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E-MTAB-4021

ABSTRACT: RNAseq profiling of C4 grass Sorghum bicolor bundle sheath and mesophyll cells

PROVIDER: E-MTAB-4021 | ExpressionAtlas | 2020-07-17

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-4021-analysis-methods.tsv	Tabular
	E-MTAB-4021-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-4021-coexpressions.tsv.gz	Tabular
	E-MTAB-4021-configuration.xml	Xml
	E-MTAB-4021-factors.xml	Xml

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RNAseq profiling of C4 grass Sorghum bicolor bundle sheath and mesophyll cells

Project description:Triplicate replicates of bundle sheath and mesophyll cell RNAseq from the C4 grass Sorghum bicolor.

2016-06-06 | E-MTAB-4021 | biostudies-arrayexpress

DNase-SEQ analysis of whole leaf and bundle sheath tissues in Zea mays, Sorghum bicolor, Setaria italica and Brachypodium distachyon.

Project description:Photosynthesis supports life on Earth but the regulatory architecture associated with photosynthesis gene expression is poorly understood. Most crops use either C3 or C4 photosynthesis with the latter allowing significantly higher efficiencies as well as improved water and nitrogen use. Here we use DNAse-SEQ to define >1 million transcription factor binding sites in leaves of grasses that either operate C3 or C4 photosynthesis and that are consistent with significant differences in the modes of gene regulation between the kingdoms of life. Leaf samples were collected from seedlings to allow for comparison of regulatory interactions between species from the same (Zea mays and Sorghum bicolor) and different (Setaria italica) C4 lineages, as well as a C3 grass (Brachypodium distachyon) in order to investigate evolution of C4 photosynthetic gene expression. Additionally bundle sheath tissues were mechanically isolated from C4 species and analysed by DNAse-SEQ to identify DNA regulatory elements controlling cell-specific gene expression patterns.

2017-07-24 | GSE97369 | GEO

Single nuclei sequencing reveals C4 photosynthesis is based on rewiring of ancestral cell identity networks

Project description:In multicellular systems changes to the patterning of gene expression drive modifications in cell function and trait evolution. One striking example is found in more than sixty plant lineages where compartmentation of photosynthesis between cell types allowed evolution of the efficient C4 pathway from the ancestral C3 state. The molecular events enabling this transition are unclear. We used single nuclei sequencing to generate a cell level expression atlas for C3 rice and C4 sorghum during photomorphogenesis. In both species a conserved cistrome was identified for each cell type and initiation of photosynthesis gene expression was conditioned by cell identity. Photosynthesis genes switching expression from mesophyll in rice to bundle sheath in sorghum acquire hallmarks of bundle sheath identity. The sorghum bundle sheath has also acquired gene networks associated with C3 guard cells. We conclude C4 photosynthesis is based on rewiring in cis that exapts cell identity networks of C3 plants.

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E-ENAD-26

Project description:Transcriptome profiling reveals regulatory and functional differentiation between Zea mays mesophyll and bundle sheath cells

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Genome-wide analysis of abscisic acid biosynthesis, catabolism, and signaling in Sorghum bicolor under saline-alkali stress

Project description:Sorghum (Sorghum bicolor) is the fifth most important cereal crop in the world. It is an annual C4 crop having a high biomass, used widely, and has a strong resistance to stress. Obviously, there are many benefits of planting sorghum on marginal soils such as saline-alkali land.

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Bundle sheath and mesophyll cell RNAseq profiling

Project description:Bundle sheath and mesophyll cell RNAseq profiling

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A common regulatory switch controls a suite of C4 traits in multiple cell types

Project description:The C4 photosynthetic pathway provided a major advantage to plants growing in hot, dry environments, including the ancestors of our most productive crops. Two traits were essential for the evolution of this pathway: increased vein density and the functionalization of bundle sheath cells for photosynthesis. Although GRAS transcriptional regulators, including SHORT ROOT (SHR), have been implicated in mediating leaf patterning in both C3 and C4 species1-4, little is known about what controls the specialized features of the cells that mediate C4 metabolism and physiology. We show in the model monocot, Setaria viridis, that SHR regulates components of multiple cell identities, including chloroplast biogenesis and photosynthetic gene expression in bundle sheath cells, a central feature of C4 plants. Furthermore, we found that it also contributes to the two-cell compartmentalization of the characteristic four-carbon shuttle pathway. Disruption of SHR function clearly reduced photosynthetic capacity and seed yield in mutant plants under heat stress. Together, these results show how cell identities are remodeled by SHR to host the suite of traits characteristic of C4 regulation, which are a main engineering target in non-C4 crops to improve climate resilience.

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C4 Photosynthesis: Gene expression in mesophyll and bundle sheath cells of bundle sheath defective2 mutant

Project description:Zea mays is a C4 plant that utilizes two distinct cell types, mesophyll (M) and bundle sheath (BS), to cooperatively fix carbon. Regulation of M and BS cell differentiation is poorly understood. Here, we explore the transcriptional networks of M and BS cells by microarray analysis. The maize mutant bundle sheath defective2 lacks the accumulation of Rubisco small and large subunits (Roth et al 1996; Brutnell et al 1999) and cannot perform the Calvin Cycle (Smith et al 1998). Therefore, this mutant provides an opportunity to study M and BS cell differentiation in a perturbed BS background, potentially revealing regulons important to cell identity. M and BS cells were independently isolated from mutant and wild-type siblings. Transcriptional profiling was then performed in a cell specific manner between mutant and wild-type.

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Project description:This study used with RNA-Seq to examine the tissue specific expression data within sorghum plants for improving the Sorghum bicolor gene annotation. We examined the RNA from tissues (spikelet, seed and stem) in Sorghum bicolor (BTx623).Total RNAs form each tissues were extracted using SDS/phenol method followed by LiCl purification

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Profiling trancriptome changes that affect vein specification in maize (Zea mays) tml (TOO MANY LATERALS) mutants

Project description:The biochemistry of C4 photosynthesis relies on a specific suite of leaf functional properties, often referred to as Kranz anatomy, where there is increased vein density and the proportion of bundle sheath cells surrounding the veins compared to C3 photosynthesizing species. From a suite of putative Kranz anatomy regulators, TML was identified. Loss of function tml mutations lead to the development of large lateral veins in positions normally occupied by smaller intermediate veins in both C3 and C4 species tested. In order to elucidate the role of TML in vein patterning, we set out to profile transcriptional changes that happen in the leaf primordia upon tml knock-out in the C4 species Zea mays.

2024-02-07 | GSE255222 | GEO

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