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 Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis

2020 ◽  
Author(s):  
Pratiti Dasgupta ◽  
Abhishek Das ◽  
Sambit Datta New ◽  
Ishani Banerjee New ◽  
Sucheta Tripathy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Low Temperature ◽  
Cold Stress ◽  
Cold Shock ◽  
Indica Rice ◽  
Cellular Reprogramming ◽  
Early Gene ◽  
Signaling Proteins ◽  
Cold Response

Abstract Background Cellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to other plant species originating in tropical and sub-tropical areas, indica rice is highly sensitive to low temperature that adversely affects its growth and grain productivity. Substantial work has been done to understand cold induced changes in gene expression in rice plants. However, adequate information is not available for early gene expression, especially in indica variety. Therefore, a transcriptome profile was generated for cold shock treated seedlings of IR64 variety to identify early responsive genes. Results The functional annotation of early DEGs shows enrichment of genes involved in altered membrane rigidity and electrolytic leakage, the onset of calcium signaling, ROS generation and activation of stress responsive transcription factors in IR64. Gene regulatory network suggests that cold shock induces Ca 2+ signaling to activate DREB/CBF pathway and other groups of transcription factors such as MYB, NAC and ZFP; for activating various cold-responsive genes. The analysis also indicates that cold induced signaling proteins like RLKs, RLCKs, CDPKs and MAPKK and ROS signaling proteins. Further, several LEA, dehydrins and Low temperature-induced-genes were upregulated under early cold shock condition, indicating the onset of water-deficit conditions. Expression profiling in different high yielding cultivars shows high expression of cold-responsive genes in Heera and CB1 indica varieties, These varieties show low levels of cold induced ROS production, electrolytic leakage and high germination rate post-cold stress, compared to IR36 and IR64. Collectively, these results suggest that these varieties may have improved adaptability to cold stress. Conclusions The results of this study provide insights about early responsive events in Oryza sativa L.ssp. indica cv IR64 in response to cold stress. Our data shows the onset of cold response is associated with upregulation of stress responsive TFs, hydrophilic proteins and signaling molecules, whereas, the genes coding for cellular biosynthetic enzymes, cell cycle control and growth-related TFs are downregulated. This study reports that the generation of ROS is integral to the early response to trigger the ROS mediated signaling events during later stages.

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.

scholarly journals Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana

2017 ◽  
Vol 35 (4) ◽  
pp. 837-854 ◽  
Author(s):  
Cristina M Alexandre ◽  
James R Urton ◽  
Ken Jean-Baptiste ◽  
John Huddleston ◽  
Michael W Dorrity ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Dna Sequences ◽  
Sequence Variation ◽  
Expression Patterns ◽  
Sequence Divergence ◽  
Chromatin Accessibility ◽  
Regulatory Dna ◽  
Regulatory Sites

AbstractVariation in regulatory DNA is thought to drive phenotypic variation, evolution, and disease. Prior studies of regulatory DNA and transcription factors across animal species highlighted a fundamental conundrum: Transcription factor binding domains and cognate binding sites are conserved, while regulatory DNA sequences are not. It remains unclear how conserved transcription factors and dynamic regulatory sites produce conserved expression patterns across species. Here, we explore regulatory DNA variation and its functional consequences within Arabidopsis thaliana, using chromatin accessibility to delineate regulatory DNA genome-wide. Unlike in previous cross-species comparisons, the positional homology of regulatory DNA is maintained among A. thaliana ecotypes and less nucleotide divergence has occurred. Of the ∼50,000 regulatory sites in A. thaliana, we found that 15% varied in accessibility among ecotypes. Some of these accessibility differences were associated with extensive, previously unannotated sequence variation, encompassing many deletions and ancient hypervariable alleles. Unexpectedly, for the majority of such regulatory sites, nearby gene expression was unaffected. Nevertheless, regulatory sites with high levels of sequence variation and differential chromatin accessibility were the most likely to be associated with differential gene expression. Finally, and most surprising, we found that the vast majority of differentially accessible sites show no underlying sequence variation. We argue that these surprising results highlight the necessity to consider higher-order regulatory context in evaluating regulatory variation and predicting its phenotypic consequences.

scholarly journals Soybean DREB1/CBF-type transcription factors function in heat and drought as well as cold stress-responsive gene expression

2015 ◽  
Vol 81 (3) ◽  
pp. 505-518 ◽  
Author(s):  
Satoshi Kidokoro ◽  
Keitaro Watanabe ◽  
Teppei Ohori ◽  
Takashi Moriwaki ◽  
Kyonoshin Maruyama ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Cold Stress ◽  
Responsive Gene

scholarly journals MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis

2019 ◽  
Author(s):  
Alexandra Plotnikova ◽  
Max J. Kellner ◽  
Magdalena Mosiolek ◽  
Michael A. Schon ◽  
Michael D. Nodine
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
High Throughput ◽  
Cellular Differentiation ◽  
High Throughput Sequencing ◽  
Profound Impact ◽  
Plant Body ◽  
Non Coding Rnas ◽  
Arabidopsis Embryogenesis

SummaryMicroRNAs (miRNAs) are short non-coding RNAs that mediate the repression of target transcripts in plants and animals. Although miRNAs are required throughout plant development, relatively little is known regarding their embryonic functions. To systematically characterize embryonic miRNAs in Arabidopsis thaliana, we developed or applied high-throughput sequencing based methods to profile hundreds of miRNAs and associated targets throughout embryogenesis. We discovered dozens of miRNAs that dynamically cleave and repress target transcripts including 30 that encode transcription factors. Transcriptome analyses indicated that these miRNA:target interactions have a profound impact on embryonic gene expression programs, and we further demonstrated that the miRNA-mediated repression of six transcription factors were individually required for embryo morphogenesis. These data indicate that the miRNA-directed repression of multiple transcription factors is critically important for the establishment of the plant body plan, and provide a foundation to further investigate how miRNAs contribute to these initial cellular differentiation events.

scholarly journals Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis

2020 ◽  
Author(s):  
Pratiti Dasgupta ◽  
Abhishek Das ◽  
Sambit Datta ◽  
Ishani Banerjee ◽  
Sucheta Tripathy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Low Temperature ◽  
Cold Stress ◽  
Cold Shock ◽  
Rice Variety ◽  
Cellular Reprogramming ◽  
Early Gene ◽  
Signaling Proteins ◽  
Cold Response

Abstract Background: Cellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to other plant species originating in tropical and sub-tropical areas, indica rice is highly sensitive to low temperature that adversely affects its growth and grain productivity. Substantial work has been done to understand cold induced changes in gene expression in rice plants. However, adequate information is not available for early gene expression, especially in indica variety. Therefore, a transcriptome profile was generated for cold shock treated seedlings of IR64 variety to identify early responsive genes. Results: The functional annotation of early DEGs shows enrichment of genes involved in altered membrane rigidity and electrolytic leakage, the onset of calcium signaling, ROS generation and activation of stress responsive transcription factors in IR64. Gene regulatory network suggests that cold shock induced Ca2+ signaling activates DREB/CBF pathway and other groups of transcription factors such as MYB, NAC and ZFP; for activating various cold-responsive genes. The analysis also indicates that cold induced signaling proteins like RLKs, RLCKs, CDPKs and MAPKK and ROS signaling proteins. Further, several late-embryogenesis-abundant (LEA), dehydrins and low temperature-induced-genes were upregulated under early cold shock condition, indicating the onset of water-deficit conditions. Expression profiling in different high yielding cultivars shows high expression of cold-responsive genes in Heera and CB1 indica varieties. These varieties show low levels of cold induced ROS production, electrolytic leakage and high germination rate post-cold stress, compared to IR36 and IR64. Collectively, these results suggest that these varieties may have improved adaptability to cold stress.Conclusions: The results of this study provide insights about early responsive events in Oryza sativa L.ssp. indica cv IR64 in response to cold stress. Our data shows the onset of cold response is associated with upregulation of stress responsive TFs, hydrophilic proteins and signaling molecules, whereas, the genes coding for cellular biosynthetic enzymes, cell cycle control and growth-related TFs are downregulated. This study reports that the generation of ROS is integral to the early response to trigger the ROS mediated signaling events during later stages.

scholarly journals Posttranslational regulation of multiple clock-related transcription factors triggers cold-inducible gene expression in Arabidopsis

2021 ◽  
Vol 118 (10) ◽  
pp. e2021048118
Author(s):  
Satoshi Kidokoro ◽  
Kentaro Hayashi ◽  
Hiroki Haraguchi ◽  
Tomona Ishikawa ◽  
Fumiyuki Soma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Cold Stress ◽  
Circadian Clock ◽  
Crop Productivity ◽  
Stress Conditions ◽  
Posttranslational Regulation ◽  
Inducible Gene Expression ◽  
Myb Proteins ◽  
Inducible Gene

Cold stress is an adverse environmental condition that affects plant growth, development, and crop productivity. Under cold stress conditions, the expression of numerous genes that function in the stress response and tolerance is induced in various plant species, and the dehydration-responsive element (DRE) binding protein 1/C-repeat binding factor (DREB1/CBF) transcription factors function as master switches for cold-inducible gene expression. Cold stress strongly induces these DREB1 genes. Therefore, it is important to elucidate the mechanisms of DREB1 expression in response to cold stress to clarify the perception and response of cold stress in plants. Previous studies indicated that the central oscillator components of the circadian clock, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), are involved in cold-inducible DREB1 expression, but the underlying mechanisms are not clear. We revealed that the clock-related MYB proteins REVEILLE4/LHY-CCA1-Like1 (RVE4/LCL1) and RVE8/LCL5 are quickly and reversibly transferred from the cytoplasm to the nucleus under cold stress conditions and function as direct transcriptional activators of DREB1 expression. We found that CCA1 and LHY suppressed the expression of DREB1s under unstressed conditions and were rapidly degraded specifically in response to cold stress, which suggests that they act as transcriptional repressors and indirectly regulate the cold-inducible expression of DREB1s. We concluded that posttranslational regulation of multiple clock-related transcription factors triggers cold-inducible gene expression. Our findings clarify the complex relationship between the plant circadian clock and the regulatory mechanisms of cold-inducible gene expression.

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.

A Study of Arabidopsis Cold Stress Tolerance Improvement via AthHOS1-Targeting HOS1-AmiRNA Approach

2021 ◽  
Author(s):  
Marzieh Karimi ◽  
Behrouz Shiran ◽  
Mohammad Rabei ◽  
Hossein Fallahi ◽  
Bojana Banović Đeri
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Circadian Rhythm ◽  
Comparative Analysis ◽  
Low Temperature ◽  
Transgenic Plants ◽  
Cold Stress ◽  
Stress Tolerance ◽  
Low Temperatures ◽  
Wild Type

Abstract In this study the artificial microRNAs (amiRNAs) technology targeting HOS1 gene was tested for its applicability for the improvement of cold stress tolerance in Landsberg-0 (Ler-0) ecotype of Arabidopsis thaliana. The chosen approach was designed to suppress AtHOS1 gene expression through the overexpression of amiRNA-HOS1. The effect of AtHOS1-amiRNA overexpression to transgenic plants’ response to cold stress was determined by Real Time PCR. The expression levels of amiRNA and its target, AtHOS1 gene, were observed in 3-week old seedlings of T3 generation and in wild-type plants after 6h, 12h, 24h, 48h and 96h of their exposure to cold stress (4ºC). Comparative analysis revealed that AtHOS1-amiRNA negatively regulated AtHOS1 in transgenic plants upon plants lengthen exposure (for 48h and 96h) to low temperature (Pearson’s correlation coefficient of -0.407; P < 0.05). Even though prolonged cold stress caused extended up regulation of AtHOS1 in wild type plants, in transgenic plants AtHOS1-amiRNA suppression disturbed expected AtHOS1 circadian rhythm by preventing further AtHOS1 up regulation. Moreover, transgenic plants showed AtHOS1 down regulation 96h after the cold stress onset, due to sufficient overexpression of AtHOS1-amiRNA, which allowed cold signaling amplification in transgenic plants. As a result of that, cold-acclimated transformed plants displayed 17% higher freezing tolerance (-1°C to -8°C) in comparison to wild type plants, demonstrating the success of chosen approach in improving Arabidopsis tolerance to low temperatures, at least in Ler-0 ecotype.

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