Discovery of alkenones with variable methylene‐interrupted double bonds: implications for the biosynthetic pathway

Alkenones (C₃₇–C₄₀) are highly specific biomarkers produced by certain haptophyte algae in ocean and lacustrine environments and have been widely used for paleoclimate studies. Unusual shorter‐chain alkenones (SCA; e.g., C₃₅ and C₃₆) have been found in environmental and culture samples, but the origin and structure of these compounds are much less understood. The marine alkenone producer, Emiliania huxleyi CCMP2758 strain, was reported with abundant C_35:2Me (?^{12, 19}) alkenones when cultured at 15°C (Prahl et al. 2006). Here we show, when this strain is cultured at 4°C–10°C, that CCMP2758 produces abundant C_35:3Me, C_36:3Me, and small amounts of C_36:3Et alkenones with unusual double‐bond positions of ?^{7, 12, 19}. We determine the double‐bond positions of the C_35:3Me and C_36:3Me alkenones by GC‐MS analysis of the dimethyl disulfide and cyclobutylamine derivatives, and we provide the first temperature calibrations based on the unsaturation ratios of the C₃₅ and C₃₆ alkenones. Previous studies have found C_35:2Me (?^{14, 19}) and C_36:2Et (?^{14, 19}) alkenones with three‐methylene interruption in the Black Sea sediments, but this is the first reported instance of alkenones with a mixed three‐ and five‐methylene interruption configuration in the double‐bond positions. The discovery of these alkenones allows us to propose a novel biosynthetic scheme, termed the SCA biosynthesis pathway, that simultaneously rationalizes the formation of both the C_35:3Me (?^{7, 12, 19}) alkenone in our culture and the ?^{14, 19} Black Sea type alkenones without invoking new desaturases for the unusual double‐bond positions.     

Synthesis of pheromones by stereoselective carbonyl olefination: A unitised construction principle

A route of synthesis for the preparation of unsaturated pheromones is presented. It permits the synthesis of monounsaturated and diunsaturated compounds, with varying position and configuration of double bonds, by stereoselective carbonyl olefination. The choice of appropriate ω-functional aldehydes and phosphoranes makes possible the synthesis of (Z)-alkenols and alkenyl acetates with the double bond in any position desired. Bifunctional synthones are used in stereoselective Wittig reactions for the preparation of diunsaturated sex attractants.     

Substrate Specificity and Regioselectivity of Δ12 and ω3 Fatty Acid Desaturases from Saccharomyces kluyveri

Δ12 and ω3 fatty acid desaturases are key enzymes in the synthesis of polyunsaturated fatty acids (PUFAs), which are important constituents of membrane glycerolipids and also precursors to signaling molecules in many organisms. In this study, we determined the substrate specificity and regioselectivity of the Δ12 and ω3 fatty acid desaturases from Saccharomyces kluyveri (Sk-FAD2 and Sk-FAD3). Based on heterologous expression in Saccharomyces cerevisiae, it was found that Sk-FAD2 converted C16–20 monounsaturated fatty acids to diunsaturated fatty acids by the introduction of a second double bond at the ν+3 position, while Sk-FAD3 recognized the ω3 position of C18 and C20. Furthermore, fatty acid analysis of major phospholipids suggested that Sk-FAD2 and Sk-FAD3 have no strong substrate specificity toward the lipid polar head group or the sn-positions of fatty acyl groups in phospholipids.     

A thioesterase bypasses the requirement for exogenous fatty acids in the plsX deletion of Streptococcus pneumoniae

PlsX is an acyl‐acyl carrier protein (ACP):phosphate transacylase that interconverts the two acyl donors in Gram‐positive bacterial phospholipid synthesis. The deletion of plsX in Staphylococcus aureus results in a requirement for both exogenous fatty acids and de novo type II fatty acid biosynthesis. Deletion of plsX (SP0037) in Streptococcus pneumoniae did not result in an auxotrophic phenotype. The ΔplsX S. pneumoniae strain was refractory to myristic acid‐dependent growth arrest, and unlike the wild‐type strain, was susceptible to fatty acid synthesis inhibitors in the presence of exogenous oleate. The ΔplsX strain contained longer chain saturated fatty acids imparting a distinctly altered phospholipid molecular species profile. An elevated pool of 18‐ and 20‐carbon saturated fatty acids was detected in the ΔplsX strain. A S. pneumoniae thioesterase (TesS, SP1408) hydrolyzed acyl‐ACP in vitro, and the ΔtesS ΔplsX double knockout strain was a fatty acid auxotroph. Thus, the TesS thioesterase hydrolyzed the accumulating acyl‐ACP in the ΔplsX strain to liberate fatty acids that were activated by fatty acid kinase to bypass a requirement for extracellular fatty acid. This work identifies tesS as the gene responsible for the difference in exogenous fatty acid growth requirement of the ΔplsX strains of S. aureus and S. pneumoniae.     

ω‐Turn: A novel β‐turn mimic in globular proteins stabilized by main‐chain to side‐chain CH···O interaction

Mimicry of structural motifs is a common feature in proteins. The 10‐membered hydrogen‐bonded ring involving the main‐chain C?O in a β‐turn can be formed using a side‐chain carbonyl group leading to Asx‐turn. We show that the N? H component of hydrogen bond can be replaced by a C^γ‐H group in the side chain, culminating in a nonconventional C? H···O interaction. Because of its shape this β‐turn mimic is designated as ω‐turn, which is found to occur ～three times per 100 residues. Three residues (i to i + 2) constitute the turn with the C? H···O interaction occurring between the terminal residues, constraining the torsion angles ?_{i + 1}, ψ_{i + 1}, ?_{i + 2} and χ′_{1(i + 2)} (using the interacting C^γ atom). Based on these angles there are two types of ω‐turns, each of which can be further divided into two groups. C^β‐branched side‐chains, and Met and Gln have high propensities to occur at i + 2; for the last two residues the carbonyl oxygen may participate in an additional interaction involving the S and amino group, respectively. With Cys occupying the i + 1 position, such turns are found in the metal‐binding sites. N‐linked glycosylation occurs at the consensus pattern Asn‐Xaa‐Ser/Thr; with Thr at i + 2, the sequence can adopt the secondary structure of a ω‐turn, which may be the recognition site for protein modification. Location between two β‐strands is the most common occurrence in protein tertiary structure, and being generally exposed ω‐turn may constitute the antigenic determinant site. It is a stable scaffold and may be used in protein engineering and peptide design. Proteins 2015; 83:203–214. © 2014 Wiley Periodicals, Inc.     

Methyl-end desaturases with ∆12 and ω3 regioselectivities enable the de novo PUFA biosynthesis in the cephalopod Octopus vulgaris

The interest in understanding the capacity of aquatic invertebrates to biosynthesise omega-3 (ω3) long-chain (≥C₂₀) polyunsaturated fatty acids (LC-PUFA) has increased in recent years. Using the common octopus Octopus vulgaris as a model species, we previously characterised a ∆5 desaturase and two elongases (i.e. Elovl2/5 and Elovl4) involved in the biosynthesis of LC-PUFA in molluscs. The aim of this study was to characterise both molecularly and functionally, two methyl-end (or ωx) desaturases that have been long regarded to be absent in most animals. O. vulgaris possess two ωx desaturase genes encoding enzymes with ∆12 and ω3 regioselectivities enabling the de novo biosynthesis of the C₁₈ PUFA 18:2ω6 (LA, linoleic acid) and 18:3ω3 (ALA, α-linolenic acid), generally regarded as dietary essential for animals. The O. vulgaris ∆12 desaturase (“ωx2”) mediates the conversion of 18:1ω9 (oleic acid) into LA, and subsequently, the ω3 desaturase (“ωx1”) catalyses the ∆15 desaturation from LA to ALA. Additionally, the O. vulgaris ω3 desaturase has ∆17 capacity towards a variety of C₂₀ ω6 PUFA that are converted to their ω3 PUFA products. Particularly relevant was the affinity of the ω3 desaturase towards 20:4ω6 (ARA, arachidonic acid) to produce 20:5ω3 (EPA, eicosapentaenoic acid), as supported by yeast heterologous expression, and enzymatic activity exhibited in vivo when paralarvae were incubated in the presence of [1-¹⁴C]20:4ω6. These results confirmed that several routes enabling EPA biosynthesis are operative in O. vulgaris whereas ARA and docosahexaenoic acid (DHA, 22:6ω3) should be considered essential fatty acids since endogenous production appears to be limited.     

MODULATION OF FATTY ACIDS IN THE MEMBRANES OF ANACYSTIS NIDULANS (CYANOBACTERIA): INCORPORATION OF ODD-NUMBERED CARBON FATTY ACIDS1

Anacystis nidulans Richt., a unicellular cyanobacterium, can incorporate exogenously supplied fatty acids, including odd-numbered carbon fatty acid (OFAs), into the acylglycerols of cell membranes. Data are presented for the uptake of undecanoic acid (11:0) into cells of A. nidulans, the subsequent elongation up to C17, and incorporation of OFA into the four major membrane acylglycerols. The incorporation of OFAs was followed by desaturation of part of the saturated fatty acid to monoenoic fatty acid. Positional analyses of the double bonds of these manoenoic fatty acids suggest that there is one desaturase that inserts a Δ⁹ bond in both odd- and even-numbered fatty acids of varying chain length. Our data also suggest that there is no positional specificity for chain length on the glycerol backbone by the acyltransferases.     

Phylogenetic diversity in freshwater‐dwelling Isochrysidales haptophytes with implications for alkenone production

Members of the order Isochrysidales are unique among haptophyte lineages in being the exclusive producers of alkenones, long‐chain ketones that are commonly used for paleotemperature reconstructions. Alkenone‐producing haptophytes are divided into three major groups based largely on molecular ecological data: Group I is found in freshwater lakes, Group II commonly occurs in brackish and coastal marine environments, and Group III consists of open ocean species. Each group has distinct alkenone distributions; however, only Groups II and III Isochrysidales currently have cultured representatives. The uncultured Group I Isochrysidales are distinguished geochemically by the presence of tri‐unsaturated alkenone isomers (C_37:3b Me, C_38:3b Et, C_38:3b Me, C_39:3b Et) present in water column and sediment samples, yet their genetic diversity, morphology, and environmental controls are largely unknown. Using small‐subunit (SSU) ribosomal RNA (rRNA) marker gene amplicon high‐throughput sequencing of environmental water column and sediment samples, we show that Group I is monophyletic with high phylogenetic diversity and contains a well‐supported clade separating the previously described “EV” clade from the “Greenland” clade. We infer the first partial large‐subunit (LSU) rRNA gene Group I sequence phylogeny, which uncovered additional well‐supported clades embedded within Group I. Relative to Group II, Group I revealed higher levels of genetic diversity despite conservation of alkenone signatures and a closer evolutionary relationship with Group III. In Group I, the presence of the tri‐unsaturated alkenone isomers appears to be conserved, which is not the case for Group II. This suggests differing environmental influences on Group I and II and perhaps uncovers evolutionary constraints on alkenone biosynthesis.     

Bioorganic chemistry of plant lipid desaturation

The desaturation of long-chain fatty acids is a ubiquitous biotransformation which plays a critical role in the biosynthesis of plant lipids. Species-specific variations lead to unusual fatty acid signatures. Of particular interest is the unique ability of desaturases to oxidize unactivated hydrocarbon chains in such a chemo-, regio- and stereoselective manner. As part of ongoing research into the structure/activity relationships of this large class of enzymes, useful mechanistic tools have been developed to probe the active site. Recently a combination of stereo- and regiospecific deuterium, sulfur and fluorine labelling has been used to study the mechanism of a soluble plant Δ⁹ desaturase. The study of several membrane-bound desaturases has led to the conclusion that the dehydrogenation (desaturation) process is initiated by a kinetically important hydrogen activation step at the carbon of the incipient double bond which is closest to the acyl terminus of the fatty acid chain. A detailed analysis of a related 1,4-desaturation process has also been carried out.     

Mass spectral studies of phytosterolins and a ketone from Trianthema pentandra

Mass spectral data of a phytosterolin and its tetraacetate from Trianthema pentandra show that sitosterol-d(+)-glucoside reported earlier¹ was a mixture of sitosteroI-d(+)-glucoside and stigmasterol-d(+)-glucoside. The structure of a ketone has been suggested as nonacos-1-en-4-one, on the basis of physicochemical data. The positions of the double bond and the carbonyl group have been established by MS and NMR data. This is the first report in plants of a C₂₉ ketone with a terminal double bond and carbonyl group at position 4.     

The efficiency of the CO2-concentrating mechanism during single-cell C4 photosynthesis

The photosynthetic efficiency of the CO₂‐concentrating mechanism in two forms of single‐cell C₄ photosynthesis in the family Chenopodiaceae was characterized. The Bienertioid‐type single‐cell C₄ uses peripheral and central cytoplasmic compartments (Bienertia sinuspersici), while the Borszczowioid single‐cell C₄ uses distal and proximal compartments of the cell (Suaeda aralocaspica). C₄ photosynthesis within a single‐cell raises questions about the efficiency of this type of CO₂‐concentrating mechanism compared with the Kranz‐type. We used measurements of leaf CO₂ isotope exchange (Δ¹³C) to compare the efficiency of the single‐cell and Kranz‐type forms of C₄ photosynthesis under various temperature and light conditions. Comparisons were made between the single‐cell C₄ and a sister Kranz form, S. eltonica[NAD malic enzyme (NAD ME) type], and with Flaveria bidentis[NADP malic enzyme (NADP‐ME) type with Kranz Atriplicoid anatomy]. There were similar levels of Δ¹³C discrimination and CO₂ leakiness (?) in the single‐cell species compared with the Kranz‐type. Increasing leaf temperature (25 to 30 °C) and light intensity caused a decrease in Δ¹³C and ? across all C₄ types. Notably, B. sinuspersici had higher Δ¹³C and ? than S. aralocaspica under lower light. These results demonstrate that rates of photosynthesis and efficiency of the CO₂‐concentrating mechanisms in single‐cell C₄ plants are similar to those in Kranz‐type.     

Formation of a Δ9-dodecenoic dibasic acid from linoleic acid by young pea leaves

A “crude plastid” preparation from young pea leaves converts linoleate [1-¹⁴C] or [U-¹⁴C] (ammonium salt or free acid) into a C₁₂ dibasic acid with a double bond at Δ⁹.     

A New Pimarane Diterpenoid from the Botryotinia fuckeliana Fungus Isolated from Deep‐Sea Water

A new pimarane diterpenoid, named botryopimarene A ( 1 ), was discovered from the fungus Botryotinia fuckeliana MCCC 3 A00494 isolated from the deep‐sea water, together with ten known compounds. The planar structure of 1 was established based on the extensive spectroscopic analyses. The absolute configurations of tricyclic system in 1 were resolved by the theoretical ECD calculation, while the 15,16‐diol moiety in the side chain was resolved by the Mo₂(OAc)₄‐induced ECD spectrum. Compound 1 , featuring a Δ⁹⁽¹¹⁾ double bond, was rarely discovered in pimarane family. Compounds 1 – 11 were tested for their cytotoxic activities using six human cancer cell lines by the MTT method. However, none of the compounds exhibited detectable cytotoxicities (IC₅₀ >20 μm ).     

Large contributions of coupled protonation equilibria to the observed enthalpy and heat capacity changes for ssDNA binding to Escherichia coli SSB protein

Many macromolecular interactions, including protein‐nucleic acid interactions, are accompanied by a substantial negative heat capacity change, the molecular origins of which have generated substantial interest. We have shown previously that temperature‐dependent unstacking of the bases within oligo(dA) upon binding to the Escherichia coli SSB tetramer dominates the binding enthalpy, ΔH_obs, and accounts for as much as a half of the observed heat capacity change, ΔC_p. However, there is still a substantial ΔC_p associated with SSB binding to ssDNA, such as oligo(dT), that does not undergo substantial base stacking. In an attempt to determine the origins of this heat capacity change, we have examined by isothermal titration calorimetry (ITC) the equilibrium binding of dT(pT)₃₄ to SSB over a broad pH range (pH 5.0–10.0) at 0.02 M, 0.2 M NaCl and 1 M NaCl (25°C), and as a function of temperature at pH 8.1. A net protonation of the SSB protein occurs upon dT(pT)₃₄ binding over this entire pH range, with contributions from at least three sets of protonation sites (pK_a1 = 5.9–6.6, pK_a2 = 8.2–8.4, and pK_a3 = 10.2–10.3) and these protonation equilibria contribute substantially to the observed ΔH and ΔC_p for the SSB‐dT(pT)₃₄ interaction. The contribution of this coupled protonation (∼ −260 to −320 cal mol⁻¹ K⁻¹) accounts for as much as half of the total ΔC_p. The values of the “intrinsic” ΔC_p,0 range from −210 ± 33 cal mol⁻¹ °K⁻¹ to −237 ± 36 cal mol⁻¹K⁻¹, independent of [NaCl]. These results indicate that the coupling of a temperature‐dependent protonation equilibria to a macromolecular interaction can result in a large negative ΔC_p, and this finding needs to be considered in interpretations of the molecular origins of heat capacity changes associated with ligand‐macromolecular interactions, as well as protein folding. Proteins 2000;Suppl 4:8–22. © 2000 Wiley‐Liss, Inc.     

The disulfide oxidoreductase SdbA is active in Streptococcus gordonii using a single C‐terminal cysteine of the CXXC motif

Recently, we identified a novel disulfide oxidoreductase, SdbA, in the oral bacterium Streptococcus gordonii. Disulfide oxidoreductases form disulfide bonds in nascent proteins using a CXXC catalytic motif. Typically, the N‐terminal cysteine interacts with substrates, whereas the C‐terminal cysteine is buried and only reacts with the first cysteine of the motif. In this study, we investigated the SdbA C⁸⁶P⁸⁷D⁸⁸C⁸⁹ catalytic motif. In vitro, SdbA single cysteine variants at the N or C‐terminal position (SdbA_C86P and SdbA_C89A) were active but displayed different susceptibility to oxidation, and N‐terminal cysteine was prone to sulfenylation. In S. gordonii, mutants with a single N‐terminal cysteine were inactive and formed unstable disulfide adducts with other proteins. Activity was partially restored by inactivation of pyruvate oxidase, a hydrogen peroxide generator. Presence of the C‐terminal cysteine alone (in the SdbA_C86P variant) could complement the ΔsdbA mutant and restore disulfide bond formation in recombinant and natural protein substrates. These results provide evidence that certain disulfide oxidoreductases can catalyze disulfide bond formation using a single cysteine of the CXXC motif, including the buried C‐terminal cysteine.     

Diethyl‐Ether Flower Washings of Dianthus cruentus Griseb. (Caryophyllaceae): Derivatization Reactions Leading to the Identification of New Wax Constituents

Some carnation species (Dianthus spp., Caryophyllaceae) exhibit a strong resistance to drought stress that is connected with the increased surface wax formation. Wax composition is unknown for the majority of Dianthus spp. Herein, mass spectral and gas chromatographic data, in combination with synthesis and chemical transformations (transesterification and synthesis of dimethyl disulfide adducts), enabled the identification of 151 constituents of diethyl‐ether washings of fresh flowers of Dianthus cruentus Griseb . from Serbia. The flower wax contained, along with the dominant ubiquitous long‐chain n‐alkanes, homologous series of n‐ and branched (iso‐ and anteiso‐) long‐chain hexyl alkanoates/alkenoates and alkyl/alkenyl benzoates. The branching position in the mentioned hexyl esters was probed by synthesis of esters of three isomeric hexanols that were spectrally characterized (¹H‐ and ¹³C‐NMR, IR, MS). The washings also contained long‐chain (Z)‐ and (E)‐alkenes (C₂₃?C₃₅) with several different double bond regiochemistries. Fifty‐five of these constituents (eight hexyl esters, two benzoates, and forty‐five alkenes) were detected for the first time in Plantae, while ten of these represent completely new compounds. The rare occurrence of these wax constituents makes them possible chemotaxonomic markers of this particular Dianthus sp.     

Technical note: A linear model for predicting δ13Cprotein

Objective : Development of a model for the prediction of δ¹³C_protein from δ¹³C_collagen and Δ¹³C_ap‐co. Model‐generated values could, in turn, serve as “consumer” inputs for multisource mixture modeling of paleodiet. Methods : Linear regression analysis of previously published controlled diet data facilitated the development of a mathematical model for predicting δ¹³C_protein (and an experimentally generated error term) from isotopic data routinely generated during the analysis of osseous remains (δ¹³C_co and Δ¹³C_ap‐co). Results : Regression analysis resulted in a two‐term linear model (δ¹³C_protein (%) = (0.78 × δ¹³C_co) ? (0.58× Δ¹³C_ap‐co) ? 4.7), possessing a high R‐value of 0.93 (r² = 0.86, P < 0.01), and experimentally generated error terms of ±1.9% for any predicted individual value of δ¹³C_protein. This model was tested using isotopic data from Formative Period individuals from northern Chile's Atacama Desert. Conclusions : The model presented here appears to hold significant potential for the prediction of the carbon isotope signature of dietary protein using only such data as is routinely generated in the course of stable isotope analysis of human osseous remains. These predicted values are ideal for use in multisource mixture modeling of dietary protein source contribution. Am J Phys Anthropol 157:694–703, 2015. © 2015 Wiley Periodicals, Inc.     

ISOLATION OF THREE NOVEL LONG‐CHAIN POLYUNSATURATED FATTY ACID Δ9‐ELONGASES AND THE TRANSGENIC ASSEMBLY OF THE ENTIRE PAVLOVA SALINA DOCOSAHEXAENOIC ACID PATHWAY IN NICOTIANA BENTHAMIANA1

The transgenic aerobic synthesis of long‐chain polyunsaturated fatty acids (LC‐PUFA) will in most land plants commence with either a Δ6‐desaturation or a Δ9‐elongation. Numerous Δ6‐desaturases have been characterized, but only one Δ9‐elongase has been reported in peer‐reviewed literature. In the present study, we describe the isolation of three additional Δ9‐elongases from the class Haptophyceae and demonstrate that the Δ9‐elongase group contains highly conserved regions, which differentiate them from other ELO‐type elongases. One such important difference is the presence of an LQxFHH motif instead of the usual LHxYHH motif, a feature that should simplify further gene discovery efforts in this group of enzymes. Moreover, the identification of the Pavlova salina (N. Carter) J. C. Green Δ9‐elongase completes the isolation of the entire P. salina docosahexaenoic acid (DHA) pathway, and we describe the assembly of this pathway in Nicotiana benthamiana. Finally, we comment on possible explanations for the widespread presence of the Δ6‐desaturated fatty acid stearidonic acid (SDA, 18:4^Δ6,9,12,15) in the plastidial lipids of organisms using the Δ9‐elongase pathway.