Molecular signatures of fossil leaves provide unexpected new evidence for extinct plant relationships

Bis-Iridoid Glycosides and Triterpenoids from Kolkwitzia amabilis and Their Potential as Inhibitors of ACC1 and ACL

A comprehensive phytochemical investigation of the twigs/leaves and flower buds of Kolkwitzia amabilis, a rare deciduous shrub native to China, led to the isolation of 39 structurally diverse compounds. These compounds include 11 iridoid glycosides (1-4 and 7-13), 20 triterpenoids (5, 6, and 14-31), and 8 phenylpropanoids (32-39). Among these, amabiliosides A (1) and B (2) represent previously undescribed bis-iridoid glycosides, while amabiliosides C (3) and D (4) feature a unique bis-iridoid-monoterpenoid indole alkaloid scaffold with a tetrahydro-β-carboline-5-carboxylic acid moiety. Amabiliacids A (5) and B (6) are 24-nor-ursane-type triterpenoids characterized by an uncommon ∆11,13(18) transannular double bond. Their chemical structures and absolute configurations were elucidated through spectroscopic data and electronic circular dichroism analyses. Compound 2 exhibited a moderate inhibitory effect against acetyl CoA carboxylase 1 (ACC1), with an IC50 value of 9.6 μM. Lonicejaposide C (8), 3β-O-trans-caffeoyl-olean-12-en-28-oic acid (29), and (23E)-coumaroylhederagenin (31) showed notable inhibitory effects on ATP-citrate lyase (ACL), with IC50 values of 3.6, 1.6, and 4.7 μM, respectively. Additionally, 3β-acetyl-ursolic acid (17) demonstrated dual inhibitory activity against both ACC1 and ACL, with IC50 values of 10.3 and 2.0 μM, respectively. The interactions of the active compounds with ACC1 and ACL enzymes were examined through molecular docking studies. From a chemotaxonomic perspective, the isolation of bis-iridoid glycosides in this study may aid in clarifying the taxonomic relationship between the genera Kolkwitzia and Lonicera within the Caprifoliaceae family. These findings highlight the importance of conserving plant species with unique and diverse secondary metabolites, which could serve as potential sources of new therapeutic agents for treating ACC1/ACL-associated diseases.

Major specialized natural products from the endangered plant Heptacodium miconioides, potential medicinal uses and insights into its longstanding unresolved systematic classification

A comprehensive phytochemical investigation of the flower buds and leaves/twigs of Heptacodium miconioides, a cultivated ornamental plant native to China and categorized as 'vulnerable', has led to the isolation of 45 structurally diverse compounds, which comprise 18 phenylpropanoids (1-4, 7-20), 11 pentacyclic triterpenoids (5, 6, 21-29), eight secoiridoid glycosides (30-37), three quinic acid derivatives (38-40), and a few miscellaneous components (41-45). Among them, (+)-α-intermedianol (1), (+)-holophyllol A (2), and (-)-pseudolarkaemin A (3) represent previously unreported enantiomeric lignans, while (+)-7'(R)-hydroxymatairesinol (4) is an undescribed naturally occurring lignan. Heptacoacids A (5) and B (6) are undescribed 24-nor-urs-28-oic acid derivatives. Their chemical structures were determined by 2D-NMR, supplemented by evidence from specific rotations and circular dichroism spectra. Given the uncertainty surrounding the systematic position of Heptacodium, integrative taxonomy (ITA), a method utilized to define contentious species, is applied. Chemotaxonomy, a vital aspect of ITA, becomes significant. By employing hierarchical clustering analysis (HCA) and syntenic pattern analysis methods, a taxonomic examination based on the major specialized natural products from the flower buds of H. miconioides and two other Caprifoliaceae plants (i.e., Lonicera japonica and Abelia × grandiflora) could offer enhanced understanding of the systematic placement of Heptacodium. Additionally, compounds 39 and 40 displayed remarkable inhibitory activities against ATP-citrate lyase (ACL), with IC50 values of 0.11 and 1.10 μM, respectively. In summary, the discovery of medical properties and refining systematic classification can establish a sturdy groundwork for conservation efforts aimed at mitigating species diversity loss while addressing human diseases.

Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity

The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today. We still know little about their origin and geographic range evolution. Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian total-evidence dating analyses. We assess the ancestral geographic origin and trace the historical biogeography of cycads with a time-stratified process-based model. Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic. Through now-vanished continental connections, Antarctica and Greenland were crucial biogeographic crossroads for cycad biogeography. Vicariance is an essential speciation mode in the deep and recent past. Their latitudinal span increased in the Jurassic and restrained toward subtropical latitudes in the Neogene in line with biogeographic inferences of high-latitude extirpations. We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present-day relict groups.

Molecular fingerprints resolve affinities of Rhynie chert organic fossils

The affinities of extinct organisms are often difficult to resolve using morphological data alone. Chemical analysis of carbonaceous specimens can complement traditional approaches, but the search for taxon-specific signals in ancient, thermally altered organic matter is challenging and controversial, partly because suitable positive controls are lacking. Here, we show that non-destructive Fourier Transform Infrared Spectroscopy (FTIR) resolves in-situ molecular fingerprints in the famous 407 Ma Rhynie chert fossil assemblage of Aberdeenshire, Scotland, an important early terrestrial Lagerstätte. Remarkably, unsupervised clustering methods (principal components analysis and K-mean) separate the fossil spectra naturally into eukaryotes and prokaryotes (cyanobacteria). Additional multivariate statistics and machine-learning approaches also differentiate prokaryotes from eukaryotes, and discriminate eukaryotic tissue types, despite the overwhelming influence of silica. We find that these methods can clarify the affinities of morphologically ambiguous taxa; in the Rhynie chert for example, we show that the problematic "nematophytes" have a plant-like composition. Overall, we demonstrate that the famously exquisite preservation of cells, tissues and organisms in the Rhynie chert accompanies similarly impressive preservation of molecular information. These results provide a compelling positive control that validates the use of infrared spectroscopy to investigate the affinity of organic fossils in chert.

Cretaceous gnetalean yields first preserved plant gum

Some liquid plant exudates (e.g. resin) can be found preserved in the fossil record. However, due to their high solubility, gums have been assumed to dissolve before fossilisation. The visual appearance of gums (water-soluble polysaccharides) is so similar to other plant exudates, particularly resin, that chemical testing is essential to differentiate them. Remarkably, Welwitschiophyllum leaves from Early Cretaceous, Brazil provide the first chemical confirmation of a preserved gum. This is despite the leaves being exposed to water twice during formation and subsequent weathering of the Crato Formation. The Welwitschiophyllum plant shares the presence of gum ducts inside leaves with its presumed extant relative the gnetalean Welwitschia. This fossil gum presents a chemical signature remarkably similar to the gum in extant Welwitschia and is distinct from those of fossil resins. We show for the first time that a water-soluble plant exudate has been preserved in the fossil record, potentially allowing us to recognise further biomolecules thought to be lost during the fossilisation process.

Proteomes of the past: the pursuit of proteins in paleontology

Introduction: Despite an extensive published literature, skepticism over the claim of original biochemicals including proteins preserved in the fossil record persists and the issue remains controversial. Workers using many different techniques including mass spectrometry, X-ray, electron microscopy and optical spectroscopic techniques, have attempted to verify proteinaceous or other biochemicals that appear endogenous to fossils found throughout the geologic column.Areas covered: This paper presents a review of the relevant literature published over the last 50 years. A comparative survey of the reported techniques used is also given.Expert opinion: Morphological and molecular investigations show that original biochemistry is geologically extensive, geographically global, and taxonomically wide-ranging. The survival of endogenous organics in fossils remains the subject of widespread and increasing research investigation.

Plant chemophenetics - A new term for plant chemosystematics/plant chemotaxonomy in the macro-molecular era

Plant chemosystematic or chemotaxonomic studies based purely on the profiles of small molecules have become obsolete as tools to study phylogenetic relationships of higher plants due to the advent of the much more powerful (macro-) molecular techniques and new methods of data analysis established in parallel to these techniques. A new term is herein proposed for the field of studies aimed at the exploitation of characteristic arrays of specialized natural products of plant taxa: plant chemophenetics. Chemophenetic studies as defined here are studies aimed at describing the array of specialized secondary metabolites in a given taxon. Thus, chemophenetic studies contribute to the phenetic description of taxa, similar to anatomical, morphological, and karyological approaches, which have already been recognized as of major importance for establishing "natural" systems, and which continue to be of the utmost importance for the description of organisms classified with the help of modern molecular methods.

Ancient Biomolecules and Evolutionary Inference

Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.

Si Nanostrip Optical Waveguide for On-Chip Broadband Molecular Overtone Spectroscopy in Near-Infrared

The ability to probe the molecular fundamental or overtone (high harmonics) vibrations is fundamental to modern healthcare monitoring techniques and sensing technologies since it provides information about the molecular structure. However, since the absorption cross section of molecular vibration overtones is much smaller compared to the absorption cross section of fundamental vibrations, their detection is challenging. Here, a silicon nanostrip rib waveguide structure is proposed for label-free on-chip overtone spectroscopy in near-infrared (NIR). Utilizing the large refractive index contrast (Δ n > 2) between the silicon core of the waveguide and the silica substrate, a broadband NIR lightwave can be efficiently guided. We show that the sensitivity for chemical detection is increased by more than 3 orders of magnitude when compared to the evanescent-wave sensing predicted by the numerical model. This spectrometer distinguished several common organic liquids such as N-methylaniline and aniline precisely without any surface modification to the waveguide through the waveguide scanning over the absorption dips in the NIR transmission spectra. Planar NIR Si nanostrip waveguide is a compact sensor that can provide a platform for accurate chemical detection. Our NIR Si nanostrip rib waveguide device can enable the development of sensors for remote, on-site monitoring of chemicals.