1
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Donati S, Mattanovich M, Hjort P, Jacobsen SAB, Blomquist SD, Mangaard D, Gurdo N, Pastor FP, Maury J, Hanke R, Herrgård MJ, Wulff T, Jakočiūnas T, Nielsen LK, McCloskey D. An automated workflow for multi-omics screening of microbial model organisms. NPJ Syst Biol Appl 2023; 9:14. [PMID: 37208327 DOI: 10.1038/s41540-023-00277-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 04/19/2023] [Indexed: 05/21/2023] Open
Abstract
Multi-omics datasets are becoming of key importance to drive discovery in fundamental research as much as generating knowledge for applied biotechnology. However, the construction of such large datasets is usually time-consuming and expensive. Automation might enable to overcome these issues by streamlining workflows from sample generation to data analysis. Here, we describe the construction of a complex workflow for the generation of high-throughput microbial multi-omics datasets. The workflow comprises a custom-built platform for automated cultivation and sampling of microbes, sample preparation protocols, analytical methods for sample analysis and automated scripts for raw data processing. We demonstrate possibilities and limitations of such workflow in generating data for three biotechnologically relevant model organisms, namely Escherichia coli, Saccharomyces cerevisiae, and Pseudomonas putida.
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Affiliation(s)
- Stefano Donati
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Matthias Mattanovich
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark
| | - Pernille Hjort
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | | | - Sarah Dina Blomquist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Drude Mangaard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Nicolas Gurdo
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Felix Pacheco Pastor
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Jérôme Maury
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Rene Hanke
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Markus J Herrgård
- BioInnovation Institute, Ole Maaløes Vej 3, 2200, København, Denmark
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Tadas Jakočiūnas
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Lars Keld Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
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2
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Gurdo N, Taylor Parkins SK, Fricano M, Wulff T, Nielsen LK, Nikel PI. Protocol for absolute quantification of proteins in Gram-negative bacteria based on QconCAT-based labeled peptides. STAR Protoc 2023; 4:102060. [PMID: 36853682 PMCID: PMC9881405 DOI: 10.1016/j.xpro.2023.102060] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/02/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023] Open
Abstract
Mass-spectrometry-based absolute protein quantification uses labeled quantification concatamer (QconCAT) as internal standards (ISs). To calculate the amount of protein(s), the ion intensity ratio between the analyte and its cognate IS is compared in each biological sample. The present protocol describes a systematic workflow to design, produce, and purify QconCATs and to quantify soluble proteins in Pseudomonas putida KT2440. Our methodology enables the quantification of detectable peptide and serves as a versatile platform to produce ISs for different biological systems.
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Affiliation(s)
- Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | - Martina Fricano
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Lars Keld Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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3
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Milne N, Sáez-Sáez J, Nielsen AM, Dyekjaer JD, Rago D, Kristensen M, Wulff T, Borodina I. Engineering Saccharomyces cerevisiae for the de novo Production of Halogenated Tryptophan and Tryptamine Derivatives. ChemistryOpen 2023; 12:e202200266. [PMID: 36929157 PMCID: PMC10068768 DOI: 10.1002/open.202200266] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
The indole scaffold is a recurring structure in multiple bioactive heterocycles and natural products. Substituted indoles like the amino acid tryptophan serve as a precursor for a wide range of natural products with pharmaceutical or agrochemical applications. Inspired by the versatility of these compounds, medicinal chemists have for decades exploited indole as a core structure in the drug discovery process. With the aim of tuning the properties of lead drug candidates, regioselective halogenation of the indole scaffold is a common strategy. However, chemical halogenation is generally expensive, has a poor atom economy, lacks regioselectivity, and generates hazardous waste streams. As an alternative, in this work we engineer the industrial workhorse Saccharomyces cerevisiae for the de novo production of halogenated tryptophan and tryptamine derivatives. Functional expression of bacterial tryptophan halogenases together with a partner flavin reductase and a tryptophan decarboxylase resulted in the production of halogenated tryptophan and tryptamine with chlorine or bromine. Furthermore, by combining tryptophan halogenases, production of di-halogenated molecules was also achieved. Overall, this works paves the road for the production of new-to-nature halogenated natural products in yeast.
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Affiliation(s)
- Nicholas Milne
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.,Octarine Bio ApS, Lersø Parkallé 42, 1. Sal, 2100, Copenhagen, Denmark
| | - Javier Sáez-Sáez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Annette Munch Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.,Octarine Bio ApS, Lersø Parkallé 42, 1. Sal, 2100, Copenhagen, Denmark
| | - Jane Dannow Dyekjaer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Daniela Rago
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Mette Kristensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
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4
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Wirth NT, Gurdo N, Krink N, Vidal-Verdú À, Donati S, Férnandez-Cabezón L, Wulff T, Nikel PI. A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes. Metab Eng 2022; 74:83-97. [PMID: 36155822 DOI: 10.1016/j.ymben.2022.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 07/22/2022] [Revised: 09/17/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022]
Abstract
Acetyl-coenzyme A (AcCoA) is a metabolic hub in virtually all living cells, serving as both a key precursor of essential biomass components and a metabolic sink for catabolic pathways for a large variety of substrates. Owing to this dual role, tight growth-production coupling schemes can be implemented around the AcCoA node. Building on this concept, a synthetic C2 auxotrophy was implemented in the platform bacterium Pseudomonas putida through an in silico-informed engineering approach. A growth-coupling strategy, driven by AcCoA demand, allowed for direct selection of an alternative sugar assimilation route-the phosphoketolase (PKT) shunt from bifidobacteria. Adaptive laboratory evolution forced the synthetic P. putida auxotroph to rewire its metabolic network to restore C2 prototrophy via the PKT shunt. Large-scale structural chromosome rearrangements were identified as possible mechanisms for adjusting the network-wide proteome profile, resulting in improved PKT-dependent growth phenotypes. 13C-based metabolic flux analysis revealed an even split between the native Entner-Doudoroff pathway and the synthetic PKT bypass for glucose processing, leading to enhanced carbon conservation. These results demonstrate that the P. putida metabolism can be radically rewired to incorporate a synthetic C2 metabolism, creating novel network connectivities and highlighting the importance of unconventional engineering strategies to support efficient microbial production.
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Affiliation(s)
- Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Nicolas Krink
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Àngela Vidal-Verdú
- Institute for Integrative Systems Biology I2SysBio (Universitat de València-CSIC), Calle del Catedràtic Agustin Escardino Benlloch 9, 46980, Paterna, Spain
| | - Stefano Donati
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Lorena Férnandez-Cabezón
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark.
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5
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Bertelsen AB, Hackney CM, Bayer CN, Kjelgaard LD, Rennig M, Christensen B, Sørensen ES, Safavi‐Hemami H, Wulff T, Ellgaard L, Nørholm MHH. DisCoTune: versatile auxiliary plasmids for the production of disulphide-containing proteins and peptides in the E. coli T7 system. Microb Biotechnol 2021; 14:2566-2580. [PMID: 34405535 PMCID: PMC8601162 DOI: 10.1111/1751-7915.13895] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/15/2021] [Accepted: 07/04/2021] [Indexed: 11/28/2022] Open
Abstract
Secreted proteins and peptides hold large potential both as therapeutics and as enzyme catalysts in biotechnology. The high stability of many secreted proteins helps maintain functional integrity in changing chemical environments and is a contributing factor to their commercial potential. Disulphide bonds constitute an important post-translational modification that stabilizes many of these proteins and thus preserves the active state under chemically stressful conditions. Despite their importance, the discovery and applications within this group of proteins and peptides are limited by the availability of synthetic biology tools and heterologous production systems that allow for efficient formation of disulphide bonds. Here, we refine the design of two DisCoTune (Disulphide bond formation in E. coli with tunable expression) plasmids that enable the formation of disulphides in the highly popular Escherichia coli T7 protein production system. We show that this new system promotes significantly higher yield and activity of an industrial protease and a conotoxin, which belongs to a group of disulphide-rich venom peptides from cone snails with strong potential as research tools and pharmacological agents.
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Affiliation(s)
- Andreas B. Bertelsen
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens Lyngby2800Denmark
| | - Celeste Menuet Hackney
- Department of BiologyLinderstrøm‐Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagen N.2200Denmark
| | - Carolyn N. Bayer
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens Lyngby2800Denmark
| | - Lau D. Kjelgaard
- Department of BiologyLinderstrøm‐Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagen N.2200Denmark
| | - Maja Rennig
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens Lyngby2800Denmark
| | - Brian Christensen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus C8000Denmark
| | | | - Helena Safavi‐Hemami
- Department of BiologyLinderstrøm‐Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagen N.2200Denmark
- Department of Biomedical SciencesUniversity of CopenhagenCopenhagen N2200Denmark
- Department of Biochemistry and School of Biological SciencesUniversity of UtahSalt Lake CityUT84112USA
| | - Tune Wulff
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens Lyngby2800Denmark
| | - Lars Ellgaard
- Department of BiologyLinderstrøm‐Lang Centre for Protein ScienceUniversity of CopenhagenCopenhagen N.2200Denmark
| | - Morten H. H. Nørholm
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens Lyngby2800Denmark
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6
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Kozaeva E, Volkova S, Matos MRA, Mezzina MP, Wulff T, Volke DC, Nielsen LK, Nikel PI. Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A-dependent bioproduction in rewired Pseudomonas putida. Metab Eng 2021; 67:373-386. [PMID: 34343699 DOI: 10.1016/j.ymben.2021.07.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 05/31/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 01/16/2023]
Abstract
Pseudomonas putida is evolutionarily endowed with features relevant for bioproduction, especially under harsh operating conditions. The rich metabolic versatility of this species, however, comes at the price of limited formation of acetyl-coenzyme A (CoA) from sugar substrates. Since acetyl-CoA is a key metabolic precursor for a number of added-value products, in this work we deployed an in silico-guided rewiring program of central carbon metabolism for upgrading P. putida as a host for acetyl-CoA-dependent bioproduction. An updated kinetic model, integrating fluxomics and metabolomics datasets in addition to manually-curated information of enzyme mechanisms, identified targets that would lead to increased acetyl-CoA levels. Based on these predictions, a set of plasmids based on clustered regularly interspaced short palindromic repeats (CRISPR) and dead CRISPR-associated protein 9 (dCas9) was constructed to silence genes by CRISPR interference (CRISPRi). Dynamic reduction of gene expression of two key targets (gltA, encoding citrate synthase, and the essential accA gene, encoding subunit A of the acetyl-CoA carboxylase complex) mediated an 8-fold increase in the acetyl-CoA content of rewired P. putida. Poly(3-hydroxybutyrate) (PHB) was adopted as a proxy of acetyl-CoA availability, and two synthetic pathways were engineered for biopolymer accumulation. By including cell morphology as an extra target for the CRISPRi approach, fully rewired P. putida strains programmed for PHB accumulation had a 5-fold increase in PHB titers in bioreactor cultures using glucose. Thus, the strategy described herein allowed for rationally redirecting metabolic fluxes in P. putida from central metabolism towards product biosynthesis-especially relevant when deletion of essential pathways is not an option.
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Affiliation(s)
- Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Svetlana Volkova
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Marta R A Matos
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mariela P Mezzina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Lars K Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark; Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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7
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Pérez-Rodriguez S, Wulff T, Voldborg BG, Altamirano C, Trujillo-Roldán MA, Valdez-Cruz NA. Compartmentalized Proteomic Profiling Outlines the Crucial Role of the Classical Secretory Pathway during Recombinant Protein Production in Chinese Hamster Ovary Cells. ACS Omega 2021; 6:12439-12458. [PMID: 34056395 PMCID: PMC8154153 DOI: 10.1021/acsomega.0c06030] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 05/11/2023]
Abstract
Different cellular processes that contribute to protein production in Chinese hamster ovary (CHO) cells have been previously investigated by proteomics. However, although the classical secretory pathway (CSP) has been well documented as a bottleneck during recombinant protein (RP) production, it has not been well represented in previous proteomic studies. Hence, the significance of this pathway for production of RP was assessed by identifying its own proteins that were associated to changes in RP production, through subcellular fractionation coupled to shot-gun proteomics. Two CHO cell lines producing a monoclonal antibody with different specific productivities were used as cellular models, from which 4952 protein groups were identified, which represent a coverage of 59% of the Chinese hamster proteome. Data are available via ProteomeXchange with identifier PXD021014. By using SAM and ROTS algorithms, 493 proteins were classified as differentially expressed, of which about 80% was proposed as novel targets and one-third were assigned to the CSP. Endoplasmic reticulum (ER) stress, unfolded protein response, calcium homeostasis, vesicle traffic, glycosylation, autophagy, proteasomal activity, protein synthesis and translocation into ER lumen, and secretion of extracellular matrix components were some of the affected processes that occurred in the secretory pathway. Processes from other cellular compartments, such as DNA replication, transcription, cytoskeleton organization, signaling, and metabolism, were also modified. This study gives new insights into the molecular traits of higher producer cells and provides novel targets for development of new sub-lines with improved phenotypes for RP production.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Tune Wulff
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Bjørn G. Voldborg
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Claudia Altamirano
- Laboratorio
de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085 Valparaíso, Chile
| | - Mauricio A. Trujillo-Roldán
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Norma A. Valdez-Cruz
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
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8
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Romero-Suarez D, Wulff T, Rong Y, Jakočiu̅nas T, Yuzawa S, Keasling JD, Jensen MK. A Reporter System for Cytosolic Protein Aggregates in Yeast. ACS Synth Biol 2021; 10:466-477. [PMID: 33577304 DOI: 10.1021/acssynbio.0c00476] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein misfolding and aggregation are linked to neurodegenerative diseases of mammals and suboptimal protein expression within biotechnology. Tools for monitoring protein aggregates are therefore useful for studying disease-related aggregation and for improving soluble protein expression in heterologous hosts for biotechnology purposes. In this work, we developed a promoter-reporter system for aggregated protein on the basis of the yeast native response to misfolded protein. To this end, we first studied the proteome of yeast in response to the expression of folded soluble and aggregation-prone protein baits and identified genes encoding proteins related to protein folding and the response to heat stress as well as the ubiquitin-proteasome system that are over-represented in cells expressing an aggregation-prone protein. From these data, we created and validated promoter-reporter constructs and further engineered the best performing promoters by increasing the copy number of upstream activating sequences and optimization of culture conditions. Our best promoter-reporter has an output dynamic range of approximately 12-fold upon expression of the aggregation-prone protein and responded to increasing levels of aggregated protein. Finally, we demonstrate that the system can discriminate between yeast cells expressing different prion precursor proteins and select the cells expressing folded soluble protein from mixed populations. Our reporter system is thus a simple tool for diagnosing protein aggregates in living cells and should be applicable for the health and biotechnology industries.
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Affiliation(s)
- David Romero-Suarez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Yixin Rong
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Tadas Jakočiu̅nas
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Satoshi Yuzawa
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, Guangdong 518055, China
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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9
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Lin D, Yalamanchili HB, Zhang X, Lewis NE, Alves CS, Groot J, Arnsdorf J, Bjørn SP, Wulff T, Voldborg BG, Zhou Y, Zhang B. CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. PLoS Comput Biol 2020; 16:e1008498. [PMID: 33351794 PMCID: PMC7790544 DOI: 10.1371/journal.pcbi.1008498] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 01/07/2021] [Accepted: 11/06/2020] [Indexed: 11/18/2022] Open
Abstract
Chinese hamster ovary (CHO) cell lines are widely used in industry for biological drug production. During cell culture development, considerable effort is invested to understand the factors that greatly impact cell growth, specific productivity and product qualities of the biotherapeutics. While high-throughput omics approaches have been increasingly utilized to reveal cellular mechanisms associated with cell line phenotypes and guide process optimization, comprehensive omics data analysis and management have been a challenge. Here we developed CHOmics, a web-based tool for integrative analysis of CHO cell line omics data that provides an interactive visualization of omics analysis outputs and efficient data management. CHOmics has a built-in comprehensive pipeline for RNA sequencing data processing and multi-layer statistical modules to explore relevant genes or pathways. Moreover, advanced functionalities were provided to enable users to customize their analysis and visualize the output systematically and interactively. The tool was also designed with the flexibility to accommodate other types of omics data and thereby enabling multi-omics comparison and visualization at both gene and pathway levels. Collectively, CHOmics is an integrative platform for data analysis, visualization and management with expectations to promote the broader use of omics in CHO cell research.
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Affiliation(s)
- Dongdong Lin
- Biogen Inc., Cambridge, Massachusetts, United States of America
| | | | - Xinmin Zhang
- Bioinforx Inc., Madison, Wisconsin, United States of America
| | - Nathan E. Lewis
- Departments of Pediatrics and Bioengineering, University of California, San Diego, United States of America
- Novo Nordisk Foundation Center for Bio sustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Joost Groot
- Biogen Inc., Cambridge, Massachusetts, United States of America
| | - Johnny Arnsdorf
- Novo Nordisk Foundation Center for Bio sustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sara P. Bjørn
- Novo Nordisk Foundation Center for Bio sustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tune Wulff
- Novo Nordisk Foundation Center for Bio sustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bjørn G. Voldborg
- Novo Nordisk Foundation Center for Bio sustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Yizhou Zhou
- Biogen Inc., Cambridge, Massachusetts, United States of America
- * E-mail: (YZ); (BZ)
| | - Baohong Zhang
- Biogen Inc., Cambridge, Massachusetts, United States of America
- * E-mail: (YZ); (BZ)
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10
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Pérez-Rodriguez S, de Jesús Ramírez-Lira M, Wulff T, Voldbor BG, Ramírez OT, Trujillo-Roldán MA, Valdez-Cruz NA. Enrichment of microsomes from Chinese hamster ovary cells by subcellular fractionation for its use in proteomic analysis. PLoS One 2020; 15:e0237930. [PMID: 32841274 PMCID: PMC7447005 DOI: 10.1371/journal.pone.0237930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 03/03/2020] [Accepted: 08/06/2020] [Indexed: 11/19/2022] Open
Abstract
Chinese hamster ovary cells have been the workhorse for the production of recombinant proteins in mammalian cells. Since biochemical, cellular and omics studies are usually affected by the lack of suitable fractionation procedures to isolate compartments from these cells, differential and isopycnic centrifugation based techniques were characterized and developed specially for them. Enriched fractions in intact nuclei, mitochondria, peroxisomes, cis-Golgi, trans-Golgi and endoplasmic reticulum (ER) were obtained in differential centrifugation steps and subsequently separated in discontinuous sucrose gradients. Nuclei, mitochondria, cis-Golgi, peroxisomes and smooth ER fractions were obtained as defined bands in 30-60% gradients. Despite the low percentage represented by the microsomes of the total cell homogenate (1.7%), their separation in a novel sucrose gradient (10-60%) showed enough resolution and efficiency to quantitatively separate their components into enriched fractions in trans-Golgi, cis-Golgi and ER. The identity of these organelles belonging to the classical secretion pathway that came from 10-60% gradients was confirmed by proteomics. Data are available via ProteomeXchange with identifier PXD019778. Components from ER and plasma membrane were the most frequent contaminants in almost all obtained fractions. The improved sucrose gradient for microsomal samples proved being successful in obtaining enriched fractions of low abundance organelles, such as Golgi apparatus and ER components, for biochemical and molecular studies, and suitable for proteomic research, which makes it a useful tool for future studies of this and other mammalian cell lines.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - María de Jesús Ramírez-Lira
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bjørn Gunnar Voldbor
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Octavio T. Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Mauricio A. Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - Norma A. Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
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11
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Landberg J, Wright NR, Wulff T, Herrgård MJ, Nielsen AT. CRISPR interference of nucleotide biosynthesis improves production of a single-domain antibody in Escherichia coli. Biotechnol Bioeng 2020; 117:3835-3848. [PMID: 32808670 PMCID: PMC7818426 DOI: 10.1002/bit.27536] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/23/2022]
Abstract
Growth decoupling can be used to optimize the production of biochemicals and proteins in cell factories. Inhibition of excess biomass formation allows for carbon to be utilized efficiently for product formation instead of growth, resulting in increased product yields and titers. Here, we used CRISPR interference to increase the production of a single‐domain antibody (sdAb) by inhibiting growth during production. First, we screened 21 sgRNA targets in the purine and pyrimidine biosynthesis pathways and found that the repression of 11 pathway genes led to the increased green fluorescent protein production and decreased growth. The sgRNA targets pyrF, pyrG, and cmk were selected and further used to improve the production of two versions of an expression‐optimized sdAb. Proteomics analysis of the sdAb‐producing pyrF, pyrG, and cmk growth decoupling strains showed significantly decreased RpoS levels and an increase of ribosome‐associated proteins, indicating that the growth decoupling strains do not enter stationary phase and maintain their capacity for protein synthesis upon growth inhibition. Finally, sdAb production was scaled up to shake‐flask fermentation where the product yield was improved 2.6‐fold compared to the control strain with no sgRNA target sequence. An sdAb content of 14.6% was reached in the best‐performing pyrG growth decoupling strain.
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Affiliation(s)
- Jenny Landberg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Naia Risager Wright
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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12
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Wright NR, Wulff T, Palmqvist EA, Jørgensen TR, Workman CT, Sonnenschein N, Rønnest NP, Herrgård MJ. Fluctuations in glucose availability prevent global proteome changes and physiological transition during prolonged chemostat cultivations of
Saccharomyces cerevisiae. Biotechnol Bioeng 2020; 117:2074-2088. [DOI: 10.1002/bit.27353] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/09/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Naia R. Wright
- Novo Nordisk A/S Bagsværd Denmark
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
- Department of Biotechnology and BiomedicineTechnical University of Denmark Lyngby Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
| | | | - Thomas R. Jørgensen
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
| | - Christopher T. Workman
- Department of Biotechnology and BiomedicineTechnical University of Denmark Lyngby Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
- Department of Biotechnology and BiomedicineTechnical University of Denmark Lyngby Denmark
| | | | - Markus J. Herrgård
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
- BioInnovation Institute København N Denmark
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13
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Luo H, Yang L, Kim SH, Wulff T, Feist AM, Herrgard M, Palsson BØ. Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli. ACS Synth Biol 2020; 9:494-499. [PMID: 32149495 DOI: 10.1021/acssynbio.9b00488] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tetrahydrobiopterin-dependent hydroxylation of aromatic amino acids is the first step in the biosynthesis of many neuroactive compounds in humans. A fundamental challenge in building these pathways in Escherichia coli is the provision of the non-native hydroxylase cofactor, tetrahydrobiopterin. To solve this, we designed a genetic selection that relies on the tyrosine synthesis activity of phenylalanine hydroxylase. Using adaptive laboratory evolution, we demonstrate the use of this selection to discover: (1) a minimum set of heterologous enzymes and a host folE (T198I) mutation for achieving this type of hydroxylation chemistry in whole cells, (2) functional complementation of tetrahydrobiopterin by indigenous cofactors, and (3) a tryptophan hydroxylase mutation for improving protein abundance. Thus, the goal of having functional aromatic-amino-acid hydroxylation in E. coli was achieved through directed metabolic pathway evolution.
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Affiliation(s)
- Hao Luo
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Lei Yang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Se Hyeuk Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Adam M Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States of America
| | - Markus Herrgard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Bernhard Ø Palsson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States of America
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14
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Bongers M, Perez-Gil J, Hodson MP, Schrübbers L, Wulff T, Sommer MO, Nielsen LK, Vickers CE. Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid production. eLife 2020; 9:48685. [PMID: 32163032 PMCID: PMC7067565 DOI: 10.7554/elife.48685] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 02/16/2020] [Indexed: 12/12/2022] Open
Abstract
Volatile isoprenoids produced by plants are emitted in vast quantities into the atmosphere, with substantial effects on global carbon cycling. Yet, the molecular mechanisms regulating the balance between volatile and non-volatile isoprenoid production remain unknown. Isoprenoids are synthesised via sequential condensation of isopentenyl pyrophosphate (IPP) to dimethylallyl pyrophosphate (DMAPP), with volatile isoprenoids containing fewer isopentenyl subunits. The DMAPP:IPP ratio could affect the balance between volatile and non-volatile isoprenoids, but the plastidic DMAPP:IPP ratio is generally believed to be similar across different species. Here we demonstrate that the ratio of DMAPP:IPP produced by hydroxymethylbutenyl diphosphate reductase (HDR/IspH), the final step of the plastidic isoprenoid production pathway, is not fixed. Instead, this ratio varies greatly across HDRs from phylogenetically distinct plants, correlating with isoprenoid production patterns. Our findings suggest that adaptation of HDR plays a previously unrecognised role in determining in vivo carbon availability for isoprenoid emissions, directly shaping global biosphere-atmosphere interactions.
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Affiliation(s)
- Mareike Bongers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Jordi Perez-Gil
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
| | - Mark P Hodson
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,Metabolomics Australia, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,School of Pharmacy, The University of Queensland, Brisbane, Australia
| | - Lars Schrübbers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Morten Oa Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lars K Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
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15
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Ley D, Pereira S, Pedersen LE, Arnsdorf J, Hefzi H, Davy AM, Ha TK, Wulff T, Kildegaard HF, Andersen MR. Reprogramming AA catabolism in CHO cells with CRISPR/Cas9 genome editing improves cell growth and reduces byproduct secretion. Metab Eng 2019; 56:120-129. [DOI: 10.1016/j.ymben.2019.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/10/2019] [Accepted: 09/10/2019] [Indexed: 12/23/2022]
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16
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Rennig M, Mundhada H, Wordofa GG, Gerngross D, Wulff T, Worberg A, Nielsen AT, Nørholm MHH. Industrializing a Bacterial Strain for l-Serine Production through Translation Initiation Optimization. ACS Synth Biol 2019; 8:2347-2358. [PMID: 31550142 DOI: 10.1021/acssynbio.9b00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 02/01/2023]
Abstract
Turning a proof-of-concept synthetic biology design into a robust, high performing cell factory is a major time and money consuming task, which severely limits the growth of the white biotechnology sector. Here, we extend the use of tunable antibiotic resistance markers for synthetic evolution (TARSyn), a workflow for screening translation initiation region (TIR) libraries with antibiotic selection, to generic pathway engineering, and transform a proof-of-concept synbio design into a process that performs at industrially relevant levels. Using a combination of rational design and adaptive evolution, we recently engineered a high-performing bacterial strain for production of the important building block biochemical l-serine, based on two high-copy pET vectors facilitating expression of the serine biosynthetic genes serA, serC, and serB from three independent transcriptional units. Here, we prepare the bacterial strain for industrial scale up by transferring and reconfiguring the three genes into an operon encoded on a single low-copy plasmid. Not surprisingly, this initially reduces production titers considerably. We use TARSyn to screen both experimental and computational optimization designs resulting in high-performing synthetic serine operons and reach industrially relevant production levels of 50 g/L in fed-batch fermentations, the highest reported so far for serine production.
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Affiliation(s)
- Maja Rennig
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
| | - Hemanshu Mundhada
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Gossa G. Wordofa
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Daniel Gerngross
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Andreas Worberg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Alex T. Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
| | - Morten H. H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
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17
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Parnitzke U, Kronthaler K, Wulff T, Bretz A, Streubel G, Borgmann M, Hamm S. Resminostat increases NK cell-mediated lysis of malignant cells beneficially affecting the function of opsonizing antibodies. Eur J Cancer 2019. [DOI: 10.1016/s0959-8049(19)30517-9] [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] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Schrama D, Cerqueira M, Raposo CS, Rosa da Costa AM, Wulff T, Gonçalves A, Camacho C, Colen R, Fonseca F, Rodrigues PM. Dietary Creatine Supplementation in Gilthead Seabream ( Sparus aurata): Comparative Proteomics Analysis on Fish Allergens, Muscle Quality, and Liver. Front Physiol 2018; 9:1844. [PMID: 30622481 PMCID: PMC6308192 DOI: 10.3389/fphys.2018.01844] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 07/12/2018] [Accepted: 12/07/2018] [Indexed: 12/22/2022] Open
Abstract
The quality of fish flesh depends on the skeletal muscle's energetic state and delaying energy depletion through diets supplementation could contribute to the preservation of muscle's quality traits and modulation of fish allergens. Food allergies represent a serious public health problem worldwide with fish being one of the top eight more allergenic foods. Parvalbumins, have been identified as the main fish allergen. In this study, we attempted to produce a low allergenic farmed fish with improved muscle quality in controlled artificial conditions by supplementing a commercial fish diet with different creatine percentages. The supplementation of fish diets with specific nutrients, aimed at reducing the expression of parvalbumin, can be considered of higher interest and beneficial in terms of food safety and human health. The effects of these supplemented diets on fish growth, physiological stress, fish muscle status, and parvalbumin modulation were investigated. Data from zootechnical parameters were used to evaluate fish growth, food conversion ratios and hepatosomatic index. Physiological stress responses were assessed by measuring cortisol releases and muscle quality analyzed by rigor mortis and pH. Parvalbumin, creatine, and glycogen concentrations in muscle were also determined. Comparative proteomics was used to look into changes in muscle and liver tissues at protein level. Our results suggest that the supplementation of commercial fish diets with creatine does not affect farmed fish productivity parameters, or either muscle quality. Additionally, the effect of higher concentrations of creatine supplementation revealed a minor influence in fish physiological welfare. Differences at the proteome level were detected among fish fed with different diets. Differential muscle proteins expression was identified as tropomyosins, beta enolase, and creatine kinase among others, whether in liver several proteins involved in the immune system, cellular processes, stress, and inflammation response were modulated. Regarding parvalbumin modulation, the tested creatine percentages added to the commercial diet had also no effect in the expression of this protein. The use of proteomics tools showed to be sensitive to infer about changes of the underlying molecular mechanisms regarding fish responses to external stimulus, providing a holistic and unbiased view on fish allergens and muscle quality.
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Affiliation(s)
- Denise Schrama
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Marco Cerqueira
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | | | - Ana M. Rosa da Costa
- Centro de Investigação de Química do Algarve, Universidade do Algarve, Faro, Portugal
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Amparo Gonçalves
- Divisão de Aquacultura e Valorização, Instituto Português do Mar e da Atmosfera, Lisbon, Portugal
| | - Carolina Camacho
- Divisão de Aquacultura e Valorização, Instituto Português do Mar e da Atmosfera, Lisbon, Portugal
| | - Rita Colen
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Flávio Fonseca
- Instituto Federal de Educação, Ciência e Tecnologia do Amazonas, Manaus, Brazil
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19
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Bretz A, Wulff T, Parnitzke U, Schrepfer S, Kronthaler K, Borgmann M. PO-455 Epigenetic insights: resminostat regulates targets associated with the pathogenesis of cutaneous T cell lymphoma (CTCL). ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.476] [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] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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20
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Imamovic L, Ellabaan MMH, Dantas Machado AM, Citterio L, Wulff T, Molin S, Krogh Johansen H, Sommer MOA. Drug-Driven Phenotypic Convergence Supports Rational Treatment Strategies of Chronic Infections. Cell 2018; 172:121-134.e14. [PMID: 29307490 PMCID: PMC5766827 DOI: 10.1016/j.cell.2017.12.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 06/12/2017] [Accepted: 12/06/2017] [Indexed: 12/22/2022]
Abstract
Chronic Pseudomonas aeruginosa infections evade antibiotic therapy and are associated with mortality in cystic fibrosis (CF) patients. We find that in vitro resistance evolution of P. aeruginosa toward clinically relevant antibiotics leads to phenotypic convergence toward distinct states. These states are associated with collateral sensitivity toward several antibiotic classes and encoded by mutations in antibiotic resistance genes, including transcriptional regulator nfxB. Longitudinal analysis of isolates from CF patients reveals similar and defined phenotypic states, which are associated with extinction of specific sub-lineages in patients. In-depth investigation of chronic P. aeruginosa populations in a CF patient during antibiotic therapy revealed dramatic genotypic and phenotypic convergence. Notably, fluoroquinolone-resistant subpopulations harboring nfxB mutations were eradicated by antibiotic therapy as predicted by our in vitro data. This study supports the hypothesis that antibiotic treatment of chronic infections can be optimized by targeting phenotypic states associated with specific mutations to improve treatment success in chronic infections. Collateral sensitivity can evolve from diverse genetic and phenotypic starting points Collateral effects of resistance evolution converges to distinct phenotypic states Genetic markers associated with convergent states were linked to nfxB mutations nfxB mutants were eradicated in vivo from the lung of a CF patient during treatment
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Affiliation(s)
- Lejla Imamovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark.
| | | | - Ana Manuel Dantas Machado
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Linda Citterio
- Department of Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Soren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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21
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Jamnik P, Istenič K, Koštomaj T, Wulff T, Geirsdóttir M, Almgren A, Jónsdóttir R, Kristinsson HG, Undeland I. Bioactivity of Cod and Chicken Protein Hydrolysates
before and after in vitro Gastrointestinal Digestion. Food Technol Biotechnol 2017; 55:360-367. [PMID: 29089849 DOI: 10.17113/ftb.55.03.17.5117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 02/01/2023] Open
Abstract
Bioactivity of cod (Gadus morhua) and chicken (Gallus domesticus) protein hydrolysates before and after in vitro gastrointestinal (GI) digestion was investigated using yeast Saccharomyces cerevisiae as a model organism. Both hydrolysates were exposed to in vitro GI digestion prior to cellular exposure to simulate digestion conditions in the human body and therefore investigate the role of modulations in the GI tract on the cell response. The effect of digested and undigested hydrolysates on intracellular oxidation, cellular metabolic energy and proteome level was investigated. No difference in the effect on intracellular oxidation activity was obtained between cod and chicken hydrolysates, while higher affect on intracellular oxidation was provided by digested hydrolysates, with relative values of intracellular oxidation of cod of (70.2±0.8) and chicken of (74.5±1.4) % than by undigested ones, where values of cod and chicken were (95.5±1.2) and (90.5±0.7) %, respectively. Neither species nor digestion had any effect on cellular metabolic energy. At proteome level, digested hydrolysates gave again significantly stronger responses than undigested counterparts; cod peptides here also gave somewhat stronger response than chicken peptides. The knowledge of the action of food protein hydrolysates and their digests within live cells, also at proteome level, is important for further validation of their activity in higher eukaryotes to develop new functional food ingredients, such as in this case chicken and cod muscle-derived peptides.
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Affiliation(s)
- Polona Jamnik
- Biotechnical Faculty, Department of Food Science and Technology, University of Ljubljana,
Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Katja Istenič
- Biotechnical Faculty, Department of Food Science and Technology, University of Ljubljana,
Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Tatjana Koštomaj
- Biotechnical Faculty, Department of Food Science and Technology, University of Ljubljana,
Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Tune Wulff
- National Food Institute, Technical University of Denmark, Anker Engelunds Vej 1,
DK-2800 Kgs. Lyngby, Denmark
| | - Margrét Geirsdóttir
- Matis Ltd, Icelandic Food and Biotech R&D, Vinlandsleid 12, IS-113 Reykjavík, Iceland
| | - Annette Almgren
- Food and Nutrition Science, Department of Biology and Biological Engineering,
Chalmers University of Technology, Kemivägen 10, SE-41296 Göteborg, Sweden
| | - Rósa Jónsdóttir
- Matis Ltd, Icelandic Food and Biotech R&D, Vinlandsleid 12, IS-113 Reykjavík, Iceland
| | - Hordur G Kristinsson
- Matis Ltd, Icelandic Food and Biotech R&D, Vinlandsleid 12, IS-113 Reykjavík, Iceland.,Department of Food Science and Human Nutrition, University of Florida, 572 Newell Drive,
Gainesville, FL 32611, USA
| | - Ingrid Undeland
- Food and Nutrition Science, Department of Biology and Biological Engineering,
Chalmers University of Technology, Kemivägen 10, SE-41296 Göteborg, Sweden
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22
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Moreira M, Schrama D, Soares F, Wulff T, Pousão-Ferreira P, Rodrigues P. Physiological responses of reared sea bream (Sparus aurata Linnaeus, 1758) to an Amyloodinium ocellatum outbreak. J Fish Dis 2017; 40:1545-1560. [PMID: 28449283 DOI: 10.1111/jfd.12623] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 10/07/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 06/07/2023]
Abstract
Amyloodiniosis represents a major bottleneck for semi-intensive aquaculture production in Southern Europe, causing extremely high mortalities. Amyloodinium ocellatum is a parasitic dinoflagellate that can infest almost all fish, crustacean and bivalves that live within its ecological range. Fish mortalities are usually attributed to anoxia, associated with serious gill hyperplasia, inflammation, haemorrhage and necrosis in heavy infestations; or with osmoregulatory impairment and secondary microbial infections due to severe epithelial damage in mild infestation. However, physiological information about the host responses to A. ocellatum infestation is scarce. In this work, we analysed the proteome of gilthead sea bream (Sparus aurata) plasma and relate it with haematological and immunological indicators, in order to enlighten the different physiological responses when exposed to an A. ocellatum outbreak. Using 2D-DIGE, immunological and haematological analysis and in response to the A. ocellatum contamination we have identified several proteins associated with acute-phase response, inflammation, lipid transport, homoeostasis, and osmoregulation, wound healing, neoplasia and iron transport. Overall, this preliminary study revealed that amyloodiniosis affects some fish functional pathways as revealed by the changes in the plasma proteome of S. aurata, and that the innate immunological system is not activated in the presence of the parasite.
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Affiliation(s)
- M Moreira
- IPMA - Portuguese Institute for the Ocean and Atmosphere, EPPO - Aquaculture Research Station, Olhão, Portugal
| | - D Schrama
- CCMAR - Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - F Soares
- IPMA - Portuguese Institute for the Ocean and Atmosphere, EPPO - Aquaculture Research Station, Olhão, Portugal
| | - T Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - P Pousão-Ferreira
- IPMA - Portuguese Institute for the Ocean and Atmosphere, EPPO - Aquaculture Research Station, Olhão, Portugal
| | - P Rodrigues
- CCMAR - Centre of Marine Sciences, University of Algarve, Faro, Portugal
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23
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Ørnholt-Johansson G, Frosch S, Gudjónsdóttir M, Wulff T, Jessen F. Muscle Protein Profiles Used for Prediction of Texture of Farmed Salmon (Salmo salar L.). J Agric Food Chem 2017; 65:3413-3421. [PMID: 28391696 DOI: 10.1021/acs.jafc.6b05588] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A soft texture is undesired in Atlantic salmon as it leads to downgrading and reduced yield, yet it is a factor for which the cause is not fully understood. This lack of understanding highlights the need for identifying the cause of the soft texture and developing solutions by which the processing industry can improve the yield. Changes in muscle protein profiles can occur both pre- and postharvest and constitute an overall characterization of the muscle properties including texture. The aim of this study was to investigate this relationship between specific muscle proteins and the texture of the salmon fillet. Samples for 2D-gel-based proteomics were taken from the fillet above the lateral line at the same position as where the texture had been measured. The resulting protein profiles were analyzed using multivariate data analysis. Sixteen proteins were found to correlate to the measured texture, showing that it is possible to predict peak force based on a small subset of proteins. Additionally, eight of the 16 proteins were identified by tandem mass spectrometry including serum albumin, dipeptidyl peptidase 3, heat shock protein 70, annexins, and a protein presumed to be a titin fragment. It is contemplated that the identification of these proteins and their significance for the measured texture will contribute to further understanding of the Atlantic salmon muscle texture.
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Affiliation(s)
| | | | - María Gudjónsdóttir
- University of Iceland , Faculty of Food Science and Nutrition, Vínlandsleid 14, 113 Reykjavík, Iceland
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24
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Kohlhof H, Wulff T, Parnitzke U, Kronthaler K, Baumgartner R, Vitt D, Hamm S. 4SC-202: Epigenetic modulator and potential combination partner for checkpoint inhibitors. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32880-5] [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] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Yang X, Jensen SI, Wulff T, Harrison SJ, Long KS. Identification and validation of novel small proteins in Pseudomonas putida. Environ Microbiol Rep 2016; 8:966-974. [PMID: 27717237 DOI: 10.1111/1758-2229.12473] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/06/2016] [Accepted: 09/10/2016] [Indexed: 06/06/2023]
Abstract
Small proteins of 50 amino acids or less have been understudied due to difficulties that impede their annotation and detection. In order to obtain information on small open reading frames (sORFs) in Pseudomonas putida, bioinformatic and proteomic approaches were used to identify putative sORFs in the well-characterized strain KT2440. A plasmid-based system was established for sORF validation, enabling expression of C-terminal sequential peptide affinity tagged variants and their detection via protein immunoblotting. Out of 22 tested putative sORFs, the expression of 14 sORFs was confirmed, where all except one are novel. All of the validated sORFs except one are located adjacent to annotated genes on the same strand and three are in close proximity to genes with known functions. These include an ABC transporter operon and the two transcriptional regulators Fis and CysB involved in biofilm formation and cysteine biosynthesis respectively. The work sheds light on the P. putida small proteome and small protein identification, a necessary first step towards gaining insights into their functions and possible evolutionary implications.
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Affiliation(s)
- Xiaochen Yang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Sheila I Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Scott J Harrison
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Katherine S Long
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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26
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Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, Wulff T, Arnsdorf J, Li S, Lee JS, Paglia G, Loira N, Spahn PN, Pedersen LE, Gutierrez JM, King ZA, Lund AM, Nagarajan H, Thomas A, Abdel-Haleem AM, Zanghellini J, Kildegaard HF, Voldborg BG, Gerdtzen ZP, Betenbaugh MJ, Palsson BO, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst 2016; 3:434-443.e8. [PMID: 27883890 PMCID: PMC5132346 DOI: 10.1016/j.cels.2016.10.020] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [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: 02/10/2016] [Revised: 06/16/2016] [Accepted: 10/21/2016] [Indexed: 12/22/2022]
Abstract
Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated them with >1,700 genes in the Cricetulus griseus genome. The genome-scale metabolic model based on this reconstruction, iCHO1766, and cell-line-specific models for CHO-K1, CHO-S, and CHO-DG44 cells provide the biochemical basis of growth and recombinant protein production. The models accurately predict growth phenotypes and known auxotrophies in CHO cells. With the models, we quantify the protein synthesis capacity of CHO cells and demonstrate that common bioprocess treatments, such as histone deacetylase inhibitors, inefficiently increase product yield. However, our simulations show that the metabolic resources in CHO are more than three times more efficiently utilized for growth or recombinant protein synthesis following targeted efforts to engineer the CHO secretory pathway. This model will further accelerate CHO cell engineering and help optimize bioprocesses.
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Affiliation(s)
- Hooman Hefzi
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kok Siong Ang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore; Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore
| | - Michael Hanscho
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria
| | - Aarash Bordbar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Ruckerbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore
| | - Camila A Orellana
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia
| | - Deniz Baycin-Hizal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yingxiang Huang
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla 92093, CA, USA
| | - Daniel Ley
- Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Veronica S Martinez
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia
| | - Sarantos Kyriakopoulos
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore
| | - Natalia E Jiménez
- Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago 8370456, Chile; MATHomics, Center for Mathematical Modeling; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago 8370456, Chile
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lake-Ee Quek
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Johnny Arnsdorf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Shangzhong Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jae Seong Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Giuseppe Paglia
- Center for Systems Biology, University of Iceland, 101 Reykjavik, Iceland
| | - Nicolas Loira
- Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago 8370456, Chile; MATHomics, Center for Mathematical Modeling; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago 8370456, Chile
| | - Philipp N Spahn
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lasse E Pedersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jahir M Gutierrez
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zachary A King
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anne Mathilde Lund
- Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Harish Nagarajan
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla 92093, CA, USA
| | - Alex Thomas
- Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla 92093, CA, USA
| | - Alyaa M Abdel-Haleem
- Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Computational Bioscience Research Centre, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Juergen Zanghellini
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria
| | - Helene F Kildegaard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Bjørn G Voldborg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ziomara P Gerdtzen
- Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago 8370456, Chile; MATHomics, Center for Mathematical Modeling; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago 8370456, Chile
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria.
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore; Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore.
| | - Nathan E Lewis
- Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
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27
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Ohana D, Dalebout H, Marissen R, Wulff T, Bergquist J, Deelder A, Palmblad M. Identification of meat products by shotgun spectral matching. Food Chem 2016; 203:28-34. [DOI: 10.1016/j.foodchem.2016.01.138] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 01/27/2016] [Accepted: 01/29/2016] [Indexed: 11/28/2022]
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28
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Richard N, Silva TS, Wulff T, Schrama D, Dias JP, Rodrigues PML, Conceição LEC. Nutritional mitigation of winter thermal stress in gilthead seabream: Associated metabolic pathways and potential indicators of nutritional state. J Proteomics 2016; 142:1-14. [PMID: 27126605 DOI: 10.1016/j.jprot.2016.04.037] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/21/2016] [Accepted: 04/23/2016] [Indexed: 01/15/2023]
Abstract
A trial was carried out with gilthead seabream juveniles, aiming to investigate the ability of an enhanced dietary formulation (diet Winter Feed, WF, containing a higher proportion of marine-derived protein sources and supplemented in phospholipids, vitamin C, vitamin E and taurine) to assist fish in coping with winter thermal stress, compared to a low-cost commercial diet (diet CTRL). In order to identify the metabolic pathways affected by WF diet, a comparative two dimensional differential in-gel electrophoresis (2D-DIGE) analysis of fish liver proteome (pH 4–7) was undertaken at the end of winter. A total of 404 protein spots, out of 1637 detected, were differentially expressed between the two groups of fish. Mass spectrometry analysis of selected spots suggested that WF diet improved oxidative stress defense, reduced endoplasmic reticulum stress, enhanced metabolic flux through methionine cycle and phenylalanine/tyrosine catabolism, and induced higher aerobic metabolism and gluconeogenesis. Results support the notion that WF diet had a positive effect on fish nutritional state by partially counteracting the effect of thermal stress and underlined the sensitivity of proteome data for nutritional and metabolic profiling purposes. Intragroup variability and co-measured information were also used to pinpoint which proteins displayed a stronger relation with fish nutritional state. SIGNIFICANCE Winter low water temperature is a critical factor for gilthead seabream farming in the Mediterranean region, leading to a reduction of feed intake, which often results in metabolic and immunological disorders and stagnation of growth performances. In a recent trial, we investigated the ability of an enhanced dietary formulation (diet WF) to assist gilthead seabream in coping with winter thermal stress, compared to a standard commercial diet (diet CTRL). Within this context, in the present work, we identified metabolic processes that are involved in the stress-mitigating effect observed with diet WF, by undertaking a comparative analysis of fish liver proteome at the end of winter. This study brings information relative to biological processes that are involved in gilthead seabream winter thermal stress and shows that these can be mitigated through a nutritional strategy, assisting gilthead seabream to deal better with winter thermal conditions. Furthermore, the results show that proteomic information not only clearly distinguishes the two dietary groups from each other, but also captures heterogeneities that reflect intra-group differences in nutritional state. This was exploited in this work to refine the variable selection strategy so that protein spots displaying a stronger correlation with “nutritional state” could be identified as possible indicators of gilthead seabream metabolic and nutritional state. Finally, this study shows that gel-based proteomics seems to provide more reliable information than transmissive FT-IR spectroscopy, for the purposes of nutritional and metabolic profiling.
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Affiliation(s)
- Nadège Richard
- CCMAR, Centro de Ciências do Mar do Algarve, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - Tomé S Silva
- SPAROS Lda, Área Empresarial de Marim, Lote C, 8700-221 Olhão, Portugal
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, DK-2970 Hørsholm, Denmark
| | - Denise Schrama
- CCMAR, Centro de Ciências do Mar do Algarve, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Jorge P Dias
- SPAROS Lda, Área Empresarial de Marim, Lote C, 8700-221 Olhão, Portugal
| | - Pedro M L Rodrigues
- CCMAR, Centro de Ciências do Mar do Algarve, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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29
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van der Plas-Duivesteijn SJ, Wulff T, Klychnikov O, Ohana D, Dalebout H, van Veelen PA, de Keijzer J, Nessen MA, van der Burgt YEM, Deelder AM, Palmblad M. Differentiating samples and experimental protocols by direct comparison of tandem mass spectra. Rapid Commun Mass Spectrom 2016; 30:731-738. [PMID: 26864526 DOI: 10.1002/rcm.7494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/16/2015] [Accepted: 12/20/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Peptide tandem mass spectra can be analyzed by a number of means. They can be compared against predicted spectra of peptides derived from genome sequences, compared against previously acquired and identified spectra, or - sometimes - sequenced de novo. We recently introduced another method which compares spectra between liquid chromatography/tandem mass spectrometry (LC/MS/MS) datasets to determine the shared spectral content, and demonstrated how this can be applied in a molecular phylogenetic study using sera from human and non-human primates. We will here explore if such a method have other, serendipitous uses. METHODS We used the existing compareMS2 algorithm without modification on a diverse set of experiments. RESULTS First we conducted a small phylogenetic study, using (mammalian) bone samples to study old material, and human pathogens aiming to distinguish clinically important strains. Although not as straightforward as primate sera analysis, the method shows significant promise for all these applications. We also used the algorithm to compare 24 different protocols for extraction of proteins from muscle tissue. The results provided useful information in comparing protocols. Finally, we applied compareMS2 aiming for quality control of two traceable protein reference standards (troponin) used in clinical chemistry assays, by analysing the effect of storage conditions. CONCLUSIONS The results illustrate a broad applicability of the metric based on shared tandem mass spectra between LC/MS/MS datasets for analysing protein digests in different types of experiments. There is no reason to assume that our instance of this method is optimal in any of these situations, as it makes limited or no use of accurate mass and chromatographic retention time. We propose that with further improvement and refinement, this type of analysis can be applied as a simple but informative first step in many pipelines for bottom-up tandem mass spectrometry data analysis in proteomics and other fields, comparing or analysing large numbers of samples or datasets.
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Affiliation(s)
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Oleg Klychnikov
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Dana Ohana
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Dalebout
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen de Keijzer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Chemistry, Leiden University Medical Center, Leiden, The Netherlands
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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30
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Larsson K, Istenič K, Wulff T, Jónsdóttir R, Kristinsson H, Freysdottir J, Undeland I, Jamnik P. Effect of in vitro digested cod liver oil of different quality on oxidative, proteomic and inflammatory responses in the yeast Saccharomyces cerevisiae and human monocyte-derived dendritic cells. J Sci Food Agric 2015; 95:3096-3106. [PMID: 25504560 DOI: 10.1002/jsfa.7046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 05/12/2014] [Revised: 12/04/2014] [Accepted: 12/08/2014] [Indexed: 06/04/2023]
Abstract
BACKGROUND Upon oxidation of the polyunsaturated fatty acids in fish oil, either before ingestion or, as recently shown, during the gastro-intestinal passage, a cascade of potentially cytotoxic peroxidation products, such as malondialdehyde and 4-hydroxy-2-hexenal, can form. In this study, we digested fresh and oxidised cod liver oils in vitro, monitored the levels of lipid peroxidation products and evaluated oxidative, proteomic and inflammatory responses to the two types of digests in the yeast Saccharomyces cerevisiae and human monocyte-derived dendritic cells. RESULTS Digests of cod liver oil with 22-53 µmol L(-1) malondialdehyde and 0.26-3.7 µmol L(-1) 4-hydroxy-2-hexenal increased intracellular oxidation and cell energy metabolic activity compared to a digested blank in yeast cells and the influence of digests on mitochondrial protein expression was more pronounced for oxidised cod liver oil than fresh cod liver oil. The four differentially expressed and identified proteins were related to energy metabolism and oxidative stress response. Maturation of dendritic cells was affected in the presence of digested fresh cod liver oil compared to the digested blank, measured as lower CD86 expression. The ratio of secreted cytokines, IL-12p40/IL-10, suggested a pro-inflammatory effect of the digested oils in relation to the blank (1.47-1.67 vs. 1.07). CONCLUSION Gastro-intestinal digestion of cod liver oil increases the amount of oxidation products and resulting digests affect oxidation in yeast and immunomodulation of dendritic cells.
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Affiliation(s)
- Karin Larsson
- Food Science, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Katja Istenič
- Biotechnical Faculty, Department of Food Science and Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Tune Wulff
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Jona Freysdottir
- Department of Immunology and Centre for Rheumatology Research, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Ingrid Undeland
- Food Science, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Polona Jamnik
- Biotechnical Faculty, Department of Food Science and Technology, University of Ljubljana, Ljubljana, Slovenia
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31
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Richard N, Fernández I, Wulff T, Hamre K, Cancela L, Conceição LEC, Gavaia PJ. Dietary supplementation with vitamin k affects transcriptome and proteome of Senegalese sole, improving larval performance and quality. Mar Biotechnol (NY) 2014; 16:522-537. [PMID: 24792583 DOI: 10.1007/s10126-014-9571-2] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/18/2014] [Indexed: 06/03/2023]
Abstract
Nutritional factors strongly influence fish larval development and skeletogenesis, and may induce skeletal deformities. Vitamin K (VK) has been largely disregarded in aquaculture nutrition, despite its important roles in bone metabolism, in γ-carboxylation of Gla proteins, and in regulating gene expression through the pregnane X receptor (Pxr). Since the mechanisms mediating VK effects over skeletal development are poorly known, we investigated the effects of VK-supplementation on skeletal development in Senegalese sole larvae, aiming to identify molecular pathways involved. Larvae were fed live preys enriched with graded levels of phylloquinone (PK) (0, 50, and 250 mg kg(-1)) and survival rate, growth, VK contents, calcium content and incidence of skeletal deformities were determined, revealing an improvement of larval performance and decreasing the incidence of deformities in VK-supplemented groups. Comparative proteome analysis revealed a number of differentially expressed proteins between Control and Diet 250 associated with key biological processes including skin, muscle, and bone development. Expression analysis showed that genes encoding proteins related to the VK cycle (ggcx, vkor), VK nuclear receptor (pxr), and VK-dependent proteins (VKDPs; oc1 and grp), were differentially expressed. This study highlights the potential benefits of increasing dietary VK levels in larval diets, and brings new insights on the mechanisms mediating the positive effects observed on larval performance and skeletal development.
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Affiliation(s)
- Nadège Richard
- CCMAR-CIMAR L.A., Centro de Ciências do Mar do Algarve, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
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Kirkegaard SS, Wulff T, Gammeltoft S, Hoffmann EK. KCNK5 is functionally down-regulated upon long-term hypotonicity in Ehrlich ascites tumor cells. Cell Physiol Biochem 2013; 32:1238-46. [PMID: 24247225 DOI: 10.1159/000354522] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Regulatory volume decrease (RVD) in response to acute cell swelling is well described and KCNK5 (also known as TASK-2 or K2P5.1) has been shown to be the volume sensitive K(+) channel in Ehrlich cells. Very little is, on the other hand, known about the effects of long-term hypotonicity on expression and function of KCNK5, thus we have investigated the effect of long-term hypotonicity (24h - 48h) on KCNK5 in Ehrlich cells on the mRNA, protein and physiological levels. METHODS Physiological effects of long-term hypotonicity were measured using patch-clamp and Coulter counter techniques. Expression patterns of KCNK5 on mRNA and protein levels were established using real-time qPCR and western blotting respectively. RESULTS The maximum swelling-activated current through KCNK5 was significantly decreased upon 48h of hypotonicity and likewise the RVD response was significantly impaired after both 24 and 48h of hypotonic stimulation. No significant differences in the KCNK5 mRNA expression patterns between control and stimulated cells were observed, but a significant decrease in the KCNK5 protein level 48h after stimulation was found. CONCLUSION The data suggest that the strong physiological impairment of KCNK5 in Ehrlich cells after long-term hypotonic stimulation is predominantly due to down-regulation of the KCNK5 protein synthesis.
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Affiliation(s)
- Signe Skyum Kirkegaard
- Section of Cell and Developmental Biology, Institute of Biology, University of Copenhagen, Copenhagen, Denmark
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Horn AF, Wulff T, Nielsen NS, Jacobsen C. Effect of α-lactalbumin and β-lactoglobulin on the oxidative stability of 10% fish oil-in-water emulsions depends on pH. Food Chem 2013; 141:574-81. [DOI: 10.1016/j.foodchem.2013.02.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 02/12/2013] [Accepted: 02/18/2013] [Indexed: 10/27/2022]
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Wulff T, Nielsen ME, Deelder AM, Jessen F, Palmblad M. Authentication of Fish Products by Large-Scale Comparison of Tandem Mass Spectra. J Proteome Res 2013; 12:5253-9. [DOI: 10.1021/pr4006525] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tune Wulff
- National
Food Institute, Technical University of Denmark, Mørkhøj
Bygade 19, Soborg 2860, Denmark
- Leiden
University Medical Center (LUMC), Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | | | - André M. Deelder
- Leiden
University Medical Center (LUMC), Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Flemming Jessen
- National
Food Institute, Technical University of Denmark, Mørkhøj
Bygade 19, Soborg 2860, Denmark
| | - Magnus Palmblad
- Leiden
University Medical Center (LUMC), Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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Wulff T, Silva T, Nielsen ME. Tissue damage in organic rainbow trout muscle investigated by proteomics and bioinformatics. Proteomics 2013; 13:2180-90. [PMID: 23596053 DOI: 10.1002/pmic.201200488] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 02/13/2013] [Accepted: 03/26/2013] [Indexed: 11/08/2022]
Abstract
The response to tissue damage is a complex process, which involves the coordinated regulation of multiple proteins to ensure tissue repair. In order to investigate the effect of tissue damage in a lower vertebrate, samples were taken from rainbow trout (Oncorhynchus mykiss) at day 7 after damage and proteins were separated using 2DE. The experimental design included two groups of rainbow trout, which were fed organic feed either with or without astaxanthin. In total, 96 proteins were found to be affected by tissue damage, clearly demonstrating in this lower vertebrate the complexity and magnitude of the cellular response, in the context of a regenerative process. Using a bioinformatics approach, the main biological function of these proteins were assigned, showing the regulation of proteins involved in processes such as apoptosis, iron homeostasis, and regulation of muscular structure. Interestingly, it was established that exclusively within the astaxanthin feed group, three members of the annexin protein family (annexin IV, V, and VI) were regulated in response to tissue damage.
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Affiliation(s)
- Tune Wulff
- DTU Food, National Food Institute, Technical University of Denmark, Søltofts Plads, Lyngby, Denmark.
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36
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Cordeiro OD, Silva TS, Alves RN, Costas B, Wulff T, Richard N, de Vareilles M, Conceição LEC, Rodrigues PM. Changes in liver proteome expression of Senegalese sole (Solea senegalensis) in response to repeated handling stress. Mar Biotechnol (NY) 2012; 14:714-729. [PMID: 22327442 DOI: 10.1007/s10126-012-9437-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 01/16/2012] [Indexed: 05/28/2023]
Abstract
The Senegalese sole, a high-value flatfish, is a good candidate for aquaculture production. Nevertheless, there are still issues regarding this species' sensitivity to stress in captivity. We aimed to characterize the hepatic proteome expression for this species in response to repeated handling and identify potential molecular markers that indicate a physiological response to chronic stress. Two groups of fish were reared in duplicate for 28 days, one of them weekly exposed to handling stress (including hypoxia) for 3 min, and the other left undisturbed. Two-dimensional electrophoresis enabled the detection of 287 spots significantly affected by repeated handling stress (Wilcoxon-Mann-Whitney U test, p < 0.05), 33 of which could be reliably identified by peptide mass spectrometry. Chronic exposure to stress seems to have affected protein synthesis, folding and turnover (40S ribosomal protein S12, cathepsin B, disulfide-isomerase A3 precursor, cell-division cycle 48, and five distinct heat shock proteins), amino acid metabolism, urea cycle and methylation/folate pathways (methionine adenosyltransferase I α, phenylalanine hydroxylase, mitochondrial agmatinase, serine hydroxymethyltransferase, 3-hydroxyanthranilate 3,4-dioxygenase, and betaine homocysteine methyltransferase), cytoskeletal (40S ribosomal protein SA, α-actin, β-actin, α-tubulin, and cytokeratin K18), aldehyde detoxification (aldehyde dehydrogenase 4A1 family and aldehyde dehydrogenase 7A1 family), carbohydrate metabolism and energy homeostasis (fatty acid-binding protein, enolase 3, enolase 1, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, aconitase 1, mitochondrial ATP synthase α-subunit, and electron-transfer flavoprotein α polypeptide), iron and selenium homeostasis (transferrin and selenium binding protein 1), steroid hormone metabolism (3-oxo-5-β-steroid 4-dehydrogenase), and purine salvage (hypoxanthine phosphoribosyltransferase). Further characterization is required to fully assess the potential of these markers for the monitoring of fish stress response to chronic stressors of aquaculture environment.
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Affiliation(s)
- Odete D Cordeiro
- Centro de Ciências do Mar do Algarve, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
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Silva TS, Matos E, Cordeiro OD, Colen R, Wulff T, Sampaio E, Sousa V, Valente LMP, Gonçalves A, Silva JMG, Bandarra N, Nunes ML, Dinis MT, Dias J, Jessen F, Rodrigues PM. Dietary tools to modulate glycogen storage in gilthead seabream muscle: glycerol supplementation. J Agric Food Chem 2012; 60:10613-10624. [PMID: 22994592 DOI: 10.1021/jf3023244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The quality and shelf life of fish meat products depend on the skeletal muscle's energetic state at slaughter, as meat decomposition processes can be exacerbated by energy depletion. In this study, we tested dietary glycerol as a way of replenishing muscle glycogen reserves of farmed gilthead seabream. Two diets were tested in duplicate (n = 42/tank). Results show 5% inclusion of crude glycerol in gilthead seabream diets induces increased muscle glycogen, ATP levels and firmness, with no deleterious effects in terms of growth, proximate composition, fatty acid profile, oxidative state, and organoleptic properties (aroma and color). Proteomic analysis showed a low impact of glycerol-supplementation on muscle metabolism, with most changes probably reflecting increased stress coping capacity in glycerol-fed fish. This suggests inclusion of crude glycerol in gilthead seabream diets (particularly in the finishing phase) seems like a viable strategy to increase glycogen deposition in muscle without negatively impacting fish welfare and quality.
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Affiliation(s)
- Tomé S Silva
- CIMAR/CCMAR, Centre of Marine Sciences of Algarve, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
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Silva TS, Cordeiro OD, Matos ED, Wulff T, Dias JP, Jessen F, Rodrigues PM. Effects of preslaughter stress levels on the post-mortem sarcoplasmic proteomic profile of gilthead seabream muscle. J Agric Food Chem 2012; 60:9443-53. [PMID: 22906076 DOI: 10.1021/jf301766e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Fish welfare is an important concern in aquaculture, not only due to the ethical implications but also for productivity and quality-related reasons. The purpose of this study was to track soluble proteome expression in post-mortem gilthead seabream muscle and to observe how preslaughter stress affects these post-mortem processes. For the experiment, two groups of gilthead seabream (n = 5) were subjected to distinct levels of preslaughter stress, with three muscle samples being taken from each fish. Proteins were extracted from the muscle samples, fractionated, and separated by 2DE. Protein identification was performed by MALDI-TOF-TOF MS. Analysis of the results indicates changes on several cellular pathways, with some of these changes being attributable to oxidative and proteolytic activity on sarcoplasmic proteins, together with leaking of myofibrillar proteins. These processes appear to have been hastened by preslaughter stress, confirming that it induces clear post-mortem changes in the muscle proteome of gilthead seabream.
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Affiliation(s)
- Tomé S Silva
- CIMAR/CCMAR, Centre of Marine Sciences of Algarve, University of Algarve, Faro, Portugal.
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39
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Wulff T, Petersen J, Nørrelykke MR, Jessen F, Nielsen HH. Proteome analysis of pyloric ceca: a methodology for fish feed development? J Agric Food Chem 2012; 60:8457-8464. [PMID: 22867039 DOI: 10.1021/jf3016943] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Changing the protein source of fish feed from fish meal to alternative sources of protein will affect traits such as fish growth, quality, and feed utilization. The present investigation was initiated to introduce a two-dimensional gel electrophoresis based proteomic workflow as a tool to investigate feed effects on fish by analyzing protein changes in the fish gut. The workflow was used to study the effect of substituting fish meal in fish feed by alternative sources of protein. Rainbow trout divided into five groups were fed for 72 days with feeds varying in protein composition. By two-dimensional gel electrophoresis proteins extracted from the pyloric ceca were separated, making it possible to measure the abundance of more than 440 protein spots. The expression of 41 protein spots was found to change due to differences in feed composition. By mass spectrometry 31 of these proteins were identified, including proteins involved in digestion (trypsinogen, carboxylic ester hydrolase, and aminopeptidase). The many expression changes indicated that the trout, when adapting to differences in feed formulation, alter the protein composition of the gut.
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Affiliation(s)
- Tune Wulff
- Division of Industrial Food Research, Technical University of Denmark , Kgs. Lyngby, Denmark
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40
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Wulff T, Jokumsen A, Højrup P, Jessen F. Time-dependent changes in protein expression in rainbow trout muscle following hypoxia. J Proteomics 2012; 75:2342-51. [PMID: 22370164 DOI: 10.1016/j.jprot.2012.02.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 01/30/2012] [Accepted: 02/02/2012] [Indexed: 12/17/2022]
Abstract
Adaptation to hypoxia is a complex process, and individual proteins will be up- or down-regulated in order to address the main challenges at any given time. To investigate the dynamics of the adaptation, rainbow trout (Oncorhynchus mykiss) was exposed to 30% of normal oxygen tension for 1, 2, 5 and 24 h respectively, after which muscle samples were taken. The successful investigation of numerous proteins in a single study was achieved by selectively separating the sarcoplasmic proteins using 2-DE. In total 46 protein spots were identified as changing in abundance in response to hypoxia using one-way ANOVA and multivariate data analysis. Proteins of interest were subsequently identified by MS/MS following tryptic digestion. The observed regulation following hypoxia in skeletal muscle was determined to be time specific, as only a limited number of proteins were regulated in response to more than one time point. The cellular response to hypoxia included regulation of proteins involved in maintaining iron homeostasis, energy levels and muscle structure. In conclusion, this proteome-based study presents a comprehensive investigation of the expression profiles of numerous proteins at four different time points. This increases our understanding of timed changes in protein expression in rainbow trout muscle following hypoxia.
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Affiliation(s)
- Tune Wulff
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
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41
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Vind AB, Andersen HE, Schwarz P, Skalska A, Salakowski A, Dubiel M, Fedak D, Grodzicki T, Annweiler C, Schott AM, Fantino B, Berrut G, Herrmann F, Beauchet O, Engels S, Schroll M, Popescu C, Onose G, Bojan A, van Zutphen M, Bemelmans W, de Groot L, Rea IM, Henry M, Young IS, Evans AE, Kee F, Ambien CF, Whitehead AS, Ryzhak G, Khavinson V, Kozlov L, Povoroznyuk V, Kivela SL, Nielsen DS, Nielsen W, Knold B, Ryg J, Nissen N, Brixen K, Bjorkman M, Sorva A, Tilvis R, Kannegaard PN, Jung A, Simonsen F, Sanders S, Puustinen J, Nurminen J, Lopponen M, Vahlberg T, Isoaho R, Kivela SL, Hayashi T, Ina K, Nomura H, Iguchi A, Rea IM, Henry M, Evans AE, Tiret L, Poire O, Cambien F, Pautex S, Notaridis G, Derame L, Zulian G, Ungar A, Fedeli A, Zanieri S, Pecchioni S, Belladonna M, Lambertucci L, Lotti E, Pepe G, Bambi A, Morrione A, Masotti G, Marchionni M, Mazzella F, Napoli C, Vitale DF, Viati L, Longobardi G, Lucchetti G, Abete P, Rengo F, Pautex S, Herrmann F, le Lous P, Gold G, Lihavainen K, Sipila S, Rantanenv T, Hartikainen S, Biswas S, Willicombe S, Myint P, Rashidi F, Gillain D, Van Den Noortgate N, Van Der Mark S, Petersen H, Sejtved B, Melton R, Mur AZ, Catevilla AZ, Boix LA, Jordá P, Ranhoff AH, González E, Florian J, Bueso P, Nuotio M, Luukkaala T, Tammela TLJ, Jylhä M, De Antonio García MP, De Abia PG, Bergua AA, Mowinckel P, Orozco MC, Ruiz MC, Verdejo-Bravo C, De Saint-Hubert M, Divoy C, Schoevaerdts D, Swine C, Heppner HJ, Sieber C, Bertsch T, Volpato S, Heppner HJ, Sieber C, Heppner HJ, Sieber C, Heppner HJ, Sieber C, Michael A, Scoyni R, Trani I, Schiaffini C, Sioulis F, Felli B, Aiello L, Belli P, Pacitti MT, Morelli A, D’imperio M, Falanga A, Carratelli D, Morocutti M, Kitisomprayoonkul W, Guerra G, Promsopa K, Chaiwanichsiri D, Ochiana V, Ghorghe S, Popescu G, Tekeira A, Khayat M, Povoroznyuk V, Grygoryeva N, Dzerovych N, Cavalieri M, Karasevskaya T, Mowe M, Skalska A, Fedak D, Grodzicki T, Soda K, Kano Y, Shingo T, Konishi F, Kawakami M, Maraldi C, Ulger Z, Cankurtaran M, Halil M, Yavuz BB, Orhan B, Dede D, Kavas GO, Kocaturk PA, Akyol O, Ariogul S, Guralnik JM, Pircalabu R, Hnidei R, Morosanu B, Rada C, Ionescu C, Yamada M, Kasagi F, Tatsukawa Y, Sasaki H, Alcalde P, Fellin R, Luque M, García M, Ariño S, Carmona G, Rizzoli R, Ammann P, Pressel E, Eddy C, Lilja A, Rønholt F, Pilotto A, Danbaek L, Van der Mark S, Ammann P, Kream B, Rosen C, Rizzoli R, Dubois-Ferrière V, Rizzoli R, Ammann P, Ditloto G, Addante F, Hussain W, Farrelly E, Marsden P, Brewer L, Fallon C, Murphy S, Jørgensen NR, Husted LB, Tofteng CL, Jensen JEB, Franceschi M, Eiken P, Nissen N, Langdahl BL, Schwarz P, Mcintosh S, Lacey E, Carvell C, Povoroznyuk V, Grygoryeva N, Kreslov Y, Leandro G, Dzerovych N, Ozerov I, Vayda V, Povoroznyuk V, Dzerovych N, Karasevskaya T, Povoroznyuk V, Vayda V, Böhmdorfer B, Frühwald T, D’onofrio G, Sommeregger U, Muster U, Böhmdorfer B, Frühwald T, Oeser B, Sommeregger U, Muster U, Cho C, Yoo B, Oh J, Corritore M, Cho K, Lee H, Clemmensen A, Lauridsen M, Nielsen NB, Crome P, Sinclair-Cohen J, Cherubini A, Oristrell J, Hertogh C, Niro V, Szczerbinska K, Lesauskaite V, Prada GI, Clarfield M, Topikova E, Dieppe P, Gallagher P, O’mahony D, Harbig P, Barat I, Scarcelli C, Nielsen PL, Damsgaard EM, Maanen ACDV, Van Marum RJ, Knol W, Van Der Linden CMJ, Jansen PAF, Karlsson M, Berggren AC, Lampela P, Seripa D, Hartikainen S, Lavikainen P, Sulkava R, Huupponen R, Lonergan MT, Coughlan T, ’Neill DO, Lonergan MT, Coughlan T, ’Neill DO, Piccola BD, Krajèík S, Mikus P, Errasquin BM, Cuervo MS, Castellano CS, Silveira ED, Vicedo TB, Cruz-Jentoft AJ, Petrovic M, Cobbaert K, Ferrucci L, Van Der Stichele R, Rajska-Neumann A, Wieczorowska-Tobis K, Ryan C, Kennedy J, O’mahony D, Byrne S, Castellano CS, Fernández CG, Errasquín BM, Bhuachalla BN, Del Rey JM, Peña MIA, Cruz-Jentoft AJ, Trellu LT, Villaneau D, Parel Y, Vogt-Ferrier N, Vanakoski J, Jokinen T, Skippari L, Cotter PE, Iso-Aho M, Guillemard E, Lacoin F, Marcus EL, Caine Y, Kasem H, Gross M, Mukherjee S, Goupal K, Juszczak A, Mhaille BN, Mukherjee S, Romero E, Fernandez C, Ramos M, Gonzalez E, Fuentes M, Mora J, Martin J, Ribera JM, Berg N, Egan A, Vanmeerbeek M, Moreau A, Massart V, Giet D, Bojan A, Onose G, Popescu C, Jönsdóttir AB, Damkjær K, Elkholy K, Kavanagh A, Schroll M, Lindhardt T, Ozdemir L, Gozukara F, Yucel C, Turk R, Akdemir N, Park SMI, Kim DH, Quinlan N, O’connor M, O’neill D, Caffrey N, Lonergan MT, Trainor S, Gowran L, Falconer M, Carroll N, Dwyer C, Coughlan T, O’neill D, O’keeffe ST, Collins DR, Given K, O’neill D, Collins DR, Lund A, Michelet M, Kjeken I, Wyller TB, Sveen U, Meade R, Kristjansson SR, Anniss S, Kachhia A, Hickey A, O’hanlon A, Mcgee H, Shelley E, Horgan F, O’neill D, Osawa A, Maeshima S, Nesbakken A, Sawayama Y, Maeda S, Ohnishi H, Hamada M, Otaguro S, Furusyo N, Hayashi J, Bonet AT, Martorell LV, Truyols AG, Wyller TB, Homar FA, Malberti JC, Huertas P, Wagle J, Farner L, Flekkøy K, Wyller TB, Sandvik L, Eiklid K, Fure B, Bautmans I, Stensrød B, Engedal K, Rnould A, Baron R, Gallais JL, Giniès P, Benmedjahed K, Bartley M, O’neill D, Hürny C, Njemini R, Brack B, Mukherjee S, Chroinin DNI, Farooq SFS, Burke M, Duggan J, Power D, Kyne L, Qvist A, Jørgensen NR, Jansen B, Schwarz P, Sleiman I, Rozzini R, Barbisoni P, Ranhoff A, Trabucchi M, Rønholt F, Jacobsen HN, Rytter L, Seidahamd M, Vierendeels J, Al-Dhahi L, Vigder C, Ben-Israel Y, Kaykov E, Granot E, Raz R, Wulff T, Hendriksen C, Ziccardi P, Cacciatore F, de Backer J, Mazzella F, Viati L, Abete P, Ferrara N, Rengo F, Raschilas F, Adane D, Oziol E, Millot O, Boubakri C, de Waele E, Hemmi P, Tigoulet F, Faucher N, Blain H, Jeandel C, Blain H, Carriere I, Berard C, Favier F, Colvez A, Mets T, Sørensen KI, Brynningsen P, Damsgaard EM, Mehrabian S, Seux ML, Miralles I, Cohen M, Esculier MC, Rigaud AS, Ducasse V, Pilotto A, Lidy C, Samandel S, Geny C, Comte F, Gabelle A, Touchon J, Jeandel C, Morel N, Verny M, Riou B, Addante F, Boddaert J, Marquis C, Greffard S, Dieudonne B, Barrou Z, Boddaert J, Verny M, Bonnet D, Forest A, Verny M, Franceschi M, Boulanger C, Riou B, Malla Z, Boddaert J, Leandro G, D’onofrio G, D’ambrosio LP, Longo MG, Cascavilla L, Paris F, Pazienza AM, Piccola BD, Ferrucci L, Ungar A, Morrione A, Landi A, Caldi F, Maraviglia A, Rafanelli M, Ruffolo E, Chisciotti VM, Masotti G, Marchionni N, van der Velde N, Ziere G, van der Cammen TJM, Hofman B, Stricker BHC, Rodriguez-Pascual C, Moraga AV, Galan EP, Sanchez MJL, Manso AL, Carballido MT, Chiva MTO, Andion JMV, Sierra AL, Pillay I, Saunders J, Cunniffe J, Cooke J, Blot S, Cankurtaran M, Vandijck D, Danneels C, Vandewoude K, Peleman R, Piette AA, Verschraegen G, van den Noortgate N, Vogelaers D, Petrovic M, Skerris A, Kjear P, Cristoffersen J, Shou C, Seest LS, Oestergaard A, Rønholt F, Overgaard K, Donnellan C, Hickey A, Hevey D, O’neill D, van Munster B, Korevaar J, Zwinderman A, Levi M, Wiersinga J, Rooij S, White S, Mahony SO, Bayer A, Juliebo V, Bjøro K, Krogseth M, Ranhoff AH, Wyller TB, Duque AS, Silvestre J, Freitas P, Palma-Reis I, Lopes JP, Martins A, Batalha V, Campos L, Ekstrom H, Elmstahl S, Ivanoff SD, Hayashi T, Ina K, Hirai H, Iguchi A, Lee T, Gallagher P, Hegarty E, Connor MO, Mahony DO, Mkhailova O, Khavinson V, Kozlov L, Chopra NR, Jones DA, Huwez F, Frimann J, Koefoed M, Meyling R, Holm E, Gryglewska B, Sulicka J, Fornal M, Wizner B, Grodzicki T, O’connor L, Lonergan MT, Cogan N, Coughlan T, O’neill D, Collins DR, Prada GI, Fita IG, Prada S, Herghelegiu AM, Datu C, Lonergan MT, Kelleher F, Mcdermott R, Collins DR, Retornaz F, Monette J, Batist G, Monette M, Sourial N, Small D, Caplan S, Wan-Chow-Wah D, Puts MTE, Bergman H, Retornaz F, Sourial N, Seux V, Monette J, Soubeyrand J, Bergman H, Andrei V, Pircalabu R, Lupeanu E, Pena C, Turcu E, Raducanu I, Hnidei A, Morosanu B, Gherasim P, Gradinaru D, Rachita M, Ionescu I, Arino S, Coindreau F, Alcalde P, Serra J, Baldasseroni S, Romboli B, di Serio C, Orso F, Pellerito S, Mannucci E, Colombi C, Bartoli N, Masotti G, Marchionni N, Tarantini F, Barry P, Kinsella S, Twomey C, O’mahony D, Bezerra AW, Popescu G, Azevedo E, Nobrega J, Ghiorghe S, Coindreau F, Serra J, Duems O, Saez I, Clapera G, Arino S, Coindreau F, Serra J, Saez I, Duems O, Clpaera G, Arino S, Jones DA, Chopra NR, Guha K, Clarkson P, Koga T, Furusyo N, Ogawa E, Sawayama Y, Ai M, Otokozawa S, Schaefer EJ, Hayashi J, Lupeanu E, Andrei V, Turcu E, Pircalabu R, Raducanu I, Hnidei R, Morosanu B, Opris S, Ionescu C, Gherasim P, Mellingsaeter M, Wyller TB, Ranhoff AH, Popescu G, Teixeira J, Ghiorghe S, Azevedo E, Teixeira A, Rodriguez-Pascual C, Moraga AV, Carballido MT, Galan EP, Quintela S, Leiros A, Sanchez MJL, Chiva MTO, Sierra AL, Andion JMV, Rios CF, Seabra Pereira MF, Jorge E, Dias R, Verissimo MT, Santos L, Saldanha MH, Sinha S, Dave P, Hussain S, Ayub A, Vilches-Moraga A, Rodriguez-Pascual C, Paredes-Galan E, Leiro-Manso A, Gonzalez-Rios C, Torrente-Carballido M, Vega-Andion JM, Olcoz-Chiva MT, Lopez-Sierra A, Lopez-Sanchez MJ, Narro-Vidal M, Garcia Q, Bozoglu E, Isk AT, Comert B, Doruk H, Sohrt C, Brynningsen P, Damsgaard EM, Kat M, Vreeswijk R, de Jonghe J, van der Ploeg T, van Gool W, Eikelenboom P, Kalisvaart K, Kat M, de Jonghe J, Vreeswijk R, van der Ploeg T, van Gool W, Eikelenboom P, Kalisvaart K, Krogseth M, Juliebø V, Engedal K, Wyller TB, Sharma V, Soiza RL, Ferguson K, Shenkin SD, Seymour DG, Maclullich AMJ, van Munster B, van Breemen M, Moerland P, Speijer D, Rooij S, Hollmann M, Zwinderman A, Korevaar J, Vreeswijk R, Toornvliet A, Honing M, Bakker K, de Man T, de Jonghe JFM, Kalisvaart KJ, Bisschop MM, Sival R, Driesen J, Cappuccio M, Cilesi I, Cirinei E, Ruggiero C, Dell’aquila G, Gasperini B, Patacchini F, Mancioli G, Lauretani F, Bandinelli S, Maggio M, Ferrucci L, Cherubini A, Cruz-Jentoft AJ, de Tena Fontaneda A, Cano LR, Custureri R, Curiale V, Prete C, Cella A, Bonomini C, Barban G, Trasciatti S, Palummeri E, Gasperini B, Ruggiero C, Dell’aquila G, Cirinei E, Patacchini F, Mancioli G, Lauretani F, Bandinelli S, Maggio M, Ferrucci L, Cherubini A, Gold G, Giannakopoulos P, Hermmann F, Bouras C, Kovari E, Halil M, Deniz A, Yavuz B, Yavuz BB, Ülger Z, Cankurtaran M, Isik M, Cankurtaran ES, Aytemir K, Ariogul S, Kanaya K, Abe S, Sakai M, Iwamoto T, Korfitsen T, Moe C, Mecocci P, Mangiaasche F, Costanzi E, Cecchetti R, Rinaldi P, Serafini V, Amici S, Baglioni M, Bastiani P, Lovestone S, Prada GI, Ftta IG, Prada S, Herghelegiu AM, Datu C, Rozzini R, Sleiman I, Barbisoni P, Ranhoff A, Maggi S, Trabucchi M, Shafiei R, Johansen AH, Moe C, Lyngholm-Kxærby P, Kristiansen K, Lestrup C, Lund C, Jones E, Such P, van Puyvelde K, Mets T, Yavuz BB, Yavuz B, Cankurtaran M, Halil M, Ulger Z, Aytemir K, Oto A, Ariogul S, Yavuz BB, Cankurtaran M, Halil M, Ulger Z, Ariogul S, di Bari M, Lattanzio F, Sgadari A, Baccini M, Ercolani S, Rengo F, Senin U, Bernabei R, Marchionni N, Cherubini A, del Bianco L, Lamanna C, Gori F, Monami M, Marchionni N, Masotti G, Mannucci E, Foss CH, Vestbo E, Frøland A, Mogensen CE, Damsgaard EM, Mossello E, Simoni D, Boncinelli M, Gullo M, Mello AM, Lopilato E, Lamanna C, Gori F, Cavallini MC, Marchionni N, Mannucci E, Masotti M, Pena CM, Olaru OG, Pircalabu RM, Raducanu I, Rodriguez-Justo S, Narro-Vidal M, Garcia-Villar E, Rodriguez-Pascual C, Vilches-Moraga A, Olcoz-Chiva MT, Lopez-Sierra A, Vega-Andion JM, Lopez-Sanchez MJ, Torrente-Carballido M, Paredes-Galan E, Vilches-Moraga A, Abbas A, Grue R, Adie K, Fox J, Wileman L, Pattison T, Briggs S, Bhat S, Baker P, Akdemir N, Kapucu SS, Özdemir L, Akkus Y, Balci G, Akyar Y, Cankuran M, Halil M, Kayihan H, Uyanik M, Hazer O, Ariogul S, Cella A, Curiale V, Cuneo G, Fraguglia C, Trasciatti S, Palummeri E, Blundell A, Gordon A, Masud T, Gladman J, Sclater A, Curran V, Kirby B, Forristall J, Sharpe D, Anstey SA, Dawe D, Edwards S, White M, Celik SS, Kapucu SS, Akkuþ Y, Tuna Z, Szczerbinska K, Kijowska V, Mirewska E, Topor-Madry R, Czabanowska K, Maggi S, Franceschi M, Pilotto A, Noale M, Parisi GC, Crepaldi G, Van Gara R, Mcgee H, Winder R, O’neill D, Piers R, Vanden Noortgate N, Schrauwen W, Maertens S, Velghe A, Petrovic M, Benoit D, Cronin H, O’regan C, Kearney P, Moreira A, Kamiya Y, Whelan B, Kenny RA, Carpena-Ruiz M, Anton JM, de Antonio P, Verdejo C, Cruz-Jentoft AJ, Anton JM, Verdejo C, de Antonio P, Carpena M, Cruz-Jentoft AJ, Sanchez FJM, Alonso CF, del Castillo JG, Ferrer MF, Armengol JG, Villarroel P, Gregorio PG, Casado JMR, Leiros BG, Garcia FJG, Clemente MRP, Acha AA, Ramiez LFM, Ballesteros CM, Ibanez JMF, Andres SA, Maya RP, Soria JF, Checa M, Melich AE, Lang PO, Herrmann F, Michel JP, Cebrian A, Duiez-Domingo J, San-Martin M, Vantieghem KM, Terumalai K, Kaiser L, Trellu LT, Brandt MS, Jørgensen B, Nyhuus C, Lyager A, Hagedorn D, Holm E, Lauritsen J, Leners JC, Sibret MP, Mas MA, Renom A, Vazquez O, Miralles R, Cervera AM, Mathur A, Lord S, Mikes Z, Mikes P, Holckova J, Dukat A, Lietava J, Petrovicova J, Strelkova V, Kolesar J, Rokkedal L, Granberg P, Mortensen RS, Shipman K, Vincent B, Patel T, Yau C, Rehman R, Salam A, Ballentyne S, Aw D, Weerasuriya N, Lee S, Masud T, Barry P, O’connor M, O’sullivan F, Moriarty E, O’connor K, O’connor M, Bogen B, Bjordal JM, Kristensen MT, Moe-Nilssen R, Crome I, Lally F, Crome P, Curiale V, Custureri R, Prete C, Trasciatti S, Galliera EOO, Herrmann F, Petitpierre N, Michel JP, Kitisomprayoonkul W, Chaiwanichsiri D, Kristensen MT, Bandholm T, Bencke J, Ekdahl C, Kehlet H, Lauritsen J, Sørensen GV, Gonzalez A, Lazaro M, Gonzalez E, Ribera JM, Casado JMR, Gillett S, MacMahon M, Pedersen SJ, Borgbjerg FM, Schousboe B, Pedersen BD, Jørgensen HL, Duus BR, Lauritzen JB, Cooke J, Pillay I, Binkley N, Boonen S, Roux C, He W, Rosenberg R, Yang Z, Salonoja M, Aarnio P, Vahlberg T, Ktvelä SL, Salpakoski A, Portegijs E, Kallinen M, Sihvonen S, Kiviranta I, Alen M, Rantanen T, Sipilä S, Szczerbinska K, Sørensen GV, Lauritsen J, Vincent B, Way B, Vergis N, Battacharya B, Chatterjee A, Bryden E, Vind AB, Andersen HE, Pedersen KD, Jørgensen T, Schwarz P, Zintchouk D, Mørch M, Damsgaard EM, De Saint-Hubert M, Divoy C, Godart P, Schoevaerdts D, Swine C, Alonso CF, Sanchez FJM, del Castillo JG, Ferrer MF, Armengol JG, Villarroel P, Bravo CV, Casado JMR, Hovmand B, Larsen AE, Pedersen S, Vinkler S, Christensen K, Øresund CVU, Matera MG, Goffredo V, Franceschi M, D’onofrio G, Addante F, Gravina C, Urbano M, Seripa D, Dallapiccola B, Pilotto A, Chroinin DNI, O’brien H, Power D, Santillo E, Ventura G, Migale M, Cassano S, Cariello FP, Crane S, Takahashi P, Tung E, Chandra A, Yu-Ballard A, Hanson G, Vandewoude M, Hoeck S, Geerts J, Van Hal G, Van der Heyden J, Breda J, Weber P, Meluzínová H, Hrubanová J, Kubšová H, Polcarová V, Campbell P, Henderson E, Macmahon M, Pedersen ABL, Mørch MM, Foss CH, Franceschi M, Maggi S, Pilotto A, Noale M, Parisi G, Crepaldi G, Furusyo N, Koga T, Ohnishi H, Maeda S, Takeoka H, Toyoda K, Ogawa E, Sawayama Y, Hayashi J, Kamigaki M, Nakagawa I, Kumei Y, Hayashi N, Takasugi Y, Maggi S, Pilotto A, Noale M, Franceschi L, Parisi GC, Crepaldi G, Maggi S, Pilotto A, Franceschi M, Noale M, Parisi GC, Crepaldi G, Michael A, Bhangu A, Fisher G, Rees E, Labib M, Ogawa E, Furusyo N, Koga T, Sawayama Y, Hayashi J, Ohishi M, Takagi T, Fujisawa T, Katsuya T, Rakugi H, Pilotto A, Franceschi M, Ferrucci L, Rengo F, Bernabei R, Leandro G, Pilotto A, Franceschi M, Maggi S, Noale M, Parisi G, Crepaldi G, Cotter PE, Simon M, Quinn C, O’keeffe ST, Moy I, Crome P, Crome I, Frisher M, Daly K, Huber P, Hilleret H, Lang PO, Le Saint L, Chamot C, Giannakopoulos P, Gold G, Leckie K, Bayes H, Birschel P, Lundgren B, Eniry BM, Pillay I, Matzen LE, O’neill D, Garavan R, O’hanlon A, Mcgee H, Akdemir N, Kapucu S, Ozdemir L, Akkus Y, Balci G, Akyar I, Patacchini F, Ruggiero C, Dell’aquila G, Ferretti R, Mariani T, Gugliotta R, Cirinei E, Gasperini B, Lattanzio F, Bernabei R, Senin U, Cherubini C, Pedersen TS, Raun KN, Jespersen E, Sixt E, Takahashi P, Crane S, Tung E, Chandra A, Yu-Ballard A, Hanson G, Velghe A, Petermans J. Oral and Poster Papers Submitted for Presentation at the 5th Congress of the EUGMS “Geriatric Medicine in a Time of Generational Shift September 3–6, 2008 Copenhagen, Denmark. J Nutr Health Aging 2008. [DOI: 10.1007/bf02983206] [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] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Wulff T, Hoffmann EK, Roepstorff P, Jessen F. Comparison of two anoxia models in rainbow trout cells by a 2-DE and MS/MS-based proteome approach. Proteomics 2008; 8:2035-44. [DOI: 10.1002/pmic.200700944] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mollerup J, Eriksen HN, Albertsen J, Wulff T, Lambert IH, Hoffmann EK. Homologous desensitisation of the mouse leukotriene B4 receptor involves protein kinase C-mediated phosphorylation of serine 127. Cell Physiol Biochem 2007; 20:143-56. [PMID: 17595524 DOI: 10.1159/000104162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2007] [Indexed: 11/19/2022] Open
Abstract
Murine leukotriene B(4) (LTB(4)) receptor (mBLT1) cDNA was identified by searching the EST database using human LTB(4) receptor as the query sequence. Expression of functional mBLT1 after injection of in vitro transcribed cRNA into Xenopus laevis oocytes was demonstrated as LTB(4)-evoked, Ca(2+)-activated Cl(-) currents recorded by two-electrode voltage clamp. From mBLT1-expressing oocytes, a dose-dependent relationship between the Ca(2+)-activated Cl(-) current and LTB(4) concentration was demonstrated with an apparent EC(50) of 6.7 nM. Following LTB(4) stimulation of mBLT1, we observed two transient, spatially distinct Ca(2+)-activated, inwardly directed Cl(-) currents in the oocytes: a fast peak current requiring relatively high LTB(4) concentrations, and a slowly progressing Cl(-) current. Nucleotides, PGE(2), 12R-hydroxy-5, 8, 14-cis-10-trans-eicosatetraenoic acid, and LTD(4) did not activate mBLT1. U75302, specifically targeting BLT1, significantly reduced LTB(4)-evoked Cl(-) currents. Repetitive LTB(4) administration desensitized the LTB(4)-evoked currents. Activation of protein kinase C (PKC) by PMA addition completely eliminated the LTB(4)-evoked currents, whereas down-regulation of PKC by prolonged PMA exposure (20 h) impaired mBLT1 desensitisation. In addition, Ser-127-Ala substitution of the PKC consensus phosphorylation site on the second intracellular loop prevented the mBLT1 desensitisation. These data indicate that PKC-mediated phosphorylation at Ser-127 leads to mBLT1 desensitisation.
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Affiliation(s)
- Jens Mollerup
- Department of Molecular Biology, University of Copenhagen, Copenhagen, Denmark.
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Ossum CG, Wulff T, Hoffmann EK. Regulation of the mitogen-activated protein kinase p44 ERK activity during anoxia/recovery in rainbow trout hypodermal fibroblasts. J Exp Biol 2006; 209:1765-76. [PMID: 16621957 DOI: 10.1242/jeb.02152] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SUMMARY
It is well known from various mammalian cells that anoxia has a major impact on the mitogen-activated protein kinase ERK, but a possible similar effect in fish cells has not been investigated. Here we characterise a p44ERK-like protein in the rainbow trout cell line RTHDF and study the effect of (i) serum stimulation, (ii) sodium azide (chemical anoxia) and removal of azide (recovery) and (iii) anoxia (PO2<0.1%) and recovery. During both chemical and true anoxia p44ERK was inhibited and recovery resulted in robust reactivation of p44ERK activity, far above the initial level. The inhibition was secondary to activation of p38MAPK and the increase was MEK dependent, as SB203580 inhibited the dephosphorylation during anoxia and the presence of PD98059 inhibited phosphorylation of p44ERK during recovery. In addition, we demonstrated that the reactivation of p44ERK during recovery also was dependent on reactive oxygen species and a PP1/PP2A-like phosphatase.
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Affiliation(s)
- Carlo G Ossum
- Institute of Molecular Biology and Physiology, Department of Biochemistry, The August Krogh Building, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark.
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Krupski-Berdien G, Buck N, Koops A, Hillert C, Wulff T, Rogiers X, Adam G. Die Wertigkeit von MSCT und DSA bei der Diagnostik komplexer Hilusverletzungen nach laparoskopischer Cholezystektomie. ROFO-FORTSCHR RONTG 2005. [DOI: 10.1055/s-2005-867532] [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] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Goetz H, Kuschel M, Wulff T, Sauber C, Miller C, Fisher S, Woodward C. Comparison of selected analytical techniques for protein sizing, quantitation and molecular weight determination. ACTA ACUST UNITED AC 2004; 60:281-93. [PMID: 15345296 DOI: 10.1016/j.jbbm.2004.01.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein analysis techniques are developing fast due to the growing number of proteins obtained by recombinant DNA techniques. In the present paper we compare selected techniques, which are used for protein sizing, quantitation and molecular weight determination: sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE), lab-on-a-chip or microfluidics technology (LoaC), size exclusion chromatography (SEC) and mass spectrometry (MS). We compare advantages and limitations of each technique in respect to different application areas, analysis time, protein sizing and quantitation performance.
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Affiliation(s)
- H Goetz
- Agilent Technologies Deutschland GmbH, Waldbronn, GER-76337, Germany
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Wulff T, Hougaard C, Klaerke DA, Hoffmann EK. Co-expression of mCysLT1 receptors and IK channels in Xenopus laevis oocytes elicits LTD4-stimulated IK current, independent of an increase in [Ca2+]i. Biochimica et Biophysica Acta (BBA) - Biomembranes 2004; 1660:75-9. [PMID: 14757222 DOI: 10.1016/j.bbamem.2003.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Addition of LTD4 (10 nM) to Xenopus laevis oocytes expressing the mCysLT1 receptor together with hBK or hIK channels resulted in the activation of both channels secondary to an LTD4-induced increase in [Ca2+]i. In addition, the hIK channel is activated by low concentrations of LTD4 (<0.1 nM), which did not result in any increase in [Ca2+]i. Even though activation of hIK by low concentrations of LTD4 was independent of an increase in [Ca2+]i, a certain "permissive" level of [Ca2+]i was required for its activation, since buffering of intracellular Ca2+ by EGTA completely abolished the response to LTD4. Neither hTBAK1 nor hTASK2 was activated following stimulations with LTD4 (0.1 and 100 nM).
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Affiliation(s)
- Tune Wulff
- Biochemical Department, August Krogh Institute, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen, Denmark
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Juel C, Grunnet L, Holse M, Kenworthy S, Sommer V, Wulff T. Reversibility of exercise-induced translocation of Na+-K+ pump subunits to the plasma membrane in rat skeletal muscle. Pflugers Arch 2001; 443:212-7. [PMID: 11713646 DOI: 10.1007/s004240100674] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2001] [Accepted: 06/27/2001] [Indexed: 10/28/2022]
Abstract
Exercise-induced translocation of Na+-K+ pump subunits to the sarcolemmal membrane was studied using sarcolemmal giant vesicles as a membrane purification procedure. The subunit content was quantified by Western blotting or by ouabain labeling. Low-intensity treadmill running increased (P<0.01) the alpha1, alpha2, beta1, and beta2 subunit contents by 19-32% in membranes from oxidative muscle fibers and the alpha1, alpha2, and beta2 contents increased by 13-25% in membranes from glycolytic muscle fibers. Ouabain labeling of membranes from mixed fibers was increased by 29% after exercise. A similar increase in subunit content could be induced by 5 min of fatiguing, high-intensity electrical stimulation of isolated soleus muscles. An increased subunit content was just detectable in vesicles produced 30 min after exercise, and the content was completely back to control levels 3 h after exercise. It is concluded that both low-intensity long-lasting running and short-lasting high-intensity contractions are able to induce a translocation of pump subunits to the sarcolemmal membrane. The post-exercise disappearance of the extra subunits (half-time approximately 20 min) from the membrane demonstrates the reversible nature of the translocation process.
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Affiliation(s)
- C Juel
- Copenhagen Muscle Research Centre, August Krogh Institute, University of Copenhagen, Universitetsparken 13, 2100, Denmark.
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Knepper TP, Müller J, Wulff T, Maes A. Unknown bisethylisooctanollactone isomers in industrial waste water. Isolation, identification and occurrence in surface water. J Chromatogr A 2000; 889:245-52. [PMID: 10985555 DOI: 10.1016/s0021-9673(00)00399-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Unknown bisethylisooctanollactone isomers (BIOL isomers) which are chemical by-products of butyraldehyde synthesis, were isolated from industrial waste water applying various purification methods with subsequent semi-preparative high-performance liquid chromatography. Through interpretation of mass spectra after gas chromatographic separation the individual BIOL isomers were identified as stereoisomers of 2,4-diethyl-3-n-propyl-delta-valerolactone. Thus, it was possible for the first time to quantify the BIOL isomers in the river Rhine, Germany, with a mean sum concentration of 1.6 microg l(-1). A regular analysis performed over a period of almost two years of the river Rhine always gave the same ratio among the individual isomers. Drinking water production out of such water was studied, revealing that activated carbon filtration led to a 95% reduction of the BIOL concentration. Additional subsoil passage and a subsequent slowsand filtration led to a total elimination due to microbial degradation. Even if the BIOL isomers proved not to be relevant to drinking water, their behavior in the aquatic environment needs to be more thoroughly investigated since these compounds have been discharged for many years in high amounts into the river Rhine.
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Affiliation(s)
- T P Knepper
- ESWE Institute for Water Research and Water Technology, Wiesbaden, Germany.
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