinant strain

Systematic metabolic analysis of recombinant Pichia pastoris under different oxygen conditions : a metabolome and fluxome based study /

L'anàlisi sistemàtic de la fisiologia cel·lular és de gran importància en la millora del coneixement sobre els microorganismes. En aquesta direcció, la biologia de sistemes ens permet l'anàlisi quantitatiu de diferents nivells fisiològics obtenint representacions in silico de les vies metabòliques estudiades que, en conjunt, s'adrecen a la millor comprensió del comportament de sistemes biològics complexos. Aquest projecte de recerca va ser dissenyat per contribuir en la comprensió de la fisiologia de Pichia pastoris sota diferents condicions d'estrès. Específicament, aquesta tesis se centre en l'estudi sistemàtic del conjunt de metabòlits lliures dins la cèl·lula i en la velocitat que aquests es transformen. En el Capítol 2, una caracterització dels principals component de la biomassa de P. pastoris es va realitzadar sota diferents condicions de. Per una altre part, la consistència dels fluxos dels metabòlits extracel·lulars van ser utilitzats per identificar la producció d'un subproducte de fermentació, arabinitol. En el Capítol 3, s'obtingué la relació entre diferents fluxos metabòlics del metabolisme central del carboni de P. pastoris mitjançant l'estudi del carboni marcat dels aminoàcids sintetitzats de novo. Posteriorment, aquest valors van ser utilitzats delimitant l'anàlisi de fluxos metabòlics sota diferents condicions d'oxigenació i producció de proteïna recombinant. Els resultat més destacats obtinguts foren la gran similitud entre els fluxos estimats per les soques productora i control en condicions equivalents. Tot i així, diferencies clares van ser observades quan es van comparar el patró de fluxos corresponents a diferents nivells d'oxigenació. L'anàlisi dels metabòlits lliures dins la cèl·lula va començar en el Capítol 4 amb l'avaluació sistemàtica de cinc protocols de parada ràpida del metabolisme en P. pastoris respecte la concentració de metanol i la temperatura. Com a resultat, la parada del metabolisme realitzada a -27ºC amb una solució de 60% v/v de metanol a ser amb la que menys pèrdues es van observar. Consecutivament, es va demostrar que cinc temps de residència són els necessaris per arribar a un estat estacionari del metabòlits intracel·lulars en cultius amb glucosa limitant. D'altra banda, sota les mateixes condicions de treball, els perfils intracel·lulars dels principals metabòlits eren similars entre els llevats P. pastoris i S. cerevisiae. En el Capítol 5, l'estequiometria redox i energètica de P. pastoris va ser validada veient un augment en els requeriments energètics d'aquesta sota condicions deficitàries d'oxigen. A més a més, es va realitzar un anàlisi termodinàmic dels metabòlits intracel·lulars mitjançant lo qual s'obtingueren millores en el patró de fluxos en la via de les pentoses fosfat conjuntament amb informació de l'estat redox del citosol. En el Capítol 6, la regulació transcripcional i termodinàmica dels fluxes del metabolisme central del carboni va ser investigada entre diferents condicions de cultiu. En general, la contribució dels diferents nivells omics en el canvi final dels fluxos metabòlics van resultar ser diferents entre els llevats P. pastoris i S. cerevisiae. Específicament, per P. pastoris, la regulació transcripcional va ser significant en la majoria de reaccions, contràriament al que s'havia descrit per S. cerevisiae. Finalment, en el Capítol 7, per una millor comprensió de l'efecte i la interacció de la disponibilitat d'oxigen i la producció d'una proteïna forania, es va realitzar un anàlisi quantitatiu del aminoàcids lliures intracel·lulars sota la producció d'aquesta proteïna i en diferents condicions d'oxigenació. Els valors obtinguts indicaren una variació significativa d'aquests aminoàcids intracel·lulars entre diferents disponibilitats d'oxigen. Sorprenentment, l'expressió d'aquesta es va veure que tenia un impacte limitat, però significant, en els pools d'aminoàcids. Amb tot, els canvis individuals observats no presentaven una correlació amb l'abundància relativa d'aquests en la proteïna recombinant, en canvi, concordava amb la variació de la composició aminoacídica de la biomassa. 90%) were obtained for all quenching procedures tested. However, quenching at -27ºC in 60% v/v methanol performed slightly better in terms of leakage minimization. Thereafter, it was demonstrated that five residence times under glucose limitation were enough to reach stable intracellular metabolite pools. Moreover, when comparing P. pastoris and S. cerevisiae metabolomes, under the same cultivation conditions, similar metabolite fingerprints were found in both yeasts, except for the lower glycolysis. In Chapter 5, the redox and energy stoichiometry of P. pastoris was validated showing increasing energy requirements as the oxygen availability became shortage. In addition, a network-embedded thermodynamic analysis of the quantitative intracellular metabolites pools was performed allowing an improvement of the non-oxidative pentose phosphate pathway fluxes as well as determination of the oxygen impact over the redox state of the cytosol. In Chapter 6, the transcriptional and thermodynamic regulations over the metabolic flow between conditions were investigated for the central carbon metabolism reactions. Overall, the different omic contributions to the final metabolic flux changes were resulted to be different between P. pastoris and S. cerevisae. Specifically, for P. pastoris, transcriptional regulation was found to be in most cases significant, contrarily to the baker yeast. Finally, in Chapter 7, to better understand the effect and interplay of oxygen availability and foreign protein secretion on central metabolism, a first quantitative metabolomic analysis of free amino acids pools in a recombinant P. pastoris strain growing under different oxygen availability conditions was performed. The values obtained indicated significant variations in the intracellular amino acid levels due to different oxygen availability conditions. Notably, even that foreign protein productivities were relatively low, recombinant protein production was found to have a limited but significant impact. However, observed changes in individual amino acids pools were not correlated with their corresponding relative abundance in the recombinant protein sequence, but to the overall cell protein amino acid compositional variations

The price of informality : how informal finance schemes defaulted in China, 1989–2015.

The default of a large number of informal finance schemes in China has caused enormous financial losses, and therefore has potential social and political significance. Analysing 354 defaulted schemes from 1989 to 2015, this study defines how they differ from other types of informal finance. It also produces an ideal-type representation of the default process and concludes that the default results from greed, increasing financial pressure at the individual level and private enterprises’ restricted access to state bank loans at the institutional level. China’s financial system should be more flexible in order to prevent further financial losses through informal financial relations

Quantitative metabolomics analysis of amino acid metabolism in recombinant Pichia pastoris under different oxygen availability conditions

Background: Environmental and intrinsic stress factors can result in the global alteration of yeast physiology, as evidenced by several transcriptional studies. Hypoxia has been shown to have a beneficial effect on the expression of recombinant proteins in Pichia pastoris growing on glucose. Furthermore, transcriptional profiling analyses revealed that oxygen availability was strongly affecting ergosterol biosynthesis, central carbon metabolism and stress responses, in particular the unfolded protein response. To contribute to the better understanding of the effect and interplay of oxygen availability and foreign protein secretion on central metabolism, a first quantitative metabolomic analysis of free amino acids pools in a recombinant P. pastoris strain growing under different oxygen availability conditions has been performed. Results: The values obtained indicate significant variations in the intracellular amino acid pools due to different oxygen availability conditions, showing an overall increase of their size under oxygen limitation. Notably, even while foreign protein productivities were relatively low (about 40-80 μg Fab/gDCW·h), recombinant protein production was found to have a limited but significant impact on the intracellular amino acid pools, which were generally decreased in the producing strain compared with the reference strain. However, observed changes in individual amino acids pools were not correlated with their corresponding relative abundance in the recombinant protein sequence, but to the overall cell protein amino acid compositional variations. Conclusions: Overall, the results obtained, combined with previous transcriptomic and proteomic analyses provide a systematic metabolic fingerprint of the oxygen availability impact on recombinant protein production in P. pastoris

Development of quantitative metabolomics for Pichia pastoris

Accurate, reliable and reproducible measurement of intracellular metabolite levels has become important for metabolic studies of microbial cell factories. A first critical step for metabolomic studies is the establishment of an adequate quenching and washing protocol, which ensures effective arrest of all metabolic activity and removal of extracellular metabolites, without causing leakage of metabolites from the cells. Five different procedures based on cold methanol quenching and cell separation by filtration were tested for metabolomics of Pichia pastoris regarding methanol content and temperature of the quenching solution as key parameters. Quantitative evaluation of these protocols was carried out through mass balance analysis, based on metabolite measurements in all sample fractions, those are whole broth, quenched and washed cells, culture filtrate and quenching and washing solution. Finally, the optimal method was used to study the time profiles of free amino acid and central carbon metabolism intermediates in glucose-limited chemostat cultures. Acceptable recoveries (>90%) were obtained for all quenching procedures tested. However, quenching at −27°C in 60% v/v methanol performed slightly better in terms of leakage minimization. We could demonstrate that five residence times under glucose limitation are enough to reach stable intracellular metabolite pools. Moreover, when comparing P. pastoris and S. cerevisiae metabolomes, under the same cultivation conditions, similar metabolite fingerprints were found in both yeasts, except for the lower glycolysis, where the levels of these metabolites in P. pastoris suggested an enzymatic capacity limitation in that part of the metabolism

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci.

Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer-promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci

Impacts of global change on Mediterranean forests and their services

The increase in aridity, mainly by decreases in precipitation but also by higher temperatures, is likely the main threat to the diversity and survival of Mediterranean forests. Changes in land use, including the abandonment of extensive crop activities, mainly in mountains and remote areas, and the increases in human settlements and demand for more resources with the resulting fragmentation of the landscape, hinder the establishment of appropriate management tools to protect Mediterranean forests and their provision of services and biodiversity. Experiments and observations indicate that if changes in climate, land use and other components of global change, such as pollution and overexploitation of resources, continue, the resilience of many forests will likely be exceeded, altering their structure and function and changing, mostly decreasing, their capacity to continue to provide their current services. A consistent assessment of the impacts of the changes, however,remains elusive due to the difficulty of obtaining simultaneous and complete data for all scales of the impacts in the same forests, areas and regions. We review the impacts of climate change and other components of global change and their interactions on the terrestrial forests of Mediterranean regions, with special attention to their impacts on ecosystem services. Management tools for counteracting the negative effects of global change on Mediterranean ecosystem- services are finally discussed

FindPath: a Matlab solution for in silico design of synthetic metabolic pathways

Supplementary data are available at Bioinformatics online.A Summary: Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files