scholarly journals A bipartite transcription factor module controlling expression in the bundle sheath of Arabidopsis thaliana

2018 ◽  
Author(s):  
Patrick J. Dickinson ◽  
Jana Kneřová ◽  
Marek Szecówka ◽  
Sean S. Stevenson ◽  
Steven J. Burgess ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Photosynthetic Efficiency ◽  
Cell Types ◽  
Bundle Sheath ◽  
Spatial Patterning ◽  
Factor Module ◽  
Bundle Sheath Cells ◽  
Necessary And Sufficient

AbstractC4 photosynthesis evolved repeatedly from the ancestral C3 state, improving photosynthetic efficiency by ∼50%. In most C4 lineages photosynthesis is compartmented between mesophyll and bundle sheath cells but how gene expression is restricted to these cell types is poorly understood. Using the C3 model Arabidopsis thaliana we identified cis-elements and transcription factors driving expression in bundle sheath strands. Upstream of the bundle sheath preferentially expressed MYB76 gene we identified a region necessary and sufficient for expression containing two cis-elements associated with the MYC and MYB families of transcription factors. MYB76 expression is reduced in mutant alleles for each. Moreover, down-regulated genes shared by both mutants are preferentially expressed in the bundle sheath. Our findings are broadly relevant for understanding the spatial patterning of gene expression, provide specific insights into mechanisms associated with evolution of C4 photosynthesis and identify a short tuneable sequence for manipulating gene expression in the bundle sheath.

scholarly journals The bundle sheath of rice is conditioned to play an active role in water transport as well as sulfur assimilation and jasmonic acid synthesis

2021 ◽  
Author(s):  
Lei Hua ◽  
Sean R. Stevenson ◽  
Ivan Reyna-Llorens ◽  
Haiyan Xiong ◽  
Stanislav Kopriva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Comparative Analysis ◽  
Jasmonic Acid ◽  
Water Transport ◽  
Acid Synthesis ◽  
Bundle Sheath ◽  
Last Common Ancestor ◽  
Bundle Sheath Cells ◽  
Sheath Cells

Abstract Leaves comprise multiple cell types but our knowledge of the patterns of gene expression that underpin their functional specialization is fragmentary. Our understanding and ability to undertake rational redesign of these cells is therefore limited. We aimed to identify genes associated with the incompletely understood bundle sheath of C3 plants, which represents a key target associated with engineering traits such as C4 photosynthesis into rice. To better understand veins, bundle sheath and mesophyll cells of rice we used laser capture microdissection followed by deep sequencing. Gene expression of the mesophyll is conditioned to allow coenzyme metabolism and redox homeostasis as well as photosynthesis. In contrast, the bundle sheath is specialized in water transport, sulphur assimilation and jasmonic acid biosynthesis. Despite the small chloroplast compartment of bundle sheath cells, substantial photosynthesis gene expression was detected. These patterns of gene expression were not associated with presence/absence of particular transcription factors in each cell type, but rather gradients in expression across the leaf. Comparative analysis with C3Arabidopsis identified a small gene-set preferentially expressed in bundle sheath cells of both species. This included genes encoding transcription factors from fourteen orthogroups, and proteins allowing water transport, sulphate assimilation and jasmonic acid synthesis. The most parsimonious explanation for our findings is that bundle sheath cells from the last common ancestor of rice and Arabidopsis was specialized in this manner, and since the species diverged these patterns of gene expression have been maintained. Significance statement The role of bundle sheath cells in C4 species have been studied intensively but this is not the case in leaves that use the ancestral C3 pathway. Here, we show that gene expression in the bundle sheath of rice is specialized to allow sulphate and nitrate reduction, water transport and jasmonate synthesis, and comparative analysis with Arabidopsis indicates ancient roles for bundle sheath cells in water transport, sulphur and jasmonate synthesis.

Comparison of photosynthetic carbon reduction (Kranz) cells having different ontogenetic origins in the C4 NADP – malic enzyme grass Arundinella hirta

1990 ◽  
Vol 68 (6) ◽  
pp. 1222-1232 ◽  
Author(s):  
Nancy G. Dengler ◽  
Ronald E. Dengler ◽  
Douglas J. Grenville
Keyword(s):  
Cell Walls ◽  
Vascular Tissue ◽  
Cell Types ◽  
Bundle Sheath ◽  
Carbon Reduction ◽  
Bundle Sheath Cells ◽  
Photosynthetic Carbon ◽  
Arundinella Hirta ◽  
Photosynthetic Carbon Reduction ◽  
Sheath Cells

The C4 grass Arundinella hirta is characterized by unusual leaf blade anatomy: photosynthetic carbon reduction takes place both within the chlorenchymatous bundle sheath cells of the longitudinal veins and within longitudinal strands of "distinctive cells" that form part of the leaf mesophyll and are often completely isolated from vascular tissue. Although they are equivalent physiologically, these two cell types have different ontogenetic origins: bundle sheath cells are delimited from procambium early in leaf development, whereas distinctive cells differentiate from ground meristem at a later developmental stage. Although the two cell types share numerous cytological features (large chloroplasts with reduced grana, thick cell walls with a suberin lamella), we also found significant differences in cell lengths, length to width ratios, cell cross-sectional areas, organelle numbers per cell cross section, phenol content of the cell walls, and numbers of pit fields in the longitudinal cell walls. The size and shape of bundle sheath cells are likely a direct consequence of procambial origin. The thicker walls of bundle sheath cells (in major veins) and their greater lignification may reflect the inductive effect of cell differentiation in the proximity of sclerenchyma and vascular tissues. Differences between major and minor vein bundle sheath cells may reflect differences in the timing of initiation of procambial strands. Our analysis of cell wall characteristics has also shown the presence of numerous primary pit fields in the transverse walls between adjacent distinctive cells in a file; plasmodesmata in these pit fields form a pathway for longitudinal symplastic transport not previously known to exist.

scholarly journals Generation of guard cell RNA-seq transcriptomes during progressive drought and recovery using an adapted INTACT protocol for Arabidopsis thaliana shoot tissue

2021 ◽  
Author(s):  
Anna van Weringh ◽  
Asher Pasha ◽  
Eddi Esteban ◽  
Paul J. Gamueda ◽  
Nicholas J. Provart
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Drought Stress ◽  
Guard Cell ◽  
Crop Production ◽  
Leaf Tissue ◽  
Cell Types ◽  
Severe Drought ◽  
Data Sets ◽  
Rna Seq

Drought is an important environmental stress that limits crop production. Guard cells (GC) act to control the rate of water loss. To better understand how GCs change their gene expression during a progressive drought we generated guard cell-specific RNA-seq transcriptomes during mild, moderate, and severe drought stress. We additionally sampled re-watered plants that had experienced severe drought stress. These transcriptomes were generated using the INTACT system to capture the RNA from GC nuclei. We optimized the INTACT protocol for Arabidopsis thaliana leaf tissue, incorporating fixation to preserve RNA during nuclear isolation. To be able to identify gene expression changes unique to GCs, we additionally generated transcriptomes from all cell types, using a 35S viral promoter to capture the nuclei of all cell types in leaves. These data sets highlight shared and unique gene expression changes between GCs and the bulk leaf tissue. The timing of gene expression changes is different between GCs and other cell types: we found that only GCs had detectable gene expression changes at the earliest drought time point. The drought responsive GC and leaf RNA-seq transcriptomes are available in the Arabidopsis ePlant at the Bio-Analytic Resource for Plant Biology website.

scholarly journals Single-nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell-type-specific gene regulatory variation

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yujuan Gui ◽  
Kamil Grzyb ◽  
Mélanie H. Thomas ◽  
Jochen Ohnmacht ◽  
Pierre Garcia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Cell Types ◽  
Mouse Strains ◽  
Cell Type ◽  
Data Set ◽  
Cell Identity ◽  
Regulatory Variation ◽  
Ventral Midbrain ◽  
Cell Type Specific

Abstract Background Cell types in ventral midbrain are involved in diseases with variable genetic susceptibility, such as Parkinson’s disease and schizophrenia. Many genetic variants affect regulatory regions and alter gene expression in a cell-type-specific manner depending on the chromatin structure and accessibility. Results We report 20,658 single-nuclei chromatin accessibility profiles of ventral midbrain from two genetically and phenotypically distinct mouse strains. We distinguish ten cell types based on chromatin profiles and analysis of accessible regions controlling cell identity genes highlights cell-type-specific key transcription factors. Regulatory variation segregating the mouse strains manifests more on transcriptome than chromatin level. However, cell-type-level data reveals changes not captured at tissue level. To discover the scope and cell-type specificity of cis-acting variation in midbrain gene expression, we identify putative regulatory variants and show them to be enriched at differentially expressed loci. Finally, we find TCF7L2 to mediate trans-acting variation selectively in midbrain neurons. Conclusions Our data set provides an extensive resource to study gene regulation in mesencephalon and provides insights into control of cell identity in the midbrain and identifies cell-type-specific regulatory variation possibly underlying phenotypic and behavioural differences between mouse strains.

scholarly journals Ribosomes act as cryosensors in plants

2020 ◽  
Author(s):  
Philip Anthony Wigge ◽  
David Guillaume-Schoepfer ◽  
Katja E Jaeger ◽  
Feng Geng ◽  
Fabrizio G Doccula ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Cold Stress ◽  
Protein Translation ◽  
Free Calcium ◽  
Cold Temperatures ◽  
Stunted Growth ◽  
Subzero Temperatures ◽  
Delayed Flowering

Cold temperatures are a threat to temperate plants, and Arabidopsis thaliana has acquired an adaptive gene expression network controlled by CBF transcription factors. The CBFs are sufficient to enable plants to survive otherwise lethal subzero temperatures. Constitutive CBF expression causes delayed flowering and stunted growth, and plants have evolved the ability to restrict CBF expression to occur only in the cold. This allows plants to anticipate likely freezing events and selectively deploy cold tolerance. The mechanism by which cold stress is sensed is however unknown. Here we show that protein translation rates in plants are proportional to temperature, and reduced translation rates trigger a rise in intracellular free calcium that activates the CAMTA transcription factors, and these directly activate cold-induced gene expression.

scholarly journals Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1321 ◽  
Author(s):  
Mahmoud Ahmed ◽  
Trang Huyen Lai ◽  
Jin Seok Hwang ◽  
Sahib Zada ◽  
Trang Minh Pham ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Transcription Factors ◽  
High Throughput Sequencing ◽  
Cell Model ◽  
Cell Types ◽  
Autophagy Gene ◽  
Occupancy Patterns ◽  
Differentiation Stage

Autophagy is the cell self-eating mechanism to maintain cell homeostasis by removing damaged intracellular proteins or organelles. It has also been implicated in the development and differentiation of various cell types including the adipocyte. Several links between adipogenic transcription factors and key autophagy genes has been suggested. In this study, we tried to model the gene expression and their transcriptional regulation during the adipocyte differentiation using high-throughput sequencing datasets of the 3T3-L1 cell model. We applied the gene expression and co-expression analysis to all and the subset of autophagy genes to study the binding, and occupancy patterns of adipogenic factors, co-factors and histone modifications on key autophagy genes. We also analyzed the gene expression of key autophagy genes under different transcription factor knockdown adipocyte cells. We found that a significant percent of the variance in the autophagy gene expression is explained by the differentiation stage of the cell. Adipogenic master regulators, such as CEBPB and PPARG target key autophagy genes directly. In addition, the same factor may also control autophagy gene expression indirectly through autophagy transcription factors such as FOXO1, TFEB or XBP1. Finally, the binding of adipogenic factors is associated with certain patterns of co-factors binding that might modulate the functions. Some of the findings were further confirmed under the knockdown of the adipogenic factors in the differentiating adipocytes. In conclusion, autophagy genes are regulated as part of the transcriptional programs through adipogenic factors either directly or indirectly through autophagy transcription factors during adipogenesis.

Cement gland-specific activation of the Xag1 promoter is regulated by co-operation of putative Ets and ATF/CREB transcription factors

Development ◽  
2002 ◽  
Vol 129 (19) ◽  
pp. 4387-4397
Author(s):  
Fiona C. Wardle ◽  
Daniel H. Wainstock ◽  
Hazel L. Sive
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Site ◽  
Reporter Gene ◽  
Binding Sites ◽  
Cement Gland ◽  
Specific Expression ◽  
Necessary And Sufficient ◽  
Do So

The cement gland marks the extreme anterior ectoderm of the Xenopus embryo, and is determined through the overlap of several positional domains. In order to understand how these positional cues activate cement gland differentiation, the promoter of Xag1, a marker of cement gland differentiation, was analyzed. Previous studies have shown that Xag1 expression can be activated by the anterior-specific transcription factor Otx2, but that this activation is indirect. 102 bp of upstream genomic Xag1 sequence restricts reporter gene expression specifically to the cement gland. Within this region, putative binding sites for Ets and ATF/CREB transcription factors are both necessary and sufficient to drive cement gland-specific expression, and cooperate to do so. Furthermore, while the putative ATF/CREB factor is activated by Otx2, a factor acting through the putative Ets-binding site is not. These results suggest that Ets-like and ATF/CREB-like family members play a role in regulating Xag1 expression in the cement gland, through integration of Otx2 dependent and independent pathways.

scholarly journals BES1 is activated by EMS1-TPD1-SERK1/2-mediated signaling to control tapetum development in Arabidopsis thaliana

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Weiyue Chen ◽  
Minghui Lv ◽  
Yanze Wang ◽  
Ping-An Wang ◽  
Yanwei Cui ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Plant Development ◽  
Family Members ◽  
Ectopic Expression ◽  
Null Mutant ◽  
Male Sterile ◽  
Receptor Like Kinase ◽  
Biochemical Analyses

Abstract BES1 and BZR1 were originally identified as two key transcription factors specifically regulating brassinosteroid (BR)-mediated gene expression. They belong to a family consisting of six members, BES1, BZR1, BEH1, BEH2, BEH3, and BEH4. bes1 and bzr1 single mutants do not exhibit any characteristic BR phenotypes, suggesting functional redundancy of these proteins. Here, by generating higher order mutants, we show that a quintuple mutant is male sterile due to defects in tapetum and microsporocyte development in anthers. Our genetic and biochemical analyses demonstrate that BES1 family members also act as downstream transcription factors in the EMS1-TPD1-SERK1/2 pathway. Ectopic expression of both TPD1 and EMS1 in bri1-116, a BR receptor null mutant, leads to the accumulation of non-phosphorylated, active BES1, similar to activation of BES1 by BRI1-BR-BAK1 signaling. These data suggest that two distinctive receptor-like kinase-mediated signaling pathways share BES1 family members as downstream transcription factors to regulate different aspects of plant development.

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