Biosynthetic origin of the saw-toothed profile in delta(13)C and delta(2)H of n-alkanes and systematic isotopic differences between n-, iso- and anteiso-alkanes in leaf waxes of land plants

n-Alkane 13C/12C indicates differential metabolic controls of fatty lipid chain extension in C3 and C4 grasses

Fundamental differences in metabolic control of fatty acids chain extension are reflected in the contrasting carbon isotopic composition profiles of C3 and C4 grasses.

Biosynthesis of barley wax β-diketones: a type-III polyketide synthase condensing two fatty acyl units

The surface coatings of cereal plants are dominated by waxy β-diketones crucial for drought resistance and, therefore, grain yield. Here, barley (Hordeum vulgare) wax analyses reveal β-diketone and associated 2-alkanol ester profiles suggesting a common C16 3-ketoacid precursor. Isotope analysis further shows that the major (C31) diketone is synthesized from two plastidial C16 acyl units. Previous studies identified a gene cluster encoding enzymes responsible for β-diketone formation in barley, but left their biochemical functions unknown. Various assays now characterize one of these enzymes as a thioesterase producing long-chain (mainly C16) 3-ketoacids, and another one as a polyketide synthase (PKS) condensing the 3-ketoacids with long-chain (mainly C16) acyl-CoAs into β-diketones. The two enzymes are localized to the plastids and Endoplasmic Reticulum (ER), respectively, implying substrate transfer between these two sub-cellular compartments. Overall, our findings define a two-step pathway involving an unprecedented PKS reaction leading directly to the β-diketone products.

Leaf cuticular waxes of wild-type Welsh onion (Allium fistulosum L.) and a wax-deficient mutant: Compounds with terminal and mid-chain functionalities

Plant cuticles cover aerial organs to limit non-stomatal water loss and protect against insects and pathogens. Cuticles contain complex mixtures of fatty acid-derived waxes, with various chain lengths and diverse functional groups. To further our understanding of the chemical diversity and biosynthesis of these compounds, this study investigated leaf cuticular waxes of Welsh onion (Allium fistulosum L.) wild type and a wax-deficient mutant. Leaf waxes were extracted with chloroform, separated using thin layer chromatography (TLC), and analyzed using gas chromatography-mass spectrometry (GC-MS). The extracts contained typical wax compound classes found in nearly all plant lineages but also two uncommon compound classes. Analyses of characteristic MS fragmentation patterns followed by comparisons with synthetic standards identified the latter as very-long-chain ketones and primary ketols. The ketols were minor compounds, with chain lengths ranging from C₂₈ to C₃₂ and carbonyls mainly on C-18 and C-20 in wild type wax, and a C₂₈ chain with C-16 carbonyl in the mutant. The ketones made up 70% of total wax in the wild type, consisting mainly of C₃₁ isomers with carbonyl group on C-14 or C-16. In contrast, the mutant wax comprised only 4% ketones, with chain lengths C₂₇ and C₂₉ and carbonyls predominantly on C-12 and C-14, respectively. A two-carbon homolog shift between wild type and mutant was also observed in the primary alcohols (a major wax compound class), whilst alkanes exhibited a four-carbon shift. Overall, the compositional data shed light on possible biosynthetic pathways to wax ketones that can be tested in future studies.

The metabolic sensitivity of hydrogen isotope fractionation differs between plant compounds

Hydrogen stable isotope analyses (δ²H) of plant derived organic compounds are a useful tool for ecological, environmental, and palaeoclimatological research. However, during organic compound synthesis, variable biosynthetic ²H-fractionation has been suggested to occur as a result of changes in plant carbon fluxes. So far, inference has been based on examining the δ²H patterns of plant compounds along environmental gradients, among plant species, and between plant organs. In an alternative approach, we used four plant species with four different types of mutations that cause impaired starch synthesis to assess whether variability in carbon metabolism affects the biosynthetic ²H-fractionation during cellulose, phytol, and acetogenic lipid synthesis. We found that mutants with impaired starch synthesis always had higher cellulose and phytol δ²H values compared to the wild type. By contrast, ²H-fractionation during acetogenic lipid biosynthesis generally did not show strong metabolic sensitivity. We rationalise these differences by considering the biosynthetic pathway of each compound and the likely source of the variable isotope fractionation. In different organic compounds, the sensitivity of variable biosynthetic ²H-fractionation to changes in C-metabolism depends on incorporation of specific H atoms from precursor molecules. As such, we determined that the similar increase in cellulose and phytol δ²H values as an effect of impaired starch synthesis most likely originates in triose-phosphates.

Leaf transition from heterotrophy to autotrophy is recorded in the intraleaf C, H and O isotope patterns of leaf organic matter

RATIONALE

Quantitatively relating ¹³ C/¹² C, ² H/¹ H and ¹⁸ O/¹⁶ O ratios of plant α-cellulose and ² H/¹ H of n-alkanes to environmental conditions and metabolic status should ideally be based on the leaf, the plant organ most sensitive to environmental change. The fact that leaf organic matter is composed of isotopically different heterotrophic and autotrophic components means that it is imperative that one be able to disentangle the relative heterotrophic and autotrophic contributions to leaf organic matter.

METHODS

We tackled this issue by two-dimensional sampling of leaf water and α-cellulose, and specific n-alkanes from greenhouse-grown immature and mature and field-grown mature banana leaves, taking advantage of their large areas and thick waxy layers. Leaf water, α-cellulose and n-alkane isotope ratios were then characterized using elemental analysis isotope ratio mass spectrometry (IRMS) or gas chromatography IRMS. A three-member (heterotrophy, autotrophy and photoheterotrophy) conceptual linear mixing model was then proposed for disentangling the relative contributions of the three trophic modes.

RESULTS

We discovered distinct spatial leaf water, α-cellulose and n-alkane isotope ratio patterns that varied with leaf developmental stages. We inferred from the conceptual model that, averaged over the leaf blade, only 20% of α-cellulose in banana leaf is autotrophically laid down in both greenhouse-grown and field-grown banana leaves, while approximately 60% and 100% of n-alkanes are produced autotrophically in greenhouse-grown and field-grown banana leaves, respectively. There exist distinct lateral (edge to midrib) gradients in autotrophic contributions of α-cellulose and n-alkanes.

CONCLUSIONS

Efforts to establish quantitative isotope-environment relationships should take into account the fact that the evaporative leaf water ¹⁸ O and ² H enrichment signal recorded in autotrophically laid down α-cellulose is significantly diluted by the heterotrophically formed α-cellulose. The δ² H value of field-grown mature banana leaf n-alkanes is much more sensitive than α-cellulose as a recorder of the growth environment. Quantitative isotope-environment relationship based on greenhouse-grown n-alkane δ² H values may not be reliable.

The effect of processing medium on the 2 H/1 H of carbon-bound hydrogen in α-cellulose extracted from higher plants

RATIONALE

Although the ² H/¹ H ratio of the carbon-bound hydrogens (C-Hs) in α-cellulose extracted from higher plants has long been used successfully for climate, environmental and metabolic studies, the assumption that bleaching with acidified NaClO₂ to remove lignin before pure α-cellulose can be obtained does not alter the ² H/¹ H ratio of α-cellulose C-Hs has nonetheless not been tested.

METHODS

For reliable application of the ² H/¹ H ratio of α-cellulose C-H, we processed plant materials representing different phytochemistries and photosynthetic carbon assimilation modes in isotopically contrasting bleaching media (with an isotopic difference of 273 mUr). All the isotope ratios were measured by elemental analyzer/isotope ratio mass spectrometry (EA/IRMS).

RESULTS

Our results show that H from the bleaching medium does appear in the final pure α-cellulose product, although the isotopic alteration to the C-H in α-cellulose due to the incorporation of processing H from the medium is small if isotopically "natural" water is used to prepare the processing medium. However, under prolonged bleaching such an isotope effect can be significant, implying that standardizing the bleaching process is necessary for reliable ² H/¹ H measurement.

CONCLUSIONS

The currently adopted method for removing lignin for α-cellulose extraction from higher plant materials with acidified NaClO₂ bleaching is considered acceptable in terms of preserving the isotopic fidelity if isotopically "natural" water is used to prepare the bleaching solution.

Novel Position-Specific 18O/16O Measurement of Carbohydrates. II. The Complete Intramolecular 18O/16O Profile of the Glucose Unit in a Starch of C4 Origin

Information about plant photosynthetic carbon assimilation, physiology, and biochemistry is locked in the ¹⁸O/¹⁶O ratios of the individual positions of higher plants carbohydrates but is under-utilized, because of the difficulty of making these determinations. We report the extension of the wet chemistry approach we used to access the ¹⁸O/¹⁶O ratio of O-3 of glucose with a novel GC/Pyrolysis/IRMS-based method, to determine the ¹⁸O/¹⁶O ratios of O-4, O-5, and O-6. The O atoms (OH groups) at positions 1, 2, 5, and 6 of glucose were protected by acetonation (converting to 1,2;5,6-di-O-isopropylidene-glucofuranose, DAGF). The DAGF was then converted to 6-bromo-6-deoxy-1,2;3,5-di-O-isopropylidene-glucofuranose (6-bromoDAGF) with the simultaneous removal of O-6 with N-bromosuccinimide and triphenylphosphine. The DAGF was also methylated at O-3 with CH₃I under the catalysis of NaH to 3-methylDAGF, which was then deacetonated to 1,2-O-isopropylidene-3-O-methyl-glucofuranose (3-methylMAGF). O-5 and O-6 were then removed as a whole from 3-methylMAGF by I₂ oxidization under the catalysis of Ph₃P and imidazole. Isotope mass balance was then applied to calculate the ¹⁸O/¹⁶O of O-5 and O-6 as a whole and O-6, respectively. Sampling at different stages of substrate conversion to product and applying a Rayleigh-type fractionation model were employed, when quantitative conversion of substrate was unachievable to calculate the δ¹⁸O of the converted substrate. Quantitative conversion of glucose with phenylhydrazine to phenylglucosazone also allowed for the calculation of δ¹⁸O₂ by applying isotope mass balance between the two. A C4 starch-derived glucose intramolecular δ¹⁸O profile is now determined: O-3 is relatively enriched (by 12.16 mUr), O-4 is relatively depleted (by 20.40-31.11 mUr), and O-2 is marginally enriched (by 2.40 mUr) against the molecular average.

Variations in hydrogen isotopic fractionation in higher plants and sediments across different latitudes: Implications for paleohydrological reconstruction

Sedimentary δD_n-alkane value is widely utilized as a reliable proxy for paleo-hydrological reconstruction. Applications of this proxy must be based upon a globally clear understanding of the relationship between leaf wax δD_n-alkane values and precipitation δD (δD_p), defined as apparent fractionation (ε_app). However, there is a critical concern about whether relatively constant ε_app values exist across different latitudes. In this study, we systematically analyzed the variations of available ε_app with latitudes based upon two compiled-new databases of higher plants and sediments over the world. We found that the total average ε_app was relatively constant, i.e., -116 ± 5‰ (n = 941), in higher plants across different latitudes without consideration of plant types (e.g., dicots, monocots, gymnosperms), and was still constant but slightly lower average ε_app, i.e., -125 ± 6‰ (n = 460), in sediments across the latitudes. The slightly lower average ε_app in sediments relative to higher plants probably derived from the contribution of aquatic plants with isotopically D-depleted ε_app in lake sediments. Interestingly, with consideration of plant types, average ε_app increased in dicots but decreased in monocots slightly from low to high latitudes. The counteraction of these competing trends generates relatively constant average ε_app values in higher plants, and resultantly constant average ε_app values occur in sediments at the global scale. It is important to elaborate relatively constant ε_app values from higher plants and sediments across different latitudes when sedimentary δD_n-alkane is utilized as a proxy for paleohydrological reconstruction.

On the contributions of photorespiration and compartmentation to the contrasting intramolecular 2H profiles of C3 and C4 plant sugars

Compartmentation of C₄ photosynthetic biochemistry into bundle sheath (BS) and mesophyll (M) cells, and photorespiration in C₃ plants is predicted to have hydrogen isotopic consequences for metabolites at both molecular and site-specific levels. Molecular-level evidence was recently reported (Zhou et al., 2016), but evidence at the site-specific level is still lacking. We propose that such evidence exists in the contrasting ²H distribution profiles of glucose samples from naturally grown C₃, C₄ and CAM plants: photorespiration contributes to the relative ²H enrichment in H⁵ and relative ²H depletion in H¹ & H⁶ (the average of the two pro-chiral Hs and in particular H^6,pro-R) in C₃ glucose, while ²H-enriched C₃ mesophyll cellular (chloroplastic) water most likely contributes to the enrichment at H⁴; export of (transferable hydrogen atoms of) NADPH from C₄ mesophyll cells to bundle sheath cells (via the malate shuttle) and incorporation of ²H-relatively unenriched BS cellular water contribute to the relative depletion of H⁴ & H⁵ respectively; shuttling of triose-phosphates (PGA: phosphoglycerate dand DHAP: dihydroacetone phosphate) between C₄ bundle sheath and mesophyll cells contributes to the relative enrichment in H¹ & H⁶ (in particular H^6,pro-R) in C₄ glucose.

Hydrogen isotopic differences between C3 and C4 land plant lipids: consequences of compartmentation in C4 photosynthetic chemistry and C3 photorespiration

The ² H/¹ H ratio of carbon-bound H in biolipids holds potential for probing plant lipid biosynthesis and metabolism. The biochemical mechanism underlying the isotopic differences between lipids from C₃ and C₄ plants is still poorly understood. GC-pyrolysis-IRMS (gas chromatography-pyrolysis-isotope ratio mass spectrometry) measurement of the ² H/¹ H ratio of leaf lipids from controlled and field grown plants indicates that the biochemical isotopic fractionation (ε² H_{lipid_biochem} ) differed between C₃ and C₄ plants in a pathway-dependent manner: ε² H_C4  > ε² H_C3 for the acetogenic pathway, ε² H_C4  < ε² H_C3 for the mevalonic acid pathway and the 1-deoxy-D-xylulose 5-phosphate pathway across all species examined. It is proposed that compartmentation of photosynthetic CO₂ fixation into C₄ mesophyll (M) and bundle sheath (BS) cells and suppression of photorespiration in C₄ M and BS cells both result in C₄ M chloroplastic pyruvate - the precursor for acetogenic pathway - being more depleted in ² H relative to pyruvate in C₃ cells. In addition, compartmentation in C₄ plants also results in (i) the transferable H of NADPH being enriched in ² H in C₄ M chloroplasts compared with that in C₃ chloroplasts for the 1-deoxy-D-xylulose 5-phosphate pathway pathway and (ii) pyruvate relatively ² H-enriched being used for the mevalonic acid pathway in the cytosol of BS cells in comparison with that in C₃ cells.

Lipid Biomarker and Isotopic Study of Community Distribution and Biomarker Preservation in a Laminated Microbial Mat from Shark Bay, Western Australia

Modern microbial mats from Shark Bay present some structural similarities with ancient stromatolites; thus, the functionality of microbial communities and processes of diagenetic preservation of modern mats may provide an insight into ancient microbial assemblages and preservation. In this study, the vertical distribution of microbial communities was investigated in a well-laminated smooth mat from Shark Bay. Biolipid and compound-specific isotopic analyses were performed to investigate the distribution of microbial communities in four distinct layers of the mat. Biomarkers indicative of cyanobacteria were more abundant in the uppermost oxic layer. Diatom markers (e.g. C25 HBI alkene, C20:4ω6 and C20:5ω3 polar lipid fatty acids (PLFAs)) were also detected in high abundance in the uppermost layer, but also in the deepest layer under conditions of permanent darkness and anoxia, where they probably used NO3 (-) for respiration. CycC19:0, an abundant PLFA of purple sulfur bacteria (PSB), was detected in all layers and presented the most (13)C-depleted values of all PLFAs, consistent with photoautotrophic PSB. Sulfur-bound aliphatic and aromatic biomarkers were detected in all layers, highlighting the occurrence of early sulfurisation which may be an important mechanism in the sedimentary preservation of functional biolipids in living and, thus, also ancient mats.

Predicting leaf wax n-alkane 2H/1H ratios: controlled water source and humidity experiments with hydroponically grown trees confirm predictions of Craig-Gordon model

The extent to which both water source and atmospheric humidity affect δ(2)H values of terrestrial plant leaf waxes will affect the interpretations of δ(2)H variation of leaf waxes as a proxy for hydrological conditions. To elucidate the effects of these parameters, we conducted a long-term experiment in which we grew two tree species, Populus fremontii and Betula occidentalis, hydroponically under combinations of six isotopically distinct waters and two different atmospheric humidities. We observed that leaf n-alkane δ(2)H values of both species were linearly related to source water δ(2)H values, but with slope differences associated with differing humidities. When a modified version of the Craig-Gordon model incorporating plant factors was used to predict the δ(2)H values of leaf water, all modelled leaf water values fit the same linear relationship with n-alkane δ(2)H values. These observations suggested a relatively constant biosynthetic fractionation factor between leaf water and n-alkanes. However, our calculations indicated a small difference in the biosynthetic fractionation factor between the two species, consistent with small differences calculated for species in other studies. At present, it remains unclear if these apparent interspecies differences in biosynthetic fractionation reflect species-specific biochemistry or a common biosynthetic fractionation factor with insufficient model parameterization.

Allocate carbon for a reason: priorities are reflected in the ¹³C/¹²C ratios of plant lipids synthesized via three independent biosynthetic pathways

It has long been theorized that carbon allocation, in addition to the carbon source and to kinetic isotopic effects associated with a particular lipid biosynthetic pathway, plays an important role in shaping the carbon isotopic composition ((13)C/(12)C) of lipids (Park and Epstein, 1961). If the latter two factors are properly constrained, valuable information about carbon allocation during lipid biosynthesis can be obtained from carbon isotope measurements. Published work of Chikaraishi et al. (2004) showed that leaf lipids isotopic shifts from bulk leaf tissue Δδ(13)C(bk-lp) (defined as δ(13)C(bulkleaftissue)-δ(13)C(lipid)) are pathway dependent: the acetogenic (ACT) pathway synthesizing fatty lipids has the largest isotopic shift, the mevalonic acid (MVA) pathway synthesizing sterols the lowest and the phytol synthesizing 1-deoxy-D-xylulose 5-phosphate (DXP) pathway gives intermediate values. The differences in Δδ(13)C(bk-lp) between C3 and C4 plants Δδ(13)C(bk-lp,C4-C3) are also pathway-dependent: Δδ(13)C(ACT)(bk-lp,C4-C3) > Δδ(13)C(DXP(bk-lp,C4-C3) > Δδ(13)C(MVA)(bk-lp,C4-C3). These pathway-dependent differences have been interpreted as resulting from kinetic isotopic effect differences of key but unspecified biochemical reactions involved in lipids biosynthesis between C3 and C4 plants. After quantitatively considering isotopic shifts caused by (dark) respiration, export-of-carbon (to sink tissues) and photorespiration, we propose that the pathway-specific differences Δδ(13)C(bk-lp,C4-C3) can be successfully explained by C4-C3 carbon allocation (flux) differences with greatest flux into the ACT pathway and lowest into the MVA pathways (when flux is higher, isotopic shift relative to source is smaller). Highest carbon allocation to the ACT pathway appears to be tied to the most stringent role of water-loss-minimization by leaf waxes (composed mainly of fatty lipids) while the lowest carbon allocation to the MVA pathway can be largely explained by the fact that sterols act as regulatory hormones and membrane fluidity modulators in rather low concentrations.

Tracing carbon sources through aquatic and terrestrial food webs using amino acid stable isotope fingerprinting

Tracing the origin of nutrients is a fundamental goal of food web research but methodological issues associated with current research techniques such as using stable isotope ratios of bulk tissue can lead to confounding results. We investigated whether naturally occurring δ(13)C patterns among amino acids (δ(13)CAA) could distinguish between multiple aquatic and terrestrial primary production sources. We found that δ(13)CAA patterns in contrast to bulk δ(13)C values distinguished between carbon derived from algae, seagrass, terrestrial plants, bacteria and fungi. Furthermore, we showed for two aquatic producers that their δ(13)CAA patterns were largely unaffected by different environmental conditions despite substantial shifts in bulk δ(13)C values. The potential of assessing the major carbon sources at the base of the food web was demonstrated for freshwater, pelagic, and estuarine consumers; consumer δ(13)C patterns of essential amino acids largely matched those of the dominant primary producers in each system. Since amino acids make up about half of organismal carbon, source diagnostic isotope fingerprints can be used as a new complementary approach to overcome some of the limitations of variable source bulk isotope values commonly encountered in estuarine areas and other complex environments with mixed aquatic and terrestrial inputs.

Intramolecular 13C pattern in hexoses from autotrophic and heterotrophic C3 plant tissues

The stable carbon isotope (13)C is used as a universal tracer in plant eco-physiology and studies of carbon exchange between vegetation and atmosphere. Photosynthesis fractionates against (13)CO(2) so that source sugars (photosynthates) are on average (13)C depleted by 20‰ compared with atmospheric CO(2). The carbon isotope distribution within sugars has been shown to be heterogeneous, with relatively (13)C-enriched and (13)C-depleted C-atom positions. The (13)C pattern within sugars is the cornerstone of (13)C distribution in plants, because all metabolites inherit the (13)C abundance in their specific precursor C-atom positions. However, the intramolecular isotope pattern in source leaf glucose and the isotope fractionation associated with key enzymes involved in sugar interconversions are currently unknown. To gain insight into these, we have analyzed the intramolecular isotope composition in source leaf transient starch, grain storage starch, and root storage sucrose and measured the site-specific isotope fractionation associated with the invertase (EC 3.2.1.26) and glucose isomerase (EC 5.3.1.5) reactions. When these data are integrated into a simple steady-state model of plant isotopic fluxes, the enzyme-dependent fractionations satisfactorily predict the observed intramolecular patterns. These results demonstrate that glucose and sucrose metabolism is the primary determinant of the (13)C abundance in source and sink tissue and is, therefore, of fundamental importance to the interpretation of plant isotopic signals.

The use of natural abundance stable isotopic ratios to indicate the presence of oxygen-containing chemical linkages between cellulose and lignin in plant cell walls

Qualitative and quantitative understanding of the chemical linkages between the three major biochemical components (cellulose, hemicellulose and lignin) of plant cell walls is crucial to the understanding of cell wall structure. Although there is convincing evidence for chemical bonds between hemicellulose and lignin and the absence of chemical bonds between hemicellulose and cellulose, there is no conclusive evidence for the presence of covalent bonds between cellulose and lignin. This is caused by the lack of selectivity of current GC/MS-, NMR- and IR-based methods for lignin characterisation as none of these techniques directly targets the possible ester and ether linkages between lignin and cellulose. We modified the widely-accepted "standard" three-step extraction method for isolating cellulose from plants by changing the order of the steps for hemicellulose and lignin removal (solubilisation with concentrated NaOH and oxidation with acetic acid-containing NaClO(2), respectively) so that cellulose and lignin could be isolated with the possible chemical bonds between them intact. These linkages were then cleaved with NaClO(2) reagent in aqueous media of contrasting (18)O/(16)O ratios. We produced cellulose with higher purity (a lower level of residual hemicellulose and no detectable lignin) than that produced by the "standard" method. Oxidative artefacts may potentially be introduced at the lignin removal stage; but testing showed this to be minimal. Cellulose samples isolated from processing plant-derived cellulose-lignin mixtures in media of contrasting (18)O/(16)O ratios were compared to provide the first quantitative evidence for the presence of oxygen-containing ester and ether bonds between cellulose and lignin in Zea mays leaves. However, no conclusive evidence for the presence or lack of similar bonds in Araucaria cunninghamii wood was obtained.