Biology subjects

Chirico, M.

Publications and source records attributed to Chirico, M..

4 recordsLinked to original sources

bioRxiv2025

Epigenomic Landscape of Oak (Quercus robur) across Seasons and Generations

O_LISeasonal fluctuations strongly shape the physiology of long-lived trees by coordinating growth, dormancy, and stress responses. Increasing evidence points to epigenetic mechanisms, particularly DNA methylation, as regulators of these processes, yet their role in long-lived trees across seasons and generations remains poorly understood. C_LIO_LIWe generated single-base resolution maps of cytosine methylation exploring the epigenetic landscape of 180 year-old mature oak (Quercus robur) trees (genetically homogeneous) along spring, summer and autumn, and in their progeny. C_LIO_LIGenome-wide DNA-methylation revealed a progressive increase in the CHH context (H = A, T or C) from Spring to Summer and Autumn, suggesting epigenetic reprogramming is happening over season. Differentially Methylated Regions (DMRs) were concentrated in promoter regions and terminal inverted repeat (TIR). Differentially methylated transposable elements (TEs) and genes were involved in leaf development and hormonal signalling. By contrast, generational differences (parents versus offspring) were most prominent in CG and CHG contexts and were concentrated in genic regions. C_LIO_LIOaks exhibit distinct seasonal and generational DNA methylation signatures, highlighting the plasticity and developmental specificity of epigenetic regulation. These findings provide a genomic foundation for understanding how epigenetic memory contributes to phenology, developmental programming and long-term adaptation in long-lived plants. C_LI

genetics↗

bioRxiv2023

Adaptation to sorbic acid in low sugar promotes resistance of spoilage yeasts to the preservative

The weak acid sorbic acid is a common preservative used in soft drink beverages to control microbial spoilage. Consumers and industry are increasingly transitioning to low-sugar food formulations, but potential impacts of reduced-sugar on preservative efficacy are barely characterised. In this study, we report enhanced sorbic acid resistance of spoilage yeasts in low-glucose conditions. We had anticipated that low glucose may induce respiratory metabolism, previously shown to be targeted by sorbic acid. However, a shift from respiratory to fermentative metabolism was correlated with the sorbic acid resistance in low glucose. Fermentation-deficient yeast species did not show the low-glucose resistance phenotype. Phenotypes observed for certain yeast deletion strains suggested roles for glucose signalling and repression pathways in the sorbic acid resistance at low glucose. This low- glucose induced sorbic acid resistance was alleviated by supplementing yeast cultures with succinic acid, a metabolic intermediate of respiratory metabolism (and a food-safe additive) that promoted respiration. The results indicate that metabolic adaptation of spoilage yeasts promotes sorbic acid resistance at low glucose, providing new insight into potential spoilage, and preservation, of foodstuffs as both food producers and consumers move towards a reduced-sugar landscape.

microbiology↗

bioRxiv2019

LYS3 encodes a prolamin-box-binding transcription factor that controls embryo growth in barley and wheat

Mutations at the LYS3 locus in barley have multiple effects on grain development, including an increase in embryo size and a decrease in endosperm starch content. The gene underlying LYS3 was identified by genetic mapping and mutations in this gene were identified in all four barley lys3 alleles. LYS3 encodes a transcription factor called Prolamin Binding Factor (PBF). Its role in controlling embryo size was confirmed using wheat TILLING mutants. To understand how PBF controls embryo development, we studied its spatial and temporal patterns of expression in developing grains. The PBF gene is expressed in both the endosperm and the embryos, but the timing of expression in these organs differs. PBF expression in wild-type embryos precedes the onset of embryo enlargement in lys3 mutants, suggesting that PBF suppresses embryo growth. We predicted the down-stream target genes of PBF in wheat and found them to be involved in a wide range of biological processes, including organ development and starch metabolism. Our work suggests that PBF may influence embryo size and endosperm starch synthesis via separate gene control networks. HIGHLIGHTSO_LILYS3 encodes a transcription factor called Prolamin Binding Factor (PBF) that is expressed in grains only. C_LIO_LIWheat and barley LYS3/PBF mutants have enlarged embryos suggesting that this gene suppresses embryo growth. C_LIO_LIThe down-stream target genes of PBF in wheat are predicted to be involved in a wide range of biological processes including organ development and starch metabolism. C_LI

plant biology↗

bioRxiv2019

A carbohydrate-binding protein, FLOURY ENDOSPERM 6 influences the initiation of A- and B-type starch granules in wheat.

Previously, we identified a quantitative trait locus on the group 4 chromosomes of Aegilops and bread wheat that controls B-type starch-granule content. Here, we identify a candidate gene by fine-mapping in Aegilops and confirm its function using wheat TILLING mutants. This gene is orthologous to the FLOURY ENDOSPERM 6 (FLO6) gene of rice and barley and the PTST2 gene of Arabidopsis. In Triticeae endosperm, reduction in the gene dose of functional FLO6 alleles results in reduction, or loss, of B-granules. This is due to repression of granule initiation in late-grain development, but has no deleterious impact on the synthesis of A-granules. The complete absence of functional FLO6, however, results in reduced numbers of normal A-type and B-type granules and the production of highly-abnormal granules that vary in size and shape. This polymorphous starch seen in a wheat flo6 triple mutant is similar to that observed in the barley mutant Franubet. Analysis of Franubet (fractured Nubet) starch suggests that the mutant A-granules are not fractured but compound, due to stimulation of granule initiation in plastids during early-grain development. Thus, in different situations in Triticeae, FLO6 either stimulates or represses granule initiation.

plant biology↗