scholarly journals Plant sulphur metabolism is stimulated by photorespiration

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Cyril Abadie ◽  
Guillaume Tcherkez
Keyword(s):  
Amino Acids ◽  
Metabolic Regulation ◽  
Biochemical Pathway ◽  
Sulphur Metabolism ◽  
Crop Breeding ◽  
Essential Information ◽  
Sulphur Nutrition ◽  
Metabolic Fluxes ◽  
Gaseous Composition ◽  
Common Target

Abstract Intense efforts have been devoted to describe the biochemical pathway of plant sulphur (S) assimilation from sulphate. However, essential information on metabolic regulation of S assimilation is still lacking, such as possible interactions between S assimilation, photosynthesis and photorespiration. In particular, does S assimilation scale with photosynthesis thus ensuring sufficient S provision for amino acids synthesis? This lack of knowledge is problematic because optimization of photosynthesis is a common target of crop breeding and furthermore, photosynthesis is stimulated by the inexorable increase in atmospheric CO2. Here, we used high-resolution 33S and 13C tracing technology with NMR and LC-MS to access direct measurement of metabolic fluxes in S assimilation, when photosynthesis and photorespiration are varied via the gaseous composition of the atmosphere (CO2, O2). We show that S assimilation is stimulated by photorespiratory metabolism and therefore, large photosynthetic fluxes appear to be detrimental to plant cell sulphur nutrition.

Promiscuous enzymes generating d-amino acids in mammals: Why they may still surprise us?

2021 ◽  
Vol 478 (5) ◽  
pp. 1175-1178
Author(s):  
Herman Wolosker ◽  
Inna Radzishevsky
Keyword(s):  
Amino Acids ◽  
Mammalian Cells ◽  
Common Property ◽  
Mammalian Brain ◽  
Intercellular Signaling ◽  
Biochemical Pathway ◽  
Recent Issue ◽  
Threonine Dehydratase ◽  
Glutamate Synthesis ◽  
Potential Biomarkers

Promiscuous catalysis is a common property of enzymes, particularly those using pyridoxal 5′-phosphate as a cofactor. In a recent issue of this journal, Katane et al. Biochem. J. 477, 4221–4241 demonstrate the synthesis and accumulation of d-glutamate in mammalian cells by promiscuous catalysis mediated by a pyridoxal 5′-phosphate enzyme, the serine/threonine dehydratase-like (SDHL). The mechanism of SDHL resembles that of serine racemase, which synthesizes d-serine, a well-established signaling molecule in the mammalian brain. d-Glutamate is present in body fluids and is degraded by the d-glutamate cyclase at the mitochondria. This study demonstrates a biochemical pathway for d-glutamate synthesis in mammalian cells and advances our knowledge on this little-studied d-amino acid in mammals. d-Amino acids may still surprise us by their unique roles in biochemistry, intercellular signaling, and as potential biomarkers of disease.

scholarly journals Carbohydrate and Amino Acid Profiles of Cotton Plant Biomass Products

Agriculture ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 2 ◽  
Author(s):  
Zhongqi He ◽  
Dan C. Olk ◽  
Haile Tewolde ◽  
Hailin Zhang ◽  
Mark Shankle
Keyword(s):  
Amino Acids ◽  
Cotton Plant ◽  
Management Practices ◽  
Plant Biomass ◽  
Plant Residues ◽  
Cotton Leaf ◽  
Essential Information ◽  
Plant Parts ◽  
Processing Strategies ◽  
Biomass Materials

To achieve the optimal and diverse utilization of cotton (Gossypium hirsutum) plant residues in various agricultural, industrial, and environmental applications, the chemical composition of cotton biomass tissues across different plant parts (e.g., seed, boll, bur, leaves, stalk, stem, and root) is of essential information. Thus, in this work, we collected field-grown whole mature cotton plants and separated them into distinct biomass fractions including main stems, leaf blades, branches, petioles, roots, and reproductive parts (mid-season growth stage) or bur, peduncles/bract, and seed cotton (pre-defoliation stage). The contents of selected carbohydrates and amino acids in these cotton biomass materials were determined. Both essential and nonessential amino acids were enriched in cotton leaf blades and reproductive parts. The distribution pattern of the selected carbohydrates differed from that of amino acids—higher contents of carbohydrate were found in roots, main stems, and branches. Although glucose was the most abundant non-structural carbohydrate in cotton plant parts at mid-season, xylose was the most abundant in most plant parts at the pre-defoliation stage. Nutritional carbohydrates and amino acids were further accumulated in seeds at pre-defoliation. The information reported in this work would be helpful in exploring and optimizing management practices and processing strategies for utilizing cotton crop biomass materials as valuable and renewable natural resources.

scholarly journals Metabolome Remodeling during the Acidogenic-Solventogenic Transition in Clostridium acetobutylicum

2011 ◽  
Vol 77 (22) ◽  
pp. 7984-7997 ◽  
Author(s):  
Daniel Amador-Noguez ◽  
Ian A. Brasg ◽  
Xiao-Jiang Feng ◽  
Nathaniel Roquet ◽  
Joshua D. Rabinowitz
Keyword(s):  
Amino Acids ◽  
Clostridium Acetobutylicum ◽  
Reducing Power ◽  
Tca Cycle ◽  
Content Type ◽  
Isotope Tracers ◽  
Metabolic Fluxes ◽  
The Tca Cycle ◽  
Concentration Changes ◽  
Almost All

ABSTRACTThe fermentation carried out by the biofuel producerClostridium acetobutylicumis characterized by two distinct phases. Acidogenesis occurs during exponential growth and involves the rapid production of acids (acetate and butyrate). Solventogenesis initiates as cell growth slows down and involves the production of solvents (butanol, acetone, and ethanol). Using metabolomics, isotope tracers, and quantitative flux modeling, we have mapped the metabolic changes associated with the acidogenic-solventogenic transition. We observed a remarkably ordered series of metabolite concentration changes, involving almost all of the 114 measured metabolites, as the fermentation progresses from acidogenesis to solventogenesis. The intracellular levels of highly abundant amino acids and upper glycolytic intermediates decrease sharply during this transition. NAD(P)H and nucleotide triphosphates levels also decrease during solventogenesis, while low-energy nucleotides accumulate. These changes in metabolite concentrations are accompanied by large changes in intracellular metabolic fluxes. During solventogenesis, carbon flux into amino acids, as well as flux from pyruvate (the last metabolite in glycolysis) into oxaloacetate, decreases by more than 10-fold. This redirects carbon into acetyl coenzyme A, which cascades into solventogenesis. In addition, the electron-consuming reductive tricarboxylic acid (TCA) cycle is shutdown, while the electron-producing oxidative (clockwise) right side of the TCA cycle remains active. Thus, the solventogenic transition involves global remodeling of metabolism to redirect resources (carbon and reducing power) from biomass production into solvent production.

scholarly journals Main Variables Affecting a Chemical-Enzymatic Method to Obtain Protein and Amino Acids from Resistant Microalgae

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
J. A. Callejo-López ◽  
M. Ramírez ◽  
J. Bolívar ◽  
D. Cantero
Keyword(s):  
Amino Acids ◽  
Enzymatic Reaction ◽  
Amino Nitrogen ◽  
Biomass Concentration ◽  
Relevant Information ◽  
High Yield ◽  
Total Biomass ◽  
Essential Information ◽  
Fresh Biomass ◽  
Alkaline Reaction

The development of microalgae uses requires further investigation in cell disruption alternatives to reduce the costs associated to this processing stage. This study aimed to evaluate the main variables affecting an extraction method to obtain protein and amino acids from microalgae. The method was based on a sequential alkaline-enzymatic process, with separate extractions and noncontrolled pH, and was applied to fresh biomass of a resistant species. The processed microalgae were composed of a consortium with Nannochloropsis sp. as predominant species. After the optimization of the pH of the alkaline reaction, the effect of the time of the alkaline reaction (30–120 min), the time (30–120 min) and temperature (40–60°C) of the enzymatic reaction, and the biomass concentration (50–150 mg·ml−1), on the extraction yields of protein and free amino nitrogen (FAN) and on the final concentration of protein in the extract, was studied using a response surface methodology. Even though all the variables and some interactions among them had a significant effect, the biomass concentration was the most important factor affecting the overall process. The results showed relevant information about the different options in order to maximize not only the response variables individually but also different combinations of them. Assays with optimized values reached maximum yields of 80.3% and 1.07% of protein (% of total protein) and FAN (% of total biomass), respectively, and a protein concentration in the extract of 15.2 mg·ml−1. The study provided the essential information of an alternative approach to obtain protein and amino acids from fresh biomass of resistant microalgae with a high yield, also opening perspectives for further research in particular aspects.

scholarly journals Single-Molecule Peptide Fingerprinting

2017 ◽  
Author(s):  
Jetty van Ginkel ◽  
Mike Filius ◽  
Malwina Szczepaniak ◽  
Pawel Tulinski ◽  
Anne S. Meyer ◽  
...  
Keyword(s):  
Amino Acids ◽  
Single Cell ◽  
Single Molecule ◽  
Medical Diagnostics ◽  
Cellular Systems ◽  
Protein Sequencing ◽  
Small Scale ◽  
Proof Of Concept ◽  
Essential Information ◽  
First Choice

ABSTRACTProteomic analyses provide essential information on molecular pathways of cellular systems and the state of a living organism. Mass spectrometry is currently the first choice for proteomic analysis. However, the requirement for a large amount of sample renders a small-scale proteomics study, such as single-cell analysis, challenging. Here we demonstrate a proof of concept of singlemolecule FRET-based protein fingerprinting. We harnessed the AAA+ protease ClpXP to scan peptides. By using donor fluorophore-labeled ClpP, we sequentially read out FRET signals from acceptor-labeled amino acids of peptides. The repurposed ClpXP exhibits uni-directional processing with high processivity and has the potential to detect low-abundance proteins. Our technique is a promising approach for sequencing protein substrates using a small amount of sample.SIGNIFICANCEProtein sequencing remains a challenge for small samples. A sensitive sequencing technology will create the opportunity for single-cell proteomics and real-time screening for on-site medical diagnostics. In order to resolve protein identity, we previously developed a computational algorithm that analyzes the ordered sequence of only two types of amino acids within a protein species. Through modification of a biological nanomachine, here we developed single-molecule fluorescence technology to linearize protein molecules and to read signals from labeled amino acids in an ordered manner. This proof of concept of singlemolecule fingerprinting will open a new door to single-molecule protein sequencing and pave the road towards the development of a new, fast, and reliable diagnostic tool.

scholarly journals TRIMER: Transcription Regulation Integrated with MEtabolic Regulation

2021 ◽  
Author(s):  
Puhua Niu ◽  
Maria J. Soto ◽  
Byung-Jun Yoon ◽  
Edward R. Dougherty ◽  
Francis J. Alexander ◽  
...  
Keyword(s):  
Transcription Regulation ◽  
Regulatory Networks ◽  
Metabolic Regulation ◽  
Simulation Framework ◽  
Data Types ◽  
Metabolic Fluxes ◽  
Gene Regulatory ◽  
Traditional Approaches ◽  
Evaluation Platform ◽  
Genome Scale

ABSTRACTAdvances in bioengineering have enabled numerous bio-based commodities. Yet most traditional approaches do not extend beyond a single metabolic pathway and do not attempt to modify gene regulatory networks in order to buffer metabolic perturbations. This is despite access to near universal technologies allowing genome-scale engineering. To help overcome this limitation, we have developed a pipeline enabling analysis of Transcription Regulation Integrated with MEtabolic Regulation (TRIMER). TRIMER utilizes a Bayesian network (BN) inferred from transcriptomic data to model the transcription factor regulatory network. TRIMER then infers the probabilities of gene states that are of relevance to the metabolism of interest, and predicts metabolic fluxes resulting from deletion of transcription factors at the genome scale. Additionally, we have developed a simulation framework to mimic the TF-regulated metabolic network, capable of generating both gene expression states and metabolic fluxes, thereby providing a fair evaluation platform for benchmarking models and predictions. Here, we present this computational pipeline. We demonstrate TRIMER’s applicability to both simulated and experimental data and show that it outperforms current approaches on both data types.

scholarly journals SALARECON connects the Atlantic salmon genome to growth and feed efficiency

2021 ◽  
Author(s):  
Maksim Zakhartsev ◽  
Filip Rotnes ◽  
Marie Gulla ◽  
Ove Øyås ◽  
Jesse C. J. van Dam ◽  
...  
Keyword(s):  
Amino Acids ◽  
Atlantic Salmon ◽  
Feed Efficiency ◽  
Metabolic Model ◽  
Quality Model ◽  
Farmed Fish ◽  
Feed Ingredients ◽  
Metabolic Fluxes ◽  
Commercial Feed ◽  
Limiting Amino Acids

Background: Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and conditions for growth and feed efficiency. Also, marine feed ingredients must be replaced to meet global demand with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which is what converts nutrients in the feed to energy and biomass, but they are currently not available for major aquaculture species such as salmon. Results: We present SALARECON, a metabolic model that links the Atlantic salmon genome to metabolic fluxes and growth. It performs well in standardized tests and reflects expected metabolic (in)capabilities. We show that it can explain observed growth under hypoxia in terms of metabolic fluxes and apply it to aquaculture by simulating growth with commercial feed ingredients. Predicted feed efficiencies and limiting amino acids agree with data, and the model suggests that marine feed efficiency can be achieved by supplementing a few amino acids to plant- and insect-based feeds. Conclusion: SALARECON is a high-quality model that makes it possible to simulate Atlantic salmon metabolism and growth from the genome. It can explain Atlantic salmon physiology and address key challenges in aquaculture.

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