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Rajpurohit H, Eiteman MA. Nutrient-Limited Operational Strategies for the Microbial Production of Biochemicals. Microorganisms 2022; 10:2226. [PMID: 36363817 PMCID: PMC9695796 DOI: 10.3390/microorganisms10112226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 08/24/2023] Open
Abstract
Limiting an essential nutrient has a profound impact on microbial growth. The notion of growth under limited conditions was first described using simple Monod kinetics proposed in the 1940s. Different operational modes (chemostat, fed-batch processes) were soon developed to address questions related to microbial physiology and cell maintenance and to enhance product formation. With more recent developments of metabolic engineering and systems biology, as well as high-throughput approaches, the focus of current engineers and applied microbiologists has shifted from these fundamental biochemical processes. This review draws attention again to nutrient-limited processes. Indeed, the sophisticated gene editing tools not available to pioneers offer the prospect of metabolic engineering strategies which leverage nutrient limited processes. Thus, nutrient- limited processes continue to be very relevant to generate microbially derived biochemicals.
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Affiliation(s)
| | - Mark A. Eiteman
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602, USA
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2
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Li G, Jian T, Liu X, Lv Q, Zhang G, Ling J. Application of Metabolomics in Fungal Research. Molecules 2022; 27:7365. [PMID: 36364192 PMCID: PMC9654507 DOI: 10.3390/molecules27217365] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 08/27/2023] Open
Abstract
Metabolomics is an essential method to study the dynamic changes of metabolic networks and products using modern analytical techniques, as well as reveal the life phenomena and their inherent laws. Currently, more and more attention has been paid to the development of metabolic histochemistry in the fungus field. This paper reviews the application of metabolomics in fungal research from five aspects: identification, response to stress, metabolite discovery, metabolism engineering, and fungal interactions with plants.
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Affiliation(s)
- Guangyao Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Tongtong Jian
- Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Xiaojin Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Qingtao Lv
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guoying Zhang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jianya Ling
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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3
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Janoska A, Verheijen JJ, Tang W, Lee Q, Sikkema B, van Gulik WM. Influence of oxygen concentration on the metabolism of Penicillium chrysogenum. Eng Life Sci 2022; 23:e2100139. [PMID: 36619886 PMCID: PMC9815084 DOI: 10.1002/elsc.202100139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/17/2022] [Accepted: 03/08/2022] [Indexed: 01/11/2023] Open
Abstract
In large-scale bioreactors, there is often insufficient mixing and as a consequence, cells experience uneven substrate and oxygen levels that influence product formation. In this study, the influence of dissolved oxygen (DO) gradients on the primary and secondary metabolism of a high producing industrial strain of Penicillium chrysogenum was investigated. Within a wide range of DO concentrations, obtained under chemostat conditions, we observed different responses from P. chrysogenum: (i) no influence on growth or penicillin production (>0.025 mmol L-1); (ii) reduced penicillin production, but no growth limitation (0.013-0.025 mmol L-1); and (iii) growth and penicillin production limitations (<0.013 mmol L-1). In addition, scale down experiments were performed by oscillating the DO concentration in the bioreactor. We found that during DO oscillation, the penicillin production rate decreased below the value observed when a constant DO equal to the average oscillating DO value was used. To understand and predict the influence of oxygen levels on primary metabolism and penicillin production, we developed a black box model that was linked to a detailed kinetic model of the penicillin pathway. The model simulations represented the experimental data during the step experiments; however, during the oscillation experiments the predictions deviated, indicating the involvement of the central metabolism in penicillin production.
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Affiliation(s)
- Agnes Janoska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jelle J. Verheijen
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Wenjung Tang
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands,DSM Biotechnology CenterAlexander Fleminglaan 1DelftNetherlands
| | - Queenie Lee
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Baukje Sikkema
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Walter M. van Gulik
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
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4
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Fast Sampling of the Cellular Metabolome. Methods Mol Biol 2021. [PMID: 34718989 DOI: 10.1007/978-1-0716-1585-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Obtaining meaningful snapshots of the metabolome of microorganisms requires rapid sampling and immediate quenching of all metabolic activity, to prevent any changes in metabolite levels after sampling. Furthermore, a suitable extraction method is required ensuring complete extraction of metabolites from the cells and inactivation of enzymatic activity, with minimal degradation of labile compounds. Finally, a sensitive, high-throughput analysis platform is needed to quantify a large number of metabolites in a small amount of sample. An issue which has often been overlooked in microbial metabolomics is the fact that many intracellular metabolites are also present in significant amounts outside the cells and may interfere with the quantification of the endo metabolome. Attempts to remove the extracellular metabolites with dedicated quenching methods often induce release of intracellular metabolites into the quenching solution. For eukaryotic microorganisms, this release can be minimized by adaptation of the quenching method. For prokaryotic cells, this has not yet been accomplished, so the application of a differential method whereby metabolites are measured in the culture supernatant as well as in total broth samples, to calculate the intracellular levels by subtraction, seems to be the most suitable approach. Here we present an overview of different sampling, quenching, and extraction methods developed for microbial metabolomics, described in the literature. Detailed protocols are provided for rapid sampling, quenching, and extraction, for measurement of metabolites in total broth samples, washed cell samples, and supernatant, to be applied for quantitative metabolomics of both eukaryotic and prokaryotic microorganisms.
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Nieland S, Barig S, Salzmann J, Gehrau F, Zamani AI, Richter A, Ibrahim J, Gräser Y, Ng CL, Stahmann K. Aspergillus fumigatus AR04 obeys Arrhenius' rule in cultivation temperature shifts from 30 to 40°C. Microb Biotechnol 2021; 14:1422-1432. [PMID: 33421319 PMCID: PMC8313250 DOI: 10.1111/1751-7915.13739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 01/01/2023] Open
Abstract
To set a benchmark in fungal growth rate, a differential analysis of prototrophic Aspergillus fumigatus AR04 with three ascomycetes applied in > 103 t year-1 scale was performed, i.e. Ashbya gosspyii (riboflavin), Aspergillus niger (citric acid) and Aspergillus oryzae (food-processing). While radial colony growth decreased 0.5-fold when A. gossypii was cultivated at 40°C instead of 28°C, A. fumigatus AR04 responded with 1.7-fold faster hyphal growth. A. niger and A. oryzae formed colonies at 40°C, but not at 43°C. Moreover, all A. fumigatus strains tested grew even at 49°C. In chemostat experiments, A. fumigatus AR04 reached steady state at a dilution rate of 0.7 h-1 at 40°C, 120% more than reported for A. gossypii at 28°C. To study mycelial growth rates under unlimited conditions, carbon dioxide increase rates were calculated from concentrations detected online in the exhaust of batch fermentations for 3 h only. All rates calculated suggest that A. fumigatus AR04 approximates Arrhenius' rule when comparing short cultivations at 30°C with those at 40°C. Linearization of the exponential phase and comparison of the slopes revealed an increase to 192% by the 10°C up-shift.
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Affiliation(s)
- Susanne Nieland
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
| | - Susann Barig
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
| | - Julian Salzmann
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
| | - Frauke Gehrau
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
| | - Arief Izzairy Zamani
- Institute of Systems BiologyUniversiti Kebangsaan MalaysiaBangiSelangor43600 UKMMalaysia
| | - Annabell Richter
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
| | - Julia Ibrahim
- Sime Darby Technology CentreUPM‐MTDC Technology Centre IIILebuh Silikon1st Floor Block BUPM 43400SerdangSelangorMalaysia
| | - Yvonne Gräser
- Institute of Microbiology and ImmunologyCharité ‐ Universitätsmedizin BerlinCorporate Member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlinGermany
- Berlin Institute of HealthHindenburgdamm 30BerlinD‐12203Germany
| | - Chyan Leong Ng
- Institute of Systems BiologyUniversiti Kebangsaan MalaysiaBangiSelangor43600 UKMMalaysia
| | - Klaus‐Peter Stahmann
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
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Gelain L, Geraldo da Cruz Pradella J, Carvalho da Costa A, van der Wielen L, van Gulik WM. A possible influence of extracellular polysaccharides on the analysis of intracellular metabolites from Trichoderma harzianum grown under carbon-limited conditions. Fungal Biol 2020; 125:368-377. [PMID: 33910678 DOI: 10.1016/j.funbio.2020.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 10/30/2020] [Accepted: 12/08/2020] [Indexed: 11/19/2022]
Abstract
Intracellular metabolites were evaluated during the continuous growth of Trichoderma harzianum P49P11 under carbon-limited conditions. Four different conditions in duplicate were investigated (10 and 20 g/L of glucose, 5.26/5.26 g/L of fructose/glucose and 10 g/L of sucrose in the feed). Differences in the values of some specific concentrations of intracellular metabolites were observed at steady-state for the duplicates. The presence of extracellular polysaccharide was confirmed in the supernatant of all conditions based on FT-IR and proton NMR. Fragments of polysaccharides from the cell wall could be released due to the shear stress and since the cells can consume them under carbon-limited conditions, this could create an unpredictable carbon flow rate into the cells. According to the values of the metabolite concentrations, it was considered that the consumption of those fragments was interfering with the analysis.
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Affiliation(s)
- Lucas Gelain
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629HZ, Delft, the Netherlands; University of Campinas, School of Chemical Engineering, Av. Albert Einstein, 500, Campinas, Brazil.
| | - José Geraldo da Cruz Pradella
- Federal University of São Paulo, Institute of Science and Technology, Av. Cesare Mansueto Giulio Lattes, 1201, S. J. Campos, Brazil
| | - Aline Carvalho da Costa
- University of Campinas, School of Chemical Engineering, Av. Albert Einstein, 500, Campinas, Brazil
| | - Luuk van der Wielen
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629HZ, Delft, the Netherlands; University of Limerick, Bernal Institute, V94 T9PX, Limerick, Ireland
| | - Walter M van Gulik
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629HZ, Delft, the Netherlands
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7
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Analysis of the proteins secreted by Trichoderma harzianum P49P11 under carbon-limited conditions. J Proteomics 2020; 227:103922. [DOI: 10.1016/j.jprot.2020.103922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023]
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Hakkaart X, Liu Y, Hulst M, El Masoudi A, Peuscher E, Pronk J, van Gulik W, Daran-Lapujade P. Physiological responses of Saccharomyces cerevisiae to industrially relevant conditions: Slow growth, low pH, and high CO 2 levels. Biotechnol Bioeng 2020; 117:721-735. [PMID: 31654410 PMCID: PMC7028085 DOI: 10.1002/bit.27210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/12/2019] [Accepted: 10/22/2019] [Indexed: 12/21/2022]
Abstract
Engineered strains of Saccharomyces cerevisiae are used for industrial production of succinic acid. Optimal process conditions for dicarboxylic‐acid yield and recovery include slow growth, low pH, and high CO2. To quantify and understand how these process parameters affect yeast physiology, this study investigates individual and combined impacts of low pH (3.0) and high CO2 (50%) on slow‐growing chemostat and retentostat cultures of the reference strain S. cerevisiae CEN.PK113‐7D. Combined exposure to low pH and high CO2 led to increased maintenance‐energy requirements and death rates in aerobic, glucose‐limited cultures. Further experiments showed that these effects were predominantly caused by low pH. Growth under ammonium‐limited, energy‐excess conditions did not aggravate or ameliorate these adverse impacts. Despite the absence of a synergistic effect of low pH and high CO2 on physiology, high CO2 strongly affected genome‐wide transcriptional responses to low pH. Interference of high CO2 with low‐pH signaling is consistent with low‐pH and high‐CO2 signals being relayed via common (MAPK) signaling pathways, notably the cell wall integrity, high‐osmolarity glycerol, and calcineurin pathways. This study highlights the need to further increase robustness of cell factories to low pH for carboxylic‐acid production, even in organisms that are already applied at industrial scale.
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Affiliation(s)
- Xavier Hakkaart
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Yaya Liu
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Mandy Hulst
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Anissa El Masoudi
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Eveline Peuscher
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Jack Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
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Cortesão M, Schütze T, Marx R, Moeller R, Meyer V. Fungal Biotechnology in Space: Why and How? GRAND CHALLENGES IN FUNGAL BIOTECHNOLOGY 2020. [DOI: 10.1007/978-3-030-29541-7_18] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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10
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Quantitative Physiology of Non-Energy-Limited Retentostat Cultures of Saccharomyces cerevisiae at Near-Zero Specific Growth Rates. Appl Environ Microbiol 2019; 85:AEM.01161-19. [PMID: 31375494 DOI: 10.1128/aem.01161-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/27/2019] [Indexed: 01/07/2023] Open
Abstract
So far, the physiology of Saccharomyces cerevisiae at near-zero growth rates has been studied in retentostat cultures with a growth-limiting supply of the carbon and energy source. Despite its relevance in nature and industry, the near-zero growth physiology of S. cerevisiae under conditions where growth is limited by the supply of non-energy substrates remains largely unexplored. This study analyzes the physiology of S. cerevisiae in aerobic chemostat and retentostat cultures grown under either ammonium or phosphate limitation. To compensate for loss of extracellular nitrogen- or phosphorus-containing compounds, establishing near-zero growth rates (μ < 0.002 h-1) in these retentostats required addition of low concentrations of ammonium or phosphate to reservoir media. In chemostats as well as in retentostats, strongly reduced cellular contents of the growth-limiting element (nitrogen or phosphorus) and high accumulation levels of storage carbohydrates were observed. Even at near-zero growth rates, culture viability in non-energy-limited retentostats remained above 80% and ATP synthesis was still sufficient to maintain an adequate energy status and keep cells in a metabolically active state. Compared to similar glucose-limited retentostat cultures, the nitrogen- and phosphate-limited cultures showed aerobic fermentation and a partial uncoupling of catabolism and anabolism. The possibility to achieve stable, near-zero growth cultures of S. cerevisiae under nitrogen or phosphorus limitation offers interesting prospects for high-yield production of bio-based chemicals.IMPORTANCE The yeast Saccharomyces cerevisiae is a commonly used microbial host for production of various biochemical compounds. From a physiological perspective, biosynthesis of these compounds competes with biomass formation in terms of carbon and/or energy equivalents. Fermentation processes functioning at extremely low or near-zero growth rates would prevent loss of feedstock to biomass production. Establishing S. cerevisiae cultures in which growth is restricted by the limited supply of a non-energy substrate therefore could have a wide range of industrial applications but remains largely unexplored. In this work we accomplished near-zero growth of S. cerevisiae through limited supply of a non-energy nutrient, namely, the nitrogen or phosphorus source, and carried out a quantitative physiological study of the cells under these conditions. The possibility to achieve near-zero-growth S. cerevisiae cultures through limited supply of a non-energy nutrient may offer interesting prospects to develop novel fermentation processes for high-yield production of bio-based chemicals.
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Liu X, Wang T, Sun X, Wang Z, Tian X, Zhuang Y, Chu J. Optimized sampling protocol for mass spectrometry-based metabolomics in Streptomyces. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0269-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
In quantitative metabolomics studies, the most crucial step was arresting snapshots of all interesting metabolites. However, the procedure customized for Streptomyces was so rare that most studies consulted the procedure from other bacteria even yeast, leading to inaccurate and unreliable metabolomics analysis. In this study, a base solution (acetone: ethanol = 1:1, mol/mol) was added to a quenching solution to keep the integrity of the cell membrane. Based on the molar transition energy (ET) of the organic solvents, five solutions were used to carry out the quenching procedures. These were acetone, isoamylol, propanol, methanol, and 60% (v/v) methanol. To the best of our knowledge, this is the first report which has utilized a quenching solution with ET values. Three procedures were also adopted for extraction. These were boiling, freezing–thawing, and grinding ethanol. Following the analysis of the mass balance, amino acids, organic acids, phosphate sugars, and sugar alcohols were measured using gas chromatography with an isotope dilution mass spectrometry. It was found that using isoamylol with a base solution (5:1, v/v) as a quenching solution and that freezing–thawing in liquid nitrogen within 50% (v/v) methanol as an extracting procedure were the best pairing for the quantitative metabolomics of Streptomyces ZYJ-6, and resulted in average recoveries of close to 100%. The concentration of intracellular metabolites obtained from this new quenching solution was between two and ten times higher than that from 60% (v/v) methanol, which until now has been the most commonly used solution. Our findings are the first systematic quantitative metabolomics tools for Streptomyces ZYJ-6 and, therefore, will be important references for research in fields such as 13C based metabolic flux analysis, multi-omic research and genome-scale metabolic model establishment, as well as for other Streptomyces.
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Wang S, Liu P, Shu W, Li C, Li H, Liu S, Xia J, Noorman H. Dynamic response of Aspergillus niger to single pulses of glucose with high and low concentrations. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0251-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Lu H, Chen H, Tang X, Yang Q, Zhang H, Chen YQ, Chen W. Evaluation of metabolome sample preparation and extraction methodologies for oleaginous filamentous fungi Mortierella alpina. Metabolomics 2019; 15:50. [PMID: 30900034 DOI: 10.1007/s11306-019-1506-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 03/04/2019] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Metabolomics has been successfully applied to guide the rational engineering of industrial strains and improve the performance of bioprocesses. Mortierella alpina has traditionally been one of the most popular industrial strains for the production of polyunsaturated fatty acids. However, a systematic comparison and optimisation of the metabolomic analysis methods of M. alpina has not yet been reported. OBJECTIVE We sought to identify potential weaknesses that are important for accurate metabolomic analysis. We also aimed to determine an efficient sample preparation protocol for metabolomics studies in the oleaginous filamentous fungus M. alpina. METHODS In this study, using GC-MS, we evaluated three sample preparation protocols and five solvent mixtures by assessment of the metabolite profile differences, the sum of peak intensities and the reproducibility of metabolite quantification. RESULTS The freeze-dried biomass had better reproducibility and recovery than fresh biomass for metabolite extraction and data normalisation that is part of a metabolomics analysis of filamentous fungi M. alpina. Methanol:water (1:1) was superior for the profiling of metabolites in oleaginous fungi M. alpina. The unbiased metabolite profiling difference between the growth phase and lipids synthesis phase revealed that the degradation of amino acids were critical nodes for the efficient synthesis of lipids in M. alpina. CONCLUSION The use of freeze-dried biomass for metabolite extraction and data normalisation was more efficient at measuring the active state of the intracellular metabolites in M. alpina. We recommend extracting the intracellular metabolites with methanol:water (1:1). An important role of amino acid oxidation in the nitrogen limitation-mediated lipid accumulation was found.
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Affiliation(s)
- Hengqian Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, China.
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, 225004, China.
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Qin Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, 225004, China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
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Tong Z, Zheng X, Tong Y, Shi YC, Sun J. Systems metabolic engineering for citric acid production by Aspergillus niger in the post-genomic era. Microb Cell Fact 2019; 18:28. [PMID: 30717739 PMCID: PMC6362574 DOI: 10.1186/s12934-019-1064-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/16/2019] [Indexed: 11/11/2022] Open
Abstract
Citric acid is the world’s largest consumed organic acid and is widely used in beverage, food and pharmaceutical industries. Aspergillus niger is the main industrial workhorse for citric acid production. Since the release of the genome sequence, extensive multi-omic data are being rapidly obtained, which greatly boost our understanding of the citric acid accumulation mechanism in A. niger to a molecular and system level. Most recently, the rapid development of CRISPR/Cas9 system facilitates highly efficient genome-scale genetic perturbation in A. niger. In this review, we summarize the impact of systems biology on the citric acid molecular regulatory mechanisms, the advances in metabolic engineering strategies for enhancing citric acid production and discuss the development and application of CRISPR/Cas9 systems for genome editing in A. niger. We believe that future systems metabolic engineering efforts will redesign and engineer A. niger as a highly optimized cell factory for industrial citric acid production.
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Affiliation(s)
- Zhenyu Tong
- Department of Grain Science and Industry, Kansas State University, Manhattan, KS, 66506, USA
| | - Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Yi Tong
- COFCO Biochemical (Anhui) Co. Ltd, Bengbu, 233000, People's Republic of China
| | - Yong-Cheng Shi
- Department of Grain Science and Industry, Kansas State University, Manhattan, KS, 66506, USA
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
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Zheng X, Yu J, Cairns TC, Zhang L, Zhang Z, Zhang Q, Zheng P, Sun J, Ma Y. Comprehensive Improvement of Sample Preparation Methodologies Facilitates Dynamic Metabolomics of Aspergillus niger. Biotechnol J 2018; 14:e1800315. [PMID: 30144348 DOI: 10.1002/biot.201800315] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/27/2018] [Indexed: 12/23/2022]
Abstract
Metabolomics is an essential discipline in industrial biotechnology. Sample preparation approaches dramatically influence data quality and, ultimately, interpretation and conclusions from metabolomic experiments. However, standardized protocols for highly reproducible metabolic datasets are limited, especially for the fungal cell factory Aspergillus niger. Here, an improved liquid chromatography-tandem mass spectrometry-based pipeline for A. niger metabolomics is developed. It is found that fast filtration with liquid nitrogen is more suitable for cell quenching, causing minimal disruption to cell integrity, and improved intracellular metabolite recovery when compared to cold methanol quenching approaches. Seven solutions are evaluated for intracellular metabolite extraction, and found acetonitrile/water (1:1, v/v) at -20 °C, combined with boiling ethanol extraction protocols, showed unbiased metabolite profiling. This improved methodology is applied to unveil the dynamic metabolite profile of one citrate over-producing A. niger isolate under citrate fermentation. Citrate precursors, especially pyruvate, oxaloacetate, and malate, are maintained at a relatively high intracellular level, which can be necessary for high citrate synthesis flux. Glutamine shows a similar trend compared to citrate production, suggesting glutamine may be involved in intracellular pH homeostasis. Taken together, this study delivers a highly standardized and improved metabolomics methodology and paves the way for systems metabolic engineering in biotechnologically important fungi.
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Affiliation(s)
- Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jiandong Yu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Timothy C Cairns
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lihui Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhidan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Qiongqiong Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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16
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Li C, Shu W, Wang S, Liu P, Zhuang Y, Zhang S, Xia J. Dynamic metabolic response of Aspergillus niger to glucose perturbation: evidence of regulatory mechanism for reduced glucoamylase production. J Biotechnol 2018; 287:28-40. [PMID: 30134150 DOI: 10.1016/j.jbiotec.2018.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/20/2018] [Accepted: 08/18/2018] [Indexed: 01/14/2023]
Abstract
Environmental gradient is an important common issue during scale-up process for protein production. To address the dynamic regulatory mechanism of Aspergillus niger being exposed to inhomogeneous glucose concentrations, glucose perturbation were experimented on the steady state of A. niger chemostat culture, and dynamic profiles of the intracellular metabolites in central carbon metabolism were tracked in a time scale of seconds. The upper glycolysis and pentose phosphate pathway showed sharp variations after glucose perturbation, while the lower glycolysis, TCA cycle and amino acid pools represented a moderate and prolonged response due to the allosteric regulation of enzymes and buffering function of metabolites with large pool sizes. Improved glucose-6-phosphate enhanced the metabolic flux to PP pathway remarkably, which provided not only more redox cofactors (NADPH) for protein synthesis but also more precursors (phosphoribosyl pyrophosphate and ribose-5-phosphate) for cell growth. Moreover, reduction of the total adenine nucleotides and major precursor amino acids indicated the upregulated RNA synthesis was required to produce stress proteins, and partially explained the drop of glucoamylase production when A. niger experienced a fluctuated glucose concentration environment. These findings would be valuable for improving bioreactor operation, design, and scale-up from engineering or genetic aspects.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Shu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shuai Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Peng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yingpping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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17
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Sevastos A, Kalampokis IF, Panagiotopoulou A, Pelecanou M, Aliferis KA. Implication of Fusarium graminearum primary metabolism in its resistance to benzimidazole fungicides as revealed by 1H NMR metabolomics. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2018; 148:50-61. [PMID: 29891377 DOI: 10.1016/j.pestbp.2018.03.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 03/24/2018] [Accepted: 03/25/2018] [Indexed: 06/08/2023]
Abstract
Fungal metabolomics is a field of high potential but yet largely unexploited. Focusing on plant-pathogenic fungi, no metabolomics studies exist on their resistance to fungicides, which represents a major issue that the agrochemical and agricultural sectors are facing. Fungal infections cause quantitative, but also qualitative yield losses, especially in the case of mycotoxin-producing species. The aim of the study was to correlate metabolic changes in Fusarium graminearum strains' metabolomes with their carbendazim-resistant level and discover corresponding metabolites-biomarkers, with primary focus on its primary metabolism. For this purpose, comparative 1H NMR metabolomics was applied to a wild-type and four carbendazim-resistant Fusarium graminearum strains following or not exposure to the fungicide. Results showed an excellent discrimination between the strains based on their carbendazim-resistance following exposure to low concentration of the fungicide (2 mg L-1). Both genotype and fungicide treatments had a major impact on fungal metabolism. Among the signatory metabolites, a positive correlation was discovered between the content of F. graminearum strains in amino acids of the aromatic and pyruvate families, l-glutamate, l-proline, l-serine, pyroglutamate, and succinate and their carbendazim-resistance level. In contrary, their content in l-glutamine and l-threonine, had a negative correlation. Many of these metabolites play important roles in fungal physiology and responses to stresses. This work represents a proof-of-concept of the applicability of 1H NMR metabolomics for high-throughput screening of fungal mutations leading to fungicide resistance, and the study of its biochemical basis, focusing on the involvement of primary metabolism. Results could be further exploited in programs of resistance monitoring, genetic engineering, and crop protection for combating fungal resistance to fungicides.
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Affiliation(s)
- A Sevastos
- Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - I F Kalampokis
- Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - A Panagiotopoulou
- Institute of Biosciences & Applications, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - M Pelecanou
- Institute of Biosciences & Applications, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - K A Aliferis
- Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Athens, Greece; Department of Plant Science, Macdonald Campus of McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada.
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18
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Lameiras F, Ras C, Ten Pierick A, Heijnen JJ, van Gulik WM. Stoichiometry and kinetics of single and mixed substrate uptake in Aspergillus niger. Bioprocess Biosyst Eng 2017; 41:157-170. [PMID: 29052015 PMCID: PMC5773628 DOI: 10.1007/s00449-017-1854-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 10/11/2017] [Indexed: 01/28/2023]
Abstract
In its natural environment, the filamentous fungus Aspergillus niger grows on decaying fruits and plant material, thereby enzymatically degrading the lignocellulosic constituents (lignin, cellulose, hemicellulose, and pectin) into a mixture of mono- and oligosaccharides. To investigate the kinetics and stoichiometry of growth of this fungus on lignocellulosic sugars, we carried out batch cultivations on six representative monosaccharides (glucose, xylose, mannose, rhamnose, arabinose, and galacturonic acid) and a mixture of these. Growth on these substrates was characterized in terms of biomass yields, oxygen/biomass ratios, and specific conversion rates. Interestingly, in combination, some of the carbon sources were consumed simultaneously and some sequentially. With a previously developed protocol, a sequential chemostat cultivation experiment was performed on a feed mixture of the six substrates. We found that the uptake of glucose, xylose, and mannose could be described with a Michaelis–Menten-type kinetics; however, these carbon sources seem to be competing for the same transport systems, while the uptake of arabinose, galacturonic acid, and rhamnose appeared to be repressed by the presence of other substrates.
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Affiliation(s)
- Francisca Lameiras
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Cor Ras
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Angela Ten Pierick
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Joseph J Heijnen
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Walter M van Gulik
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands.
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Kapoore RV, Vaidyanathan S. Towards quantitative mass spectrometry-based metabolomics in microbial and mammalian systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0363. [PMID: 27644979 PMCID: PMC5031630 DOI: 10.1098/rsta.2015.0363] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/27/2016] [Indexed: 05/03/2023]
Abstract
Metabolome analyses are a suite of analytical approaches that enable us to capture changes in the metabolome (small molecular weight components, typically less than 1500 Da) in biological systems. Mass spectrometry (MS) has been widely used for this purpose. The key challenge here is to be able to capture changes in a reproducible and reliant manner that is representative of the events that take place in vivo Typically, the analysis is carried out in vitro, by isolating the system and extracting the metabolome. MS-based approaches enable us to capture metabolomic changes with high sensitivity and resolution. When developing the technique for different biological systems, there are similarities in challenges and differences that are specific to the system under investigation. Here, we review some of the challenges in capturing quantitative changes in the metabolome with MS based approaches, primarily in microbial and mammalian systems.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Rahul Vijay Kapoore
- Advanced Biomanufacturing Centre, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Seetharaman Vaidyanathan
- Advanced Biomanufacturing Centre, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
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20
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Lu H, Cao W, Ouyang L, Xia J, Huang M, Chu J, Zhuang Y, Zhang S, Noorman H. Comprehensive reconstruction and in silico analysis of Aspergillus niger genome-scale metabolic network model that accounts for 1210 ORFs. Biotechnol Bioeng 2016; 114:685-695. [PMID: 27696371 DOI: 10.1002/bit.26195] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/29/2016] [Indexed: 12/26/2022]
Abstract
Aspergillus niger is one of the most important cell factories for industrial enzymes and organic acids production. A comprehensive genome-scale metabolic network model (GSMM) with high quality is crucial for efficient strain improvement and process optimization. The lack of accurate reaction equations and gene-protein-reaction associations (GPRs) in the current best model of A. niger named GSMM iMA871, however, limits its application scope. To overcome these limitations, we updated the A. niger GSMM by combining the latest genome annotation and literature mining technology. Compared with iMA871, the number of reactions in iHL1210 was increased from 1,380 to 1,764, and the number of unique ORFs from 871 to 1,210. With the aid of our transcriptomics analysis, the existence of 63% ORFs and 68% reactions in iHL1210 can be verified when glucose was used as the only carbon source. Physiological data from chemostat cultivations, 13 C-labeled and molecular experiments from the published literature were further used to check the performance of iHL1210. The average correlation coefficients between the predicted fluxes and estimated fluxes from 13 C-labeling data were sufficiently high (above 0.89) and the prediction of cell growth on most of the reported carbon and nitrogen sources was consistent. Using the updated genome-scale model, we evaluated gene essentiality on synthetic and yeast extract medium, as well as the effects of NADPH supply on glucoamylase production in A. niger. In summary, the new A. niger GSMM iHL1210 contains significant improvements with respect to the metabolic coverage and prediction performance, which paves the way for systematic metabolic engineering of A. niger. Biotechnol. Bioeng. 2017;114: 685-695. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hongzhong Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Weiqiang Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Liming Ouyang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Mingzhi Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Henk Noorman
- DSM Biotechnology Center, Delft, The Netherlands
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21
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Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology. Anal Chim Acta 2016; 938:18-32. [DOI: 10.1016/j.aca.2016.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023]
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22
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Vrabl P, Artmann DJ, Schinagl CW, Burgstaller W. Rapid sample processing for intracellular metabolite studies in Penicillium ochrochloron CBS 123.824: the FiltRes-device combines cold filtration of methanol quenched biomass with resuspension in extraction solution. SPRINGERPLUS 2016; 5:966. [PMID: 27429876 PMCID: PMC4932030 DOI: 10.1186/s40064-016-2649-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 06/23/2016] [Indexed: 11/10/2022]
Abstract
Background Many issues concerning sample processing for intracellular metabolite studies in filamentous fungi still need to be solved, e.g. how to reduce the contact time of the biomass to the quenching solution in order to minimize metabolite leakage. Since the required time to separate the biomass from the quenching solution determines the contact time, speeding up this step is thus of utmost interest. Recently, separation approaches based on cold-filtration were introduced as promising alternative to cold-centrifugation, which exhibit considerably reduced contact times. In previous works we were unable to obtain a compact pellet from cold methanol quenched samples of the filamentous fungus Penicillium ochrochloron CBS 123.824 via centrifugation. Therefore our aim was to establish for this organism a separation technique based on cold-filtration to determine intracellular levels of a selected set of nucleotides. Results We developed a cold-filtration based technique as part of our effort to revise the entire sample processing method and analytical procedure. The Filtration-Resuspension (FiltRes) device combined in a single apparatus (1) a rapid cold-filtration and (2) a rapid resuspension of the biomass in hot extraction solution. Unique to this is the injection of the extraction solution from below the membrane filter (FiltRes-principle). This caused the mycelial cake to detach completely from the filter membrane and to float upwards so that the biomass could easily be transferred into preheated tubes for metabolite extraction. The total contact time of glucose-limited chemostat mycelium to the quenching solution could be reduced to 15.7 ± 2.5 s, whereby each washing step added another 10–15 s. We evaluated critical steps like filtration time, temperature profile, reproducibility of results, and using the energy charge (EC) as a criterion, effectiveness of enzyme destruction during the transition in sample temperature from cold to hot. As control we used total broth samples quenched in hot ethanol. Averaged over all samples an EC of 0.93 ± 0.020 was determined with the FiltRes-principle compared to 0.89 ± 0.049 with heat stopped total broth samples. Conclusions We concluded that for P. ochrochloron this technique is a reliable sample processing method for intracellular metabolite analysis, which might offer also other possible applications. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2649-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pamela Vrabl
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Desiree J Artmann
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Christoph W Schinagl
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Wolfgang Burgstaller
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
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