Abstract
Analysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance during anaerobiosis in different plant species. This may be due to the fact that a combination of primary effects, changes due to the presence or absence of oxygen, and secondary effects, responses to primary changes or tissue and developmental responses, are measured together and not differentiated from each other. In order to dissect out these responses, the effect of the presence or absence of oxygen was investigated using three different experimental designs using rice (Oryza sativa) as a model system. A total of 110 metabolites and 9,596 transcripts were found to change significantly in response to oxygen availability in at least one experiment. However, only one-quarter of these showed complementary responses to oxygen in all three experiments, allowing the core response to oxygen availability to be defined. A total of 10 metabolites and 1,136 genes could be defined as aerobic responders (up-regulated in the presence of oxygen and down-regulated in its absence), and 13 metabolites and 730 genes could be defined as anaerobic responders (up-regulated in the absence of oxygen and down-regulated in its presence). Defining core sets of transcripts that were sensitive to oxygen provided insights into alterations in metabolism, specifically carbohydrate and lipid metabolism and the putative regulatory mechanisms that allow rice to grow under anaerobic conditions. Transcript abundance of a specific set of transcription factors was sensitive to oxygen availability during all of the different experiments conducted, putatively identifying primary regulators of gene expression under anaerobic conditions. Combined with the possibility of selective transcript degradation, these transcriptional processes are involved in the core response of rice to anaerobiosis.
Highlights
Analysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance during anaerobiosis in different plant species
More global analysis of these studies reveals that the number of genes that displayed significant changes in abundance varied greatly between species; in Arabidopsis, only 1,266 transcripts were altered in abundance in response to anoxia (Klok et al, 2002; Liu et al, 2005), 3,134 probe sets were observed to change sig
An analysis of changes in transcript abundance during germination between aerobic and anaerobic conditions revealed that there was little difference up to 3 h after imbibition (HAI); as a result, transcriptomic data for aerobic and anaerobic germinated seeds at this time point were not differentiated by principal component analysis (PCA) analysis (Fig. 1B; Supplemental Fig. S1)
Summary
Analysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance during anaerobiosis in different plant species. Transcript abundance of a specific set of transcription factors was sensitive to oxygen availability during all of the different experiments conducted, putatively identifying primary regulators of gene expression under anaerobic conditions. More global analysis of these studies reveals that the number of genes that displayed significant changes in abundance varied greatly between species; in Arabidopsis, only 1,266 transcripts were altered in abundance in response to anoxia (Klok et al, 2002; Liu et al, 2005), 3,134 probe sets were observed to change sig-. The expression of a NAC transcription factor from Arabidopsis has been shown to increase tolerance to low-oxygen treatments (Christianson et al, 2009)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.