Biology subjects

Tahmasebi, A.

Publications and source records attributed to Tahmasebi, A..

3 recordsLinked to original sources

bioRxiv2022

Nitrogen and phosphorus deficiencies alter primary and secondary metabolites of soybean roots

Nitrogen (N) and phosphorus (P) are two essential plant macronutrients that can limit plant growth by different mechanisms. We aimed to shed light on how soybean respond to low nitrogen (LN), low phosphorus (LP) and their combined deficiency (LNP). Generally, these conditions triggered changes in gene expression of the same processes, including cell wall organization, defense response, response to oxidative stress, and photosynthesis, however, response was different in each condition. A typical primary response to LN and LP was detected also in soybean, i.e., the enhanced uptake of N and P, respectively, by upregulation of genes for the corresponding transporters. The regulation of genes involved in cell wall organization showed that in LP roots tended to produce more casparian strip, in LN more secondary wall biosynthesis occurred, and in LNP reduction in expression of genes involved in secondary wall production accompanied by cell wall loosening was observed. Flavonoid biosynthesis also showed distinct pattern of regulation in different conditions: more anthocyanin production in LP, and more isoflavonoid production in LN and LNP, which we confirmed also on the metabolite level. Interestingly, in soybean the nutrient deficiencies reduced defense response by lowering expression of genes involved in defense response, suggesting a role of N and P nutrition in plant disease resistance. In conclusion, we provide detailed information on how LN, LP, and LNP affect different processes in soybean roots on the molecular and physiological levels.

plant biology↗

bioRxiv2021

Integrative system biology analysis of barley transcriptome - hormonal signaling against biotic stress

Biotic stresses are environmental factors that cause a variety of crop diseases and damages. In contrast, crops trigger specific transduction signaling pathways that the hormones are the central players. Integrative OMICS for systems genetic engineering approach contributes in the understanding of molecular mechanisms. In this research, the system biology approaches were applied to discover particular molecular interactions between biotic stresses and hormonal signaling in barley. The meta-analysis of the data identified a total of 1232 and 304 differentially expressed genes (DEGs) respectively so that were significantly involved in defense processes and hormone signaling. A total of 24 TFs belonged to 15 conserved families and 6 TFs belonged to 6 conserved families were identified for biotic and hormonal data respectively, whereas NF-YC, GNAT, and whirly families were the most abundant groups. The functional analysis of the upstream regions for over-represented cis-acting elements revealed that were involved activation of transcription factors in response to pathogens and hormones. Based on the co-expression analysis, 6 and 7 distinct co-expression modules related to biotic stresses and hormonal signaling were respectively uncovered. The gene network analysis also identified novel hub genes such as TIM10, DRT101, ADG1, and TRA2 which may be involved in regulating defense responses to biotic stresses. In addition, many new genes with unknown function were obtained. Since this study represents a first preliminary curated system biology analysis of barley transcriptomic responses to biotic stresses and hormone treatments, introduces important candidate genes that may be beneficial to crop biotechnologists to accelerate genetic engineering programs.

systems biology↗

bioRxiv2021

New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

BackgroundSPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes. ResultsWe analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs. ConclusionThis comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1 and AtPHO1;H1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.

evolutionary biology↗