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Bergum OET, Singleton AH, Røst LM, Bodein A, Scott-Boyer MP, Rye MB, Droit A, Bruheim P, Otterlei M. SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated. Front Microbiol 2024; 15:1373344. [PMID: 38596376 PMCID: PMC11002266 DOI: 10.3389/fmicb.2024.1373344] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
The DNA damage inducible SOS response in bacteria serves to increase survival of the species at the cost of mutagenesis. The SOS response first initiates error-free repair followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response. Escherichia coli was grown in batch cultivation in bioreactors to ensure highly controlled conditions, and a low dose of the antibiotic ciprofloxacin was used to activate the SOS response while avoiding extensive cell death. Our results show that expression of genes involved in error-free and error-prone repair were both induced shortly after DNA damage, thus, challenging the established perception that the expression of error-prone repair genes is delayed. By combining transcriptomics and a sub-proteomics approach termed signalomics, we found that the temporal segregation of error-free and error-prone repair is primarily regulated after transcription, supporting the current literature. Furthermore, the heterology index (i.e., the binding affinity of LexA to the SOS box) was correlated to the maximum increase in gene expression and not to the time of induction of SOS genes. Finally, quantification of metabolites revealed increasing pyrimidine pools as a late feature of the SOS response. Our results elucidate how the SOS response is coordinated, showing a rapid transcriptional response and temporal regulation of mutagenesis on the protein and metabolite levels.
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Affiliation(s)
| | - Amanda Holstad Singleton
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Antoine Bodein
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Morten Beck Rye
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Arnaud Droit
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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Dankel SN, Kalleklev TL, Tungland SL, Stafsnes MH, Bruheim P, Aloysius TA, Lindquist C, Skorve J, Nygård OK, Madsen L, Bjørndal B, Sydnes MO, Berge RK. Changes in Plasma Pyruvate and TCA Cycle Metabolites upon Increased Hepatic Fatty Acid Oxidation and Ketogenesis in Male Wistar Rats. Int J Mol Sci 2023; 24:15536. [PMID: 37958519 PMCID: PMC10648824 DOI: 10.3390/ijms242115536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/06/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Altered hepatic mitochondrial fatty acid β-oxidation and associated tricarboxylic acid (TCA) cycle activity contributes to lifestyle-related diseases, and circulating biomarkers reflecting these changes could have disease prognostic value. This study aimed to determine hepatic and systemic changes in TCA-cycle-related metabolites upon the selective pharmacologic enhancement of mitochondrial fatty acid β-oxidation in the liver, and to elucidate the mechanisms and potential markers of hepatic mitochondrial activity. Male Wistar rats were treated with 3-thia fatty acids (e.g., tetradecylthioacetic acid (TTA)), which target mitochondrial biogenesis, mitochondrial fatty acid β-oxidation, and ketogenesis predominantly in the liver. Hepatic and plasma concentrations of TCA cycle intermediates and anaplerotic substrates (LC-MS/MS), plasma ketones (colorimetric assay), and acylcarnitines (HPLC-MS/MS), along with associated TCA-cycle-related gene expression (qPCR) and enzyme activities, were determined. TTA-induced hepatic fatty acid β-oxidation resulted in an increased ratio of plasma ketone bodies/nonesterified fatty acid (NEFA), lower plasma malonyl-CoA levels, and a higher ratio of plasma acetylcarnitine/palmitoylcarnitine (C2/C16). These changes were associated with decreased hepatic and increased plasma pyruvate concentrations, and increased plasma concentrations of succinate, malate, and 2-hydroxyglutarate. Expression of several genes encoding TCA cycle enzymes and the malate-oxoglutarate carrier (Slc25a11), glutamate dehydrogenase (Gdh), and malic enzyme (Mdh1 and Mdh2) were significantly increased. In conclusion, the induction of hepatic mitochondrial fatty acid β-oxidation by 3-thia fatty acids lowered hepatic pyruvate while increasing plasma pyruvate, as well as succinate, malate, and 2-hydroxyglutarate.
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Affiliation(s)
- Simon Nitter Dankel
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
| | - Tine-Lise Kalleklev
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
| | - Siri Lunde Tungland
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, N-4021 Stavanger, Norway (M.O.S.)
| | - Marit Hallvardsdotter Stafsnes
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway (P.B.)
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway (P.B.)
| | - Thomas Aquinas Aloysius
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
| | - Carine Lindquist
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
| | - Jon Skorve
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
| | - Ottar Kjell Nygård
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
- Department of Heart Disease, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Lise Madsen
- Department of Clinical Medicine, University of Bergen, N-5021 Bergen, Norway;
| | - Bodil Bjørndal
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
- Department of Sports, Food and Natural Sciences, Western Norway University of Applied Sciences, N-5020 Bergen, Norway
| | - Magne Olav Sydnes
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, N-4021 Stavanger, Norway (M.O.S.)
| | - Rolf Kristian Berge
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
- Department of Heart Disease, Haukeland University Hospital, N-5021 Bergen, Norway
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Hallan SI, Øvrehus MA, Darshi M, Montemayor D, Langlo KA, Bruheim P, Sharma K. Metabolic Differences in Diabetic Kidney Disease Patients with Normoalbuminuria versus Moderately Increased Albuminuria. Kidney360 2023; 4:1407-1418. [PMID: 37612821 PMCID: PMC10615383 DOI: 10.34067/kid.0000000000000248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Key Points The pathophysiological mechanisms of diabetic kidney disease (DKD) with normal (nonalbuminuric DKD) versus moderately increased albuminuria (A-DKD) are not well-understood. Fatty acid biosynthesis and oxydation, gluconeogenesis, TCA cycle, and glucose-alanine cycle were more disturbed in patients with A-DKD compared with those with nonalbuminuric DKD with identical eGFR. DKD patients with and without microalbuminuria could represent different clinical phenotypes. Background The pathophysiological mechanisms of diabetic kidney disease (DKD) with normal versus moderately increased albuminuria (nonalbuminuric DKD [NA-DKD] and A-DKD) are currently not well-understood and could have implications for diagnosis and treatment. Methods Fourteen patients with NA-DKD with urine albumin–creatinine ratio <3 mg/mmol, 26 patients with A-DKD with albumin–creatinine ratio 3–29 mg/mmol, and 60 age- and sex-matched healthy controls were randomly chosen from a population-based cohort study (Nord-Trøndelag Health Study-3, Norway). Seventy-four organic acids, 21 amino acids, 21 biogenic acids, 40 acylcarnitines, 14 sphingomyelins, and 88 phosphatidylcholines were quantified in urine. One hundred forty-six patients with diabetes from the US-based Chronic Renal Insufficiency Cohort study were used to verify main findings. Results Patients with NA-DKD and A-DKD had similar age, kidney function, diabetes treatment, and other traditional risk factors. Still, partial least-squares discriminant analysis showed strong metabolite-based separation (R2, 0.82; Q2, 0.52), with patients with NA-DKD having a metabolic profile positioned between the profiles of healthy controls and patients with A-DKD. Seventy-five metabolites contributed significantly to separation between NA-DKD and A-DKD (variable importance in projection scores ≥1.0) with propionylcarnitine (C3), phosphatidylcholine C38:4, medium-chained (C8) fatty acid octenedioic acid, and lactic acid as the top metabolites (variable importance in projection scores, 2.7–2.2). Compared with patients with NA-DKD, those with A-DKD had higher levels of short-chained acylcarnitines, higher long-chained fatty acid levels with more double bounds, higher branched-chain amino acid levels, and lower TCA cycle intermediates. The main findings were similar by random forest analysis and in the Chronic Renal Insufficiency Cohort study. Formal enrichment analysis indicated that fatty acid biosynthesis and oxydation, gluconeogenesis, TCA cycle, and glucose-alanine cycle were more disturbed in patients with A-DKD compared with those with NA-DKD with identical eGFR. We also found indications of a Warburg-like effect in patients with A-DKD (i.e. , metabolism of glucose to lactate despite adequate oxygen). Conclusion DKD patients with normoalbuminuria differ substantially in their metabolic disturbances compared with patients with moderately increase albuminuria and could represent different clinical phenotypes.
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Affiliation(s)
- Stein I Hallan
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Nephrology, St. Olav Hospital, Trondheim, Norway
| | | | - Manjula Darshi
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, Texas
| | - Daniel Montemayor
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, Texas
| | - Knut A Langlo
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Nephrology, St. Olav Hospital, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kumar Sharma
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, Texas
- Department of Nephrology, University of Texas Health San Antonio, San Antonio, Texas
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Singleton AH, Bergum OET, Søgaard CK, Røst LM, Olsen CE, Blindheim FH, Ræder SB, Bjørnstad FA, Sundby E, Hoff BH, Bruheim P, Otterlei M. Activation of multiple stress responses in Staphylococcus aureus substantially lowers the minimal inhibitory concentration when combining two novel antibiotic drug candidates. Front Microbiol 2023; 14:1260120. [PMID: 37822747 PMCID: PMC10564113 DOI: 10.3389/fmicb.2023.1260120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023] Open
Abstract
The past few decades have been plagued by an increasing number of infections caused by antibiotic resistant bacteria. To mitigate the rise in untreatable infections, we need new antibiotics with novel targets and drug combinations that reduce resistance development. The novel β-clamp targeting antimicrobial peptide BTP-001 was recently shown to have a strong additive effect in combination with the halogenated pyrrolopyrimidine JK-274. In this study, the molecular basis for this effect was examined by a comprehensive proteomic and metabolomic study of the individual and combined effects on Staphylococcus aureus. We found that JK-274 reduced activation of several TCA cycle enzymes, likely via increasing the cellular nitric oxide stress, and BTP-001 induced oxidative stress in addition to inhibiting replication, translation, and DNA repair processes. Analysis indicated that several proteins linked to stress were only activated in the combination and not in the single treatments. These results suggest that the strong additive effect is due to the activation of multiple stress responses that can only be triggered by the combined effect of the individual mechanisms. Importantly, the combination dose required to eradicate S. aureus was well tolerated and did not affect cell viability of immortalized human keratinocyte cells, suggesting a species-specific response. Our findings demonstrate the potential of JK-274 and BTP-001 as antibiotic drug candidates and warrant further studies.
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Affiliation(s)
- Amanda Holstad Singleton
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Caroline Krogh Søgaard
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Cecilie Elisabeth Olsen
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Fredrik Heen Blindheim
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Synnøve Brandt Ræder
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Frithjof A. Bjørnstad
- Department of Materials Science and Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Eirik Sundby
- Department of Materials Science and Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Bård Helge Hoff
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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Scheffold J, Bruheim P, Kjesbu JS, Jang M. Serum-free alginate-C2C12 cells microcapsule as a model of alternative animal protein source. Front Nutr 2023; 10:1184178. [PMID: 37252232 PMCID: PMC10213942 DOI: 10.3389/fnut.2023.1184178] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 04/27/2023] [Indexed: 05/31/2023] Open
Abstract
Due to the climate change crisis, and environmental impacts of the traditional meat sector, the production of artificial animal protein based on in vitro cell culture technology is proposed as an alternative. Furthermore, since traditional animal serum-supplemented cultures pose scientific challenges such as batch variation and contamination risks, artificial animal protein cultures are currently in urgent need of not only serum-free cultures, but also microcarrier culture systems for scalability. However, serum-free microcarrier-based culture system for the differentiation of muscle cells is not available to date. Therefore, we established an edible alginate microcapsules culture system for the differentiation of C2C12 cells in serum-free conditions. Furthermore, metabolites related to central carbon metabolism were profiled based on targeted metabolomics using mass spectrometry. The C2C12 cells cultured in alginate microcapsules displayed high viability throughout 7 days and successfully differentiated within 4 days in serum and serum-free cultures except for AIM-V cultures, which was confirmed by CK activity and MHC immunostaining. Lastly, to the best of our knowledge, this is the first report to compare metabolite profiles between monolayer and alginate microcapsule culture systems. Alginate microcapsule culture showed higher levels of intracellular glycolysis and TCA cycle intermediates, lactate, and the contribution of essential amino acids compared to the monolayer culture. We believe our serum-free alginate microcapsule culture system is adaptable to different species of muscle cells and contributes to future food technology as a proof of concept for the scalability of alternative animal protein source production.
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Jaramillo-Jimenez A, Giil LM, Germán Borda M, Tovar-Rios DA, Andre Kristiansen K, Bruheim P, Aarsland D, Barreto GE, Kristian Berge R. Serum TCA cycle metabolites in Lewy Bodies Dementia and Alzheimer's Disease: Network analysis and cognitive prognosis. Mitochondrion 2023; 71:17-25. [PMID: 37172667 DOI: 10.1016/j.mito.2023.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 03/27/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
Abnormalities in the Tri-Carboxylic-Acid (TCA) cycle have been documented in dementia. Through network analysis, TCA cycle metabolites could indirectly reflect known dementia-related abnormalities in biochemical pathways, and key metabolites might be associated with prognosis. This study analyzed TCA cycle metabolites as predictors of cognitive decline in a mild dementia cohort and explored potential interactions with the diagnosis of Lewy Body Dementia (LBD) or Alzheimer's Disease (AD) and APOE-ε4 genotype. We included 145 mild dementia patients (LBD = 59; AD = 86). Serum TCA cycle metabolites were analyzed at baseline, and partial correlation networks were conducted. Cognitive performance was measured annually over 5-years with the Mini-mental State Examination. Longitudinal mixed-effects Tobit models evaluated each baseline metabolite as a predictor of 5-years cognitive decline. APOE-ε4 and diagnosis interactions were explored. Results showed comparable metabolite concentrations in LBD and AD. Multiple testing corrected networks showed larger coefficients for a negative correlation between pyruvate - succinate and positive correlations between fumarate - malate and citrate - Isocitrate in both LBD and AD. In the total sample, adjusted mixed models showed significant associations between baseline citrate concentration and longitudinal MMSE scores. In APOE-ε4 carriers, baseline isocitrate predicted MMSE scores. We conclude that, in mild dementia, serum citrate concentrations could be associated with subsequent cognitive decline, as well as isocitrate concentrations in APOE-ε4 carriers. Downregulation of enzymatic activity in the first half of the TCA cycle (decarboxylating dehydrogenases), with upregulation in the latter half (dehydrogenases only), might be indirectly reflected in serum TCA cycle metabolites' networks.
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Affiliation(s)
- Alberto Jaramillo-Jimenez
- Centre for Age-Related Medicine (SESAM), Stavanger University Hospital. Stavanger, Norway; Faculty of Health Sciences, University of Stavanger. Stavanger, Norway; Grupo de Neurociencias de Antioquia, Universidad de Antioquia, School of Medicine. Medellín, Colombia; Semillero de Investigación SINAPSIS, Universidad de Antioquia, School of Medicine. Medellín, Colombia; Semillero de Investigación NeuroCo, Universidad de Antioquia, School of Medicine & School of Engenieering. Medellín, Colombia.
| | - Lasse M Giil
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Miguel Germán Borda
- Centre for Age-Related Medicine (SESAM), Stavanger University Hospital. Stavanger, Norway; Faculty of Health Sciences, University of Stavanger. Stavanger, Norway; Semillero de Neurociencias y Envejecimiento, Ageing Institute, Medical School, Pontificia Universidad Javeriana. Bogotá, Colombia
| | - Diego A Tovar-Rios
- Centre for Age-Related Medicine (SESAM), Stavanger University Hospital. Stavanger, Norway; Faculty of Health Sciences, University of Stavanger. Stavanger, Norway; Universidad Del Valle, Grupo de Investigación en Estadística Aplicada - INFERIR, Faculty of Engineering, Santiago De Cali, Colombia; Universidad Del Valle, Prevención y Control de la Enfermedad Crónica - PRECEC, Faculty of Health, Santiago De Cali, Colombia
| | - Kåre Andre Kristiansen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Dag Aarsland
- Centre for Age-Related Medicine (SESAM), Stavanger University Hospital. Stavanger, Norway; Department of Old Age Psychiatry, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - George E Barreto
- Department of Biological Sciences, University of Limerick, Ireland
| | - Rolf Kristian Berge
- The Lipid Research Group, Department of Clinical Science, University of Bergen, Bergen, Norway
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Rau EM, Aasen IM, Bartosova Z, Bruheim P, Ertesvåg H. Utilizing lipidomics and fatty acid synthase inhibitors to explore lipid accumulation in two thraustochytrid species. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103091] [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: 04/08/2023]
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8
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García-Calvo L, Rane DV, Everson N, Humlebrekk ST, Mathiassen LF, Mæhlum AHM, Malmo J, Bruheim P. Central carbon metabolite profiling reveals vector-associated differences in the recombinant protein production host Escherichia coli BL21. Front Chem Eng 2023. [DOI: 10.3389/fceng.2023.1142226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
The Gram-negative bacterium Escherichia coli is the most widely used host for recombinant protein production, both as an industrial expression platform and as a model system at laboratory scale. The recombinant protein production industry generates proteins with direct applications as biopharmaceuticals and in technological processes central to a plethora of fields. Despite the increasing economic significance of recombinant protein production, and the importance of E. coli as an expression platform and model organism, only few studies have focused on the central carbon metabolic landscape of E. coli during high-level recombinant protein production. In the present work, we applied four targeted CapIC- and LC-MS/MS methods, covering over 60 metabolites, to perform an in-depth metabolite profiling of the effects of high-level recombinant protein production in strains derived from E. coli BL21, carrying XylS/Pm vectors with different characteristics. The mass-spectrometric central carbon metabolite profiling was complemented with the study of growth kinetics and protein production in batch bioreactors. Our work shows the robustness in E. coli central carbon metabolism when introducing increased plasmid copy number, as well as the greater importance of induction of recombinant protein production as a metabolic challenge, especially when strong promoters are used.
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Thorfinnsdottir LB, Bø GH, Booth JA, Bruheim P. Survival of Escherichia coli after high-antibiotic stress is dependent on both the pregrown physiological state and incubation conditions. Front Microbiol 2023; 14:1149978. [PMID: 36970700 PMCID: PMC10036391 DOI: 10.3389/fmicb.2023.1149978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/17/2023] [Indexed: 03/12/2023] Open
Abstract
IntroductionThe survival of bacterial cells exposed to antibiotics depends on the mode of action, the antibiotics concentration, and the duration of treatment. However, it also depends on the physiological state of the cells and the environmental conditions. In addition, bacterial cultures contain sub-populations that can survive high antibiotic concentrations, so-called persisters. Research on persisters is challenging due to multiple mechanisms for their formation and low fractions, down to and below one millionth of the total cell population. Here, we present an improved version of the persister assay used to enumerate the amount of persisters in a cell population.MethodsThe persister assay with high antibiotic stress exposure was performed at both growth supporting and non-supporting conditions. Escherichia coli cells were pregrown to various growth stages in shake flasks and bench-top bioreactors. In addition, the physiological state of E. coli before antibiotic treatment was determined by quantitative mass spectrometry-based metabolite profiling.ResultsSurvival of E. coli strongly depended on whether the persister assay medium supported growth or not. The results were also highly dependent on the type of antibiotic and pregrown physiological state of the cells. Therefore, applying the same conditions is critical for consistent and comparable results. No direct connection was observed between antibiotic efficacy to the metabolic state. This also includes the energetic state (i.e., the intracellular concentration of ATP and the adenylate energy charge), which has earlier been hypothesized to be decisive for persister formation.DiscussionThe study provides guides and suggestions for the design of future experimentation in the research fields of persisters and antibiotic tolerance.
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Affiliation(s)
| | - Gaute Hovde Bø
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - James Alexander Booth
- Department of Microbiology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
- *Correspondence: Per Bruheim,
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10
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Eide M, Goksøyr A, Yadetie F, Gilabert A, Bartosova Z, Frøysa HG, Fallahi S, Zhang X, Blaser N, Jonassen I, Bruheim P, Alendal G, Brun M, Porte C, Karlsen OA. Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod. Front Physiol 2023; 14:1129089. [PMID: 37035678 PMCID: PMC10073473 DOI: 10.3389/fphys.2023.1129089] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/07/2023] [Indexed: 04/11/2023] Open
Abstract
Lipid metabolism is essential in maintaining energy homeostasis in multicellular organisms. In vertebrates, the peroxisome proliferator-activated receptors (PPARs, NR1C) regulate the expression of many genes involved in these processes. Atlantic cod (Gadus morhua) is an important fish species in the North Atlantic ecosystem and in human nutrition, with a highly fatty liver. Here we study the involvement of Atlantic cod Ppar a and b subtypes in systemic regulation of lipid metabolism using two model agonists after in vivo exposure. WY-14,643, a specific PPARA ligand in mammals, activated cod Ppara1 and Ppara2 in vitro. In vivo, WY-14,643 caused a shift in lipid transport both at transcriptional and translational level in cod. However, WY-14,643 induced fewer genes in the fatty acid beta-oxidation pathway compared to that observed in rodents. Although GW501516 serves as a specific PPARB/D ligand in mammals, this compound activated cod Ppara1 and Ppara2 as well as Pparb in vitro. In vivo, it further induced transcription of Ppar target genes and caused changes in lipid composition of liver and plasma. The integrative approach provide a foundation for understanding how Ppars are engaged in regulating lipid metabolism in Atlantic cod physiology. We have shown that WY-14,643 and GW501516 activate Atlantic cod Ppara and Pparb, affect genes in lipid metabolism pathways, and induce changes in the lipid composition in plasma and liver microsomal membranes. Particularly, the combined transcriptomic, proteomics and lipidomics analyses revealed that effects of WY-14,643 on lipid metabolism are similar to what is known in mammalian studies, suggesting conservation of Ppara functions in mediating lipid metabolic processes in fish. The alterations in the lipid profiles observed after Ppar agonist exposure suggest that other chemicals with similar Ppar receptor affinities may cause disturbances in the lipid regulation of fish. Model organism: Atlantic cod (Gadus morhua). LSID: urn:lsid:zoobank.org:act:389BE401-2718-4CF2-BBAE-2E13A97A5E7B. COL Identifier: 6K72F.
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Affiliation(s)
- Marta Eide
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Anders Goksøyr
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- *Correspondence: Anders Goksøyr,
| | - Fekadu Yadetie
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Alejandra Gilabert
- Institute of Environmental Assessment and Water Research, Spanish National Research Council (CSIC), Barcelona, Spain
- Faculty of Science, National Distance Education University (UNED), Madrid, Spain
| | - Zdenka Bartosova
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Håvard G. Frøysa
- Department of Mathematics, University of Bergen, Bergen, Norway
- Institute of Marine Research (IMR), Bergen, Norway
| | - Shirin Fallahi
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Xiaokang Zhang
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Nello Blaser
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Inge Jonassen
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Guttorm Alendal
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Morten Brun
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Cinta Porte
- Institute of Environmental Assessment and Water Research, Spanish National Research Council (CSIC), Barcelona, Spain
| | - Odd André Karlsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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11
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Carracedo S, Lirussi L, Alsøe L, Segers F, Wang C, Bartosova Z, Bohov P, Tekin NB, Kong XY, Esbensen QY, Chen L, Wennerström A, Kroustallaki P, Ceolotto D, Tönjes A, Berge RK, Bruheim P, Wong G, Böttcher Y, Halvorsen B, Nilsen H. SMUG1 regulates fat homeostasis leading to a fatty liver phenotype in mice. DNA Repair (Amst) 2022; 120:103410. [DOI: 10.1016/j.dnarep.2022.103410] [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] [Received: 04/07/2022] [Revised: 08/08/2022] [Accepted: 10/01/2022] [Indexed: 11/25/2022]
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12
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Jang M, Pete ES, Bruheim P. The impact of serum-free culture on HEK293 cells: From the establishment of suspension and adherent serum-free adaptation cultures to the investigation of growth and metabolic profiles. Front Bioeng Biotechnol 2022; 10:964397. [PMID: 36147538 PMCID: PMC9485887 DOI: 10.3389/fbioe.2022.964397] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/12/2022] [Indexed: 12/05/2022] Open
Abstract
Serum-free cultures are preferred for application in clinical cell therapy and facilitate the purification processes of bioproducts, such as vaccines and recombinant proteins. It can replace traditional cell culture - eliminating potential issues posed by animal-derived serum supplementation, such as lot to lot variation and risks of pathogen infection from the host animal. However, adapting cells to serum-free conditions can be challenging and time-consuming, and is cell line and medium dependent. In addition, the knowledge of the impact of serum-free culture on cellular metabolism is limited. Herein, we successfully established serum-free suspension and adherent cultures through two adaptation procedures for HEK293 cells in serum-free Freestyle 293 medium. Furthermore, growth kinetics and intracellular metabolic profiles related to central carbon metabolism were investigated. The entire adaptation procedure took 1 month, and high cell viability (>90%) was maintained throughout. The serum-free adherent culture showed the best growth performance, measured as the highest cell density and growth rate. The largest differences in metabolic profiles were observed between culture modes (adherent vs. suspension), followed by culture medium condition (control growth medium vs. serum-free medium). Metabolic differences related to the adaptation procedures were only seen in suspension cultures. Interestingly, the intracellular itaconate concentration was significantly higher in suspension cells compared to adherent cells. Furthermore, when the cells back-adapted from serum-free to serum-supplemented control medium, their metabolic profiles were immediately reversed, highlighting the effect of extracellular components on metabolic phenotype. This study provides strategies for efficient serum-free cultivation and deeper insights into the cellular responses related to growth and metabolism responses to diverse culture conditions.
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13
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Jang M, Scheffold J, Bruheim P. Isolation and cultivation of primary muscle cells from Lobster (Homarus gammarus). In Vitro Cell Dev Biol Anim 2022; 58:446-451. [PMID: 35829896 DOI: 10.1007/s11626-022-00698-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Mi Jang
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway
| | - Jana Scheffold
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway.
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14
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Røst LM, Louet C, Bruheim P, Flo TH, Gidon A. Pyruvate Supports RET-Dependent Mitochondrial ROS Production to Control Mycobacterium avium Infection in Human Primary Macrophages. Front Immunol 2022; 13:891475. [PMID: 35874747 PMCID: PMC9298545 DOI: 10.3389/fimmu.2022.891475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
Macrophages deploy a variety of antimicrobial programs to contain mycobacterial infection. Upon activation, they undergo extensive metabolic reprogramming to meet an increase in energy demand, but also to support immune effector functions such as secretion of cytokines and antimicrobial activities. Here, we report that mitochondrial import of pyruvate is linked to production of mitochondrial ROS and control of Mycobacterium avium (M. avium) infection in human primary macrophages. Using chemical inhibition, targeted mass spectrometry and single cell image analysis, we showed that macrophages infected with M. avium switch to aerobic glycolysis without any major imbalances in the tricarboxylic acid cycle volume or changes in the energy charge. Instead, we found that pyruvate import contributes to hyperpolarization of mitochondria in infected cells and increases production of mitochondrial reactive oxygen species by the complex I via reverse electron transport, which reduces the macrophage burden of M. avium. While mycobacterial infections are extremely difficult to treat and notoriously resistant to antibiotics, this work stresses out that compounds specifically inducing mitochondrial reactive oxygen species could present themself as valuable adjunct treatments.
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Affiliation(s)
- Lisa Marie Røst
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Claire Louet
- Center of Molecular Inflammation Research (CEMIR), Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Trude Helen Flo
- Center of Molecular Inflammation Research (CEMIR), Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- *Correspondence: Alexandre Gidon, ; Trude Helen Flo,
| | - Alexandre Gidon
- Center of Molecular Inflammation Research (CEMIR), Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- *Correspondence: Alexandre Gidon, ; Trude Helen Flo,
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15
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Kumar K, Bruheim P. Nutrient-depended metabolic switching during batch cultivation of Streptomyces coelicolor explored with absolute quantitative mass spectrometry-based metabolite profiling. 3 Biotech 2022; 12:80. [PMID: 35242495 PMCID: PMC8882213 DOI: 10.1007/s13205-022-03146-x] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/10/2022] [Indexed: 11/27/2022] Open
Abstract
The well-known secondary metabolite-producing bacterium Streptomyces coelicolor is a natural choice for the development of super-hosts optimized for the heterologous expression of antibiotic biosynthetic gene clusters (BGCs). In this study, we used S. coelicolor M145 and its derivative strain M1146 where all active BGCs have been deleted and generated high-resolution quantitative time series metabolite profiles under two cultivation conditions (phosphate and nitrogen limitation to cease growth and trigger secondary metabolism). Five targeted LC-MS/MS-based methods were used to quantify intracellular primary metabolites covering phosphorylated metabolites, amino acids, organic acids, (deoxy) nucleoside/sugar phosphates, Nicotinamide adenine dinucleotide (NAD), and Coenzyme A (CoA). The nitrogen limitation resulted in a sharp decline in respiration and an immediate drop in the cell mass concentration. Intracellularly, a reduction in the level of the metabolites next to α-ketoglutarate in the tricarboxylic acid cycle and a decrease in the NADH pool were among the most prominent adaptation to this nutrient limitation. Phosphate limitation evoked a different adaptation of the metabolite pools as most of the phosphorylated metabolite pools except 6-phosphogluconic acid (6PG) pool were downregulated. 13C-isotope-labeling experiments revealed the simultaneous activity of both glycolysis and gluconeogenesis during the co-utilization of glucose and glutamate. The S. coelicolor M1146 strain had similar time-series metabolite profile dynamics as the parent M145 strain, except for a visibly increased 6PG pool in the stationary phase. In general, the nutrient limitation had a larger effect on the metabolite pool levels than the absence of secondary metabolite production in M1146. This study provides new insight into the primary carbon metabolism and its link to the secondary metabolism which is needed for further optimization of both super-host genotype and cultivation conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03146-x.
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Affiliation(s)
- Kanhaiya Kumar
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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16
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Simensen V, Schulz C, Karlsen E, Bråtelund S, Burgos I, Thorfinnsdottir LB, García-Calvo L, Bruheim P, Almaas E. Experimental determination of Escherichia coli biomass composition for constraint-based metabolic modeling. PLoS One 2022; 17:e0262450. [PMID: 35085271 PMCID: PMC8794083 DOI: 10.1371/journal.pone.0262450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/24/2021] [Indexed: 12/03/2022] Open
Abstract
Genome-scale metabolic models (GEMs) are mathematical representations of metabolism that allow for in silico simulation of metabolic phenotypes and capabilities. A prerequisite for these predictions is an accurate representation of the biomolecular composition of the cell necessary for replication and growth, implemented in GEMs as the so-called biomass objective function (BOF). The BOF contains the metabolic precursors required for synthesis of the cellular macro- and micromolecular constituents (e.g. protein, RNA, DNA), and its composition is highly dependent on the particular organism, strain, and growth condition. Despite its critical role, the BOF is rarely constructed using specific measurements of the modeled organism, drawing the validity of this approach into question. Thus, there is a need to establish robust and reliable protocols for experimental condition-specific biomass determination. Here, we address this challenge by presenting a general pipeline for biomass quantification, evaluating its performance on Escherichia coli K-12 MG1655 sampled during balanced exponential growth under controlled conditions in a batch-fermentor set-up. We significantly improve both the coverage and molecular resolution compared to previously published workflows, quantifying 91.6% of the biomass. Our measurements display great correspondence with previously reported measurements, and we were also able to detect subtle characteristics specific to the particular E. coli strain. Using the modified E. coli GEM iML1515a, we compare the feasible flux ranges of our experimentally determined BOF with the original BOF, finding that the changes in BOF coefficients considerably affect the attainable fluxes at the genome-scale.
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Affiliation(s)
- Vetle Simensen
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Christian Schulz
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Emil Karlsen
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Signe Bråtelund
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Idun Burgos
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Lilja Brekke Thorfinnsdottir
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Laura García-Calvo
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology Department of Public Health and General Practice, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- * E-mail:
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17
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Rau EM, Bartosova Z, Kristiansen KA, Aasen IM, Bruheim P, Ertesvåg H. Overexpression of Two New Acyl-CoA:Diacylglycerol Acyltransferase 2-Like Acyl-CoA:Sterol Acyltransferases Enhanced Squalene Accumulation in Aurantiochytrium limacinum. Front Microbiol 2022; 13:822254. [PMID: 35145505 PMCID: PMC8821962 DOI: 10.3389/fmicb.2022.822254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Thraustochytrids are heterotrophic marine eukaryotes known to accumulate large amounts of triacylglycerols, and they also synthesize terpenoids like carotenoids and squalene, which all have an increasing market demand. However, a more extensive knowledge of the lipid metabolism is needed to develop thraustochytrids for profitable biomanufacturing. In this study, two putative type-2 Acyl-CoA:diacylglycerol acyltransferases (DGAT2) genes of Aurantiochytrium sp. T66, T66ASATa, and T66ASATb, and their homologs in Aurantiochytrium limacinum SR21, AlASATa and AlASATb, were characterized. In A. limacinum SR21, genomic knockout of AlASATb reduced the amount of the steryl esters of palmitic acid, SE (16:0), and docosahexaenoic acid, SE (22:6). The double mutant of AlASATa and AlASATb produced even less of these steryl esters. The expression and overexpression of T66ASATb and AlASATb, respectively, enhanced SE (16:0) and SE (22:6) production more significantly than those of T66ASATa and AlASATa. In contrast, these mutations did not significantly change the level of triacylglycerols or other lipid classes. The results suggest that the four genes encoded proteins possessing acyl-CoA:sterol acyltransferase (ASAT) activity synthesizing both SE (16:0) and SE (22:6), but with the contribution from AlASATb and T66ASATb being more important than that of AlASATa and T66ASATa. Furthermore, the expression and overexpression of T66ASATb and AlASATb enhanced squalene accumulation in SR21 by up to 88%. The discovery highlights the functional diversity of DGAT2-like proteins and provides valuable information on steryl ester and squalene synthesis in thraustochytrids, paving the way to enhance squalene production through metabolic engineering.
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Affiliation(s)
- E-Ming Rau
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Zdenka Bartosova
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Kåre Andre Kristiansen
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Inga Marie Aasen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Helga Ertesvåg
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
- *Correspondence: Helga Ertesvåg,
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18
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Jang M, Scheffold J, Røst LM, Cheon H, Bruheim P. Serum-free cultures of C2C12 cells show different muscle phenotypes which can be estimated by metabolic profiling. Sci Rep 2022; 12:827. [PMID: 35039582 PMCID: PMC8764040 DOI: 10.1038/s41598-022-04804-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022] Open
Abstract
In vitro skeletal muscle cell production is emerging in the field of artificial lab-grown meat as alternative future food. Currently, there is an urgent paradigm shift towards a serum replacement culture system. Surprisingly, little is known about the impact of serum-free culture on skeletal muscle cells to date. Therefore, we performed metabolic profiling of the C2C12 myoblasts and myotubes in serum-free mediums (B27, AIM-V) and compared it with conventional serum supplementation culture. Furthermore, cell morphology, viability, and myogenic differentiation were observed for 7 days of cultivation. Intriguingly, the metabolic difference is more dominant between the cell status than medium effects. In addition, proliferative myoblast showed more distinct metabolic differences than differentiated myotubes in different culture conditions. The intracellular levels of GL3P and UDP-GlcNAc were significantly increased in myotubes versus myoblast. Non-essential amino acids and pyruvate reduction and transamination showed significant differences among serum, B27, and AIM-V cultures. Intracellular metabolite profiles indicated that C2C12 myotubes cultured in serum and B27 had predominant glycolytic and oxidative metabolism, respectively, indicating fast and slow types of muscle confirmed by MHC immunostaining. This work might be helpful to understand the altered metabolism of skeletal muscle cells in serum-free culture and contribute to future artificial meat research work.
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Affiliation(s)
- Mi Jang
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway
| | - Jana Scheffold
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway
| | - Hyejeong Cheon
- PoreLab, Department of Physics, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway.
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Kumar K, Bruheim P. A comparative study at bioprocess and metabolite levels of superhost strain Streptomyces coelicolor M1152 and its derivative M1581 heterologously expressing chloramphenicol biosynthetic gene cluster. Biotechnol Bioeng 2021; 119:145-161. [PMID: 34636422 DOI: 10.1002/bit.27958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/20/2021] [Accepted: 10/03/2021] [Indexed: 11/09/2022]
Abstract
Microbial superhost strains should provide an ideal platform for the efficient homologous or heterologous phenotypic expression of biosynthetic gene clusters (BGCs) of new and novel bioactive molecules. Our aim in the current study was to perform a comparative study at the bioprocess and metabolite levels of the previously designed superhost strain Streptomyces coelicolor M1152 and its derivative strain S. coelicolor M1581 heterologously expressing chloramphenicol BGC. Parent strain M1152 was characterized by a higher specific growth rate, specific CO2 evolution rate, and a higher specific l-glutamate consumption rate as compared with M1581. Intracellular primary central metabolites (nucleoside/sugar phosphates, amino acids, organic acids, and CoAs) were quantified using four targeted LC-MS/MS-based methods. The metabolite pathways in the nonantibiotic producing S. coelicolor host strain were flooded with carbon from both carbon sources, whereas in antibiotic-producing strain, the carbon of l-glutamate seems to be draining out through excreting synthesized antibiotic. The 13 C-isotope-labeling experiments revealed the bidirectionality in the glycolytic pathway and reversibility in the non-oxidative part of PPP even with continuous uptake of d-glucose. The change in the primary metabolites due to the insertion of BGC disclosed a clear linkage between the primary and secondary metabolites.
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Affiliation(s)
- Kanhaiya Kumar
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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20
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Kumar K, Bruheim P. Large dependency of intracellular NAD and CoA pools on cultivation conditions in Saccharomyces cerevisiae. BMC Res Notes 2021; 14:372. [PMID: 34556160 PMCID: PMC8461857 DOI: 10.1186/s13104-021-05783-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/13/2021] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE The objective of this study was to investigate the variation of NAD and CoA metabolite pools in Saccharomyces cerevisiae cultivated under various cultivation conditions. This study complements a previous report on glycolytic, pentose phosphate pathway, tricarboxylic acid cycle, amino acids, and deoxy-/nucleoside phosphate pools determined under the same cultivation conditions. RESULTS S. cerevisiae pellets from batch (four carbohydrate sources) and chemostat (carbon-, nitrogen-, phosphate-limited and a range of dilution rates) bioreactor cultivations were extracted and analyzed with two recently established absolute quantitative liquid chromatography mass spectrometry (LC-MS/MS) methods for NAD and CoA metabolites. Both methods apply 13C internal standard dilution strategy for the enhanced analytical accuracy and precision. Individual metabolite pools were relatively constant for the different growth rates within the same mode of cultivation, but large differences were observed among some of the modes, i.e. NAD metabolites were 10 to 100-fold lower in nitrogen limited chemostats compared to the other modes, and phosphate limited chemostats were characterized with much lower CoA metabolite pools. The results complement the previous results and together provide a comprehensive insight into primary metabolite pools variations at a large range in growth and carbon source consumption rates.
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Affiliation(s)
- Kanhaiya Kumar
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
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21
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Bartosova Z, Gonzalez SV, Voigt A, Bruheim P. High Throughput Semiquantitative UHPSFC-MS/MS Lipid Profiling and Lipid Class Determination. J Chromatogr Sci 2021; 59:670-680. [PMID: 33479755 PMCID: PMC8217741 DOI: 10.1093/chromsci/bmaa121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Indexed: 01/02/2023]
Abstract
High throughput and high-resolution lipid analyses are important for many biological model systems and research questions. This comprises both monitoring at the individual lipid species level and broad lipid classes. Here, we present a nontarget semiquantitative lipidomics workflow based on ultrahigh performance supercritical fluid chromatography (UHPSFC)-mass spectrometry (MS). The optimized chromatographic conditions enable the base-line separation of both nonpolar and polar classes in a single 7-minute run. Ionization efficiencies of lipid classes vary 10folds in magnitude and great care must be taken in a direct interpretation of raw data. Therefore, the inclusion of internal standards or experimentally determined Response factors (RF) are highly recommended for the conversion of raw abundances into (semi) quantitative data. We have deliberately developed an algorithm for automatic semiquantification of lipid classes by RF. The workflow was tested and validated using a bovine liver extract with satisfactory results. The RF corrected data provide a more representative relative lipid class determination, but also the interpretation of individual lipid species should be performed on RF corrected data. In addition, semiquantification can be improved by using internal or also external standards when more accurate quantitative data are of interest but this requires validation for all new sample types. The workflow established greatly extends the potential of nontarget UHPSFC–MS/MS based analysis.
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Affiliation(s)
- Zdenka Bartosova
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim Norway
| | - Susana Villa Gonzalez
- Department of Chemistry, NTNU Norwegian University of Science and Technology, Høgskoleringen 5, N-7491 Trondheim, Norway
| | - André Voigt
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim Norway
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22
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Abdollahi P, Vandsemb EN, Elsaadi S, Røst LM, Yang R, Hjort MA, Andreassen T, Misund K, Slørdahl TS, Rø TB, Sponaas AM, Moestue S, Bruheim P, Børset M. Phosphatase of regenerating liver-3 regulates cancer cell metabolism in multiple myeloma. FASEB J 2021; 35:e21344. [PMID: 33566385 DOI: 10.1096/fj.202001920rr] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/11/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022]
Abstract
Cancer cells often depend on microenvironment signals from molecules such as cytokines for proliferation and metabolic adaptations. PRL-3, a cytokine-induced oncogenic phosphatase, is highly expressed in multiple myeloma cells and associated with poor outcome in this cancer. We studied whether PRL-3 influences metabolism. Cells transduced to express PRL-3 had higher aerobic glycolytic rate, oxidative phosphorylation, and ATP production than the control cells. PRL-3 promoted glucose uptake and lactate excretion, enhanced the levels of proteins regulating glycolysis and enzymes in the serine/glycine synthesis pathway, a side branch of glycolysis. Moreover, mRNAs for these proteins correlated with PRL-3 expression in primary patient myeloma cells. Glycine decarboxylase (GLDC) was the most significantly induced metabolism gene. Forced GLDC downregulation partly counteracted PRL-3-induced aerobic glycolysis, indicating GLDC involvement in a PRL-3-driven Warburg effect. AMPK, HIF-1α, and c-Myc, important metabolic regulators in cancer cells, were not mediators of PRL-3's metabolic effects. A phosphatase-dead PRL-3 mutant, C104S, promoted many of the metabolic changes induced by wild-type PRL-3, arguing that important metabolic effects of PRL-3 are independent of its phosphatase activity. Through this study, PRL-3 emerges as one of the key mediators of metabolic adaptations in multiple myeloma.
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Affiliation(s)
- Pegah Abdollahi
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Laboratory Clinic, St. Olavs University Hospital, Trondheim, Norway
| | - Esten N Vandsemb
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Samah Elsaadi
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lisa M Røst
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rui Yang
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Laboratory Clinic, St. Olavs University Hospital, Trondheim, Norway
| | - Magnus A Hjort
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Children's Clinic, St. Olavs University Hospital, Trondheim, Norway
| | - Trygve Andreassen
- MR Core Facility, Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kristine Misund
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Clinic of Medicine, St. Olavs University Hospital, Trondheim, Norway
| | - Tobias S Slørdahl
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Clinic of Medicine, St. Olavs University Hospital, Trondheim, Norway
| | - Torstein B Rø
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Children's Clinic, St. Olavs University Hospital, Trondheim, Norway
| | - Anne-Marit Sponaas
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Siver Moestue
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Pharmacy, Faculty of Health Sciences, Nord University, Bodø, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Magne Børset
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Immunology and Transfusion Medicine, St. Olavs University Hospital, Trondheim, Norway
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23
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Sumabe BK, Ræder SB, Røst LM, Sharma A, Donkor ES, Mosi L, Duodu S, Bruheim P, Otterlei M. Nucleoside Analogues Are Potent Inducers of Pol V-mediated Mutagenesis. Biomolecules 2021; 11:843. [PMID: 34198819 PMCID: PMC8227612 DOI: 10.3390/biom11060843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/18/2022] Open
Abstract
Drugs targeting DNA and RNA in mammalian cells or viruses can also affect bacteria present in the host and thereby induce the bacterial SOS system. This has the potential to increase mutagenesis and the development of antimicrobial resistance (AMR). Here, we have examined nucleoside analogues (NAs) commonly used in anti-viral and anti-cancer therapies for potential effects on mutagenesis in Escherichia coli, using the rifampicin mutagenicity assay. To further explore the mode of action of the NAs, we applied E. coli deletion mutants, a peptide inhibiting Pol V (APIM-peptide) and metabolome and proteome analyses. Five out of the thirteen NAs examined, including three nucleoside reverse transcriptase inhibitors (NRTIs) and two anti-cancer drugs, increased the mutation frequency in E. coli by more than 25-fold at doses that were within reported plasma concentration range (Pl.CR), but that did not affect bacterial growth. We show that the SOS response is induced and that the increase in mutation frequency is mediated by the TLS polymerase Pol V. Quantitative mass spectrometry-based metabolite profiling did not reveal large changes in nucleoside phosphate or other central carbon metabolite pools, which suggests that the SOS induction is an effect of increased replicative stress. Our results suggest that NAs/NRTIs can contribute to the development of AMR and that drugs inhibiting Pol V can reverse this mutagenesis.
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Affiliation(s)
- Balagra Kasim Sumabe
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway; (B.K.S.); (S.B.R.)
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. BOX LG 54 Accra, Ghana; (L.M.); (S.D.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. BOX LG 54 Accra, Ghana
| | - Synnøve Brandt Ræder
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway; (B.K.S.); (S.B.R.)
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway; (L.M.R.); (P.B.)
| | - Animesh Sharma
- Proteomics and Modomics Experimental Core Facility (PROMEC), NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway;
| | - Eric S. Donkor
- Department of Medical Microbiology, University of Ghana Medical School, P.O. Box 4236 Accra, Ghana;
| | - Lydia Mosi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. BOX LG 54 Accra, Ghana; (L.M.); (S.D.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. BOX LG 54 Accra, Ghana
| | - Samuel Duodu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. BOX LG 54 Accra, Ghana; (L.M.); (S.D.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. BOX LG 54 Accra, Ghana
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway; (L.M.R.); (P.B.)
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway; (B.K.S.); (S.B.R.)
- Clinic of Laboratory medicine, St. Olav University Hospital, NO-7006 Trondheim, Norway
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24
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Rutkis R, Strazdina I, Lasa Z, Bruheim P, Kalnenieks U. Ethanologenesis and respiration in a pyruvate decarboxylase-deficient Zymomonas mobilis. BMC Res Notes 2021; 14:208. [PMID: 34049566 PMCID: PMC8161578 DOI: 10.1186/s13104-021-05625-5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/19/2021] [Indexed: 11/10/2022] Open
Abstract
Objective Zymomonas mobilis is an alpha-proteobacterium with a rapid ethanologenic pathway, involving Entner–Doudoroff (E–D) glycolysis, pyruvate decarboxylase (Pdc) and two alcohol dehydrogenase (ADH) isoenzymes. Pyruvate is the end-product of the E–D pathway and the substrate for Pdc. Construction and study of Pdc-deficient strains is of key importance for Z. mobilis metabolic engineering, because the pyruvate node represents the central branching point, most novel pathways divert from ethanol synthesis. In the present work, we examined the aerobic metabolism of a strain with partly inactivated Pdc. Results Relative to its parent strain the mutant produced more pyruvate. Yet, it also yielded more acetaldehyde, the product of the Pdc reaction and the substrate for ADH, although the bulk ADH activity was similar in both strains, while the Pdc activity in the mutant was reduced by half. Simulations with the kinetic model of Z. mobilis E-D pathway indicated that, for the observed acetaldehyde to ethanol production ratio in the mutant, the ratio between its respiratory NADH oxidase and ADH activities should be significantly higher, than the measured values. Implications of this finding for the directionality of the ADH isoenzyme operation in vivo and interactions between ADH and Pdc are discussed. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05625-5.
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Affiliation(s)
- Reinis Rutkis
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Inese Strazdina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Zane Lasa
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Uldis Kalnenieks
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia.
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25
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Bjune MS, Lindquist C, Hallvardsdotter Stafsnes M, Bjørndal B, Bruheim P, Aloysius TA, Nygård O, Skorve J, Madsen L, Dankel SN, Berge RK. Plasma 3-hydroxyisobutyrate (3-HIB) and methylmalonic acid (MMA) are markers of hepatic mitochondrial fatty acid oxidation in male Wistar rats. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158887. [PMID: 33454435 DOI: 10.1016/j.bbalip.2021.158887] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Discovery of specific markers that reflect altered hepatic fatty acid oxidation could help to detect an individual's risk of fatty liver, type 2 diabetes and cardiovascular disease at an early stage. Lipid and protein metabolism are intimately linked, but our understanding of this crosstalk remains limited. METHODS In male Wistar rats, we used synthetic fatty acid analogues (3-thia fatty acids) as a tool to induce hepatic fatty acid oxidation and mitochondrial biogenesis, to gain new insight into the link between fatty acid oxidation, amino acid metabolism and TCA cycle-related intermediate metabolites in liver and plasma. RESULTS Rats treated with 3-thia fatty acids had 3-fold higher hepatic, but not adipose and skeletal muscle, expression of the thioesterase 3-hydroxyisobutyryl-CoA hydrolase (Hibch), which controls the formation of 3-hydroxyisobutyrate (3-HIB) in the valine degradation pathway. Consequently, 3-thia fatty acid-stimulated hepatic fatty acid oxidation and ketogenesis was accompanied by decreased plasma 3-HIB and increased methylmalonic acid (MMA) concentrations further downstream in BCAA catabolism. The higher plasma MMA corresponded to higher MMA-CoA hydrolase activity and hepatic expression of GTP-specific succinyl-CoA synthase (Suclg2) and succinate dehydrogenase (Sdhb), and lower MMA-CoA mutase activity. Plasma 3-HIB correlated positively to plasma and hepatic concentrations of TAG, plasma total fatty acids, plasma NEFA and insulin/glucose ratio, while the reverse correlations were seen for MMA. CONCLUSION Our study provides new insight into TCA cycle-related metabolic changes associated with altered hepatic fatty acid flux, and identifies 3-HIB and MMA as novel circulating markers reflective of mitochondrial β-oxidation in male Wistar rats.
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Affiliation(s)
| | - Carine Lindquist
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marit Hallvardsdotter Stafsnes
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Bodil Bjørndal
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Thomas A Aloysius
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ottar Nygård
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, Bergen, Norway
| | - Jon Skorve
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Lise Madsen
- Institute of Marine Research, NO-5817 Bergen, Norway
| | - Simon N Dankel
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Rolf Kristian Berge
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, Bergen, Norway.
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26
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Jin Y, Harvey TN, Bartosova Z, Hassani S, Bruheim P, Sandve SR, Vik JO. Diet and Life Stage-Associated Lipidome Remodeling in Atlantic Salmon. J Agric Food Chem 2021; 69:3787-3796. [PMID: 33754702 PMCID: PMC8041299 DOI: 10.1021/acs.jafc.0c07281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/17/2020] [Revised: 03/05/2021] [Accepted: 03/15/2021] [Indexed: 05/07/2023]
Abstract
Salmon is an important source of long-chain highly unsaturated fatty acids (LC-HUFAs) such as 22:6n-3 [docosahexaenoic acid (DHA)]. In the present study, we conducted two identical experiments on salmon in freshwater (FW) and seawater (SW) stages, with a diet switch from fish oil (high in LC-HUFA) to vegetable oil (low in LC-HUFA) and vice versa. Our aim was to investigate the diet and life stage-specific features of lipid uptake (gut), processing (liver), and deposition (muscle). The lipid composition changed much faster in the gut of SW fish relative to FW fish, suggesting that the former had a higher rate of lipid absorption and transport. SW fish also had higher expression of phospholipid synthesis and lipoprotein formation genes in the gut, whereas FW fish had higher expression of lipid synthesis genes in the liver. All phospholipids except PC-44:12 and PE-44:12 were less abundant in SW, suggesting that SW fish have a higher requirement for DHA.
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Affiliation(s)
- Yang Jin
- Center
of Integrative Genetics (CIGENE), Norwegian
University of Life Sciences, 1430 Aas, Norway
| | - Thomas Nelson Harvey
- Center
of Integrative Genetics (CIGENE), Norwegian
University of Life Sciences, 1430 Aas, Norway
| | - Zdenka Bartosova
- Department
of Biotechnology and Food Science, Norwegian
University of Science and Technology, 7491 Trondheim, Norway
| | - Sahar Hassani
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Aas, Norway
| | - Per Bruheim
- Department
of Biotechnology and Food Science, Norwegian
University of Science and Technology, 7491 Trondheim, Norway
| | - Simen Rød Sandve
- Center
of Integrative Genetics (CIGENE), Norwegian
University of Life Sciences, 1430 Aas, Norway
| | - Jon Olav Vik
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Aas, Norway
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27
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Kumar K, Venkatraman V, Bruheim P. Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae. Microb Cell Fact 2021; 20:64. [PMID: 33750414 PMCID: PMC7941957 DOI: 10.1186/s12934-021-01557-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 11/17/2020] [Accepted: 03/01/2021] [Indexed: 11/19/2022] Open
Abstract
Background Saccharomyces cerevisiae is a well-known popular model system for basic biological studies and serves as a host organism for the heterologous production of commercially interesting small molecules and proteins. The central metabolism is at the core to provide building blocks and energy to support growth and survival in normal situations as well as during exogenous stresses and forced heterologous protein production. Here, we present a comprehensive study of intracellular central metabolite pool profiling when growing S. cerevisiae on different carbon sources in batch cultivations and at different growth rates in nutrient-limited glucose chemostats. The latest versions of absolute quantitative mass spectrometry-based metabolite profiling methodology were applied to cover glycolytic and pentose phosphate pathway metabolites, tricarboxylic acid cycle (TCA), complete amino acid, and deoxy-/nucleoside phosphate pools. Results Glutamate, glutamine, alanine, and citrate were the four most abundant metabolites for most conditions tested. The amino acid is the dominant metabolite class even though a marked relative reduction compared to the other metabolite classes was observed for nitrogen and phosphate limited chemostats. Interestingly, glycolytic and pentose phosphate pathway (PPP) metabolites display the largest variation among the cultivation conditions while the nucleoside phosphate pools are more stable and vary within a closer concentration window. The overall trends for glucose and nitrogen-limited chemostats were increased metabolite pools with the increasing growth rate. Next, comparing the chosen chemostat reference growth rate (0.12 h−1, approximate one-fourth of maximal unlimited growth rate) illuminates an interesting pattern: almost all pools are lower in nitrogen and phosphate limited conditions compared to glucose limitation, except for the TCA metabolites citrate, isocitrate and α-ketoglutarate. Conclusions This study provides new knowledge-how the central metabolism is adapting to various cultivations conditions and growth rates which is essential for expanding our understanding of cellular metabolism and the development of improved phenotypes in metabolic engineering. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01557-8.
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Affiliation(s)
- Kanhaiya Kumar
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Vishwesh Venkatraman
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
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28
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Bartosova Z, Ertesvåg H, Nyfløt EL, Kämpe K, Aasen IM, Bruheim P. Combined Metabolome and Lipidome Analyses for In-Depth Characterization of Lipid Accumulation in the DHA Producing Aurantiochytrium sp. T66. Metabolites 2021; 11:metabo11030135. [PMID: 33669117 PMCID: PMC7996494 DOI: 10.3390/metabo11030135] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/19/2022] Open
Abstract
Thraustochytrids are marine heterotrophic microorganisms known for their potential to accumulate docosahexaenoic acid (DHA)-enriched lipids. There have been many attempts to improve thraustochytrid DHA bioprocesses, especially through traditional optimization of cultivation and media conditions. Nevertheless, thraustochytrid-based bioprocesses are still not commercially competitive for high volume-low cost production of DHA. Thus, it is realized that genetic and metabolic engineering strategies are needed for the development of commercially competitive thraustochytrid DHA cell factories. Here, we present an analytical workflow for high resolution phenotyping at metabolite and lipid levels to generate deeper insight into the thraustochytrid physiology, with particular focus on central carbon and redox metabolism. We use time-series sampling during unlimited growth and nitrogen depleted triggering of DHA synthesis and lipid accumulation (LA) to show-case our methodology. The mass spectrometric absolute quantitative metabolite profiling covered glycolytic, pentose phosphate pathway (PPP) and tricarboxylic acid cycle (TCA) metabolites, amino acids, complete (deoxy)nucleoside phosphate pools, CoA and NAD metabolites, while semiquantitative high-resolution supercritical fluid chromatography MS/MS was applied for the lipid profiling. Interestingly, trace amounts of a triacylglycerols (TG) with DHA incorporated in all three acyl positions was detected, while TGs 16:0_16:0_22:6 and 16:0_22:6_22:6 were among the dominant lipid species. The metabolite profiling data indicated that lipid accumulation is not limited by availability of the acyl chain carbon precursor acetyl-CoA nor reducing power (NADPH) but rather points to the TG head group precursor glycerol-3-phosphate as the potential cause at the metabolite level for the gradual decline in lipid production throughout the cultivation. This high-resolution phenotyping provides new knowledge of changes in the central metabolism during growth and LA in thraustochytrids and will guide target selection for metabolic engineering needed for further improvements of this DHA cell factory.
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Affiliation(s)
- Zdenka Bartosova
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Z.B.); (H.E.); (E.L.N.); (K.K.)
| | - Helga Ertesvåg
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Z.B.); (H.E.); (E.L.N.); (K.K.)
| | - Eirin Lishaugen Nyfløt
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Z.B.); (H.E.); (E.L.N.); (K.K.)
| | - Kristoffer Kämpe
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Z.B.); (H.E.); (E.L.N.); (K.K.)
| | - Inga Marie Aasen
- Biotechnology and Nanomedicine, SINTEF Industry, 4730 Trondheim, Norway;
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Z.B.); (H.E.); (E.L.N.); (K.K.)
- Correspondence:
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29
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Skedsmo FS, Espenes A, Tranulis MA, Matiasek K, Gunnes G, Bjerkås I, Moe L, Røed SS, Berendt M, Fredholm M, Rohdin C, Shelton GD, Bruheim P, Stafsnes MH, Bartosova Z, Hermansen LC, Stigen Ø, Jäderlund KH. Impaired NDRG1 functions in Schwann cells cause demyelinating neuropathy in a dog model of Charcot-Marie-Tooth type 4D. Neuromuscul Disord 2020; 31:56-68. [PMID: 33334662 DOI: 10.1016/j.nmd.2020.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 04/17/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 11/25/2022]
Abstract
Mutations in the N-myc downstream-regulated gene 1 (NDRG1) cause degenerative polyneuropathy in ways that are poorly understood. We have investigated Alaskan Malamute dogs with neuropathy caused by a missense mutation in NDRG1. In affected animals, nerve levels of NDRG1 protein were reduced by more than 70% (p< 0.03). Nerve fibers were thinly myelinated, loss of large myelinated fibers was pronounced and teased fiber preparations showed both demyelination and remyelination. Inclusions of filamentous material containing actin were present in adaxonal Schwann cell cytoplasm and Schmidt-Lanterman clefts. This condition strongly resembles the human Charcot-Marie-Tooth type 4D. However, the focally folded myelin with adaxonal infoldings segregating the axon found in this study are ultrastructural changes not described in the human disease. Furthermore, lipidomic analysis revealed a profound loss of peripheral nerve lipids. Our data suggest that the low levels of mutant NDRG1 is insufficient to support Schwann cells in maintaining myelin homeostasis.
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Affiliation(s)
- Fredrik S Skedsmo
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway.
| | - Arild Espenes
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - Michael A Tranulis
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - Kaspar Matiasek
- Section of Clinical & Comparative Neuropathology, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität, Veterinärstr. 13, D-80539 Munich, Germany
| | - Gjermund Gunnes
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - Inge Bjerkås
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - Lars Moe
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - Susan Skogtvedt Røed
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - Mette Berendt
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlægevej 16, 1870 Frederiksberg C, Denmark
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 2, 1870 Frederiksberg C, Denmark
| | - Cecilia Rohdin
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Ultunaalléen 5A, 756 51 Uppsala, Sweden; Anicura Albano Small Animal Hospital, Rinkebyvägen 21, 182 36 Danderyd, Sweden
| | - G Diane Shelton
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0709, United States of America
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Sem Sælands vei 6, 7034 Trondheim, Norway
| | - Marit H Stafsnes
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Sem Sælands vei 6, 7034 Trondheim, Norway
| | - Zdenka Bartosova
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Sem Sælands vei 6, 7034 Trondheim, Norway
| | - Lene C Hermansen
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Universitetstunet 3, 1433 Ås, Norway
| | - Øyvind Stigen
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - Karin H Jäderlund
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway
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30
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Fontana D, Mauri M, Renso R, Docci M, Crespiatico I, Røst LM, Jang M, Niro A, D'Aliberti D, Massimino L, Bertagna M, Zambrotta G, Bossi M, Citterio S, Crescenzi B, Fanelli F, Cassina V, Corti R, Salerno D, Nardo L, Chinello C, Mantegazza F, Mecucci C, Magni F, Cavaletti G, Bruheim P, Rea D, Larsen S, Gambacorti-Passerini C, Piazza R. ETNK1 mutations induce a mutator phenotype that can be reverted with phosphoethanolamine. Nat Commun 2020; 11:5938. [PMID: 33230096 PMCID: PMC7684297 DOI: 10.1038/s41467-020-19721-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/27/2020] [Indexed: 11/09/2022] Open
Abstract
Recurrent somatic mutations in ETNK1 (Ethanolamine-Kinase-1) were identified in several myeloid malignancies and are responsible for a reduced enzymatic activity. Here, we demonstrate in primary leukemic cells and in cell lines that mutated ETNK1 causes a significant increase in mitochondrial activity, ROS production, and Histone H2AX phosphorylation, ultimately driving the increased accumulation of new mutations. We also show that phosphoethanolamine, the metabolic product of ETNK1, negatively controls mitochondrial activity through a direct competition with succinate at mitochondrial complex II. Hence, reduced intracellular phosphoethanolamine causes mitochondria hyperactivation, ROS production, and DNA damage. Treatment with phosphoethanolamine is able to counteract complex II hyperactivation and to restore a normal phenotype.
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Affiliation(s)
- Diletta Fontana
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Mario Mauri
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Rossella Renso
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Mattia Docci
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Ilaria Crespiatico
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Lisa M Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Mi Jang
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Antonio Niro
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Deborah D'Aliberti
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Luca Massimino
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Mayla Bertagna
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Giovanni Zambrotta
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Mario Bossi
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Stefania Citterio
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milano, Italy
| | - Barbara Crescenzi
- Centro Ricerche Emato-Oncologiche, University of Perugia, Perugia, Italy
| | - Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - Valeria Cassina
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Roberta Corti
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Domenico Salerno
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Luca Nardo
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Clizia Chinello
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Francesco Mantegazza
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Cristina Mecucci
- Centro Ricerche Emato-Oncologiche, University of Perugia, Perugia, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Guido Cavaletti
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Delphine Rea
- Service d'Hématologie adulte, Hôpital Saint-Louis, Paris, France
| | - Steen Larsen
- X-lab, Center for Healthy Aging, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.,Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Carlo Gambacorti-Passerini
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy.,Hematology and Clinical Research Unit, San Gerardo Hospital, Monza, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy. .,Hematology and Clinical Research Unit, San Gerardo Hospital, Monza, Italy. .,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre (B4), University of Milano - Bicocca, Milan, Italy.
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Fuchino K, Bruheim P. An assessment of serial co-cultivation approach for generating novel Zymomonas mobilis strains. BMC Res Notes 2020; 13:422. [PMID: 32894180 PMCID: PMC7487726 DOI: 10.1186/s13104-020-05261-5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/28/2020] [Indexed: 11/21/2022] Open
Abstract
Objective The alphaproteobacterium Zymomonas mobilis is an efficient ethanol producer, and Z. mobilis-based biorefinery shows great potential for biofuel production. Serial co-cultivation is an emerging approach that promotes inter-species interactions which can improve or rewire the metabolic features in industrially useful microorganisms by inducing frequent mutations. We applied this method to assess if it improves or rewires the desirable physiological features of Z. mobilis, especially ethanol production. Results We performed serial co-culture of Z. mobilis with the baker’s yeast, Saccharomyces cerevisiae. We observed filamentation of Z. mobilis cells in the co-culture, indicating that the Z. mobilis cells were exposed to stress due to the presence of a competitor. After 50 times of serial transfers, we characterized the generated Z. mobilis strains, showing that long term co-culture did not drive significant changes in either the growth or profile of excreted metabolites in the generated strains. In line with this, whole genome sequencing of the generated Z. mobilis strains revealed only minor genetic variations from the parental strain. 50 generations of Z. mobilis monoculture did not induce morphological changes or any significant genetic variations. The result indicates that the method needs to be carefully optimized for Z. mobilis strain improvement.
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Affiliation(s)
- Katsuya Fuchino
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
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Abstract
BACKGROUND Ethanologenic alphaproteobacterium Zymomonas mobilis has been acknowledged as a promising biofuel producer. There have been numerous efforts to engineer this species applicable for an industrial-scale bioethanol production. Although Z. mobilis is robustly resilient to certain abiotic stress such as ethanol, the species is known to be sensitive to saline stress at a mild concentration, which hampers its industrial use as an efficient biocatalyst. To overcome this issue, we implemented a laboratory adaptive evolution approach to obtain salt tolerant Z. mobilis strain. RESULTS During an adaptive evolution, we biased selection by cell morphology to exclude stressed cells. The evolved strains significantly improved growth and ethanol production in the medium supplemented with 0.225 M NaCl. Furthermore, comparative metabolomics revealed that the evolved strains did not accumulate prototypical osmolytes, such as proline, to counter the stress during their growth. The sequenced genomes of the studied strains suggest that the disruption of ZZ6_1149 encoding carboxyl-terminal protease was likely responsible for the improved phenotype. CONCLUSIONS The present work successfully generated strains able to grow and ferment glucose under the saline condition that severely perturbs parental strain physiology. Our approach to generate strains, cell shape-based diagnosis and selection, might be applicable to other kinds of strain engineering in Z. mobilis.
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Affiliation(s)
- Katsuya Fuchino
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
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33
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Røst LM, Shafaei A, Fuchino K, Bruheim P. Zwitterionic HILIC tandem mass spectrometry with isotope dilution for rapid, sensitive and robust quantification of pyridine nucleotides in biological extracts. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1144:122078. [PMID: 32222674 DOI: 10.1016/j.jchromb.2020.122078] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 12/13/2022]
Abstract
The pyridine nucleotides nicotineamide adenine dinucleotide (NAD) and nicotineamide adenine dinucleotide phosphate (NADP) are conserved coenzymes across all domains of life, and are involved in more than 200 different hydride transfer reactions supporting essential catabolic and anabolic functions. The intracellular levels of these metabolites, and the ratio of their oxidized to reduced forms regulate an extensive network of reactions ranging beyond metabolism. Hence, monitoring their intracellular levels provides information about, but not limited to, the metabolic state of a cell or tissue. Interconversion between oxidized and reduced forms, varying pH liability and varying intracellular concentrations of the different species leaves absolute quantification of the pyridine nucleotides analytically challenging. These polar metabolites are poorly retained on conventional reverseed-phase stationary phases without ion-pair reagents that contaminates the LC-system. Herein we demonstrate that zwitterionic HILIC-tandem mass spectroemtry can be applied to successfully resolve the pyridine nucleotides in biological extracts in a fast, robust and highly sensitive way. The presented method applies isotope dilution to compensate potential loss of these labile metabolites and is validated for low, medium and high biomass samples of two popular biological model systems; Escherichia coli and the human cell line JJN-3. High stability and rapid sample preparation without solvent removal allows for long sequence runs, making this method ideal for high-throughput analysis of biological extracts.
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Affiliation(s)
- Lisa M Røst
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Armaghan Shafaei
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Katsuya Fuchino
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway.
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34
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Skedsmo FS, Malachin G, Våge DI, Hammervold MM, Salvesen Ø, Ersdal C, Ranheim B, Stafsnes MH, Bartosova Z, Bruheim P, Jäderlund KH, Matiasek K, Espenes A, Tranulis MA. Demyelinating polyneuropathy in goats lacking prion protein. FASEB J 2019; 34:2359-2375. [PMID: 31907995 DOI: 10.1096/fj.201902588r] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 10/23/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 01/01/2023]
Abstract
Studies in mice with ablation of Prnp, the gene that encodes the cellular prion protein (PrPC ), have led to the hypothesis that PrPC is important for peripheral nerve myelin maintenance. Here, we have used a nontransgenic animal model to put this idea to the test; namely, goats that, due to a naturally occurring nonsense mutation, lack PrPC . Teased nerve fiber preparation revealed a demyelinating pathology in goats without PrPC . Affected nerves were invaded by macrophages and T cells and displayed vacuolated fibers, shrunken axons, and onion bulbs. Peripheral nerve lipid composition was similar in young goats with or without PrPC , but markedly different between corresponding groups of adult goats, reflecting the progressive nature of the neuropathy. This is the first report of a subclinical demyelinating polyneuropathy caused by loss of PrPC function in a nontransgenic mammal.
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Affiliation(s)
- Fredrik S Skedsmo
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Giulia Malachin
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Dag Inge Våge
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Mie Marie Hammervold
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Øyvind Salvesen
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Cecilie Ersdal
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Birgit Ranheim
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Marit H Stafsnes
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Zdenka Bartosova
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Karin H Jäderlund
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Kaspar Matiasek
- Section of Clinical & Comparative Neuropathology, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Arild Espenes
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Michael A Tranulis
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
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35
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Kalnenieks U, Balodite E, Strähler S, Strazdina I, Rex J, Pentjuss A, Fuchino K, Bruheim P, Rutkis R, Pappas KM, Poole RK, Sawodny O, Bettenbrock K. Improvement of Acetaldehyde Production in Zymomonas mobilis by Engineering of Its Aerobic Metabolism. Front Microbiol 2019; 10:2533. [PMID: 31798541 PMCID: PMC6868117 DOI: 10.3389/fmicb.2019.02533] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/21/2019] [Indexed: 01/29/2023] Open
Abstract
Acetaldehyde is a valuable product of microbial biosynthesis, which can be used by the chemical industry as the entry point for production of various commodity chemicals. In ethanologenic microorganisms, like yeast or the bacterium Zymomonas mobilis, this compound is the immediate metabolic precursor of ethanol. In aerobic cultures of Z. mobilis, it accumulates as a volatile, inhibitory byproduct, due to the withdrawal of reducing equivalents from the alcohol dehydrogenase reaction by respiration. The active respiratory chain of Z. mobilis with its low energy-coupling efficiency is well-suited for regeneration of NAD+ under conditions when acetaldehyde, but not ethanol, is the desired catabolic product. In the present work, we sought to improve the capacity Z. mobilis to synthesize acetaldehyde, based on predictions of a stoichiometric model of its central metabolism developed herein. According to the model analysis, the main objectives in the course of engineering acetaldehyde producer strains were determined to be: (i) reducing ethanol synthesis via reducing the activity of alcohol dehydrogenase (ADH), and (ii) enhancing the respiratory capacity, either by overexpression of the respiratory NADH dehydrogenase (NDH), or by mutation of other components of respiratory metabolism. Several mutants with elevated respiration rate, decreased alcohol dehydrogenase activity, or a combination of both, were obtained. They were extensively characterized by determining their growth rates, product yields, oxygen consumption rates, ADH, and NDH activities, transcription levels of key catabolic genes, as well as concentrations of central metabolites under aerobic culture conditions. Two mutant strains were selected, with acetaldehyde yield close to 70% of the theoretical maximum value, almost twice the previously published yield for Z. mobilis. These strains can serve as a basis for further development of industrial acetaldehyde producers.
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Affiliation(s)
- Uldis Kalnenieks
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Elina Balodite
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Steffi Strähler
- Max-Planck-Institute for Dynamics of Complex Technical Systems, Analysis and Redesign of Biological Networks, Magdeburg, Germany
| | - Inese Strazdina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Julia Rex
- Institute for System Dynamics, University of Stuttgart, Stuttgart, Germany
| | - Agris Pentjuss
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Katsuya Fuchino
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Reinis Rutkis
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Katherine M Pappas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens (NKUA), Athens, Greece
| | - Robert K Poole
- Department of Molecular Biology and Biotechnology, The Krebs Institute, University of Sheffield, Sheffield, United Kingdom
| | - Oliver Sawodny
- Institute for System Dynamics, University of Stuttgart, Stuttgart, Germany
| | - Katja Bettenbrock
- Max-Planck-Institute for Dynamics of Complex Technical Systems, Analysis and Redesign of Biological Networks, Magdeburg, Germany
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Navarro MOP, Simionato AS, Pérez JCB, Barazetti AR, Emiliano J, Niekawa ETG, Andreata MFDL, Modolon F, Dealis ML, Araújo EJDA, Carlos TM, Scarpelim OJ, da Silva DB, Chryssafidis AL, Bruheim P, Andrade G. Fluopsin C for Treating Multidrug-Resistant Infections: In vitro Activity Against Clinically Important Strains and in vivo Efficacy Against Carbapenemase-Producing Klebsiella pneumoniae. Front Microbiol 2019; 10:2431. [PMID: 31708901 PMCID: PMC6824035 DOI: 10.3389/fmicb.2019.02431] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 10/08/2019] [Indexed: 11/22/2022] Open
Abstract
The increasing emergence of multidrug-resistant (MDR) organisms in hospital infections is causing a global public health crisis. The development of drugs with effective antibiotic action against such agents is of the highest priority. In the present study, the action of Fluopsin C against MDR clinical isolates was evaluated under in vitro and in vivo conditions. Fluopsin C was produced in cell suspension culture of Pseudomonas aeruginosa LV strain, purified by liquid adsorption chromatography and identified by mass spectrometric analysis. Bioactivity, bacterial resistance development risk against clinically important pathogenic strains and toxicity in mammalian cell were initially determined by in vitro models. In vivo toxicity was evaluated in Tenebrio molitor larvae and mice. The therapeutic efficacy of intravenous Fluopsin C administration was evaluated in a murine model of Klebsiella pneumoniae (KPC) acute sepsis, using six different treatments. The in vitro results indicated MIC and MBC below 2 μg/mL and low bacterial resistance development frequency. Electron microscopy showed that Fluopsin C may have altered the exopolysaccharide matrix and caused disruption of the cell wall of MDR bacteria. Best therapeutic results were achieved in mice treated with a single dose of 2 mg/kg and in mice treated with two doses of 1 mg/kg, 8 h apart. Furthermore, acute and chronic histopathological studies demonstrated absent nephrotoxicity and moderate hepatotoxicity. The results demonstrated the efficacy of Fluopsin C against MDR organisms in in vitro and in vivo models, and hence it can be a novel therapeutic agent for the control of severe MDR infections.
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Affiliation(s)
| | - Ane Stefano Simionato
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | | | - André Riedi Barazetti
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | - Janaina Emiliano
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | - Erika Tyemi Goya Niekawa
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | | | - Fluvio Modolon
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | - Mickely Liuti Dealis
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | | | | | | | - Denise Brentan da Silva
- Biological and Health Sciences Centre, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Andreas Lazaros Chryssafidis
- Veterinary Toxicology Laboratory, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Galdino Andrade
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina, Brazil
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37
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Volkova YA, Averina EB, Vasilenko DA, Sedenkova KN, Grishin YK, Bruheim P, Kuznetsova TS, Zefirov NS. Unexpected Heterocyclization of Electrophilic Alkenes by Tetranitromethane in the Presence of Triethylamine. Synthesis of 5-Nitroisoxazoles. J Org Chem 2019; 84:3192-3200. [PMID: 30726081 DOI: 10.1021/acs.joc.8b03086] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel reaction of tetranitromethane with electrophilic alkenes in the presence of triethylamine affording substituted 5-nitroisoxazoles is described. Triethylamine reacts with tetranitromethane to generate N-nitrotriethylammonium and trinitromethanide. This process provides the heterocyclization of electrophilic alkenes. A variety of α,β-unsaturated aldehydes, ketones, esters, amides, phosphonates, nitro, and sulfur compounds was involved in the heterocyclization reaction, and a wide range of functionalized 5-nitroisoxazoles was obtained in good to high yields. The scope and limitations of the reaction and the mechanistic proposal are discussed.
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Affiliation(s)
- Yulia A Volkova
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory, 1-3 , Moscow 119992 , Russia
| | - Elena B Averina
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory, 1-3 , Moscow 119992 , Russia
| | - Dmitry A Vasilenko
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory, 1-3 , Moscow 119992 , Russia
| | - Kseniya N Sedenkova
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory, 1-3 , Moscow 119992 , Russia
| | - Yuri K Grishin
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory, 1-3 , Moscow 119992 , Russia
| | - Per Bruheim
- Department of Biotechnology , Norwegian University of Science and Technology , Sem Selands vei 6/8 , N-7431 Trondheim , Norway
| | - Tamara S Kuznetsova
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory, 1-3 , Moscow 119992 , Russia
| | - Nikolai S Zefirov
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory, 1-3 , Moscow 119992 , Russia
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38
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Volkova YA, Averina EB, Grishin YK, Bruheim P, Kuznetsova TS, Zefirov NS. Retraction of “Unexpected Heterocyclization of Electrophilic Alkenes by Tetranitromethane in the Presence of Triethylamine. Synthesis of 3-Nitroisoxazoles”. J Org Chem 2019; 84:3742. [DOI: 10.1021/acs.joc.8b02967] [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: 11/30/2022]
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39
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Øvrehus MA, Bruheim P, Ju W, Zelnick LR, Langlo KA, Sharma K, de Boer IH, Hallan SI. Gene Expression Studies and Targeted Metabolomics Reveal Disturbed Serine, Methionine, and Tyrosine Metabolism in Early Hypertensive Nephrosclerosis. Kidney Int Rep 2018; 4:321-333. [PMID: 30775629 PMCID: PMC6365407 DOI: 10.1016/j.ekir.2018.10.007] [Citation(s) in RCA: 20] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 02/07/2023] Open
Abstract
Introduction Hypertensive nephrosclerosis is among the leading causes of end-stage renal disease, but its pathophysiology is poorly understood. We wanted to explore early metabolic changes using gene expression and targeted metabolomics analysis. Methods We analyzed gene expression in kidneys biopsied from 20 patients with nephrosclerosis and 31 healthy controls with an Affymetrix array. Thirty-one amino acids were measured by liquid chromatography coupled with mass spectrometry (LC-MS) in urine samples from 62 patients with clinical hypertensive nephrosclerosis and 33 age- and sex-matched healthy controls, and major findings were confirmed in an independent cohort of 45 cases and 15 controls. Results Amino acid catabolism and synthesis were strongly underexpressed in hypertensive nephrosclerosis (13- and 7-fold, respectively), and these patients also showed gene expression patterns indicating decreased fatty acid oxidation (12-fold) and increased interferon gamma (10-fold) and cellular defense response (8-fold). Metabolomics analysis revealed significant distribution differences in 11 amino acids in hypertensive nephrosclerosis, among them tyrosine, phenylalanine, dopamine, homocysteine, and serine, with 30% to 70% lower urine excretion. These findings were replicated in the independent cohort. Integrated gene-metabolite pathway analysis showed perturbations of renal dopamine biosynthesis. There were also significant differences in homocysteine/methionine homeostasis and the serine pathway, which have strong influence on 1-carbon metabolism. Several of these disturbances could be interconnected through reduced regeneration of tetrahydrofolate and tetrahydrobiopterin. Conclusion Early hypertensive nephrosclerosis showed perturbations of intrarenal biosynthesis of dopamine, which regulates natriuresis and blood pressure. There were also disturbances in serine/glycine and methionine/homocysteine metabolism, which may contribute to endothelial dysfunction, atherosclerosis, and renal fibrosis.
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Affiliation(s)
- Marius A Øvrehus
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Nephrology, St Olav Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Wenjun Ju
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Leila R Zelnick
- Kidney Research Institute, University of Washington, Seattle, Washington, USA.,Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Knut A Langlo
- Department of Nephrology, St Olav Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Kumar Sharma
- University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Ian H de Boer
- Kidney Research Institute, University of Washington, Seattle, Washington, USA.,Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Stein I Hallan
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Nephrology, St Olav Hospital, Trondheim University Hospital, Trondheim, Norway
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Søgaard CK, Blindheim A, Røst LM, Petrović V, Nepal A, Bachke S, Liabakk NB, Gederaas OA, Viset T, Arum CJ, Bruheim P, Otterlei M. "Two hits - one stone"; increased efficacy of cisplatin-based therapies by targeting PCNA's role in both DNA repair and cellular signaling. Oncotarget 2018; 9:32448-32465. [PMID: 30197755 PMCID: PMC6126690 DOI: 10.18632/oncotarget.25963] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 06/06/2018] [Accepted: 07/31/2018] [Indexed: 01/08/2023] Open
Abstract
Low response rate and rapid development of resistance against commonly used chemotherapeutic regimes demand new multi-targeting anti-cancer strategies. In this study, we target the stress-related roles of the scaffold protein PCNA with a cell-penetrating peptide containing the PCNA-interacting motif APIM. The APIM-peptide increased the efficacy of cisplatin-based therapies in a muscle-invasive bladder cancer (MIBC) solid tumor model in rat and in bladder cancer (BC) cell lines. By combining multiple omics-levels, from gene expression to proteome/kinome and metabolome, we revealed a unique downregulation of the EGFR/ERBB2 and PI3K/Akt/mTOR pathways in the APIM-peptide-cisplatin combination treated cells. Additionally, the combination treatment reduced the expression of anti-apoptotic proteins and proteins involved in development of resistance to cisplatin. Concurrently, we observed increased levels of DNA breaks in combination treated cells, suggesting that the APIM-peptide impaired PCNA - DNA repair protein interactions and reduced the efficacy of repair. This was also seen in cisplatin-resistant cells, which notably was re-sensitized to cisplatin by the APIM-peptide. Our data indicate that the increased efficacy of cisplatin treatment is mediated both via downregulation of known oncogenic signaling pathways and inhibition of DNA repair/translesion synthesis (TLS), thus the APIM-peptide hits both nuclear and cytosolic functions of PCNA. The novel multi-targeting strategy of the APIM-peptide could potentially improve the efficacy of chemotherapeutic regiments for treatment of MIBC, and likely other solid tumors.
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Affiliation(s)
- Caroline Krogh Søgaard
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Augun Blindheim
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Department of Urology and Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Lisa M Røst
- Department of Biotechnology and Food Science, NTNU, Trondheim, Norway
| | - Voin Petrović
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anala Nepal
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Siri Bachke
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Nina-Beate Liabakk
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Odrun A Gederaas
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Trond Viset
- Department of Pathology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Carl-Jørgen Arum
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Department of Urology and Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU, Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.,APIM Therapeutics A/S, Trondheim, Norway
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41
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Olaisen C, Kvitvang HFN, Lee S, Almaas E, Bruheim P, Drabløs F, Otterlei M. The role of PCNA as a scaffold protein in cellular signaling is functionally conserved between yeast and humans. FEBS Open Bio 2018; 8:1135-1145. [PMID: 29988559 PMCID: PMC6026702 DOI: 10.1002/2211-5463.12442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/19/2018] [Accepted: 05/01/2018] [Indexed: 12/11/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA), a member of the highly conserved DNA sliding clamp family, is an essential protein for cellular processes including DNA replication and repair. A large number of proteins from higher eukaryotes contain one of two PCNA-interacting motifs: PCNA-interacting protein box (PIP box) and AlkB homologue 2 PCNA-interacting motif (APIM). APIM has been shown to be especially important during cellular stress. PIP box is known to be functionally conserved in yeast, and here, we show that this is also the case for APIM. Several of the 84 APIM-containing yeast proteins are associated with cellular signaling as hub proteins, which are able to interact with a large number of other proteins. Cellular signaling is highly conserved throughout evolution, and we recently suggested a novel role for PCNA as a scaffold protein in cellular signaling in human cells. A cell-penetrating peptide containing the APIM sequence increases the sensitivity toward the chemotherapeutic agent cisplatin in both yeast and human cells, and both yeast and human cells become hypersensitive when the Hog1/p38 MAPK pathway is blocked. These results suggest that the interactions between APIM-containing signaling proteins and PCNA during the DNA damage response is evolutionary conserved between yeast and mammals and that PCNA has a role in cellular signaling also in yeast.
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Affiliation(s)
- Camilla Olaisen
- Department of Clinical and Molecular MedicineFaculty of Medicine and Health SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Hans Fredrik N. Kvitvang
- Department of Biotechnology and Food ScienceFaculty of Natural SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Sungmin Lee
- Department of Biotechnology and Food ScienceFaculty of Natural SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Eivind Almaas
- Department of Biotechnology and Food ScienceFaculty of Natural SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Per Bruheim
- Department of Biotechnology and Food ScienceFaculty of Natural SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Finn Drabløs
- Department of Clinical and Molecular MedicineFaculty of Medicine and Health SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Marit Otterlei
- Department of Clinical and Molecular MedicineFaculty of Medicine and Health SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
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42
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Petrovic V, Nepal A, Olaisen C, Bachke S, Hira J, Søgaard CK, Røst LM, Misund K, Andreassen T, Melø TM, Bartsova Z, Bruheim P, Otterlei M. Anti-Cancer Potential of Homemade Fresh Garlic Extract Is Related to Increased Endoplasmic Reticulum Stress. Nutrients 2018; 10:nu10040450. [PMID: 29621132 PMCID: PMC5946235 DOI: 10.3390/nu10040450] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/14/2022] Open
Abstract
The use of garlic and garlic-based extracts has been linked to decreased incidence of cancer in epidemiological studies. Here we examine the molecular and cellular activities of a simple homemade ethanol-based garlic extract (GE). We show that GE inhibits growth of several different cancer cells in vitro, as well as cancer growth in vivo in a syngeneic orthotopic breast cancer model. Multiple myeloma cells were found to be especially sensitive to GE. The GE was fractionated using solid-phase extractions, and we identified allicin in one GE fraction; however, growth inhibitory activities were found in several additional fractions. These activities were lost during freeze or vacuum drying, suggesting that the main anti-cancer compounds in GE are volatile. The anti-cancer activity was stable for more than six months in −20 °C. We found that GE enhanced the activities of chemotherapeutics, as well as MAPK and PI3K inhibitors. Furthermore, GE affected hundreds of proteins involved in cellular signalling, including changes in vital cell signalling cascades regulating proliferation, apoptosis, and the cellular redox balance. Our data indicate that the reduced proliferation of the cancer cells treated by GE is at least partly mediated by increased endoplasmic reticulum (ER) stress.
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Affiliation(s)
- Voin Petrovic
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Anala Nepal
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Camilla Olaisen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Siri Bachke
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Jonathan Hira
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Caroline K Søgaard
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Lisa M Røst
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Kristine Misund
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Trygve Andreassen
- MR core facility, Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Torun M Melø
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Zdenka Bartsova
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
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43
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Stafsnes MH, Røst LM, Bruheim P. Improved phosphometabolome profiling applying isotope dilution strategy and capillary ion chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1083:278-283. [PMID: 29571119 DOI: 10.1016/j.jchromb.2018.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/04/2018] [Accepted: 02/05/2018] [Indexed: 12/27/2022]
Abstract
The phosphometabolome is comprised of all phosphorylated metabolites including the major metabolite classes sugar phosphates and nucleoside phosphates. Phosphometabolites are invaluable in any cell as a part of primary- and energy- metabolism, and as building blocks in the biosynthesis of macromolecules. Here, we report quantitative profiling of the phosphometabolome by applying capillary ion chromatography-tandem mass spectrometry (capIC-MS/MS), ensuring improved chromatographic separation, robustness and quantitative precision. Baseline separation was achieved for six out of eight tested hexose phosphates. Quantitative precision and reproducibility was improved by introducing a fully uniformly (U) 13C-labeled biological extract and applying an isotope dilution (ID) correction strategy. A 13C-labeled biological extract does in principle contain internal standards (IS) for all metabolites, but low abundant metabolites pose a challenge, and solutions to this are discussed. The extreme reproducibility and reliability of this capIC-MS/MS method was demonstrated by running the instrumentation continuously for ten days.
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Affiliation(s)
- Marit H Stafsnes
- NTNU Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Norway
| | - Lisa M Røst
- NTNU Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Norway
| | - Per Bruheim
- NTNU Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Norway.
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44
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Giskeødegård GF, Hansen AF, Bertilsson H, Gonzalez SV, Kristiansen KA, Bruheim P, Mjøs SA, Angelsen A, Bathen TF, Tessem MB. Metabolic markers in blood can separate prostate cancer from benign prostatic hyperplasia. Br J Cancer 2015; 113:1712-9. [PMID: 26633561 PMCID: PMC4702000 DOI: 10.1038/bjc.2015.411] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 10/28/2015] [Accepted: 11/04/2015] [Indexed: 02/06/2023] Open
Abstract
Background: An individualised risk-stratified screening for prostate cancer (PCa) would select the patients who will benefit from further investigations as well as therapy. Current detection methods suffer from low sensitivity and specificity, especially for separating PCa from benign prostatic conditions. We have investigated the use of metabolomics analyses of blood samples for separating PCa patients and controls with benign prostatic hyperplasia (BPH). Methods: Blood plasma and serum samples from 29 PCa patient and 21 controls with BPH were analysed by metabolomics analysis using magnetic resonance spectroscopy, mass spectrometry and gas chromatography. Differences in blood metabolic patterns were examined by multivariate and univariate statistics. Results: By combining results from different methodological platforms, PCa patients and controls were separated with a sensitivity and specificity of 81.5% and 75.2%, respectively. Conclusions: The combined analysis of serum and plasma samples by different metabolomics measurement techniques gave successful discrimination of PCa and controls, and provided metabolic markers and insight into the processes characteristic of PCa. Our results suggest changes in fatty acid (acylcarnitines), choline (glycerophospholipids) and amino acid metabolism (arginine) as markers for PCa compared with BPH.
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Affiliation(s)
- Guro F Giskeødegård
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.,St Olav University Hospital, Trondheim 7006, Norway
| | - Ailin Falkmo Hansen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Helena Bertilsson
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.,Department of Urology, NTNU, Trondheim 7491, Norway
| | | | | | - Per Bruheim
- Department of Biotechnology, NTNU, Trondheim 7491, Norway
| | - Svein A Mjøs
- Department of Chemistry, University of Bergen, Bergen 5020, Norway
| | - Anders Angelsen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.,St Olav University Hospital, Trondheim 7006, Norway
| | - Tone Frost Bathen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - May-Britt Tessem
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.,St Olav University Hospital, Trondheim 7006, Norway
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45
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Kvitvang HFN, Bruheim P. Fast filtration sampling protocol for mammalian suspension cells tailored for phosphometabolome profiling by capillary ion chromatography - tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 998-999:45-9. [PMID: 26151192 DOI: 10.1016/j.jchromb.2015.06.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 11/16/2022]
Abstract
Capillary ion chromatography (capIC) is the premium separation technology for low molecular phosphometabolites and nucleotides in biological extracts. Removal of excessive amounts of salt during sample preparation stages is a prerequisite to enable high quality capIC separation in combination with reproducible and sensitive MS detection. Existing sampling protocols for mammalian cells used for GC-MS and LC-MS metabolic profiling can therefore not be directly applied to capIC separations. Here, the development of a fast filtration sampling protocol for mammalian suspension cells tailored for quantitative profiling of the phosphometabolome on capIC-MS/MS is presented. The whole procedure from sampling the culture to transfer of filter to quenching and extraction solution takes less than 10s. To prevent leakage it is critical that a low vacuum pressure is applied, and satisfactorily reproducibility was only obtained by usage of a vacuum pressure controlling device. A vacuum of 60mbar was optimal for filtration of multiple myeloma Jjn-3 cell cultures through 5μm polyvinylidene (PVDF) filters. A quick deionized water (DI-water) rinse step prior to extraction was tested, and significantly higher metabolite yields were obtained during capIC-MS/MS analyses in this extract compared to extracts prepared by saline and reduced saline (25%) washing steps only. In addition, chromatographic performance was dramatically improved. Thus, it was verified that a quick DI-water rinse is tolerated by the cells and can be included as the final stage during filtration. Over 30 metabolites were quantitated in JJN-3 cell extracts by using the optimized sampling protocol with subsequent capIC-MS/MS analysis, and up to 2 million cells can be used in a single filtration step for the chosen filter and vacuum pressure. The technical set-up is also highly advantageous for microbial metabolome filtration protocols after optimization of vacuum pressure and washing solutions, and the reduced salt content of the extract will also improve the quality of LC-MS analysis due to lower salt adduct ion formation.
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Affiliation(s)
- Hans F N Kvitvang
- Department of Biotechnology, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology, NTNU Norwegian University of Science and Technology, Trondheim, Norway.
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46
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Lien SK, Niedenführ S, Sletta H, Nöh K, Bruheim P. Fluxome study of Pseudomonas fluorescens reveals major reorganisation of carbon flux through central metabolic pathways in response to inactivation of the anti-sigma factor MucA. BMC Syst Biol 2015; 9:6. [PMID: 25889900 PMCID: PMC4351692 DOI: 10.1186/s12918-015-0148-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/27/2015] [Indexed: 11/25/2022]
Abstract
Background The bacterium Pseudomonas fluorescens switches to an alginate-producing phenotype when the pleiotropic anti-sigma factor MucA is inactivated. The inactivation is accompanied by an increased biomass yield on carbon sources when grown under nitrogen-limited chemostat conditions. A previous metabolome study showed significant changes in the intracellular metabolite concentrations, especially of the nucleotides, in mucA deletion mutants compared to the wild-type. In this study, the P. fluorescens SBW25 wild-type and an alginate non-producing mucA- ΔalgC double-knockout mutant are investigated through model-based 13C-metabolic flux analysis (13C-MFA) to explore the physiological consequences of MucA inactivation at the metabolic flux level. Intracellular metabolite extracts from three carbon labelling experiments using fructose as the sole carbon source are analysed for 13C-label incorporation in primary metabolites by gas and liquid chromatography tandem mass spectrometry. Results From mass isotopomer distribution datasets, absolute intracellular metabolic reaction rates for the wild type and the mutant are determined, revealing extensive reorganisation of carbon flux through central metabolic pathways in response to MucA inactivation. The carbon flux through the Entner-Doudoroff pathway was reduced in the mucA- ΔalgC mutant, while flux through the pentose phosphate pathway was increased. Our findings also indicated flexibility of the anaplerotic reactions through down-regulation of the pyruvate shunt in the mucA- ΔalgC mutant and up-regulation of the glyoxylate shunt. Conclusions Absolute metabolic fluxes and metabolite levels give detailed, integrated insight into the physiology of this industrially, medically and agriculturally important bacterial species and suggest that the most efficient way of using a mucA- mutant as a cell factory for alginate production would be to use non-growing conditions and nitrogen deprivation. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0148-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stina K Lien
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491, Trondheim, Norway.
| | - Sebastian Niedenführ
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425, Jülich, Germany.
| | - Håvard Sletta
- Department of Bioprocess technology, SINTEF Materials and Chemistry, Sem Sælands vei 2a, N-7465, Trondheim, Norway.
| | - Katharina Nöh
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425, Jülich, Germany.
| | - Per Bruheim
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491, Trondheim, Norway.
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47
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Gederaas OA, Søgaard CD, Viset T, Bachke S, Bruheim P, Arum CJ, Otterlei M. Increased Anticancer Efficacy of Intravesical Mitomycin C Therapy when Combined with a PCNA Targeting Peptide. Transl Oncol 2014; 7:812-23. [PMID: 25500092 PMCID: PMC4311026 DOI: 10.1016/j.tranon.2014.10.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/13/2014] [Accepted: 10/13/2014] [Indexed: 12/21/2022] Open
Abstract
Non-muscle-invasive bladder cancers (NMIBCs) are tumors confined to the mucosa or the mucosa/submucosa. An important challenge in treatment of NMIBC is both high recurrence and high progression rates. Consequently, more efficacious intravesical treatment regimes are in demand. Inhibition of the cell's DNA repair systems is a new promising strategy to improve cancer therapy, and proliferating cell nuclear antigen (PCNA) is a new promising target. PCNA is an essential scaffold protein in multiple cellular processes including DNA replication and repair. More than 200 proteins, many involved in stress responses, interact with PCNA through the AlkB homologue 2 PCNA-interacting motif (APIM), including several proteins directly or indirectly involved in repair of DNA interstrand crosslinks (ICLs). In this study, we targeted PCNA with a novel peptide drug containing the APIM sequence, ATX-101, to inhibit repair of the DNA damage introduced by the chemotherapeutics. A bladder cancer cell panel and two different orthotopic models of bladder cancer in rats, the AY-27 implantation model and the dietary BBN induction model, were applied. ATX-101 increased the anticancer efficacy of the ICL-inducing drug mitomycin C (MMC), as well as bleomycin and gemcitabine in all bladder cancer cell lines tested. Furthermore, we found that ATX-101 given intravesically in combination with MMC penetrated the bladder wall and further reduced the tumor growth in both the slow growing endogenously induced and the rapidly growing transplanted tumors. These results suggest that ATX-101 has the potential to improve the efficacy of current MMC treatment in NMIBC.
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Affiliation(s)
- Odrun A Gederaas
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Caroline D Søgaard
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Trond Viset
- Department of Pathology and Medical Genetics, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Siri Bachke
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim Norway
| | - Carl-Jørgen Arum
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Department of Urology and Surgery, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Marit Otterlei
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; APIM Therapeutics A/S, Trondheim, Norway.
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48
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Janeckova H, Kalivodova A, Najdekr L, Friedecky D, Hron K, Bruheim P, Adam T. Untargeted metabolomic analysis of urine samples in the diagnosis of some inherited metabolic disorders. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2014; 159:582-5. [PMID: 25482736 DOI: 10.5507/bp.2014.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 09/15/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Metabolomics is becoming an important tool in clinical research and the diagnosis of human diseases. It has been used in the diagnosis of inherited metabolic disorders with pronounced biochemical abnormalities. The aim of this study was to determine if it could be applied in the diagnosis of inherited metabolic disorders (IMDs) with less clear biochemical profiles from urine samples using an untargeted metabolomic approach. METHODS A total of 14 control urine samples and 21 samples from infants with cystinuria, maple syrup urine disease, adenylosuccinate lyase deficiency and galactosemia were tested. Samples were analyzed by liquid chromatography on aminopropyl column in aqueous normal phase separation system using gradient elution of acetonitrile/ammonium acetate. Detection was performed by time-of-flight mass spectrometer fitted with electrospray ionisation in positive mode. The data were statistically processed using principal component analysis (PCA), principal component discriminant function analysis (PCA-DFA) and partial least squares (PLS) regression. RESULTS All patient samples were first distinguished from controls using unsupervised PCA. Discrimination of the patient samples was then unambiguously verified using supervised PCA-DFA. Known markers of the diseases in question were successfully confirmed and a potential new marker emerged from the PLS regression. CONCLUSION This study showed that untargeted metabolomics can be applied in the diagnosis of mild IMDs with less clear biochemical profiles.
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Affiliation(s)
- Hana Janeckova
- Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc, Czech Republic.,Laboratory of Metabolomics, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc
| | - Alzbeta Kalivodova
- Laboratory of Metabolomics, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc.,Department of Mathematical Analysis and Applications of Mathematics, Faculty of Science, Palacky University Olomouc
| | - Lukas Najdekr
- Laboratory of Metabolomics, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc
| | - David Friedecky
- Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc, Czech Republic.,Laboratory of Metabolomics, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc
| | - Karel Hron
- Department of Mathematical Analysis and Applications of Mathematics, Faculty of Science, Palacky University Olomouc
| | - Per Bruheim
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Saelands vei 6/8, NO-7491 Trondheim, Norway
| | - Tomas Adam
- Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc, Czech Republic.,Laboratory of Metabolomics, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc
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49
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Kvitvang HFN, Kristiansen KA, Lien SK, Bruheim P. Quantitative analysis of amino and organic acids by methyl chloroformate derivatization and GC-MS/MS analysis. Methods Mol Biol 2014; 1198:137-145. [PMID: 25270928 DOI: 10.1007/978-1-4939-1258-2_10] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Alkyl chloroformates are known for their ability to produce mixed anhydrides, and they have found use as versatile derivatization reagents for gas chromatographic (GC) separation of amino- and organic acids. Triple-quadrupole mass spectrometers are excellent detectors for high sensitive and selective analysis. Here, we describe a methyl chloroformate (MCF) GC-MS/MS method for the quantitative analysis of metabolites containing amino- and/or carboxylic groups. The method covers over 60 metabolites with quantitation limits down to the low picomole range injected on column, and any metabolite with amino- and/or carboxylic acid functional groups that yield a stable and volatile MCF derivative can be included in the method. Absolute quantitation can be achieved by including a stable isotope-coded derivatization agent (d3-MCF) and deuterated alcohol solvent (e.g., d4-methanol). As the carboxylic and amino groups are differently labeled, the former from the solvent methanol while the latter from MCF, this approach can also be used to identify a number of amino and carboxylic groups in unknown analytes in an extract.
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Affiliation(s)
- Hans Fredrik Nyvold Kvitvang
- NTNU Department of Biotechnology, Norwegian University of Science and Technology, Sem Selands vei 6/8, 7491, Trondheim, Norway
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50
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Bruheim P, Kvitvang HFN, Villas-Boas SG. Stable isotope coded derivatizing reagents as internal standards in metabolite profiling. J Chromatogr A 2013; 1296:196-203. [DOI: 10.1016/j.chroma.2013.03.072] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 03/22/2013] [Accepted: 03/25/2013] [Indexed: 12/26/2022]
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