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Laakko T, Korkealaakso A, Yildirir BF, Batys P, Liljeström V, Hokkanen A, Nonappa, Penttilä M, Laukkanen A, Miserez A, Södergård C, Mohammadi P. Accelerated Engineering of ELP-based Materials through Hybrid Biomimetic-De Novo Predictive Molecular Design. Adv Mater 2024:e2312299. [PMID: 38710202 DOI: 10.1002/adma.202312299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/28/2024] [Indexed: 05/08/2024]
Abstract
Efforts to engineer high-performance protein-based materials inspired by nature have mostly focused on altering naturally occurring sequences to confer the desired functionalities, whereas de novo design lags significantly behind and calls for unconventional innovative approaches. Here, using partially disordered elastin-like polypeptides (ELPs) as initial building blocks we show that de novo engineering of protein materials can be accelerated through hybrid biomimetic design, which we achieve by integrating computational modeling, deep neural network, and recombinant DNA technology. This generalizable approach involves incorporating a series of de novo-designed sequences with α-helical conformation and genetically encoding them into biologically inspired intrinsically disordered repeating motifs. The new ELP variants maintained structural conformation and showed tunable supramolecular self-assembly out of thermal equilibrium with phase behavior in vitro. We illustrate the effective translation of the predicted molecular designs in structural and functional materials. The proposed methodology can be applied to a broad range of partially disordered biomacromolecules and potentially pave the way toward the discovery of novel structural proteins. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Timo Laakko
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | | | - Burcu Firatligil Yildirir
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 6, Tampere, FI-33720, Finland
| | - Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow, PL-30239, Poland
| | - Ville Liljeström
- Department of Applied Physics, School of Science, Aalto University, Aalto, FI-00076, Finland
| | - Ari Hokkanen
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Nonappa
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 6, Tampere, FI-33720, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Anssi Laukkanen
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore, 637553, Singapore
- School of Biological Sciences, NTU, 637551, Singapore
| | - Caj Södergård
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., VTT, FI-02044, Finland
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Toivari M, Vehkomäki ML, Ruohonen L, Penttilä M, Wiebe MG. Production of D-glucaric acid with phosphoglucose isomerase-deficient Saccharomyces cerevisiae. Biotechnol Lett 2024; 46:69-83. [PMID: 38064042 PMCID: PMC10787697 DOI: 10.1007/s10529-023-03443-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/14/2023] [Accepted: 10/17/2023] [Indexed: 01/14/2024]
Abstract
D-Glucaric acid is a potential biobased platform chemical. Previously mainly Escherichia coli, but also the yeast Saccharomyces cerevisiae, and Pichia pastoris, have been engineered for conversion of D-glucose to D-glucaric acid via myo-inositol. One reason for low yields from the yeast strains is the strong flux towards glycolysis. Thus, to decrease the flux of D-glucose to biomass, and to increase D-glucaric acid yield, the four step D-glucaric acid pathway was introduced into a phosphoglucose isomerase deficient (Pgi1p-deficient) Saccharomyces cerevisiae strain. High D-glucose concentrations are toxic to the Pgi1p-deficient strains, so various feeding strategies and use of polymeric substrates were studied. Uniformly labelled 13C-glucose confirmed conversion of D-glucose to D-glucaric acid. In batch bioreactor cultures with pulsed D-fructose and ethanol provision 1.3 g D-glucaric acid L-1 was produced. The D-glucaric acid titer (0.71 g D-glucaric acid L-1) was lower in nitrogen limited conditions, but the yield, 0.23 g D-glucaric acid [g D-glucose consumed]-1, was among the highest that has so far been reported from yeast. Accumulation of myo-inositol indicated that myo-inositol oxygenase activity was limiting, and that there would be potential to even higher yield. The Pgi1p-deficiency in S. cerevisiae provides an approach that in combination with other reported modifications and bioprocess strategies would promote the development of high yield D-glucaric acid yeast strains.
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Affiliation(s)
- Mervi Toivari
- VTT Technical Research Centre of Finland Ltd, Tekniikantie 21, P.O. Box 1000, 02044, Espoo, Finland.
| | - Maija-Leena Vehkomäki
- VTT Technical Research Centre of Finland Ltd, Tekniikantie 21, P.O. Box 1000, 02044, Espoo, Finland
| | - Laura Ruohonen
- VTT Technical Research Centre of Finland Ltd, Tekniikantie 21, P.O. Box 1000, 02044, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd, Tekniikantie 21, P.O. Box 1000, 02044, Espoo, Finland
| | - Marilyn G Wiebe
- VTT Technical Research Centre of Finland Ltd, Tekniikantie 21, P.O. Box 1000, 02044, Espoo, Finland
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Kakko N, Rantasalo A, Koponen T, Vidgren V, Kannisto M, Maiorova N, Nygren H, Mojzita D, Penttilä M, Jouhten P. Inducible Synthetic Growth Regulation Using the ClpXP Proteasome Enhances cis,cis-Muconic Acid and Glycolic Acid Yields in Saccharomyces cerevisiae. ACS Synth Biol 2023; 12:1021-1033. [PMID: 36976676 PMCID: PMC10127448 DOI: 10.1021/acssynbio.2c00467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Engineered microbial cells can produce sustainable chemistry, but the production competes for resources with growth. Inducible synthetic control over the resource use would enable fast accumulation of sufficient biomass and then divert the resources to production. We developed inducible synthetic resource-use control overSaccharomyces cerevisiae by expressing a bacterial ClpXP proteasome from an inducible promoter. By individually targeting growth-essential metabolic enzymes Aro1, Hom3, and Acc1 to the ClpXP proteasome, cell growth could be efficiently repressed during cultivation. The ClpXP proteasome was specific to the target proteins, and there was no reduction in the targets when ClpXP was not induced. The inducible growth repression improved product yields from glucose (cis,cis-muconic acid) and per biomass (cis,cis-muconic acid and glycolic acid). The inducible ClpXP proteasome tackles uncertainties in strain optimization by enabling model-guided repression of competing, growth-essential, and metabolic enzymes. Most importantly, it allows improving production without compromising biomass accumulation when uninduced; therefore, it is expected to mitigate strain stability and low productivity challenges.
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Affiliation(s)
- Natalia Kakko
- VTT Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
- School of Chemical Engineering, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16300, Espoo FI-00076 AALTO, Finland
| | - Anssi Rantasalo
- VTT Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Tino Koponen
- VTT Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Virve Vidgren
- VTT Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Matti Kannisto
- VTT Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Natalia Maiorova
- VTT Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Heli Nygren
- VTT Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
- School of Chemical Engineering, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16300, Espoo FI-00076 AALTO, Finland
| | - Paula Jouhten
- VTT Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
- School of Chemical Engineering, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16300, Espoo FI-00076 AALTO, Finland
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Pylkkänen R, Werner D, Bishoyi A, Weil D, Scoppola E, Wagermaier W, Safeer A, Bahri S, Baldus M, Paananen A, Penttilä M, Szilvay GR, Mohammadi P. The complex structure of Fomes fomentarius represents an architectural design for high-performance ultralightweight materials. Sci Adv 2023; 9:eade5417. [PMID: 36812306 PMCID: PMC9946349 DOI: 10.1126/sciadv.ade5417] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
High strength, hardness, and fracture toughness are mechanical properties that are not commonly associated with the fleshy body of a fungus. Here, we show with detailed structural, chemical, and mechanical characterization that Fomes fomentarius is an exception, and its architectural design is a source of inspiration for an emerging class of ultralightweight high-performance materials. Our findings reveal that F. fomentarius is a functionally graded material with three distinct layers that undergo multiscale hierarchical self-assembly. Mycelium is the primary component in all layers. However, in each layer, mycelium exhibits a very distinct microstructure with unique preferential orientation, aspect ratio, density, and branch length. We also show that an extracellular matrix acts as a reinforcing adhesive that differs in each layer in terms of quantity, polymeric content, and interconnectivity. These findings demonstrate how the synergistic interplay of the aforementioned features results in distinct mechanical properties for each layer.
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Affiliation(s)
- Robert Pylkkänen
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Daniel Werner
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, D-14476 Potsdam, Germany
| | - Ajit Bishoyi
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Dominik Weil
- KLA-Tencor GmbH, Moritzburger Weg 67, Dresden 01109, Germany
| | - Ernesto Scoppola
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, D-14476 Potsdam, Germany
| | - Wolfgang Wagermaier
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, D-14476 Potsdam, Germany
| | - Adil Safeer
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Salima Bahri
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Arja Paananen
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Géza R. Szilvay
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
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Pylkkänen R, Mohammadi P, Liljeström V, Płaziński W, Beaune G, Timonen JVI, Penttilä M. β-1,3-Glucan synthesis, novel supramolecular self-assembly, characterization and application. Nanoscale 2022; 14:15533-15541. [PMID: 36194159 DOI: 10.1039/d2nr02731c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
β-1,3-Glucans are ubiquitously observed in various biological systems with diverse physio-ecological functions, yet their underlying assembly mechanism and multiscale complexation in vitro remains poorly understood. Here, we provide for the first-time evidence of unidentified β-1,3-glucan supramolecular complexation into intricate hierarchical architectures over several length scales. We mediated these unique assemblies using a recombinantly produced β-1,3-glucan phosphorylase (Ta1,3BGP) by fine-tuning solution conditions during particle nucleation and growth. We report a synthesis of interconnected parallel hexagonal lamellae composed of 8 nm thick sheets of highly expanded paracrystals. The architecture consists of β-1,3-glucan triple-helices with considerable inter-intra hydrogen bonding within, as well as in between adjacent triple-helices. The results extend our understanding of β-1,3-glucan molecular organization and shed light on different aspects of the crystallization processes of biomolecules into structures unseen by nature. The presented versatile synthesis yields new materials for diverse medical and industrial applications.
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Affiliation(s)
- Robert Pylkkänen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland.
- VTT Technical Research Centre of Finland, FI-02044 VTT, Finland
| | | | - Ville Liljeström
- Nanomicroscopy Center, OtaNano, Aalto University, FI-00076 Aalto, Finland
| | - Wojciech Płaziński
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Krakow, Poland
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland
| | - Grégory Beaune
- Nanomicroscopy Center, OtaNano, Aalto University, FI-00076 Aalto, Finland
| | - Jaakko V I Timonen
- Department of Applied Physics, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Merja Penttilä
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland.
- VTT Technical Research Centre of Finland, FI-02044 VTT, Finland
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6
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Pylkkänen R, Mohammadi P, Liljeström V, Płaziński W, Beaune G, Timonen JVI, Penttilä M. Correction: β-1,3-Glucan synthesis, novel supramolecular self-assembly, characterization and application. Nanoscale 2022; 14:15542. [PMID: 36260479 DOI: 10.1039/d2nr90202h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Correction for 'β-1,3-Glucan synthesis, novel supramolecular self-assembly, characterization and application' by Robert Pylkkänen et al., Nanoscale, 2022, https://doi.org/10.1039/D2NR02731C.
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Affiliation(s)
- Robert Pylkkänen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland.
- VTT Technical Research Centre of Finland, FI-02044 VTT, Finland
| | | | - Ville Liljeström
- Nanomicroscopy Center, OtaNano, Aalto University, FI-00076 Aalto, Finland
| | - Wojciech Płaziński
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Krakow, Poland
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland
| | - Grégory Beaune
- Nanomicroscopy Center, OtaNano, Aalto University, FI-00076 Aalto, Finland
| | - Jaakko V I Timonen
- Department of Applied Physics, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Merja Penttilä
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland.
- VTT Technical Research Centre of Finland, FI-02044 VTT, Finland
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Ylinen A, de Ruijter JC, Jouhten P, Penttilä M. PHB production from cellobiose with Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:124. [PMID: 35729556 PMCID: PMC9210708 DOI: 10.1186/s12934-022-01845-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Replacement of petrochemical-based materials with microbially produced biodegradable alternatives calls for industrially attractive fermentation processes. Lignocellulosic materials offer non-edible alternatives for cultivated sugars, but require often use of expensive sugar releasing enzymes, such as β-glucosidases. These cellulose treatment costs could be reduced if microbial production hosts could use short cellodextrins such as cellobiose directly as their substrates. In this study, we demonstrate production of poly(hydroxybutyrate) (PHB) in yeast Saccharomyces cerevisiae using cellobiose as a sole carbon source. Yeast strains expressing PHB pathway genes from Cupriavidus necator and cellodextrin transporter gene CDT-1 from Neurospora crassa were complemented either with β-glucosidase gene GH1-1 from N. crassa or with cellobiose phosphorylase gene cbp from Ruminococcus flavefaciens. These cellobiose utilization routes either with Gh1-1 or Cbp enzymes differ in energetics and dynamics. However, both routes enabled higher PHB production per consumed sugar and higher PHB accumulation % of cell dry weight (CDW) than use of glucose as a carbon source. As expected, the strains with Gh1-1 consumed cellobiose faster than the strains with Cbp, both in flask and bioreactor batch cultures. In shake flasks, higher final PHB accumulation % of CDW was reached with Cbp route (10.0 ± 0.3%) than with Gh1-1 route (8.1 ± 0.2%). However, a higher PHB accumulation was achieved in better aerated and pH-controlled bioreactors, in comparison to shake flasks, and the relative performance of strains switched. In bioreactors, notable PHB accumulation levels per CDW of 13.4 ± 0.9% and 18.5 ± 3.9% were achieved with Cbp and Gh1-1 routes, respectively. The average molecular weights of accumulated PHB were similar using both routes; approximately 500 kDa and 450 kDa for strains expressing either cbp or GH1-1 genes, respectively. The formation of PHB with high molecular weights, combined with efficient cellobiose conversion, demonstrates a highly potential solution for improving attractiveness of sustainable polymer production using microbial cells.
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Affiliation(s)
- Anna Ylinen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.
| | - Jorg C de Ruijter
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland
| | - Paula Jouhten
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 00076, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 00076, Espoo, Finland
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Sabzevari M, Szedmak S, Penttilä M, Jouhten P, Rousu J. Strain design optimization using reinforcement learning. PLoS Comput Biol 2022; 18:e1010177. [PMID: 35658018 PMCID: PMC9200333 DOI: 10.1371/journal.pcbi.1010177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 06/15/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022] Open
Abstract
Engineered microbial cells present a sustainable alternative to fossil-based synthesis of chemicals and fuels. Cellular synthesis routes are readily assembled and introduced into microbial strains using state-of-the-art synthetic biology tools. However, the optimization of the strains required to reach industrially feasible production levels is far less efficient. It typically relies on trial-and-error leading into high uncertainty in total duration and cost. New techniques that can cope with the complexity and limited mechanistic knowledge of the cellular regulation are called for guiding the strain optimization.
In this paper, we put forward a multi-agent reinforcement learning (MARL) approach that learns from experiments to tune the metabolic enzyme levels so that the production is improved. Our method is model-free and does not assume prior knowledge of the microbe’s metabolic network or its regulation. The multi-agent approach is well-suited to make use of parallel experiments such as multi-well plates commonly used for screening microbial strains.
We demonstrate the method’s capabilities using the genome-scale kinetic model of Escherichia coli, k-ecoli457, as a surrogate for an in vivo cell behaviour in cultivation experiments. We investigate the method’s performance relevant for practical applicability in strain engineering i.e. the speed of convergence towards the optimum response, noise tolerance, and the statistical stability of the solutions found. We further evaluate the proposed MARL approach in improving L-tryptophan production by yeast Saccharomyces cerevisiae, using publicly available experimental data on the performance of a combinatorial strain library.
Overall, our results show that multi-agent reinforcement learning is a promising approach for guiding the strain optimization beyond mechanistic knowledge, with the goal of faster and more reliably obtaining industrially attractive production levels.
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Affiliation(s)
- Maryam Sabzevari
- Department of Computer Science, Aalto University, Espoo, Finland
- * E-mail: ,
| | - Sandor Szedmak
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Paula Jouhten
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Juho Rousu
- Department of Computer Science, Aalto University, Espoo, Finland
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Rautio N, Ylitolonen L, Haapea M, Huovinen H, Alakokkare AE, Niemelä S, Miettunen J, Penttilä M, Koponen H, Seppälä J, Isohanni M, Jääskeläinen E. Off-label prescribing of antipsychotics: prescribing practices and clinical experiences of Finnish physicians. Eur Psychiatry 2022. [PMCID: PMC9567249 DOI: 10.1192/j.eurpsy.2022.876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Introduction
Off-label use of antipsychotics has increased in many countries. In adult populations antipsychotics off-label prescriptions varied from 40 to 75% of all AP users.
Objectives
To examine the off-label prescribing practices and experiences of antipsychotic medication in Finland.
Methods
An electronic questionnaire on physicians’ prescription practices of antipsychotics, especially for off-label use, was sent in 2019 for physicians (n=1195) in different health care facilities including primary health care, occupational health care, in- and outpatient mental health services and services for substance abuse. The sample was selected by systematic and convenience sampling covering five university hospital areas in Finland.
Results
In total, 216 physicians (18% of the target sample) participated in the study, and 94% had prescribed antipsychotics for off-label use. The most common off-label indications were insomnia and anxiety. The most common antipsychotic used was quetiapine. Off-label antipsychotics was not prescribed as a first-choice medication: 99% of the physicians reported that the patients with off-label use have previously had other medications for the corresponding symptoms. In all, 88% of clinicians monitored the patients’ clinical condition, whereas metabolic values were followed more rarely. About 68% of physicians reported more benefit than harm from the antipsychotics off-label
use.
Conclusions
Antipsychotics are often prescribed for off-label use, most commonly for insomnia and anxiety. Most of the physicians see more benefits than harms for the patient in off-label use. There is a need to analyse the long-term benefits and harms of off-label use of antipsychotics and create more detailed treatment algorithms and clinical recommendations for such use.
Disclosure
No significant relationships.
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Mohammadi P, Gandier JA, Wagermaier W, Miserez A, Penttilä M. Bioinspired Functionally Graded Composite Assembled Using Cellulose Nanocrystals and Genetically Engineered Proteins with Controlled Biomineralization. Adv Mater 2021; 33:e2102658. [PMID: 34467572 DOI: 10.1002/adma.202102658] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Nature provides unique insights into design strategies evolved by living organisms to construct robust materials with a combination of mechanical properties that are challenging to replicate synthetically. Hereby, inspired by the impact-resistant dactyl club of the stomatopod, a mineralized biocomposite is rationally designed and produced in the complex shapes of dental implant crowns exhibiting high strength, stiffness, and fracture toughness. This material consists of an expanded helicoidal organization of cellulose nanocrystals (CNCs) mixed with genetically engineered proteins that regulate both binding to CNCs and in situ growth of reinforcing apatite crystals. Critically, the structural properties emerge from controlled self-assembly across multiple length scales regulated by rational engineering and phase separation of the protein components. This work replicates multiscale biomanufacturing of a model biological material and also offers an innovative platform to synthesize multifunctional biocomposites whose properties can be finely regulated by colloidal self-assembly and engineering of its constitutive protein building blocks.
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Affiliation(s)
- Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd, VTT, Espoo, FI-02044, Finland
| | - Julie-Anne Gandier
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, Espoo, FI-16100, Finland
| | - Wolfgang Wagermaier
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg1, 14476, Potsdam, Germany
| | - Ali Miserez
- Centre for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 639798, Singapore
- School of Biological Sciences, 60 Nanyang Drive, NTU, Singapore, 637551, Singapore
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd, VTT, Espoo, FI-02044, Finland
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Allahverdiyeva Y, Aro EM, van Bavel B, Escudero C, Funk C, Heinonen J, Herfindal L, Lindblad P, Mäkinen S, Penttilä M, Sivonen K, Skogen Chauton M, Skomedal H, Skjermo J. NordAqua, a Nordic Center of Excellence to develop an algae-based photosynthetic production platform. Physiol Plant 2021; 173:507-513. [PMID: 33709388 DOI: 10.1111/ppl.13394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/25/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
NordAqua is a multidisciplinary Nordic Center of Excellence funded by NordForsk Bioeconomy program (2017-2022). The research center promotes Blue Bioeconomy and endeavours to reform the use of natural resources in a environmentally sustainable way. In this short communication, we summarize particular outcomes of the consortium. The key research progress of NordAqua includes (1) improving of photosynthetisis, (2) developing novel photosynthetic cell factories that function in a "solar-driven direct CO2 capture to target bioproducts" mode, (3) promoting the diversity of Nordic cyanobacteria and algae as an abundant and resilient alternative for less sustainable forest biomass and for innovative production of biochemicals, and (4) improving the bio-based wastewater purification and nutrient recycling technologies to provide new tools for integrative circular economy platforms.
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Affiliation(s)
- Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Bert van Bavel
- Section of Environmental Pollutants, Norwegian Institute for Water Research, Oslo, Norway
| | - Carlos Escudero
- Section of Environmental Pollutants, Norwegian Institute for Water Research, Oslo, Norway
| | | | - Jarna Heinonen
- Department of Management and Entrepreneurship, School of Economics, University of Turku, Turku, Finland
| | - Lars Herfindal
- Centre for Pharmacy, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Sari Mäkinen
- Department of Production Systems, Natural Resources Institute Finland, Jokioinen, Finland
| | - Merja Penttilä
- Devision of Industrial Biotechnology and Food Solutions, VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | | | - Hanne Skomedal
- Division of Biotechnology and Plant Health, NIBIO, Ås, Norway
| | - Jorunn Skjermo
- Department of Fisheries and New Biomarine Industry, SINTEF Ocean, Trondheim, Norway
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12
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Ylinen A, Maaheimo H, Anghelescu-Hakala A, Penttilä M, Salusjärvi L, Toivari M. Production of D-lactic acid containing polyhydroxyalkanoate polymers in yeast Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2021; 48:6253250. [PMID: 33899921 PMCID: PMC9113173 DOI: 10.1093/jimb/kuab028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/13/2021] [Indexed: 11/13/2022]
Abstract
Polyhydroxyalkanoates (PHAs) provide biodegradable and bio-based alternatives to conventional plastics. Incorporation of 2-hydroxy acid monomers into polymer, in addition to 3-hydroxy acids, offers possibility to tailor the polymer properties. In this study, poly(D-lactic acid) (PDLA) and copolymer P(LA-3HB) were produced and characterized for the first time in the yeast Saccharomyces cerevisiae. Expression of engineered PHA synthase PhaC1437Ps6–19, propionyl-CoA transferase Pct540Cp, acetyl-CoA acetyltransferase PhaA, and acetoacetyl-CoA reductase PhaB1 resulted in accumulation of 3.6% P(LA-3HB) and expression of engineered enzymes PhaC1Pre and PctMe resulted in accumulation of 0.73% PDLA of the cell dry weight (CDW). According to NMR, P(LA-3HB) contained D-lactic acid repeating sequences. For reference, expression of PhaA, PhaB1, and PHA synthase PhaC1 resulted in accumulation 11% poly(hydroxybutyrate) (PHB) of the CDW. Weight average molecular weights of these polymers were comparable to similar polymers produced by bacterial strains, 24.6, 6.3, and 1 130 kDa for P(LA-3HB), PDLA, and PHB, respectively. The results suggest that yeast, as a robust and acid tolerant industrial production organism, could be suitable for production of 2-hydroxy acid containing PHAs from sugars or from 2-hydroxy acid containing raw materials. Moreover, the wide substrate specificity of PHA synthase enzymes employed increases the possibilities for modifying copolymer properties in yeast in the future.
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Affiliation(s)
- Anna Ylinen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | | | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Espoo, Finland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
| | - Laura Salusjärvi
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Espoo, Finland
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13
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Nappa M, Lienemann M, Tossi C, Blomberg P, Jäntti J, Tittonen IJ, Penttilä M. Solar-Powered Carbon Fixation for Food and Feed Production Using Microorganisms-A Comparative Techno-Economic Analysis. ACS Omega 2020; 5:33242-33252. [PMID: 33403286 PMCID: PMC7774257 DOI: 10.1021/acsomega.0c04926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
This study evaluates the techno-economic feasibility of five solar-powered concepts for the production of autotrophic microorganisms for food and feed production; the main focus is on three concepts based on hydrogen-oxidizing bacteria (HOB), which are further compared to two microalgae-related concepts. Two locations with markedly different solar conditions are considered (Finland and Morocco), in which Morocco was found to be the most economically competitive for the cultivation of microalgae in open ponds and closed systems (1.4 and 1.9 € kg-1, respectively). Biomass production by combined water electrolysis and HOB cultivation results in higher costs for all three considered concepts. Among these, the lowest production cost of 5.3 € kg-1 is associated with grid-assisted electricity use in Finland, while the highest production cost of >9.1 € kg-1 is determined for concepts using solely photovoltaics and/or photoelectrochemical technology for on-site electricity production and solar-energy conversion to H2 by water electrolysis. All assessed concepts are capital intensive. Furthermore, a sensitivity analysis suggests that the production costs of HOB biomass can be lowered down to 2.1 € kg-1 by optimization of the process parameters among which volumetric productivity, electricity strategy, and electricity costs have the highest cost-saving potentials. The study reveals that continuously available electricity and H2 supply are essential for the development of a viable HOB concept due to the capital intensity of the needed technologies. In addition, volumetric productivity is the key parameter that needs to be optimized to increase the economic competitiveness of HOB production.
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Affiliation(s)
- Marja Nappa
- VTT
Technical Research Centre of Finland Ltd, Espoo 02150, Finland
| | | | - Camilla Tossi
- School
of Electrical Engineering, Department of Electronics and Nanoengineering, Aalto University, Espoo 02150, Finland
| | - Peter Blomberg
- VTT
Technical Research Centre of Finland Ltd, Espoo 02150, Finland
| | - Jussi Jäntti
- VTT
Technical Research Centre of Finland Ltd, Espoo 02150, Finland
| | - Ilkka Juhani Tittonen
- School
of Electrical Engineering, Department of Electronics and Nanoengineering, Aalto University, Espoo 02150, Finland
| | - Merja Penttilä
- VTT
Technical Research Centre of Finland Ltd, Espoo 02150, Finland
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14
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Voutilainen S, Heinonen M, Andberg M, Jokinen E, Maaheimo H, Pääkkönen J, Hakulinen N, Rouvinen J, Lähdesmäki H, Kaski S, Rousu J, Penttilä M, Koivula A. Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods. Appl Microbiol Biotechnol 2020; 104:10515-10529. [PMID: 33147349 PMCID: PMC7671976 DOI: 10.1007/s00253-020-10960-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 11/29/2022]
Abstract
In this work, deoxyribose-5-phosphate aldolase (Ec DERA, EC 4.1.2.4) from Escherichia coli was chosen as the protein engineering target for improving the substrate preference towards smaller, non-phosphorylated aldehyde donor substrates, in particular towards acetaldehyde. The initial broad set of mutations was directed to 24 amino acid positions in the active site or in the close vicinity, based on the 3D complex structure of the E. coli DERA wild-type aldolase. The specific activity of the DERA variants containing one to three amino acid mutations was characterised using three different substrates. A novel machine learning (ML) model utilising Gaussian processes and feature learning was applied for the 3rd mutagenesis round to predict new beneficial mutant combinations. This led to the most clear-cut (two- to threefold) improvement in acetaldehyde (C2) addition capability with the concomitant abolishment of the activity towards the natural donor molecule glyceraldehyde-3-phosphate (C3P) as well as the non-phosphorylated equivalent (C3). The Ec DERA variants were also tested on aldol reaction utilising formaldehyde (C1) as the donor. Ec DERA wild-type was shown to be able to carry out this reaction, and furthermore, some of the improved variants on acetaldehyde addition reaction turned out to have also improved activity on formaldehyde. KEY POINTS: • DERA aldolases are promiscuous enzymes. • Synthetic utility of DERA aldolase was improved by protein engineering approaches. • Machine learning methods aid the protein engineering of DERA.
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Affiliation(s)
- Sanni Voutilainen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
| | - Markus Heinonen
- Department of Computer Science, Aalto University, Espoo, Finland
- Helsinki Institute for Information Technology, Espoo, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Emmi Jokinen
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Johan Pääkkönen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FI-80101, Joensuu, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FI-80101, Joensuu, Finland
| | - Juha Rouvinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FI-80101, Joensuu, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Samuel Kaski
- Department of Computer Science, Aalto University, Espoo, Finland
- Helsinki Institute for Information Technology, Espoo, Finland
| | - Juho Rousu
- Department of Computer Science, Aalto University, Espoo, Finland
- Helsinki Institute for Information Technology, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
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15
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Pylkkänen R, Mohammadi P, Arola S, de Ruijter JC, Sunagawa N, Igarashi K, Penttilä M. In Vitro Synthesis and Self-Assembly of Cellulose II Nanofibrils Catalyzed by the Reverse Reaction of Clostridium thermocellum Cellodextrin Phosphorylase. Biomacromolecules 2020; 21:4355-4364. [PMID: 32960595 DOI: 10.1021/acs.biomac.0c01162] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In nature, various organisms produce cellulose as microfibrils, which are processed into their nano- and microfibrillar and/or crystalline components by humans in order to obtain desired material properties. Interestingly, the natural synthesis machinery can be circumvented by enzymatically synthesizing cellulose from precursor molecules in vitro. This approach is appealing for producing tailor-made cellulosic particles and materials because it enables optimization of the reaction conditions for cellulose synthesis in order to generate particles with a desired morphology in their pure form. Here, we present enzymatic cellulose synthesis catalyzed by the reverse reaction of Clostridium thermocellum cellodextrin phosphorylase in vitro. We were able to produce cellulose II nanofibril networks in all conditions tested, using varying concentrations of the glycosyl acceptors d-glucose or d-cellobiose (0.5, 5, and 50 mM). We show that shorter cellulose chains assemble into flat ribbon-like fibrils with greater diameter, while longer chains assemble into cylindrical fibrils with smaller diameter.
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Affiliation(s)
- Robert Pylkkänen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Espoo, Finland.,VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Suvi Arola
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Jorg C de Ruijter
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, 113-8657 Tokyo, Japan
| | - Kiyohiko Igarashi
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland.,Department of Biomaterial Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, 113-8657 Tokyo, Japan
| | - Merja Penttilä
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Espoo, Finland.,VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
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16
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de Ruijter JC, Igarashi K, Penttilä M. The Lipomyces starkeyi gene Ls120451 encodes a cellobiose transporter that enables cellobiose fermentation in Saccharomyces cerevisiae. FEMS Yeast Res 2020; 20:foaa019. [PMID: 32310262 PMCID: PMC7204792 DOI: 10.1093/femsyr/foaa019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/17/2020] [Indexed: 12/14/2022] Open
Abstract
Processed lignocellulosic biomass is a source of mixed sugars that can be used for microbial fermentation into fuels or higher value products, like chemicals. Previously, the yeast Saccharomyces cerevisiae was engineered to utilize its cellodextrins through the heterologous expression of sugar transporters together with an intracellular expressed β-glucosidase. In this study, we screened a selection of eight (putative) cellodextrin transporters from different yeast and fungal hosts in order to extend the catalogue of available cellobiose transporters for cellobiose fermentation in S. cerevisiae. We confirmed that several in silico predicted cellodextrin transporters from Aspergillus niger were capable of transporting cellobiose with low affinity. In addition, we found a novel cellobiose transporter from the yeast Lipomyces starkeyi, encoded by the gene Ls120451. This transporter allowed efficient growth on cellobiose, while it also grew on glucose and lactose, but not cellotriose nor cellotetraose. We characterized the transporter more in-depth together with the transporter CdtG from Penicillium oxalicum. CdtG showed to be slightly more efficient in cellobiose consumption than Ls120451 at concentrations below 1.0 g/L. Ls120451 was more efficient in cellobiose consumption at higher concentrations and strains expressing this transporter grew slightly slower, but produced up to 30% more ethanol than CdtG.
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Affiliation(s)
- Jorg C de Ruijter
- VTT Technical Research Centre of Finland, Tietotie 2, FI-02150 Espoo, Finland
| | - Kiyohiko Igarashi
- VTT Technical Research Centre of Finland, Tietotie 2, FI-02150 Espoo, Finland
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yajoi, Bunkyo, Tokyo 113–8657, Japan
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Tietotie 2, FI-02150 Espoo, Finland
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17
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Vartiainen E, Blomberg P, Ilmén M, Andberg M, Toivari M, Penttilä M. Evaluation of synthetic formaldehyde and methanol assimilation pathways in Yarrowia lipolytica. Fungal Biol Biotechnol 2019; 6:27. [PMID: 31890234 PMCID: PMC6918578 DOI: 10.1186/s40694-019-0090-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/03/2019] [Indexed: 11/10/2022] Open
Abstract
Background Crude glycerol coming from biodiesel production is an attractive carbon source for biological production of chemicals. The major impurity in preparations of crude glycerol is methanol, which is toxic for most microbes. Development of microbes, which would not only tolerate the methanol, but also use it as co-substrate, would increase the feasibility of bioprocesses using crude glycerol as substrate. Results To prevent methanol conversion to CO2 via formaldehyde and formate, the formaldehyde dehydrogenase (FLD) gene was identified in and deleted from Yarrowia lipolytica. The deletion strain was able to convert methanol to formaldehyde without expression of heterologous methanol dehydrogenases. Further, it was shown that expression of heterologous formaldehyde assimilating enzymes could complement the deletion of FLD. The expression of either 3-hexulose-6-phosphate synthase (HPS) enzyme of ribulose monosphosphate pathway or dihydroxyacetone synthase (DHAS) enzyme of xylulose monosphosphate pathway restored the formaldehyde tolerance of the formaldehyde sensitive Δfld1 strain. Conclusions In silico, the expression of heterologous formaldehyde assimilation pathways enable Y. lipolytica to use methanol as substrate for growth and metabolite production. In vivo, methanol was shown to be converted to formaldehyde and the enzymes of formaldehyde assimilation were actively expressed in this yeast. However, further development is required to enable Y. lipolytica to efficiently use methanol as co-substrate with glycerol.
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Affiliation(s)
- Eija Vartiainen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Peter Blomberg
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Marja Ilmén
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
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18
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Rantasalo A, Landowski CP, Kuivanen J, Korppoo A, Reuter L, Koivistoinen O, Valkonen M, Penttilä M, Jäntti J, Mojzita D. A universal gene expression system for fungi. Nucleic Acids Res 2019; 46:e111. [PMID: 29924368 PMCID: PMC6182139 DOI: 10.1093/nar/gky558] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/07/2018] [Indexed: 12/02/2022] Open
Abstract
Biotechnological production of fuels, chemicals and proteins is dependent on efficient production systems, typically genetically engineered microorganisms. New genome editing methods are making it increasingly easy to introduce new genes and functionalities in a broad range of organisms. However, engineering of all these organisms is hampered by the lack of suitable gene expression tools. Here, we describe a synthetic expression system (SES) that is functional in a broad spectrum of fungal species without the need for host-dependent optimization. The SES consists of two expression cassettes, the first providing a weak, but constitutive level of a synthetic transcription factor (sTF), and the second enabling strong, at will tunable expression of the target gene via an sTF-dependent promoter. We validated the SES functionality in six yeast and two filamentous fungi species in which high (levels beyond organism-specific promoters) as well as adjustable expression levels of heterologous and native genes was demonstrated. The SES is an unprecedentedly broadly functional gene expression regulation method that enables significantly improved engineering of fungi. Importantly, the SES system makes it possible to take in use novel eukaryotic microbes for basic research and various biotechnological applications.
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Affiliation(s)
- Anssi Rantasalo
- VTT Technical Research Centre of Finland, Espoo, P.O. Box 1000, FI-02044 VTT, Finland
| | | | - Joosu Kuivanen
- VTT Technical Research Centre of Finland, Espoo, P.O. Box 1000, FI-02044 VTT, Finland
| | - Annakarin Korppoo
- VTT Technical Research Centre of Finland, Espoo, P.O. Box 1000, FI-02044 VTT, Finland
| | - Lauri Reuter
- VTT Technical Research Centre of Finland, Espoo, P.O. Box 1000, FI-02044 VTT, Finland
| | - Outi Koivistoinen
- VTT Technical Research Centre of Finland, Espoo, P.O. Box 1000, FI-02044 VTT, Finland
| | - Mari Valkonen
- VTT Technical Research Centre of Finland, Espoo, P.O. Box 1000, FI-02044 VTT, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, P.O. Box 1000, FI-02044 VTT, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland, Espoo, P.O. Box 1000, FI-02044 VTT, Finland
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland, Espoo, P.O. Box 1000, FI-02044 VTT, Finland
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19
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Lienemann M, TerAvest MA, Pitkänen J, Stuns I, Penttilä M, Ajo‐Franklin CM, Jäntti J. Towards patterned bioelectronics: facilitated immobilization of exoelectrogenic Escherichia coli with heterologous pili. Microb Biotechnol 2018; 11:1184-1194. [PMID: 30296001 PMCID: PMC6196383 DOI: 10.1111/1751-7915.13309] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/02/2018] [Accepted: 08/07/2018] [Indexed: 12/01/2022] Open
Abstract
Biosensors detect signals using biological sensing components such as redox enzymes and biological cells. Although cellular versatility can be beneficial for different applications, limited stability and efficiency in signal transduction at electrode surfaces represent a challenge. Recent studies have shown that the Mtr electron conduit from Shewanella oneidensis MR-1 can be produced in Escherichia coli to generate an exoelectrogenic model system with well-characterized genetic tools. However, means to specifically immobilize this organism at solid substrates as electroactive biofilms have not been tested previously. Here, we show that mannose-binding Fim pili can be produced in exoelectrogenic E. coli and can be used to selectively attach cells to a mannose-coated material. Importantly, cells expressing fim genes retained current production by the heterologous Mtr electron conduit. Our results demonstrate the versatility of the exoelectrogenic E. coli system and motivate future work that aims to produce patterned biofilms for bioelectronic devices that can respond to various biochemical signals.
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Affiliation(s)
| | - Michaela A. TerAvest
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMIUSA
- The Molecular FoundryLawrence Berkeley National LaboratoryMolecular Biophysics and Integrated Bioimaging DivisionSynthetic Biology InstituteBerkeleyCAUSA
| | - Juha‐Pekka Pitkänen
- VTT Technical Research Centre of Finland LtdEspooFinland
- Current affiliation: Solar Foods LtdHelsinkiFinland
| | - Ingmar Stuns
- VTT Technical Research Centre of Finland LtdEspooFinland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland LtdEspooFinland
| | - Caroline M. Ajo‐Franklin
- The Molecular FoundryLawrence Berkeley National LaboratoryMolecular Biophysics and Integrated Bioimaging DivisionSynthetic Biology InstituteBerkeleyCAUSA
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland LtdEspooFinland
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20
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Fang W, Nonappa, Vitikainen M, Mohammadi P, Koskela S, Soikkeli M, Westerholm-Parvinen A, Landowski CP, Penttilä M, Linder MB, Laaksonen P. Coacervation of resilin fusion proteins containing terminal functionalities. Colloids Surf B Biointerfaces 2018; 171:590-596. [PMID: 30098537 DOI: 10.1016/j.colsurfb.2018.07.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/11/2018] [Accepted: 07/23/2018] [Indexed: 12/16/2022]
Abstract
Liquid-liquid phase transition known as coacervation of resilin-like-peptide fusion proteins containing different terminal domains were investigated. Two different modular proteins were designed and produced and their behavior were compared to a resilin-like-peptide without terminal domains. The size of the particle-like coacervates was modulated by the protein concentration, pH and temperature. The morphology and three-dimensional (3D) structural details of the coacervate particles were investigated by cryogenic transmission electron microscopy (cryo-TEM) and tomography (cryo-ET) reconstruction. Selective adhesion of the coacervates on cellulose and graphene surfaces was demonstrated.
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Affiliation(s)
- Wenwen Fang
- Department of Bioproducts and Biosystems, Aalto University, Espoo, FI-00076, AALTO, Finland
| | - Nonappa
- Department of Bioproducts and Biosystems, Aalto University, Espoo, FI-00076, AALTO, Finland; Department of Applied Physics, Aalto University, Espoo, FI-00076, AALTO, Finland
| | - Marika Vitikainen
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044, VTT, Finland
| | - Pezhman Mohammadi
- Department of Bioproducts and Biosystems, Aalto University, Espoo, FI-00076, AALTO, Finland
| | - Salla Koskela
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044, VTT, Finland
| | - Miika Soikkeli
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044, VTT, Finland
| | | | | | - Merja Penttilä
- Department of Bioproducts and Biosystems, Aalto University, Espoo, FI-00076, AALTO, Finland; VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044, VTT, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, Aalto University, Espoo, FI-00076, AALTO, Finland
| | - Päivi Laaksonen
- Department of Bioproducts and Biosystems, Aalto University, Espoo, FI-00076, AALTO, Finland.
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21
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Mohammadi P, Aranko AS, Lemetti L, Cenev Z, Zhou Q, Virtanen S, Landowski CP, Penttilä M, Fischer WJ, Wagermaier W, Linder MB. Phase transitions as intermediate steps in the formation of molecularly engineered protein fibers. Commun Biol 2018; 1:86. [PMID: 30271967 PMCID: PMC6123624 DOI: 10.1038/s42003-018-0090-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/08/2018] [Indexed: 12/19/2022] Open
Abstract
A central concept in molecular bioscience is how structure formation at different length scales is achieved. Here we use spider silk protein as a model to design new recombinant proteins that assemble into fibers. We made proteins with a three-block architecture with folded globular domains at each terminus of a truncated repetitive silk sequence. Aqueous solutions of these engineered proteins undergo liquid-liquid phase separation as an essential pre-assembly step before fibers can form by drawing in air. We show that two different forms of phase separation occur depending on solution conditions, but only one form leads to fiber assembly. Structural variants with one-block or two-block architectures do not lead to fibers. Fibers show strong adhesion to surfaces and self-fusing properties when placed into contact with each other. Our results show a link between protein architecture and phase separation behavior suggesting a general approach for understanding protein assembly from dilute solutions into functional structures.
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Affiliation(s)
- Pezhman Mohammadi
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland.
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Laura Lemetti
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Zoran Cenev
- Department of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, 02150, Espoo, Finland
| | - Quan Zhou
- Department of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, 02150, Espoo, Finland
| | - Salla Virtanen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | | | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., 02150, Espoo, Finland
| | | | - Wolfgang Wagermaier
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland.
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22
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Koivuranta K, Castillo S, Jouhten P, Ruohonen L, Penttilä M, Wiebe MG. Enhanced Triacylglycerol Production With Genetically Modified Trichosporon oleaginosus. Front Microbiol 2018; 9:1337. [PMID: 29977232 PMCID: PMC6021488 DOI: 10.3389/fmicb.2018.01337] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/31/2018] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial pyruvate dehydrogenase (PDH) is important in the production of lipids in oleaginous yeast, but other yeast may bypass the mitochondria (PDH bypass), converting pyruvate in the cytosol to acetaldehyde, then acetate and acetyl CoA which is further converted to lipids. Using a metabolic model based on the oleaginous yeast Yarrowia lipolytica, we found that introduction of this bypass to an oleaginous yeast should result in enhanced yield of triacylglycerol (TAG) on substrate. Trichosporon oleaginosus (formerly Cryptococcus curvatus) is an oleaginous yeast which can produce TAGs from both glucose and xylose. Based on the sequenced genome, it lacks at least one of the enzymes needed to complete the PDH bypass, acetaldehyde dehydrogenase (ALD), and may also be deficient in pyruvate decarboxylase and acetyl-CoA synthetase under production conditions. We introduced these genes to T. oleaginosus in various combinations and demonstrated that the yield of TAG on both glucose and xylose was improved, particularly at high C/N ratio. Expression of a phospholipid:diacyltransferase encoding gene in conjunction with the PDH bypass further enhanced lipid production. The yield of TAG on xylose (0.27 g/g) in the engineered strain approached the theoretical maximum yield of 0.289 g/g. Interestingly, TAG production was also enhanced compared to the control in some strains which were given only part of the bypass pathway, suggesting that these genes may contribute to alternative routes to cytoplasmic acetyl CoA. The metabolic model indicated that the improved yield of TAG on substrate in the PDH bypass was dependent on the production of NADPH by ALD. NADPH for lipid synthesis is otherwise primarily supplied by the pentose phosphate pathway (PPP). This would contribute to the greater improvement of TAG production from xylose compared to that observed from glucose when the PDH bypass was introduced, since xylose enters metabolism through the non-oxidative part of the PPP. Yield of TAG from xylose in the engineered strains (0.21–0.27 g/g) was comparable to that obtained from glucose and the highest so far reported for lipid or TAG production from xylose.
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Affiliation(s)
- Kari Koivuranta
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Sandra Castillo
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Paula Jouhten
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Laura Ruohonen
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Marilyn G Wiebe
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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23
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Abstract
Sustainable production of chemicals, materials, and pharmaceuticals is increasingly performed by genetically engineered cell factories. Engineering of complex metabolic routes or cell behavior control systems requires robust and predictable gene expression tools. In this challenging task, orthogonality is a fundamental prerequisite for such tools. In this study, we developed and characterized in depth a comprehensive gene expression toolkit that allows accurate control of gene expression in Saccharomyces cerevisiae without marked interference with native cellular regulation. The toolkit comprises a set of transcription factors, designed to function as synthetic activators or repressors, and transcription-factor-dependent promoters, which together provide a broad expression range surpassing, at high end, the strongest native promoters. Modularity of the developed tools is demonstrated by establishing a novel bistable genetic circuit with robust performance to control a heterologous metabolic pathway and enabling on-demand switching between two alternative metabolic branches.
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Affiliation(s)
- Anssi Rantasalo
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Joosu Kuivanen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT Espoo, Finland
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24
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Kuivanen J, Holmström S, Lehtinen B, Penttilä M, Jäntti J. A High-throughput workflow for CRISPR/Cas9 mediated combinatorial promoter replacements and phenotype characterization in yeast. Biotechnol J 2018; 13:e1700593. [PMID: 29729128 DOI: 10.1002/biot.201700593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/05/2018] [Accepted: 04/19/2018] [Indexed: 01/24/2023]
Abstract
Due to the rapidly increasing sequence information on gene variants generated by evolution and our improved abilities to engineer novel biological activities, microbial cells can be evolved for the production of a growing spectrum of compounds. For high productivity, efficient carbon channeling towards the end product is a key element. In large scale production systems the genetic modifications that ensure optimal performance cannot be dependent on plasmid-based regulators, but need to be engineered stably into the host genome. Here we describe a CRISPR/Cas9 mediated high-throughput workflow for combinatorial and multiplexed replacement of native promoters with synthetic promoters and the following high-throughput phenotype characterization in the yeast Saccharomyces cerevisiae. The workflow is demonstrated with three central metabolic genes, ZWF1, PGI1 and TKL1 encoding a glucose-6-phosphate dehydrogenase, phosphoglucose isomerase and transketolase, respectively. The synthetic promoter donor DNA libraries were generated by PCR and transformed to yeast cells. A 50% efficiency was achieved for simultaneous replacement at three individual loci using short 60-bp flanking homology sequences in the donor promoters. Phenotypic strain characterization was validated and demonstrated using liquid handling automation and 150 µl cultivation volume in 96-well plate format. The established workflow offers a robust platform for automated engineering and improvement of yeast strains.
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Affiliation(s)
- Joosu Kuivanen
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Sami Holmström
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Birgitta Lehtinen
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
- Current address: Life Science Graduate School Zurich, Institute of Molecular Systems biology (IMSB), Department of Biology (D-BIOL), ETH Zurich
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
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25
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Griffo A, Hähl H, Grandthyll S, Müller F, Paananen A, Ilmén M, Szilvay GR, Landowski CP, Penttilä M, Jacobs K, Laaksonen P. Single-Molecule Force Spectroscopy Study on Modular Resilin Fusion Protein. ACS Omega 2017; 2:6906-6915. [PMID: 31457277 PMCID: PMC6644949 DOI: 10.1021/acsomega.7b01133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/26/2017] [Indexed: 05/05/2023]
Abstract
The adhesive and mechanical properties of a modular fusion protein consisting of two different types of binding units linked together via a flexible resilin-like-polypeptide domain are quantified. The adhesive domains have been constructed from fungal cellulose-binding modules (CBMs) and an amphiphilic hydrophobin HFBI. This study is carried out by single-molecule force spectroscopy, which enables stretching of single molecules. The fusion proteins are designed to self-assemble on the cellulose surface, leading into the submonolayer of proteins having the HFBI pointing away from the surface. A hydrophobic atomic force microscopy (AFM) tip can be employed for contacting and lifting the single fusion protein from the HFBI-functionalized terminus by the hydrophobic interaction between the tip surface and the hydrophobic patch of the HFBI. The work of rupture, contour length at rupture and the adhesion forces of the amphiphilic end domains are evaluated under aqueous environment at different pHs.
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Affiliation(s)
- Alessandra Griffo
- Department
of Bioproducts and Biosystems BIO, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Hendrik Hähl
- Department
of Experimental Physics, Saarland University, 66123 Saarbrücken, Germany
| | - Samuel Grandthyll
- Department
of Experimental Physics, Saarland University, 66123 Saarbrücken, Germany
| | - Frank Müller
- Department
of Experimental Physics, Saarland University, 66123 Saarbrücken, Germany
| | - Arja Paananen
- VTT
Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044 Espoo, Finland
| | - Marja Ilmén
- VTT
Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044 Espoo, Finland
| | - Géza R. Szilvay
- VTT
Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044 Espoo, Finland
| | | | - Merja Penttilä
- Department
of Bioproducts and Biosystems BIO, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- VTT
Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044 Espoo, Finland
| | - Karin Jacobs
- Department
of Experimental Physics, Saarland University, 66123 Saarbrücken, Germany
| | - Päivi Laaksonen
- Department
of Bioproducts and Biosystems BIO, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
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26
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Salusjärvi L, Toivari M, Vehkomäki ML, Koivistoinen O, Mojzita D, Niemelä K, Penttilä M, Ruohonen L. Production of ethylene glycol or glycolic acid from D-xylose in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2017; 101:8151-8163. [PMID: 29038973 DOI: 10.1007/s00253-017-8547-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/05/2017] [Accepted: 09/17/2017] [Indexed: 11/26/2022]
Abstract
The important platform chemicals ethylene glycol and glycolic acid were produced via the oxidative D-xylose pathway in the yeast Saccharomyces cerevisiae. The expression of genes encoding D-xylose dehydrogenase (XylB) and D-xylonate dehydratase (XylD) from Caulobacter crescentus and YagE or YjhH aldolase and aldehyde dehydrogenase AldA from Escherichia coli enabled glycolic acid production from D-xylose up to 150 mg/L. In strains expressing only xylB and xylD, 29 mg/L 2-keto-3-deoxyxylonic acid [(S)-4,5-dihydroxy-2-oxopentanoic acid] (2K3DXA) was produced and D-xylonic acid accumulated to ca. 9 g/L. A significant amount of D-xylonic acid (ca. 14%) was converted to 3-deoxypentonic acid (3DPA), and also, 3,4-dihydroxybutyric acid was formed. 2K3DXA was further converted to glycolaldehyde when genes encoding by either YagE or YjhH aldolase from E. coli were expressed. Reduction of glycolaldehyde to ethylene glycol by an endogenous aldo-keto reductase activity resulted further in accumulation of ethylene glycol of 14 mg/L. The possibility of simultaneous production of lactic and glycolic acids was evaluated by expression of gene encoding lactate dehydrogenase ldhL from Lactobacillus helveticus together with aldA. Interestingly, this increased the accumulation of glycolic acid to 1 g/L. The D-xylonate dehydratase activity in yeast was notably low, possibly due to inefficient Fe-S cluster synthesis in the yeast cytosol, and leading to D-xylonic acid accumulation. The dehydratase activity was significantly improved by targeting its expression to mitochondria or by altering the Fe-S cluster metabolism of the cells with FRA2 deletion.
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Affiliation(s)
- Laura Salusjärvi
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Maija-Leena Vehkomäki
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Outi Koivistoinen
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Klaus Niemelä
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Laura Ruohonen
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
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27
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Rahman MM, Andberg M, Thangaraj SK, Parkkinen T, Penttilä M, Jänis J, Koivula A, Rouvinen J, Hakulinen N. The Crystal Structure of a Bacterial l-Arabinonate Dehydratase Contains a [2Fe-2S] Cluster. ACS Chem Biol 2017; 12:1919-1927. [PMID: 28574691 DOI: 10.1021/acschembio.7b00304] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-l-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg2+ ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of l-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.
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Affiliation(s)
- Mohammad Mubinur Rahman
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Senthil Kumar Thangaraj
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Tarja Parkkinen
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Janne Jänis
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Juha Rouvinen
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Nina Hakulinen
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
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28
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Miskovic L, Alff-Tuomala S, Soh KC, Barth D, Salusjärvi L, Pitkänen JP, Ruohonen L, Penttilä M, Hatzimanikatis V. A design-build-test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models. Biotechnol Biofuels 2017; 10:166. [PMID: 28674555 PMCID: PMC5485749 DOI: 10.1186/s13068-017-0838-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/06/2017] [Indexed: 05/28/2023]
Abstract
BACKGROUND Recent advancements in omics measurement technologies have led to an ever-increasing amount of available experimental data that necessitate systems-oriented methodologies for efficient and systematic integration of data into consistent large-scale kinetic models. These models can help us to uncover new insights into cellular physiology and also to assist in the rational design of bioreactor or fermentation processes. Optimization and Risk Analysis of Complex Living Entities (ORACLE) framework for the construction of large-scale kinetic models can be used as guidance for formulating alternative metabolic engineering strategies. RESULTS We used ORACLE in a metabolic engineering problem: improvement of the xylose uptake rate during mixed glucose-xylose consumption in a recombinant Saccharomyces cerevisiae strain. Using the data from bioreactor fermentations, we characterized network flux and concentration profiles representing possible physiological states of the analyzed strain. We then identified enzymes that could lead to improved flux through xylose transporters (XTR). For some of the identified enzymes, including hexokinase (HXK), we could not deduce if their control over XTR was positive or negative. We thus performed a follow-up experiment, and we found out that HXK2 deletion improves xylose uptake rate. The data from the performed experiments were then used to prune the kinetic models, and the predictions of the pruned population of kinetic models were in agreement with the experimental data collected on the HXK2-deficient S. cerevisiae strain. CONCLUSIONS We present a design-build-test cycle composed of modeling efforts and experiments with a glucose-xylose co-utilizing recombinant S. cerevisiae and its HXK2-deficient mutant that allowed us to uncover interdependencies between upper glycolysis and xylose uptake pathway. Through this cycle, we also obtained kinetic models with improved prediction capabilities. The present study demonstrates the potential of integrated "modeling and experiments" systems biology approaches that can be applied for diverse applications ranging from biotechnology to drug discovery.
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Affiliation(s)
- Ljubisa Miskovic
- Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Keng Cher Soh
- Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Dorothee Barth
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | | | | | - Laura Ruohonen
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
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29
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Fang W, Paananen A, Vitikainen M, Koskela S, Westerholm-Parvinen A, Joensuu JJ, Landowski CP, Penttilä M, Linder MB, Laaksonen P. Elastic and pH-Responsive Hybrid Interfaces Created with Engineered Resilin and Nanocellulose. Biomacromolecules 2017; 18:1866-1873. [PMID: 28440631 DOI: 10.1021/acs.biomac.7b00294] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We investigated how a genetically engineered resilin fusion protein modifies cellulose surfaces. We characterized the pH-responsive behavior of a resilin-like polypeptide (RLP) having terminal cellulose binding modules (CBM) and showed its binding to cellulose nanofibrils (CNF). Characterization of the resilin fusion protein at different pHs revealed substantial conformational changes of the protein, which were observed as swelling and contraction of the protein layer bound to the nanocellulose surface. In addition, we showed that employment of the modified resilin in cellulose hydrogel and nanopaper increased their modulus of stiffness through a cross-linking effect.
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Affiliation(s)
- Wenwen Fang
- Department of Bioproducts and Biosystems, Aalto University , Espoo, FI-00076 Aalto, Finland
| | - Arja Paananen
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
| | - Marika Vitikainen
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
| | - Salla Koskela
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
| | | | - Jussi J Joensuu
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
| | | | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., Espoo, FI-02044 VTT, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, Aalto University , Espoo, FI-00076 Aalto, Finland
| | - Päivi Laaksonen
- Department of Bioproducts and Biosystems, Aalto University , Espoo, FI-00076 Aalto, Finland
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30
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Ribas D, Sá-Pessoa J, Soares-Silva I, Paiva S, Nygård Y, Ruohonen L, Penttilä M, Casal M. Yeast as a tool to express sugar acid transporters with biotechnological interest. FEMS Yeast Res 2017; 17:fox005. [DOI: 10.1093/femsyr/fox005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/10/2017] [Indexed: 11/13/2022] Open
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31
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Kludas J, Arvas M, Castillo S, Pakula T, Oja M, Brouard C, Jäntti J, Penttilä M, Rousu J. Machine Learning of Protein Interactions in Fungal Secretory Pathways. PLoS One 2016; 11:e0159302. [PMID: 27441920 PMCID: PMC4956264 DOI: 10.1371/journal.pone.0159302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/30/2016] [Indexed: 12/18/2022] Open
Abstract
In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict protein interactions in other, related species. In our methodology, we combine several state of the art machine learning approaches, namely, multiple kernel learning (MKL), pairwise kernels and kernelized structured output prediction in the supervised graph inference framework. For MKL, we apply recently proposed centered kernel alignment and p-norm path following approaches to integrate several feature sets describing the proteins, demonstrating improved performance. For graph inference, we apply input-output kernel regression (IOKR) in supervised and semi-supervised modes as well as output kernel trees (OK3). In our experiments simulating increasing genetic distance, Input-Output Kernel Regression proved to be the most robust prediction approach. We also show that the MKL approaches improve the predictions compared to uniform combination of the kernels. We evaluate the methods on the task of predicting protein-protein-interactions in the secretion pathways in fungi, S.cerevisiae, baker's yeast, being the source, T. reesei being the target of the inter-species transfer learning. We identify completely novel candidate secretion proteins conserved in filamentous fungi. These proteins could contribute to their unique secretion capabilities.
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Affiliation(s)
- Jana Kludas
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland
| | - Mikko Arvas
- VTT Technical Research Centre of Finland, Espoo, Finland
| | | | - Tiina Pakula
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Merja Oja
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Céline Brouard
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Juho Rousu
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland
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32
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Andberg M, Aro-Kärkkäinen N, Carlson P, Oja M, Bozonnet S, Toivari M, Hakulinen N, O'Donohue M, Penttilä M, Koivula A. Characterization and mutagenesis of two novel iron-sulphur cluster pentonate dehydratases. Appl Microbiol Biotechnol 2016; 100:7549-63. [PMID: 27102126 DOI: 10.1007/s00253-016-7530-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/15/2016] [Accepted: 03/29/2016] [Indexed: 10/21/2022]
Abstract
We describe here the identification and characterization of two novel enzymes belonging to the IlvD/EDD protein family, the D-xylonate dehydratase from Caulobacter crescentus, Cc XyDHT, (EC 4.2.1.82), and the L-arabonate dehydratase from Rhizobium leguminosarum bv. trifolii, Rl ArDHT (EC 4.2.1.25), that produce the corresponding 2-keto-3-deoxy-sugar acids. There is only a very limited amount of characterization data available on pentonate dehydratases, even though the enzymes from these oxidative pathways have potential applications with plant biomass pentose sugars. The two bacterial enzymes share 41 % amino acid sequence identity and were expressed and purified from Escherichia coli as homotetrameric proteins. Both dehydratases were shown to accept pentonate and hexonate sugar acids as their substrates and require Mg(2+) for their activity. Cc XyDHT displayed the highest activity on D-xylonate and D-gluconate, while Rl ArDHT functioned best on D-fuconate, L-arabonate and D-galactonate. The configuration of the OH groups at C2 and C3 position of the sugar acid were shown to be critical, and the C4 configuration also contributed substantially to the substrate recognition. The two enzymes were also shown to contain an iron-sulphur [Fe-S] cluster. Our phylogenetic analysis and mutagenesis studies demonstrated that the three conserved cysteine residues in the aldonic acid dehydratase group of IlvD/EDD family members, those of C60, C128 and C201 in Cc XyDHT, and of C59, C127 and C200 in Rl ArDHT, are needed for coordination of the [Fe-S] cluster. The iron-sulphur cluster was shown to be crucial for the catalytic activity (kcat) but not for the substrate binding (Km) of the two pentonate dehydratases.
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Affiliation(s)
- Martina Andberg
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland.
| | - Niina Aro-Kärkkäinen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Paul Carlson
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Merja Oja
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Sophie Bozonnet
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.,CNRS, UMR5504, F-31400, Toulouse, France
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FI-80101, Joensuu, Finland
| | - Michael O'Donohue
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.,CNRS, UMR5504, F-31400, Toulouse, France
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
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Rantasalo A, Czeizler E, Virtanen R, Rousu J, Lähdesmäki H, Penttilä M, Jäntti J, Mojzita D. Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae. PLoS One 2016; 11:e0148320. [PMID: 26901642 PMCID: PMC4762949 DOI: 10.1371/journal.pone.0148320] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 01/15/2016] [Indexed: 12/26/2022] Open
Abstract
This work describes the development and characterization of a modular synthetic expression system that provides a broad range of adjustable and predictable expression levels in S. cerevisiae. The system works as a fixed-gain transcription amplifier, where the input signal is transferred via a synthetic transcription factor (sTF) onto a synthetic promoter, containing a defined core promoter, generating a transcription output signal. The system activation is based on the bacterial LexA-DNA-binding domain, a set of modified, modular LexA-binding sites and a selection of transcription activation domains. We show both experimentally and computationally that the tuning of the system is achieved through the selection of three separate modules, each of which enables an adjustable output signal: 1) the transcription-activation domain of the sTF, 2) the binding-site modules in the output promoter, and 3) the core promoter modules which define the transcription initiation site in the output promoter. The system has a novel bidirectional architecture that enables generation of compact, yet versatile expression modules for multiple genes with highly diversified expression levels ranging from negligible to very strong using one synthetic transcription factor. In contrast to most existing modular gene expression regulation systems, the present system is independent from externally added compounds. Furthermore, the established system was minimally affected by the several tested growth conditions. These features suggest that it can be highly useful in large scale biotechnology applications.
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Affiliation(s)
- Anssi Rantasalo
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Elena Czeizler
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 Aalto, Espoo, Finland
| | - Riitta Virtanen
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Juho Rousu
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 Aalto, Espoo, Finland
| | - Harri Lähdesmäki
- Aalto University, Department of Computer Science, P.O. Box 15400, FI-00076 Aalto, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
- * E-mail:
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Castillo S, Barth D, Arvas M, Pakula TM, Pitkänen E, Blomberg P, Seppanen-Laakso T, Nygren H, Sivasiddarthan D, Penttilä M, Oja M. Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. Biotechnol Biofuels 2016; 9:252. [PMID: 27895706 PMCID: PMC5117618 DOI: 10.1186/s13068-016-0665-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/10/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis. RESULTS A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model. CONCLUSIONS The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes.
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Affiliation(s)
- Sandra Castillo
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | - Dorothee Barth
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | - Mikko Arvas
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | - Tiina M. Pakula
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | - Esa Pitkänen
- Department of Computer Science, University of Helsinki, P.O. 68 (Gustaf Hällströmin katu 2b), 00014 Helsinki, Finland
| | - Peter Blomberg
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | | | - Heli Nygren
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | | | - Merja Penttilä
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | - Merja Oja
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
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Pakula TM, Nygren H, Barth D, Heinonen M, Castillo S, Penttilä M, Arvas M. Genome wide analysis of protein production load in Trichoderma reesei. Biotechnol Biofuels 2016; 9:132. [PMID: 27354857 PMCID: PMC4924338 DOI: 10.1186/s13068-016-0547-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/07/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei (teleomorph Hypocrea jecorina) is a widely used industrial host organism for protein production. In industrial cultivations, it can produce over 100 g/l of extracellular protein, mostly constituting of cellulases and hemicellulases. In order to improve protein production of T. reesei the transcriptional regulation of cellulases and secretory pathway factors have been extensively studied. However, the metabolism of T. reesei under protein production conditions has not received much attention. RESULTS To understand the physiology and metabolism of T. reesei under protein production conditions we carried out a well-controlled bioreactor experiment with extensive analysis. We used minimal media to make the data amenable for modelling and three strain pairs to cover different protein production levels. With RNA-sequencing transcriptomics we detected the concentration of the carbon source as the most important determinant of the transcriptome. As the major transcriptional response concomitant to protein production we detected the induction of selected genes that were putatively regulated by xyr1 and were related to protein transport, amino acid metabolism and transcriptional regulation. We found novel metabolic responses such as production of glycerol and a cellotriose-like compound. We then used this cultivation data for flux balance analysis of T. reesei metabolism and demonstrate for the first time the use of genome wide stoichiometric metabolic modelling for T. reesei. We show that our model can predict protein production rate and provides novel insight into the metabolism of protein production. We also provide this unprecedented cultivation and transcriptomics data set for future modelling efforts. CONCLUSIONS The use of stoichiometric modelling can open a novel path for the improvement of protein production in T. reesei. Based on this we propose sulphur assimilation as a major limiting factor of protein production. As an organism with exceptional protein production capabilities modelling of T. reesei can provide novel insight also to other less productive organisms.
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Affiliation(s)
- Tiina M. Pakula
- />VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | - Heli Nygren
- />VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | - Dorothee Barth
- />VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | - Markus Heinonen
- />Department of Information and Computer Science, Aalto University, PO Box 15400, 00076 Espoo, Finland
- />Helsinki Institute for Information Technology HIIT, Espoo, Finland
| | - Sandra Castillo
- />VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | - Merja Penttilä
- />VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
| | - Mikko Arvas
- />VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland
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Landowski CP, Huuskonen A, Wahl R, Westerholm-Parvinen A, Kanerva A, Hänninen AL, Salovuori N, Penttilä M, Natunen J, Ostermeier C, Helk B, Saarinen J, Saloheimo M. Enabling Low Cost Biopharmaceuticals: A Systematic Approach to Delete Proteases from a Well-Known Protein Production Host Trichoderma reesei. PLoS One 2015; 10:e0134723. [PMID: 26309247 PMCID: PMC4550459 DOI: 10.1371/journal.pone.0134723] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/13/2015] [Indexed: 11/22/2022] Open
Abstract
The filamentous fungus Trichoderma reesei has tremendous capability to secrete proteins. Therefore, it would be an excellent host for producing high levels of therapeutic proteins at low cost. Developing a filamentous fungus to produce sensitive therapeutic proteins requires that protease secretion is drastically reduced. We have identified 13 major secreted proteases that are related to degradation of therapeutic antibodies, interferon alpha 2b, and insulin like growth factor. The major proteases observed were aspartic, glutamic, subtilisin-like, and trypsin-like proteases. The seven most problematic proteases were sequentially removed from a strain to develop it for producing therapeutic proteins. After this the protease activity in the supernatant was dramatically reduced down to 4% of the original level based upon a casein substrate. When antibody was incubated in the six protease deletion strain supernatant, the heavy chain remained fully intact and no degradation products were observed. Interferon alpha 2b and insulin like growth factor were less stable in the same supernatant, but full length proteins remained when incubated overnight, in contrast to the original strain. As additional benefits, the multiple protease deletions have led to faster strain growth and higher levels of total protein in the culture supernatant.
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Affiliation(s)
| | - Anne Huuskonen
- VTT Technical Research Centre of Finland, Espoo, Finland
| | | | | | | | | | | | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, Finland
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Mehtiö T, Toivari M, Wiebe MG, Harlin A, Penttilä M, Koivula A. Production and applications of carbohydrate-derived sugar acids as generic biobased chemicals. Crit Rev Biotechnol 2015; 36:904-16. [DOI: 10.3109/07388551.2015.1060189] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Tuomas Mehtiö
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Mervi Toivari
- VTT Technical Research Centre of Finland, Espoo, Finland
| | | | - Ali Harlin
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland, Espoo, Finland
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Andberg M, Penttilä M, Saloheimo M. Swollenin from Trichoderma reesei exhibits hydrolytic activity against cellulosic substrates with features of both endoglucanases and cellobiohydrolases. Bioresour Technol 2015; 181:105-13. [PMID: 25643956 DOI: 10.1016/j.biortech.2015.01.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 05/21/2023]
Abstract
The cellulolytic and hemicellulolytic enzymes of Trichoderma reesei comprise one of the best characterised enzyme systems involved in lignocellulose degradation. In this paper, swollenin (SWOI), a protein recognised based on its sequence similarity with plant expansins, has been characterised. SWOI and its catalytic domain were subjected to analysis of their hydrolytic activity on different soluble carbohydrate polymers. By measuring the production of reducing ends, zymogram-, and viscosity analysis, SWOI was shown to have activity on substrates containing β-1,4 glucosidic bonds, i.e. carboxymethyl cellulose, hydroxyethyl cellulose and β-glucan. The formation of oligosaccharides from β-glucan was analysed by HPLC and showed cellobiose as the main reaction product. SWOI was also able to hydrolyse soluble cello-oligosaccharides and the products formed were all consistent with SWOI cleaving a cellobiose unit off the substrate. In conclusion, the T. reesei swollenin showed a unique mode of action with similarities with action of both endoglucanases and cellobiohydrolases.
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Affiliation(s)
- Martina Andberg
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT Espoo, Finland.
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Markku Saloheimo
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT Espoo, Finland
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Isohanni M, Miettunen J, Isohanni I, Penttilä M, Husa A, Seppälä J, Murray G, Rissanen I, Jääskeläinen E. Long-term Antipsychotic Treatment, Brain Volumes and Clinical Outcomes of Midlife Schizophrenia in the Northern Finland 1966 Birth Cohort. Eur Psychiatry 2015. [DOI: 10.1016/s0924-9338(15)30687-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Penttilä M, Moilanen J, Haapea M, Isohanni M, Möller H, Koponen H, Miettunen J, Jääskeläinen E. Duration of Untreated Psychosis and the Use of Antipsychotic Medication During the Course of Illness in the Northern Finland 1966 Birth Cohort. Eur Psychiatry 2015. [DOI: 10.1016/s0924-9338(15)30229-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Richard P, Viljanen K, Penttilä M. Overexpression of PAD1 and FDC1 results in significant cinnamic acid decarboxylase activity in Saccharomyces cerevisiae. AMB Express 2015; 5:12. [PMID: 25852989 PMCID: PMC4384992 DOI: 10.1186/s13568-015-0103-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/09/2015] [Indexed: 11/10/2022] Open
Abstract
The S. cerevisiae PAD1 gene had been suggested to code for a cinnamic acid decarboxylase, converting trans-cinnamic acid to styrene. This was suggested for the reason that the over-expression of PAD1 resulted in increased tolerance toward cinnamic acid, up to 0.6 mM. We show that by over-expression of the PAD1 together with the FDC1 the cinnamic acid decarboxylase activity can be increased significantly. The strain over-expressing PAD1 and FDC1 tolerated cinnamic acid concentrations up to 10 mM. The cooperation of Pad1p and Fdc1p is surprising since the PAD1 has a mitochondrial targeting sequence and the FDC1 codes for a cytosolic protein. The cinnamic acid decarboxylase activity was also seen in the cell free extract. The activity was 0.019 μmol per minute and mg of extracted protein. The overexpression of PAD1 and FDC1 resulted also in increased activity with the hydroxycinnamic acids ferulic acid, p-coumaric acid and caffeinic acid. This activity was not seen when FDC1 was overexpressed alone. An efficient cinnamic acid decarboxylase is valuable for the genetic engineering of yeast strains producing styrene. Styrene can be produced from endogenously produced L-phenylalanine which is converted by a phenylalanine ammonia lyase to cinnamic acid and then by a decarboxylase to styrene.
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Kuivanen J, Penttilä M, Richard P. Metabolic engineering of the fungal D-galacturonate pathway for L-ascorbic acid production. Microb Cell Fact 2015; 14:2. [PMID: 25566698 PMCID: PMC4299797 DOI: 10.1186/s12934-014-0184-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 12/19/2014] [Indexed: 11/29/2022] Open
Abstract
Background Synthetic L-ascorbic acid (vitamin C) is widely used as a preservative and nutrient in food and pharmaceutical industries. In the current production method, D-glucose is converted to L-ascorbic acid via several biochemical and chemical steps. The main source of L-ascorbic acid in human nutrition is plants. Several alternative metabolic pathways for L-ascorbic acid biosynthesis are known in plants. In one of them, D-galacturonic acid is the precursor. D-Galacturonic acid is also the main monomer in pectin, a plant cell wall polysaccharide. Pectin is abundant in biomass and is readily available from several waste streams from fruit and sugar processing industries. Results In the present work, we engineered the filamentous fungus Aspergillus niger for the conversion of D-galacturonic acid to L-ascorbic acid. In the generated pathway, the native D-galacturonate reductase activity was utilized while the gene coding for the second enzyme in the fungal D-galacturonic acid pathway, an L-galactonate consuming dehydratase, was deleted. Two heterologous genes coding for enzymes from the plant L-ascorbic acid pathway – L-galactono-1,4-lactone lactonase from Euglena gracilis (EgALase) and L-galactono-1,4-lactone dehydrogenase from Malpighia glabra (MgGALDH) – were introduced into the A. niger strain. Alternatively, an unspecific L-gulono-1,4-lactone lactonase (smp30) from the animal L-ascorbic acid pathway was introduced in the fungal strain instead of the plant L-galactono-1,4-lactone lactonase. In addition, a strain with the production pathway inducible with D-galacturonic acid was generated by using a bidirectional and D-galacturonic acid inducible promoter from the fungus. Even though, the lactonase enzyme activity was not observed in the resulting strains, they were capable of producing L-ascorbic acid from pure D-galacturonic acid or pectin-rich biomass in a consolidated bioprocess. Product titers up to 170 mg/l were achieved. Conclusions In the current study, an L-ascorbic acid pathway using D-galacturonic acid as a precursor was introduced to a microorganism for the first time. This is also the first report on an engineered filamentous fungus for L-ascorbic acid production and a proof-of-concept of consolidated bioprocess for the production.
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Affiliation(s)
- Joosu Kuivanen
- VTT Technical Research Centre of Finland, PO Box 1000, 02044 VTT, Espoo, Finland.
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, PO Box 1000, 02044 VTT, Espoo, Finland.
| | - Peter Richard
- VTT Technical Research Centre of Finland, PO Box 1000, 02044 VTT, Espoo, Finland.
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Turkia H, Sirén H, Penttilä M, Pitkänen JP. Capillary electrophoresis with laser-induced fluorescence detection for studying amino acid uptake by yeast during beer fermentation. Talanta 2015; 131:366-71. [DOI: 10.1016/j.talanta.2014.07.101] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/28/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022]
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Gourlay K, Hu J, Arantes V, Penttilä M, Saddler JN. The use of carbohydrate binding modules (CBMs) to monitor changes in fragmentation and cellulose fiber surface morphology during cellulase- and Swollenin-induced deconstruction of lignocellulosic substrates. J Biol Chem 2014; 290:2938-45. [PMID: 25527502 DOI: 10.1074/jbc.m114.627604] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Although the actions of many of the hydrolytic enzymes involved in cellulose hydrolysis are relatively well understood, the contributions that amorphogenesis-inducing proteins might contribute to cellulose deconstruction are still relatively undefined. Earlier work has shown that disruptive proteins, such as the non-hydrolytic non-oxidative protein Swollenin, can open up and disaggregate the less-ordered regions of lignocellulosic substrates. Within the cellulosic fraction, relatively disordered, amorphous regions known as dislocations are known to occur along the length of the fibers. It was postulated that Swollenin might act synergistically with hydrolytic enzymes to initiate biomass deconstruction within these dislocation regions. Carbohydrate binding modules (CBMs) that preferentially bind to cellulosic substructures were fluorescently labeled. They were imaged, using confocal microscopy, to assess the distribution of crystalline and amorphous cellulose at the fiber surface, as well as to track changes in surface morphology over the course of enzymatic hydrolysis and fiber fragmentation. Swollenin was shown to promote targeted disruption of the cellulosic structure at fiber dislocations.
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Affiliation(s)
- Keith Gourlay
- From the Forest Products Biotechnology/Bioenergy Group, Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada and
| | - Jinguang Hu
- From the Forest Products Biotechnology/Bioenergy Group, Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada and
| | - Valdeir Arantes
- From the Forest Products Biotechnology/Bioenergy Group, Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada and
| | - Merja Penttilä
- the VTT Technical Research Centre of Finland, Metallimiehenkuja 2 (Espoo), FI-02044 VTT, Finland
| | - Jack N Saddler
- From the Forest Products Biotechnology/Bioenergy Group, Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada and
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Aguiar TQ, Ribeiro O, Arvas M, Wiebe MG, Penttilä M, Domingues L. Investigation of protein secretion and secretion stress in Ashbya gossypii. BMC Genomics 2014; 15:1137. [PMID: 25523110 PMCID: PMC4320514 DOI: 10.1186/1471-2164-15-1137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/20/2014] [Indexed: 11/27/2022] Open
Abstract
Background Ashbya gossypii is a filamentous Saccharomycete used for the industrial production of riboflavin that has been recently explored as a host system for recombinant protein production. To gain insight into the protein secretory pathway of this biotechnologically relevant fungus, we undertook genome-wide analyses to explore its secretome and its transcriptional responses to protein secretion stress. Results A computational pipeline was used to predict the inventory of proteins putatively secreted by A. gossypii via the general secretory pathway. The proteins actually secreted by this fungus into the supernatants of submerged cultures in minimal and rich medium were mapped by two-dimensional gel electrophoresis, revealing that most of the A. gossypii secreted proteins have an isoelectric point between 4 and 6, and a molecular mass above 25 kDa. These analyses together indicated that 1-4% of A. gossypii proteins are likely to be secreted, of which less than 33% are putative hydrolases. Furthermore, transcriptomic analyses carried out in A. gossypii cells under recombinant protein secretion conditions and dithiothreitol-induced secretion stress unexpectedly revealed that a conventional unfolded protein response (UPR) was not activated in any of the conditions, as the expression levels of several well-known UPR target genes (e.g. IRE1, KAR2, HAC1 and PDI1 homologs) remained unaffected. However, several other genes involved in protein unfolding, endoplasmatic reticulum-associated degradation, proteolysis, vesicle trafficking, vacuolar protein sorting, secretion and mRNA degradation were up-regulated by dithiothreitol-induced secretion stress. Conversely, the transcription of several genes encoding secretory proteins, such as components of the glycosylation pathway, was severely repressed by dithiothreitol Conclusions This study provides the first insights into the secretion stress response of A. gossypii, as well as a basic understanding of its protein secretion potential, which is more similar to that of yeast than to that of other filamentous fungi. Contrary to what has been widely described for yeast and fungi, a conventional UPR was not observed in A. gossypii, but alternative protein quality control mechanisms enabled it to cope with secretion stress. These data will help provide strategies for improving heterologous protein secretion in A. gossypii. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1137) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
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Taberman H, Andberg M, Parkkinen T, Jänis J, Penttilä M, Hakulinen N, Koivula A, Rouvinen J. Structure and function of a decarboxylating Agrobacterium tumefaciens keto-deoxy-d-galactarate dehydratase. Biochemistry 2014; 53:8052-60. [PMID: 25454257 DOI: 10.1021/bi501290k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Agrobacterium tumefaciens (At) strain C58 contains an oxidative enzyme pathway that can function on both d-glucuronic and d-galacturonic acid. The corresponding gene coding for At keto-deoxy-d-galactarate (KDG) dehydratase is located in the same gene cluster as those coding for uronate dehydrogenase (At Udh) and galactarolactone cycloisomerase (At Gci) which we have previously characterized. Here, we present the kinetic characterization and crystal structure of At KDG dehydratase, which catalyzes the next step, the decarboxylating hydrolyase reaction of KDG to produce α-ketoglutaric semialdehyde (α-KGSA) and carbon dioxide. The crystal structures of At KDG dehydratase and its complexes with pyruvate and 2-oxoadipic acid, two substrate analogues, were determined to 1.7 Å, 1.5 Å, and 2.1 Å resolution, respectively. Furthermore, mass spectrometry was used to confirm reaction end-products. The results lead us to propose a structure-based mechanism for At KDG dehydratase, suggesting that while the enzyme belongs to the Class I aldolase protein family, it does not follow a typical retro-aldol condensation mechanism.
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Affiliation(s)
- Helena Taberman
- Department of Chemistry, University of Eastern Finland , FI-80101 Joensuu, Finland
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Aro-Kärkkäinen N, Toivari M, Maaheimo H, Ylilauri M, Pentikäinen OT, Andberg M, Oja M, Penttilä M, Wiebe MG, Ruohonen L, Koivula A. L-arabinose/D-galactose 1-dehydrogenase of Rhizobium leguminosarum bv. trifolii characterised and applied for bioconversion of L-arabinose to L-arabonate with Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2014; 98:9653-65. [PMID: 25236800 DOI: 10.1007/s00253-014-6039-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/13/2014] [Accepted: 08/18/2014] [Indexed: 10/24/2022]
Abstract
Four potential dehydrogenases identified through literature and bioinformatic searches were tested for L-arabonate production from L-arabinose in the yeast Saccharomyces cerevisiae. The most efficient enzyme, annotated as a D-galactose 1-dehydrogenase from the pea root nodule bacterium Rhizobium leguminosarum bv. trifolii, was purified from S. cerevisiae as a homodimeric protein and characterised. We named the enzyme as a L-arabinose/D-galactose 1-dehydrogenase (EC 1.1.1.-), Rl AraDH. It belongs to the Gfo/Idh/MocA protein family, prefers NADP(+) but uses also NAD(+) as a cofactor, and showed highest catalytic efficiency (k cat/K m) towards L-arabinose, D-galactose and D-fucose. Based on nuclear magnetic resonance (NMR) and modelling studies, the enzyme prefers the α-pyranose form of L-arabinose, and the stable oxidation product detected is L-arabino-1,4-lactone which can, however, open slowly at neutral pH to a linear L-arabonate form. The pH optimum for the enzyme was pH 9, but use of a yeast-in-vivo-like buffer at pH 6.8 indicated that good catalytic efficiency could still be expected in vivo. Expression of the Rl AraDH dehydrogenase in S. cerevisiae, together with the galactose permease Gal2 for L-arabinose uptake, resulted in production of 18 g of L-arabonate per litre, at a rate of 248 mg of L-arabonate per litre per hour, with 86 % of the provided L-arabinose converted to L-arabonate. Expression of a lactonase-encoding gene from Caulobacter crescentus was not necessary for L-arabonate production in yeast.
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Mojzita D, Oja M, Rintala E, Wiebe M, Penttilä M, Ruohonen L. Transcriptome of Saccharomyces cerevisiae during production of D-xylonate. BMC Genomics 2014; 15:763. [PMID: 25192596 PMCID: PMC4176587 DOI: 10.1186/1471-2164-15-763] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 08/29/2014] [Indexed: 11/24/2022] Open
Abstract
Background Production of D-xylonate by the yeast S. cerevisiae provides an example of bioprocess development for sustainable production of value-added chemicals from cheap raw materials or side streams. Production of D-xylonate may lead to considerable intracellular accumulation of D-xylonate and to loss of viability during the production process. In order to understand the physiological responses associated with D-xylonate production, we performed transcriptome analyses during D-xylonate production by a robust recombinant strain of S. cerevisiae which produces up to 50 g/L D-xylonate. Results Comparison of the transcriptomes of the D-xylonate producing and the control strain showed considerably higher expression of the genes controlled by the cell wall integrity (CWI) pathway and of some genes previously identified as up-regulated in response to other organic acids in the D-xylonate producing strain. Increased phosphorylation of Slt2 kinase in the D-xylonate producing strain also indicated that D-xylonate production caused stress to the cell wall. Surprisingly, genes encoding proteins involved in translation, ribosome structure and RNA metabolism, processes which are commonly down-regulated under conditions causing cellular stress, were up-regulated during D-xylonate production, compared to the control. The overall transcriptional responses were, therefore, very dissimilar to those previously reported as being associated with stress, including stress induced by organic acid treatment or production. Quantitative PCR analyses of selected genes supported the observations made in the transcriptomic analysis. In addition, consumption of ethanol was slower and the level of trehalose was lower in the D-xylonate producing strain, compared to the control. Conclusions The production of organic acids has a major impact on the physiology of yeast cells, but the transcriptional responses to presence or production of different acids differs considerably, being much more diverse than responses to other stresses. D-Xylonate production apparently imposed considerable stress on the cell wall. Transcriptional data also indicated that activation of the PKA pathway occurred during D-xylonate production, leaving cells unable to adapt normally to stationary phase. This, together with intracellular acidification, probably contributes to cell death. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-763) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dominik Mojzita
- VTT Technical Research Centre of Finland, P,O, Box 1000, Espoo FI-02044 VTT, Finland.
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Koivuranta KT, Ilmén M, Wiebe MG, Ruohonen L, Suominen P, Penttilä M. L-lactic acid production from D-xylose with Candida sonorensis expressing a heterologous lactate dehydrogenase encoding gene. Microb Cell Fact 2014; 13:107. [PMID: 25104116 PMCID: PMC4249597 DOI: 10.1186/s12934-014-0107-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/15/2014] [Indexed: 11/10/2022] Open
Abstract
Background Bioplastics, like polylactic acid (PLA), are renewable alternatives for petroleum-based plastics. Lactic acid, the monomer of PLA, has traditionally been produced biotechnologically with bacteria. With genetic engineering, yeast have the potential to replace bacteria in biotechnological lactic acid production, with the benefits of being acid tolerant and having simple nutritional requirements. Lactate dehydrogenase genes have been introduced to various yeast to demonstrate this potential. Importantly, an industrial lactic acid producing process utilising yeast has already been implemented. Utilisation of D-xylose in addition to D-glucose in production of biochemicals such as lactic acid by microbial fermentation would be beneficial, as it would allow lignocellulosic raw materials to be utilised in the production processes. Results The yeast Candida sonorensis, which naturally metabolises D-xylose, was genetically modified to produce L-lactic acid from D-xylose by integrating the gene encoding L-lactic acid dehydrogenase (ldhL) from Lactobacillus helveticus into its genome. In microaerobic, CaCO3-buffered conditions a C. sonorensis ldhL transformant having two copies of the ldhL gene produced 31 g l−1 lactic acid from 50 g l−1 D-xylose free of ethanol. Anaerobic production of lactic acid from D-xylose was assessed after introducing an alternative pathway of D-xylose metabolism, i.e. by adding a xylose isomerase encoded by XYLA from Piromyces sp. alone or together with the xylulokinase encoding gene XKS1 from Saccharomyces cerevisiae. Strains were further modified by deletion of the endogenous xylose reductase encoding gene, alone or together with the xylitol dehydrogenase encoding gene. Strains of C. sonorensis expressing xylose isomerase produced L-lactic acid from D-xylose in anaerobic conditions. The highest anaerobic L-lactic acid production (8.5 g l−1) was observed in strains in which both the xylose reductase and xylitol dehydrogenase encoding genes had been deleted and the xylulokinase encoding gene from S. cerevisiae was overexpressed. Conclusions Integration of two copies of the ldhL gene in C. sonorensis was sufficient to obtain good L-lactic acid production from D-xylose. Under anaerobic conditions, the ldhL strain with exogenous xylose isomerase and xylulokinase genes expressed and the endogenous xylose reductase and xylitol dehydrogenase genes deleted had the highest L- lactic acid production.
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Affiliation(s)
- Kari T Koivuranta
- VTT Technical Research Centre of Finland, Espoo FI-02044 VTT, Finland.
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Valkonen M, Penttilä M, Benčina M. Intracellular pH responses in the industrially important fungus Trichoderma reesei. Fungal Genet Biol 2014; 70:86-93. [PMID: 25046860 DOI: 10.1016/j.fgb.2014.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/07/2014] [Accepted: 07/08/2014] [Indexed: 12/14/2022]
Abstract
Preserving an optimal intracellular pH is critical for cell fitness and productivity. The pH homeostasis of the industrially important filamentous fungus Trichoderma reesei (Hypocrea jecorina) is largely unexplored. We analyzed the impact of growth conditions on regulation of intracellular pH of the strain Rut-C30 and the strain M106 derived from the Rut-C30 that accumulates L-galactonic acid-from provided galacturonic acid-as a consequence of L-galactonate dehydratase deletion. For live-cell measurements of intracellular pH, we used the genetically encoded ratiometric pH-sensitive fluorescent protein RaVC. Glucose and lactose, used as carbon sources, had specific effects on intracellular pH of T. reesei. The growth in lactose-containing medium extensively acidified cytosol, while intracellular pH of hyphae cultured in a medium with glucose remained at a higher level. The strain M106 maintained higher intracellular pH in the presence of D-galacturonic acid than its parental strain Rut-C30. Acidic external pH caused significant acidification of cytosol. Altogether, the pH homeostasis of T. reesei Rut-C30 strain is sensitive to extracellular pH and the degree of acidification depends on carbon source.
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Affiliation(s)
- Mari Valkonen
- VTT Technical Research Centre of Finland, Espoo, Finland.
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Mojca Benčina
- Laboratory of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; Centre of Excellence EN-FIST, 1000 Ljubljana, Slovenia.
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