Biology subjects

Roston, R. L.

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

7 recordsLinked to original sources

bioRxiv2025

Lipid Metabolism and Contact Site Homologs Are Enriched at the Chloroplast Envelope-Thylakoid Interface

Biogenesis and maintenance of the photosynthetic thylakoid membrane requires transport of lipids from their site of synthesis in the chloroplast envelopes to their destination in the thylakoid. While vesicle trafficking is likely involved, we hypothesized a complementary mechanism involving direct membrane interactions. Using domain homology and proteomic profiling of chloroplast membrane fractions, we identified candidate lipid transport proteins enriched in a distinct, intermediate-density membrane population. This fraction was enriched in lipid metabolic enzymes and proteins homologous to known membrane organization factors. Several candidates, including TVP38 FAMILY PROTEIN (TVPFP), PLASMA MEMBRANE FUSION PROTEIN (PMFP), and LETM1-LIKE, localized to discrete subdomains within chloroplasts. Loss- of-function tvpfp or pmfp mutants exhibited altered chloroplast ultrastructure, including changes in thylakoid-envelope proximity, supporting their roles in maintaining membrane architecture. These findings identify a specialized chloroplast membrane region enriched in lipid-related functions and offer a foundation for elucidating the molecular architecture of these regions.

biochemistry↗

bioRxiv2024

Coenzyme M: An Archaeal Antioxidant as an Agricultural Biostimulant

Rising global food demand necessitates improved crop yields. Biostimulants offer a potential solution to meet these demands. Among them, antioxidants have shown potential to improve yield, nutritional quality and resilience to climate change. However, large-scale production of many antioxidants is challenging. Here, we investigate Coenzyme M (CoM), a small, achiral antioxidant from archaea, as a potential biostimulant, investigating its effects on growth and physiology. CoM significantly increased biomass of the model plant Arabidopsis thaliana in a concentration-dependent manner consistent with it being metabolized. In tobacco, CoM increased photosynthetic light capture capacity, consistent with observed growth improvements. Interestingly, this effect was independent of carbon capture rates. Furthermore, CoM promoted early-stage shoot growth in various crops species, including tobacco, basil, cannabis, and soybean. Our results suggest CoM is a promising, scalable biostimulant with potential to modify photosynthesis and enhance crop productivity. Key PointsO_LIAntioxidant application improves plant growth but is typically too expensive to use widely. C_LIO_LICoenzyme M is a small, easily made antioxidant of Archaeal origin. C_LIO_LIApplied exogenously, Coenzyme M conditionally increases plant biomass. C_LIO_LICoenzyme M represents an antioxidant with potential to be a widely used biostimulant. C_LI

plant biology↗

bioRxiv2023

Rhythmic lipid and gene expression responses to chilling in panicoid grasses

Chilling stress threatens plant growth and development, particularly affecting membrane fluidity and cellular integrity. Understanding plant membrane responses to chilling stress is important for unraveling the molecular mechanisms of stress tolerance. Whereas core transcriptional responses to chilling stress and stress tolerance are conserved across species, the associated changes in membrane lipids appear to be less conserved, as which lipids are affected by chilling stress varies by species. Here, we investigated changes in gene expression and membrane lipids in response to chilling stress during one diurnal cycle in sorghum (Sorghum bicolor), Urochloa (browntop signal grass, Urochloa fusca) (lipids only), and foxtail millet (Setaria italica), leveraging their evolutionary relatedness and differing levels of chilling-stress tolerance. We show that most chilling-induced lipid changes are conserved across the three species, while we observed distinct, time-specific responses in chilling-tolerant foxtail millet, indicating the presence of a finely orchestrated adaptive mechanism. We detected diurnal rhythmicity in lipid responses to chilling stress in the three grasses, which were also present in Arabidopsis (Arabidopsis thaliana), suggesting the conservation of rhythmic patterns across species and highlighting the importance of accounting for diurnal effects. When integrating lipid datasets with gene expression profiles, we identified potential candidate genes that showed corresponding transcriptional changes in response to chilling stress, providing insights into the differences in regulatory mechanisms between chilling-sensitive sorghum and chilling-tolerant foxtail millet. Significance StatementPlants respond to low-temperature stress in myriad ways. While core transcriptional changes are conserved across species, specific adaptive strategies do exist. However, membrane lipid responses during chilling do not appear to be conserved. Here, we collected samples from control and chilling stress-treated seedlings [PSC4] to assess gene expression and membrane lipids in three panicoid grasses to show that lipid metabolic changes follow a daily rhythm. Lipid changes in chilling-tolerant foxtail millet occurred at specific time points, partly explaining the difficulty in finding conserved chilling-induced lipid changes in previous reports. We identified specific orthologs in sorghum and foxtail millet that showed a correlation between gene expression and lipid metabolic changes; these orthologs may be used as potential target genes for developing chilling-tolerant sorghum varieties.

plant biology↗

bioRxiv2020

Predicting transcriptional responses to cold stress across plant species

Although genome sequence assemblies are available for a growing number of plant species, gene expression responses to stimuli have been catalogued for only a subset of these species. Many genes show altered transcription patterns in response to abiotic stresses. However, orthologous genes in related species often exhibit different responses to a given stress. Accordingly, data on the regulation of gene expression in one species are not reliable predictors of orthologous gene responses in a related species. Here, we trained a supervised classification algorithm to identify genes that transcriptionally respond to cold stress. A model trained with only features calculated directly from genome assemblies exhibited only modest decreases in performance relative to models trained using genomic, chromatin, and evolution/diversity features. Models trained with data from one species successfully predicted which genes would respond to cold stress in other related species. Cross-species predictions remained accurate when training was performed in cold-sensitive species and predictions were performed in cold-tolerant species and vice versa. Models trained with data on gene expression in multiple species outperformed models trained with data from any single species. These results suggest that classifiers trained on stress data from well-studied species may suffice for predicting gene expression patterns in related, less-studied species with sequenced genomes.

plant biology↗

bioRxiv2020

Using computational modeling to teach metabolism as a dynamic system improves student performance

Understanding metabolic function requires knowledge of the dynamics, interdependence, and regulation of biochemical networks. However, current approaches are not optimal to develop the needed mechanistic understanding, and misconceptions about biological processes persist even after graduation. To address these issues, we developed a computational modeling and simulation approach that employs scaffolded learning to teach biochemistry students about the regulation of metabolism. The power of the approach lies in students abilities to alter any component or connection in a modeled system and instantly observe the effects of their changes. We find that students who use our approach perform better on biochemistry metabolism questions compared to students in a course that did not use this approach. We also investigated performance by gender and found that our modules may have the potential to increase equity in education. We noted that students are generally positive about the approach and appreciate its benefits. Our modules provide life science instructors with a dynamic and systems-driven approach to teach metabolic regulation and control that improves learning and also equips students with important technical skills.

scientific communication and education↗

bioRxiv2017

Parallels between artificial selection in temperate maize and natural selection in the cold-adapted crop-wild relative Tripsacum

Artificial selection has produced varieties of domesticated maize which thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and sub-tropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full-length reference transcriptome for Tripsacum dactyloides generated using long-read isoseq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis, a critical component of cold acclimation on other cold adapted plant lineages, were enriched among those genes experiencing more rapid rates of protein sequence evolution in T. dactyloides. In contrast with previous studies of parallel selection, we find that there is a significant overlap between the genes which were targets of artificial selection during the adaptation of maize to temperate climates and those which were targets of natural selection in temperate adapted T. dactyloides. This overlap between the targets of natural and artificial selection suggests genetic changes in crop-wild relatives associated with adaptation to new environments may be useful guides for identifying genetic targets for breeding efforts aimed at adapting crops to a changing climate.

plant biology↗

bioRxiv2017

Differentially regulated ortholog analysis demonstrations that early transcriptional responses to cold have diverged slowly than downstream responses in panicoid grasses

Cross-species comparisons of transcriptional regulation have the potential to identify functionally constrained transcriptional regulation and genes for which a change in transcriptional regulation correlates with a change in phenotype. Conventional differential gene expression analysis and a different approach based on identifying differentially regulated orthologs (DROs) are compared using paired time course gene expression data from two species which respond similarly to cold - maize (Zea mays) and sorghum (Sorghum bicolor). Both approaches suggest that, for genes conserved at syntenic positions for millions of years, the majority of cold responsive transcriptional regulation is species specific, although initial transcriptional responses to cold appear to be more conserved between the two species than later responses. In maize, the promoters of genes with both species specific and conserved transcriptional responses to cold tend to contain more micrococcal nuclease hypersensitive sites in their promoters, a proxy for open chromatin. However, genes with conserved patterns of transcriptional regulation between the two species show lower ratios of nonsynonymous to synonymous substitutions consistent with this population of genes experiencing stronger purifying selection. We hypothesize that cold responsive transcriptional regulation is a fast evolving and largely neutral molecular phenotype for the majority of genes in Andropogoneae, while a smaller core set of genes involved in perceiving and responding to cold stress are subject to functionally constrained cold responsive regulation.

genetics↗