Biology subjects

Amir, R.

Publications and source records attributed to Amir, R..

5 recordsLinked to original sources

bioRxiv2025

Methionine Triggers Metabolic, Transcriptional, and Epigenetic Reprogramming in Arabidopsis Leaves

Methionine (Met) is a central metabolite in plants, as it serves as a precursor for S-adenosylmethionine (SAM), a key methyl donor for epigenetic and metabolic processes. Met is also an essential amino acid that limits the nutritional value of plant-based diets. Understanding how altered Met levels affect the metabolome, transcriptome, and epigenetic regulation of plant leaves remains an open challenge. This study investigates the impact of ectopic Met accumulation in SSE Arabidopsis leaves of transgenic lines expressing a deregulated form of AtCGS (AtD-CGS) under the seed-specific phaseolin promoter. Unexpected activation of the phaseolin promoter in leaves led to AtD-CGS expression and variable Met accumulation among progeny, despite genetic homozygosity. High-Met (HM) plants showed elevated amino acid and sugar levels, enrichment of stress-related transcripts, and suppression of Met biosynthetic genes, while Low-Met (LM) plants showed reduced Met levels and increased non-CG DNA methylation, especially in centromeric and promoter regions. Integrated transcriptome and methylome analyses revealed that high Met levels were associated with the upregulation of stress hormone pathways (abscisic acid, jasmonate, salicylic acid, and ethylene), downregulation of key epigenetic regulators (e.g., MET1, CMTs), and broader transcriptional reprogramming. By contrast, low Met (LM) lines displayed similar expression levels of genes as control plants. Our findings reveal a complex regulatory network whereby Met accumulation reprograms metabolism, gene expression, and DNA methylation patterns. These results suggest feedback between sulfur-carbon metabolism, stress adaptation, and epigenetic control, positioning Met as both a nutrient and a signaling hub in plant physiology.

plant biology↗

bioRxiv2025

Elevated methionine induces DNA hypermethylation of transposable elements in Arabidopsis

Methionine (Met) is a key sulfur-containing amino acid and the precursor of S-adenosylmethionine (SAM), the universal methyl donor for DNA and histone methylation. While reduced SAM availability is known to cause DNA hypomethylation, the effects of elevated Met/SAM remain poorly understood. Here, we examined the Arabidopsis thaliana mto1 mutant, which accumulates Met and SAM due to a mutation in cystathionine {gamma}-synthase, the first committed enzyme of Met biosynthesis. Whole-genome bisulfite sequencing (WGBS) analysis revealed widespread hypermethylation in mto1, particularly in non-CG contexts (CHG and CHH), with the strongest changes in pericentromeric heterochromatin. Hypermethylation was concentrated in transposable elements (TEs), especially retrotransposon families such as Gypsy and Copia. Transcriptome profiling showed that TE-genes (TEGs) were broadly downregulated, consistent with reinforced TE silencing due to the hypermethylation. Despite these epigenetic changes, expression of core DNA methyltransferases and demethylases was largely unchanged, suggesting that increased SAM availability enhances enzymatic activity rather than gene expression. In addition, [~]25% of protein-coding genes were differentially expressed in mto1, though most changes were not directly linked to promoter- or gene-body methylation. Instead, the strong bias toward hypermethylation of TEs and repression of TEGs suggests that elevated Met/SAM primarily affects gene expression indirectly. Together, these findings demonstrate that an excess of Met/SAM reinforces heterochromatic DNA methylation and transposon silencing, providing new insights into the connection between amino acid metabolism and epigenetic regulation in plants.

plant biology↗

bioRxiv2023

Conversion of methionine biosynthesis in E. coli from trans- to direct-sulfurylation enhances extracellular methionine levels

Methionine is an essential amino acid in mammals and a critical metabolite in all organisms. As such, various applications, including food, feed, and pharmaceuticals, necessitate the addition of L-methionine. Although amino acids and other metabolites are commonly produced through bacterial fermentation, high-yield biosynthesis of L-methionine remains a significant challenge due to the strict cellular regulation of the biosynthesis pathway. As a result, methionine is produced primarily synthetically, resulting in a racemic mixture of D,L-methionine. This study aimed to enhance methionine bio-production yields in E. coli by replacing its highly regulated trans-sulfurylation pathway with the more common direct-sulfurylation pathway used by other bacteria. To this end, we generated an auxotroph E. coli strain (MG1655) by simultaneously deleting metA and metB genes and complementing them with metX and metY from different bacteria. Complementation of the genetically modified E. coli with metX/metY from Cyclobacterium marinum or Deinococcus geothermalis, together with the deletion of the global repressor metJ and overexpression of the transporter YjeH, resulted in a substantial increase of up to 126 and 160-fold methionine relative to the wild-type strain, respectively, and accumulation of up to 700 mg/L using minimal MOPS medium and 2 ml culture. Our findings provide a method to study methionine biosynthesis and a chassis for enhancing L-methionine production by fermentation. HighlightsO_LIReplacement of E. coli metA and metB with metX and metY recovered its growth C_LIO_LIThe engineered E. coli has a 160-fold increase in extracellular methionine levels C_LIO_LISelection of different metX and metY leads to varying growth rates and enhanced methionine levels C_LI

biochemistry↗

bioRxiv2022

Self-Assembly of Tunable Intrinsically DisorderedPeptide Amphiphiles

Intrinsically disordered peptide amphiphiles (IDPAs) present a novel class of synthetic conjugates that consist of short hydrophilic polypeptides anchored to hydrocarbon chains. These hybrid polymer-lipid block constructs spontaneously self-assemble into dispersed nanoscopic aggregates or ordered mesophases in aqueous solution due to hydrophobic interactions. Yet, the possible sequence variations and their influence on the self-assembly structures is vast and have hardly been explored. Here, we measure the nanoscopic self-assembled structures of four IDPA systems that differ by their amino acid sequence. We show that permutations in the charge pattern along the sequence remarkably alter the headgroup conformation and consequently alters the pH-triggered phase transitions between spherical, cylindrical micelles and hexagonal condensed phases. We demonstrate that even a single amino acid mutation is sufficient to tune structural transitions in the condensed IDPA mesophases, while peptide conformations remain unfolded and disordered. Furthermore, alteration of the peptide sequence can render IDPAs to become susceptible to enzymatic cleavage and induces enzymatically activated phase transitions. These results hold great potential for embedding multiple functionalities into lipid nanoparticle delivery systems by incorporating IDPAs with desired properties.

biophysics↗

bioRxiv2020

Real-time Ratiometric Imaging of Micelles Assembly State in a Microfluidic Cancer-on-a-chip

The performance of supramolecular nanocarriers as drug delivery systems depends on their stability in the complex and dynamic biological media. After administration, nanocarriers are challenged by confronting different barriers such as shear stress and proteins present in blood, endothelial wall, extracellular matrix and eventually cancer cell membranes. While early disassembly will result in a premature drug release, extreme stability of the nanocarriers can lead to poor drug release and low efficiency. Therefore, comprehensive understanding of the stability and assembly state of supramolecular carriers in each stage of delivery is a key factor for the rational design of these systems. One of the key challenges is that current 2D in vitro models do not provide exhaustive information, as they do not fully recapitulate the 3D tumor microenvironment. This deficiency of the 2D models complexity is the main reason for the differences observed in vivo when testing the performance of supramolecular nanocarriers. Herein, we present a real-time monitoring study of self-assembled micelles stability and extravasation, combining spectral confocal microscopy and a microfluidic tumor-on-a-chip. The combination of advanced imaging and a reliable organ-on-a-chip model allow us to track micelle disassembly by following the spectral properties of the amphiphiles in space and time during the crucial steps of drug delivery. The spectrally active micelles were introduced under flow and their position and conformation followed during the crossing of barriers by spectral imaging, revealing the interplay between carrier structure, micellar stability and extravasation. Integrating the ability of the micelles to change their fluorescent properties when disassembled, spectral confocal imaging and 3D microfluidic tumor blood vessel-on-a-chip, resulted in the establishment of a robust testing platform, suitable for real-time imaging and evaluation of supramolecular drug delivery carriers stability.

bioengineering↗