Deciphering energy‐associated gene networks operating in the response of Arabidopsis plants to stress and nutritional cues

Abstract

SUMMARYPlants need to continuously adjust their transcriptome in response to various stresses that lead to inhibition of photosynthesis and the deprivation of cellular energy. This adjustment is triggered in part by a coordinated re-programming of the energy-associated transcriptome to slow down photosynthesis and activate other energy-promoting gene networks. Therefore, understanding the stress-related transcriptional networks of genes belonging to energy-associated pathways is of major importance for engineering stress tolerance. In a bioinformatics approach developed by our group, termed 'gene coordination', we previously divided genes encoding for enzymes and transcription factors in Arabidopsis thaliana into three clusters, displaying altered coordinated transcriptional behaviors in response to multiple biotic and abiotic stresses (Plant Cell, 23, 2011, 1264. Enrichment analysis indicated further that genes controlling energy-associated metabolism operate as a compound network in response to stress. In the present paper, we describe in detail the network association of genes belonging to six central energy-associated pathways in each of these three clusters described in our previous paper. Our results expose extensive stress-associated intra-and inter-pathway interactions between genes from these pathways, indicating that genes encoding proteins involved in energy-associated metabolism are expressed in a highly coordinated manner. We also provide examples showing that this approach can be further utilized to elucidate candidate genes for stress tolerance and functions of isozymes.

Perturbed porphyrin biosynthesis contributes to differential herbicidal symptoms in photodynamically stressed rice (Oryza sativa) treated with 5-aminolevulinic acid and oxyfluorfen

“…4C). The strong expression of FC, which plays an essential role in heme synthesis, ensures the supply of cofactors for hemoproteins that may be required in response to ALA-and OF-induced photodynamic stress as well as the stress conditions caused by norflurazon (NF), paraquat, wounding, ozone, and drought [24,32,[51][52][53][54]. Transcript levels of HO1 encoding HO, which catalyzes the formation of biliverdin-IXα from heme [55], decreased in ALA-and OF-treated plants, whereas transcript levels of HO2 greatly increased after 2 days of both treatments (Fig.…”

Increased expression of Fe-chelatase leads to increased metabolic flux into heme and confers protection against photodynamically induced oxidative stress

“…In addition, heme is required for the upregulation of ROS scavengers (catalase, peroxidases) during plant stress response . The strong expression of FeCh1, which plays an essential role in heme synthesis, ensures the supply of cofactors for hemoproteins that may be required in response to the stress conditions including those caused by norflurazon (NF), paraquat, wounding, ozone, and drought Ujwal et al 2002;Nagai et al 2007;Moulin et al 2008;Phung et al 2011;Avin-Wittenberg et al 2012). Stressinduced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression, and the specific accumulation of the chlorophyll intermediates MgProto IX and its monomethylester (ME) are proposed to coincide with these changes, suggesting that they may be important for plastid-to-nucleus signaling (Strand et al 2003;Alawady and Grimm 2005;Pontier et al 2007;Barajas-López et al 2013).…”

Plant Abiotic Stress:‘Omics’ Approach

“…Stress response in Arabidopsis thaliana was associated with a co-ordinated re-programming of the energy-associated transcriptome. The result from this study shows a sharp decrease in the rate of photosynthesis while other energy promoting networks were activated [9]. Similar to transcriptional network protein and metabolites network can be constructed using nodes and edges.…”