Low temperature regulates Arabidopsis Lhcb gene expression in a light-independent manner

Transcriptome analysis and differential expression in Arabidopsis thaliana in response to rohitukine (a chromone alkaloid) treatment

Rohitukine is a chromone alkaloid and precursor of potent anticancer drugs flavopiridol, P-276-00, and 2,6-dichloro-styryl derivative (11d) (IIIM-290). The metabolite is reported to possess anticancer, anti-inflammatory, antiadipogenic, immunomodulatory, gastroprotective, anti-implantation, antidyslipidemic, anti-arthritic, and anti-fertility properties. However, the physiological role of rohitukine in plant system is yet to be explored. Here, we studied the effect of rohitukine isolated from Dysoxylum gotadhora on Arabidopsis thaliana. The A. thaliana plants grown on a medium fortified with different rohitukine concentrations showed a significant effect on the growth and development. The root growth of A. thaliana seedlings showed considerable inhibition when grown on medium containing 1.0 mM of rohitukine. Transcriptomic analysis indicated the expression of 895 and 932 genes in control and treated samples respectively at a cut-off of FPKM ≥ 1 and P-value < 0.05. Gene ontology (GO) analysis revealed the upregulation of genes related to photosynthesis, membrane transport, antioxidation, xenobiotic degradation, and some transcription factors (TFs) in response to rohitukine. Conversely, rohitukine downregulated several genes including RNA helicases and those involved in nitrogen compound metabolism. The RNA-seq result was also validated by real-time qRT-PCR analysis. In light of these results, we discuss (i) likely ecological importance of rohitukine in parent plant as well as (ii) comparison between responses to rohitukine treatment in plants and mammals.

Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis)

Polyploids generated by the replication of a single genome (autopolyploid) or synthesis of two or more distinct genomes (allopolyploid) usually show significant advantages over their diploid progenitors in biological characteristics, including growth and development, nutrient accumulation, and plant resistance. Whereas, the impacts of genomic replication on transcription regulation and chromatin structure in pak choi have not been explored fully. In this study, we observed the transcriptional and genomic structural alterations between diploid B. rapa (AA) and artificial autotetraploid B. rapa (AAAA) using RNA-seq and Hi-C. RNA-seq revealed 1,786 differentially expressed genes (DEGs) between the diploids and autotetraploids, including 717 down-regulated and 1,069 up-regulated genes in autotetraploids. Of all the 1,786 DEGs, 23 DEGs (10 down-regulated DEGs in autotetraploids) were involved in Compartment A-B shifts, while 28 DEGs (20 up-regulated DEGs in autotetraploids) participated in Compartment B-A shifts. Moreover, there were 15 DEGs in activated topologically associating domains (TADs) (9 up-regulated DEGs in diploids) and 80 DEGs in repressed TADs (49 down-regulated DEGs in diploids). Subsequently, eight DEGs with genomic structural variants were selected as potential candidate genes, including four DEGs involved in photosynthesis (BraA01003143, BraA09002798, BraA04002224, and BraA08000594), three DEGs related to chloroplast (BraA05002974, BraA05001662, and BraA04001148), and one DEG associated with disease resistance (BraA09004451), which all showed high expression in autotetraploids. Overall, our results demonstrated that integrative RNA-seq and Hi-C analysis can identify related genes to phenotypic traits and also provided new insights into the molecular mechanism of the growth advantage of polyploids.

Transcriptional profiling reveals changes in gene regulation and signaling transduction pathways during temperature stress in wucai (Brassica campestris L.)

Background

Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a cold-tolerant plant that is vulnerable to high temperature. This study explored the response mechanism of wucai to low temperature. In this study, wucai seedlings were treated with different temperatures, including low temperature (LT), high temperature (HT), and a control.

Results

According to transcriptomics analysis, the number of differentially expressed genes (DEGs) in HT and LT was 10,702 and 7267, respectively, compared with the control. The key genes associated with the physiological response of wucai to the treatments were analyzed. The Kyoto Encyclopedia of Genes and Genomes and Gene Ontology annotations indicated the importance of the photosynthesis and photosynthetic-antenna protein pathways. We found that a high-temperature environment greatly inhibited the expression of important genes in the photosynthetic pathway (BrLhc superfamily members, PsaD, PsaE, PsaD, PsaD, PsbO, PsbP, PsbQ, PsbR, PsbS, PsbW, PsbY, Psb27, and Psb28), whereas low temperature resulted in the expression of certain key genes (BrLhc superfamily members, Psa F, Psa H, Psb S, Psb H, Psb 28). In addition, the wucai seedlings exhibited better photosynthetic performance under low-temperature conditions than high-temperature conditions.

Conclusions

Based on the above results, we speculate that upon exposure to low temperature, the plants developed higher cold tolerance by upregulating the expression of genes related to photosynthesis. Conversely, high-temperature stress inhibited the expression of pivotal genes and weakened the self-regulating ability of the plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07981-9.

Transcriptomic Analysis of Verbena bonariensis Leaves Under Low-Temperature Stress

Verbena bonariensis is a valuable plant for both ornament and flower border. As a major constraint, low temperature affects the growing development and survival of V. bonariensis. However, there are few systematic studies in terms of molecular mechanism on the tolerance of low temperature in V. bonariensis. In this study, Illumina sequencing technology was applied to analyze the cold resistance mechanism of plants. Six cDNA libraries were obtained from two samples of two groups, the cold-treated group and the control group. A total of 271,920 unigenes were produced from 406,641 assembled transcripts. Among these, 19,003 differentially expressed genes (DEGs) (corrected p-value <0.01, |log2(fold change) | >3) were obtained, including 9852 upregulated and 9151 downregulated genes. The antioxidant enzyme system, photosynthesis, plant hormone signal transduction, fatty acid metabolism, starch and sucrose metabolism pathway, and transcription factors were analyzed. Based on these results, series of candidate genes related to cold stress were screened out and discussed. The physiological indexes related to response mechanism of low temperature were tested. Eleven upregulated DEGs were validated by Quantitative Real-time PCR. In this study, we provided the transcriptome sequence resource of V. bonariensis and used these data to realize its molecular mechanism under cold stress. The results contributed to valuable clues for genetic studies and helped to screen candidate genes for cold-resistance breeding.

Combination analysis of the physiology and transcriptome provides insights into the mechanism of silver nanoparticles phytotoxicity

Silver nanoparticles (AgNPs) have adverse impacts on plants when released into environments, but their toxic mechanism is still a matter of debate. Here we present a combined analysis of physiology and transcriptome of Arabidopsis thaliana leaves exposure to 30 mg L^-1 AgNPs and Ag⁺ for six days to explore the toxicity mechanism of AgNPs on Arabidopsis. Both transcriptomic and physiological results showed that AgNPs induced reactive oxygen species (ROS) accumulation and damaged photosynthesis. The toxicity of AgNPs is not merely attributable to Ag⁺ release and much higher photosynthetic toxicity and ROS accumulation were observed in 30 mg L^-1 AgNPs than that in 0.12 mg L^-1 Ag⁺. About 60% genes were similarly up- or down-regulated at the same concentration of AgNPs and Ag⁺ and these genes were enriched in photosynthesis and response to the stimulus. However, 302 genes, including those involved in glucosinolates synthesis, were specifically regulated under AgNPs treatments. In conclusion, more than the released Ag⁺, nanoparticle-specific effects are responsible for the toxicity of AgNPs in Arabidopsis thaliana.

Gateway-compatible tissue-specific vectors for plant transformation

BACKGROUND

Understanding regulation of developmental events has increasingly required the use of tissue-specific expression of diverse genes affecting plant growth and environmental responses.

FINDINGS

To allow for cloning of presumptive promoters with tissue-specific activities, we created two plant expression vectors with multiple cloning sites upstream of a Gateway cassette for expression of either untagged or YFP-tagged genes of interest. For fast and easy tissue-specific expression of desired genes, we further developed an initial set of Gateway-compatible tissue-specific gene expression vectors that allow for the expression of YFP-tagged or untagged proteins driven by the ALCOHOL DEHYDROGENASE1, CHLOROPHYLL A/B BINDING PROTEIN 1, COBRA LIKE1, EXPANSIN7, LATERAL ORGAN BOUNDARIES-DOMAIN 16, SCARECROW, UBIQUITIN10, and WOODEN LEG upstream regulatory regions.

CONCLUSIONS

These vectors provide an invaluable resource to the plant community, allowing for rapid generation of a variety of tissue-specific expression constructs.

Integration of low temperature and light signaling during cold acclimation response in Arabidopsis

Certain plants increase their freezing tolerance in response to low nonfreezing temperatures, an adaptive process named cold acclimation. Light has been shown to be required for full cold acclimation, although how light and cold signals integrate and cross-talk to enhance freezing tolerance still remains poorly understood. Here, we show that HY5 levels are regulated by low temperature transcriptionally, via a CBF- and ABA-independent pathway, and posttranslationally, via protein stabilization through nuclear depletion of COP1. Furthermore, we demonstrate that HY5 positively regulates cold-induced gene expression through the Z-box and other cis-acting elements, ensuring the complete development of cold acclimation. These findings uncover unexpected functions for HY5, COP1, and the Z-box in Arabidopsis response to low temperature, provide insights on how cold and light signals integrate to optimize plant survival under freezing temperatures, and reveal the complexity of the molecular mechanisms plants have evolved to respond and adapt to their fluctuating natural environment.

The plastid hexokinase pHXK: a node of convergence for sugar and plastid signals in Arabidopsis

The inhibitors to plastid gene expression (PGE) were effective in preventing nuclear photosynthetic gene expression only if applied within the first 2-3 days of Arabidopsis seedling development. However, the signal transduction processes are still unknown. In this investigation, we found 3% glucose with 1mM chloramphenicol co-treatment repressed LHCB transcript significantly in mature Arabidopsis seedlings, while effective solo glucose treatment needed a concentration of 7%. The repressive effects of glucose and chloramphenicol on LHCB expression were inhibited in phxk (plastid hexokinase) mutant. pHXK enzyme activities, location, function in signal transduction, and cross talk to plastid GUN1 protein (a key signaling factor) were also investigated. The data suggest that pHXK may be a node of convergence for sugar-mediated and PGE-derived signals in Arabidopsis.

Abscisic acid, high-light, and oxidative stress down-regulate a photosynthetic gene via a promoter motif not involved in phytochrome-mediated transcriptional regulation

In etiolated seedlings, light perceived by phytochrome promotes the expression of light-harvesting chlorophyll a/b protein of photosystem II (Lhcb) genes. However, excess of photosynthetically active radiation can reduce Lhcb expression. Here, we investigate the convergence and divergence of phytochrome, high-light stress and abscisic acid (ABA) signaling, which could connect these processes. Etiolated Arabidopsis thaliana seedlings bearing an Lhcb promoter fused to a reporter were exposed to continuous far-red light to activate phytochrome and not photosynthesis, and treated with ABA. We identified a cis-acting region of the promoter required for down-regulation by ABA. This region contains a CCAC sequence recently found to be necessary for ABI4-binding to an Lhcb promoter. However, we did not find a G-box-binding core motif often associated with the ABI4-binding site in genes promoted by light and repressed by ABI4. Mutations involving this motif also impaired the responses to reduced water potential, the response to high photosynthetic light and the response to methyl viologen but not the response to low temperature or to Norflurazon. We propose a model based on current and previous findings, in which hydrogen peroxide produced in the chloroplasts under high light conditions interacts with the ABA signaling network to regulate Lhcb expression. Since the mutation that affects high-light and methyl viologen responses does not affect phytochrome-mediated responses, the regulation by retrograde and phytochrome signaling can finally be separated at the target promoter level.

Arabidopsis mutants deregulated in RCI2A expression reveal new signaling pathways in abiotic stress responses

To uncover new pathways involved in low-temperature signal transduction, we screened for mutants altered in cold-induced expression of RCI2A, an Arabidopsis gene that is not a member of the CBF/DREB1 regulon and is induced not only by low temperature but also by abscisic acid (ABA), dehydration (DH) and NaCl. This was accomplished by generating a line of Arabidopsis carrying a transgene consisting of the RCI2A promoter fused to the firefly luciferase coding sequence. A number of mutants showing low or high RCI2A expression in response to low temperature were identified. These mutants also displayed deregulated RCI2A expression in response to ABA, DH or NaCl. Interestingly, however, they were not altered in stress-induced expression of RD29A, a CBF/DREB1-target gene, suggesting that the mutations affect signaling intermediates of CBF/DREB1-independent regulatory pathways. Several mutants showed alterations in their tolerance to freezing, DH or salt stress, as well as in their ABA sensitivity, which indicates that the signaling intermediates defined by the corresponding mutations play an important role in Arabidopsis tolerance to abiotic stresses. Based on the mutants identified, we discuss the involvement of CBF/DREB1-independent pathways in modulating stress signaling.

Developmental and stress regulation of RCI2A and RCI2B, two cold-inducible genes of arabidopsis encoding highly conserved hydrophobic proteins

The capability of most higher plants to tolerate environmental conditions strongly depends on their developmental stage. In addition, environmental factors have pleiotropic effects on many developmental processes. The interaction between plant development and environmental conditions implies that some genes must be regulated by both environmental factors and developmental cues. To understand their developmental regulation and obtain possible clues on their functions, we have isolated genomic clones for RCI2A and RCI2B, two genes from Arabidopsis ecotype Columbia (Col), whose expression is induced in response to low temperature, dehydration, salt stress, and abscisic acid. The promoters of RCI2A and RCI2B were fused to the uidA (GUS)-coding sequence and the resulting constructs used to transform Arabidopsis. GUS activity was analyzed in transgenic plants during development under both stressed and unstressed conditions. Transgenic plants with either the RCI2A or RCI2B promoter showed strong GUS expression during the first stages of seed development and germination, in vascular bundles, pollen, and most interestingly in guard cells. When transgenic plants were exposed to low temperature, dehydration, salt stress, or abscisic acid, reporter gene expression was induced in most tissues. These results indicate that RCI2A and RCI2B are regulated at transcriptional level during plant development and in response to different environmental stimuli and treatments. The potential role of RCI2A and RCI2B in plant development and stress response is discussed.

Sucrose availability on the aerial part of the plant promotes morphogenesis and flowering of Arabidopsis in the dark

Conditions to promote dark morphogenesis and flower-ing in Arabidopsis have previously been limited to liquid cultures and to a few laboratory ecotypes. We have obtained development and flowering of Arabidopsis plants under complete darkness by growing them on vertical Petri dishes containing solid agar medium with sucrose. Under these conditions, all the ecotypes tested were able to develop, giving rise to etiolated plants that flowered after producing a certain number of leaves. Dark-grown plants showed similarities with phytochrome-deficient mutants and were different from de-etiolated or constitutive photomorphogenesis mutants such as det and cop. Late- and early-flowering ecotypes, showing large differences in flowering time and leaf number under long days, flowered with a similar number of leaves when grown in the dark. Rapid dark flowering of late-flowering ecotypes was not an effect of darkness but the result of the interaction between dark and sucrose availability at the aerial part of the plant, since sucrose also had an effect when plants were grown in the light. Gibberellin-deficient and insensitive mutants were delayed in the initiation of flowers in the dark, indicating a role for these hormones in flowering promotion in the dark. The late-flowering phenotype of mutants at different loci of the autonomous and long-day-dependent flowering induction pathways was rescued in dark growth conditions. However, the late-flowering phenotype of ft and fwa mutants was not rescued by sucrose either in the dark or in the light, suggesting a different role for these genes in flowering induction.

The Arabidopsis CBF gene family is composed of three genes encoding AP2 domain-containing proteins whose expression Is regulated by low temperature but not by abscisic acid or dehydration

We have identified two genes from Arabidopsis that show high similarity with CBF1, a gene encoding an AP2 domain-containing transcriptional activator that binds to the low-temperature-responsive element CCGAC and induces the expression of some cold-regulated genes, increasing plant freezing tolerance. These two genes, which we have named CBF2 and CBF3, also encode proteins containing AP2 DNA-binding motifs. Furthermore, like CBF1, CBF2 and CBF3 proteins also include putative nuclear-localization signals and potential acidic activation domains. The CBF2 and CBF3 genes are linked to CBF1, constituting a cluster on the bottom arm of chromosome IV. The high level of similarity among the three CBF genes, their tandem organization, and the fact that they have the same transcriptional orientation all suggest a common origin. CBF1, CBF2, and CBF3 show identical expression patterns, being induced very rapidly by low-temperature treatment. However, in contrast to most of the cold-induced plant genes characterized, they are not responsive to abscisic acid or dehydration. Taken together, all of these data suggest that CBF2 and CBF3 may function as transcriptional activators, controlling the level of low-temperature gene expression and promoting freezing tolerance through an abscisic acid-independent pathway.