Understanding metabolite transport and metabolism in C-4 plants through RNA-seq

Schlueter U, Denton AK, Bräutigam A. Understanding metabolite transport and metabolism in C-4 plants through RNA-seq. Current Opinion in Plant Biology. 2016;31:83-90.RNA-seq, the measurement of steady-state RNA levels by next generation sequencing, has enabled quantitative transcriptome analyses of complex traits in many species without requiring the parallel sequencing of their genomes. The complex trait of C-4 photosynthesis, which increases photosynthetic efficiency via a biochemical pump that concentrates CO2 around RubisCO, has evolved convergently multiple times. Due to these interesting properties, C-4 photosynthesis has been analyzed in a series of comparative RNA-seq projects. These projects compared both species with and without the C-4 trait and different tissues or organs within a C-4 plant. The RNA-seq studies were evaluated by comparing to earlier single gene studies. The studies confirmed the marked changes expected for C-4 signature genes, but also revealed numerous new players in C-4 metabolism showing that the C-4 cycle is more complex than previously thought, and suggesting modes of integration into the underlying C-3 metabolism

Comparative Transcriptome Atlases Reveal Altered Gene Expression Modules between Two Cleomaceae C-3 and C-4 Plant Species

Külahoglu C, Denton AK, Sommer M, et al. Comparative Transcriptome Atlases Reveal Altered Gene Expression Modules between Two Cleomaceae C-3 and C-4 Plant Species. Plant Cell. 2014;26(8):3243-3260.C-4 photosynthesis outperforms the ancestral C-3 state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C-3 backgrounds. However, the genetic architecture of C-4 photosynthesis remains largely unknown. To define the divergence in gene expression modules between C-3 and C-4 photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C-4) and Tarenaya hassleriana (C-3), by RNA sequencing. Overall, the gene expression profiles appear remarkably similar between the C-3 and C-4 species. We found that known C-4 genes were recruited to photosynthesis from different expression domains in C-3, including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. Furthermore, we identified a structure-related module recruited from the C-3 root. Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C-4 bundle sheath cells. A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C-4 leaf

Phosphate starvation causes different stress responses in the lipid metabolism of tomato leaves and roots

Plants have evolved various acclimation responses to cope with phosphate depletion, including several changes in lipid metabolism. Thereby membrane phospholipids are dephosphorylated and can be used as an internal phosphate source, while galactolipids are incorporated into the membrane to maintain membrane functionality. Still little is known about the lipidomic and transcriptomic response of plants other than Arabidopsis thaliana upon phosphate starvation. Therefore, we employed lipidomics and transcriptomics to characterize the phosphate starvation response of lipid metabolism in tomato leaves and roots.Overall, phospholipid levels decreased and galactolipids increased during the acclimation response. In addition, an early increase of triacylglycerol was observed. Interestingly, there were major differences in the acclimation response of tomato leaves and roots: leaves mainly accumulated polyunsaturated triacylglycerol, while roots showed a massive increase in galactolipid content. In line with these results, we observed transcriptional induction of phospholipid degradation and galactolipid synthesis pathways in both analyzed tissues. In contrast, other aspects of the transcriptional response, in particular, the induction of phospholipid degradation, ER-localized fatty acid desaturation and triacylglycerol assembly differed between tomato leaves and roots.These results suggest a different modulation of degraded phospholipids toward triacylglycerols and galactolipids in phosphate-starved tomato leaves and roots. Possibly the availability and composition of acyl-CoA pools and ER-derived precursors trigger the synthesis of triacylglycerols or galactolipids. As the mechanism of triacylglycerol accumulation is poorly characterized outside of seed oil formation, these findings enhance our understanding of the phosphate starvation response and of how storage lipids accumulate under stress in vegetative tissue. Previous article in issu

Fig S1-7 All Supplemental Figures

Figure S1. Setup of developmental slices, enzyme/metabolite data deconvolution method, and validation of separation method. Figure S2. Metabolite levels in BS and M of the developmental slices (full data in dataset S1). Figure S3. Contextual data of developmental section pairing, and library complexity for inter-study comparison. Figure S4. Transcript coverage of genes (or their orthologs) that were significantly enriched in the BS in Chang_2012, but in M in here Denton_2016. Figure S5. Transcript coverage of examples genes from conflict set 1 (definition and gene list in dataset S5). Figure S6. Expression of marker genes/categories used to evaluate the co-purification of additional tissues. Figure S7. AlaAT and 40S ribosome distributions

Seaton Computing Center Before Renovation_03

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Supplemental Table1 Bioinformatis Parameters

Non-default parameters used for bioinformatics tools in this study

Supplemental_Table2 Numbers of Signifiant Differences

Quantification of the number of significant differences in expression found between BS and M in each study and developmental category. Significance was calculated with edgeR for all studies, and additionally with contamDE for Denton_2016