Biology subjects

Last, R. L.

Publications and source records attributed to Last, R. L..

13 recordsLinked to original sources

bioRxiv2026

Spatial expression evolution of duplicated genes post-whole genome duplication in cultivated tomato

The mechanisms by which whole genome duplication contributes to expression divergence of duplicate genes, which can impact the evolution of form and function, has been a long-standing question in evolutionary biology. We compared expression patterns of paralogs derived from the most recent Solanaceae-specific genome triplication event across 23 tissues and inferred ancestral expression states to investigate patterns of expression evolution. While the partitioning of ancestral expression states is traditionally considered the second most common (after the gene loss) trajectory of duplicate expression evolution, we found that the ancestral expression states tended to be retained by most (~66%) duplicates, with ~6% of gene lineages experiencing expression gain events and ~20% experiencing expression losses. The genes that gained expression in fruit tissues are significantly enriched with functions associated with fruit quality. Notably, asymmetrical expression divergence is prevalent among duplicates, especially when ancestral genes were either not expressed or were highly expressed. Our study demonstrates the utility of integrating paralog expression comparisons with phylogenetic analyses to document the potential evolutionary history of spatial expression patterns and gain insight into how expression divergence contributes to the evolution of function across tissues.

plant biology↗

bioRxiv2023

Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

BackgroundMitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, henceforth, the rhizobiome, can harbor beneficial microbes that alleviate stress impacts. However, the factors influencing the recruitment of the rhizobiome during stress are unclear. We conducted an experiment to understand bacterial rhizobiome responses to short-term drought for two crop species: switchgrass and common bean. We used 16S rRNA and 16S rRNA gene sequencing to investigate the impact of drought severity on the recruitment of active bacterial rhizobiome members. We included planted and unplanted conditions to distinguish the environment-versus plant-mediated drivers of the active rhizobiome. ResultsThough each crop had a distinct rhizobiome, there were differences in the active microbiome structure between drought and watered and between planted and unplanted treatments. Despite their different community structures, the drought rhizobiome dynamics were similar across the two crops. However, the presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought only observed for the bean rhizobiome. The switchgrass rhizobiome was stable despite differences in the rhizosphere metabolite profiles between planted and unplanted treatments. Specifically, steroidal saponins and diterpennoids were enriched in drought, planted switchgrass soils. ConclusionsWe conclude that rhizobiome benefits to resist short-term drought are crop-specific, with the possibility of decoupling of plant exudation and rhizobiome responses, as we observed in switchgrass. We propose bacterial taxa uniquely associated with common bean plants during the short-term drought, which could be further evaluated to determine any plant benefit during drought.

microbiology↗

bioRxiv2023

Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes

Solanaceae (nightshade family) species synthesize a remarkable array of clade- and tissue-specific specialized metabolites. Protective acylsugars, one such class of structurally diverse metabolites, are produced by AcylSugar AcylTransferases from sugars and acyl-coenzyme A esters. Published research revealed trichome acylsugars composed of glucose and sucrose cores in species across the family. In addition, acylsugars were analyzed across a small fraction of the >1200 species in the phenotypically megadiverse Solanum genus, with a handful containing inositol and glycosylated inositol cores. The current study sampled several dozen species across subclades of the Solanum to get a more detailed view of acylsugar chemodiversity. In depth characterization of acylsugars from the Clade II species Solanum melongena (brinjal eggplant) led to the identification of eight unusual structures with inositol or inositol glycoside cores, and hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis of 31 additional species in the Solanum genus revealed striking acylsugar diversity with some traits restricted to specific clades and species. Acylinositols and inositol-based acyldisaccharides were detected throughout much of the genus. In contrast, acylglucoses and acylsucroses were more restricted in distribution. Analysis of tissue-specific transcriptomes and interspecific acylsugar acetylation differences led to the identification of the S. melongena AcylSugar AcylTransferase 3-Like 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct from previously characterized acylsugar acetyltransferases, which are in the ASAT4 clade, and appears to be a functionally divergent ASAT3. This study provides a foundation for investigating the evolution and function of diverse Solanum acylsugar structures and harnessing this diversity in breeding and synthetic biology.

plant biology↗

bioRxiv2023

Identification of anti-fungal bioactive terpenoids from the bioenergy crop switchgrass (Panicum virgatum)

Plant derived bioactive small molecules have attracted attention of scientists across fundamental and applied scientific disciplines. We seek to understand the influence of these phytochemicals on functional phytobiomes. Increased knowledge of specialized metabolite bioactivities could inform strategies for sustainable crop production. Our recent investigations of metabolomes of the upland and lowland ecotypes of the bioenergy crop switchgrass (Panicum virgatum) revealed large differences in types and abundances of terpenoid specialized metabolites. We hypothesized that - consistent with accumulating evidence that switchgrass genotype impacts microbiome assembly - differential terpenoid accumulation contributes to switchgrass ecotype-specific microbiome composition. An initial in vitro plate-based disc diffusion screen of 18 switchgrass root derived fungal isolates revealed differential responses to upland- and lowland-isolated metabolites. To identify specific fungal growth-modulating metabolites, we tested fractions from root extracts on three ecologically important fungal isolates - Linnemania elongata, Trichoderma sp. and Fusarium sp. Saponins and diterpenoids were identified as the most prominent antifungal metabolites. Finally, analysis of liquid chromatography-purified terpenoids revealed fungal inhibition structure - activity relationships (SAR). Saponin antifungal activity was primarily determined by the number of sugar moieties - saponins glycosylated at a single core position were inhibitory whereas saponins glycosylated at two core positions were inactive. Saponin core hydroxylation and acetylation were also associated with reduced activity. Diterpenoid activity required the presence of an intact furan ring for strong fungal growth inhibition. This study demonstrates that switchgrass genotype-specific metabolites differentially inhibit fungal isolates from the root and rhizosphere, supporting the hypothesis that these small molecules contribute to microbiome assembly and function.

plant biology↗

bioRxiv2022

Identification of BAHD acyltransferases associated with acylinositol biosynthesis in Solanum quitoense (naranjilla)

Plants make a variety of specialized metabolites that can mediate interactions with animals, microbes and competitor plants. Understanding how plants synthesize these compounds enables studies of their biological roles by manipulating their synthesis in vivo as well as producing them in vitro. Acylsugars are a group of protective metabolites that accumulate in the trichomes of many Solanaceae family plants. Acylinositol biosynthesis is of interest because it appears to be restricted to a subgroup of species within the Solanum genus. Previous work characterized a triacylinositol acetyltransferase involved in acylinositol biosynthesis in the Andean fruit plant Solanum quitoense (lulo or naranjillo). We characterized three additional S. quitoense trichome expressed enzymes, and found that virus induced gene silencing of each caused changes in acylinositol accumulation. Surprisingly, the in vitro triacylinositol products of these enzymes are distinct from those that accumulate in planta. These enzymes, nonetheless, provide an opportunities to test the biological impact and properties of these triacylinositols in vitro.

plant biology↗

bioRxiv2022

Natural Variation Meets Synthetic Biology: Promiscuous Trichome Expressed Acyltransferases from Nicotiana acuminata

Acylsugars are defensive, trichome-synthesized sugar esters produced in plants across the Solanaceae (nightshade) family. Although assembled from simple metabolites and synthesized by a relatively short core biosynthetic pathway, tremendous within- and across-species acylsugar structural variation is documented across the family. To advance our understanding of the diversity and the synthesis of acylsugars within the Nicotiana genus, trichome extracts were profiled across the genus coupled with transcriptomics-guided enzyme discovery and in vivo and in vitro analysis. Differences in the types of sugar cores, numbers of acylations, and acyl chain structures contributed to over 300 unique annotated acylsugars throughout Nicotiana. Placement of acyl chain length into a phylogenetic context revealed that an unsaturated acyl chain type was detected in a few closely-related species. A comparative transcriptomics approach identified trichome-enriched Nicotiana acuminata acylsugar biosynthetic candidate enzymes. > 25 acylsugar variants could be produced in a single enzyme assay with four acylsugar acyltransferases (NacASAT1-4) together with structurally diverse acyl-CoAs and sucrose. Liquid chromatography coupled with mass spectrometry screening of in vitro products revealed the ability of these enzymes to make acylsugars not present in Nicotiana plant extracts. In vitro acylsugar production also provided insights into acyltransferase acyl donor promiscuity and acyl acceptor specificity as well as regiospecificity of some ASATs. This study suggests that promiscuous Nicotiana acyltransferases can be used as synthetic biology tools to produce novel and potentially useful metabolites. ONE SENTENCE SUMMARYAnalysis of Nicotiana glandular trichome metabolites and BAHD acyltransferases revealed diverse sucrose and glucose based acylesters.

biochemistry↗

bioRxiv2021

It happened again: convergent evolution of acylglucose specialized metabolism in black nightshade and wild tomato

Plants synthesize myriad phylogenetically-restricted specialized (aka secondary) metabolites with diverse structures. Metabolism of acylated sugar esters in epidermal glandular secreting trichomes across the Solanaceae (nightshade) family are ideal for investigating the mechanisms of evolutionary metabolic diversification. We developed methods to structurally analyze acylhexose mixtures by 2D NMR, which led to the insight that the Old World species black nightshade (Solanum nigrum) accumulates acylglucoses and acylinositols in the same tissue. Detailed in vitro biochemistry - cross validated by in vivo virus induced gene silencing - revealed two unique features of the four-step acylglucose biosynthetic pathway: a trichome-expressed, neofunctionalized invertase-like enzyme, SnASFF1, converts BAHD-produced acylsucroses to acylglucoses, which in turn are substrates for the first-reported acylglucose acyltransferase, SnAGAT1. This biosynthetic pathway evolved independently from that recently described in the wild tomato S. pennellii, reinforcing that acylsugar biosynthesis is evolutionarily dynamic with independent examples of primary metabolic enzyme cooption and additional variation in BAHD acyltransferases. TeaserAnalysis of plant protective surface hair chemistry revealed evolutionary mechanisms leading to metabolic innovation.

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

Switchgrass metabolomics reveals striking genotypic and developmental differences in saponins

Switchgrass (Panicum virgatum L.) is a bioenergy crop that grows productively on lands not suitable for food production, and is an excellent target for low-pesticide input biomass production. We hypothesize that resistance to insect pests and microbial pathogens is influenced by low molecular weight compounds known as specialized metabolites. We employed untargeted liquid chromatography-mass spectrometry (LC-MS), quantitative gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy to identify differences in switchgrass ecotype metabolomes. This analysis revealed striking differences between upland and lowland switchgrass metabolomes as well as distinct developmental profiles. Terpenoid and polyphenol derived specialized metabolites were identified, including steroidal saponins, di- and sesqui-terpenoids and flavonoids. The saponins are especially abundant in switchgrass extracts and have diverse aglycone cores and sugar moieties. We report seven structurally distinct steroidal saponin classes with unique steroidal cores and glycosylated at one or two positions. Quantitative GC-MS revealed differences in total saponin concentrations in leaf blade, leaf sheath, stem, rhizome and root. The quantitative data also demonstrated that saponin concentrations is higher in roots of lowland than upland ecotype plants, suggesting ecotypic specific biosynthesis and/or biological functions. These results enable future testing of these specialized metabolites on biotic and abiotic stress tolerance and can inform development of low-input bioenergy crops. One sentence summaryIntegrated mass-spectrometry and nuclear magnetic resonance spectroscopy based metabolomics reveal that switchgrass accumulates structurally diverse terpenoids and phenolics, which vary in abundance and structure in a tissue- and ecotype-specific manner.

plant biology↗

bioRxiv2020

Solanaceae specialized metabolism in a non-model plant: trichome acylinositol biosynthesis

Plants make hundreds of thousands of biologically active specialized metabolites varying widely in structure, biosynthesis and the processes that they influence. An increasing number of these compounds are documented to protect plants from harmful insects, pathogens, or herbivores, or mediate interactions with beneficial organisms including pollinators and nitrogen fixing microbes. Acylsugars - one class of protective compounds - are made in glandular trichomes of plants across the Solanaceae family. While most described acylsugars are acylsucroses, published examples also include acylsugars with hexose cores. The South American fruit crop Solanum quitoense (Naranjilla) produces acylsugars that contain a myo-inositol core. We identified an enzyme that acetylates triacylinositols, a function homologous to the last step in the Solanum lycopersicum acylsucrose biosynthetic pathway. Our analysis reveals parallels between S. lycopersicum acylsucrose and S. quitoense acylinositol biosynthesis, suggesting a common evolutionary origin. Material availabilityThe author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Robert L. Last (lastr@msu.edu). One sentence summaryEvidence that the final step in Solanum quitoense acylinositol biosynthesis evolved from an acylsucrose acetyltransferase enzyme.

biochemistry↗

bioRxiv2020

Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

Plants produce phylogenetically and spatially restricted, as well as structurally diverse specialized metabolites via multistep metabolic pathways. Hallmarks of specialized metabolic evolution include enzymatic promiscuity, recruitment of primary metabolic enzymes and genomic clustering of pathway genes. Solanaceae plant glandular trichomes produce defensive acylsugars, with aliphatic sidechains that vary in length across the family. We describe a tomato gene cluster on chromosome 7 involved in medium chain acylsugar accumulation due to trichome specific acyl-CoA synthetase and enoyl-CoA hydratase genes. This cluster co-localizes with a tomato steroidal alkaloid gene cluster forming a supercluster, and is syntenic to a chromosome 12 region containing another acylsugar pathway gene. We reconstructed the evolutionary events leading to emergence of this gene cluster and found that its phylogenetic distribution correlates with medium chain acylsugar accumulation across the Solanaceae. This work reveals dynamics behind emergence of novel enzymes from primary metabolism, gene cluster evolution and cell-type specific metabolite diversity.

plant biology↗

bioRxiv2018

Evolution of metabolic novelty: a trichome-expressed invertase creates specialized metabolic diversity in wild tomato

Plants produce myriad taxonomically restricted specialized metabolites. This diversity - and our ability to correlate genotype with phenotype - makes the evolution of these ecologically and medicinally important compounds interesting and experimentally tractable. Trichomes of tomato and other nightshade family plants produce structurally diverse protective compounds termed acylsugars. While cultivated tomato (Solanum lycopersicum) accumulates strictly acylsucroses, the South American wild relative Solanum pennellii produces copious amounts of acylglucoses. Genetic, transgenic and biochemical dissection of the S. pennellii acylglucose biosynthetic pathway identified a trichome gland cell expressed invertase-like enzyme that hydrolyzes acylsucroses (Sopen03g040490). This enzyme acts on the pyranose ring-acylated acylsucroses found in the wild tomato but not the furanose ring-decorated acylsucroses of cultivated tomato. These results show that modification of the core acylsucrose biosynthetic pathway leading to loss of furanose ring acylation set the stage for co-option of a general metabolic enzyme to produce a new class of protective compounds.

plant biology↗

bioRxiv2017

Multi-omic analysis of a hyper-diverse plant metabolic pathway reveals evolutionary routes to biological innovation

The diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome-localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenetics in non-model species. Our results reveal that hundreds of acylsugars are produced across the Solanaceae family and even within a single plant, revealing this phenotype to be hyper-diverse. The relatively short biosynthetic pathway experienced repeated cycles of innovation over the last 100 million years that include gene duplication and divergence, gene loss, evolution of substrate preference and promiscuity. This study provides mechanistic insights into the emergence of plant chemical novelty, and offers a template for investigating the [~]300,000 non-model plant species that remain underexplored.

genomics↗