Biology subjects

Marik, D.

Publications and source records attributed to Marik, D..

3 recordsLinked to original sources

bioRxiv2025

Genome-wide association study, network analysis, and reverse genetics pinpoint novel genes associated with seedling root growth variation of Arabidopsis thaliana under drought

Development of drought-resilient crops requires a precise understanding of molecular signaling in the root, the primary organ encountering drought. This study unraveled novel genetic loci contributing to drought tolerance by exploiting the natural variation in seedling root growth of Arabidopsis thaliana under PEG-induced drought stress. Through a genome-wide association study (GWAS) of 207 worldwide Arabidopsis thaliana ecotypes from regions with varied rainfall, 68 protein-coding genes were identified, associated with the top 50 single-nucleotide polymorphisms (P < 10- 3), explaining 63% of the observed variation in root length. Subsequent network and functional enrichment analyses of the GWAS-delineated genes demarcated key biological processes crucial for maintaining root growth under drought, including DNA repair, tRNA editing, protein folding and quality control, cell cycle regulation, stress granule assembly, and the pyridoxal 5'-phosphate (PLP) salvage pathway regulating oxidative stress in roots. Expression level polymorphisms, promoter cis-element variations, and amino acid substitutions affecting predicted protein dynamics, with phenotype and climate associations, were identified. Finally, reverse genetic evaluation using T-DNA insertion knockout/knockdown mutants confirmed a direct association of the identified candidate genes, AT1G06690 (PLP pathway), AT4G26990 and RBP45C (stress granule assembly), ACD55.5 (protein folding), PCMP-A4 (RNA modification), SKS6 and ANAC094 (cell wall remodeling), and INCENP (cell cycle regulation), with seedling drought tolerance. Furthermore, the knockdown of AT1G06690 led to higher accumulation of hydrogen peroxide in root tissues, inhibiting growth. Future translation of the current findings into crops will provide new tools for the improvement of drought tolerance by modulating root traits through biotechnology and breeding.

genetics↗

bioRxiv2025

A desert endophyte, Priestia megaterium SI1-IITJ, improves fluoride stress tolerance by reducing fluoride content of plant tissues and perturbing salt tolerance and defense genes of Arabidopsis thaliana

We isolated a fluoride (F-)-resistant bacterium, Priestia megaterium SI1-IITJ, from thse internal root tissues of several Thar Desert plants, Aerva javanica, Cyperus conglomeratus, Senna tora, and Tephrosia purpurea, tolerating up to 100 mM NaF. The root endophytic behavior of the isolate was confirmed by scanning electron microscopy. SI1-IITJ possesses plant growth-promoting properties, including auxin production (19.8 g mL-1), phosphate solubilization (index 3.64), ACC deaminase (0.54 mmol -ketobutyrate mL-1) and nitrate reductase (0.65 mol mL-1 nitrite) activities, revealed by biochemical tests and whole genome sequencing. SI1-IITJ extrudes F- from the cell, possibly through an F- efflux transporter, CrcB, identified in its genome. Significant growth improvements were observed in Arabidopsis thaliana under F- stress in hydroponics and soil culture upon coculture with SI1-IITJ, which improved the chlorophyll content by 1.6%, total nitrogen by 30.4%, and reduced reactive oxygen species by 48.9% and F- content by 63.9% in plant tissues. A differential gene expression analysis of A. thaliana by transcriptome sequencing indicated an unperturbed F- exporter, AtFEX1, but up-regulation of 55 genes regulating root meristem growth, cell wall modification, chlorophyll biosynthesis, Fe homeostasis, and high salt- and abiotic stress-responsive genes. On the other hand, 103 genes were down-regulated, suppressing systemic acquired resistance, plant defense, and H2O2 production. In conclusion, our results provide genomic insights into the mechanisms of F- toxicity alleviation and plant growth enhancement by a desert PGPR, highlighting Priestia megaterium SI1-IITJ as a potential biofertilizer for mitigating F- stress in plants.

plant biology↗

bioRxiv2024

AP2/ERF transcription factors enriched in the drought-response transcriptome of the Thar desert tree Prosopis cineraria show higher copy number and greater DNA-binding affinity than orthologs in drought-sensitive species

We sequenced the drought-response transcriptome of the keystone tree species Prosopis cineraria from the Indian Thar desert to understand the key factors in its drought tolerance mechanism. We identified a network of genes activated in P. cineraria involved in osmotic stress response, phytohormone, calcium, and phosphorelay signal transduction. Of these, up-regulation of 54 APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factor genes, validated by real-time PCR, suggests their key role in the drought tolerance of P. cineraria. We conducted a genome-wide study of the AP2/ERF superfamily in P. cineraria, classifying its 232 proteins into 15 clades and analyzing their protein structures, gene structure, and promoter organization. The P. cineraria genome contains more copies of AP2/ERF genes than drought-sensitive plants. Further, we identified sequence polymorphisms in AP2/ERF genes between Arabian and Indian cultivars of P. cineraria. We modeled the DNA-protein complex structures of AP2/ERFs from drought-tolerant and sensitive species using AlphaFold to compare their DNA binding ability. Though the DNA binding domain (DBD) is relatively conserved across species, the unstructured region of these proteins possesses different charge distributions, which might contribute differently to their DNA search and binding. Using all-atom molecular dynamics simulations, we teased out a higher number of specific DBD-DNA hydrogen bonds in P. cineraria, leading to a stronger DNA-binding affinity compared to drought-sensitive Arabidopsis thaliana. These results directly support copy number expansion of AP2/ERF transcription factors and the evolution of their structures for more efficient DNA search and binding as drought adaptation mechanisms in P. cineraria.

plant biology↗