This clustering outcome suggests that the genes typically affected by abiotic and oxidative MLN4924 905579-51-3 stresses were affected to a different degree, or not at all, during treatment with the two mitochondrial inhibitors. Thus, MapMan and cluster analysis each indicated that the Arabidopsis leaf transcriptome did not strongly respond as though the leaves had been subjected to an abiotic or oxidative stress, even with increased ROS production during AA treatment. This result is consistent with observed differences between effects of AA and H2O2 on gene expression in leaves, and a growing body of evidence suggesting that the origin and type of ROS,, as well as the amount of ROS from a given subcellular origin are factors distinguished by plant cells, leading to distinct gene expression responses. Rather than an association with abiotic or oxidative stress, the cluster analysis showed that the genes affected by the mitochondrial inhibitors were most similarly affected under the biotic stress conditions of pathogen challenge and bacterial elicitor exposure. Also, MapMan analysis showed ����biotic stress���� to be one of the most statistically significant functional gene categories for both AA and MFA treatments. This category includes genes encoding diseaseresistance proteins with TIR, TIR-NBS, TIR-NBS-LRR, and CCNBS- LRR domain signatures and genes encoding proteases and avirulence-responsive proteins. Other affected functional categories for AA and MFA showed transcript changes previously observed with biotic stress, specifically pathogen attack. Photosynthesis rates decrease, accompanied by down-regulation of transcripts for associated photosynthesis genes, in a variety of plant-pathogen interactions. As noted above, AA and MFA treatments resulted in striking down-regulation of genes related to photosynthesis. Repression of auxin signaling, which the functional category analysis suggests occurred with AA and MFA treatment, appears to be an important WY 14643 PPAR inhibitor protective plant response to pathogens,. Increased expression of genes for ethylene synthesis is observed with pathogen challenge, and ethylene functional categories were significant and up-regulated overall with AA and MFA treatment. Lastly, for MFA-treated leaves, functional categories for salicylic acid, well-known for its role in plant defense were affected, with most genes up-regulated. Transcriptome changes suggesting increases in the amino acid pool of the leaves were also consistent with plant responses to pathogens, although the changes differed between the two inhibitor treatments.