High temperature acclimation through PIF4 signaling

Mechanisms of plant acclimation to multiple abiotic stresses

Plants frequently encounter a range of abiotic stresses and their combinations. Even though stresses rarely occur in isolation, research on plant stress resilience typically focuses on single environmental stressors. Plant responses to abiotic stress combinations are often distinct from corresponding individual stresses. Factors determining the outcomes of combined stresses are complex and multifaceted. In this review, we summarize advancements in our understanding of the mechanisms underlying plant responses to co-occurring (combined and sequential) abiotic stresses, focusing on morphological, physiological, developmental, and molecular aspects. Comprehensive understanding of plant acclimation, including the signaling and response mechanisms to combined and individual stresses, can contribute to the development of strategies for enhancing plant resilience in dynamic environments.

Differential biochemical responses of seven Indian wheat genotypes to temperature stress

BACKGROUND

Changes in the temperature induction response are potential tools for the empirical assessment of plant cell tolerance. This technique is used to identify thermotolerant lines in field crops. In the present investigation, ten-day-old seedlings of six wheat genotypes released by Dr. PDKV, Akola, Maharashtra, India were exposed to gradual increases in high temperature and duration (control 25 °C to 30 °C for 1 h, 34 °C for 1 h, 38 °C for 2 h and 42 °C for 3 h) to investigate their effects on some physiological and biochemical parameters to provide basic information for improving heat-tolerant cultivars.

RESULTS

Proline levels increased with increasing temperature up to 34 °C for 1 h but then decreased at higher temperatures (depending on genotype). Notably, proline levels decreased at 38 °C for 2 h in PDKV-Washim, AKAW-3722, and PDKV Sardar and at 42 °C for 3 h in all the genotypes. The relative leaf water content (RLWC) and chlorophyll 'b' content significantly decreased with increasing temperature. Hydrogen peroxide (H₂O₂) levels increased with temperature. The enzyme activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), and peroxidase also increased with temperature. However, these parameters, along with other biochemical indicators, generally decreased at 42 °C for 3 h.

CONCLUSION

This study revealed positive relationships between increasing temperatures. Hydrogen peroxide levels and the activities of SOD, APX, and peroxidase enzymes across all the genotypes. The AKAW-4627 genotype presented better maintenance of physiological and biochemical parameters and lower H₂O₂ levels, indicating greater heat tolerance. Compared with PDKV-Washim and AKAW-3722, which are more susceptible to high temperatures, the WSM-109-04, AKAW-4627 and PDKV Sardar genotypes presented better adaptability to heat stress. These findings suggest that selecting wheat genotypes with higher proline accumulation and better maintenance of physiological and biochemical parameters under heat stress, such as AKAW-4627, can help in the development of heat-tolerant wheat cultivars.

LlbHLH87 interacts with LlSPT to modulate thermotolerance via activation of LlHSFA2 and LlEIN3 in lily

Basic helix-loop-helix (bHLH) proteins comprise one of the largest families of transcription factors in plants, which play roles in plant development, secondary metabolism, and the response to biotic/abiotic stresses. However, the roles of bHLH proteins in thermotolerance are largely unknown. Herein, we identified a heat-inducible member of the bHLH family in lily (Lilium longiflorum), named LlbHLH87, which plays a role in thermotolerance. LlbHLH87 was rapidly induced by transient heat stress, and its encoded protein was localized to the nucleus, exhibiting transactivation activity in both yeast and plant cells. Overexpression of LlbHLH87 in Arabidopsis enhanced basal thermotolerance, while silencing of LlbHLH87 in lily reduced basal thermotolerance. Further analysis showed that LlbHLH87 bound to the promoters of HEAT STRESS TRANSCRIPTION FACTOR A2 (LlHSFA2) and ETHYLENE-INSENSITIVE 3 (LlEIN3) to directly activate their expression. In addition, LlbHLH87 interacted with itself and with SPATULA (LlSPT) protein. LlSPT was activated by extended heat stress and its protein competed for the homologous interaction of LlbHLH87, which reduced the transactivation ability of LlbHLH87 for target genes. Compared with that observed under LlbHLH87 overexpression alone, co-overexpression of LlbHLH87 and LlSPT reduced the basal thermotolerance of lily to sudden heat shock, but improved its thermosensitivity to prolonged heat stress treatment. Overall, our data demonstrated that LlbHLH87 regulates thermotolerance via activation of LlEIN3 and LlHSFA2, along with an antagonistic interaction with LlSPT.

MPK4-mediated phosphorylation of PHYTOCHROME INTERACTING FACTOR4 controls thermosensing by regulating histone variant H2A.Z deposition

Plants can perceive a slight upsurge in ambient temperature and respond by undergoing morphological changes, such as elongated hypocotyls and early flowering. The dynamic functioning of PHYTOCHROME INTERACTING FACTOR4 (PIF4) in thermomorphogenesis is well established, although the complete regulatory pathway involved in thermosensing remains elusive. We establish that an increase in temperature from 22 to 28 °C induces upregulation and activation of MITOGEN-ACTIVATED PROTEIN KINASE 4 (MPK4) in Arabidopsis (Arabidopsis thaliana), subsequently leading to the phosphorylation of PIF4. Phosphorylated PIF4 represses the expression of ACTIN-RELATED PROTEIN 6 (ARP6), which is required for mediating the deposition of histone variant H2A.Z at its target loci. Furthermore, we demonstrate that variations in ARP6 expression in PIF4 phosphor-null and phosphor-mimetic seedlings affect hypocotyl growth at 22 and 28 °C by modulating the regulation of ARP6-mediated H2A.Z deposition at the loci of genes involved in elongating hypocotyl cells. Interestingly, the expression of MPK4 is also controlled by H2A.Z deposition in a temperature-dependent manner. Taken together, these findings highlight the regulatory mechanism of thermosensing by which MPK4-mediated phosphorylation of PIF4 affects ARP6-mediated H2A.Z deposition at the genes involved in hypocotyl cell elongation.

LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes

Ethylene signaling has been indicated as a potential positive regulator of plant warm ambient temperature response, but its underlying molecular mechanisms are largely unknown. Here, we show that LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes. We found that the presence of warm ambient temperature activates ethylene signaling through EIN2 and EIN3, leading to an interaction between LHP1 and accumulated EIN2-C to co-regulate a subset of LHP1-bound genes marked by H3K27me3 and H3K4me3 bivalency. Furthermore, we demonstrate that INO80 is recruited to bivalent genes by interacting with EIN2-C and EIN3, promoting H3K4me3 enrichment and facilitating transcriptional activation in response to a warm ambient temperature. Together, our findings illustrate a mechanism wherein ethylene signaling orchestrates LHP1 and INO80 to regulate warm ambient temperature response by activating specific bivalent genes in Arabidopsis.

CCaP1/CCaP2/CCaP3 interact with plasma membrane H+-ATPases and promote thermo-responsive growth by regulating cell wall modification in Arabidopsis

Arabidopsis plants adapt to warm temperatures by promoting hypocotyl growth primarily through the basic helix-loop-helix transcription factor PIF4 and its downstream genes involved in auxin responses, which enhance cell division. In the current study, we discovered that cell wall-related calcium-binding protein 2 (CCaP2) and its paralogs CCaP1 and CCaP3 function as positive regulators of thermo-responsive hypocotyl growth by promoting cell elongation in Arabidopsis. Interestingly, mutations in CCaP1/CCaP2/CCaP3 do not affect the expression of PIF4-regulated classic downstream genes. However, they do noticeably reduce the expression of xyloglucan endotransglucosylase/hydrolase genes, which are involved in cell wall modification. We also found that CCaP1/CCaP2/CCaP3 are predominantly localized to the plasma membrane, where they interact with the plasma membrane H+-ATPases AHA1/AHA2. Furthermore, we observed that vanadate-sensitive H+-ATPase activity and cell wall pectin and hemicellulose contents are significantly increased in wild-type plants grown at warm temperatures compared with those grown at normal growth temperatures, but these changes are not evident in the ccap1-1 ccap2-1 ccap3-1 triple mutant. Overall, our findings demonstrate that CCaP1/CCaP2/CCaP3 play an important role in controlling thermo-responsive hypocotyl growth and provide new insights into the alternative pathway regulating hypocotyl growth at warm temperatures through cell wall modification mediated by CCaP1/CCaP2/CCaP3.

JASMONATE ZIM-domain protein 3 regulates photomorphogenesis and thermomorphogenesis through inhibiting PIF4 in Arabidopsis

Light and temperature are 2 major environmental factors that affect the growth and development of plants during their life cycle. Plants have evolved complex mechanisms to adapt to varying external environments. Here, we show that JASMONATE ZIM-domain protein 3 (JAZ3), a jasmonic acid signaling component, acts as a factor to integrate light and temperature in regulating seedling morphogenesis. JAZ3 overexpression transgenic lines display short hypocotyls under red, far-red, and blue light and warm temperature (28 °C) conditions compared to the wild type in Arabidopsis (Arabidopsis thaliana). We show that JAZ3 interacts with the transcription factor PHYTOCHROME-INTERACTING FACTOR4 (PIF4). Interestingly, JAZ3 spontaneously undergoes liquid-liquid phase separation (LLPS) in vitro and in vivo and promotes LLPS formation of PIF4. Moreover, transcriptomic analyses indicate that JAZ3 regulates the expression of genes involved in many biological processes, such as response to auxin, auxin-activated signaling pathway, regulation of growth, and response to red light. Finally, JAZ3 inhibits the transcriptional activation activity and binding ability of PIF4. Collectively, our study reveals a function and molecular mechanism of JAZ3 in regulating plant growth in response to environmental factors such as light and temperature.

Temperature Effect on Rhizome Development in Perennial rice

Traditional agriculture is becoming increasingly not adapted to global climate change. Compared with annual rice, perennial rice has strong environmental adaptation and needs fewer natural resources and labor inputs. Rhizome, a kind of underground stem for rice to achieve perenniallity, can grow underground horizontally and then bend upward, developing into aerial stems. The temperature has a great influence on plant development. To date, the effect of temperature on rhizome development is still unknown. Fine temperature treatment of Oryza longistaminata (OL) proved that compared with higher temperatures (28-30 ℃), lower temperature (17-19 ℃) could promote the sprouting of axillary buds and enhance negative gravitropism of branches, resulting in shorter rhizomes. The upward growth of branches was earlier at low temperature than that at high temperature, leading to a high frequency of shorter rhizomes and smaller branch angles. Comparative transcriptome showed that plant hormones played an essential role in the response of OL to temperature. The expressions of ARF17, ARF25 and FucT were up-regulated at low temperature, resulting in prospectively asymmetric auxin distribution, which subsequently induced asymmetric expression of IAA20 and WOX11 between the upper and lower side of the rhizome, further leading to upward growth of the rhizome. Cytokinin and auxin are phytohormones that can promote and inhibit bud outgrowth, respectively. The auxin biosynthesis gene YUCCA1 and cytokinin oxidase/dehydrogenase gene CKX4 and CKX9 were up-regulated, while cytokinin biosynthesis gene IPT4 was down-regulated at high temperature. Moreover, the D3 and D14 in strigolactones pathways, negatively regulating bud outgrowth, were up-regulated at high temperature. These results indicated that cytokinin, auxins, and strigolactones jointly control bud outgrowth at different temperatures. Our research revealed that the outgrowth of axillary bud and the upward growth of OL rhizome were earlier at lower temperature, providing clues for understanding the rhizome growth habit under different temperatures, which would be helpful for cultivating perennial rice.

High-throughput field phenotyping reveals that selection in breeding has affected the phenology and temperature response of wheat in the stem elongation phase

Crop growth and phenology are driven by seasonal changes in environmental variables, with temperature as one important factor. However, knowledge about genotype-specific temperature response and its influence on phenology is limited. Such information is fundamental to improve crop models and adapt selection strategies. We measured the increase in height of 352 European winter wheat varieties in 4 years to quantify phenology, and fitted an asymptotic temperature response model. The model used hourly fluctuations in temperature to parameterize the base temperature (Tmin), the temperature optimum (rmax), and the steepness (lrc) of growth responses. Our results show that higher Tmin and lrc relate to an earlier start and end of stem elongation. A higher rmax relates to an increased final height. Both final height and rmax decreased for varieties originating from the continental east of Europe towards the maritime west. A genome-wide association study (GWAS) indicated a quantitative inheritance and a large degree of independence among loci. Nevertheless, genomic prediction accuracies (GBLUPs) for Tmin and lrc were low (r≤0.32) compared with other traits (r≥0.59). As well as known, major genes related to vernalization, photoperiod, or dwarfing, the GWAS indicated additional, as yet unknown loci that dominate the temperature response.

Functional insight into multi-omics-based interventions for climatic resilience in sorghum (Sorghum bicolor): a nutritionally rich cereal crop

MAIN CONCLUSION

The article highlights omics-based interventions in sorghum to combat food and nutritional scarcity in the future. Sorghum with its unique ability to thrive in adverse conditions, has become a tremendous highly nutritive, and multipurpose cereal crop. It is resistant to various types of climatic stressors which will pave its way to a future food crop. Multi-omics refers to the comprehensive study of an organism at multiple molecular levels, including genomics, transcriptomics, proteomics, and metabolomics. Genomic studies have provided insights into the genetic diversity of sorghum and led to the development of genetically improved sorghum. Transcriptomics involves analysing the gene expression patterns in sorghum under various conditions. This knowledge is vital for developing crop varieties with enhanced stress tolerance. Proteomics enables the identification and quantification of the proteins present in sorghum. This approach helps in understanding the functional roles of specific proteins in response to stress and provides insights into metabolic pathways that contribute to resilience and grain production. Metabolomics studies the small molecules, or metabolites, produced by sorghum, provides information about the metabolic pathways that are activated or modified in response to environmental stress. This knowledge can be used to engineer sorghum varieties with improved metabolic efficiency, ultimately leading to better crop yields. In this review, we have focused on various multi-omics approaches, gene expression analysis, and different pathways for the improvement of Sorghum. Applying omics approaches to sorghum research allows for a holistic understanding of its genome function. This knowledge is invaluable for addressing challenges such as climate change, resource limitations, and the need for sustainable agriculture.

LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes

Ethylene signaling has been indicated as a potential positive regulator of plant warm ambient temperature response but its underlying molecular mechanisms are largely unknown. Here, we show that LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes. We found that the presence of warm ambient temperature activates ethylene signaling through EIN2 and EIN3, leading to an interaction between LHP1 and accumulated EIN2-C to co-regulate a subset of LHP1-bound genes marked by H3K27me3 and H3K4me3 bivalency. Furthermore, we demonstrate that INO80 is recruited to bivalent genes by interacting with EIN2-C and EIN3, promoting H3K4me3 enrichment and facilitating transcriptional activation in response to warm ambient temperature. Together, our findings illustrate a novel mechanism wherein ethylene signaling orchestrates LHP1 and INO80 to regulate warm ambient temperature response through activating specific bivalent genes in Arabidopsis.

Update on stomata development and action under abiotic stress

Stomata, key gatekeepers of plant hydration, have long been known to play a pivotal role in mitigating the impacts of abiotic stressors. However, the complex molecular mechanisms underscoring this role remain unresolved fully and continue to be the subject of research. In the context of water-use efficiency (WUE), a key indicator of a plant's ability to conserve water, this aspect links intrinsically with stomatal behavior. Given the pivotal role of stomata in modulating water loss, it can be argued that the complex mechanisms governing stomatal development and function will significantly influence a plant's WUE under different abiotic stress conditions. Addressing these calls for a concerted effort to strengthen plant adaptability through advanced, targeted research. In this vein, recent studies have illuminated how specific stressors trigger alterations in gene expression, orchestrating changes in stomatal pattern, structure, and opening. This reveals a complex interplay between stress stimuli and regulatory sequences of essential genes implicated in stomatal development, such as MUTE, SPCH, and FAMA. This review synthesizes current discoveries on the molecular foundations of stomatal development and behavior in various stress conditions and their implications for WUE. It highlights the imperative for continued exploration, as understanding and leveraging these mechanisms guarantee enhanced plant resilience amid an ever-changing climatic landscape.

Recent advances in auxin biosynthesis and homeostasis

The plant proliferation is linked with auxins which in turn play a pivotal role in the rate of growth. Also, auxin concentrations could provide insights into the age, stress, and events leading to flowering and fruiting in the sessile plant kingdom. The role in rejuvenation and plasticity is now evidenced. Interest in plant auxins spans many decades, information from different plant families for auxin concentrations, transcriptional, and epigenetic evidences for gene regulation is evaluated here, for getting an insight into pattern of auxin biosynthesis. This biosynthesis takes place via an tryptophan-independent and tryptophan-dependent pathway. The independent pathway initiated before the tryptophan (trp) production involves indole as the primary substrate. On the other hand, the trp-dependent IAA pathway passes through the indole pyruvic acid (IPyA), indole-3-acetaldoxime (IAOx), and indole acetamide (IAM) pathways. Investigations on trp-dependent pathways involved mutants, namely yucca (1-11), taa1, nit1, cyp79b and cyp79b2, vt2 and crd, and independent mutants of tryptophan, ins are compiled here. The auxin conjugates of the IAA amide and ester-linked mutant gh3, iar, ilr, ill, iamt1, ugt, and dao are remarkable and could facilitate the assimilation of auxins. Efforts are made herein to provide an up-to-date detailed information about biosynthesis leading to plant sustenance. The vast information about auxin biosynthesis and homeostasis is consolidated in this review with a simplified model of auxin biosynthesis with keys and clues for important missing links since auxins can enable the plants to proliferate and override the environmental influence and needs to be probed for applications in sustainable agriculture.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-023-03709-6.

CsMYBL2 homologs modulate the light and temperature stress-regulated anthocyanin and catechins biosynthesis in tea plants (Camellia sinensis)

Anthocyanin and catechin production in tea (Camellia sinensis) leaves can positively affect tea quality; however, their regulatory mechanisms are not fully understood. Here we report that, while the CsMYB75- or CsMYB86-directed MYB-bHLH-WD40 (MBW) complexes differentially activate anthocyanin or catechin biosynthesis in tea leaves, respectively, CsMYBL2a and CsMYBL2b homologs negatively modified the light- and temperature-induced anthocyanin and catechin production in both Arabidopsis and tea plants. The MBW complexes activated both anthocyanin synthesis genes and the downstream repressor genes CsMYBL2a and CsMYBL2b. Overexpression of CsMYBL2b, but not CsMYBL2a, repressed Arabidopsis leaf anthocyanin accumulation and seed coat proanthocyanin production. CsMYBL2b strongly and CsMYBL2a weakly repressed the activating effects of CsMYB75/CsMYB86 on CsDFR and CsANS, due to their different EAR and TLLLFR domains and interactions with CsTT8/CsGL3, interfering with the functions of activating MBW complexes. CsMYBL2b and CsMYBL2a in tea leaves play different roles in fine-tuning CsMYB75/CsMYB86-MBW activation of biosynthesis of anthocyanins and catechins, respectively. The CsbZIP1-CsmiR858a-CsMYBL2 module mediated the UV-B- or cold-activated CsMYB75/CsMYB86 regulation of anthocyanin/catechin biosynthesis by repressing CsMYBL2a and CsMYBL2b. Similarly, the CsCOP1-CsbZIP1-CsPIF3 module, and BR signaling as well, mediated the high temperature repression of anthocyanin and catechin biosynthesis through differentially upregulating CsMYBL2b and CsMYBL2a, respectively. The present study provides new insights into the complex regulatory networks in environmental stress-modified flavonoid production in tea plant leaves.

Regulatory Mechanisms of Heat Stress Response and Thermomorphogenesis in Plants

As worldwide warming intensifies, the average temperature of the earth continues to increase. Temperature is a key factor for the growth and development of all organisms and governs the distribution and seasonal behavior of plants. High temperatures lead to various biochemical, physiological, and morphological changes in plants and threaten plant productivity. As sessile organisms, plants are subjected to various hostile environmental factors and forced to change their cellular state and morphological architecture to successfully deal with the damage they suffer. Therefore, plants have evolved multiple strategies to cope with an abnormal rise in temperature. There are two main mechanisms by which plants respond to elevated environmental temperatures. One is the heat stress response, which is activated under extremely high temperatures; the other is the thermomorphogenesis response, which is activated under moderately elevated temperatures, below the heat-stress range. In this review, we summarize recent progress in the study of these two important heat-responsive molecular regulatory pathways mediated, respectively, by the Heat Shock Transcription Factor (HSF)-Heat Shock Protein (HSP) pathway and PHYTOCHROME INTER-ACTING FACTOR 4 (PIF4) pathways in plants and elucidate the regulatory mechanisms of the genes involved in these pathways to provide comprehensive data for researchers studying the heat response. We also discuss future perspectives in this field.

Regulation Mechanism of Plant Pigments Biosynthesis: Anthocyanins, Carotenoids, and Betalains

Anthocyanins, carotenoids, and betalains are known as the three major pigments in the plant kingdom. Anthocyanins are flavonoids derived from the phenylpropanoid pathway. They undergo acylation and glycosylation in the cytoplasm to produce anthocyanin derivatives and deposits in the cytoplasm. Anthocyanin biosynthesis is regulated by the MBW (comprised by R2R3-MYB, basic helix-loop-helix (bHLH) and WD40) complex. Carotenoids are fat-soluble terpenoids whose synthetic genes also are regulated by the MBW complex. As precursors for the synthesis of hormones and nutrients, carotenoids are not only synthesized in plants, but also synthesized in some fungi and bacteria, and play an important role in photosynthesis. Betalains are special water-soluble pigments that exist only in Caryophyllaceae plants. Compared to anthocyanins and carotenoids, the synthesis and regulation mechanism of betalains is simpler, starting from tyrosine, and is only regulated by MYB (myeloblastosis). Recently, a considerable amount of novel information has been gathered on the regulation of plant pigment biosynthesis, specifically with respect to aspects. In this review, we summarize the knowledge and current gaps in our understanding with a view of highlighting opportunities for the development of pigment-rich plants.

Long-day photoperiod and cool temperature induce flowering in cassava: Expression of signaling genes

Cassava is a staple food crop in the tropics, and is of particular importance in Africa. Recent development of genomic selection technology have improved the speed of cassava breeding; however, cassava flower initiation and development remains a bottleneck. The objectives of the current studies were to elucidate the effect of photoperiod, temperature and their interactions on the time of flowering and flower development in controlled environments, and to use RNA-sequencing to identify transcriptome expression underlying these environmental responses. Compared to a normal tropical day-length of 12 h, increasing the photoperiod by 4 h or decreasing the air temperature from 34/31 to 22°/19°C (day/night) substantially hastened the time to flowering. For both photoperiod and temperature, the environment most favorable for flowering was opposite the one for storage root harvest index. There was a pronounced treatment interaction: at warm day-time temperatures, percent flowering was low, and photoperiod had little effect. In contrast, at cooler temperatures, percent flowering increased, and long-day (LD) photoperiod had a strong effect in hastening flowering. In response to temperature, many differentially expressed genes in the sugar, phase-change, and flowering-time-integrator pathways had expression/flowering patterns in the same direction as in Arabidopsis (positive or negative) even though the effect of temperature on flowering operates in the reverse direction in cassava compared to Arabidopsis. Three trehalose-6-phosphate-synthase-1 (TPS1) genes and four members of the SPL gene family had significantly increased expression at cool temperature, suggesting sugar signaling roles in flower induction. In response to LD photoperiod, regulatory genes were expressed as in Arabidopsis and other LD flowering plants. Several hormone-related genes were expressed in response to both photoperiod and temperature. In summary, these findings provide insight on photoperiod and temperature responses and underlying gene expression that may assist breeding programs to manipulate flowering for more rapid crop improvement.

MEDIATOR SUBUNIT17 integrates jasmonate and auxin signaling pathways to regulate thermomorphogenesis

Plant adjustment to environmental changes involves complex crosstalk between extrinsic and intrinsic cues. In the past two decades, extensive research has elucidated the key roles of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and the phytohormone auxin in thermomorphogenesis. In this study, we identified a previously unexplored role of jasmonate (JA) signaling components, the Mediator complex, and their integration with auxin signaling during thermomorphogenesis in Arabidopsis (Arabidopsis thaliana). Warm temperature induces expression of JA signaling genes including MYC2, but, surprisingly, this transcriptional activation is not JA dependent. Warm temperature also promotes accumulation of the JA signaling receptor CORONATINE INSENSITIVE1 (COI1) and degradation of the JA signaling repressor JASMONATE-ZIM-DOMAIN PROTEIN9, which probably leads to de-repression of MYC2, enabling it to contribute to the expression of MEDIATOR SUBUNIT17 (MED17). In response to warm temperature, MED17 occupies the promoters of thermosensory genes including PIF4, YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE19 (IAA19), and IAA29. Moreover, MED17 facilitates enrichment of H3K4me3 on the promoters of PIF4, YUC8, IAA19, and IAA29 genes. Interestingly, both occupancy of MED17 and enrichment of H3K4me3 on these thermomorphogenesis-related promoters are dependent on PIF4 (or PIFs). Altered accumulation of COI1 under warm temperature in the med17 mutant suggests the possibility of a feedback mechanism. Overall, this study reveals the role of the Mediator complex as an integrator of JA and auxin signaling pathways during thermomorphogenesis.

Expression profile, transcriptional and post-transcriptional regulation of genes involved in hydrogen sulphide metabolism connecting the balance between development and stress adaptation in plants: a data-mining bioinformatics approach

Recent research focused on novel aspects of sulphur and sulphur-containing molecules in fundamental plant processes has highlighted the importance of these compounds. Currently, the focus has shifted to the efficacy of hydrogen sulphide (H₂ S) as signalling compounds that regulate different development and stress mitigation in plants. Accordingly, we used an in silico approach to study the differential expression patterns of H₂ S metabolic genes at different growth/development stages and their tissue-specific expression patterns under a range of abiotic stresses. Moreover, to understand the multilevel regulation of genes involved in H₂ S metabolism, we performed computation-based promoter analysis, alternative splice variant analysis, prediction of putative miRNA targets and co-expression network analysis. Gene expression analysis suggests that H₂ S biosynthesis is highly influenced by developmental and stress stimuli. The functional annotation of promoter structures reveales a wide range of plant hormone and stress responsive cis-regulatory elements (CREs) that regulate H₂ S metabolism. Co-expression analysis suggested that genes involved in H₂ S metabolism are also associated with different metabolic processes. In this data-mining study, the primary focus was to understand the genetic architecture governing pathways of H₂ S metabolism in different cell compartments under various developmental and stress signalling cascades. The present study will help to understand the genetic architecture of H₂ S metabolism via cysteine metabolism and the functional roles of these genes in development and stress tolerance mechanisms.

Multilevel regulation of anthocyanin-promoting R2R3-MYB transcription factors in plants

Anthocyanins are common secondary metabolites in plants that confer red, blue, and purple colorations in plants and are highly desired by consumers for their visual appearance and nutritional quality. In the last two decades, the anthocyanin biosynthetic pathway and transcriptional regulation of anthocyanin biosynthetic genes (ABGs) have been well characterized in many plants. From numerous studies on model plants and horticultural crops, many signaling regulators have been found to control anthocyanin accumulation via regulation of anthocyanin-promoting R2R3-MYB transcription factors (so-called R2R3-MYB activators). The regulatory mechanism of R2R3-MYB activators is mediated by multiple environmental factors (e.g., light, temperature) and internal signals (e.g., sugar, ethylene, and JA) in complicated interactions at multiple levels. Here, we summarize the transcriptional control of R2R3-MYB activators as a result of natural variations in the promoter of their encoding genes, upstream transcription factors and epigenetics, and posttranslational modifications of R2R3-MYB that determine color variations of horticultural plants. In addition, we focus on progress in elucidating the integrated regulatory network of anthocyanin biosynthesis mediated by R2R3-MYB activators in response to multiple signals. We also highlight a few gene cascade modules involved in the regulation of anthocyanin-related R2R3-MYB to provide insights into anthocyanin production in horticultural plants.

PIF4: Integrator of light and temperature cues in plant growth

Plants are sessile and lack behavioural responses to avoid extreme environmental changes linked to annual seasons. For survival, they have evolved elaborate sensory systems coordinating their architecture and physiology with fluctuating diurnal and seasonal temperatures. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) was initially identified as a key component of the Arabidopsis thaliana phytochrome signalling pathway. It was then identified as playing a central role in promoting plant hypocotyl growth via the activation of auxin synthesis and signalling-related genes. Recent studies expanded its known regulatory functions to thermomorphogenesis and defined PIF4 as a central molecular hub for the integration of environmental light and temperature cues. The present review comprehensively summarizes recent progress in our understanding of PIF4 function in Arabidopsis thaliana, including PIF4-mediated photomorphogenesis and thermomorphogenesis, and the contribution of PIF4 to plant growth via the integration of environmental light and temperature cues. Remaining questions and possible directions for future research on PIF4 are also discussed.

Small RNAs: The Essential Regulators in Plant Thermotolerance

Small RNAs (sRNAs) are a class of non-coding RNAs that consist of 21-24 nucleotides. They have been extensively investigated as critical regulators in a variety of biological processes in plants. sRNAs include two major classes: microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis and functional pathways. Due to global warming, high-temperature stress has become one of the primary causes for crop loss worldwide. Recent studies have shown that sRNAs are involved in heat stress responses in plants and play essential roles in high-temperature acclimation. Genome-wide studies for heat-responsive sRNAs have been conducted in many plant species using high-throughput sequencing. The roles for these sRNAs in heat stress response were also unraveled subsequently in model plants and crops. Exploring how sRNAs regulate gene expression and their regulatory mechanisms will broaden our understanding of sRNAs in thermal stress responses of plant. Here, we highlight the roles of currently known miRNAs and siRNAs in heat stress responses and acclimation of plants. We also discuss the regulatory mechanisms of sRNAs and their targets that are responsive to heat stress, which will provide powerful molecular biological resources for engineering crops with improved thermotolerance.

Drought and High Temperature Stress in Sorghum: Physiological, Genetic, and Molecular Insights and Breeding Approaches

Sorghum is one of the staple crops for millions of people in Sub-Saharan Africa (SSA) and South Asia (SA). The future climate in these sorghum production regions is likely to have unexpected short or long episodes of drought and/or high temperature (HT), which can cause significant yield losses. Therefore, to achieve food and nutritional security, drought and HT stress tolerance ability in sorghum must be genetically improved. Drought tolerance mechanism, stay green, and grain yield under stress has been widely studied. However, novel traits associated with drought (restricted transpiration and root architecture) need to be explored and utilized in breeding. In sorghum, knowledge on the traits associated with HT tolerance is limited. Heat shock transcription factors, dehydrins, and genes associated with hormones such as auxin, ethylene, and abscisic acid and compatible solutes are involved in drought stress modulation. In contrast, our understanding of HT tolerance at the omic level is limited and needs attention. Breeding programs have exploited limited traits with narrow genetic and genomic resources to develop drought or heat tolerant lines. Reproductive stages of sorghum are relatively more sensitive to stress compared to vegetative stages. Therefore, breeding should incorporate appropriate pre-flowering and post-flowering tolerance in a broad genetic base population and in heterotic hybrid breeding pipelines. Currently, more than 240 QTLs are reported for drought tolerance-associated traits in sorghum prospecting discovery of trait markers. Identifying traits and better understanding of physiological and genetic mechanisms and quantification of genetic variability for these traits may enhance HT tolerance. Drought and HT tolerance can be improved by better understanding mechanisms associated with tolerance and screening large germplasm collections to identify tolerant lines and incorporation of those traits into elite breeding lines. Systems approaches help in identifying the best donors of tolerance to be incorporated in the SSA and SA sorghum breeding programs. Integrated breeding with use of high-throughput precision phenomics and genomics can deliver a range of drought and HT tolerant genotypes that can improve yield and resilience of sorghum under drought and HT stresses.

Crosstalk between Light- and Temperature-Mediated Processes under Cold and Heat Stress Conditions in Plants

Extreme temperatures are among the most important stressors limiting plant growth and development. Results indicate that light substantially influences the acclimation processes to both low and high temperatures, and it may affect the level of stress injury. The interaction between light and temperature in the regulation of stress acclimation mechanisms is complex, and both light intensity and spectral composition play an important role. Higher light intensities may lead to overexcitation of the photosynthetic electron transport chain; while different wavelengths may act through different photoreceptors. These may induce various stress signalling processes, leading to regulation of stomatal movement, antioxidant and osmoregulation capacities, hormonal actions, and other stress-related pathways. In recent years, we have significantly expanded our knowledge in both light and temperature sensing and signalling. The present review provides a synthesis of results for understanding how light influences the acclimation of plants to extreme low or high temperatures, including the sensing mechanisms and molecular crosstalk processes.

XBAT31 regulates thermoresponsive hypocotyl growth through mediating degradation of the thermosensor ELF3 in Arabidopsis

Elevated ambient temperature has wide effects on plant growth and development. ELF3, a proposed thermosensor, negatively regulates protein activity of the growth-promoting factor PIF4, and such an inhibitory effect is subjected to attenuation at warm temperature. However, how ELF3 stability is regulated at warm temperature remains enigmatic. Here, we report the identification of XBAT31 as the E3 ligase that mediates ELF3 degradation in response to warm temperature in Arabidopsis XBAT31 interacts with ELF3, ubiquitinates ELF3, and promotes ELF3 degradation via the 26S proteasome. Mutation of XBAT31 results in enhanced accumulation of ELF3 and reduced hypocotyl elongation at warm temperature. In contrast, overexpression of XBAT31 accelerates ELF3 degradation and promotes hypocotyl growth. Furthermore, XBAT31 interacts with the B-box protein BBX18, and the XBAT31-mediated ELF3 degradation is dependent on BBX18 Thus, our findings reveal that XBAT31-mediated destruction of ELF3 represents an additional regulatory layer of complexity in temperature signaling during plant thermomorphogenesis.

Metabolic control of histone demethylase activity involved in plant response to high temperature

Jumonji C (JmjC) domain proteins are histone lysine demethylases that require ferrous iron and alpha-ketoglutarate (or α-KG) as cofactors in the oxidative demethylation reaction. In plants, α-KG is produced by isocitrate dehydrogenases (ICDHs) in different metabolic pathways. It remains unclear whether fluctuation of α-KG levels affects JmjC demethylase activity and epigenetic regulation of plant gene expression. In this work, we studied the impact of loss of function of the cytosolic ICDH (cICDH) gene on the function of histone demethylases in Arabidopsis thaliana. Loss of cICDH resulted in increases of overall histone H3 lysine 4 trimethylation (H3K4me3) and enhanced mutation defects of the H3K4me3 demethylase gene JMJ14. Genetic analysis suggested that the cICDH mutation may affect the activity of other demethylases, including JMJ15 and JMJ18 that function redundantly with JMJ14 in the plant thermosensory response. Furthermore, we show that mutation of JMJ14 affected both the gene activation and repression programs of the plant thermosensory response and that JMJ14 and JMJ15 repressed a set of genes that are likely to play negative roles in the process. The results provide evidence that histone H3K4 demethylases are involved in the plant response to elevated ambient temperature.

Mapping and identification of CsSh5.1, a gene encoding a xyloglucan galactosyltransferase required for hypocotyl elongation in cucumber (Cucumis sativus L.)

CsSh5.1, which controls hypocotyl elongation under high temperature conditions in cucumber, was mapped to a 57.1 kb region on chromosome 5 containing a candidate gene encoding a xyloglucan galactosyltransferase. Hypocotyl growth is a vital process in seedling establishment. Hypocotyl elongation after germination relies more on longitudinal cell elongation than cell division. Cell elongation is largely determined by the extensibility of the cell wall. Here, we identified a spontaneous mutant in cucumber (Cucumis sativus L.), sh5.1, which exhibits a temperature-insensitive short hypocotyl phenotype. Genetic analysis showed that the phenotype of sh5.1 was controlled by a recessive nuclear gene. CsSh5.1 was mapped to a 57.1 kb interval on chromosome 5, containing eight predicted genes. Sequencing analysis revealed that the Csa5G171710 is the candidate gene of CsSh5.1, which was further confirmed via co-segregation analysis and genomic DNA sequencing in natural cucumber variations. The result indicated that hypocotyl elongation might be controlled by this gene. CsSh5.1 encodes a xyloglucan galactosyltransferase that specifically adds galactose to xyloglucan and forms galactosylated xyloglucans, which determine the strength and extensibility of the cell walls. CsSh5.1 expression in wild-type (WT) hypocotyl was significantly higher than that in sh5.1 hypocotyl under high temperature, suggesting its important role in hypocotyl cell elongation under high temperature. The identification of CsSh5.1 is helpful for elucidating the function of xyloglucan galactosyltransferase in cell wall expansion and understanding the mechanism of hypocotyl elongation in cucumber.

PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) negatively regulates anthocyanin accumulation by inhibiting PAP1 transcription in Arabidopsis seedlings

Anthocyanin accumulation is a striking symptom of plant environmental response and plays an important role in plant adaptation to adverse stimuli. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) is a member of the PIFs family that directly interacts with light-activated phytochromes, and it can not only regulate various light responses but also optimize growth as a key integrator of multiple signaling pathways. However, the mechanism by which PIF4 participates in the regulation of anthocyanin accumulation remains to be elucidated. In this study, we found that anthocyanin accumulation was effectively induced by white light in Arabidopsis Col-0, but such an effect was impaired in the overexpression line PIF4OX. Consistently, the transcript level of PAP1 that encodes a key transcript factor involved in regulating anthocyanin biosynthesis was significantly decreased in PIF4OX compared with Col-0. Moreover, the expression of PAP1 was markedly lower in pap1-D/PIF4OX than pap1-D, as a result, the phenotype that highly accumulates anthocyanins in leaves of pap1-D caused by PAP1 overexpressing was almost eliminated in pap1-D/PIF4OX. Analyses through chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and electrophoretic mobility shift assay (EMSA) revealed that PIF4 could directly bind to the G-box motif present in the promoter of PAP1. Furthermore, transient transcriptional expression analysis showed that PIF4 could weaken the transcriptional activity of the PAP1 promoter, and the G-box motif is necessary for the effect of PIF4. Subsequently, when the seedlings shifted from darkness to light and grew under constant red light and short-day photoperiod, it was found that the PAP1 transcription level and anthocyanin content in pif4-2/pap1-D were significantly higher than pap1-D, implying that PIF4 mutation can strengthen PAP1's effect on anthocyanin biosynthesis under these conditions. Taken together, the results indicate that PIF4 negatively regulates anthocyanin accumulation in Arabidopsis through transcriptional suppression of PAP1 by directly binding to the G-box motif of the promoter.

Phosphoproteomic Analysis of Thermomorphogenic Responses in Arabidopsis

Plants rapidly adapt to elevated ambient temperature by adjusting their growth and developmental programs. To date, a number of experiments have been carried out to understand how plants sense and respond to warm temperatures. However, how warm temperature signals are relayed from thermosensors to transcriptional regulators is largely unknown. To identify new early regulators of plant thermo-responsiveness, we performed phosphoproteomic analysis using TMT (Tandem Mass Tags) labeling and phosphopeptide enrichment with Arabidopsis etiolated seedlings treated with or without 3h of warm temperatures (29°C). In total, we identified 13,160 phosphopeptides in 5,125 proteins with 10,700 quantifiable phosphorylation sites. Among them, 200 sites (180 proteins) were upregulated, while 120 sites (87 proteins) were downregulated by elevated temperature. GO (Gene Ontology) analysis indicated that phosphorelay-related molecular function was enriched among the differentially phosphorylated proteins. We selected ATL6 (ARABIDOPSIS TOXICOS EN LEVADURA 6) from them and expressed its native and phosphorylation-site mutated (S343A S357A) forms in Arabidopsis and found that the mutated form of ATL6 was less stable than that of the native form both in vivo and in cell-free degradation assays. Taken together, our data revealed extensive protein phosphorylation during thermo-responsiveness, providing new candidate proteins/genes for studying plant thermomorphogenesis in the future.

Hydrogen sulfide (H2S) signaling in plant development and stress responses

ABSTRACT

Hydrogen sulfide (H₂S) was initially recognized as a toxic gas and its biological functions in mammalian cells have been gradually discovered during the past decades. In the latest decade, numerous studies have revealed that H₂S has versatile functions in plants as well. In this review, we summarize H₂S-mediated sulfur metabolic pathways, as well as the progress in the recognition of its biological functions in plant growth and development, particularly its physiological functions in biotic and abiotic stress responses. Besides direct chemical reactions, nitric oxide (NO) and hydrogen peroxide (H₂O₂) have complex relationships with H₂S in plant signaling, both of which mediate protein post-translational modification (PTM) to attack the cysteine residues. We also discuss recent progress in the research on the three types of PTMs and their biological functions in plants. Finally, we propose the relevant issues that need to be addressed in the future research.

GRAPHIC ABSTRACT

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s42994-021-00035-4.

Characterization of novel regulators for heat stress tolerance in tomato from Indian sub-continent

The footprint of tomato cultivation, a cool region crop that exhibits heat stress (HS) sensitivity, is increasing in the tropics/sub-tropics. Knowledge of novel regulatory hot spots from varieties growing in the Indian sub-continent climatic zones could be vital for developing HS-resilient crops. Comparative transcriptome-wide signatures of a tolerant (CLN1621L) and sensitive (CA4) cultivar pair shortlisted from a pool of varieties exhibiting variable thermo-sensitivity using physiological-, survival- and yield-related traits revealed redundant to cultivar-specific HS regulation. The antagonistically expressing genes encode enzymes and proteins that have roles in plant defence and abiotic stresses. Functional characterization of three antagonistic genes by overexpression and silencing established Solyc09g014280 (Acylsugar acyltransferase) and Solyc07g056570 (Notabilis) that are up-regulated in tolerant cultivar, as positive regulators of HS tolerance and Solyc03g020030 (Pin-II proteinase inhibitor), that are down-regulated in CLN1621L, as negative regulator of thermotolerance. Transcriptional assessment of promoters of these genes by SNPs in stress-responsive cis-elements and promoter swapping experiments in opposite cultivar background showed inherent cultivar-specific orchestration of transcription factors in regulating transcription. Moreover, overexpression of three ethylene response transcription factors (ERF.C1/F4/F5) also improved HS tolerance in tomato. This study identifies several novel HS tolerance genes and provides proof of their utility in tomato thermotolerance.

Glycosyltransferase UGT76F1 is involved in the temperature-mediated petiole elongation and the BR-mediated hypocotyl growth in Arabidopsis

The signaling network formed by external environmental signals and endogenous hormone signals is an important basis for the adaptive growth of plants. We recently identified a UDP-glucosyltransferase gene, UGT76F1, which controls the glucosylation of auxin precursor IPyA and mediates light-temperature signaling to regulate auxin-dependent hypocotyl elongation in Arabidopsis. However, it is unclear whether UGT76F1 is involved in the adaptive growth of other tissues and whether it is related to the signaling of other hormones besides auxin. Here we investigated the petiole elongation of UGT76F1 overexpression lines and knockout mutant lines, and also studied the effects of UGT76F1 on BR signaling. Experimental results indicated that UGT76F1 is involved in the PIF4-mediated petiole growth under high temperature and that UGT76F1 is also related to the BR signaling in controlling hypocotyl growth. These results suggest that UGT76F1 may have a wider significance in the plant adaptations to surrounding environments.

The cold response regulator CBF1 promotes Arabidopsis hypocotyl growth at ambient temperatures

Light and temperature are two core environmental factors that coordinately regulate plant growth and survival throughout their entire life cycle. However, the mechanisms integrating light and temperature signaling pathways in plants remain poorly understood. Here, we report that CBF1, an AP2/ERF-family transcription factor essential for plant cold acclimation, promotes hypocotyl growth under ambient temperatures in Arabidopsis. We show that CBF1 increases the protein abundance of PIF4 and PIF5, two phytochrome-interacting bHLH-family transcription factors that play pivotal roles in modulating plant growth and development, by directly binding to their promoters to induce their gene expression, and by inhibiting their interaction with phyB in the light. Moreover, our data demonstrate that CBF1 promotes PIF4/PIF5 protein accumulation and hypocotyl growth at both 22°C and 17°C, but not at 4°C, with a more prominent role at 17°C than at 22°C. Together, our study reveals that CBF1 integrates light and temperature control of hypocotyl growth by promoting PIF4 and PIF5 protein abundance in the light, thus providing insights into the integration mechanisms of light and temperature signaling pathways in plants.

WRKY33-PIF4 loop is required for the regulation of H2O2 homeostasis

The reactive oxygen species (ROS) are continuously produced and are essential for mediating the growth and development of plants. However too much accumulation of ROS can result in the oxidative damage to cells, especially under the adverse environmental conditions. Plants have evolved sophisticated strategies to regulate the homeostasis of H₂O₂. In this study, we generated transgenic Arabidopsis plants in the Ws ecotype (Ws) background in which WRKY33 is co-suppressed (csWRKY33/Ws). Compared with Ws, csWRKY33/Ws plants accumulate more H₂O₂. RNA-seq analysis indicated that in csWRKY33/Ws plants, expression of oxidative stress related genes such as ascorbate peroxidase 2 (APX2) is affected. Over-expression of APX2 can rescue the phenotype of csWRKY33/Ws, suggesting that the changes in the growth of csWRKY33/Ws is duo to the higher accumulation of H₂O₂. Analysis of the CHIP-seq data suggested that WRKY33 can directly regulate the expression of PIF4, vice versa. qPCR analysis also confirmed that the mutual regulation between WRKY33 and PIF4. Similar to that of csWRKY33/Ws, and the accumulation of H₂O₂ in pif4 also increased. Taken together, our results reveal a WRKY33-PIF4 regulatory loop that appears to play an important role in regulating the growth and development of seedlings by mediating H₂O₂ homeostasis.

Mutation of DELAYED GREENING1 impairs chloroplast RNA editing at elevated ambient temperature in Arabidopsis

Chloroplasts are important for plant growth and development. RNA editing in chloroplast converts cytidines (Cs) to uridines (Us) at specific transcript positions and provides a correction mechanism to restore conserved codons or creates start or stop codons. However, the underlined molecular mechanism is not yet fully understood. In the present study, we identified a thermo-sensitive mutant in leaf color 1 (tsl1) and found that TSL1 is allelic to DELAYED GREENING 1 (DG1). The missense mutation of DG1 in tsl1 mutant confers a high temperature sensitivity and impaired chloroplast development at an elevated ambient temperature in Arabidopsis. Subsequent analysis showed that chloroplast RNA editing at several sites including accD-1568, ndhD-2, and petL-5 is impaired in tsl1 mutant plants grown at an elevated temperature. DG1 interacts with MORF2 and other proteins such as DYW1 and DYW2 involved in chloroplast RNA editing. In vitro RNA electrophoretic mobility shift assay demonstrated that DG1 binds to RNA targets such as accD, ndhD, and petL. Thus, our results revealed that DG1 is important for maintaining chloroplast mRNA editing in Arabidopsis.

Transgenic Breeding Approaches for Improving Abiotic Stress Tolerance: Recent Progress and Future Perspectives

The recent rapid climate changes and increasing global population have led to an increased incidence of abiotic stress and decreased crop productivity. Environmental stresses, such as temperature, drought, nutrient deficiency, salinity, and heavy metal stresses, are major challenges for agriculture, and they lead to a significant reduction in crop growth and productivity. Abiotic stress is a very complex phenomenon, involving a variety of physiological and biochemical changes in plant cells. Plants exposed to abiotic stress exhibit enhanced levels of ROS (reactive oxygen species), which are highly reactive and toxic and affect the biosynthesis of chlorophyll, photosynthetic capacity, and carbohydrate, protein, lipid, and antioxidant enzyme activities. Transgenic breeding offers a suitable alternative to conventional breeding to achieve plant genetic improvements. Over the last two decades, genetic engineering/transgenic breeding techniques demonstrated remarkable developments in manipulations of the genes for the induction of desired characteristics into transgenic plants. Transgenic approaches provide us with access to identify the candidate genes, miRNAs, and transcription factors (TFs) that are involved in specific plant processes, thus enabling an integrated knowledge of the molecular and physiological mechanisms influencing the plant tolerance and productivity. The accuracy and precision of this phenomenon assures great success in the future of plant improvements. Hence, transgenic breeding has proven to be a promising tool for abiotic stress improvement in crops. This review focuses on the potential and successful applications, recent progress, and future perspectives of transgenic breeding for improving abiotic stress tolerance and productivity in plants.

IPyA glucosylation mediates light and temperature signaling to regulate auxin-dependent hypocotyl elongation in Arabidopsis

Auxin is a class of plant hormone that plays a crucial role in the life cycle of plants, particularly in the growth response of plants to ever-changing environments. Since the auxin responses are concentration-dependent and higher auxin concentrations might often be inhibitory, the optimal endogenous auxin level must be closely controlled. However, the underlying mechanism governing auxin homeostasis remains largely unknown. In this study, a UDP-glycosyltransferase (UGT76F1) was identified from Arabidopsis thaliana, which participates in the regulation of auxin homeostasis by glucosylation of indole-3-pyruvic acid (IPyA), a major precursor of the auxin indole-3-acetic acid (IAA) biosynthesis, in the formation of IPyA glucose conjugates (IPyA-Glc). In addition, UGT76F1 was found to mediate hypocotyl growth by modulating active auxin levels in a light- and temperature-dependent manner. Moreover, the transcription of UGT76F1 was demonstrated to be directly and negatively regulated by PIF4, which is a key integrator of both light and temperature signaling pathways. This study sheds a light on the trade-off between IAA biosynthesis and IPyA-Glc formation in controlling auxin levels and reveals a regulatory mechanism for plant growth adaptation to environmental changes through glucosylation of IPyA.

Difference Between Day and Night Temperatures Affects Stem Elongation in Tomato (Solanum lycopersicum) Seedlings via Regulation of Gibberellin and Auxin Synthesis

Temperature is a critical environmental factor governing plant growth and development. The difference between day temperature (DT) and night temperature (NT), abbreviated as DIF, influences plant architecture. Subjecting plants to artificial DIF treatments is an effective strategy in ornamental horticulture. For example, negative DIF (when DT - NT < 0) generally inhibits stem elongation, resulting in dwarf plants. However, the mechanisms underlying stem growth regulation by DIF remains to be completely elucidated. In this study, we aimed to analyze the growth, transcriptome, and phytohormone profiles of tomato (Solanum lycopersicum) seedlings grown under different DIF treatments. Under positive DIF (when DT - NT > 0), in contrast to the control temperature (25°C/20°C, DT/NT), high temperature (30°C/25°C) increased stem length and thickness, as well as the number of xylem vessels. Conversely, compared with the positive high temperature DIF treatment (30°C/25°C), under negative DIF treatment (25°C/30°C) stem elongation was inhibited, but stem thickness and the number of xylem vessels were not affected. The negative DIF treatment decreased the expression of gibberellin (GA)-, auxin-, and cell wall-related genes in the epicotyl, as well as the concentrations of GAs and indole-3-acetic acid (IAA). The expression of these genes and concentrations of these hormones increased under high temperature compared to those under the control temperature positive DIF. Our results suggest that stem length in tomato seedlings is controlled by changes in GA and IAA biosynthesis in response to varying day and night temperatures.

Arabidopsis histone deacetylase HDA15 directly represses plant response to elevated ambient temperature

Elevated ambient temperatures affect plant growth and substantially impact biomass and crop yield. Recent results have indicated that chromatin remodelling is critical in plant thermal responses but how histone modification dynamics affects plant thermal response has not been clearly demonstarted. Here we show that Arabidopsis histone deacetylase genes HDA9, HDA15 and HDA19 play distinct roles in plant response to elevated ambient temperature. hda9 and hda19 mutants showed a warm-temperature-insensitive phenotype at 27°C, whereas hda15 plants displayed a constitutive warm-temperature-induced phenotype at 20°C and an enhanced thermal response at 27°C. The hda19 mutation led to upregulation of genes mostly related to stress response at both 20 and 27°C. The hda15 mutation resulted in upregulation of many warm temperature-responsive as well as metabolic genes at 20 and 27°C, while hda9 led to differential expression of a large number of genes at 20°C and impaired induction of warm-temperature-responsive genes at 27°C. HDA15 is associated with thermosensory mark genes at 20°C and that the association is decreased after shifting to 27°C, indicating that HDA15 is a direct repressor of plant thermal-responsive genes at normal temperature. In addition, as hda9, the hda15 mutation also led to upregulation of many metabolic genes and accumulation of primary metabolites. Furthermore, we show that HDA15 interacts with the transcription factor HFR1 (long Hypocotyl in Far Red1) to cooperatively repress warm-temperature response. Our study demonstrates that the histone deacetylases target to different sets of genes and play distinct roles in plant response to elevated ambient temperature.

Natural variations of growth thermo-responsiveness determined by SAUR26/27/28 proteins in Arabidopsis thaliana

How diversity in growth thermo-responsiveness is generated for local adaptation is a long-standing biological question. We investigated molecular genetic basis of natural variations in thermo-responsiveness of plant architecture in Arabidopsis thaliana. We measured the extent of rosette architecture at 22°C and 28°C in a set of 69 natural accessions and determined their thermo-responsiveness of plant architecture. A genome-wide association study was performed to identify major loci for variations in thermo-responsiveness. The SAUR26 subfamily, a new subfamily of SAUR genes, was identified as a major locus for the thermo-responsive architecture variations. The expression of SAUR26/27/28 is modulated by temperature and PIF4. Extensive natural polymorphisms in these genes affect their RNA expression levels and protein activities and influence the thermo-responsiveness of plant architecture. In addition, the SAUR26 subfamily genes exhibit a high variation frequency and their variations are associated with the local temperature climate. This study reveals that the SAUR26 subfamily is a key variation for thermo-responsive architecture and suggests a preference for generating diversity for local adaptation through signaling connectors.

Identification of flowering-time genes in mast flowering plants using De Novo transcriptomic analysis

Mast flowering is synchronised highly variable flowering by a population of perennial plants over a wide geographical area. High seeding years are seen as a threat to native and endangered species due to high predator density caused by the abundance of seed. An understanding of the molecular pathways that influence masting behaviour in plants could provide better prediction of a forthcoming masting season and enable conservation strategies to be deployed. The goal of this study was to identify candidate flowering genes that might be involved in regulating mast flowering. To achieve this, high-throughput large-scale RNA-sequencing was performed on two masting plant species, Celmisia lyallii (Asteraceae), and Chionochloa pallens (Poaceae) to develop a reference transcriptome for functional and molecular analysis. An average total of 33 million 150 base-paired reads, for both species, were assembled using the Trinity pipeline, resulting in 151,803 and 348,649 transcripts respectively for C. lyallii and C. pallens. For both species, about 56% of the unigenes were annotated with gene descriptions to known proteins followed by Gene Ontology analysis, categorising them on the basis of putative biological processes, molecular function, and cellular localization. A total of 543 transcripts from C. lyallii and 470 transcripts from C. pallens were also mapped to unique flowering-time proteins identified in Arabidopsis thaliana, suggesting the conservation of the flowering network in these wild alpine plants growing in natural field conditions. Expression analysis of several selected homologous flowering-pathway genes showed seasonal and photoperiodic variations. These genes can further be analysed to understand why seasonal cues, such as the increasing photoperiod in spring, that triggers the annual flowering of most plants, are insufficient to always trigger flowering in masting plants and to uncover the molecular basis of how additional cues (such as temperature during the previous growing seasons) then determines flowering in mast years.

Class I TCP Transcription Factors Target the Gibberellin Biosynthesis Gene GA20ox1 and the Growth-Promoting Genes HBI1 and PRE6 during Thermomorphogenic Growth in Arabidopsis

Plants respond to a rise in ambient temperature by increasing the growth of petioles and hypocotyls. In this work, we show that Arabidopsis thaliana class I TEOSINTE BRANCHED 1, CYCLOIDEA, PCF (TCP) transcription factors TCP14 and TCP15 are required for optimal petiole and hypocotyl elongation under high ambient temperature. These TCPs influence the levels of the DELLA protein RGA and the expression of growth-related genes, which are induced in response to an increase in temperature. However, the class I TCPs are not required for the induction of the auxin biosynthesis gene YUCCA8 or for auxin-dependent gene expression responses. TCP15 directly targets the gibberellin biosynthesis gene GA20ox1 and the growth regulatory genes HBI1 and PRE6. Several of the genes regulated by TCP15 are also targets of the growth regulator PIF4 and show an enrichment of PIF4- and TCP-binding motifs in their promoters. PIF4 binding to GA20ox1 and HBI1 is enhanced in the presence of the TCPs, indicating that TCP14 and TCP15 directly participate in the induction of genes involved in gibberellin biosynthesis and cell expansion by high temperature functionally interacting with PIF4. In addition, overexpression of HBI1 rescues the growth defects of tcp14 tcp15 double mutants, suggesting that this gene is a major outcome of regulation by both class I TCPs during thermomorphogenesis.

Auxin and Cell Wall Crosstalk as Revealed by the Arabidopsis thaliana Cellulose Synthase Mutant Radially Swollen 1

Plant cells sheath themselves in a complex lattice of polysaccharides, proteins and enzymes forming an integral matrix known as the cell wall. Cellulose microfibrils, the primary component of cell walls, are synthesized at the plasma membrane by CELLULOSE SYNTHASE A (CESA) proteins throughout cellular growth and are responsible for turgor-driven anisotropic expansion. Associations between hormone signaling and cell wall biosynthesis have long been suggested, but recently direct links have been found revealing hormones play key regulatory roles in cellulose biosynthesis. The radially swollen 1 (rsw1) allele of Arabidopsis thaliana CESA1 harbors a single amino acid change that renders the protein unstable at high temperatures. We used the conditional nature of rsw1 to investigate how auxin contributes to isotropic growth. We found that exogenous auxin treatment reduces isotropic swelling in rsw1 roots at the restrictive temperature of 30�C. We also discovered decreases in auxin influx between rsw1 and wild-type roots via confocal imaging of AUX1-YFP, even at the permissive temperature of 19�C. Moreover, rsw1 displayed mis-expression of auxin-responsive and CESA genes. Additionally, we found altered auxin maxima in rsw1 mutant roots at the onset of swelling using DII-VENUS and DR5:vYFP auxin reporters. Overall, we conclude disrupted cell wall biosynthesis perturbs auxin transport leading to altered auxin homeostasis impacting both anisotropic and isotropic growth that affects overall root morphology.

Overexpression of OsPIL1 enhanced biomass yield and saccharification efficiency in switchgrass

Switchgrass (Panicum virgatum L.) is a herbaceous cellulosic biofuel plant with broad adaptability. However, the intrinsic recalcitrance of biomass and limited land for switchgrass planting hinder its utilization as feedstock for biofuel ethanol production. The OsPIL1 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 1) gene encodes a basic helix-loop-helix transcription factor. Its expression is induced by light, which facilitated the expression of cell wall-related genes, promoted cell elongation and resulted in longer internode in rice. Here, we introduced the OsPIL1 gene into switchgrass by Agrobacterium-mediated transformation with the aim of improving biomass yield of transgenic switchgrass plants. The transgenic plants were verified by PCR, Southern-blotting, RT-PCR and qRT-PCR tests, respectively. The transgenic plants overexpression of OsPIL1 showed increased plant height and biomass yield. Microscopy analysis showed that the length of epidermal cells of transgenic plants was longer than that of wild type. OsPIL1 overexpressed transgenic switchgrass plants also released more soluble sugar after enzymatic hydrolysis, indicating improved saccharification efficiency. The results suggest OsPIL1 can be used as a useful molecular tool in improving plant biomass and saccharification efficiency with the purpose of plant fiber biofuel ethanol production.

Unraveling Field Crops Sensitivity to Heat Stress：Mechanisms, Approaches, and Future Prospects

The astonishing increase in temperature presents an alarming threat to crop production worldwide. As evident by huge yield decline in various crops, the escalating drastic impacts of heat stress (HS) are putting global food production as well as nutritional security at high risk. HS is a major abiotic stress that influences plant morphology, physiology, reproduction, and productivity worldwide. The physiological and molecular responses to HS are dynamic research areas, and molecular techniques are being adopted for producing heat tolerant crop plants. In this article, we reviewed recent findings, impacts, adoption, and tolerance at the cellular, organellar, and whole plant level and reported several approaches that are used to improve HS tolerance in crop plants. Omics approaches unravel various mechanisms underlying thermotolerance, which is imperative to understand the processes of molecular responses toward HS. Our review about physiological and molecular mechanisms may enlighten ways to develop thermo-tolerant cultivars and to produce crop plants that are agriculturally important in adverse climatic conditions.

SEUSS and PIF4 Coordinately Regulate Light and Temperature Signaling Pathways to Control Plant Growth

Plants continuously monitor environmental conditions (such as light and temperature) and adjust their growth and development accordingly. The transcription factor PHYTOCHROME-INTERACTING FACTOR4 (PIF4) regulates both light and temperature signaling pathways. Here, we identified ENHANCED PHOTOMORPHOGENIC2 (EPP2) as a new repressor of photomorphogenesis in red, far-red, and blue light. Map-based cloning revealed that EPP2 encodes the SEUSS (SEU) transcription regulator. The C terminus of SEU has transcriptional activation activity, and SEU physically interacts with PIF4. Moreover, SEU promotes the expression of many genes, including auxin biosynthetic and responsive genes, and regulates IAA levels in plants. SEU associates with the regulatory regions of INDOLE-3-ACETIC ACID INDUCIBLE6 (IAA6) and IAA19 in a PIF4-independent manner, whereas the binding of PIF4 to these genes requires SEU. Furthermore, mutations in SEU affect H3K4me3 methylation at IAA6 and IAA19, and SEU positively regulates warm temperature-mediated hypocotyl growth together with PIF4. Collectively, our results reveal that SEU acts as a central regulator integrating light and temperature signals to control plant growth by coordinating with PIF4.

Genome-Wide Identification and Characterization of Warming-Related Genes in Brassica rapa ssp. pekinensis

For sustainable crop cultivation in the face of global warming, it is important to unravel the genetic mechanisms underlying plant adaptation to a warming climate and apply this information to breeding. Thermomorphogenesis and ambient temperature signaling pathways have been well studied in model plants, but little information is available for vegetable crops. Here, we investigated genes responsive to warming conditions from two Brassica rapa inbred lines with different geographic origins: subtropical (Kenshin) and temperate (Chiifu). Genes in Gene Ontology categories “response to heat”, “heat acclimation”, “response to light intensity”, “response to oxidative stress”, and “response to temperature stimulus” were upregulated under warming treatment in both lines, but genes involved in “response to auxin stimulus” were upregulated only in Kenshin under both warming and minor-warming conditions. We identified 16 putative high temperature (HT) adaptation-related genes, including 10 heat-shock response genes, 2 transcription factor genes, 1 splicing factor gene, and 3 others. BrPIF4, BrROF2, and BrMPSR1 are candidate genes that might function in HT adaptation. Auxin response, alternative splicing of BrHSFA2, and heat shock memory appear to be indispensable for HT adaptation in B. rapa. These results lay the foundation for molecular breeding and marker development to improve warming tolerance in B. rapa.

Essential Roles of Local Auxin Biosynthesis in Plant Development and in Adaptation to Environmental Changes

It has been a dominant dogma in plant biology that the self-organizing polar auxin transport system is necessary and sufficient to generate auxin maxima and minima that are essential for almost all aspects of plant growth and development. However, in the past few years, it has become clear that local auxin biosynthesis is required for a suite of developmental processes, including embryogenesis, endosperm development, root development, and floral initiation and patterning. Moreover, it was discovered that local auxin biosynthesis maintains optimal plant growth in response to environmental signals, including light, temperature, pathogens, and toxic metals. In this article, I discuss the recent progress in auxin biosynthesis research and the paradigm shift in recognizing the important roles of local auxin biosynthesis in plant biology.

POWERDRESS-mediated histone deacetylation is essential for thermomorphogenesis in Arabidopsis thaliana

Ambient temperature affects plant growth and even minor changes can substantially impact crop yields. The underlying mechanisms of temperature perception and response are just beginning to emerge. Chromatin remodeling, via the eviction of the histone variant H2A.Z containing nucleosomes, is a critical component of thermal response in plants. However, the role of histone modifications remains unknown. Here, through a forward genetic screen, we identify POWERDRESS (PWR), a SANT-domain containing protein known to interact with HISTONE DEACETYLASE 9 (HDA9), as a novel factor required for thermomorphogenesis in Arabidopsis thaliana. We show that mutations in PWR impede thermomorphogenesis, exemplified by attenuated warm temperature-induced hypocotyl/petiole elongation and early flowering. We show that inhibitors of histone deacetylases diminish temperature-induced hypocotyl elongation, which demonstrates a requirement for histone deacetylation in thermomorphogenesis. We also show that elevated temperature is associated with deacetylation of H3K9 at the +1 nucleosomes of PHYTOCHROME INTERACTING FACTOR4 (PIF4) and YUCCA8 (YUC8), and that PWR is required for this response. There is global misregulation of genes in pwr mutants at elevated temperatures. Meta-analysis revealed that genes that are misregulated in pwr mutants display a significant overlap with genes that are H2A.Z-enriched in their gene bodies, and with genes that are differentially expressed in mutants of the components of the SWR1 complex that deposits H2A.Z. Our findings thus uncover a role for PWR in facilitating thermomorphogenesis and suggest a potential link between histone deacetylation and H2A.Z nucleosome dynamics in plants.

Plant growth and development is influenced by a variety of external environmental cues. Ambient temperature affects almost all stages of plant development but the underlying molecular mechanisms remain largely unknown. In this paper, the authors show that histone deacetylation, an important chromatin remodeling processes, is essential for eliciting warm temperature-induced growth responses in plants; a process called thermomorphogenesis. The authors identify POWERDRESS, a protein known to interact with HISTONE DEACETYLASE 9, as a novel player essential for thermomorphogenesis in Arabidopsis. Another chromatin remodeling mechanism that is known to play a role in thermal response is the eviction of histone variant H2A.Z containing nucleosomes. Through transcriptome studies and meta-analysis, the authors demonstrate statistical associations between gene regulations conferred through PWR-mediated histone H3 deacetylation and those conferred by histone H2A.Z eviction/incorporation dynamics. This study identifies a novel gene that is essential for thermomorphogenesis and points to a possible link between two seemingly distinct chromatin-remodeling processes in regulating gene expression in plants.