Biology subjects

Bennett, A. A.

Publications and source records attributed to Bennett, A. A..

6 recordsLinked to original sources

bioRxiv2024

Characterization of root exudates of black oat in the presence of interspecific weed species neighbours and intraspecific neighbours, and their effects on root traits

Root exudates are composed of primary and secondary organic compounds that function as signalling molecules and play important roles in plant-environment interactions. The quantity and composition of root exudates vary depending on the species, genotype, and environmental conditions, including the presence and identity of neighbouring plants. Although cover crops are commonly used in agricultural practices for their ecosystem services, such as weed suppression, pathogen control, and soil structure improvement, studies on their root exudates are limited. Our study provides the first characterization of the root exudates of black oat interacting with weed neighbours, redroot pigweed and blackgrass, as well as with neighbours of the same species, black oat. We investigated how these interactions influence the black oat root exudation patterns. Furthermore, we investigated the impact of black oat presence on neighbours and how exposure to black oat root exudate treatments affects the root traits of weeds. The upregulated compounds detected in root exudates in response to neighbouring plants primarily belonged to the organic oxygen compounds superclass, with most of which identified as amino acids and carbohydrates. In the presence of redroot pigweed, a general increase in root exudation was observed, with amino acids and sugar sulphates being upregulated. The presence of black oat had varying effects among the neighbouring plants. While significant decreases observed and black oat in redroot pigweed root traits, an increase was observed in blackgrass. Similarly, more pronounced effects were observed in redroot pigweed compared to blackgrass upon root exudate application. This study provides a characterization and insights into the dynamic nature of root exudates and their influence on root traits and plant interactions.

plant biology↗

bioRxiv2022

Characterization and visualization of global metabolomic responses of Brachypodium distachyon to environmental changes

Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from tandem liquid chromatography mass spectrometry (LC-MS/MS) can be identified, limiting our understanding of how different metabolite classes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS of leaves, roots and other organs of Brachypodium distachyon, a model Poaceae species, under 17 different organ-condition combinations, including copper deficiency, heat stress, low phosphate and arbuscular mycorrhizal symbiosis (AMS). We used a combination of information theory-based metrics and machine learning-based identification of metabolite structural classes to assess metabolomic changes. Both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We also found that one week of copper deficiency shielded the root metabolome, but not the leaf metabolome, from perturbation due to heat stress. Using a recently published deep learning based method for metabolite class predictions, we analyzed the responsiveness of each metabolite class to environmental change, which revealed significant perturbations of various lipid classes and phenylpropanoids such as cinnamic acids and flavonoids. Co-accumulation analysis further identified condition-specific metabolic biomarkers. Finally, to make these results publicly accessible, we developed a novel visualization platform on the Bioanalytical Resource website, where significantly perturbed metabolic classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and plant stress adaptation.

plant biology↗

bioRxiv2021

Computational metabolomics illuminates the lineage-specific diversification of resin glycoside acylsugars in the morning glory (Convolvulaceae) family

Acylsugars are a class of plant defense compounds produced across many distantly related families. Members of the horticulturally important morning glory (Convolvulaceae) family produce a diverse sub-class of acylsugars called resin glycosides (RGs), which comprise oligosaccharide cores, hydroxyacyl chain(s), and decorating aliphatic and aromatic acyl chains. While many RG structures are characterized, the extent of structural diversity of this class in different genera and species is not known. In this study, we asked whether there has been lineage-specific diversification of RG structures in different Convolvulaceae species that may suggest diversification of the underlying biosynthetic pathways. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was performed from root and leaf extracts of 26 species sampled in a phylogeny-guided manner. LC-MS/MS revealed thousands of peaks with signature RG fragmentation patterns with one species producing over 300 signals, mirroring the diversity in Solanaceae-type acylsugars. A novel RG from Dichondra argentea was characterized using Nuclear Magnetic Resonance spectroscopy, supporting previous observations of RGs with open hydroxyacyl chains instead of closed macrolactone ring structures. Substantial lineage-specific differentiation in utilization of sugars, hydroxyacyl chains, and decorating acyl chains was discovered, especially among Ipomoea and Convolvulus - the two largest genera in Convolvulaceae. Adopting a computational, knowledge-based strategy, we further developed a high-recall workflow that successfully explained ~72% of the MS/MS fragments, predicted the structural components of 11/13 previously characterized RGs, and partially annotated ~45% of the RGs. Overall, this study improves our understanding of phytochemical diversity and lays a foundation for characterizing the evolutionary mechanisms underlying RG diversification.

plant biology↗

bioRxiv2020

Ancestral class-promiscuity as a driver of functional diversity in the BAHD acyltransferase family in plants

Large enzyme families catalyze metabolic diversification by virtue of their ability to use diverse chemical scaffolds. How enzyme families attain such functional diversity is not clear. Here, we addressed this question using BAHD acyltransferases as a model, and identified the routes by which duplication, promiscuity and sequence changes influenced BAHD diversification. This fast-evolving family expanded drastically during land plant evolution from 1-5 copies in algae to [~]100 copies in diploid angiosperm genomes. In vitro characterization of fourteen BAHDs against a substrate panel and compilation of >160 published activities revealed the wide prevalence of promiscuity among BAHDs. Using phylogenetic analysis, we predicted the substrate classes that the ancestral enzymes were likely capable of using prior to land plant origins. While the anthocyanin acylation activity was fixed in BAHDs later near the origin of angiosperms, in vitro testing of BAHDs from non-seed plant lineages suggested that the ability to acylate anthocyanins likely existed promiscuously millions of years prior to its fixation. Motif enrichment analysis in anthocyanin-acylating BAHDs identified two motifs fixed in the largest anthocyanin acylating clade. Molecular dynamic simulations and enzyme kinetics revealed the important role of an active site tryptophan, whose bulkiness, hydrophobicity and aromaticity are critical for anthocyanin acylation. Our results thus describe the molecular processes in robust, evolvable enzymes that drive emergence of functional diversity in enzyme families. One sentence summaryUsing a combination of phylogenetics, biochemistry and protein structure analysis, we investigated how the BAHD acyltransferase family evolved to use a structurally diverse array of substrates.

plant biology↗

bioRxiv2020

Migration through a major Andean ecogeographic disruption as a driver of genotypic and phenotypic diversity in a wild tomato species

The large number of species on our planet arises from the phenotypic variation and reproductive isolation occurring at the population level. In this study, we sought to understand the origins of such population-level variation in defensive acylsugar chemistry and mating systems in Solanum habrochaites - a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-Associated-Digestion Sequencing (RAD-seq) of 50 S. habrochaites accessions, we identified eight population clusters generated via isolation and hybridization dynamics of 4-6 ancestral populations. Estimation of heterozygosity, fixation index, isolation by distance, and migration probabilities, allowed identification of multiple barriers to gene flow leading to the establishment of extant populations. One major barrier is the Amotape-Huancabamba Zone (AHZ) - a geographical feature in the Andes with high endemism, where the mountainous range breaks up into isolated microhabitats. The AHZ was associated with emergence of alleles for novel reproductive and acylsugar phenotypes. These alleles led to the evolution of self-compatibility in the northern populations, where alleles for novel defense-related enzyme variants were also found to be fixed. We identified geographical distance as a major force causing population differentiation in the central/southern part of the range, where S. habrochaites was also inferred to have originated. Findings presented here highlight the role of the diverse ecogeography of Peru and Ecuador in generating new, reproductively isolated populations, and enhance our understanding of the microevolutionary processes that lay a path to speciation.

plant biology↗

bioRxiv2020

Assessing extraction methods and diversity of anthocyanins from purple-fleshed sweet potatoes grown in cooler climates

Anthocyanins are economically valuable phytochemicals of significant relevance to human health. Multiple fruit and vegetable sources for industrial-scale anthocyanin purification exist, however, each source has distinct anthocyanin levels and profiles conferred by modifications to the central anthocyanidin core. In this study, we assessed three purple-fleshed and one orange-fleshed cultivars of sweet potato, with the goal of studying their anthocyanin yield and diversity when this warm-weather crop is grown in cooler, northern latitudes. Comparison of multiple anthocyanin extraction methods revealed acidified ethanol extraction of lyophilized roots as the optimal method, producing a high, average yield of [~]800 mg anthocyanins/100g dry weight. Mass spectrometric analysis of sweet potato extracts identified eighteen high-confidence anthocyanins - all derived from peonidin and cyanidin cores - contributing to over 90% of the total anthocyanin signal. The concentrations of different anthocyanins were variable between the three purple-fleshed cultivars, while low anthocyanin accumulation was observed in the orange-fleshed cultivar. Further assessment of the untargeted high-resolution mass spectrometry data using MS/MS molecular networking revealed existence of low-abundance anthocyanins with delphinidin and pelargonidin cores, as well as over 250 peaks comprising of potential anthocyanins and flavonoids. These results provide a comprehensive insight into anthocyanin yields of purple-fleshed sweet potato grown in the northern latitudes and reveal the large diversity of anthocyanins and flavonoids in this popular crop.

plant biology↗