A new insight into isotopic fractionation associated with decarboxylation in organisms: implications for amino acid isotope approaches in biogeoscience

Abstract Stable nitrogen (15N/14N) and carbon (13C/12C) isotopic compositions of amino acids in organisms have widely been employed as a powerful tool to evaluate resource utilization and trophic connection among organisms in diverse ecosystems. However, little is known about the physiological factors or mechanisms responsible for determining the isotopic discrimination (particularly for carbon) within amino acids of organisms. In the present study, we investigated the inter-trophic discrimination of nitrogen and carbon isotopes within amino acids (Δδ15NAA and Δδ13CAA, respectively) using four consumer–diet pairs. Each pairing illustrates a metabolic perspective of isotopic fractionation of amino acids. The Δδ15NAA values in these combinations reveal a trend consistent with those observed in many other combinations in previous studies. This further validates a standard scenario: the deamination preferentially removes 14N amino group from diet-derived amino acids, leaving behind the 15N-enriched amino acids in consumer biomass. The Δδ15NAA values thus mirror the activity of amino acid deamination in consumers. In contrast, the trends in the Δδ13CAA value suggest a different metabolic fate for the amino acid carbon isotope. Based on our results, we predict the following scenario: decarboxylation preferentially removes 12C α-carbon (i.e., carbonyl-carbon) from pyruvic acid in glycolysis, and from α-ketoglutaric acid in the tricarboxylic acid cycle, leaving behind the 13C-enriched both pyruvic and α-ketoglutaric acids. The 13C is then transferred to amino acids that are synthesized from the 13C-enriched precursor molecules within consumers. The Δδ13CAA values therefore mirror the pathways of de novo amino acid synthesis in consumers. The proposed link between nitrogen and carbon isotopes can refine our knowledge of the potential processes affecting the isotopic fractionation within diet and consumer compartments, as well as environmental samples. Graphical abstract

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Mechanism of De Novo Branched-Chain Amino Acid Synthesis as an Alternative Electron Sink in Hypoxic Aspergillus nidulans Cells

Applied and Environmental Microbiology ◽

10.1128/aem.02135-09 ◽

2010 ◽

Vol 76 (5) ◽

pp. 1507-1515 ◽

Cited By ~ 36

Author(s):

Motoyuki Shimizu ◽

Tatsuya Fujii ◽

Shunsuke Masuo ◽

Naoki Takaya

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Aspergillus Nidulans ◽

De Novo ◽

Acid Synthesis ◽

Branched Chain Amino Acids ◽

Amino Acid Synthesis ◽

Lactate Dehydrogenase Activity ◽

Branched Chain Amino Acid ◽

Branched Chain

ABSTRACT Although branched-chain amino acids are synthesized as building blocks of proteins, we found that the fungus Aspergillus nidulans excretes them into the culture medium under hypoxia. The transcription of predicted genes for synthesizing branched-chain amino acids was upregulated by hypoxia. A knockout strain of the gene encoding the large subunit of acetohydroxy acid synthase (AHAS), which catalyzes the initial reaction of the synthesis, required branched-chain amino acids for growth and excreted very little of them. Pyruvate, a substrate for AHAS, increased the amount of hypoxic excretion in the wild-type strain. These results indicated that the fungus responds to hypoxia by synthesizing branched-chain amino acids via a de novo mechanism. We also found that the small subunit of AHAS regulated hypoxic branched-chain amino acid production as well as cellular AHAS activity. The AHAS knockout resulted in higher ratios of NADH/NAD+ and NADPH/NADP+ under hypoxia, indicating that the branched-chain amino acid synthesis contributed to NAD+ and NADP+ regeneration. The production of branched-chain amino acids and the hypoxic induction of involved genes were partly repressed in the presence of glucose, where cells produced ethanol and lactate and increased levels of lactate dehydrogenase activity. These indicated that hypoxic branched-chain amino acid synthesis is a unique alternative mechanism that functions in the absence of glucose-to-ethanol/lactate fermentation and oxygen respiration.

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Petasis vs. Strecker Amino Acid Synthesis: Convergence, Divergence and Opportunities in Organic Synthesis

Molecules ◽

10.3390/molecules26061707 ◽

2021 ◽

Vol 26 (6) ◽

pp. 1707

Author(s):

Wayiza Masamba

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Organic Synthesis ◽

Acid Synthesis ◽

Physical Sciences ◽

Amino Acid Synthesis

α-Amino acids find widespread applications in various areas of life and physical sciences. Their syntheses are carried out by a multitude of protocols, of which Petasis and Strecker reactions have emerged as the most straightforward and most widely used. Both reactions are three-component reactions using the same starting materials, except the nucleophilic species. The differences and similarities between these two important reactions are highlighted in this review.

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New aspects of amino acid metabolism in cancer

British Journal of Cancer ◽

10.1038/s41416-019-0620-5 ◽

2019 ◽

Vol 122 (2) ◽

pp. 150-156 ◽

Cited By ~ 31

Author(s):

Lisa Vettore ◽

Rebecca L. Westbrook ◽

Daniel A. Tennant

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Cancer Cells ◽

Cancer Metabolism ◽

Acid Synthesis ◽

Response To Therapy ◽

Direct Role ◽

Amino Acid Synthesis ◽

Metabolic Coupling ◽

Abundant Supply

AbstractAn abundant supply of amino acids is important for cancers to sustain their proliferative drive. Alongside their direct role as substrates for protein synthesis, they can have roles in energy generation, driving the synthesis of nucleosides and maintenance of cellular redox homoeostasis. As cancer cells exist within a complex and often nutrient-poor microenvironment, they sometimes exist as part of a metabolic community, forming relationships that can be both symbiotic and parasitic. Indeed, this is particularly evident in cancers that are auxotrophic for particular amino acids. This review discusses the stromal/cancer cell relationship, by using examples to illustrate a number of different ways in which cancer cells can rely on and contribute to their microenvironment – both as a stable network and in response to therapy. In addition, it examines situations when amino acid synthesis is driven through metabolic coupling to other reactions, and synthesis is in excess of the cancer cell’s proliferative demand. Finally, it highlights the understudied area of non-proteinogenic amino acids in cancer metabolism and their potential role.

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Proteasome Inhibition in Brassica napus Roots Increases Amino Acid Synthesis to Offset Reduced Proteolysis

Plant and Cell Physiology ◽

10.1093/pcp/pcaa047 ◽

2020 ◽

Vol 61 (6) ◽

pp. 1028-1040

Author(s):

Dan Pereksta ◽

Dillon King ◽

Fahmida Saki ◽

Amith Maroli ◽

Elizabeth Leonard ◽

...

Keyword(s):

Amino Acid ◽

Brassica Napus ◽

De Novo ◽

Metabolic Response ◽

Sugar Metabolism ◽

Proteasome Inhibition ◽

Acid Synthesis ◽

Amino Acid Synthesis ◽

Amino Acid Depletion ◽

Metabolic Activities

Abstract Cellular homeostasis is maintained by the proteasomal degradation of regulatory and misfolded proteins, which sustains the amino acid pool. Although proteasomes alleviate stress by removing damaged proteins, mounting evidence indicates that severe stress caused by salt, metal(oids), and some pathogens can impair the proteasome. However, the consequences of proteasome inhibition in plants are not well understood and even less is known about how its malfunctioning alters metabolic activities. Lethality causes by proteasome inhibition in non-photosynthetic organisms stem from amino acid depletion, and we hypothesized that plants respond to proteasome inhibition by increasing amino acid biosynthesis. To address these questions, the short-term effects of proteasome inhibition were monitored for 3, 8 and 48 h in the roots of Brassica napus treated with the proteasome inhibitor MG132. Proteasome inhibition did not affect the pool of free amino acids after 48 h, which was attributed to elevated de novo amino acid synthesis; these observations coincided with increased levels of sulfite reductase and nitrate reductase activities at earlier time points. However, elevated amino acid synthesis failed to fully restore protein synthesis. In addition, transcriptome analysis points to perturbed abscisic acid signaling and decreased sugar metabolism after 8 h of proteasome inhibition. Proteasome inhibition increased the levels of alternative oxidase but decreased aconitase activity, most sugars and tricarboxylic acid metabolites in root tissue after 48 h. These metabolic responses occurred before we observed an accumulation of reactive oxygen species. We discuss how the metabolic response to proteasome inhibition and abiotic stress partially overlap in plants.

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New Enzymatic Method of Chiral Amino Acid Synthesis by Dynamic Kinetic Resolution of Amino Acid Amides: Use of Stereoselective Amino Acid Amidases in the Presence of α-Amino-ε-Caprolactam Racemase

Applied and Environmental Microbiology ◽

10.1128/aem.00807-07 ◽

2007 ◽

Vol 73 (16) ◽

pp. 5370-5373 ◽

Cited By ~ 46

Author(s):

Shigenori Yamaguchi ◽

Hidenobu Komeda ◽

Yasuhisa Asano

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Kinetic Resolution ◽

Acid Synthesis ◽

Enzymatic Method ◽

Ochrobactrum Anthropi ◽

Dynamic Kinetic Resolution ◽

Amino Acid Synthesis

ABSTRACT d- and l-amino acids were produced from l- and d-amino acid amides by d-aminopeptidase from Ochrobactrum anthropi C1-38 and l-amino acid amidase from Pseudomonas azotoformans IAM 1603, respectively, in the presence of α-amino-ε-caprolactam racemase from Achromobacter obae as the catalyst by dynamic kinetic resolution of amino acid amides.

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Target of Rapamycin Inhibition in Chlamydomonas reinhardtii Triggers de Novo Amino Acid Synthesis by Enhancing Nitrogen Assimilation

The Plant Cell ◽

10.1105/tpc.18.00159 ◽

2018 ◽

Vol 30 (10) ◽

pp. 2240.1-2254 ◽

Cited By ~ 19

Author(s):

Umarah Mubeen ◽

Jessica Jüppner ◽

Jessica Alpers ◽

Dirk K. Hincha ◽

Patrick Giavalisco

Keyword(s):

Amino Acid ◽

Chlamydomonas Reinhardtii ◽

Nitrogen Assimilation ◽

De Novo ◽

Acid Synthesis ◽

Target Of Rapamycin ◽

Amino Acid Synthesis

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Biosynthesis of Amino Acids in Xanthomonas oryzae pv. oryzae Is Essential to Its Pathogenicity

Microorganisms ◽

10.3390/microorganisms7120693 ◽

2019 ◽

Vol 7 (12) ◽

pp. 693 ◽

Cited By ~ 1

Author(s):

Ting Li ◽

Zhaohong Zhan ◽

Yunuan Lin ◽

Maojuan Lin ◽

Qingbiao Xie ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Bacterial Growth ◽

Acid Synthesis ◽

Xanthomonas Oryzae ◽

Host Responses ◽

Amino Acid Synthesis ◽

Rice Bacterial Blight ◽

Nutrient Environment ◽

Blight Disease

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of rice bacterial blight disease, which causes a large reduction in rice production. The successful interaction of pathogens and plants requires a particular nutrient environment that allows pathogen growth and the initiation of both pathogen and host responses. Amino acid synthesis is essential for bacterial growth when bacteria encounter amino acid-deficient environments, but the effects of amino acid synthesis on Xoo pathogenicity are unclear. Here, we systemically deleted the essential genes (leuB, leuC, leuD, ilvC, thrC, hisD, trpC, argH, metB, and aspC) involved in the synthesis of different amino acids and analyzed the effects of these mutations on Xoo virulence. Our results showed that leucine, isoleucine, valine, histidine, threonine, arginine, tryptophan, and cysteine syntheses are essential to Xoo infection. We further studied the role of leucine in the interaction between pathogens and hosts and found that leucine could stimulate some virulence-related responses and regulate Xoo pathogenicity. Our findings highlight that amino acids not only act as nutrients for bacterial growth but also play essential roles in the Xoo and rice interaction.

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Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C3 and C4 plants

Nature Plants ◽

10.1038/s41477-021-01042-5 ◽

2021 ◽

Author(s):

Haim Treves ◽

Anika Küken ◽

Stéphanie Arrivault ◽

Hirofumi Ishihara ◽

Ines Hoppe ◽

...

Keyword(s):

Amino Acid ◽

Higher Plants ◽

Tricarboxylic Acid Cycle ◽

Empirical Studies ◽

Crop Improvement ◽

Lipid Synthesis ◽

Acid Synthesis ◽

Central Carbon Metabolism ◽

Amino Acid Synthesis

AbstractPhotosynthesis-related pathways are regarded as a promising avenue for crop improvement. Whilst empirical studies have shown that photosynthetic efficiency is higher in microalgae than in C3 or C4 crops, the underlying reasons remain unclear. Using a tailor-made microfluidics labelling system to supply 13CO2 at steady state, we investigated in vivo labelling kinetics in intermediates of the Calvin Benson cycle and sugar, starch, organic acid and amino acid synthesis pathways, and in protein and lipids, in Chlamydomonas reinhardtii, Chlorella sorokiniana and Chlorella ohadii, which is the fastest growing green alga on record. We estimated flux patterns in these algae and compared them with published and new data from C3 and C4 plants. Our analyses identify distinct flux patterns supporting faster growth in photosynthetic cells, with some of the algae exhibiting faster ribulose 1,5-bisphosphate regeneration and increased fluxes through the lower glycolysis and anaplerotic pathways towards the tricarboxylic acid cycle, amino acid synthesis and lipid synthesis than in higher plants.

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