International Journal of Molecular Sciences

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Open AccessEditorial

Regulatory Mechanisms of Transcription Factors in Plant Morphology and Function 2.0

by Tomotsugu Koyama

Int. J. Mol. Sci. 2024, 25(4), 2010; https://doi.org/10.3390/ijms25042010 - 7 Feb 2024

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Abstract

In plants, gene regulation underlies organ development and responses to environmental changes [...] Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

Research

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16 pages, 9382 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of Homeobox Transcription Factors in Phoma sorghina var. saccharum Causing Sugarcane Twisted Leaf Disease

by Yixue Bao, Jinlan Deng, Sehrish Akbar, Zhenzhen Duan, Chi Zhang, Wenfeng Lin, Suyan Wu, Yabing Yue, Wei Yao, Jianlong Xu and Muqing Zhang

Int. J. Mol. Sci. 2024, 25(10), 5346; https://doi.org/10.3390/ijms25105346 - 14 May 2024

Cited by 1 | Viewed by 1371

Abstract

A homeobox transcription factor is a conserved transcription factor, ubiquitous in eukaryotes, that regulates the tissue formation of structure, cell differentiation, proliferation, and cancer. This study identified the homeobox transcription factor family and its distribution in Phoma sorghina var. saccharum at the whole [...] Read more.

A homeobox transcription factor is a conserved transcription factor, ubiquitous in eukaryotes, that regulates the tissue formation of structure, cell differentiation, proliferation, and cancer. This study identified the homeobox transcription factor family and its distribution in Phoma sorghina var. saccharum at the whole genome level. It elucidated the gene structures and evolutionary characteristics of this family. Additionally, knockout experiments were carried out and the preliminary function of these transcription factors was studied. Through bioinformatics approaches, nine homeobox transcription factors (PsHOX1–PsHOX9) were identified in P. sorghina var. saccharum, and these contained HOX-conserved domains and helix–turn–helix secondary structures. Nine homeobox gene deletion mutants were obtained using the homologous recombinant gene knockout technique. Protoplast transformation was mediated by polyethylene glycol (PEG) and the transformants were identified using PCR. The knockouts of PsHOX1, PsHOX2, PsHOX3, PsHOX4, PsHOX6, PsHOX8, and PsHOX9 genes resulted in a smaller growth diameter in P. sorghina var. saccharum. In contrast, the knockouts of the PsHOX3, PsHOX6, and PsHOX9 genes inhibited the formation of conidia and led to a significant decrease in the pathogenicity. This study’s results will provide insights for understanding the growth and development of P. sorghina var. saccharum. The pathogenic mechanism of the affected sugarcane will provide an essential theoretical basis for preventing and controlling sugarcane twisted leaf disease. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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24 pages, 4579 KiB

Open AccessArticle

Are TaNAC Transcription Factors Involved in Promoting Wheat Yield by cis-Regulation of TaCKX Gene Family?

by Adnan Iqbal, Joanna Bocian, Mateusz Przyborowski, Wacław Orczyk and Anna Nadolska-Orczyk

Int. J. Mol. Sci. 2024, 25(4), 2027; https://doi.org/10.3390/ijms25042027 - 7 Feb 2024

Cited by 3 | Viewed by 1324

Abstract

NAC transcription factors (TFs) are one of the largest TF families in plants, and TaNACs have been known to participate in the regulation of the transcription of many yield-regulating genes in bread wheat. The TaCKX gene family members (GFMs) have already been shown [...] Read more.

NAC transcription factors (TFs) are one of the largest TF families in plants, and TaNACs have been known to participate in the regulation of the transcription of many yield-regulating genes in bread wheat. The TaCKX gene family members (GFMs) have already been shown to regulate yield-related traits, including grain mass and number, leaf senescence, and root growth. The genes encode cytokinin (CK) degrading enzymes (CKXs) and are specifically expressed in different parts of developing wheat plants. The aim of the study was to identify and characterize TaNACs involved in the cis-regulation of TaCKX GFMs. After analysis of the initial transcription factor data in 1.5 Kb cis-regulatory sequences of a total of 35 homologues of TaCKX GFMs, we selected five of them, namely TaCKX1-3A, TaCKX22.1-3B, TaCKX5-3D, TaCKX9-1B, and TaCKX10, and identified five TaNAC genes: TaNACJ-1, TaNAC13a, TaNAC94, TaNACBr-1, and TaNAC6D, which are potentially involved in the cis-regulation of selected TaCKX genes, respectively. Protein feature analysis revealed that all of the selected TaNACs have a conserved NAC domain and showed a stable tertiary structure model. The expression profile of the selected TaNACs was studied in 5 day-old seedling roots, 5–6 cm inflorescences, 0, 4, 7, and 14 days-after-pollination (DAP) spikes, and the accompanying flag leaves. The expression pattern showed that all of the selected TaNACs were preferentially expressed in seedling roots, 7 and 14 DAP spikes, and flag leaves compared to 5–6 cm inflorescence and 0 and 4 DAP spikes and flag leaves in Kontesa and Ostka spring wheat cultivars (cvs.). In conclusion, the results of this study highlight the potential role of the selected TaNACs in the regulation of grain productivity, leaf senescence, root growth, and response to various stresses. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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17 pages, 3152 KiB

Open AccessArticle

Upregulation of Wheat Heat Shock Transcription Factor TaHsfC3-4 by ABA Contributes to Drought Tolerance

by Zhenyu Ma, Baihui Zhao, Huaning Zhang, Shuonan Duan, Zihui Liu, Xiulin Guo, Xiangzhao Meng and Guoliang Li

Int. J. Mol. Sci. 2024, 25(2), 977; https://doi.org/10.3390/ijms25020977 - 12 Jan 2024

Cited by 3 | Viewed by 1561

Abstract

Drought stress can seriously affect the yield and quality of wheat (Triticum aestivum). So far, although few wheat heat shock transcription factors (Hsfs) have been found to be involved in the stress response, the biological functions of them, especially the members [...] Read more.

Drought stress can seriously affect the yield and quality of wheat (Triticum aestivum). So far, although few wheat heat shock transcription factors (Hsfs) have been found to be involved in the stress response, the biological functions of them, especially the members of the HsfC (heat shock transcription factor C) subclass, remain largely unknown. Here, we identified a class C encoding gene, TaHsfC3-4, based on our previous omics data and analyzed its biological function in transgenic plants. TaHsfC3-4 encodes a protein containing 274 amino acids and shows the basic characteristics of the HsfC class. Gene expression profiles revealed that TaHsfC3-4 was constitutively expressed in many tissues of wheat and was induced during seed maturation. TaHsfC3-4 could be upregulated by PEG and abscisic acid (ABA), suggesting that this Hsf may be involved in the regulation pathway depending on ABA in drought resistance. Further results represented that TaHsfC3-4 was localized in the nucleus but had no transcriptional activation activity. Notably, overexpression of TaHsfC3-4 in Arabidopsis thaliana pyr1pyl1pyl2pyl4 (pyr1pyl124) quadruple mutant plants complemented the ABA-hyposensitive phenotypes of the quadruple mutant including cotyledon greening, root elongation, seedling growth, and increased tolerance to drought, indicating positive roles of TaHsfC3-4 in the ABA signaling pathway and drought tolerance. Furthermore, we identified TaHsfA2-11 as a TaHsfC3-4-interacting protein by yeast two-hybrid (Y2H) screening. The experimental data show that TaHsfC3-4 can indeed interact with TaHsfA2-11 in vitro and in vivo. Moreover, transgenic Arabidopsis TaHsfA2-11 overexpression lines exhibited enhanced drought tolerance, too. In summary, our study confirmed the role of TaHsfC3-4 in response to drought stress and provided a target locus for marker-assisted selection breeding to improve drought tolerance in wheat. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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14 pages, 3362 KiB

Open AccessArticle

Gene Cloning and Characterization of Transcription Factor FtNAC10 in Tartary Buckwheat (Fagopyrum tataricum (L.) Gaertn.)

by Jinghuan Li, Xiaohua Li, Caihua Jia and Dahui Liu

Int. J. Mol. Sci. 2023, 24(22), 16317; https://doi.org/10.3390/ijms242216317 - 14 Nov 2023

Viewed by 1198

Abstract

NAC transcription factors play a significant role in plant stress responses. In this study, an NAC transcription factor, with a CDS of 792 bp encoding 263 amino acids, was cloned from Fagopyrum tataricum (L.) Gaertn. (F. tataricum), a minor cereal crop, [...] Read more.

NAC transcription factors play a significant role in plant stress responses. In this study, an NAC transcription factor, with a CDS of 792 bp encoding 263 amino acids, was cloned from Fagopyrum tataricum (L.) Gaertn. (F. tataricum), a minor cereal crop, which is rich in flavonoids and highly stress resistant. The transcription factor was named FtNAC10 (NCBI accession number: MK614506.1) and characterized as a member of the NAP subgroup of NAC transcriptions factors. The gene exhibited a highly conserved N-terminal, encoding about 150 amino acids, and a highly specific C-terminal. The resulting protein was revealed to be hydrophilic, with strong transcriptional activation activity. FtNAC10 expression occurred in various F. tataricum tissues, most noticeably in the root, and was regulated differently under various stress treatments. The over-expression of FtNAC10 in transgenic Arabidopsis thaliana (A. thaliana) seeds inhibited germination, and the presence of FtNAC10 enhanced root elongation under saline and drought stress. According to phylogenetic analysis and previous reports, our experiments indicate that FtNAC10 may regulate the stress response or development of F. tataricum through ABA-signaling pathway, although the mechanism is not yet known. This study provides a reference for further analysis of the regulatory function of FtNAC10 and the mechanism that underlies stress responses in Tartary buckwheat. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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16 pages, 10180 KiB

Open AccessArticle

Expression Patterns and Functional Analysis of Three SmTAT Genes Encoding Tyrosine Aminotransferases in Salvia miltiorrhiza

by Shuai Dong, Long Wang, Huiting Qin, Hongbin Zhan, Donghao Wang and Xiaoyan Cao

Int. J. Mol. Sci. 2023, 24(21), 15575; https://doi.org/10.3390/ijms242115575 - 25 Oct 2023

Viewed by 1404

Abstract

Tyrosine aminotransferase (TAT, E.C. 2.6.1.5) is a pyridoxal phosphate-dependent aminotransferase that is widely found in living organisms. It catalyzes the transfer of the amino group on tyrosine to α-ketoglutarate to produce 4-hydroxyphenylpyruvic acid (4-HPP) and is the first enzyme for tyrosine degradation. Three [...] Read more.

Tyrosine aminotransferase (TAT, E.C. 2.6.1.5) is a pyridoxal phosphate-dependent aminotransferase that is widely found in living organisms. It catalyzes the transfer of the amino group on tyrosine to α-ketoglutarate to produce 4-hydroxyphenylpyruvic acid (4-HPP) and is the first enzyme for tyrosine degradation. Three SmTATs have been identified in the genome of Salvia miltiorrhiza (a model medicinal plant), but their information is very limited. Here, the expression profiles of the three SmTAT genes (SmTAT1, SmTAT2, and SmTAT3) were studied. All three genes expressed in different tissues and responded to methyl jasmonate stimuli. SmTAT proteins are localized in the cytoplasm. The recombinant SmTATs were subjected to in vitro biochemical properties. All three recombinant enzymes had TAT activities and SmTAT1 had the highest catalytic activity for tyrosine, followed by SmTAT3. Also, SmTAT1 preferred the direction of tyrosine deamination to 4-HPP, while SmTAT2 preferred transamination of 4-HPP to tyrosine. In parallel, transient overexpression of SmTATs in tobacco leaves revealed that all three SmTAT proteins catalyzed tyrosine to 4-HPP in vivo, with SmTAT1 exhibiting the highest enzymatic activity. Overall, our results lay a foundation for the production of tyrosine-derived secondary metabolites via metabolic engineering or synthetic biology in the future. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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20 pages, 11986 KiB

Open AccessArticle

Comprehensive Functional Analysis of the bZIP Family in Bletilla striata Reveals That BsbZIP13 Could Respond to Multiple Abiotic Stresses

by Ru Zhou, Guangming Zhao, Siting Zheng, Siyuan Xie, Chan Lu, Shuai Liu, Zhezhi Wang and Junfeng Niu

Int. J. Mol. Sci. 2023, 24(20), 15202; https://doi.org/10.3390/ijms242015202 - 15 Oct 2023

Cited by 1 | Viewed by 1524

Abstract

Basic leucine zipper (bZIP) transcription factors (TFs) are one of the largest families involved in plant physiological processes such as biotic and abiotic responses, growth, and development, etc. In this study, 66 members of the bZIP family were identified in Bletilla striata, [...] Read more.

Basic leucine zipper (bZIP) transcription factors (TFs) are one of the largest families involved in plant physiological processes such as biotic and abiotic responses, growth, and development, etc. In this study, 66 members of the bZIP family were identified in Bletilla striata, which were divided into 10 groups based on their phylogenetic relationships with AtbZIPs. A structural analysis of BsbZIPs revealed significant intron–exon differences among BsbZIPs. A total of 63 bZIP genes were distributed across 16 chromosomes in B. striata. The tissue-specific and germination stage expression patterns of BsbZIPs were based on RNA-seq. Stress-responsive expression analysis revealed that partial BsbZIPs were highly expressed under low temperatures, wounding, oxidative stress, and GA treatments. Furthermore, subcellular localization studies indicated that BsbZIP13 was localized in the nucleus. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays suggested that BsbZIP13 could interact with multiple BsSnRK2s. The results of this study provide insightful data regarding bZIP TF as one of the stress response regulators in B. striata, while providing a theoretical basis for transgenic and functional studies of the bZIP gene family in B. striata. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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15 pages, 5754 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of WRKY Gene Family in Melastoma dodecandrum

by Ruonan Tang, Yunjun Zhu, Songmin Yang, Fei Wang, Guizhen Chen, Jinliao Chen, Kai Zhao, Zhongjian Liu and Donghui Peng

Int. J. Mol. Sci. 2023, 24(19), 14904; https://doi.org/10.3390/ijms241914904 - 5 Oct 2023

Cited by 2 | Viewed by 1871

Abstract

WRKY is one of the largest transcription factor families in plants and plays an important role in plant growth and development as well as in abiotic and biological stresses. However, there is little information about the WRKY family in Melastoma dodecandrum. In [...] Read more.

WRKY is one of the largest transcription factor families in plants and plays an important role in plant growth and development as well as in abiotic and biological stresses. However, there is little information about the WRKY family in Melastoma dodecandrum. In this study, 126 WRKY members were identified in M. dodecandrum. According to phylogenetic analysis, they were divided into three major groups, and group II was further divided into five subgroups. MedWRKY genes were unevenly distributed on 12 chromosomes. Additionally, the gene structure and sequence composition were similar within the same group and differed between groups, suggesting their functional diversity. The promoter sequence analysis identified a number of cis-acting elements related to plant growth and development, stress response, and secondary metabolite synthesis in the WRKY gene family. The collinearity analysis showed that gene replication events were the main driving force of MedWRKY gene evolution. The transcriptome data and RT-qPCR analysis suggested that MedWRKY genes had higher expression in the roots and ripe fruit of M. dodecandrum. In short, this paper lays a foundation for further study of the functions and molecular mechanism of M. dodecandrum WRKY gene family. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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21 pages, 5155 KiB

Open AccessArticle

Transcriptomic Profiling of Embryogenic and Non-Embryogenic Callus Provides New Insight into the Nature of Recalcitrance in Cannabis

by Mohsen Hesami, Marco Pepe, Maxime de Ronne, Mohsen Yoosefzadeh-Najafabadi, Kristian Adamek, Davoud Torkamaneh and Andrew Maxwell Phineas Jones

Int. J. Mol. Sci. 2023, 24(19), 14625; https://doi.org/10.3390/ijms241914625 - 27 Sep 2023

Cited by 3 | Viewed by 2623

Abstract

Differential gene expression profiles of various cannabis calli including non-embryogenic and embryogenic (i.e., rooty and embryonic callus) were examined in this study to enhance our understanding of callus development in cannabis and facilitate the development of improved strategies for plant regeneration and biotechnological [...] Read more.

Differential gene expression profiles of various cannabis calli including non-embryogenic and embryogenic (i.e., rooty and embryonic callus) were examined in this study to enhance our understanding of callus development in cannabis and facilitate the development of improved strategies for plant regeneration and biotechnological applications in this economically valuable crop. A total of 6118 genes displayed significant differential expression, with 1850 genes downregulated and 1873 genes upregulated in embryogenic callus compared to non-embryogenic callus. Notably, 196 phytohormone-related genes exhibited distinctly different expression patterns in the calli types, highlighting the crucial role of plant growth regulator (PGRs) signaling in callus development. Furthermore, 42 classes of transcription factors demonstrated differential expressions among the callus types, suggesting their involvement in the regulation of callus development. The evaluation of epigenetic-related genes revealed the differential expression of 247 genes in all callus types. Notably, histone deacetylases, chromatin remodeling factors, and EMBRYONIC FLOWER 2 emerged as key epigenetic-related genes, displaying upregulation in embryogenic calli compared to non-embryogenic calli. Their upregulation correlated with the repression of embryogenesis-related genes, including LEC2, AGL15, and BBM, presumably inhibiting the transition from embryogenic callus to somatic embryogenesis. These findings underscore the significance of epigenetic regulation in determining the developmental fate of cannabis callus. Generally, our results provide comprehensive insights into gene expression dynamics and molecular mechanisms underlying the development of diverse cannabis calli. The observed repression of auxin-dependent pathway-related genes may contribute to the recalcitrant nature of cannabis, shedding light on the challenges associated with efficient cannabis tissue culture and regeneration protocols. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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17 pages, 4518 KiB

Open AccessArticle

Genome-Wide Analysis of WUSCHEL-Related Homeobox Gene Family in Sacred Lotus (Nelumbo nucifera)

by Gui-Zhen Chen, Jie Huang, Zhi-Cong Lin, Fei Wang, Song-Min Yang, Xiao Jiang, Sagheer Ahmad, Yu-Zhen Zhou, Siren Lan, Zhong-Jian Liu and Dong-Hui Peng

Int. J. Mol. Sci. 2023, 24(18), 14216; https://doi.org/10.3390/ijms241814216 - 18 Sep 2023

Cited by 9 | Viewed by 1442

Abstract

WUSCHEL-related homeobox (WOX) is a plant-specific transcription factor (TF), which plays an essential role in the regulation of plant growth, development, and abiotic stress responses. However, little information is available on the specific roles of WOX TFs in sacred lotus (Nelumbo nucifera [...] Read more.

WUSCHEL-related homeobox (WOX) is a plant-specific transcription factor (TF), which plays an essential role in the regulation of plant growth, development, and abiotic stress responses. However, little information is available on the specific roles of WOX TFs in sacred lotus (Nelumbo nucifera), which is a perennial aquatic plant with important edible, ornamental, and medicinal values. We identified 15 WOX TFs distributing on six chromosomes in the genome of N. nucifera. A total of 72 WOX genes from five species were divided into three clades and nine subclades based on the phylogenetic tree. NnWOXs in the same subclades had similar gene structures and conserved motifs. Cis-acting element analysis of the promoter regions of NnWOXs found many elements enriched in hormone induction, stress responses, and light responses, indicating their roles in growth and development. The Ka/Ks analysis showed that the WOX gene family had been intensely purified and selected in N. nucifera. The expression pattern analysis suggested that NnWOXs were involved in organ development and differentiation of N. nucifera. Furthermore, the protein–protein interaction analysis showed that NnWOXs might participate in the growth, development, and metabolic regulation of N. nucifera. Taken together, these findings laid a foundation for further analysis of NnWOX functions. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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23 pages, 8419 KiB

Open AccessArticle

Comprehensive Analysis and Characterization of the GATA Gene Family, with Emphasis on the GATA6 Transcription Factor in Poplar

by Kai Zhao, Siyuan Nan, Yajing Li, Changhong Yu, Lieding Zhou, Jia Hu, Xia Jin, Youzhi Han and Shengji Wang

Int. J. Mol. Sci. 2023, 24(18), 14118; https://doi.org/10.3390/ijms241814118 - 14 Sep 2023

Cited by 1 | Viewed by 1410

Abstract

GATA transcription factors are ubiquitously present in eukaryotic organisms and play a crucial role in multiple biological processes, such as plant growth, stress response, and hormone signaling. However, the study of GATA factors in poplar is currently limited to a small number of [...] Read more.

GATA transcription factors are ubiquitously present in eukaryotic organisms and play a crucial role in multiple biological processes, such as plant growth, stress response, and hormone signaling. However, the study of GATA factors in poplar is currently limited to a small number of proteins, despite their evident functional importance. In this investigation, we utilized the most recent genome annotation and stringent criteria to identify 38 GATA transcription factor genes in poplar. Subsequently, we conducted a comprehensive analysis of this gene family, encompassing phylogenetic classification, protein characterization, analysis of promoter cis-acting elements, and determination of chromosomal location. Our examination of gene duplication events indicated that both tandem and segmental duplications have contributed to the expansion of the GATA gene family in poplar, with segmental duplication potentially being a major driving force. By performing collinearity analysis of genes across six different species, we identified 74 pairs of co-linear genes, which provide valuable insights for predicting gene functions from a comparative genomics perspective. Furthermore, through the analysis of gene expression patterns, we identified five GATA genes that exhibited differential expression in leaf–stem–root tissues and eight genes that were responsive to salt stress. Of particular interest was GATA6, which displayed strong induction by salt stress and overlapped between the two gene sets. We discovered that GATA6 encodes a nuclear-localized protein with transcription activation activity, which is continuously induced by salt stress in leaf and root tissues. Moreover, we constructed a co-expression network centered around GATA6, suggesting the potential involvement of these genes in the growth, development, and response to abiotic stress processes in poplar through cell transport systems and protein modification mechanisms, such as vesicle-mediated transport, intracellular transport, ubiquitination, and deubiquitination. This research provides a foundation for further exploration of the functions and mechanisms of GATA transcription factors in poplar. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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16 pages, 15471 KiB

Open AccessArticle

Genome-Wide Identification of the NF-Y Gene Family and Their Involvement in Bolting and Flowering in Flowering Chinese Cabbage

by Zhehao Jiang, Yuting Wang, Wenxiang Li, Yudan Wang, Xiaojuan Liu, Xi Ou, Wei Su, Shiwei Song and Riyuan Chen

Int. J. Mol. Sci. 2023, 24(15), 11898; https://doi.org/10.3390/ijms241511898 - 25 Jul 2023

Cited by 4 | Viewed by 1712

Abstract

Flowering Chinese cabbage (Brassica campestris L. ssp. Chinensis var. utilis Tsen et Lee) is a widely consumed vegetable in southern China with significant economic value. Developing product organs in the flowering Chinese cabbage involves two key processes: bolting and flowering. Nuclear factor [...] Read more.

Flowering Chinese cabbage (Brassica campestris L. ssp. Chinensis var. utilis Tsen et Lee) is a widely consumed vegetable in southern China with significant economic value. Developing product organs in the flowering Chinese cabbage involves two key processes: bolting and flowering. Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor known for its crucial role in various plant developmental processes. However, there is limited information available on the involvement of this gene family during flowering during Chinese cabbage development. In this study, 49 BcNF-Y genes were identified and characterized along with their physicochemical properties, gene structure, chromosomal location, collinearity, and expression patterns. We also conducted subcellular localization, yeast two-hybrid, and transcriptional activity assays on selected BcNF-Y genes. The findings of this study revealed enhanced expression levels of specific BcNF-Y genes during the stalk development and flowering stages in flowering Chinese cabbage. Notably, BcNF-YA8, BcNF-YB14, BcNF-YB20, and BcNF-YC5 interacted with BcRGA1, a negative regulator of GA signaling, indicating their potential involvement in GA-mediated stalk development. This study provides valuable insights into the role of BcNF-Y genes in flowering Chinese cabbage development and suggests that they are potential candidates for further investigating the key regulators of cabbage bolting and flowering. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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21 pages, 1416 KiB

Open AccessArticle

Transcriptome Dynamics Underlying Planticine^®-Induced Defense Responses of Tomato (Solanum lycopersicum L.) to Biotic Stresses

by Roksana Rakoczy-Lelek, Małgorzata Czernicka, Magdalena Ptaszek, Anna Jarecka-Boncela, Ewa M. Furmanczyk, Kinga Kęska-Izworska, Marlena Grzanka, Łukasz Skoczylas, Nikodem Kuźnik, Sylwester Smoleń, Alicja Macko-Podgórni, Klaudia Gąska, Aneta Chałańska, Krzysztof Ambroziak and Hubert Kardasz

Int. J. Mol. Sci. 2023, 24(7), 6494; https://doi.org/10.3390/ijms24076494 - 30 Mar 2023

Cited by 4 | Viewed by 3798

Abstract

The induction of natural defense mechanisms in plants is considered to be one of the most important strategies used in integrated pest management (IPM). Plant immune inducers could reduce the use of chemicals for plant protection and their harmful impacts on the environment. [...] Read more.

The induction of natural defense mechanisms in plants is considered to be one of the most important strategies used in integrated pest management (IPM). Plant immune inducers could reduce the use of chemicals for plant protection and their harmful impacts on the environment. Planticine^® is a natural plant defense biostimulant based on oligomers of α(1→4)-linked D-galacturonic acids, which are biodegradable and nontoxic. The aim of this study was to define the molecular basis of Planticine’s biological activity and the efficacy of its use as a natural plant resistance inducer in greenhouse conditions. Three independent experiments with foliar application of Planticine^® were carried out. The first experiment in a climatic chamber (control environment, no pest pressure) subjected the leaves to RNA-seq analysis, and the second and third experiments in greenhouse conditions focused on efficacy after a pest infestation. The result was the RNA sequencing of six transcriptome libraries of tomatoes treated with Planticine^® and untreated plants; a total of 3089 genes were found to be differentially expressed genes (DEGs); among them, 1760 and 1329 were up-regulated and down-regulated, respectively. DEG analysis indicated its involvement in such metabolic pathways and processes as plant-pathogen interaction, plant hormone signal transduction, MAPK signaling pathway, photosynthesis, and regulation of transcription. We detected up-regulated gene-encoded elicitor and effector recognition receptors (ELRR and ERR), mitogen-activated protein kinase (MAPKs) genes, and transcription factors (TFs), i.e., WRKY, ERF, MYB, NAC, bZIP, pathogenesis-related proteins (PRPs), and resistance-related metabolite (RRMs) genes. In the greenhouse trials, foliar application of Planticine^® proved to be effective in reducing the infestation of tomato leaves by the biotrophic pathogen powdery mildew and in reducing feeding by thrips, which are insect herbivores. Prophylactic and intervention use of Planticine^® at low infestation levels allows the activation of plant defense mechanisms. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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Review

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16 pages, 1822 KiB

Open AccessReview

Transcriptional Regulators of Plant Adaptation to Heat Stress

by Xuejing Wang, Nicholas Wui Kiat Tan, Fong Yi Chung, Nobutoshi Yamaguchi, Eng-Seng Gan and Toshiro Ito

Int. J. Mol. Sci. 2023, 24(17), 13297; https://doi.org/10.3390/ijms241713297 - 27 Aug 2023

Cited by 6 | Viewed by 2826

Abstract

Heat stress (HS) is becoming an increasingly large problem for food security as global warming progresses. As sessile species, plants have evolved different mechanisms to cope with the disruption of cellular homeostasis, which can impede plant growth and development. Here, we summarize the [...] Read more.

Heat stress (HS) is becoming an increasingly large problem for food security as global warming progresses. As sessile species, plants have evolved different mechanisms to cope with the disruption of cellular homeostasis, which can impede plant growth and development. Here, we summarize the mechanisms underlying transcriptional regulation mediated by transcription factors, epigenetic regulators, and regulatory RNAs in response to HS. Additionally, cellular activities for adaptation to HS are discussed, including maintenance of protein homeostasis through protein quality control machinery, and autophagy, as well as the regulation of ROS homeostasis via a ROS-scavenging system. Plant cells harmoniously regulate their activities to adapt to unfavorable environments. Lastly, we will discuss perspectives on future studies for improving urban agriculture by increasing crop resilience to HS. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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31 pages, 5638 KiB

Open AccessReview

Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms

by Mughair Abdul Aziz and Khaled Masmoudi

Int. J. Mol. Sci. 2023, 24(12), 9813; https://doi.org/10.3390/ijms24129813 - 6 Jun 2023

Cited by 8 | Viewed by 2693

Abstract

The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop’s salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances [...] Read more.

The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop’s salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant’s adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant’s physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs’ genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na⁺ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop’s adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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Open AccessReview

Transcription Factors-Regulated Leaf Senescence: Current Knowledge, Challenges and Approaches

by Jie Cao, Hairong Liu, Shuya Tan and Zhonghai Li

Int. J. Mol. Sci. 2023, 24(11), 9245; https://doi.org/10.3390/ijms24119245 - 25 May 2023

Cited by 19 | Viewed by 2975

Abstract

Leaf senescence is a complex biological process regulated at multiple levels, including chromatin remodeling, transcription, post-transcription, translation, and post-translational modifications. Transcription factors (TFs) are crucial regulators of leaf senescence, with NAC and WRKY families being the most studied. This review summarizes the progress [...] Read more.

Leaf senescence is a complex biological process regulated at multiple levels, including chromatin remodeling, transcription, post-transcription, translation, and post-translational modifications. Transcription factors (TFs) are crucial regulators of leaf senescence, with NAC and WRKY families being the most studied. This review summarizes the progress made in understanding the regulatory roles of these families in leaf senescence in Arabidopsis and various crops such as wheat, maize, sorghum, and rice. Additionally, we review the regulatory functions of other families, such as ERF, bHLH, bZIP, and MYB. Unraveling the mechanisms of leaf senescence regulated by TFs has the potential to improve crop yield and quality through molecular breeding. While significant progress has been made in leaf senescence research in recent years, our understanding of the molecular regulatory mechanisms underlying this process is still incomplete. This review also discusses the challenges and opportunities in leaf senescence research, with suggestions for possible strategies to address them. Full article

(This article belongs to the Special Issue Regulatory Mechanism of Transcription Factors in Plant Morphology and Function 2.0)

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