C-4 sterol demethylation enzymes distinguish bacterial and eukaryotic sterol synthesis.

Sterols are essential eukaryotic lipids that are required for a variety of physiological roles. The diagenetic products of sterol lipids, sterane hydrocarbons, are preserved in ancient sedimentary rocks and are utilized as geological biomarkers, indicating the presence of both eukaryotes and oxic environments throughout Earth's history. However, a few bacterial species are also known to produce sterols, bringing into question the significance of bacterial sterol synthesis for our interpretation of sterane biomarkers. Recent studies suggest that bacterial sterol synthesis may be distinct from what is observed in eukaryotes. In particular, phylogenomic analyses of sterol-producing bacteria have failed to identify homologs of several key eukaryotic sterol synthesis enzymes, most notably those required for demethylation at the C-4 position. In this study, we identified two genes of previously unknown function in the aerobic methanotrophic γ-Proteobacterium Methylococcus capsulatus that encode sterol demethylase proteins (Sdm). We show that a Rieske-type oxygenase (SdmA) and an NAD(P)-dependent reductase (SdmB) are responsible for converting 4,4-dimethylsterols to 4α-methylsterols. Identification of intermediate products synthesized during heterologous expression of SdmA-SdmB along with 13C-labeling studies support a sterol C-4 demethylation mechanism distinct from that of eukaryotes. SdmA-SdmB homologs were identified in several other sterol-producing bacterial genomes but not in any eukaryotic genomes, indicating that these proteins are unrelated to the eukaryotic C-4 sterol demethylase enzymes. These findings reveal a separate pathway for sterol synthesis exclusive to bacteria and show that demethylation of sterols evolved at least twice-once in bacteria and once in eukaryotes.

Experimental and Computational Modeling of H-Bonded Arginine-Tyrosine Groupings in Aprotic Environments.

H-bonds between neutral tyrosine and arginine in nonpolar environments are modeled by small-molecule phenol/guanidine complexes. From the temperature and concentration dependence of UV spectra, a value of ΔH° = -74 ± 4 kJ mol-1 is deduced for the formation of H-bonded p-cresol/dodecylguanidine in hexane. ΔE = -71 kJ mol-1 is computed with density functional theory (in vacuo). In dimethyl sulfoxide or crystals, (p-phenolyl)alkylguanidines form head-to-tail homodimers with two strong H-bonding interactions, as evidenced by UV, IR, and NMR spectral shifts, strong IR continuum absorbance bands, and short O···N distances in X-ray crystal structures. Phenol/alkylguanidine H-bonded complexes consist of polarizable rapidly interconverting tautomers, with the proton shift from phenol to guanidine increasing with increase in the polarity of the aprotic solvent. As measured by NMR, both groups in these strongly H-bonded neutral complexes can simultaneously appear to be predominantly protonated. These systems serve as models for the hypothetical hydrogen-Bonded Uncharged (aRginine + tYrosine), or "BU(RY)", motifs in membrane proteins.

NMR Tube Degradation Method for Sugar Analysis of Glycosides.

The sugar subunits of natural glycosides can be conveniently determined by acid hydrolysis and (1)H NMR spectroscopy without isolation or derivatization. The chemical shifts, coupling constants, and integral ratios of the anomeric signals allow each monosaccharide to be identified and its molar ratio to other monosaccharides to be quantified. The NMR data for the anomeric signals of 28 monosaccharides and three disaccharides are reported. Application of the method is demonstrated with the flavonoid glycoside naringin (1), the aminoglycoside antibiotics kanamycin (2) and tobramycin (3), and the saponin digitonin (4).

"Green" synthesis of unnatural poly(Amino Acid)s with Zwitterionic character and pH-responsive solution behavior, mediated by linear-dendritic laccase complexes.

This article describes the enzyme-catalyzed "green" synthesis of an unnatural poly(amino acid). dl-Tyrosine was polymerized under environmentally friendly conditions using linear-dendritic laccase complexes as initiators and water as solvent. The influence of the dendron generation in the linear-dendritic copolymers, the monomer concentration, and time and temperature on the polymer yields and molecular masses was investigated. Depending on the reaction conditions poly(tyrosine) with molecular mass (Mw) up to 82 kDa could be obtained in yields ranging between 45 and 69%. It was found that the linear-dendritic laccase complexes can induce further chain growth upon addition of fresh monomer to the preformed poly(tyrosine) in a fashion resembling the classic "living" polymerization. The structure of the poly(tyrosine) was investigated by NMR, FT-IR, and MALDI-TOF and it was discovered that the polymer chains consist of phenol repeating units linked together by C-C and C-O bonds randomly distributed along the backbone of the polymers. The materials formed are completely water-soluble and behave as typical poly(zwitterions) changing charge and size with the medium pH. DLS measurements reveal that the zeta potential of the polymers can vary between +15 mV at pH 1.2 with hydrodynamic diameter (Dh) = 6.7 nm to -35 mV at pH 11.8 and Dh = 10 nm. The isoelectric point was found at pH = 2.3-2.6, where Dh of the polymer is at the minimum (2.4 nm).

Structural identities of four glycosylated lipids in the oral bacterium Streptococcus mutans UA159.

The cariogenic bacterium Streptococcus mutans is an important dental pathogen that forms biofilms on tooth surfaces, which provide a protective niche for the bacterium where it secretes organic acids leading to the demineralization of tooth enamel. Lipids, especially glycolipids are likely to be key components of these biofilm matrices. The UA159 strain of S. mutans was among the earliest microorganisms to have its genome sequenced. While the lipids of other S. mutans strains have been identified and characterized, lipid analyses of UA159 have been limited to a few studies on its fatty acids. Here we report the structures of the four major glycolipids from stationary-phase S. mutans UA159 cells grown in standing cultures. These were shown to be monoglucosyldiacylglycerol (MGDAG), diglucosyldiacylglycerol (DGDAG), diglucosylmonoacylglycerol (DGMAG) and, glycerophosphoryldiglucosyldiacylglycerol (GPDGDAG). The structures were determined by high performance thin-layer chromatography, mass spectrometry and nuclear magnetic resonance spectroscopy. The glycolipids were identified by accurate, high resolution, and tandem mass spectrometry. The identities of the sugar units in the glycolipids were determined by a novel and highly efficient NMR method. All sugars were shown to have alpha-glycosidic linkages and DGMAG was shown to be acylated in the sn-1 position by NMR. This is the first observation of unsubstituted DGMAG in any organism and the first mass spectrometry data for GPDGDAG.

Unusual macrocyclic lactone sex pheromone of Parcoblatta lata, a primary food source of the endangered red-cockaded woodpecker.

Wood cockroaches in the genus Parcoblatta, comprising 12 species endemic to North America, are highly abundant in southeastern pine forests and represent an important prey of the endangered red-cockaded woodpecker, Picoides borealis. The broad wood cockroach, Parcoblatta lata, is among the largest and most abundant of the wood cockroaches, constituting >50% of the biomass of the woodpecker's diet. Because reproduction in red-cockaded woodpeckers is affected dramatically by seasonal and spatial changes in arthropod availability, monitoring P. lata populations could serve as a useful index of habitat suitability for woodpecker conservation and forest management efforts. Female P. lata emit a volatile, long-distance sex pheromone, which, once identified and synthesized, could be deployed for monitoring cockroach populations. We describe here the identification, synthesis, and confirmation of the chemical structure of this pheromone as (4Z,11Z)-oxacyclotrideca-4,11-dien-2-one [= (3Z,10Z)-dodecadienolide; herein referred to as "parcoblattalactone"]. This macrocyclic lactone is a previously unidentified natural product and a previously unknown pheromonal structure for cockroaches, highlighting the great chemical diversity that characterizes olfactory communication in cockroaches: Each long-range sex pheromone identified to date from different genera belongs to a different chemical class. Parcoblattalactone was biologically active in electrophysiological assays and attracted not only P. lata but also several other Parcoblatta species in pine forests, underscoring its utility in monitoring several endemic wood cockroach species in red-cockaded woodpecker habitats.

Structural identities of four glycosylated lipids in the oral bacterium Streptococcus mutans UA159.

The cariogenic bacterium Streptococcus mutans is an important dental pathogen that forms biofilms on tooth surfaces, which provide a protective niche for the bacterium where it secretes organic acids leading to the demineralization of tooth enamel. Lipids, especially glycolipids are likely to be key components of these biofilm matrices. The UA159 strain of S. mutans was among the earliest microorganisms to have its genome sequenced. While the lipids of other S. mutans strains have been identified and characterized, lipid analyses of UA159 have been limited to a few studies on its fatty acids. Here we report the structures of the four major glycolipids from stationary-phase S. mutans UA159 cells grown in standing cultures. These were shown to be monoglucosyldiacylglycerol (MGDAG), diglucosyldiacylglycerol (DGDAG), diglucosylmonoacylglycerol (DGMAG) and, glycerophosphoryldiglucosyldiacylglycerol (GPDGDAG). The structures were determined by high performance thin-layer chromatography, mass spectrometry and nuclear magnetic resonance spectroscopy. The glycolipids were identified by accurate, high resolution, and tandem mass spectrometry. The identities of the sugar units in the glycolipids were determined by a novel and highly efficient NMR method. All sugars were shown to have α-glycosidic linkages and DGMAG was shown to be acylated in the sn-1 position by NMR. This is the first observation of unsubstituted DGMAG in any organism and the first mass spectrometry data for GPDGDAG.

Nanogram-scale preparation and NMR analysis for mass-limited small volatile compounds.

Semiochemicals are often produced in infinitesimally small quantities, so their isolation requires large amounts of starting material, not only requiring significant effort in sample preparation, but also resulting in a complex mixture of compounds from which the bioactive compound needs to be purified and identified. Often, compounds cannot be unambiguously identified by their mass spectra alone, and NMR analysis is required for absolute chemical identification, further exacerbating the situation because NMR is relatively insensitive and requires large amounts of pure analyte, generally more than several micrograms. We developed an integrated approach for purification and NMR analysis of <1 µg of material. Collections from high performance preparative gas-chromatography are directly eluted with minimal NMR solvent into capillary NMR tubes. With this technique, (1)H-NMR spectra were obtained on 50 ng of geranyl acetate, which served as a model compound, and reasonable H-H COSY NMR spectra were obtained from 250 ng of geranyl acetate. This simple off-line integration of preparative GC and NMR will facilitate the purification and chemical identification of novel volatile compounds, such as insect pheromones and other semiochemicals, which occur in minute (sub-nanogram), and often limited, quantities.

Quantitative analyses of mixtures of 2-deuterio-1-vinylcyclobutanes.

Making distinctions between two stereoisomers characterized by diastereotopic deuterium atoms can ordinarily be achieved using standard NMR spectroscopic methods. Mixtures of stereoisomers having both diastereotopic and enantiotopic deuterium labels, however, may be difficult to analyze quantitatively. The present work introduces a simple way to gain quantitative analyses of mixtures of the four stereoisomeric 2-deuterio-1-vinylcyclobutanes, an essential prerequisite to establishing the stereochemical characteristics of the thermal stereomutations of vinylcyclobutane and its structural isomerizations to cyclohexene. The unconventional NMR method introduced and validated in this work will likely prove convenient and generally applicable to related stereochemical investigations.

Quantitative analysis of sugars in wood hydrolyzates with 1H NMR during the autohydrolysis of hardwoods.

The focus of this work was to determine the utility of (1)H NMR spectroscopy in the quantification of sugars resulting from the solubilization of hemicelluloses during the autohydrolysis of hardwoods and the use of this technique to evaluate the kinetics of this process over a range of temperatures and times. Yields of residual xylan, xylooligomers, xylose, glucose, and the degraded products of sugars, i.e., furfural and HMF (5-hydroxymethyl furfural), were determined. The monosaccharide and oligomer contents were quantified with a recently developed high resolution (1)H NMR spectroscopic analysis. This method provided precise measurement of the residual xylan and cellulose remaining in the extracted wood samples and xylose and glucose in the hydrolyzates. NMR was found to exhibit good repeatability and provided carbohydrate compositional results comparable to published methods for sugar maple and aspen woods.

Quantitative analyses of stereoisomeric 3,4-d2-cyclohexenes in the presence of 3,6-d2-cyclohexenes.

The challenging analytical problem posed by mixtures of the four isomeric 3,4-d(2)-cyclohexenes and the three isomeric 3,6-d(2)-cyclohexenes has been solved through a novel one-dimensional NMR spectroscopic method dependent on recording (13)C resonances while broadband decoupling both proton and deuteron nuclei. Upfield deuterium perturbations of (13)C chemical shifts in chair conformationally locked cyclohexane derivatives readily secured from a mixture of the seven deuterium-labeled cyclohexenes allow quantitative analytical assessments of the four possible 3,4-d(2)-cyclohexenes in the mixture. This analytical capability is an essential prerequisite for uncovering the relative participations of the four possible stereochemical paths followed by the thermal structural isomerizations of vinylcyclobutane to cyclohexene. The unconventional NMR method validated in this work will likely prove invaluable in related stereochemical investigations.

Unambiguous NMR spectral assignments of salvinorin A.

The complete assignments of the (1)H and (13)C NMR spectra of the hallucinogenic neoclerodane diterpenoid salvinorin A were determined in three different NMR solvents using HSQC, HMBC and COSY. Solvent systems are described that allow the resolution of all (1)H signals. Virtual coupling was observed for the protons at C-2, C-3 and C-4 in the 600 MHz (1)H spectrum in CDCl(3). The complete assignments of the (1)H and (13)C NMR spectra of salvinorin B are also reported.

Submicro scale NMR sample preparation for volatile chemicals.

A simple, inexpensive, and highly efficient NMR sample preparation technique for volatile chemicals has been devised using a micropreparative GC system. The recovery efficiency of a volatile chemical using this technique was >80% with sample sizes of 0.05 to 0.5 microg. The purity of the acquired NMR samples was sufficient for high sensitive NMR analyses including two dimensional experiments.

Biosynthesis of tunicamycin and metabolic origin of the 11-carbon dialdose sugar, tunicamine.

Tunicamycin is a reversible inhibitor of polyprenol-phosphate: N-acetylhexosamine-1-phosphate translocases and is produced by several Streptomyces species. We have examined tunicamycin biosynthesis, an important but poorly characterized biosynthetic pathway. Biosynthetic precursors have been identified by incorporating radioactive and stable isotopes, and by determining the labeling pattern using electrospray ionization-collision induced dissociation-mass spectrometry (ESI-CID-MS), and proton, deuterium, and C-13 nuclear magnetic resonance (NMR) spectroscopy. Preparation and analysis of [uracil-5-(2)H]-labeled tunicamycin established the complete ESI-CID-MS fragmentation pathway for the major components of the tunicamycin complex. Competitive metabolic experiments indicate that 7 deuteriums incorporate into tunicamycin from [6,6'-(2)H,(2)H]-labeled D-glucose, 6 of which arise from D-GlcNAc and 1 from uridine and/or D-ribose. Inverse correlation NMR experiments (heteronuclear single-quantum coherence (HSQC)) of (13)C-labeled tunicamycin enriched from D-[1-(13)C]glucose suggest that the unique tunicamine 11-carbon dialdose sugar backbone arises from a 5-carbon furanose precursor derived from uridine and a 6-carbon N-acetylamino-pyranose precursor derived from UDP-D-N-acetylglucosamine. The equivalent incorporation of (13)C into both the alpha-1" and beta-11' anomeric carbons of tunicamycin supports a direct biosynthesis via 6-carbon metabolism. It also indicates that the tunicamine motif and the alpha-1"-linked GlcNAc residue are both derived from the same metabolic pool of UDP-GlcNAc, without significant differential metabolic processing. A biosynthetic pathway is therefore proposed for tunicamycin for the first time: an initial formation of the 11-carbon tunicamine sugar motif from uridine and UDP-GlcNAc via uridine-5'-aldehyde and UDP-4-keto-6-ene-N-acetylhexosamine, respectively, and subsequent formation of the anomeric-to-anomeric alpha, beta-1",11'-glycosidic bond.