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A simple microscale method for determining the relative stereochemistry of statine units.

ABSTRACT: A simple method to determine the relative stereochemistry of statine amino acids (gamma-amino-beta-hydroxyacids) by using (1)H NMR spectroscopy is described. Configurational assignment of statine units within complex natural products is possible without degradation or derivatization as the syn and anti diastereomers can be distinguished by using a combination of chemical shift and coupling constant information derived from the alpha-methylene ABX system. Seventy-three examples are provided, demonstrating the scope and limitations of the methodology. These examples range in complexity from simple statine units to cyclic depsipeptides, such as tamandarin B.

SUBMITTER: Preciado A

PROVIDER: S-EPMC2765571 | biostudies-other | 2008 Dec

REPOSITORIES: biostudies-other

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A simple microscale method for determining the relative stereochemistry of statine units.

Preciado Alejandro A Williams Philip G PG

The Journal of organic chemistry 20081201 23

A simple method to determine the relative stereochemistry of statine amino acids (gamma-amino-beta-hydroxyacids) by using (1)H NMR spectroscopy is described. Configurational assignment of statine units within complex natural products is possible without degradation or derivatization as the syn and anti diastereomers can be distinguished by using a combination of chemical shift and coupling constant information derived from the alpha-methylene ABX system. Seventy-three examples are provided, demo ...[more]

PMID: 18989929

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Project description:Background:Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns. Methods:We used TIGER-rates to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into partitions based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as k-means. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder. Results:Simulations did not highlight any misbehaviour of our partitioning approach, even under difficult parameter conditions or missing data. In all eight phylogenetic datasets, partitioning using TIGER-rates and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position. We compared the resulting topologies and node support for these eight datasets as well as for the phylogenomic dataset. Discussion:We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNA sequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge.

Project description:Background and Aims:Boraginales are often characterized by a dense cover of stiff, mineralized trichomes, which may act as a first line of defence against herbivores. Recent studies have demonstrated that the widely reported silica and calcium carbonate in plant trichomes may be replaced by calcium phosphate. The present study investigates mineralization patterns in 42 species from nine families of the order Boraginales to investigate detailed patterns of mineralization and the possible presence of a phylogenetic signal in different mineralization patterns. Methods:The distribution of biominerals was analysed by scanning electron microscopy (SEM) including cryo-SEM and energy-dispersive X-ray analyses with element mapping. The observed distribution of biominerals was plotted onto a published phylogeny of the Boraginales. Three colours were selected to represent the principal elements: Si (red), Ca (green) and P (blue). Key Results:Calcium carbonate was present in the mineralized trichomes of all 42 species investigated, silica in 30 and calcium phosphate in 25; multiple mineralization with calcium carbonate and silica or calcium phosphate was found in all species, and 13 of the species were mineralized with all three biominerals. Trichome tips featured the most regular pattern - nearly all were exclusively mineralized with either silica or calcium phosphate. Biomineralization of the trichome shafts and bases was found to be more variable between species. However, the trichome bases were also frequently mineralized with calcium phosphate or silica, indicating that not only the tip is under functional constraints requiring specific patterns of chemical heterogeneity. The complete absence of either silica or phosphate may be an additional feature with systematic relevance. Conclusions:This study demonstrates that complex, site-specific and differential biomineralization is widespread across the order Boraginales. Calcium phosphate, only recently first reported as a structural plant biomineral, is common and appears to be functionally analogous to silica. A comparison with the phylogeny of Boraginales additionally reveals striking phylogenetic patterns. Most families show characteristic patterns of biomineralization, such as the virtual absence of calcium phosphate in Cordiaceae and Boraginaceae, the triple biomineralization of Heliotropiaceae and Ehretiaceae, or the absence of silica in Namaceae and Codonaceae. The complex chemical and phylogenetic patterns indicate that trichome evolution and functionalities are anything but simple and follow complex functional and phylogenetic constraints.

Dataset Information

A simple microscale method for determining the relative stereochemistry of statine units.

Publications

A simple microscale method for determining the relative stereochemistry of statine units.

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