Meta-analysis of transcriptomic responses to biotic and abiotic stress in tomato

A wide range of biotic stresses (BS) and abiotic stresses (AS) adversely affect plant growth and productivity worldwide. The study of individual genes cannot be considered as an effective approach for the understanding of tolerance mechanisms, since these stresses are frequent and often in combination with each other, and a large number of genes are involved in these mechanisms. The availability of high-throughput genomic data has enabled the discovery of the role of transcription factors (TFs) in regulatory networks. A meta-analysis of BS and AS responses was performed by analyzing a total of 391 microarray samples from 23 different experiments and 2,336 differentially expressed genes (DEGs) involved in multiple stresses were identified. We identified 1,862 genes differentially regulated in response to BS was much greater than that regulated by AS, 835 genes, and found 15.4% or 361 DEGs with the conserved expression between AS and BS. The greatest percent of genes related to the cellular process (>76% genes), metabolic process (>76% genes) and response to stimulus (>50%). About 4.2% of genes involved in BS and AS responses belonged to the TF families. We identified several genes, which encode TFs that play an important role in AS and BS responses. These proteins included Jasmonate Ethylene Response Factor 1 (JERF1), SlGRAS6, MYB48, SlERF4, EIL2, protein LATE ELONGATED HYPOCOTYL (LHY), SlERF1, WRKY 26, basic leucine zipper TF, inducer of CBF expression 1-like, pti6, EIL3 and WRKY 11. Six of these proteins, JERF1, MYB48, protein LHY, EIL3, EIL2 and SlGRAS6, play central roles in these mechanisms. This research promoted a new approach to clarify the expression profiles of various genes under different conditions in plants, detected common genes from differentially regulated in response to these conditions and introduced them as candidate genes for improving plant tolerance through genetic engineering approach.

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Genome-wide systematic characterization and its regulatory expression reprogramming process of the bZIP transcription factors during trauma response in Camellia sinensis

Canadian Journal of Forest Research ◽

10.1139/cjfr-2018-0135 ◽

2018 ◽

Vol 48 (11) ◽

pp. 1279-1291

Author(s):

Yajie Xue ◽

Zaibao Zhang ◽

Lei Wang ◽

Yajun Yu ◽

Jinbin Xiao ◽

...

Keyword(s):

Phylogenetic Relationship ◽

Camellia Sinensis ◽

Leucine Zipper ◽

Expression Profiles ◽

Functional Characterization ◽

Gene Expression Profiles ◽

Bzip Transcription Factor ◽

Motif Analysis ◽

Basic Leucine Zipper ◽

Tea Tree

Basic leucine zipper (bZIP) transcription factor (TF) genes regulate numerous biological processes, as well as biotic and abiotic responses. Although the genome of the tea tree (Camellia sinensis (L.) Kuntze) has been released, knowledge regarding the bZIP TF family in C. sinensis, e.g., phylogenetic relationship and transcriptional gene expression profiles, remains limited. In this study, we characterized 77 bZIP genes in C. sinensis based on transcriptomic and genomic data and divided them into 11 groups according to their phylogenetic relationship with those in Arabidopsis, which allowed us to identify 14 pairs of orthologous proteins shared by Arabidopsis and C. sinensis and 19 pairs of paralogous proteins in C. sinensis. Conserved motif analysis of CsbZIP proteins showed high group specificity. Our classification was supported by the predicted specificities based on DNA-binding domains, as well as the dimerization property based on characteristic features in the basic and hinge regions and the leucine zipper. Specifically, they indicated that some highly conserved amino acid residues exist across each major group in the tree of land plant life. Expression profiling analyses indicate that the CsbZIP genes are likely involved in response to trauma, and a model was established to display the unique expression of each group during different time intervals after wounding. This work provides useful clues for further functional characterization of the CsbZIP TFs.

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Identification and characterization of the bZIP transcription factor family in yellowhorn

Journal of Forestry Research ◽

10.1007/s11676-020-01129-3 ◽

2020 ◽

Vol 32 (1) ◽

pp. 273-284 ◽

Cited By ~ 1

Author(s):

Qiaoying Chang ◽

Xin Lu ◽

Zhi Liu ◽

Zhimin Zheng ◽

Song Yu

Keyword(s):

Transcription Factor ◽

Leucine Zipper ◽

Molecular Mechanisms ◽

Bzip Transcription Factor ◽

Biological Functions ◽

Transcription Factor Family ◽

Promoter Regions ◽

Basic Leucine Zipper ◽

Biotic Stresses ◽

Bzip Transcription Factor Family

AbstractThe basic leucine zipper (bZIP) transcription factor family is one of the largest and most diverse families in plants, regulating plant growth and development and playing an essential role in response to abiotic and biotic stresses. However, little is known about the biological functions of bZIP proteins in yellowhorn (Xanthoceras sorbifolium). Recently, 64 XsbZIP genes were identified in the yellowhorn genome and found to be disproportionately distributed in linkage groups. The XsbZIP proteins clustered into 11 groups based on their phylogenetic relationships with AtbZIP, ZmbZIP and GmbZIP proteins. Five intron patterns in the basic and hinge regions and additional conserved motifs were defined, both supporting the group classification and possibly contributing to their functional diversity. Compared to tandem duplication, the segment duplication greatly contributed to the expansion of yellowhorn bZIP genes. In addition, most XsbZIP genes harbor several stress responsive cis-elements in their promoter regions. Moreover, the RNA-seq and qRT-PCR data indicated XsbZIP genes were extensively involved in response to various stresses, including salt (NaCl), cold and abscisic acid, with possibly different molecular mechanisms. These results provide a new understanding of the biological functions of bZIP transcription factors in yellowhorn.

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Genome wide in-silico miRNA and target network prediction from stress responsive Horsegram (Macrotyloma uniflorum) accessions

Scientific Reports ◽

10.1038/s41598-020-73140-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Jeshima Khan Yasin ◽

Bharat Kumar Mishra ◽

M. Arumugam Pillai ◽

Nidhi Verma ◽

Shabir H. Wani ◽

...

Keyword(s):

Energy Conservation ◽

Stress Tolerance ◽

Regulatory Networks ◽

Expression Profiles ◽

Abiotic Stress Tolerance ◽

Functional Characterization ◽

Moisture Stress ◽

Biotic And Abiotic Stress ◽

Macrotyloma Uniflorum ◽

Regulatory Rnas

Abstract Horsegram (Macrotyloma uniflorum (Lam.) Verdc.) is a drought hardy food and fodder legume of Indo-African continents with diverse germplasm sources demonstrating alternating mechanisms depicting contrasting adaptations to different climatic zones. Tissue specific expression of genes contributes substantially to location specific adaptations. Regulatory networks of such adaptive genes are elucidated for downstream translational research. MicroRNAs are small endogenous regulatory RNAs which alters the gene expression profiles at a particular time and type of tissue. Identification of such small regulatory RNAs in low moisture stress hardy crops can help in cross species transfer and validation confirming stress tolerance ability. This study outlined prediction of conserved miRNAs from transcriptome shotgun assembled sequences and EST sequences of horsegram. We could validate eight out of 15 of the identified miRNAs to demonstrate their role in deficit moisture stress tolerance mechanism of horsegram variety Paiyur1 with their target networks. The putative mumiRs were related to other food legumes indicating the presence of gene regulatory networks. Differential miRNA expression among drought specific tissues indicted the probable energy conservation mechanism. Targets were identified for functional characterization and regulatory network was constructed to find out the probable pathways of post-transcriptional regulation. The functional network revealed mechanism of biotic and abiotic stress tolerance, energy conservation and photoperiod responsiveness.

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Melatonin and Its Protective Role against Biotic Stress Impacts on Plants

Biomolecules ◽

10.3390/biom10010054 ◽

2019 ◽

Vol 10 (1) ◽

pp. 54 ◽

Cited By ~ 25

Author(s):

Mohamed Moustafa-Farag ◽

Abdulwareth Almoneafy ◽

Ahmed Mahmoud ◽

Amr Elkelish ◽

Marino B. Arnao ◽

...

Keyword(s):

Plant Resistance ◽

Biotic Stress ◽

Growth Regulation ◽

Protective Role ◽

Virus Concentration ◽

Plant Tolerance ◽

Biotic And Abiotic Stress ◽

Interaction Models ◽

Biotic Stresses

Biotic stress causes immense damage to agricultural products worldwide and raises the risk of hunger in many areas. Plants themselves tolerate biotic stresses via several pathways, including pathogen-associated molecular patterns (PAMPs), which trigger immunity and plant resistance (R) proteins. On the other hand, humans use several non-ecofriendly methods to control biotic stresses, such as chemical applications. Compared with chemical control, melatonin is an ecofriendly compound that is an economical alternative strategy which can be used to protect animals and plants from attacks via pathogens. In plants, the bactericidal capacity of melatonin was verified against Mycobacterium tuberculosis, as well as multidrug-resistant Gram-negative and -positive bacteria under in vitro conditions. Regarding plant–bacteria interaction, melatonin has presented effective antibacterial activities against phytobacterial pathogens. In plant–fungi interaction models, melatonin was found to play a key role in plant resistance to Botrytis cinerea, to increase fungicide susceptibility, and to reduce the stress tolerance of Phytophthora infestans. In plant–virus interaction models, melatonin not only efficiently eradicated apple stem grooving virus (ASGV) from apple shoots in vitro (making it useful for the production of virus-free plants) but also reduced tobacco mosaic virus (TMV) viral RNA and virus concentration in infected Nicotiana glutinosa and Solanum lycopersicum seedlings. Indeed, melatonin has unique advantages in plant growth regulation and increasing plant resistance effectiveness against different forms of biotic and abiotic stress. Although considerable work has been done regarding the role of melatonin in plant tolerance to abiotic stresses, its role in biotic stress remains unclear and requires clarification. In our review, we summarize the work that has been accomplished so far; highlight melatonin’s function in plant tolerance to pathogens such as bacteria, viruses, and fungi; and determine the direction required for future studies on this topic.

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Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum

BMC Genomics ◽

10.1186/s12864-021-08215-8 ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Jan Deneweth ◽

Yves Van de Peer ◽

Vanessa Vermeirssen

Keyword(s):

Gene Regulation ◽

Transposable Elements ◽

Regulatory Networks ◽

Expression Profiles ◽

Meta Analysis ◽

Light Stress ◽

Plant Stress ◽

Stress Conditions ◽

Specific Gene ◽

Regulatory Motifs

Abstract Background Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Several TEs can contribute to gene regulation by influencing expression of nearby genes as stress-responsive regulatory motifs. To delineate TE-mediated plant stress regulatory networks, we took a 2-step computational approach consisting of identifying TEs in the proximity of stress-responsive genes, followed by searching for cis-regulatory motifs in these TE sequences and linking them to known regulatory factors. Through a systematic meta-analysis of RNA-seq expression profiles and genome annotations, we investigated the relation between the presence of TE superfamilies upstream, downstream or within introns of nearby genes and the differential expression of these genes in various stress conditions in the TE-poor Arabidopsis thaliana and the TE-rich Solanum lycopersicum. Results We found that stress conditions frequently expressed genes having members of various TE superfamilies in their genomic proximity, such as SINE upon proteotoxic stress and Copia and Gypsy upon heat stress in A. thaliana, and EPRV and hAT upon infection, and Harbinger, LINE and Retrotransposon upon light stress in S. lycopersicum. These stress-specific gene-proximal TEs were mostly located within introns and more detected near upregulated than downregulated genes. Similar stress conditions were often related to the same TE superfamily. Additionally, we detected both novel and known motifs in the sequences of those TEs pointing to regulatory cooption of these TEs upon stress. Next, we constructed the regulatory network of TFs that act through binding these TEs to their target genes upon stress and discovered TE-mediated regulons targeted by TFs such as BRB/BPC, HD, HSF, GATA, NAC, DREB/CBF and MYB factors in Arabidopsis and AP2/ERF/B3, NAC, NF-Y, MYB, CXC and HD factors in tomato. Conclusions Overall, we map TE-mediated plant stress regulatory networks using numerous stress expression profile studies for two contrasting plant species to study the regulatory role TEs play in the response to stress. As TE-mediated gene regulation allows plants to adapt more rapidly to new environmental conditions, this study contributes to the future development of climate-resilient plants.

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Genome-wide identification and analysis of the basic leucine zipper (bZIP) transcription factor gene family in Ustilaginoidea virens

Genome ◽

10.1139/gen-2017-0089 ◽

2017 ◽

Vol 60 (12) ◽

pp. 1051-1059 ◽

Cited By ~ 11

Author(s):

Weixiao Yin ◽

Peng Cui ◽

Wei Wei ◽

Yang Lin ◽

Chaoxi Luo

Keyword(s):

Transcription Factor ◽

Phylogenetic Relationships ◽

Leucine Zipper ◽

Expression Profiles ◽

Pathogenic Fungi ◽

Bzip Transcription Factor ◽

Basic Leucine Zipper ◽

Ustilaginoidea Virens ◽

Infection Period ◽

Genome Wide

The basic leucine zipper (bZIP) transcription factor (TF) family is one of the largest and most diverse TF families widely distributed across the eukaryotes. The bZIP TF family plays an important role in growth, development, and response to abiotic or biotic stresses, which have been well characterized in plants, but not in plant pathogenic fungi. In this study, we performed genome-wide and systematic bioinformatics analysis of bZIP genes in the fungus Ustilaginoidea virens, the causal agent of rice false smut disease. We identified 28 bZIP family members in the U. virens genome by searching for the bZIP domain in predicted genes. The gene structures, motifs, and phylogenetic relationships were analyzed for bZIP genes in U. virens (UvbZIP). Together with bZIP proteins from two other fungi, the bZIP genes can be divided into eight groups according to their phylogenetic relationships. Based on RNA-Seq data, the expression profiles of UvbZIP genes at different infection stages were evaluated. Results showed that 17 UvbZIP genes were up-regulated during the infection period. Furthermore, 11 infection-related UvbZIP genes were investigated under H2O2 stress and the expression level of eight genes were changed, which confirmed their role in stress tolerance and pathogenicity. In summary, our genome-wide systematic characterization and expression analysis of UvbZIP genes provided insight into the molecular function of these genes in U. virens and provides a reference for other pathogens.

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Systematic Analysis of the bZIP Family in Tobacco and Functional Characterization of NtbZIP62 Involvement in Salt Stress

Agronomy ◽

10.3390/agronomy11010148 ◽

2021 ◽

Vol 11 (1) ◽

pp. 148

Author(s):

Zhiyuan Li ◽

Jiangtao Chao ◽

Xiaoxu Li ◽

Gongbo Li ◽

Dean Song ◽

...

Keyword(s):

Salt Stress ◽

Leucine Zipper ◽

Expression Profiles ◽

Functional Characterization ◽

Segmental Duplications ◽

Basic Leucine Zipper ◽

Systematic Analysis ◽

Duplication Events ◽

Tobacco Genome ◽

Gene Structures

The basic leucine zipper (bZIP) transcription factors play important regulatory roles, influencing plant growth and responses to environmental stresses. In the present study, 132 bZIP genes identified in the tobacco genome were classified into 11 groups with Arabidopsis and tomato bZIP members, based on the results of a phylogenetic analysis. An examination of gene structures and conserved motifs revealed relatively conserved exon/intron structures and motif organization within each group. The results of an investigation of whole-genome duplication events indicated that segmental duplications were crucial for the expansion of the bZIP gene family in tobacco. Expression profiles confirmed that the NtbZIP genes are differentially expressed in various tissues, and several genes are responsive to diverse stresses. Notably, NtbZIP62, which was identified as an AtbZIP37/ABF3 homolog, was highly expressed in response to salinity. Subcellular localization analyses proved that NtbZIP62 is a nuclear protein. Furthermore, the overexpression of NtbZIP62 in tobacco significantly enhanced the salt stress tolerance of the transgenic plants. The results of this study may be relevant for future functional analyses of the bZIP genes in tobacco.

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Basic Leucine zipper (bZIP) transcription factor genes and their response to drought stress in ginseng, Panax ginseng C.A. Meyer

10.21203/rs.2.20019/v1 ◽

2020 ◽

Author(s):

Hongjie Li ◽

Jing Chen ◽

Qi Zhao ◽

Yilai Han ◽

Chunyu Sun ◽

...

Keyword(s):

Transcription Factor ◽

Drought Stress ◽

Leucine Zipper ◽

Bzip Transcription Factor ◽

Functional Categories ◽

Basic Leucine Zipper ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses ◽

Transcription Factor Genes ◽

Alternatively Spliced

Abstract Background: As a famous and important medicinal herb in the world, ginseng contains numerous bioactive components that are remarkable for mankind's health. The basic leucine zipper (bZIP) transcription factor genes play important roles in many biological processes and plant response to abiotic and biotic stresses. Nevertheless, these genes remain unknown in ginseng. Results: Here, we report 91 bZIP genes, designated as PgbZIP genes, identified from ginseng. These PgbZIP genes were alternatively spliced into 273 transcripts. Phylogenetic analysis grouped the PgbZIP genes into ten groups, including A, B, C, D, E, F, G, H, I and S. Gene Ontology (GO) categorized the PgbZIP genes into a number of functional categories, suggesting that they have substantially diversified in functionality, even though their putative proteins share a number of conserved motifs. These 273 PgbZIP transcripts expressed quite differentially across 14 different tissues, the roots of different aged, and the roots of different cultivars. However, the expression of these transcripts was coordinated as they formed a co-expression network. Furthermore, we studied their response to drought stress in ginseng using five representatives of the PgbZIP genes, including PgbZIP25 , PgbZIP38 , PgbZIP39 , PgbZIP53 and PgbZIP54 . The results showed that these PgbZIP genes all responded to drought stress in ginseng, but the magnitudes of their response to drought stress varied. Conclusions: These results provide knowledge and resources for deeper functional analysis of PgbZIP genes and molecular tools for enhanced drought tolerance breeding in ginseng.

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Meta-Analysis of Expression of the Stress Tolerance Associated Genes and Uncover their Cis-Regulatory Elements in Rice (Oryza sativa L.)

The Open Bioinformatics Journal ◽

10.2174/1875036202013010039 ◽

2020 ◽

Vol 13 (1) ◽

pp. 39-49 ◽

Cited By ~ 1

Author(s):

Nikwan Shariatipour ◽

Bahram Heidari

Keyword(s):

Oryza Sativa ◽

Stress Tolerance ◽

Abiotic Stresses ◽

Regulatory Networks ◽

Oryza Sativa L ◽

Expression Profiles ◽

Meta Analysis ◽

Regulatory Elements ◽

Significant Differential Expression ◽

Bioinformatics Tools

Background: Rice contributes to the staple food of more than half of the world’s population. However, its productivity is influenced by various biotic and abiotic stresses. Genetic engineering and plant breeding tools help to overcome the adverse effects of environmental stresses. The advanced bioinformatics tools provide information for a better understanding of the mechanisms underlying stress tolerance, gene expression profiles and functions of the important genes and cis-regulatory elements involved in better performance under abiotic stresses. Objective: To identify the key genes involved in the tolerance mechanism for abiotic stresses and their regulatory networks in rice (Oryza sativa L.). Methods: A total of 152 various microarray datasets associated with nine rice trials were retrieved for expression meta-analysis through various bioinformatics tools. Results: The results indicated that 29593, 202798, 73224 and 25241 genes represented significant differential expression under cold, drought, salinity and heat stress conditions compared with the control condition, respectively. Twenty three highly overexpressed genes were identified under the evaluated abiotic stresses. The transcription regulatory activity of differentially expressed genes was mainly due to hormone, light and stress-responsive cis-acting regulatory elements among which ABRE, ARE, CGTCA-motif, GARE-motif, TGACG-motif, G-box, G-Box, GAG-motif, GA-motif, TCT-motif, Box 4, Sp1, HSE, MBS and TC-rich repeats were the most important in the promoter sites of the identified up-regulated genes. The results of cis-acting regulatory analysis suggest that 15 cis-acting regulatory elements were contributed to the tolerance mechanisms for abiotic stresses. Conclusion: The result of expression meta-analysis in this study provides an insight for plant breeders for better understanding the function of the genes and their regulatory mechanism in plants (especially cereals) exposed to different abiotic stresses. The outcome of this study suggests practical approaches for designing unified breeding programmes to breed multi-abiotic stress-tolerant species.

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Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

BMC Genomics ◽

10.1186/s12864-021-07624-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Hongjie Li ◽

Jing Chen ◽

Qi Zhao ◽

Yilai Han ◽

Li Li ◽

...

Keyword(s):

Transcription Factor ◽

Drought Stress ◽

Leucine Zipper ◽

Bzip Transcription Factor ◽

Plant Responses ◽

Basic Leucine Zipper ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses ◽

Transcription Factor Genes ◽

Alternatively Spliced

Abstract Background Ginseng is an important medicinal herb in Asia and Northern America. The basic leucine zipper (bZIP) transcription factor genes play important roles in many biological processes and plant responses to abiotic and biotic stresses, such as drought stress. Nevertheless, the genes remain unknown in ginseng. Results Here, we report 91 bZIP genes identified from ginseng, designated PgbZIP genes. These PgbZIP genes were alternatively spliced into 273 transcripts. Phylogenetic analysis grouped the PgbZIP genes into ten groups, including A, B, C, D, E, F, G, H, I and S. Gene Ontology (GO) categorized the PgbZIP genes into five functional subcategories, suggesting that they have diversified in functionality, even though their putative proteins share a number of conserved motifs. These 273 PgbZIP transcripts expressed differentially across 14 tissues, the roots of different ages and the roots of different genotypes. However, the transcripts of the genes expressed coordinately and were more likely to form a co-expression network. Furthermore, we studied the responses of the PgbZIP genes to drought stress in ginseng using a random selection of five PgbZIP genes, including PgbZIP25, PgbZIP38, PgbZIP39, PgbZIP53 and PgbZIP54. The results showed that all five PgbZIP genes responded to drought stress in ginseng, indicating that the PgbZIP genes play important roles in ginseng responses to drought stress. Conclusions These results provide knowledge and gene resources for deeper functional analysis of the PgbZIP genes and molecular tools for enhanced drought tolerance breeding in ginseng.

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