Stable isotope fingerprinting: a novel method for identifying plant, fungal, or bacterial origins of amino acids

Larsen, Thomas; Taylor, D. Lee; Leigh, Mary Beth; O’Brien, Diane M.

doi:10.1890/08-1695.1

Cited by 212 publications

(316 citation statements)

References 53 publications

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“…Pathway? Considering those atoms proposed to be derived from LLys, these give a mean δ 13 C g value of −30.2‰ (Table 1), compatible with literature values for amino acids from C 3 plants (39). The key difference between the two postulated alternative routes-via cadaverine or via L-2-amino-adipic-6-semialdehyde-is that the former involves a symmetrical intermediate, whereas the latter does not.…”

Section: Resultssupporting

confidence: 83%

A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol

Romek

Nun

Remaud

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Tramadol, previously only known as a synthetic analgesic, has now been found in the bark and wood of roots of the African medicinal tree Nauclea latifolia. At present, no direct evidence is available as to the biosynthetic pathway of its unusual skeleton. To provide guidance as to possible biosynthetic precursors, we have adopted a novel approach of retro-biosynthesis based on the position-specific distribution of isotopes in the extracted compound. Relatively recent developments in isotope ratio monitoring by 13 C NMR spectrometry make possible the measurement of the nonstatistical position-specific natural abundance distribution of 13 C (δ 13 C i ) within the molecule with better than 1‰ precision. Very substantial variation in the 13 C positional distribution is found: between δ 13 C i = −11 and −53‰. Distribution is not random and it is argued that the pattern observed can substantially be interpreted in relation to known causes of isotope fractionation in natural products. Thus, a plausible biosynthetic scheme based on sound biosynthetic principals of precursorsubstrate relationships can be proposed. In addition, data obtained from the 18 O/ 16 O ratios in the oxygen atoms of the compound add support to the deductions made from the carbon isotope analysis. This paper shows how the use of 13 C NMR at natural abundance can help with proposing a biosynthetic route to compounds newly found in nature or those difficult to tackle by conventional means.NMR spectrometry | position-specific isotope analysis | retro-biosynthesis | tramadol | Nauclea latifolia

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Section: Resultssupporting

confidence: 83%

A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol

Romek

Nun

Remaud

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…The fidelity of the δ 15 N-AA patterns observed in this study indicates a broad range of new potential in coral-based paleoceanographic studies of the marine N cycle. Some examples of future potential include (i) the reconstruction of δ 15 N of average exported production from the surface ocean, independent of complicating assumptions about any single species or biomarker (36); (ii) reconstruction of phytoplankton trophic structure through time; and (iii) a possible new tracer for variations in algal community structure, based on evolving studies of the tracer potential in compound-specific stable isotope patterns (37,38).…”

Section: Resultsmentioning

confidence: 99%

Nutrient regime shift in the western North Atlantic indicated by compound-specific δ ¹⁵ N of deep-sea gorgonian corals

Sherwood

Lehmann

Schubert

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

160

172

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Despite the importance of the nitrogen (N) cycle on marine productivity, little is known about variability in N sources and cycling in the ocean in relation to natural and anthropogenic climate change. Beyond the last few decades of scientific observation, knowledge depends largely on proxy records derived from nitrogen stable isotopes ( δ 15 N) preserved in sediments and other bioarchives. Traditional bulk δ 15 N measurements, however, represent the combined influence of N source and subsequent trophic transfers, often confounding environmental interpretation. Recently, compound-specific analysis of individual amino acids ( δ 15 N-AA) has been shown as a means to deconvolve trophic level versus N source effects on the δ 15 N variability of bulk organic matter. Here, we demonstrate the first use of δ 15 N-AA in a paleoceanographic study, through analysis of annually secreted growth rings preserved in the organic endoskeletons of deep-sea gorgonian corals. In the Northwest Atlantic off Nova Scotia, coral δ 15 N is correlated with increasing presence of subtropical versus subpolar slope waters over the twentieth century. By using the new δ 15 N-AA approach to control for variable trophic processing, we are able to interpret coral bulk δ 15 N values as a proxy for nitrate source and, hence, slope water source partitioning. We conclude that the persistence of the warm, nutrient-rich regime since the early 1970s is largely unique in the context of the last approximately 1,800 yr. This evidence suggests that nutrient variability in this region is coordinated with recent changes in global climate and underscores the broad potential of δ 15 N-AA for paleoceanographic studies of the marine N cycle.

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“…LDA was conducted on d 13 C AA values normalized to their means as N(d 13 C AAi ) 5 d 13 C AAi 2 ( P n i~1 d 13 C AAi )/n, where n is the number of samples used to calculate the mean and AA i is an AA for sample i. The training set used for the LDA was composed of marine producer and bacterial N(d 13 C AA ) values from Larsen et al (2009Larsen et al ( , 2012 where ''marine producers'' include seagrasses, seaweeds, and microbial mats (mats of cyanobacteria, photosynthetic sulfur bacteria, and Archaea). PCA was conducted on d 15 N AA (Phe, Sr-AA, and Tr-AA), TP Glu-Phe , and N(d 13 C AA ) values standardized by dividing each AA i or TP by its standard deviation.…”

Section: Methodsmentioning

confidence: 99%

“…These d 13 C patterns are preserved in essential AAs (EAAs) during trophic transfers and thus can act as ''fingerprints'' of producer source in consumers. Larsen et al (2009) In this study, we investigate zooplankton trophic status and potential linkage to particle cycling in midwaters of the oligotrophic North Pacific Subtropical Gyre (NPSG) for the first time using CSIA. We determine d 15 N AA and d 13 C AA values for epi-and mesopelagic zooplankton and suspended particles and use this information to (1) investigate the drivers of change in suspended particle d 15 N values with depth, (2) determine whether depth variability in zooplankton d 15 N values is driven by changes in food source N isotope composition or changes in trophic position, and (3) establish the biosynthetic origin of material supporting zooplankton food webs and contributing to suspended particle cycling in midwaters.…”

mentioning

confidence: 99%

Midwater zooplankton and suspended particle dynamics in the North Pacific Subtropical Gyre: A stable isotope perspective

Hannides

Popp

Choy

et al. 2013

Limnology & Oceanography

158

147

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We used amino acid (AA) compound-specific isotope analysis (d 15 N AA and d 13 C AA values) of midwater zooplankton and suspended particles to examine their dynamics in the mesopelagic zone. Suspended particle d 15 N AA values increased by up to 14% with depth, whereas particle trophic status (measured as trophic position, TP) remained constant at 1.6 6 0.07. Applying a Rayleigh distillation model to these results gave an observed kinetic isotope fractionation of 5.7 6 0.4%, similar to that previously measured for protein hydrolysis. AA-based degradation index values also decreased with depth on the particles, whereas a measure of heterotrophic resynthesis (SV) remained constant at 1.2 6 0.3. The main mechanism driving 15 N enrichment of suspended particles appears to be isotope fractionation associated with heterotrophic degradation, rather than a change in trophic status or N source with depth. In zooplankton the ''source'' AA phenylalanine (Phe) became 15 N enriched by up to 3.5% with depth, whereas zooplankton TP increased by up to 0.65 between the surface ocean and midwaters. Both changes in the d 15 N values of food resources at the base of the zooplankton food web and changes in zooplankton TP drive observed zooplankton 15 N enrichment with depth. Midwater zooplankton d 15 N Phe values were lower by 5-8% compared with suspended particles, indicating this organic matter pool is not a significant zooplankton food resource at depth. Instead, 62-88% of the N sustaining midwater zooplankton is surface derived, obtained through consumption of sinking particles, carnivory of vertical migrants, or direct feeding in surface waters at night.

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Stable isotope fingerprinting: a novel method for identifying plant, fungal, or bacterial origins of amino acids

Cited by 212 publications

References 53 publications

A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol

A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol

Nutrient regime shift in the western North Atlantic indicated by compound-specific δ ¹⁵ N of deep-sea gorgonian corals

Midwater zooplankton and suspended particle dynamics in the North Pacific Subtropical Gyre: A stable isotope perspective

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Stable isotope fingerprinting: a novel method for identifying plant, fungal, or bacterial origins of amino acids

Cited by 212 publications

References 53 publications

A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol

A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol

Nutrient regime shift in the western North Atlantic indicated by compound-specific δ 15 N of deep-sea gorgonian corals

Midwater zooplankton and suspended particle dynamics in the North Pacific Subtropical Gyre: A stable isotope perspective

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Nutrient regime shift in the western North Atlantic indicated by compound-specific δ ¹⁵ N of deep-sea gorgonian corals