scholarly journals Assessing the potential of amino acid <sup>13</sup>C patterns as a carbon source tracer in marine sediments: effects of algal growth conditions and sedimentary diagenesis

2015 ◽  
Vol 12 (16) ◽  
pp. 4979-4992 ◽  
Author(s):  
T. Larsen ◽  
L. T. Bach ◽  
R. Salvatteci ◽  
Y. V. Wang ◽  
N. Andersen ◽  
...  

Abstract. Burial of organic carbon in marine sediments has a profound influence in marine biogeochemical cycles and provides a sink for greenhouse gases such as CO2 and CH4. However, tracing organic carbon from primary production sources as well as its transformations in the sediment record remains challenging. Here we examine a novel but growing tool for tracing the biosynthetic origin of amino acid carbon skeletons, based on naturally occurring stable carbon isotope patterns in individual amino acids (δ13CAA). We focus on two important aspects for δ13CAA utility in sedimentary paleoarchives: first, the fidelity of source diagnostic of algal δ13CAA patterns across different oceanographic growth conditions, and second, the ability of δ13CAA patterns to record the degree of subsequent microbial amino acid synthesis after sedimentary burial. Using the marine diatom Thalassiosira weissflogii, we tested under controlled conditions how δ13CAA patterns respond to changing environmental conditions, including light, salinity, temperature, and pH. Our findings show that while differing oceanic growth conditions can change macromolecular cellular composition, δ13CAA isotopic patterns remain largely invariant. These results emphasize that δ13CAA patterns should accurately record biosynthetic sources across widely disparate oceanographic conditions. We also explored how δ13CAA patterns change as a function of age, total nitrogen and organic carbon content after burial, in a marine sediment core from a coastal upwelling area off Peru. Based on the four most informative amino acids for distinguishing between diatom and bacterial sources (i.e., isoleucine, lysine, leucine and tyrosine), bacterially derived amino acids ranged from 10 to 15 % in the sediment layers from the last 5000 years, and up to 35 % during the last glacial period. The greater bacterial contributions in older sediments indicate that bacterial activity and amino acid resynthesis progressed, approximately as a function of sediment age, to a substantially larger degree than suggested by changes in total organic nitrogen and carbon content. It is uncertain whether archaea may have contributed to sedimentary δ13CAA patterns we observe, and controlled culturing studies will be needed to investigate whether δ13CAA patterns can differentiate bacterial from archeal sources. Further research efforts are also needed to understand how closely δ13CAA patterns derived from hydrolyzable amino acids represent total sedimentary proteineincous material, and more broadly sedimentary organic nitrogen. Overall, however, both our culturing and sediment studies suggest that δ13CAA patterns in sediments will represent a novel proxy for understanding both primary production sources, and the direct bacterial role in the ultimate preservation of sedimentary organic matter.

2015 ◽  
Vol 12 (2) ◽  
pp. 1613-1651 ◽  
Author(s):  
T. Larsen ◽  
L. T. Bach ◽  
R. Salvatteci ◽  
Y. V. Wang ◽  
N. Andersen ◽  
...  

Abstract. Burial of organic carbon in marine sediments has a profound influence in marine biogeochemical cycles, and provides a sink for greenhouse gases such as CO2 and CH4. However, tracing organic carbon from primary production sources as well as its transformations in the sediment record remains challenging. Here we examine a novel but growing tool for tracing biosynthetic origin of amino acid carbon skeletons, based on natural occurring stable carbon isotope patterns in individual amino acids (δ13CAA). We focus on two important aspects for δ13CAA utility in sedimentary paleoarchives: first, the fidelity of source diagnostic of algal δ13CAA patterns across different oceanographic growth conditions; and second, the ability of δ13CAA patterns to record the degree of subsequent microbial amino acid synthesis after sedimentary burial. Using the marine diatom Thalassiosira weissflogii, we tested under controlled conditions how δ13CAA patterns respond to changing environmental conditions, including light, salinity, temperature, and pH. Our findings show that while differing oceanic growth conditions can change macromolecular cellular composition, δ13CAA isotopic patterns remain largely invariant. These results underscore that δ13CAA patterns should accurately record biosynthetic sources across widely disparate oceanographic conditions. We also explored how δ13CAA patterns change as a function of age, total nitrogen and organic carbon content after burial, in a marine sediment core from a coastal upwelling area off Peru. Based on the four most informative amino acids for distinguishing between diatom and bacterial sources (i.e. isoleucine, lysine, leucine and tyrosine), bacterial derived amino acids ranged from 10–15% in the sediment layers from the last 5000 years to 35% during the last glacial period. The larger bacterial fractions in older sediments indicate that bacterial activity and amino acid resynthesis progressed, approximately as a function of sediment age, to a substantially larger degree than suggested by changes in total organic nitrogen and carbon content. Taken together, these culturing and sediment studies suggest that δ13CAA patterns in sediments represent a novel proxy for understanding both primary production sources, as well as direct bacterial role in the ultimate preservation of sedimentary organic matter.


Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1707
Author(s):  
Wayiza Masamba

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.


1998 ◽  
Vol 201 (16) ◽  
pp. 2445-2453 ◽  
Author(s):  
J Wang ◽  
AE Douglas

When corals and allied animals are deprived of their symbiotic algae, the ammonium content in their tissues rises. This is commonly interpreted as evidence for nitrogen recycling (i.e. algal assimilation of animal waste ammonium into amino acids that are released back to the animal), but it can also be explained as nitrogen conservation by the animal (i.e. reduced net ammonium production in response to the receipt of algal photosynthetic carbon). This study discriminated between these interpretations in two ways. First, the increased ammonium concentration in the sea anemone Aiptasia pulchella, caused by darkness or depletion of the alga Symbiodinium, was partially or completely reversed by supplementing the medium with organic carbon compounds (e.g. &lt;IMG src="/images/symbols/&agr ;.gif" WIDTH="9" HEIGHT="12" ALIGN= "BOTTOM" NATURALSIZEFLAG="3"&gt;-ketoglutarate). Second, the activity of the ammonium-assimilating enzyme glutamine synthetase and the concentration of protein amino acids in the free amino acid pool of the animal, which were depressed by darkness and algal depletion, were restored by exogenous carbon compounds. It is concluded that organic carbon, whether derived from algal photosynthate or exogenously, promotes the animal's capacity for ammonium assimilation and reduces ammonium production from amino acid degradation. These processes contribute to nitrogen conservation in the animal, but they confound the interpretation of various studies on nitrogen recycling by symbiotic algae.


2019 ◽  
Vol 122 (2) ◽  
pp. 150-156 ◽  
Author(s):  
Lisa Vettore ◽  
Rebecca L. Westbrook ◽  
Daniel A. Tennant

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.


2007 ◽  
Vol 73 (16) ◽  
pp. 5370-5373 ◽  
Author(s):  
Shigenori Yamaguchi ◽  
Hidenobu Komeda ◽  
Yasuhisa Asano

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.


2019 ◽  
Vol 7 (12) ◽  
pp. 693 ◽  
Author(s):  
Ting Li ◽  
Zhaohong Zhan ◽  
Yunuan Lin ◽  
Maojuan Lin ◽  
Qingbiao Xie ◽  
...  

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.


2010 ◽  
Vol 76 (5) ◽  
pp. 1507-1515 ◽  
Author(s):  
Motoyuki Shimizu ◽  
Tatsuya Fujii ◽  
Shunsuke Masuo ◽  
Naoki Takaya

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.


2002 ◽  
Vol 22 (19) ◽  
pp. 6681-6688 ◽  
Author(s):  
Peichuan Zhang ◽  
Barbara C. McGrath ◽  
Jamie Reinert ◽  
DeAnne S. Olsen ◽  
Li Lei ◽  
...  

ABSTRACT The GCN2 eIF2α kinase is essential for activation of the general amino acid control pathway in yeast when one or more amino acids become limiting for growth. GCN2's function in mammals is unknown, but must differ, since mammals, unlike yeast, can synthesize only half of the standard 20 amino acids. To investigate the function of mammalian GCN2, we have generated a Gcn2 −/− knockout strain of mice. Gcn2 −/− mice are viable, fertile, and exhibit no phenotypic abnormalities under standard growth conditions. However, prenatal and neonatal mortalities are significantly increased in Gcn2 −/− mice whose mothers were reared on leucine-, tryptophan-, or glycine-deficient diets during gestation. Leucine deprivation produced the most pronounced effect, with a 63% reduction in the expected number of viable neonatal mice. Cultured embryonic stem cells derived from Gcn2 −/− mice failed to show the normal induction of eIF2α phosphorylation in cells deprived of leucine. To assess the biochemical effects of the loss of GCN2 in the whole animal, liver perfusion experiments were conducted. Histidine limitation in the presence of histidinol induced a twofold increase in the phosphorylation of eIF2α and a concomitant reduction in eIF2B activity in perfused livers from wild-type mice, but no changes in livers from Gcn2 −/− mice.


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