The Kandelia obovata transcription factor KoWRKY40 enhances cold tolerance in transgenic Arabidopsis

Genome-wide identification of WRKY transcription factors in Casuarina equisetifolia and the function analysis of CeqWRKY11 in response to NaCl/NaHCO3 stresses

BACKGROUND

Casuarina equisetifolia (C. equisetifolia) is a woody species with many excellent features. It has natural resistance against drought, salt and saline-alkali stresses. WRKY transcription factors (TFs) play significant roles in plant response to abiotic stresses, therefore, molecular characterization of WRKY gene family under abiotic stresses holds great significance for improvement of forest trees through molecular biological tools. At present, WRKY TFs from C. equisetifolia have not been thoroughly studied with respect to their role in salt and saline-alkali stresses response. The current study was conducted to bridge the same knowledge gap.

RESULTS

A total of 64 WRKYs were identified in C. equisetifolia and divided into three major groups i.e. group I, II and III, consisting of 10, 42 and 12 WRKY members, respectively. The WRKY members in group II were further divided into 5 subgroups according to their homology with Arabidopsis counterparts. WRKYs belonging to the same group exhibited higher similarities in gene structure and the presence of conserved motifs. Promoter analysis data showed the presence of various response elements, especially those related to hormone signaling and abiotic stresses, such as ABRE (ABA), TGACG (MeJA), W-box ((C/T) TGAC (T/C)) and TC-rich motif. Tissue specific expression data showed that CeqWRKYs were mainly expressed in root under normal growth conditions. Furthermore, most of the CeqWRKYs were up-regulated by NaCl and NaHCO3 stresses with few of WRKYs showing early responsiveness to both stresses while few others exhibiting late response. Although the expressions of CeqWRKYs were also induced by cold stress, the response was delayed compared with other stresses. Transgenic C. equisetifolia plants overexpressing CeqWRKY11 displayed lower electrolyte leakage, higher chlorophyll content, and enhanced tolerance to both stresses. The higher expression of abiotic stress related genes, especially CeqHKT1 and CeqPOD7, in overexpression lines points to the maintenance of optimum Na+/K+ ratio, and ROS scavenging as possible key molecular mechanisms underlying salt stress tolerance.

CONCLUSIONS

Our results show that CeqWRKYs might be key regulators of NaCl and NaHCO3 stresses response in C. equisetifolia. In addition, positive correlation of CeqWRKY11 expression with increased stress tolerance in C. equisetifolia encourages further research on other WRKY family members through functional genomic tools. The best candidates could be incorporated in other woody plant species for improving stress tolerance.

Identification of WRKY Family Members and Characterization of the Low-Temperature-Stress-Responsive WRKY Genes in Luffa (Luffa cylindrica L.)

The plant-specific WRKY transcription factor family members have diverse regulatory effects on the genes associated with many plant processes. Although the WRKY proteins in Arabidopsis thaliana and other species have been thoroughly investigated, there has been relatively little research on the WRKY family in Luffa cylindrica, which is one of the most widely grown vegetables in China. In this study, we performed a genome-wide analysis to identify L. cylindrica WRKY genes, which were subsequently classified and examined in terms of their gene structures, chromosomal locations, promoter cis-acting elements, and responses to abiotic stress. A total of 62 LcWRKY genes (471-2238 bp) were identified and divided into three phylogenetic groups (I, II, and III), with group II further divided into five subgroups (IIa, IIb, IIc, IId, and IIe) in accordance with the classification in other plants. The LcWRKY genes were unevenly distributed across 13 chromosomes. The gene structure analysis indicated that the LcWRKY genes contained 0-11 introns (average of 4.4). Moreover, 20 motifs were detected in the LcWRKY proteins with conserved motifs among the different phylogenetic groups. Two subgroup IIc members (LcWRKY16 and LcWRKY31) contained the WRKY sequence variant WRKYGKK. Additionally, nine cis-acting elements related to diverse responses to environmental stimuli were identified in the LcWRKY promoters. The subcellular localization analysis indicated that three LcWRKY proteins (LcWRKY43, LcWRKY7, and LcWRKY23) are localized in the nucleus. The tissue-specific LcWRKY expression profiles reflected the diversity in LcWRKY expression. The RNA-seq data revealed the effects of low-temperature stress on LcWRKY expression. The cold-induced changes in expression were verified via a qRT-PCR analysis of 24 differentially expressed WRKY genes. Both LcWRKY7 and LcWRKY12 were highly responsive to the low-temperature treatment (approximately 110-fold increase in expression). Furthermore, the LcWRKY8, LcWRKY12, and LcWRKY59 expression levels increased by more than 25-fold under cold conditions. Our findings will help clarify the evolution of the luffa WRKY family while also providing valuable insights for future studies on WRKY functions.

Research progress on the physiological response and molecular mechanism of cold response in plants

Low temperature is a critical environmental stress factor that restricts crop growth and geographical distribution, significantly impacting crop quality and yield. When plants are exposed to low temperatures, a series of changes occur in their external morphology and internal physiological and biochemical metabolism. This article comprehensively reviews the alterations and regulatory mechanisms of physiological and biochemical indices, such as membrane system stability, redox system, fatty acid content, photosynthesis, and osmoregulatory substances, in response to low-temperature stress in plants. Furthermore, we summarize recent research on signal transduction and regulatory pathways, phytohormones, epigenetic modifications, and other molecular mechanisms mediating the response to low temperatures in higher plants. In addition, we outline cultivation practices to improve plant cold resistance and highlight the cold-related genes used in molecular breeding. Last, we discuss future research directions, potential application prospects of plant cold resistance breeding, and recent significant breakthroughs in the research and application of cold resistance mechanisms.

The complete mitochondrial genome of the Kandelia obovata Sheue, H.Y.Liu & J.W.H.Yong (Rhizophoraceae)

Kandelia obovata Sheue, H.Y.Liu & J.W.H.Yong is one of the most cold-resistant true mangrove species, and it is widely distributed from the South China Sea to southern Japan. In the current study, the complete mitochondrial genome sequence of K. obovata was assembled using Illumina reads. It is the first mitochondrial genome of the Kandelia genus within the family Rhizophoraceae to be sequenced. The mitochondrial genome size is 312,146 bp with a total of 49 predicted genes, including 29 protein-coding genes, 17 transfer RNA genes, and 3 ribosomal RNA genes. The overall GC content of the genome is 41.87%. A phylogenetic tree constructed using nine complete mitochondrial genomes revealed that K. obovata is more closely related to Bruguiera species. This study enriches the plastid genome of Kandelia, furnishing valuable genetic insights for the investigation of evolutionary and population genetics in Kandelia and other mangrove species.

A novel ABA-induced transcript factor from Millettia pinnata, MpAITR1, enhances salt and drought tolerance through ABA signaling in transgenic Arabidopsis

Abiotic stress, such as salt and drought stress, seriously limits plant growth and crop yield. Abscisic acid (ABA) is essential in regulating plant responses to abiotic stress via signal perception, transduction, and transcriptional regulation. Pongamia (Millettia pinnata) is a kind of semi-mangrove plant with strong stress tolerance and can grow in fresh and sea water. However, the molecular mechanism of the ABA signaling pathway mediating the environmental tolerance of Pongamia is still scarce so far. AITR (ABA-Induced Transcription Repressor) was a recently identified small conserved family of transcription factor in angiosperms, which played controversial roles in response to abiotic stresses in different species. Here, we identified an ABA-induced gene, MpAITR1, which encoded a nucleus localization transcriptional factor in Pongamia. MpAITR1 was highly induced by ABA and salt treatments in roots and leaves. Heterologous expression of MpAITR1 in Arabidopsis increased sensitivity to ABA, moreover, enhanced tolerance to salt and drought stress. The expression levels of some ABA-responsive and stress-responsive genes were altered in transgenic plants compared to wild-type plants under the ABA, salt, and drought stress, which was consistent with the stress-tolerant phenotype of transgenic plants. These results reveal that MpAITR1 positively modulates ABA signaling pathways and enhances the tolerance to salt and drought stress by regulating downstream target genes. Taken together, MpAITR1 from the semi-mangrove plant Pongamia serves as a potential candidate for stress-tolerant crop breeding.

AeWRKY32 from okra regulates anthocyanin accumulation and cold tolerance in Arabidopsis

Okra (Abelmoschus esculentus L.) is a tropical crop species, and its growth and development are severely affected by cold stress. Recent studies have identified a potential association between WRKY transcription factors and the cold response mechanism of crops. In this study, the AeWRKY32 transcription factor that encodes 482 amino acids was amplified from A. esculentus, and its expression level was found to be the highest in the okra flower. AeWRKY32 localized to the nucleus and displayed transcriptional activation capability. Under normal conditions, overexpression of AeWRKY32 induced anthocyanin accumulation, with higher expression levels of AtCHS1, AtCHI4, AtF3H1, and AtDFR2 in transgenic Arabidopsis. Under cold stress, anthocyanin levels were further elevated in transgenic Arabidopsis plants. At the same time, AeWRKY32 overexpression promoted ABA biosynthesis, inhibited H2O2 and O2- generation, induced stomatal closure, reduced electrolyte leakage, and thus improved the cold resistance of transgenic Arabidopsis. Furthermore, under cold stress, the expression profiles of AtCOR413, AtCOR15B, AtCBF1, and AtCBF2 were upregulated in transgenic Arabidopsis. Overall, our study provides evidence that AeWRKY32 serves as a crucial regulator in both anthocyanin accumulation and cold tolerance of transgenic Arabidopsis. Our findings could provide insights into the molecular mechanism linking AeWRKYs to plant cold tolerance.

An Aquaporin Gene (KoPIP2;1) Isolated from Mangrove Plant Kandelia obovata Had Enhanced Cold Tolerance of Transgenic Arabidopsis thaliana

Aquaporins (AQPs) are essential channel proteins that play central roles in maintaining water homeostasis. Here, a novel aquaporin gene, named KoPIP2;1, was cloned from the mangrove plant Kandelia obovata by RACE technology. The KoPIP2;1 gene was 1404 bp in length with an open reading frame (ORF) of 852 bp, encoded with 283 amino acids. Database comparisons revealed that KoPIP2;1 protein shared the highest identity (91.26%) with the aquaporin HbPIP2;2, which was isolated from Hevea brasiliensis. Gene expression analysis revealed that the KoPIP2;1 gene was induced higher in leaves than in stems and roots of K. obovata under cold stress. Transient expression of KoPIP2;1 in Nicotiana benthamiana epidermal cells revealed that the KoPIP2;1 protein was localized to the plasma membrane. Overexpressing KoPIP2;1 in Arabidopsis significantly enhanced the lateral root number of the transgenic lines. KoPIP2;1 transgenic Arabidopsis demonstrated better growth, elevated proline content, increased superoxide dismutase (SOD) and peroxidase (POD) activities, and reduced malondialdehyde (MDA) content compared with the wild-type Arabidopsis when exposed to cold stress. The findings suggest that overexpression of KoPIP2;1 probably conferred cold tolerance of transgenic Arabidopsis by enhancing osmoregulation and antioxidant capacity. This present data presents a valuable gene resource that contributes to the advancement of our understanding of aquaporins and their potential application in enhancing plant stress tolerance.

Genome-wide analysis of the WRKY genes and their important roles during cold stress in white clover

Background

White clover (Trifolium repens L) is a high-quality forage grass with a high protein content, but it is vulnerable to cold stress, which can negatively affect its growth and development. WRKY transcription factor is a family of plant transcription factors found mainly in higher plants and plays an important role in plant growth, development, and stress response. Although WRKY transcription factors have been studied extensively in other plants, it has been less studied in white clover.

Methods and Results

In the present research, we have performed a genome-wide analysis of the WRKY gene family of white clover, in total, there were 145 members of WRKY transcription factors identified in white clover. The characterization of the TrWRKY genes was detailed, including conserved motif analysis, phylogenetic analysis, and gene duplication analysis, which have provided a better understanding of the structure and evolution of the TrWRKY genes in white clover. Meanwhile, the genetic regulation network (GRN) containing TrWRKY genes was reconstructed, and Gene Ontology (GO) annotation analysis of these function genes showed they contributed to regulation of transcription process, response to wounding, and phosphorylay signal transduction system, all of which were important processes in response to abiotic stress. To determine the TrWRKY genes function under cold stress, the RNA-seq dataset was analyzed; most of TrWRKY genes were highly upregulated in response to cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiment, implying they are involved in various gene regulation pathways in response to cold stress.

Conclusion

The results of this study provide insights that will be useful for further functional analyses of TrWRKY genes in response to biotic or abiotic stresses in white clover. These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold stress, which is important to understand the molecular mechanism of cold tolerance in white clover and improve its cold tolerance.

Genome-wide identification and analysis of the WRKY gene family and low-temperature stress response in Prunus sibirica

BACKGROUND

WRKY transcription factors are a prominent gene family in plants, playing a crucial role in various biological processes including development, metabolism, defense, differentiation, and stress response. Although the WRKY gene family has been extensively studied and analysed in numerous plant species, research on Prunus sibirica's WRKY genes (PsWRKY) remains lacking.

RESULTS

This study analysed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, and Gene ontology (GO) annotation of PsWRKY gene family members using bioinformatics methods based on the whole-genome data of P. sibirica. In total, 55 WRKYs were identified in P. sibirica and were heterogeneously distributed on eight chromosomes. Based on the phylogenetic analysis, these WRKYs were classified into three major groups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Members of different subfamilies have different cis-acting elements, conserved motifs, and intron-exon structures, indicating functional heterogeneity of the WRKY family. Prediction of subcellular localisation indicated that PsWRKYs were mainly located in the nucleus. Twenty pairs of duplicated genes were identified, and segmental duplication events may play an important role in PsWRKY gene family expansion. Analysis of the Ka/Ks ratio showed that the PsWRKY family's homologous genes were primarily purified by selection. Additionally, GO annotation analysis showed that the WRKY gene family was mainly involved in responses to stimuli, immune system processes, and reproductive processes. Furthermore, quantitative real-time PCR (qRT-PCR) analysis showed that 23 PsWRKYs were highly expressed in one or more tissues (pistils and roots) and PsWRKYs showed specific expression patterns under different low-temperature stress conditions.

CONCLUSIONS

Our results provide a scientific basis for the further exploration and functional validation of WRKYs in P. sibirica.

Description and genomic characterization of Gallaecimonas kandeliae sp. nov., isolated from the sediments of mangrove plant Kandelia obovate

The genus Gallaecimonas, proposed by Rodríguez-Blanco et al. (Int J Syst Evol Microbiol 60:504-509, 2010), is mainly isolated from marine environments. So far, only three species have been identified and characterized in this genus. In this study, a new Gallaecimonas strain named Q10^T was isolated from the sediments of mangrove plant Kandelia obovate taken from Dapeng district, Shenzhen, China. Strain Q10^T was a Gram-stain-negative, non-motile, strictly aerobic, rod-shaped bacterium, and grew with 0-8.0% (w/v) NaCl, at 10-45 °C and at pH 5.5-8.5. Phylogenetic analysis indicated that strain Q10^T and the three Gallaecimonas species formed a clade in the tree, with 16S rRNA gene sequence similarities ranging from 96.0 to 97.0%. The major respiratory quinone is Q8. The polar lipids comprised aminolipid, aminophospholipid, diphosphatidylglycerol, glycolipid, phosphatidylethanolamine, phosphatidylglycerol, glycophospholipid and phospholipid. The predominant fatty acids are C_16:0, C_17:1ω8c, summed feature 3 (C_16:1ω7c/C_16:1ω6c), and iso-C_16:0. The complete genome of strain Q10^T is 3,836,841 bp with a G+C content of 62.6 mol%. The orthologous proteins analysis revealed 55 unique proteins in strain Q10^T related to important biological processes, especially three frataxins related to iron-sulfur cluster assembly, which may play a pivotal role in environmental adaptability of this species. Based on polyphasic taxonomic data, strain Q10^T is considered to represent a novel species within the genus Gallaecimonas, for which the name Gallaecimonas kandelia sp. nov. is proposed. The type strain is Q10^T (=KCTC 92860^T=MCCC 1K08421^T). These results contribute to a better understanding of general features and taxonomy of the genus Gallaecimonas.

Genome-Wide Identification and Characterization of WRKY Transcription Factors and Their Expression Profile in Loropetalum chinense var. rubrum

The WRKY gene family plays important roles in plant growth and development, as well as in the responses to biotic and abiotic stresses. Loropetalum chinense var. rubrum has high ornamental and medicinal value. However, few WRKY genes have been reported in this plant, and their functions remain unknown. To explore the roles that the WRKY genes play in L. chinense var. rubrum, we identified and characterized 79 LcWRKYs through BLAST homology analysis and renamed them (as LcWRKY1-79) based on their distribution on the chromosomes of L. chinense var. rubrum. In this way, according to their structural characteristics and phylogenetic analysis, they were divided into three groups containing 16 (Group I), 52 (Group II), and 11 (Group III) WRKYs, respectively. LcWRKYs in the same group have similar motifs and gene structures; for instance, Motifs 1, 2, 3, 4, and 10 constitute the WRKY domain and zinc-finger structure. The LcWRKY promoter region contains light response elements (ACE, G-box), stress response elements (TC-rich repeats), hormone response elements (TATC-box, TCA-element), and MYB binding sites (MBS, MBSI). Synteny analysis of LcWRKYs allowed us to establish orthologous relationships among the WRKY gene families of Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum L., Vitis vinifera L., Oryza sativa L., and Zea mays L.; furthermore, analysis of the transcriptomes of mature leaves and flowers from different cultivars demonstrated the cultivar-specific LcWRKY gene expression. The expression levels of certain LcWRKY genes also presented responsive changes from young to mature leaves, based on an analysis of the transcriptome in leaves at different developmental stages. White light treatment led to a significant decrease in the expression of LcWRKY6, 18, 24, 34, 36, 44, 48, 61, 62, and 77 and a significant increase in the expression of LcWRKY41, blue light treatment led to a significant decrease in the expression of LcWRKY18, 34, 50, and 77 and a significant increase in the expression of LcWRKY36 and 48. These results enable a better understanding of LcWRKYs, facilitating the further exploration of their genetic functions and the molecular breeding of L. chinense var. rubrum.

Genome-wide investigation of the WRKY transcription factor gene family in weeping forsythia: expression profile and cold and drought stress responses

Weeping forsythia is a wide-spread shrub in China with important ornamental, medicinal and ecological values. It is widely distributed in China's warm temperate zone. In plants, WRKY transcription factors play important regulatory roles in seed germination, flower development, fruit ripening and coloring, and biotic and abiotic stress response. To date, WRKY transcription factors have not been systematically studied in weeping forsythia. In this study, we identified 79 WRKY genes in weeping forsythia and classified them according to their naming rules in Arabidopsis thaliana. Phylogenetic tree analysis showed that, except for IIe subfamily, whose clustering was inconsistent with A. thaliana clustering, other subfamily clustering groups were consistent. Cis-element analysis showed that WRKY genes related to pathogen resistance in weeping forsythia might be related to methyl jasmonate and salicylic acid-mediated signaling pathways. Combining cis-element and expression pattern analyses of WRKY genes showed that more than half of WRKY genes were involved in light-dependent development and morphogenesis in different tissues. The gene expression results showed that 13 WRKY genes were involved in drought response, most of which might be related to the abscisic acid signaling pathway, and a few of which might be regulated by MYB transcription factors. The gene expression results under cold stress showed that 17 WRKY genes were involved in low temperature response, and 9 of them had low temperature responsiveness cis-elements. Our study of WRKY family in weeping forsythia provided useful resources for molecular breeding and important clues for their functional verification.

Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance

BACKGROUND

Kandelia obovata is an important mangrove species extensively distributed in Eastern Asia that is susceptible to low-temperature stress. NAC (NAM, ATAF1/2 and CUC2) domain proteins are transcription factors (TFs) that play various roles in plant growth and development and in the plant response to environmental stresses. Nevertheless, genome-wide analyses of K. obovata NAC genes (KoNACs) and their responses to chilling stress have rarely been studied.

METHODS

The KoNAC gene family was identified and characterized using bioinformatic analysis, the subcellular location of some NAC proteins was confirmed using confocal microscopy analysis, and the KoNACs that responded to chilling stress were screened using RNA-seq and qRT-PCR analysis.

RESULTS

A total of 79 KoNACs were identified, and they were unequally distributed across all 18 chromosomes of K. obovata. The KoNAC proteins could be divided into 16 subgroups according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana. The KoNACs exhibited greater synteny with A. thaliana sequences than with Oryza sativa sequences, indicating that KoNACs underwent extensive evolution after the divergence of dicotyledons and monocotyledons. Segmental duplication was the main driving force of the expansions of KoNAC genes. Confocal microscopy analysis verified that the four randomly selected KoNACs localized to the nucleus, indicating the accuracy of the bioinformatic predictions. Tissue expression pattern analysis demonstrated that some KoNAC genes showed tissue-specific expression, suggesting that these KoNACs might be important for plant development and growth. Additionally, the expression levels of 19 KoNACs were significantly (15 positively and 4 negatively) induced by cold treatment, demonstrating that these KoNACs might play important roles during cold stress responses and might be candidate genes for the genetic engineering of K. obovata with enhanced chilling stress tolerance. Coexpression network analysis revealed that 381 coexpressed pairs (between 13 KoNACs and 284 other genes) were significantly correlated.

CONCLUSIONS

Seventy-nine KoNACs were identified in K. obovata, nineteen of which displayed chilling-induced expression patterns. These genes may serve as candidates for functional analyses of KoNACs engaged in chilling stress. Our results lay the foundation for evolutionary analyses of KoNACs and their molecular mechanisms in response to environmental stress.

Review of the Mechanisms by Which Transcription Factors and Exogenous Substances Regulate ROS Metabolism under Abiotic Stress

Reactive oxygen species (ROS) are signaling molecules that regulate many biological processes in plants. However, excess ROS induced by biotic and abiotic stresses can destroy biological macromolecules and cause oxidative damage to plants. As the global environment continues to deteriorate, plants inevitably experience abiotic stress. Therefore, in-depth exploration of ROS metabolism and an improved understanding of its regulatory mechanisms are of great importance for regulating cultivated plant growth and developing cultivars that are resilient to abiotic stresses. This review presents current research on the generation and scavenging of ROS in plants and summarizes recent progress in elucidating transcription factor-mediated regulation of ROS metabolism. Most importantly, the effects of applying exogenous substances on ROS metabolism and the potential regulatory mechanisms at play under abiotic stress are summarized. Given the important role of ROS in plants and other organisms, our findings provide insights for optimizing cultivation patterns and for improving plant stress tolerance and growth regulation.

Importance of FaWRKY71 in Strawberry (Fragaria × ananassa) Fruit Ripening

WRKY transcription factors play a nonnegligible role in plant growth and development, but little is known about the involvement of WRKY transcription factors in the regulation of fruit ripening. In this study, FaWRKY71 was identified to be closely related to fruit maturation in octoploid strawberry. FaWRKY71 protein localized in the nucleus and responded to cold, salt, low phosphate, ABA, and light quality in strawberry seedlings. The temporal and spatial pattern expression analysis indicated that FaWRKY71 was expressed in all the detected tissues, especially in the full red fruits. In addition, FaWRKY71 gave rise to the accumulation of anthocyanin content by promoting the expression of structural genes FaF3’H, FaLAR, FaANR, and transport factors FaTT19 and FaTT12 in the flavonoid pathway, and softening the texture of strawberry via up-regulating the abundance of FaPG19 and FaPG21. Furthermore, FaWRKY71 was a positive regulator that mediated resistance against reactive oxygen species by enhancing the enzyme activities of SOD, POD, and CAT, reducing the amount of MDA. Altogether, this study provides new and comprehensive insight into the regulatory mechanisms facilitating fruit ripening in strawberry.