A pervasive phosphorylation cascade modulation of plant transcription factors in response to abiotic stress

Integrative physiological and transcriptomic analysis provides insights on the molecular basis of ABA-enhanced drought tolerance in pear (Pyrus betulaefolia)

BACKGROUND

Drought stress could suppress the carbon assimilation and limit nutrient uptake of pear plants, thus affecting their growth and severely impacting the quality and yield of pear fruit. ABA is a stress hormone and is reported to alleviate drought stress in numerous plants. However, whether and how ABA functions in the drought responses of pear plants is yet explored.

RESULTS

Here, to address this gap, pear seedlings (Pyrus betulaefolia) were used and subjected to PEG-induced drought conditions with or without additional ABA in various doses. The results showed that while drought caused severe leaf water loss and damage, applying ABA at 50 µM and 100 µM dramatically amended the phenomenon, as indicated by the markedly increased relative water content, and notably decreased relative electrolyte leakage and malondialdehyde content. Based on the results of RNA sequencing and related physiological indices, it was found that drought grossly disrupted chlorophyll synthesis and photosynthesis. It induced the over-production of reactive oxygen species (ROS) and broke the ROS homeostasis, despite the pronounced increases in ABA biosynthesis/content and signaling, flavonoid synthesis, and antioxidant enzyme activities, as well as sugar metabolism. However, ABA applications significantly elevated the expressions of genes in chlorophyll synthesis and photosynthesis, partially boosting the SPAD and Fv/Fm values. In addition, ABA treatments further prominently accelerate the synthesis processes of ABA, flavonoids, and antioxidant enzymes by up-regulating the corresponding genes, resulting in endogenous ABA accumulation and enzymatic activity improvement, thereby expediting the ROS scavenging. Of course, the sugar metabolism pathway was also outstandingly enhanced to balance the growth and stress response of pear seedlings. Moreover, through WGCNA analysis, the core turquoise module associated with ABA-attenuated drought stress was identified, and a portion of key transcription factors (TFs) and some hub genes were characterized, particularly for ERF, WRKY, MYB, bHLH, NAC in TFs, and CSP, COR, and DHN in hub genes. Overall, our study reveals that exogenous ABA could help pear plants to efficiently scavenge drought-induced ROS by improving their photosynthesis capacity, ABA accumulation, sugar catabolism, enzymatic antioxidant system, etc. These results will provide a scientific basis and practical direction for utilizing ABA to mitigate the adverse effects of water starvation resulting from the persistent high temperature on pear plants in summer.

CONCLUSION

50 µM and 100 µM ABA application ameliorated the drought damage in pear seedlings, and the working routes are associated with reinforcement in the photosystem, ABA biosynthesis and signaling, flavonoid accumulation, and sugar metabolism, as well as enzymatic activities in ROS scavenging. The relevant regulatory network is complex, primarily concerned with ERF, WRKY, MYB, bHLH, and NAC TFs, with a focus on the potential target genes named CSP, COR, and DHN.

NAC transcription factors as biological macromolecules responded to abiotic stress: A comprehensive review

NAC transcription factors (NAC TFs) represent a large and vital family of transcription factors in the plant kingdom, playing a central role in regulating plant growth, developmental processes, and responses to abiotic stresses. As key regulators, NAC TFs fine-tune the expression of downstream genes, thereby actively contributing to the adaptation of crops to various abiotic stresses. The functions of NAC TFs are controlled by several complex signaling pathways, including those involving phytohormones (such as abscisic acid (ABA) and ethylene (ET)), reactive oxygen species (ROS), and mitogen-activated protein kinases (MAPKs). This review highlights recent advances in the biological functions and signaling pathways of NAC TFs in crops under abiotic stress conditions, such as drought, salinity, and extreme temperatures. It also offers prospects for further exploration of the complex mechanisms by which NAC TFs operate within signaling networks, with the aim of developing food crops with enhanced physiological traits.

Genome-Wide Identification and Expression Profiling of the SPL Transcription Factor Family in Response to Abiotic Stress in Centipedegrass

SQUAMOSA promoter-binding protein-like (SPL) transcription factors play a critical role in the regulation of gene expression and are indispensable in orchestrating plant growth and development while also improving resistance to environmental stressors. Although it has been identified across a wide array of plant species, there have been no comprehensive studies on the SPL gene family in centipedegrass [Eremochloa ophiuroides (Munro) Hack.], which is an important warm-season perennial C4 turfgrass. In this study, 19 potential EoSPL genes in centipedegrass were identified and assigned the names EoSPL1-EoSPL19. Gene structure and motif analysis demonstrated that there was relative consistency among the branches of the phylogenetic tree. Five pairs of segmental duplication events were detected within centipedegrass. Ten EoSPL genes were predicted to be targeted by miR156. Additionally, the EoSPL genes were found to be predominantly expressed in leaves and demonstrated diverse responses to abiotic stress (salt, drought, glufosinate ammonium, aluminum, and cold). This study offers a comprehensive insight into the SPL gene family in centipedegrass, creating a foundation for elucidating the functions of EoSPL genes and investigating their involvement in abiotic stress responses.

Ecophysiological, transcriptomic and metabolomic analyses shed light on the response mechanism of Bruguiera gymnorhiza to upwelling stress

Mangroves, due to their unique habitats, endure dual stressors from land to ocean and ocean to land directions. While extensive researches have been conducted on land-ocean stressors, studies on ocean-land stressors like upwelling are considerably scarce. In this study, ecophysiological, transcriptome, and metabolome analyses were conducted to determine the responses of mangrove plant (Bruguiera gymnorhiza, B. gymnorhiza) to upwelling stress. The results suggested that upwelling stress in B. gymnorhiza induces oxidative stress and membrane damage, which are mitigated by the synergistic actions of antioxidant enzymes and osmoprotectants. Transcriptomic and metabolomic analyses revealed that upregulated genes related to oxidation-reduction and carbohydrate metabolism, along with accumulated metabolites such as amino acids, lipids, phenols, and organic acids, contribute to enhancing antioxidant capacity and maintaining osmotic balance. Further analysis identified key KEGG pathways involved in the response to upwelling stress, including amino acid metabolism, carbohydrate and energy metabolism, flavonoid biosynthesis, and plant hormone signal transduction. These findings provide vital information into the multi-level response mechanisms of mangrove plants to upwelling stress.

Genome-wide identification of the EIN3/EIL transcription factor family and their responses under abiotic stresses in Medicago sativa

BACKGROUND

Medicago sativa, often referred to as the "king of forage", is prized for its high content of protein, minerals, carbohydrates, and digestible nutrients. However, various abiotic stresses can hinder its growth and development, ultimately resulting in reduced yield and quality, including water deficiency, high salinity, and low temperature. The ethylene-insensitive 3 (EIN3)/ethylene-insensitive 3-like (EIL) transcription factors are key regulators in the ethylene signaling pathway in plants, playing crucial roles in development and in the response to abiotic stresses. Research on the EIN3/EIL gene family has been reported for several species, but minimal information is available for M. sativa.

RESULTS

In this study, we identified 10 MsEIN3/EIL genes from the M. sativa genome (cv. Zhongmu No.1), which were classified into three clades based on phylogenetic analysis. The conserved structural domains of the MsEIN3/EIL genes include motifs 1, 2, 3, 4, and 9. Gene duplication analyses suggest that segmental duplication (SD) has played a significant role in the expansion of the MsEIN3/EIL gene family throughout evolution. Analysis of the cis-acting elements in the promoters of MsEIN3/EIL genes indicates their potential to respond to various hormones and environmental stresses. We conducted a further analysis of the tissue-specific expression of the MsEIN3/EIL genes and assessed the gene expression profiles of MsEIN3/EIL under various stresses using transcriptome data, including cold, drought, salt and abscisic acid treatments. The results showed that MsEIL1, MsEIL4, and MsEIL5 may act as positive regulatory factors involved in M. sativa's response to abiotic stress, providing important genetic resources for molecular design breeding.

CONCLUSION

This study investigated MsEIN3/EIL genes in M. sativa and identified three candidate transcription factors involved in the regulation of abiotic stresses. These findings will offer valuable insights into uncovering the molecular mechanisms underlying various stress responses in M. sativa.

Genome-wide identification of bHLH transcription factors in Kenaf (Hibiscus cannabinus L.) and gene function analysis of HcbHLH88

Among plants' transcription factor families, the bHLHs family has a significant influence on plant development processes and stress tolerance. However, there have been no relevant studies performed on the bHLHs family in kenaf (Hibiscus cannabinus L). Here, the bHLH transcription factors in kenaf were found using bioinformatics, and a total of 141 kenaf HcbHLH transcription factors were identified. Phylogenetic analysis revealed that these transcription factors were irregularly distributed on 18 chromosomes and separated into 20 subfamilies. Additionally, utilizing the transcriptome data under diverse abiotic pressures, the expression of HcbHLH members was analyzed under different stress conditions. A typical HcbHLH abiotic stress transcription factor, HcbHLH88, was exposed to salt, drought, heavy metals, and ABA. The findings revealed that HcbHLH88 might be activated under salt, drought, cadmium stress, and ABA conditions. Furthermore, HcbHLH88's function under salt stress conditions was studied after it was silenced using the virus-induced gene silencing (VIGS) technique. Reduced antioxidant enzyme activity and stunted plant development were seen in VIGS-silenced seedlings. Stress-related genes were shown to be considerably downregulated in the HcbHLH88-silenced kenaf plants, according to the qRT-PCR study. In conclusion, this study provides the first systematic gene family analysis of the kenaf bHLH gene family and provides a preliminary validation of the salt tolerance function of the HcbHLH88 gene. This study lays the foundation for future research on the regulatory mechanisms of bHLH genes in response to abiotic stresses.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01504-y.

bZIP Transcription Factors: Structure, Modification, Abiotic Stress Responses and Application in Plant Improvement

Plant growth, yield, and distribution are significantly impacted by abiotic stresses, affecting global ecosystems and forestry practices. However, plants have evolved complex adaptation mechanisms governed by numerous genes and transcription factors (TFs) to manage these stresses. Among these, bZIP (basic leucine zipper) is a crucial regulator orchestrating morphological adaptations. This review aims to elucidate the multifaceted roles of bZIP TFs in plant species. We discuss the morphological changes induced by stress stimuli and the pivotal functions of bZIP TFs in mediating these responses. While several publications have explored the mechanisms of bZIP TFs in response to abiotic stresses, this review delves into the intricate regulatory networks, summarizing alternative splicing and post-translational modifications, signaling networks interacting with bZIP TFs, and genetic engineering of bZIP TFs. By synthesizing current research, this review provides an updated discussion on bZIP interactions with other proteins to regulate stresses such as cold, heat, drought, and salt. Additionally, it offers avenues for future research and applications of bZIP TFs to improve abiotic stress resilience in plants through genetic engineering.

Major transcription factor families at the nexus of regulating abiotic stress response in millets: a comprehensive review

Millets stand out as a sustainable crop with the potential to address the issues of food insecurity and malnutrition. These small-seeded, drought-resistant cereals have adapted to survive a broad spectrum of abiotic stresses. Researchers are keen on unravelling the regulatory mechanisms that empower millets to withstand environmental adversities. The aim is to leverage these identified genetic determinants from millets for enhancing the stress tolerance of major cereal crops through genetic engineering or breeding. This review sheds light on transcription factors (TFs) that govern diverse abiotic stress responses and play role in conferring tolerance to various abiotic stresses in millets. Specifically, the molecular functions and expression patterns of investigated TFs from various families, including bHLH, bZIP, DREB, HSF, MYB, NAC, NF-Y and WRKY, are comprehensively discussed. It also explores the potential of TFs in developing stress-tolerant crops, presenting a comprehensive discussion on diverse strategies for their integration.

Genome-wide identification and expression pattern analysis of the kiwifruit GRAS transcription factor family in response to salt stress

BACKGROUND

GRAS is a family of plant-specific transcription factors (TFs) that play a vital role in plant growth and development and response to adversity stress. However, systematic studies of the GRAS TF family in kiwifruit have not been reported.

RESULTS

In this study, we used a bioinformatics approach to identify eighty-six AcGRAS TFs located on twenty-six chromosomes and phylogenetic analysis classified them into ten subfamilies. It was found that the gene structure is relatively conserved for these genes and that fragmental duplication is the prime force for the evolution of AcGRAS genes. However, the promoter region of the AcGRAS genes mainly contains cis-acting elements related to hormones and environmental stresses, similar to the results of GO and KEGG enrichment analysis, suggesting that hormone signaling pathways of the AcGRAS family play a vital role in regulating plant growth and development and adversity stress. Protein interaction network analysis showed that the AcGRAS51 protein is a relational protein linking DELLA, SCR, and SHR subfamily proteins. The results demonstrated that 81 genes were expressed in kiwifruit AcGRAS under salt stress, including 17 differentially expressed genes, 13 upregulated, and four downregulated. This indicates that the upregulated AcGRAS55, AcGRAS69, AcGRAS86 and other GRAS genes can reduce the salt damage caused by kiwifruit plants by positively regulating salt stress, thus improving the salt tolerance of the plants.

CONCLUSIONS

These results provide a theoretical basis for future exploration of the characteristics and functions of more AcGRAS genes. This study provides a basis for further research on kiwifruit breeding for resistance to salt stress. RT-qPCR analysis showed that the expression of 3 AcGRAS genes was elevated under salt stress, indicating that AcGRAS exhibited a specific expression pattern under salt stress conditions.