Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)

From swamp to field: how genes from mangroves and its associates can enhance crop salinity tolerance

Salinity stress is a critical challenge in crop production and requires innovative strategies to enhance the salt tolerance of plants. Insights from mangrove species, which are renowned for their adaptability to high-salinity environments, provides valuable genetic targets and resources for improving crops. A significant hurdle in salinity stress is the excessive uptake of sodium ions (Na+) by plant roots, causing disruptions in cellular balance, nutrient deficiencies, and hampered growth. Specific ion transporters and channels play crucial roles in maintaining a low Na+/K+ ratio in root cells which is pivotal for salt tolerance. The family of high-affinity potassium transporters, recently characterized in Avicennia officinalis, contributes to K+ homeostasis in transgenic Arabidopsis plants even under high-salt conditions. The salt overly sensitive pathway and genes related to vacuolar-type H+-ATPases hold promise for expelling cytosolic Na+ and sequestering Na+ in transgenic plants, respectively. Aquaporins contribute to mangroves' adaptation to saline environments by regulating water uptake, transpiration, and osmotic balance. Antioxidant enzymes mitigate oxidative damage, whereas genes regulating osmolytes, such as glycine betaine and proline, provide osmoprotection. Mangroves exhibit increased expression of stress-responsive transcription factors such as MYB, NAC, and CBFs under high salinity. Moreover, genes involved in various metabolic pathways, including jasmonate synthesis, triterpenoid production, and protein stability under salt stress, have been identified. This review highlights the potential of mangrove genes to enhance salt tolerance of crops. Further research is imperative to fully comprehend and apply these genes to crop breeding to improve salinity resilience.

Functional characterization of plant specific Indeterminate Domain (IDD) transcription factors in tomato (Solanum lycopersicum L.)

Plant-specific transcription factors (TFs) are responsible for regulating the genes involved in the development of plant-specific organs and response systems for adaptation to terrestrial environments. This includes the development of efficient water transport systems, efficient reproductive organs, and the ability to withstand the effects of terrestrial factors, such as UV radiation, temperature fluctuations, and soil-related stress factors, and evolutionary advantages over land predators. In rice and Arabidopsis, INDETERMINATE DOMAIN (IDD) TFs are plant-specific TFs with crucial functions, such as development, reproduction, and stress response. However, in tomatoes, IDD TFs remain uncharacterized. Here, we examined the presence, distribution, structure, characteristics, and expression patterns of SlIDDs. Database searches, multiple alignments, and motif alignments suggested that 24 TFs were related to Arabidopsis IDDs. 18 IDDs had two characteristic C2H2 domains and two C2HC domains in their coding regions. Expression analyses suggest that some IDDs exhibit multi-stress responsive properties and can respond to specific stress conditions, while others can respond to multiple stress conditions in shoots and roots, either in a tissue-specific or universal manner. Moreover, co-expression database analyses suggested potential interaction partners within IDD family and other proteins. This study functionally characterized SlIDDs, which can be studied using molecular and bioinformatics methods for crop improvement.

Genome-Wide Analysis of Q-Type C2H2 ZFP Genes in Response to Biotic and Abiotic Stresses in Sugar Beet

A plant's Q-type C2H2-type ZFP plays key roles in plant growth and development and responses to biotic and abiotic stresses. Sugar beet (Beta vulgaris L.) is an important crop for sugar production. Salt stress and viral infection significantly reduce the root yield and sugar content of sugar beet. However, there is a lack of comprehensive genome-wide analyses of Q-type C2H2 ZFPs and their expression patterns in sugar beet under stress. In this study, 35 sugar beet Q-type C2H2 ZFPs (BvZFPs) containing at least one conserved "QALGGH" motif were identified via bioinformatics techniques using TBtools software. According to their evolutionary relationship, the BvZFPs were classified into five subclasses. Within each subclass, the physicochemical properties and motif compositions showed strong similarities. A Ka/Ks analysis indicated that the BvZFPs were conserved during evolution. Promoter cis-element analysis revealed that most BvZFPs are associated with elements related to phytohormone, biotic or abiotic stress, and plant development. The expression data showed that the BvZFPs in sugar beet are predominantly expressed in the root. In addition, BvZFPs are involved in the response to abiotic and biotic stresses, including salt stress and viral infection. Overall, these results will extend our understanding of the Q-type C2H2 gene family and provide valuable information for the biological breeding of sugar beet against abiotic and biotic stresses in the future.

Identification of Transcriptional Networks Involved in De Novo Organ Formation in Tomato Hypocotyl Explants

Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. In previous work, we established Solanum lycopersicum "Micro-Tom" explants without the addition of exogenous hormones as a model to investigate wound-induced de novo organ formation. The current working model indicates that cell reprogramming and founder cell activation requires spatial and temporal regulation of auxin-to-cytokinin (CK) gradients in the apical and basal regions of the hypocotyl combined with extensive metabolic reprogramming of some cells in the apical region. In this work, we extended our transcriptomic analysis to identify some of the gene regulatory networks involved in wound-induced organ regeneration in tomato. Our results highlight a functional conservation of key TF modules whose function is conserved during de novo organ formation in plants, which will serve as a valuable resource for future studies.

C2H2 Zinc Finger Proteins Response to Abiotic Stress in Plants

Abiotic stresses have already exhibited the negative effects on crop growth and development, thereby influencing crop quality and yield. Therefore, plants have developed regulatory mechanisms to adopt against such harsh changing environmental conditions. Recent studies have shown that zinc finger protein transcription factors play a crucial role in plant growth and development as well as in stress response. C2H2 zinc finger proteins are one of the best-studied types and have been shown to play diverse roles in the plant abiotic stress responses. However, the C2H2 zinc finger network in plants is complex and needs to be further studied in abiotic stress responses. Here in this review, we mainly focus on recent findings on the regulatory mechanisms, summarize the structural and functional characterization of C2H2 zinc finger proteins, and discuss the C2H2 zinc finger proteins involved in the different signal pathways in plant responses to abiotic stress.

Genome-wide identification and expression analyses of C2H2 zinc finger transcription factors in Pleurotus ostreatus

The C2H2-type zinc finger proteins (C2H2-ZFPs) regulate various developmental processes and abiotic stress responses in eukaryotes. Yet, a comprehensive analysis of these transcription factors which could be used to find candidate genes related to the control the development and abiotic stress tolerance has not been performed in Pleurotus ostreatus. To fill this knowledge gap, 18 C2H2-ZFs were identified in the P. ostreatus genome. Phylogenetic analysis indicated that these proteins have dissimilar amino acid sequences. In addition, these proteins had variable protein characteristics, gene intron-exon structures, and motif compositions. The expression patterns of PoC2H2-ZFs in mycelia, primordia, and young and mature fruiting bodies were investigated using qRT-PCR. The expression of some PoC2H2-ZFs is regulated by auxin and cytokinin. Moreover, members of PoC2H2-ZFs expression levels are changed dramatically under heat and cold stress, suggesting that these genes may participate in abiotic stress responses. These findings could be used to study the role of P. ostreatus-derived C2H2-ZFs in development and stress tolerance.

Differential Physiological, Transcriptomic, and Metabolomic Responses of Paspalum wettsteinii Under High-Temperature Stress

Global warming has far-reaching effects on plant growth and development. As a warm-season forage grass, Paspalum wettsteinii is highly adaptable to high temperatures. However, the response mechanism of P. wettsteinii under high-temperature stress is still unclear. Therefore, we investigated the physiological indicators, transcriptome and metabolome of P. wettsteinii under different heat stress treatments. Plant height, the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and the contents of soluble sugar, proline, chlorophyll a, and chlorophyll b increased and then decreased, while the malondialdehyde (MDA) content decreased and then increased with increasing heat stress. Transcriptomic analysis revealed that genes related to energy and carbohydrate metabolism, heat shock proteins (HSPs), and transcription factors (TFs), secondary metabolite biosynthesis and the antioxidant system significantly changed to varying degrees. Metabolomic analysis showed that only free fatty acids were downregulated, while amino acids and their derivatives, organic acids, flavonoids, and sugars were both up- and downregulated under heat stress. These combined analyses revealed that growth was promoted at 25-40°C, while at 45°C, excess reactive oxygen species (ROS) damage reduced antioxidant and osmoregulatory effects and inactivated genes associated with the light and electron transport chains (ETCs), as well as damaged the PS II system and inhibited photosynthesis. A small number of genes and metabolites were upregulated to maintain the basic growth of P. wettsteinii. The physiological and biochemical changes in response to high-temperature stress were revealed, and the important metabolites and key genes involved in the response to high temperature were identified, providing an important reference for the physiological and molecular regulation of high-temperature stress in plants.

SlHair2 Regulates the Initiation and Elongation of Type I Trichomes on Tomato Leaves and Stems

Trichomes are hair-like structures that are essential for abiotic and biotic stress responses. Tomato Hair (H), encoding a C2H2 zinc finger protein, was found to regulate the multicellular trichomes on stems. Here, we characterized Solyc10g078990 (hereafter Hair2, H2), its closest homolog, to examine whether it was involved in trichome development. The H2 gene was highly expressed in the leaves, and its protein contained a single C2H2 domain and was localized to the nucleus. The number and length of type I trichomes on the leaves and stems of knock-out h2 plants were reduced when compared to the wild-type, while overexpression increased their number and length. An auto-activation test with various truncated forms of H2 using yeast two-hybrid (Y2H) suggested that H2 acts as a transcriptional regulator or co-activator and that its N-terminal region is important for auto-activation. Y2H and pull-down analyses showed that H2 interacts with Woolly (Wo), which regulates the development of type I trichomes in tomato. Luciferase complementation imaging assays confirmed that they had direct interactions, implying that H2 and Wo function together to regulate the development of trichomes. These results suggest that H2 has a role in the initiation and elongation of type I trichomes in tomato.

OBV (obscure vein), a C2H2 zinc finger transcription factor, positively regulates chloroplast development and bundle sheath extension formation in tomato (Solanum lycopersicum) leaf veins

Leaf veins play an important role in plant growth and development, and the bundle sheath (BS) is believed to greatly improve the photosynthetic efficiency of C₄ plants. The OBV mutation in tomato (Solanum lycopersicum) results in dark veins and has been used widely in processing tomato varieties. However, physiological performance has difficulty explaining fitness in production. In this study, we confirmed that this mutation was caused by both the increased chlorophyll content and the absence of bundle sheath extension (BSE) in the veins. Using genome-wide association analysis and map-based cloning, we revealed that OBV encoded a C₂H₂L domain class transcription factor. It was localized in the nucleus and presented cell type-specific gene expression in the leaf veins. Furthermore, we verified the gene function by generating CRISPR/Cas9 knockout and overexpression mutants of the tomato gene. RNA sequencing analysis revealed that OBV was involved in regulating chloroplast development and photosynthesis, which greatly supported the change in chlorophyll content by mutation. Taken together, these findings demonstrated that OBV affected the growth and development of tomato by regulating chloroplast development in leaf veins. This study also provides a solid foundation to further decipher the mechanism of BSEs and to understand the evolution of photosynthesis in land plants.

A C2H2-Type Zinc-Finger Protein from Millettia pinnata, MpZFP1, Enhances Salt Tolerance in Transgenic Arabidopsis

C2H2 zinc finger proteins (ZFPs) play important roles in plant development and response to abiotic stresses, and have been studied extensively. However, there are few studies on ZFPs in mangroves and mangrove associates, which represent a unique plant community with robust stress tolerance. MpZFP1, which is highly induced by salt stress in the mangrove associate Millettia pinnata, was cloned and functionally characterized in this study. MpZFP1 protein contains two zinc finger domains with conserved QALGGH motifs and targets to the nucleus. The heterologous expression of MpZFP1 in Arabidopsis increased the seeds' germination rate, seedling survival rate, and biomass accumulation under salt stress. The transgenic plants also increased the expression of stress-responsive genes, including RD22 and RD29A, and reduced the accumulation of reactive oxygen species (ROS). These results indicate that MpZFP1 is a positive regulator of plant responses to salt stress due to its activation of gene expression and efficient scavenging of ROS.

Genome wide identification and expression analysis of pepper C2H2 zinc finger transcription factors in response to anthracnose pathogen Colletotrichum truncatum

Although, the C₂H₂ zinc finger (ZF) family of plant transcription factors have been implicated in multiple biological processes, they are yet to be characterized in the economically important chilli pepper (Capsicum annuum). In this study, a total of 79 C₂H₂ ZF genes were identified in the pepper genome. Phylogenetic analysis categorized the pepper C₂H₂ ZF (CaZF) members into five subfamilies each with unique conserved domains and functions. Genomic organization revealed that CaZF genes have variable number of introns consistent with the characteristics defined by the evolutionary analysis. Segmental duplication-based purifying selection contributed to the expansion of CaZF genes in pepper. Additionally, 11 CaZF genes were identified as targets for 38 miRNAs indicating their role in post-transcriptional silencing-mediated genetic regulation. Gene expression analysis revealed that 18 CaZF genes were differentially expressed post-infection with the anthrocnose pathogen Colletotrichum truncatum, uncovering their potential function in pepper response to biotic stresses. Moreover, CaZFs were significantly induced post-treatment with methyl jasmonate and ethylene indicating their role in defense signaling. Notably, the MeJA responsive cis-elements were detected in the promoter regions of majority of CaZF genes, suggesting that CaZFs may be implicated in defense-responsive signal cross talking. Additionally, 18 CaZF genes were differentially expressed under drought and heat treatment, indicating their involvement in plant response to abiotic stresses. Overall, a comprehensive analysis of CaZF gene family in pepper provided significant insights into the understanding of C₂H₂ ZF-mediated stress regulation network, which would benefit the genetic improvement of pepper and other allied plants.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02601-x.

Comparative transcriptome analysis of defense response of rice to Nilaparvata lugens and Chilo suppressalis infestation

The brown planthopper (BPH, Nilaparvata lugens) and striped stem borer (SSB, Chilo suppressalis) are two of the most devastating insect pests in rice, causing significant losses of rice yield. Plants evolve multiple defense responses in the process of coexisting with pests. According to different pest infestation, the plants selectively activate related pathways and downstream gene expression. However, there are very few reports of differences in defense signaling pathways after rice was attacked by BPH or SSB. We determined the transcriptional responses of rice infested with BPH and SSB for 3 and 6 h using Illumina sequencing. By comparing the difference in gene changes caused by BPH and SSB infestation in rice, multiple signal pathways and gene expression patterns, including phytohormones, secondary metabolites, plant-pathogen interaction, reactive oxygen species, defense response, transcription factors, protease inhibitor and chitinase were found significantly different. Our results provide a basis for further exploring the molecular mechanism of rice defense response caused by BPH and SSB infestation, which will add to further understanding the interactions between plants and insects, and could provide valuable resources that could be applied in insect-resistant crop breeding.