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Resistance Exercise Reduces Kynurenine Pathway Metabolites in Breast Cancer Patients Undergoing Radiotherapy
MESI-STRAT

Abstract (Expand)

Purpose: Evidence from preclinical studies and trials in healthy volunteers suggests that exercise may modulate the levels of tryptophan (TRP) metabolites along the kynurenine (KYN) pathway. As KYN and … downstream KYN metabolites are known to promote cancer progression by inhibiting anti-tumor immune responses and by promoting the motility of cancer cells, we investigated if resistance exercise can also control the levels of KYN pathway metabolites in breast cancer patients undergoing radiotherapy (NCT01468766). Patients and Methods: Chemotherapy-naïve breast cancer patients (n = 96) were either randomized to an exercise/intervention group (IG) or a control group (CG). The IG participated in a 12-week supervised progressive resistance exercise program twice a week, whereas the CG received a supervised relaxation program. Serum levels of TRP and KYN as well as urine levels of kynurenic acid (KYNA) and neurotoxic quinolinic acid (QUINA) were assessed before (t0), after radiotherapy, and mid-term of the exercise intervention (t1) and after the exercise intervention (t2). Additionally, 24 healthy women (HIG) participated in the exercise program to investigate potential differences in its effects on KYN metabolites in comparison to the breast cancer patients. Results: At baseline (t0) the breast cancer patients showed a significantly elevated serum KYN/TRP ratio and urine QUINA/KYNA ratio, as well as increased urine QUINA levels in comparison to the healthy women. In response to exercise the healthy women and the breast cancer patients differed significantly in the levels of urine QUINA and the QUINA/KYNA ratio. Most importantly, serum KYN levels and the KYN/TRP ratio were significantly reduced in exercising patients (IG) compared to non-exercising patients (CG) both at t1 and t2. Conclusion: Resistance exercise may represent a potent non-pharmacological avenue to counteract an activation of the KYN pathway in breast cancer patients undergoing radiotherapy.

Authors: Philipp Zimmer, Frank Schmidt, Mirja Tamara Prentzell, Bianca Berdel, Joachim Wiskemann, Karl-Heinz Kellner, Jürgen Debus, Cornelia Ulrich, Christiane Opitz, Karen Steindorf

Date Published: 25th Sep 2019

Journal: Front. Oncol.

Tryptophan metabolism as a common therapeutic target in cancer, neurodegeneration and beyond
MESI-STRAT

Abstract (Expand)

L-Tryptophan (Trp) metabolism through the kynurenine pathway (KP) is involved in the regulation of immunity, neuronal function and intestinal homeostasis. Imbalances in Trp metabolism in disorders … ranging from cancer to neurodegenerative disease have stimulated interest in therapeutically targeting the KP, particularly the main rate-limiting enzymes indoleamine-2,3-dioxygenase 1 (IDO1), IDO2 and tryptophan-2,3-dioxygenase (TDO) as well as kynurenine monooxygenase (KMO). However, although small-molecule IDO1 inhibitors showed promise in early-stage cancer immunotherapy clinical trials, a phase III trial was negative. This Review summarizes the physiological and pathophysiological roles of Trp metabolism, highlighting the vast opportunities and challenges for drug development in multiple diseases.

Authors: Michael Platten, Ellen A. A. Nollen, Ute F. Röhrig, Francesca Fallarino, Christiane Opitz

Date Published: 1st May 2019

Journal: Nat Rev Drug Discov

Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio.
DigiSal

Abstract (Expand)

Zebrafish is a useful modeling organism for the study of vertebrate development, immune response, and metabolism. Metabolic studies can be aided by mathematical reconstructions of the metabolic network … of zebrafish. These list the substrates and products of all biochemical reactions that occur in the zebrafish. Mathematical techniques such as flux-balance analysis then make it possible to predict the possible metabolic flux distributions that optimize, for example, the turnover of food into biomass. The only available genome-scale reconstruction of zebrafish metabolism is ZebraGEM. In this study, we present ZebraGEM 2.0, an updated and validated version of ZebraGEM. ZebraGEM 2.0 is extended with gene-protein-reaction associations (GPRs) that are required to integrate genetic data with the metabolic model. To demonstrate the use of these GPRs, we performed an in silico genetic screening for knockouts of metabolic genes and validated the results against published in vivo genetic knockout and knockdown screenings. Among the single knockout simulations, we identified 74 essential genes, whose knockout stopped growth completely. Among these, 11 genes are known have an abnormal knockout or knockdown phenotype in vivo (partial), and 41 have human homologs associated with metabolic diseases. We also added the oxidative phosphorylation pathway, which was unavailable in the published version of ZebraGEM. The updated model performs better than the original model on a predetermined list of metabolic functions. We also determined a minimal feed composition. The oxidative phosphorylation pathways were validated by comparing with published experiments in which key components of the oxidative phosphorylation pathway were pharmacologically inhibited. To test the utility of ZebraGEM2.0 for obtaining new results, we integrated gene expression data from control and Mycobacterium marinum-infected zebrafish larvae. The resulting model predicts impeded growth and altered histidine metabolism in the infected larvae.

Authors: L. van Steijn, F. J. Verbeek, H. P. Spaink, R. M. H. Merks

Date Published: 20th Jun 2019

Journal: Zebrafish

Modulation of Neuro-Dopamine Homeostasis in Juvenile Female Atlantic Cod ( Gadus morhua) Exposed to Polycyclic Aromatic Hydrocarbons and Perfluoroalkyl Substances.
Systems toxicology of Atlantic cod

Abstract (Expand)

The dopaminergic effect of PAH and PFAS mixtures, prepared according to environmentally relevant concentrations, has been studied in juvenile female Atlantic cod ( Gadus morhua). Benzo[a]pyrene, … dibenzothiophene, fluorene, naphthalene, phenanthrene, and pyrene were used to prepare a PAH mixture, while PFNA, PFOA, PFOS, and PFTrA were used to prepare a PFAS mixture. Cod were injected intraperitoneally twice, with either a low (1x) or high (20x) dose of each compound mixture or their combinations. After 2 weeks of exposure, levels of plasma 17beta-estradiol (E2) were significantly elevated in high PAH/high PFAS treated group. Brain dopamine/metabolite ratios (DOPAC/dopamine and HVA+DOPAC/dopamine) changed with E2 plasma levels, except for high PAH/low PFAS and low PAH/high PFAS treated groups. On the transcript levels, th mRNA inversely correlated with dopamine/metabolite ratios and gnrh2 mRNA levels. Respective decreases and increases of drd1 and drd2a after exposure to the high PAH dose were observed. Specifically, high PFAS exposure decreased both drds, leading to high plasma E2 concentrations. Other studied end points suggest that these compounds, at different doses and combinations, have different toxicity threshold and modes of action. These effects indicate potential alterations in the feedback signaling processes within the dopaminergic pathway by these contaminant mixtures.

Authors: Essa Ahsan Khan, L. B. Bertotto, Karina Dale, R. Lille-Langoy, Fekadu Yadetie, Odd André Karlsen, Anders Goksøyr, D. Schlenk, A. Arukwe

Date Published: 18th Jun 2019

Journal: Environ Sci Technol

Contaminant accumulation and biological responses in Atlantic cod (Gadus morhua) caged at a capped waste disposal site in Kollevag, Western Norway.
Systems toxicology of Atlantic cod

Abstract (Expand)

The aim of this study was to assess whether fish in Kollevag, a sheltered bay on the western coast of Norway, previously utilized as a waste disposal site, could be affected by environmental contaminants … leaking from the waste. Farmed, juvenile Atlantic cod (Gadus morhua) were caged for six weeks at three different locations in Kollevag bay and at one reference location. Sediments and cod samples (bile and liver) were analyzed for polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), brominated flame retardants (BFRs), per-and polyfluoroalkyl substances (PFASs) and polycyclic aromatic hydrocarbon (PAH) metabolites, revealing a contamination gradient at the four stations. Furthermore, hepatosomatic index (HSI) and Fulton's condition factor (CF) were significantly lower in cod caged closest to the disposal site. Levels and activities of biomarker proteins, such as vitellogenin (Vtg), metallothionein (Mt), and biotransformation and oxidative stress enzymes, including cytochrome P450 1a and 3a (Cyp1a, Cyp3a), glutathione s-transferase (Gst) and catalase (Cat), were quantified in blood plasma and liver tissue. Hepatic Cat and Gst activities were significantly reduced in cod caged at the innermost stations in Kollevag, indicating modulation of oxidative stress responses. However, these results contrasted with reduced hepatic lipid peroxidation. Significant increases in transcript levels were observed for genes involved in lipid metabolism (fasn and acly) in cod liver, while transcript levels of ovarian steroidogenic enzyme genes such as p450scc, cyp19, 3beta-hsd and 20beta-hsd showed significant station-dependent increases. Cyp1a and Vtg protein levels were however not significantly altered in cod caged in Kollevag. Plasma levels of estradiol (E2) and testosterone (T) were determined by enzyme immunoassay (EIA) and showed elevated E2 levels, but only at the innermost station. We conclude that the bay of Kollevag did not fullfill adequate environmental condition based on environmental quality standards (EQSs) for chemicals in coastal waters. Following a six weeks caging period, environmental contaminants accumulated in cod tissues and effects were observed on biomarker responses, especially those involved in reproductive processes in cod ovary.

Authors: Karina Dale, M. B. Muller, Zhanna Tairova, Essa Ahsan Khan, K. Hatlen, M. Grung, Fekadu Yadetie, R. Lille-Langoy, Nello Blaser, H. J. Skaug, J. L. Lyche, A. Arukwe, Ketil Hylland, Odd André Karlsen, Anders Goksøyr

Date Published: 26th Feb 2019

Journal: Mar Environ Res

Diastereoselective synthesis of vicinal amino alcohols
TRALAMINOL

Abstract (Expand)

The vicinal amino alcohol is a common motif in natural products and pharmaceuticals. Amino acidsconstitute a natural, inexpensive, and enantiopure choice of starting material for the synthesis of … suchfunctionalities. However, the matters concerning diastereoselectivity are not obvious. This Perspectivetakes a look in thefield of diastereoselective synthesis of vicinal amino alcohols starting from amino acidsusing various methods. https://pubs.rsc.org/en/content/articlepdf/2012/ob/c2ob25357g

Authors: Oskari K. Karjalainen, Ari M. P. Koskinen

Date Published: 2012

Journal: Org. Biomol. Chem.

Chemoenzymatic Hydroxymethylation of Carboxylic Acids by Tandem Stereodivergent Biocatalytic Aldol Reaction and Chemical Decarboxylation
TRALAMINOL

Abstract (Expand)

Chiral 2-substituted 3-hydroxycarboxylic acid derivatives are valuable building blocks for the preparation of naturally occurring and synthetic biologically active molecules. Current methodologies for … the preparation of these compounds are still limited for large-scale production due to the high costs, limited microbial strains, low yields, difficult downstream processing, and limited range of structures. We report an effective chemoenzymatic method for the synthesis of enantiomerically pure 2 substituted 3 hydroxycarboxylic esters. The strategy comprises: i) a stereoselective aldol addition of 2 oxoacids to methanal catalyzed by two enantiocomplementary 2 oxoacid aldolases, ii) oxidative decarboxylation, and iii) esterification. Compounds with S-configuration were obtained in 69-80% isolated yields (94-99% ee), and the R enantiomers in 57-88% (88-95% ee), using a substrate concentration range of 0.1-1.0 M. The method developed offers a versatile alternative route to this important class of chiral building blocks, and highlights the exciting opportunities available for using natural enzymes with minimal active site modification.

Authors: Roser Marín-Valls, Karel Hernández, Michael Bolte, Jesús Joglar, Jordi Bujons, Pere Clapés

Date Published: 8th Jul 2019

Journal: ACS Catal.

One‐Pot Cascade Synthesis of (3S)‐Hydroxyketones Catalyzed by Transketolase via Hydroxypyruvate Generated in Situ from d‐Serine by d‐Amino Acid Oxidase
TRALAMINOL

Abstract (Expand)

We described an efficient in situ generation of hydroxypyruvate from d‐serine catalyzed by a d‐amino acid oxidase from Rhodotorula gracilis. This strategy revealed an interesting alternative to the … conventional chemical synthesis of hydroxypyruvate starting from toxic bromopyruvate or to the enzymatic transamination from l‐serine requiring an additional substrate as amino acceptor. Hydroxypyruvate thus produced was used as donor substrate of transketolases from Escherichia coli or from Geobacillus stearothermophilus catalyzing the stereoselective formation of a carbon−carbon bond. The enzymatic cascade reaction was performed in one‐pot in the presence of d‐serine and appropriate aldehydes for the synthesis of valuable (3S)‐hydroxyketones, which were obtained with high enantio‐ and diastereoselectivity and in good yield. The efficiency of the process was based on the irreversibility of both reactions allowing complete conversion of d‐serine and aldehydes.

Authors: None

Date Published: 6th Jun 2019

Journal: Volume361, Issue11 Special Issue: Biocatalysis, Pages 2550-2558

Second-Generation Engineering of a Thermostable Transketolase (TK Gst ) for Aliphatic Aldehyde Acceptors with Either Improved or Reversed Stereoselectivity
TRALAMINOL

Abstract (Expand)

The transketolase from Geobacillus stearothermophilus (TKGst) is a thermostable enzyme with notable high activity and stability at elevated temperatures, but it accepts non‐α‐hydroxylated aldehydes … only with low efficiency. Here we report a protein engineering study of TKGst based on double‐site saturation mutagenesis either at Leu191 or at Phe435 in combination with Asp470; these are the residues responsible for substrate binding in the active site. Screening of the mutagenesis libraries resulted in several positive variants with activity towards propanal up to 7.4 times higher than that of the wild type. Variants F435L/D470E and L191V/D470I exhibited improved (73 % ee, 3S) and inverted (74 % ee, 3R) stereoselectivity, respectively, for propanal. L191V, L382F/E, F435L, and D470/D470I were concluded to be positive mutations at Leu191, Leu382, Phe435, and Asp470 both for activity and for stereoselectivity improvement. These results should benefit further engineering of TKGst for various applications in asymmetric carboligation.

Authors: Chaoqiang Zhou, Thangavelu Saravanan, Marion Lorillière, Dongzhi Wei, Franck Charmantray, Laurence Hecquet, Wolf Dieter Fessner, Dong Yi

Date Published: 2nd Mar 2017

Journal: ChemBioChem

Aldolase-Catalyzed Asymmetric Synthesis of N-Heterocycles by Addition of Simple Aliphatic Nucleophiles to Aminoaldehydes
TRALAMINOL

Abstract (Expand)

Nitrogen heterocycles are structural motifs found in many bioactive natural products and of utmost importance in pharmaceutical drug development. In this work, a stereoselective synthesis of functionalized … N‐heterocycles was accomplished in two steps, comprising the biocatalytic aldol addition of ethanal and simple aliphatic ketones such as propanone, butanone, 3‐pentanone, cyclobutanone, and cyclopentanone to N‐Cbz‐protected aminoaldehydes using engineered variants of d‐fructose‐6‐phosphate aldolase from Escherichia coli (FSA) or 2‐deoxy‐d‐ribose‐5‐phosphate aldolase from Thermotoga maritima (DERATma) as catalysts. FSA catalyzed most of the additions of ketones while DERATma was restricted to ethanal and propanone. Subsequent treatment with hydrogen in the presence of palladium over charcoal, yielded low‐level oxygenated N‐heterocyclic derivatives of piperidine, pyrrolidine and N‐bicyclic structures bearing fused cyclobutane and cyclopentane rings, with stereoselectivities of 96–98 ee and 97:3 dr in isolated yields ranging from 35 to 79%.

Authors: Raquel Roldán, Karel Hernández, Jesús Joglar, Jordi Bujons, Teodor Parella, Wolf Dieter Fessner, Pere Clapés

Date Published: 6th Jun 2019

Journal: Adv. Synth. Catal.

Living on the edge: substrate competition explains loss of robustness in mitochondrial fatty-acid oxidation disorders.
FAIRDOM

Abstract (Expand)

BACKGROUND: Defects in genes involved in mitochondrial fatty-acid oxidation (mFAO) reduce the ability of patients to cope with metabolic challenges. mFAO enzymes accept multiple substrates of different … chain length, leading to molecular competition among the substrates. Here, we combined computational modeling with quantitative mouse and patient data to investigate whether substrate competition affects pathway robustness in mFAO disorders. RESULTS: First, we used comprehensive biochemical analyses of wild-type mice and mice deficient for medium-chain acyl-CoA dehydrogenase (MCAD) to parameterize a detailed computational model of mFAO. Model simulations predicted that MCAD deficiency would have no effect on the pathway flux at low concentrations of the mFAO substrate palmitoyl-CoA. However, high concentrations of palmitoyl-CoA would induce a decline in flux and an accumulation of intermediate metabolites. We proved computationally that the predicted overload behavior was due to substrate competition in the pathway. Second, to study the clinical relevance of this mechanism, we used patients' metabolite profiles and generated a humanized version of the computational model. While molecular competition did not affect the plasma metabolite profiles during MCAD deficiency, it was a key factor in explaining the characteristic acylcarnitine profiles of multiple acyl-CoA dehydrogenase deficient patients. The patient-specific computational models allowed us to predict the severity of the disease phenotype, providing a proof of principle for the systems medicine approach. CONCLUSION: We conclude that substrate competition is at the basis of the physiology seen in patients with mFAO disorders, a finding that may explain why these patients run a risk of a life-threatening metabolic catastrophe.

Authors: Karen Van Eunen, C. M. Volker-Touw, A. Gerding, A. Bleeker, J. C. Wolters, W. J. van Rijt, A. M. Martines, K. E. Niezen-Koning, R. M. Heiner, H. Permentier, A. K. Groen, D. J. Reijngoud, Terry G.J. Derks, Barbara Bakker

Date Published: 7th Dec 2016

Journal: BMC Biol

CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genes
DigiSal

Abstract (Expand)

Atlantic salmon can synthesize polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic acid (20:5n-3), arachidonic acid (20:4n-6) and docosahexaenoic acid (22:6n-3) via activities of very long … chain fatty acyl elongases (Elovls) and fatty acyl desaturases (Fads), albeit to a limited degree. Understanding molecular mechanisms of PUFA biosynthesis and regulation is a pre-requisite for sustainable use of vegetable oils in aquafeeds as current sources of fish oils are unable to meet increasing demands for omega-3 PUFAs. By generating CRISPR-mediated elovl2 partial knockout (KO), we have shown that elovl2 is crucial for multi-tissue synthesis of 22:6n-3 in vivo and that endogenously synthesized PUFAs are important for transcriptional regulation of lipogenic genes in Atlantic salmon. The elovl2-KOs showed reduced levels of 22:6n-3 and accumulation of 20:5n-3 and docosapentaenoic acid (22:5n-3) in the liver, brain and white muscle, suggesting inhibition of elongation. Additionally, elovl2-KO salmon showed accumulation of 20:4n-6 in brain and white muscle. The impaired synthesis of 22:6n-3 induced hepatic expression of sterol regulatory element binding protein-1 (srebp-1), fatty acid synthase-b, Δ6fad-a, Δ5fad and elovl5. Our study demonstrates key roles of elovl2 at two penultimate steps of PUFA synthesis in vivo and suggests Srebp-1 as a main regulator of endogenous PUFA synthesis in Atlantic salmon.

Authors: Alex K. Datsomor, Nikola Zic, Keshuai Li, Rolf E. Olsen, Yang Jin, Jon Olav Vik, Rolf B. Edvardsen, Fabian Grammes, Anna Wargelius, Per Winge

Date Published: 1st Dec 2019

Journal: Sci Rep

Delivering on open data: Current practices in data sharing, and challenges ahead!
FAIRDOM, FAIRDOM user meeting

Abstract

Not specified

Author: Timon Oefelein

Date Published: 20th Nov 2018

Journal: SCS

Human iPSC-derived RPE and retinal organoids reveal impaired alternative splicing of genes involved in pre-mRNA splicing in PRPF31 autosomal dominant retinitis pigmentosa
Stress granules

Abstract (Expand)

Mutations in pre-mRNA processing factors (PRPFs) cause 40% of autosomal dominant retinitis pigmentosa (RP), but it is unclear why mutations in ubiquitously expressed PRPFs cause retinal disease. To … understand the molecular basis of this phenotype, we have generated RP type 11 (PRPF31-mutated) patient-specific retinal organoids and retinal pigment epithelium (RPE) from induced pluripotent stem cells (iPSC). Impaired alternative splicing of genes encoding pre-mRNA splicing proteins occurred in patient-specific retinal cells and Prpf31+/− mouse retinae, but not fibroblasts and iPSCs, providing mechanistic insights into retinal-specific phenotypes of PRPFs. RPE was the most affected, characterised by loss of apical-basal polarity, reduced trans-epithelial resistance, phagocytic capacity, microvilli, and cilia length and incidence. Disrupted cilia morphology was observed in patient-derived-photoreceptors that displayed progressive features associated with degeneration and cell stress. In situ gene-editing of a pathogenic mutation rescued key structural and functional phenotypes in RPE and photoreceptors, providing proof-of-concept for future therapeutic strategies. eTOC PRPF31 is a ubiquitously expressed pre-mRNA processing factor that when mutated causes autosomal dominant RP. Using a patient-specific iPSC approach, Buskin and Zhu et al. show that retinal-specific defects result from altered splicing of genes involved in the splicing process itself, leading to impaired splicing, loss of RPE polarity and diminished phagocytic ability as well as reduced cilia incidence and length in both photoreceptors and RPE.

Authors: Adriana Buskin, Lili Zhu, Valeria Chichagova, Basudha Basu, Sina Mozaffari-Jovin, David Dolan, Alastair Droop, Joseph Collin, Revital Bronstein, Sudeep Mehrotra, Michael Farkas, Gerrit Hilgen, Kathryn White, Dean Hallam, Katarzyna Bialas, Git Chung, Carla Mellough, Yuchun Ding, Natalio Krasnogor, Stefan Przyborski, Jumana Al-Aama, Sameer Alharthi, Yaobo Xu, Gabrielle Wheway, Katarzyna Szymanska, Martin McKibbin, Chris F Inglehearn, David J Elliott, Susan Lindsay, Robin R Ali, David H Steel, Lyle Armstrong, Evelyne Sernagor, Eric Pierce, Reinhard Luehrmann, Sushma Nagaraja Grellscheid, Colin A Johnson, Majlinda Lako

Date Published: No date defined

Journal: Not specified

Circadian protein regulation in the green lineage I. A phospho-dawn anticipates light onset before proteins peak in daytime.
Millar group

Abstract (Expand)

BioRxiv preprint, 4 April 2018. Abstract: Daily light-dark cycles (LD) drive dynamic regulation of plant and algal transcriptomes via photoreceptor pathways and 24-hour, circadian rhythms. Diel regulation … of protein levels and modifications has been less studied. Ostreococcus tauri, the smallest free-living eukaryote, provides a minimal model proteome for the green lineage. Here, we compare transcriptome data under LD to the algal proteome and phosphoproteome, assayed using shotgun mass-spectrometry. Under 10% of 855 quantified proteins were rhythmic but two-thirds of 860 phosphoproteins showed rhythmic modification(s). Most rhythmic proteins peaked in the daytime. Model simulations showed that light-stimulated protein synthesis largely accounts for this distribution of protein peaks. Prompted by apparently dark-stable proteins, we sampled during prolonged dark adaptation, where stable RNAs and very limited change to the proteome suggested a quiescent, cellular “dark state”. In LD, acid-directed and proline-directed protein phosphorylation sites were regulated in antiphase. Strikingly, 39% of rhythmic phospho-sites reached peak levels just before dawn. This anticipatory phosphorylation is distinct from light-responsive translation but consistent with plant phosphoprotein profiles, suggesting that a clock-regulated phospho-dawn prepares green cells for daytime functions.

Authors: Zeenat B. Noordally, Matthew M. Hindle, Sarah F. Martin, Daniel Seaton, Ian Simpson, Thierry Le Bihan, Andrew Millar

Date Published: No date defined

Journal: Not specified

Molecular basis of flowering under natural long-day conditions in Arabidopsis.
Regulation of flowering time in natural conditions

Abstract (Expand)

Plants sense light and temperature changes to regulate flowering time. Here, we show that expression of the Arabidopsis florigen gene, FLOWERING LOCUS T (FT), peaks in the morning during spring, a … different pattern than we observe in the laboratory. Providing our laboratory growth conditions with a red/far-red light ratio similar to open-field conditions and daily temperature oscillation is sufficient to mimic the FT expression and flowering time in natural long days. Under the adjusted growth conditions, key light signalling components, such as phytochrome A and EARLY FLOWERING 3, play important roles in morning FT expression. These conditions stabilize CONSTANS protein, a major FT activator, in the morning, which is probably a critical mechanism for photoperiodic flowering in nature. Refining the parameters of our standard growth conditions to more precisely mimic plant responses in nature can provide a powerful method for improving our understanding of seasonal response.

Authors: Y. H. Song, A. Kubota, M. S. Kwon, M. F. Covington, N. Lee, E. R. Taagen, D. Laboy Cintron, D. Y. Hwang, R. Akiyama, S. K. Hodge, H. Huang, N. H. Nguyen, D. A. Nusinow, A. J. Millar, K. K. Shimizu, T. Imaizumi

Date Published: 27th Sep 2018

Journal: Nat Plants

Subcellular Distribution of NAD+ between Cytosol and Mitochondria Determines the Metabolic Profile of Human Cells.
NAD COMPARTMENTATION

Abstract (Expand)

The mitochondrial NAD pool is particularly important for the maintenance of vital cellular functions. Although at least in some fungi and plants, mitochondrial NAD is imported from the cytosol by carrier … proteins, in mammals, the mechanism of how this organellar pool is generated has remained obscure. A transporter mediating NAD import into mammalian mitochondria has not been identified. In contrast, human recombinant NMNAT3 localizes to the mitochondrial matrix and is able to catalyze NAD(+) biosynthesis in vitro. However, whether the endogenous NMNAT3 protein is functionally effective at generating NAD(+) in mitochondria of intact human cells still remains to be demonstrated. To modulate mitochondrial NAD(+) content, we have expressed plant and yeast mitochondrial NAD(+) carriers in human cells and observed a profound increase in mitochondrial NAD(+). None of the closest human homologs of these carriers had any detectable effect on mitochondrial NAD(+) content. Surprisingly, constitutive redistribution of NAD(+) from the cytosol to the mitochondria by stable expression of the Arabidopsis thaliana mitochondrial NAD(+) transporter NDT2 in HEK293 cells resulted in dramatic growth retardation and a metabolic shift from oxidative phosphorylation to glycolysis, despite the elevated mitochondrial NAD(+) levels. These results suggest that a mitochondrial NAD(+) transporter, similar to the known one from A. thaliana, is likely absent and could even be harmful in human cells. We provide further support for the alternative possibility, namely intramitochondrial NAD(+) synthesis, by demonstrating the presence of endogenous NMNAT3 in the mitochondria of human cells.

Authors: M. R. VanLinden, C. Dolle, I. K. Pettersen, V. A. Kulikova, Marc Niere, G. Agrimi, S. E. Dyrstad, F. Palmieri, A. A. Nikiforov, K. J. Tronstad, Mathias Ziegler

Date Published: 13th Nov 2015

Journal: J Biol Chem

Mechanistic model of temperature influence on flowering through whole-plant accumulation of FT
Regulation of flowering time in natural conditions

Abstract

BioRxiv preprint:

Authors: Hannah A Kinmonth-Schultz, Melissa J MacEwen, Daniel Seaton, Andrew Millar, Takato Imaizumi, Soo-Hyung Kim

Date Published: No date defined

Journal: Not specified

The Carbon Switch at the Level of Pyruvate and Phosphoenolpyruvate in Sulfolobus solfataricus P2.
HOTSOLUTE

Abstract (Expand)

Sulfolobus solfataricus P2 grows on different carbohydrates as well as alcohols, peptides and amino acids. Carbohydrates such as D-glucose or D-galactose are degraded via the modified, branched … Entner-Doudoroff (ED) pathway whereas growth on peptides requires the Embden-Meyerhof-Parnas (EMP) pathway for gluconeogenesis. As for most hyperthermophilic Archaea an important control point is established at the level of triosephophate conversion, however, the regulation at the level of pyruvate/phosphoenolpyruvate conversion was not tackled so far. Here we describe the cloning, expression, purification and characterization of the pyruvate kinase (PK, SSO0981) and the phosphoenolpyruvate synthetase (PEPS, SSO0883) of Sul. solfataricus. The PK showed only catabolic activity [catalytic efficiency (PEP): 627.95 mM(-1)s(-1), 70 degrees C] with phosphoenolpyruvate as substrate and ADP as phosphate acceptor and was allosterically inhibited by ATP and isocitrate (K i 0.8 mM). The PEPS was reversible, however, exhibited preferred activity in the gluconeogenic direction [catalytic efficiency (pyruvate): 1.04 mM(-1)s(-1), 70 degrees C] and showed some inhibition by AMP and alpha-ketoglutarate. The gene SSO2829 annotated as PEPS/pyruvate:phosphate dikinase (PPDK) revealed neither PEPS nor PPDK activity. Our studies suggest that the energy charge of the cell as well as the availability of building blocks in the citric acid cycle and the carbon/nitrogen balance plays a major role in the Sul. solfataricus carbon switch. The comparison of regulatory features of well-studied hyperthermophilic Archaea reveals a close link and sophisticated coordination between the respective sugar kinases and the kinetic and regulatory properties of the enzymes at the level of PEP-pyruvate conversion.

Authors: Patrick Haferkamp, B. Tjaden, Lu Shen, C. Brasen, Theresa Kouril, Bettina Siebers

Date Published: 30th Apr 2019

Journal: Front Microbiol

Phosphoglycerate kinase acts as a futile cycle at high temperature.
SulfoSys, SulfoSys - Biotec

Abstract (Expand)

In (hyper)thermophilic organisms metabolic processes have to be adapted to function optimally at high temperature. We compared the gluconeogenic conversion of 3-phosphoglycerate via 1,3-bisphosphoglycerate … to glyceraldehyde-3-phosphate at 30 degrees C and at 70 degrees C. At 30 degrees C it was possible to produce 1,3-bisphosphoglycerate from 3-phosphoglycerate with phosphoglycerate kinase, but at 70 degrees C, 1,3-bisphosphoglycerate was dephosphorylated rapidly to 3-phosphoglycerate, effectively turning the phosphoglycerate kinase into a futile cycle. When phosphoglycerate kinase was incubated together with glyceraldehyde 3-phosphate dehydrogenase it was possible to convert 3-phosphoglycerate to glyceraldehyde 3-phosphate, both at 30 degrees C and at 70 degrees C, however, at 70 degrees C only low concentrations of product were observed due to thermal instability of glyceraldehyde 3-phosphate. Thus, thermolabile intermediates challenge central metabolic reactions and require special adaptation strategies for life at high temperature.

Authors: Theresa Kouril, J. J. Eicher, Bettina Siebers, Jacky Snoep

Date Published: 7th Oct 2017

Journal: Microbiology

The FAIR Guiding Principles for scientific data management and stewardship
Sustainable co-production

Abstract

Not specified

Authors: Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim Clark, Mercè Crosas, Ingrid Dillo, Olivier Dumon, Scott Edmunds, Chris T. Evelo, Richard Finkers, Alejandra Gonzalez-Beltran, Alasdair J.G. Gray, Paul Groth, Carole Goble, Jeffrey S. Grethe, Jaap Heringa, Peter A.C ’t Hoen, Rob Hooft, Tobias Kuhn, Ruben Kok, Joost Kok, Scott J. Lusher, Maryann E. Martone, Albert Mons, Abel L. Packer, Bengt Persson, Philippe Rocca-Serra, Marco Roos, Rene van Schaik, Susanna-Assunta Sansone, Erik Schultes, Thierry Sengstag, Ted Slater, George Strawn, Morris A. Swertz, Mark Thompson, Johan van der Lei, Erik van Mulligen, Jan Velterop, Andra Waagmeester, Peter Wittenburg, Katherine Wolstencroft, Jun Zhao, Barend Mons

Date Published: 15th Mar 2016

Journal: Sci. Data

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017
FAIRDOM, FAIRDOM & LiSyM & de.NBI Data Structuring Training

Abstract

Not specified

Authors: Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Mike Hucka, Sarah M. Keating, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath

Date Published: 25th Apr 2018

Journal: Not specified

Harmonizing semantic annotations for computational models in biology
FAIRDOM

Abstract

Not specified

Authors: Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba, Samuel H Friedman, Alan Garny, John H Gennari, Padraig Gleeson, Martin Golebiewski, Mike Hucka, Nick Juty, Chris Myers, Brett G Olivier, Herbert M Sauro, Martin Scharm, Jacky Snoep, Vasundra Toure, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath

Date Published: 21st Nov 2018

Journal: Not specified

Simultaneous Clostridial fermentation, lipase-catalyzed esterification, and ester extraction to enrich diesel with butyl butyrate.
BESTER

Abstract (Expand)

The recovery of 1-butanol from fermentation broth is energy-intensive since typical concentrations in fermentation broth are below 20 g L(-1). To prevent butanol inhibition and high downstream processing … costs, we aimed at producing butyl esters instead of 1-butanol. It is shown that it is possible to perform simultaneously clostridial fermentation, esterification of the formed butanol to butyl butyrate, and extraction of this ester by hexadecane. The very high partition coefficient of butyl butyrate pulls the esterification towards the product side even at fermentation pH and relatively low butanol concentrations. The hexadecane extractant is a model diesel compound and is nontoxic to the cells. If butyl butyrate enriched diesel can directly be used as car fuel, no product recovery is required. A proof-of-principle experiment for the one-pot bio-ester production from glucose led to 5 g L(-1) butyl butyrate in the hexadecane phase. The principle may be extended to a wide range of esters, especially to longer chain ones.

Authors: C. van den Berg, A. S. Heeres, L. A. van der Wielen, A. J. Straathof

Date Published: No date defined

Journal: Biotechnol Bioeng

In situ esterification and extractive fermentation for butyl butyrate production with Clostridium tyrobutyricum.
BESTER

Abstract (Expand)

Butyl butyrate (BB) is a valuable chemical that can be used as flavor, fragrance, extractant, and so on in various industries. Meanwhile, BB can also be used as a fuel source with excellent compatibility … as gasoline, aviation kerosene, and diesel components. The conventional industrial production of BB is highly energy-consuming and generates various environmental pollutants. Recently, there have been tremendous interests in producing BB from renewable resources through biological routes. In this study, based on the fermentation using the hyper-butyrate producing strain Clostridium tyrobutyricum ATCC 25755, efficient BB production through in situ esterification was achieved by supplementation of lipase and butanol into the fermentation. Three commercially available lipases were assessed and the one from Candida sp. (recombinant, expressed in Aspergillus niger) was identified with highest catalytic activity for BB production. Various conditions that might affect BB production in the fermentation have been further evaluated, including the extractant type, enzyme loading, agitation, pH, and butanol supplementation strategy. Under the optimized conditions (5.0 g L(-1) of enzyme loading, pH at 5.5, butanol kept at 10.0 g L(-1) ), 34.7 g L(-1) BB was obtained with complete consumption of 50 g L(-1) glucose as the starting substrate. To our best knowledge, the BB production achieved in this study is the highest among the ever reported from the batch fermentation process. Our results demonstrated an excellent biological platform for renewable BB production from low-value carbon sources. Biotechnol. Bioeng. 2017;114: 1428-1437. (c) 2017 Wiley Periodicals, Inc.

Authors: Z. T. Zhang, S. Taylor, Y. Wang

Date Published: No date defined

Journal: Biotechnol Bioeng

Atlantic salmon raised with diets low in long-chain polyunsaturated n-3 fatty acids in freshwater have a Mycoplasma-dominated gut microbiota at sea
GenoSysFat, DigiSal

Abstract (Expand)

Factors affecting the establishment of the gut microbiota in animals living in marine environments remain largely unknown. In terrestrial animals, however, it is well established that the juvenile … environment has a major impact on the gut microbiota later in life. Atlantic salmon Salmo salar is an anadromous fish important in aquaculture with a juvenile freshwater stage and an adult seawater stage. For wild salmon, there are major dietary changes with respect to availability of long-chain polyunsaturated n-3 fatty acids (LC-n-3 PUFA) with lower abundance in freshwater systems. The aim of our work was therefore to determine the effect of a juvenile freshwater diet with high LC-n-3 PUFA, as compared to a diet low in LC-n-3 PUFA (designed to increase the endogenous LC-n-3 PUFA production), on the transition to a seawater gut microbiota for Atlantic salmon. We found a juvenile freshwater microbiota high in Firmicutes for fish raised with low LC-n-3 PUFA, while the microbiota for fish given high LC-n-3 PUFA feed was high in Proteobacteria. One hundred days after transfer to a common sea cage, fish that were given low LC-n-3 PUFA diets in freshwater showed significantly higher (p = 0.02, Kruskal-Wallis) Mycoplasma content (90 ± 7%; mean ± SD) compared to fish raised on a high LC-n-3 PUFA diet in freshwater (25 ± 31% Mycoplasma). Shotgun metagenome sequencing from fish raised with a low LC-n-3 PUFA diet identified a salmon-associated Mycoplasma in sea, being distinct from currently known Mycoplasma. The genome sequence information indicated a mutualistic lifestyle of this bacterium. Mycoplasma has also previously been identified as dominant (>70%) in sea-living adult Atlantic salmon. Taken together, our results suggest that the juvenile freshwater diet influences the establishment of the gut microbiota in marine Atlantic salmon.

Authors: Yang Jin, Inga Leena Angell, Sandve Simen, Lars Snipen, Y Olsen, Knut Rudi

Date Published: 24th Jan 2019

Journal: Aquacult. Environ. Interact.

Draft genome sequence of the docosahexaenoic acid producing thraustochytrid Aurantiochytrium sp. T66.
Auromega

Abstract (Expand)

Thraustochytrids are unicellular, marine protists, and there is a growing industrial interest in these organisms, particularly because some species, including strains belonging to the genus Aurantiochytrium, … accumulate high levels of docosahexaenoic acid (DHA). Here, we report the draft genome sequence of Aurantiochytrium sp. T66 (ATCC PRA-276), with a size of 43 Mbp, and 11,683 predicted protein-coding sequences. The data has been deposited at DDBJ/EMBL/Genbank under the accession LNGJ00000000. The genome sequence will contribute new insight into DHA biosynthesis and regulation, providing a basis for metabolic engineering of thraustochytrids.

Authors: B. Liu, H. Ertesvag, I. M. Aasen, O. Vadstein, T. Brautaset, T. M. Heggeset

Date Published: No date defined

Journal: Genom Data

Rev1 contributes to proper mitochondrial function via the PARP-NAD+-SIRT1-PGC1α axis
Dynamic interplay between nuclei and mitochondria in ageing cells

Abstract (Expand)

Nucleic acids, which constitute the genetic material of all organisms, are continuously exposed to endogenous and exogenous damaging agents, representing a significant challenge to genome stability and … genome integrity over the life of a cell or organism. Unrepaired DNA lesions, such as single- and double-stranded DNA breaks (SSBs and DSBs), and single-stranded gaps can block progression of the DNA replication fork, causing replicative stress and/or cell cycle arrest. However, translesion synthesis (TLS) DNA polymerases, such as Rev1, have the ability to bypass some DNA lesions, which can circumvent the process leading to replication fork arrest and minimize replicative stress. Here, we show that Rev1-deficiency in mouse embryo fibroblasts or mouse liver tissue is associated with replicative stress and mitochondrial dysfunction. In addition, Rev1-deficiency is associated with high poly(ADP) ribose polymerase 1 (PARP1) activity, low endogenous NAD+, low expression of SIRT1 and PGC1α and low adenosine monophosphate (AMP)-activated kinase (AMPK) activity. We conclude that replication stress via Rev1-deficiency contributes to metabolic stress caused by compromized mitochondrial function via the PARP-NAD+-SIRT1-PGC1α axis.

Authors: Nima Borhan Fakouri, Jon Ambæk Durhuus, Christine Elisabeth Regnell, Maria Angleys, Claus Desler, Md Mahdi Hasan-Olive, Ana Martín-Pardillos, Anastasia Tsaalbi-Shtylik, Kirsten Thomsen, Martin Lauritzen, Vilhelm A. Bohr, Niels de Wind, Linda Hildegard Bergersen, Tim Rasmussen

Date Published: 1st Dec 2017

Journal: Sci Rep

NAD + Replenishment Improves Lifespan and Healthspan in Ataxia Telangiectasia Models via Mitophagy and DNA Repair
Dynamic interplay between nuclei and mitochondria in ageing cells

Abstract (Expand)

Ataxia telangiectasia (A-T) is a rare autosomal recessive disease characterized by progressive neurodegeneration and cerebellar ataxia. A-T is causally linked to defects in ATM, a master regulator of … the response to and repair of DNA double-strand breaks. The molecular basis of cerebellar atrophy and neurodegeneration in A-T patients is unclear. Here we report and examine the significance of increased PARylation, low NAD+, and mitochondrial dysfunction in ATM-deficient neurons, mice, and worms. Treatments that replenish intracellular NAD+ reduce the severity of A-T neuropathology, normalize neuromuscular function, delay memory loss, and extend lifespan in both animal models. Mechanistically, treatments that increase intracellular NAD+ also stimulate neuronal DNA repair and improve mitochondrial quality via mitophagy. This work links two major theories on aging, DNA damage accumulation, and mitochondrial dysfunction through nuclear DNA damage-induced nuclear-mitochondrial signaling, and demonstrates that they are important pathophysiological determinants in premature aging of A-T, pointing to therapeutic interventions.

Authors: Evandro Fei Fang, Henok Kassahun, Deborah L. Croteau, Morten Scheibye-Knudsen, Krisztina Marosi, Huiming Lu, Raghavendra A. Shamanna, Sumana Kalyanasundaram, Ravi Chand Bollineni, Mark A. Wilson, Wendy B. Iser, Bradley N. Wollman, Marya Morevati, Jun Li, Jesse S. Kerr, Qiping Lu, Tyler B. Waltz, Jane Tian, David A. Sinclair, Mark P. Mattson, Marianne B. Nilsen, Vilhelm A. Bohr

Date Published: 1st Oct 2016

Journal: Cell Metabolism

Predicting strain engineering strategies using iKS1317: a genome‐scale metabolic model of Streptomyces coelicolor
INBioPharm

Abstract

Not specified

Authors: Tjasa Kumelj, Snorre Sulheim, Alexander Wentzel, Eivind Almaas

Date Published: 7th Dec 2018

Journal: Biotechnol. J.

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