Genome-Wide Identification and Characterization of Cucumber BPC Transcription Factors and Their Responses to Abiotic Stresses and Exogenous Phytohormones

BASIC PENTACYSTEINE (BPC) is a small transcription factor family that functions in diverse growth and development processes in plants. However, the roles of BPCs in plants, especially cucumber (Cucumis sativus L.), in response to abiotic stress and exogenous phytohormones are still unclear. Here, we identified four BPC genes in the cucumber genome, and classified them into two groups according to phylogenetic analysis. We also investigated the gene structures and detected five conserved motifs in these CsBPCs. Tissue expression pattern analysis revealed that the four CsBPCs were expressed ubiquitously in both vegetative and reproductive organs. Additionally, the transcriptional levels of the four CsBPCs were induced by various abiotic stress and hormone treatments. Overexpression of CsBPC2 in tobacco (Nicotiana tabacum) inhibited seed germination under saline, polyethylene glycol, and abscisic acid (ABA) conditions. The results suggest that the CsBPC genes may play crucial roles in cucumber growth and development, as well as responses to abiotic stresses and plant hormones. CsBPC2 overexpression in tobacco negatively affected seed germination under hyperosmotic conditions. Additionally, CsBPC2 functioned in ABA-inhibited seed germination and hypersensitivity to ABA-mediated responses. Our results provide fundamental information for further research on the biological functions of BPCs in development and abiotic stress responses in cucumber and other plant species.

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Genome-Wide Characterization and Abiotic Stresses Expression Analysis of Annexin Family Genes in Poplar

International Journal of Molecular Sciences ◽

10.3390/ijms23010515 ◽

2022 ◽

Vol 23 (1) ◽

pp. 515

Author(s):

Hui Wei ◽

Ali Movahedi ◽

Guoyuan Liu ◽

Yixin Li ◽

Shiwei Liu ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Abiotic Stresses ◽

Growth And Development ◽

Woody Plant ◽

Calcium Dependent ◽

Genome Wide ◽

Duplication Events ◽

Gene Structures ◽

Similar Gene

Poplar is an illustrious industrial woody plant with rapid growth, providing a range of materials, and having simple post-treatment. Various kinds of environmental stresses limit its output. Plant annexin (ANN) is a calcium-dependent phospholipid-binding protein involved in plant metabolism, growth and development, and cooperatively regulating drought resistance, salt tolerance, and various stress responses. However, the features of the PtANN gene family and different stress responses remain unknown in poplar. This study identified 12 PtANN genes in the P. trichocarpa whole-genome and PtANNs divided into three subfamilies based on the phylogenetic tree. The PtANNs clustered into the same clade shared similar gene structures and conserved motifs. The 12 PtANN genes were located in ten chromosomes, and segmental duplication events were illustrated as the main duplication method. Additionally, the PtANN4 homogenous with AtANN1 was detected localized in the cytoplasm and plasma membrane. In addition, expression levels of PtANNs were induced by multiple abiotic stresses, which indicated that PtANNs could widely participate in response to abiotic stress. These results revealed the molecular evolution of PtANNs and their profiles in response to abiotic stress.

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Genome-Wide Characterization of Cucumber (Cucumis sativus L.) GRAS Genes and Their Response to Various Abiotic Stresses

Horticulturae ◽

10.3390/horticulturae6040110 ◽

2020 ◽

Vol 6 (4) ◽

pp. 110

Author(s):

Caixia Li ◽

Shaoyun Dong ◽

Xiaoping Liu ◽

Kailiang Bo ◽

Han Miao ◽

...

Keyword(s):

Transcription Factors ◽

Abiotic Stress ◽

Cucumis Sativus ◽

Stress Responses ◽

Abiotic Stresses ◽

Transcriptional Analysis ◽

Cucumis Sativus L ◽

Genome Wide ◽

Cucumber Genome ◽

Multiple Signaling

The GRAS (gibberellic acid insensitive, repressor of GAI, and scarecrow) proteins are a family of plant-specific transcription factors that regulate plant growth, development, and stress response. Currently, the role of GRAS transcription factors in various abiotic stress responses has not been systematically studied in cucumber (Cucumis sativus L.), a popular vegetable crop. Here, we provide a comprehensive bioinformatics analysis of the 35 GRAS genes identified in the cucumber genome. In this study, cucumber genotypes, i.e., “CG104”, which is stress-tolerant, and genotype “CG37”, which is stress-sensitive, were examined to provide insight on potential differences in the GRAS-regulated abiotic stress pathways. Transcriptional analysis by RNA-seq or qRT-PCR of these two genotypes revealed common and divergent functions of CsGRAS genes regulated by low and high temperatures, salinity, and by exposure to the phytohormones gibberellin (GA) and abscisic acid (ABA). Notably, CsGRAS2 (DELLA) and CsGRAS26 (LISCL) were regulated by all abiotic stresses and hormone treatments, suggesting that they may function in the biological cross-talk between multiple signaling pathways. This study provides candidate genes for improving cucumber tolerance to various environmental stresses.

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Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview

Metabolites ◽

10.3390/metabo11070445 ◽

2021 ◽

Vol 11 (7) ◽

pp. 445

Author(s):

Morena M. Tinte ◽

Kekeletso H. Chele ◽

Justin J. J. van der Hooft ◽

Fidele Tugizimana

Keyword(s):

Machine Learning ◽

Abiotic Stress ◽

Stress Responses ◽

Abiotic Stresses ◽

Industrial Revolution ◽

Chemical Space ◽

Big Data Analytics ◽

Plant Responses ◽

Next Generation ◽

Computational Tools

Plants are constantly challenged by changing environmental conditions that include abiotic stresses. These are limiting their development and productivity and are subsequently threatening our food security, especially when considering the pressure of the increasing global population. Thus, there is an urgent need for the next generation of crops with high productivity and resilience to climate change. The dawn of a new era characterized by the emergence of fourth industrial revolution (4IR) technologies has redefined the ideological boundaries of research and applications in plant sciences. Recent technological advances and machine learning (ML)-based computational tools and omics data analysis approaches are allowing scientists to derive comprehensive metabolic descriptions and models for the target plant species under specific conditions. Such accurate metabolic descriptions are imperatively essential for devising a roadmap for the next generation of crops that are resilient to environmental deterioration. By synthesizing the recent literature and collating data on metabolomics studies on plant responses to abiotic stresses, in the context of the 4IR era, we point out the opportunities and challenges offered by omics science, analytical intelligence, computational tools and big data analytics. Specifically, we highlight technological advancements in (plant) metabolomics workflows and the use of machine learning and computational tools to decipher the dynamics in the chemical space that define plant responses to abiotic stress conditions.

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Genome-Wide Analysis of Poplar SQUAMOSA-Promoter-Binding Protein (SBP) Family under Salt Stress

Forests ◽

10.3390/f12040413 ◽

2021 ◽

Vol 12 (4) ◽

pp. 413

Author(s):

Qing Guo ◽

Li Li ◽

Kai Zhao ◽

Wenjing Yao ◽

Zihan Cheng ◽

...

Keyword(s):

Salt Stress ◽

Abiotic Stress ◽

Stress Responses ◽

Growth And Development ◽

Binding Protein ◽

Gene Segment ◽

Gene Expression Pattern ◽

Genome Wide Analysis ◽

Genome Wide ◽

Squamosa Promoter Binding Protein

SQUAMOSA promoter binding protein (SBP) is a kind of plant-specific transcription factor, which plays a crucial role in stress responses and plant growth and development by activating and inhibiting the transcription of multiple target genes. In this study, a total of 30 SBP genes were identified from Populus trichocarpa genome and randomly distributed on 16 chromosomes in poplar. According to phylogenetic analysis, the PtSBPs can be divided into six categories, and 14 out of the genes belong to VI. Furthermore, the SBP genes in VI were proved to have a targeting relationship with miR156. The homeopathic element analysis showed that the promoters of poplar SBP genes mainly contain the elements involved in growth and development, abiotic stress and hormone response. In addition, there existed 10 gene segment duplication events in the SBP gene duplication analysis. Furthermore, there were four poplar and Arabidopsis orthologous gene pairs among the poplar SBP members. What is more, poplar SBP gene family has diverse gene expression pattern under salt stress. As many as nine SBP members were responding to high salt stress and six members possibly participated in growth development and abiotic stress. Yeast two-hybrid experiments indicated that PtSBPs can form heterodimers to interact in the transcriptional regulatory networks. The genome-wide analysis of poplar SBP family will contribute to function characterization of SBP genes in woody plants.

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WRKY Proteins: Signaling and Regulation of Expression during Abiotic Stress Responses

The Scientific World JOURNAL ◽

10.1155/2015/807560 ◽

2015 ◽

Vol 2015 ◽

pp. 1-17 ◽

Cited By ~ 121

Author(s):

Aditya Banerjee ◽

Aryadeep Roychoudhury

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Biotic Stress ◽

Abiotic Stresses ◽

Abiotic Stress Tolerance ◽

Plant Signaling ◽

Biological Functions ◽

Abiotic And Biotic Stress ◽

Regulation Of Expression ◽

Wrky Proteins

WRKY proteins are emerging players in plant signaling and have been thoroughly reported to play important roles in plants under biotic stress like pathogen attack. However, recent advances in this field do reveal the enormous significance of these proteins in eliciting responses induced by abiotic stresses. WRKY proteins act as major transcription factors, either as positive or negative regulators. Specific WRKY factors which help in the expression of a cluster of stress-responsive genes are being targeted and genetically modified to induce improved abiotic stress tolerance in plants. The knowledge regarding the signaling cascade leading to the activation of the WRKY proteins, their interaction with other proteins of the signaling pathway, and the downstream genes activated by them are altogether vital for justified targeting of theWRKYgenes. WRKY proteins have also been considered to generate tolerance against multiple abiotic stresses with possible roles in mediating a cross talk between abiotic and biotic stress responses. In this review, we have reckoned the diverse signaling pattern and biological functions of WRKY proteins throughout the plant kingdom along with the growing prospects in this field of research.

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Genome-Wide Identification of Barley ABC Genes and Their Expression in Response to Abiotic Stress Treatment

Plants ◽

10.3390/plants9101281 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1281

Author(s):

Ziling Zhang ◽

Tao Tong ◽

Yunxia Fang ◽

Junjun Zheng ◽

Xian Zhang ◽

...

Keyword(s):

Abiotic Stress ◽

Amino Acid ◽

Stress Responses ◽

Transmembrane Domain ◽

Profile Analysis ◽

Tissue Expression ◽

Expression Profile Analysis ◽

Genome Wide ◽

Tissue Expression Profile ◽

Amino Acid Length

Adenosine triphosphate-binding cassette transporters (ABC transporters) participate in various plant growth and abiotic stress responses. In the present study, 131 ABC genes in barley were systematically identified using bioinformatics. Based on the classification method of the family in rice, these members were classified into eight subfamilies (ABCA–ABCG, ABCI). The conserved domain, amino acid composition, physicochemical properties, chromosome distribution, and tissue expression of these genes were predicted and analyzed. The results showed that the characteristic motifs of the barley ABC genes were highly conserved and there were great diversities in the homology of the transmembrane domain, the number of exons, amino acid length, and the molecular weight, whereas the span of the isoelectric point was small. Tissue expression profile analysis suggested that ABC genes possess non-tissue specificity. Ultimately, 15 differentially expressed genes exhibited diverse expression responses to stress treatments including drought, cadmium, and salt stress, indicating that the ABCB and ABCG subfamilies function in the response to abiotic stress in barley.

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Genome-wide characterization of NtHD-ZIP IV: different roles in abiotic stress response and glandular Trichome induction

BMC Plant Biology ◽

10.1186/s12870-019-2023-4 ◽

2019 ◽

Vol 19 (1) ◽

Author(s):

Hongying Zhang ◽

Xudong Ma ◽

Wenjiao Li ◽

Dexin Niu ◽

Zhaojun Wang ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Stress Responses ◽

Leucine Zipper ◽

Regulatory Gene ◽

Glandular Trichomes ◽

Glandular Trichome ◽

Tissue Expression ◽

Abiotic Stress Response ◽

Epidermal Development

Abstract Background The plant-specific homeodomain-leucine zipper class IV (HD-ZIP IV) gene family has been involved in the regulation of epidermal development. Results Fifteen genes coding for HD-ZIP IV proteins were identified (NtHD-ZIP-IV-1 to NtHD-ZIP-IV-15) based on the genome of N. tabacum. Four major domains (HD, ZIP, SAD and START) were present in these proteins. Tissue expression pattern analysis indicated that NtHD-ZIP-IV-1, − 2, − 3, − 10, and − 12 may be associated with trichome development; NtHD-ZIP-IV-8 was expressed only in cotyledons; NtHD-ZIP-IV-9 only in the leaf and stem epidermis; NtHD-ZIP-IV-11 only in leaves; and NtHD-ZIP-IV-15 only in the root and stem epidermis. We found that jasmonates may induce the generation of glandular trichomes, and that NtHD-ZIP-IV-1, − 2, − 5, and − 7 were response to MeJA treatment. Dynamic expression under abiotic stress and after application of phytohormones indicated that most NtHD-ZIP IV genes were induced by heat, cold, salt and drought. Furthermore, most of these genes were induced by gibberellic acid, 6-benzylaminopurine, and salicylic acid, but were inhibited by abscisic acid. NtHD-ZIP IV genes were sensitive to heat, but insensitive to osmotic stress. Conclusion NtHD-ZIP IV genes are implicated in a complex regulatory gene network controlling epidermal development and abiotic stress responses. The present study provides evidence to elucidate the gene functions of NtHD-ZIP IVs during epidermal development and stress response.

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Nitric oxide function during oxygen deprivation in physiological and stress processes

Journal of Experimental Botany ◽

10.1093/jxb/eraa442 ◽

2020 ◽

Author(s):

Isabel Manrique-Gil ◽

Inmaculada Sánchez-Vicente ◽

Isabel Torres-Quezada ◽

Oscar Lorenzo

Keyword(s):

Nitric Oxide ◽

Stress Responses ◽

Abiotic Stresses ◽

Growth And Development ◽

Energy Supply ◽

Molecular Mechanisms ◽

Environmental Cues ◽

Biotic And Abiotic Stresses ◽

Proteolytic Pathway ◽

The Impact

Abstract Plants are aerobic organisms that have evolved to maintain specific requirements for oxygen (O2), leading to a correct respiratory energy supply during growth and development. There are certain plant developmental cues and biotic or abiotic stress responses where O2 is scarce. This O2 deprivation known as hypoxia may occur in hypoxic niches of plant-specific tissues and during adverse environmental cues such as pathogen attack and flooding. In general, plants respond to hypoxia through a complex reprogramming of their molecular activities with the aim of reducing the impact of stress on their physiological and cellular homeostasis. This review focuses on the fine-tuned regulation of hypoxia triggered by a network of gaseous compounds that includes O2, ethylene, and nitric oxide. In view of recent scientific advances, we summarize the molecular mechanisms mediated by phytoglobins and by the N-degron proteolytic pathway, focusing on embryogenesis, seed imbibition, and germination, and also specific structures, most notably root apical and shoot apical meristems. In addition, those biotic and abiotic stresses that comprise hypoxia are also highlighted.

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Identification and Expression Analysis of Stress-Associated Proteins (SAPs) Containing A20/AN1 Zinc Finger in Cucumber

Plants ◽

10.3390/plants9030400 ◽

2020 ◽

Vol 9 (3) ◽

pp. 400

Author(s):

Wei Lai ◽

Yong Zhou ◽

Rao Pan ◽

Liting Liao ◽

Juncheng He ◽

...

Keyword(s):

Gene Family ◽

Zinc Finger ◽

Expression Analysis ◽

Stress Responses ◽

Tissue Expression ◽

Future Research ◽

Transcriptional Responses ◽

Cucumis Sativus L ◽

Tissue Expression Analysis ◽

Associated Proteins

Stress-associated proteins (SAPs) are a class of zinc finger proteins that confer tolerance to a variety of abiotic and biotic stresses in diverse plant species. However, in cucumber (Cucumis sativus L.), very little is known about the roles of SAP gene family members in regulating plant growth, development, and stress responses. In this study, a total of 12 SAP genes (named as CsSAP1-CsSAP12) were identified in the cucumber genome, which were unevenly distributed on six chromosomes. Gene duplication analysis detected one tandem duplication and two segmental duplication events. Phylogenetic analysis of SAP proteins from cucumber and other plants suggested that they could be divided into seven groups (sub-families), and proteins in the same group generally had the same arrangement of AN1 (ZnF-AN1) and A20 (ZnF-A20) domains. Most of the CsSAP genes were intronless and harbored a number of stress- and hormone-responsive cis-elements in their promoter regions. Tissue expression analysis showed that the CsSAP genes had a broad spectrum of expression in different tissues, and some of them displayed remarkable alteration in expression during fruit development. RT-qPCR results indicated that all the selected CsSAP genes displayed transcriptional responses to cold, drought, and salt stresses. These results enable the first comprehensive description of the SAP gene family in cucumber and lay a solid foundation for future research on the biological functions of CsSAP genes.

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(456) Abiotic Stress Responses in Cucumber (Cucumis sativus L.) Plants Expressing the Arabidopsis thaliana Transcriptional Activators-CBF1and CBF3

HortScience ◽

10.21273/hortsci.40.4.1036e ◽

2005 ◽

Vol 40 (4) ◽

pp. 1036E-1037

Author(s):

Mohamed Tawfik ◽

Alejandra Ferenczi ◽

Daniel Enter ◽

Rebecca Grumet

Keyword(s):

Oxidative Stress ◽

Abiotic Stress ◽

Drought Stress ◽

Stress Responses ◽

Stress Resistance ◽

Photochemical Efficiency ◽

Leaf Damage ◽

Cucumis Sativus L ◽

Oxidative Stresses ◽

Major Factors

Abiotic stresses (e.g., salinity, drought, cold, oxidative stress) can be major factors limiting plant productivity worldwide. We sought to increase abiotic stress resistance in cucumber by expressing the A. thaliana transcription factors CBF1and CBF3, which regulate genes responsible for enhanced dehydration-stress resistance in Arabidopsis. Our previous studies in the greenhouse and field demonstrated increased salinity tolerance in CBF-expressing cucumber lines. In the current studies, we tested response of CBF-cucumber plants to drought, chilling, and oxidative stresses. Transgenic cucumber plants subjected to drought stress in the greenhouse showed elevated levels of the stress-inducible compatible solute, proline, compared to the nontransgenic controls. Preliminary results also indicate greater photochemical efficiency in CBF-expressing plants under drought stress conditions compared to the nontransgenic controls. Under nonstressed conditions, there were no significant differences in growth between the transgenic and the nontransgenic cucumber plants; however, after a cycle of drought stress, CBF-cucumber lines had less growth reduction compared to the nontransgenic counterparts. The advantage in growth was less pronounced after a second cycle of drought. We also evaluated the transgenic cucumber plants under chilling conditions (i.e., low, nonfreezing temperatures within the 0 to 12 °C range). Based on plant height and cotyledon and leaf damage measurements, transgenic cucumber seedlings did not show chilling tolerance compared to the wild-type control. The response of transgenic CBF-cucumber plants to oxidative stress using methyl viologen is also being evaluated.

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