Strength comparison between cold-inducible promoters of Arabidopsis cor15a and cor15b genes in potato and tobacco

Arabidopsis as a model for translational research

Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage laboratory and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, and molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.

Genome-Wide Identification and Expression Analysis of GASA Genes in Hevea brasiliensis Reveals Their Involvement in Response to Cold Stress

The Gibberellic Acid Stimulated in Arabidopsis (GASA) gene family is regulated by gibberellins and plays a crucial role in regulating plant growth and development. Based on rubber tree genome data, 18 HbGASA genes, designated HbGASA1 to HbGASA18, were identified in Hevea brasiliensis. Comprehensive bioinformatics analyses were performed to characterize gene structures, chromosomal distributions, syntenic relationships, protein architectures, phylogenetic evolution, and expression profiles. The expression patterns of HbGASA genes under low-temperature stress were further validated by quantitative real-time polymerase chain reactions (qRT-PCR). The results demonstrated that the 18 HbGASA genes were unevenly distributed across 10 chromosomes. The encoded proteins ranged from 88 to 253 amino acids in length, and the number of exons varied from 2 to 4. Phylogenetic analysis clustered these genes into three distinct clades. Conserved motif analysis identified 10 conserved motifs, with Motif 1 and Motif 2 being highly conserved across all members. Promoter analysis revealed multiple hormone-responsive and stress-related regulatory cis-acting elements. Transcripts of the 18 HbGASA genes were detected in various tissues, and significant differences were observed in their expression levels. Under cold stress, qRT-PCR results showed that multiple HbGASA genes were significantly up-regulated. This study provides valuable insights into the structure, evolution, and functional diversification of GASA genes in the important tropical crop, H. brasiliensis.

Warm temperature-triggered developmental reprogramming requires VIL1-mediated, genome-wide H3K27me3 accumulation in Arabidopsis

Changes in ambient temperature immensely affect developmental programs in many species. Plants adapt to high ambient growth temperature in part by vegetative and reproductive developmental reprogramming, known as thermo-morphogenesis. Thermo-morphogenesis is accompanied by massive changes in the transcriptome upon temperature change. Here, we show that transcriptome changes induced by warm ambient temperature require VERNALIZATION INSENSITIVE 3-LIKE 1 (VIL1), a facultative component of the Polycomb repressive complex PRC2, in Arabidopsis. Warm growth temperature elicits genome-wide accumulation of H3K27me3 and VIL1 is necessary for the warm temperature-mediated accumulation of H3K27me3. Consistent with its role as a mediator of thermo-morphogenesis, loss of function of VIL1 results in hypo-responsiveness to warm ambient temperature. Our results show that VIL1 is a major chromatin regulator in responses to high ambient temperature.

Overexpression of a Malus baccata CBF transcription factor gene, MbCBF1, Increases cold and salinity tolerance in Arabidopsis thaliana

CBFs play a crucial role when plants are in adverse environmental conditions for growth. However, there are few reports on the role of CBF gene in stress responses of Malus plant. In this experiment, a new CBF TF was separated from M. baccata which was named MbCBF1. MbCBF1 protein was found to be localized in the nucleus after subcellular localization. Furthermore, the expression of MbCBF1 was highly accumulated in new leaves and roots due to the high influence of cold and high salt in M. baccata seedlings. After introducing MbCBF1 into A. thaliana, transgenic A. thaliana can better adapt to the living conditions of cold and high salt. The increased expression of MbCBF1 in A. thaliana also increased the contents of proline, remarkablely improved the activities of SOD, POD and CAT, but the content of MDA was decreased. Although the chlorophyll content also decreased, it decreased less in transgenic plants. In short, above date showed that MbCBF1 has a positive effect on improving A. thaliana cold and high salt tolerance. MbCBF1 can regulate the expression of its downstream gene in transgenic lines, up-regulate the expression of key genes COR15a, RD29a/bandCOR6.6/47 related to low temperature under cold conditions and NCED3, CAT1, P5CS1, RD22, DREB2A,PIF1/4, SOS1 and SnRK2.4 related to salt stress under high salt conditions, so as to further improve the adaptability and tolerance of the transgenic plants to low temperature and high salt environment.

Performance of abiotic stress-inducible synthetic promoters in genetically engineered hybrid poplar (Populus tremula × Populus alba)

Abiotic stresses can cause significant damage to plants. For sustainable bioenergy crop production, it is critical to generate resistant crops to such stress. Engineering promoters to control the precise expression of stress resistance genes is a very effective way to address the problem. Here we developed stably transformed Populus tremula × Populus alba hybrid poplar (INRA 717-1B4) containing one-of-six synthetic drought stress-inducible promoters (SDs; SD9-1, SD9-2, SD9-3, SD13-1, SD18-1, and SD18-3) identified previously by transient transformation assays. We screened green fluorescent protein (GFP) induction in poplar under osmotic stress conditions. Of six transgenic lines containing synthetic promoter, three lines (SD18-1, 9-2, and 9-3) had significant GFP expression in both salt and osmotic stress treatments. Each synthetic promoter employed heptamerized repeats of specific and short cis-regulatory elements (7 repeats of 7-8 bases). To verify whether the repeats of longer sequences can improve osmotic stress responsiveness, a transgenic poplar containing the synthetic promoter of the heptamerized entire SD9 motif (20 bases, containing all partial SD9 motifs) was generated and measured for GFP induction under osmotic stress. The heptamerized entire SD9 motif did not result in higher GFP expression than the shorter promoters consisting of heptamerized SD9-1, 9-2, and 9-3 (partial SD9) motifs. This result indicates that shorter synthetic promoters (~50 bp) can be used for versatile control of gene expression in transgenic poplar. These synthetic promoters will be useful tools to engineer stress-resilient bioenergy tree crops in the future.

Isolation and Functional Analysis of MbCBF2, a Malus baccata (L.) Borkh CBF Transcription Factor Gene, with Functions in Tolerance to Cold and Salt Stress in Transgenic Arabidopsis thaliana

CBF transcription factors (TFs) are key regulators of plant stress tolerance and play an integral role in plant tolerance to adverse growth environments. However, in the current research situation, there are few reports on the response of the CBF gene to Begonia stress. Therefore, this experiment investigated a novel CBF TF gene, named MbCBF2, which was isolated from M. baccata seedlings. According to the subcellular localization results, the MbCBF2 protein was located in the nucleus. In addition, the expression level of MbCBF2 was higher in new leaves and roots under low-temperature and high-salt induction. After the introduction of MbCBF2 into Arabidopsis thaliana, the adaptability of transgenic A. thaliana to cold and high-salt environments was significantly enhanced. In addition, the high expression of MbCBF2 can also change many physiological indicators in transgenic A. thaliana, such as increased chlorophyll and proline content, superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activity, and reduced malondialdehyde (MDA) content. Therefore, it can be seen from the above results that MbCBF2 can positively regulate the response of A. thaliana to low-temperature and osmotic stress. In addition, MbCBF2 can also regulate the expression of its downstream genes in transgenic lines. It can not only positively regulate the expression of the downstream key genes AtCOR15a, AtERD10, AtRD29a/b and AtCOR6.6/47, related to cold stress at low temperatures, but can also positively regulate the expression of the downstream key genes AtNCED3, AtCAT1, AtP5CS, AtPIF1/4 and AtSnRK2.4, related to salt stress. That is, the overexpression of the MbCBF2 gene further improved the adaptability and tolerance of transgenic plants to low-temperature and high-salt environments.

The Research on the Osmotic Stress Gene Mining Model Based on the Arabidopsis Genome

In the field of the bioinformatics, during osmotic stress response genes mining processing, it is also very crucial to verify experimental data obtained in the course of complex experiments by using the computer. Aim of this paper is taking Arabidopsis thaliana as the experimental crop, designing technology roadmap, taking advantage of the skills of function and programming, then designing algorithms. After using the program to predict the transcription start point, the promoter sequence is extracted and simplified. In addition, different alignment methods are classified. Then, comparing the promoter sequence with the cis-element and using the formula for further processing. Finally, get the probability P value, which provide further help to experts and scholars on the basis of probability values to determine the correlation between the osmotic stress. The experimental data source of chromosomal sequences is received from Genbank database files, and cis-element sequence that associated with osmotic stress is collected from TRANSFAC and TRRD database. From this, the authors not only used the Arabidopsis promoter as the experimental data, but also use a variety of eukaryotic promoters include promoters GhNHX1 rice, cotton OsNHX1 promoter, as a comparison. Wherein the data obtained in the biological laboratory, which in the course of running the program, 70% have been verified. P value close to 0.8, this article will be treated as the promoter contains osmotic stress cis-elements, the expression of gene induced by osmotic stress. For thaliana, cotton and rice, programs running average time was 51s, 72s and 114s. Through the use of some commonly used bioinformatics gene mining algorithms, MEME algorithm and BioProspector algorithm for the same data have been processed, the average running time of the system is increasing with the increase of data. Running time of MEME algorithm increases from 60s to reach 198s, BioProspector algorithm increases from 45s to 150s model process used herein were 50s, 75s, 110s, 135s. At the same time, the authors can see in the three algorithms, the model algorithm used herein with respect to the first two more optimized. To ensure the accuracy rate, meanwhile has high speed and stabilization of higher.

The Expression of CARK1 or RCAR11 Driven by Synthetic Promoters Increases Drought Tolerance in Arabidopsis thaliana

Drought stress hinders plant growth and development, and abscisic acid (ABA) stimulates plants to respond to drought. Here, to increase plant tolerance to drought, we designed three synthetic promoters (Ap, Dp, ANDp) to determine transcription activity and drought stress resistance in plants resulting from combinations of (1) synthetic promoters and (2) the functional genes CARK1 (cytosolic ABA receptor kinase 1) and RCAR11 (regulatory components of ABA receptor 11). Transient expression of eGFP and the dual-luciferase assay demonstrated that the basal transcriptional activities of Ap and ANDp were present at low levels under normal conditions, while the synthetic promoters were apparently induced upon either treatment of exogenous ABA or co-transformation with effector DREB2A (dehydration-responsive element binding protein 2A). Analysis of the transgenic plants (Ap:CARK1, Dp:CARK1, ANDp:CARK1, and Dp:RCAR11-Ap:CARK1) showed that the synthetic promoters Ap, Dp, and ANDp increased the expression of exogenous genes in transgenic plants upon treatment of ABA or d-mannitol. ANDp:CARK1 and Dp:RCAR11-Ap:CARK1 transgenic plants were sensitive to ABA and d-mannitol during cotyledon greening and root growth. A drought tolerance assay revealed that ANDp:CARK1 and Dp:RCAR11-Ap:CARK1 exhibited a higher survival rate than others upon drought stress. These results indicate that the combinations ANDp:CARK1 and Dp:RCAR11-Ap:CARK1 can be used to generate drought stress resistance in plants.

Expression analysis and promoter methylation under osmotic and salinity stress of TaGAPC1 in wheat (Triticum aestivum L)

Cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPC) catalyzes a key reaction in glycolysis and encoded by a multi-gene family which showed instability expression under abiotic stress. DNA methylation is an epigenetic modification that plays an important role in gene regulation in response to abiotic stress. The comprehension of DNA methylation at promoter region of TaGAPC1 can provide insights into the transcription regulation mechanisms of plant genes under abiotic stress. In this study, we cloned TaGAPC1 genes and its promoters from two wheat genomes, then investigated the expression patterns of TaGAPC1 under osmotic and salinity stress, and analyzed the promoter sequences. Moreover, the methylation patterns of promoters under stress were confirmed. Expression analysis indicated that TaGAPC1 was induced inordinately by stresses in two wheat genotypes with contrasting drought tolerance. Several stress-related cis-acting elements (MBS, DRE, GT1 and LTR et al.) were located in its promoters. Furthermore, the osmotic and salinity stress induced the demethylation of CG and CHG nucleotide in the promoter region of Changwu134. The methylation level of CHG and CHH in promoter of Zhengyin1 was always increased under stresses, and the CG contexts remained unchanged. The cytosine loci of stress-related cis-acting elements also showed different methylation changes in this process. These results provide insights into the relationship between promoter methylation and gene expression, promoting the function investigation of GAPC.

Oil palm drought inducible DREB1 induced expression of DRE/CRT- and non-DRE/CRT-containing genes in lowland transgenic tomato under cold and PEG treatments

Dehydration-responsive element binding (DREB) transcription factor plays an important role in controlling the expression of abiotic stress responsive genes. An intronless oil palm EgDREB1 was isolated and confirmed to be a nuclear localized protein. Electrophoretic mobility shift and yeast one-hybrid assays validated its ability to interact with DRE/CRT motif. Its close evolutionary relation to the dicot NtDREB2 suggests a universal regulatory role. In order to determine its involvement in abiotic stress response, functional characterization was performed in oil palm seedlings subjected to different levels of drought severity and in EgDREB1 transgenic tomato seedlings treated by abiotic stresses. Its expression in roots and leaves was compared with several antioxidant genes using quantitative real-time PCR. Early accumulation of EgDREB1 in oil palm roots under mild drought suggests possible involvement in the initiation of signaling communication from root to shoot. Ectopic expression of EgDREB1 in T1 transgenic tomato seedlings enhanced expression of DRE/CRT and non-DRE/CRT containing genes, including tomato peroxidase (LePOD), ascorbate peroxidase (LeAPX), catalase (LeCAT), superoxide dismutase (LeSOD), glutathione reductase (LeGR), glutathione peroxidase (LeGP), heat shock protein 70 (LeHSP70), late embryogenesis abundant (LeLEA), metallothionine type 2 (LeMET2), delta 1-pyrroline-5- carboxylate synthetase (LePCS), ABA-aldehyde oxidase (LeAAO) and 9-cis- Epoxycarotenoid dioxygenase (LeECD) under PEG treatment and cold stress (4 °C). Altogether, these findings suggest that EgDREB1 is a functional regulator in enhancing tolerance to drought and cold stress.

Tomato SlRbohB, a member of the NADPH oxidase family, is required for disease resistance against Botrytis cinerea and tolerance to drought stress

NADPH oxidases (also known as respiratory burst oxidase homologs, Rbohs) are key enzymes that catalyze the generation of reactive oxygen species (ROS) in plants. In the present study, eight SlRboh genes were identified in tomato and their possible involvement in resistance to Botrytis cinerea and drought tolerance was examined. Expression of SlRbohs was induced by B. cinerea and Pseudomonas syringae pv. tomato but displayed distinct patterns. Virus-induced gene silencing based silencing of SlRbohB resulted in reduced resistance to B. cinerea but silencing of other SlRbohs did not affect the resistance. Compared to non-silenced plants, the SlRbohB-silenced plants accumulated more ROS and displayed attenuated expression of defense genes after infection with B. cinerea. Silencing of SlRbohB also suppressed flg22-induced ROS burst and the expression of SlLrr22, a marker gene related to PAMP-triggered immunity (PTI). Transient expression of SlRbohB in Nicotiana benthamiana led to enhanced resistance to B. cinerea. Furthermore, silencing of SlRbohB resulted in decreased drought tolerance, accelerated water loss in leaves and the altered expression of drought-responsive genes. Our data demonstrate that SlRbohB positively regulates the resistance to B. cinerea, flg22-induced PTI, and drought tolerance in tomato.