scholarly journals Transcription Factors in Plant Stress Responses: Challenges and Potential for Sugarcane Improvement

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 491 ◽  
Author(s):  
Talha Javed ◽  
Rubab Shabbir ◽  
Ahmad Ali ◽  
Irfan Afzal ◽  
Uroosa Zaheer ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Target Genes ◽  
Plant Stress ◽  
Growth And Yield ◽  
Abiotic And Biotic Stresses ◽  
Cis Acting ◽  
Biotic Stresses ◽  
Signal Perception ◽  
Wide Range

Increasing vulnerability of crops to a wide range of abiotic and biotic stresses can have a marked influence on the growth and yield of major crops, especially sugarcane (Saccharum spp.). In response to various stresses, plants have evolved a variety of complex defense systems of signal perception and transduction networks. Transcription factors (TFs) that are activated by different pathways of signal transduction and can directly or indirectly combine with cis-acting elements to modulate the transcription efficiency of target genes, which play key regulators for crop genetic improvement. Over the past decade, significant progresses have been made in deciphering the role of plant TFs as key regulators of environmental responses in particular important cereal crops; however, a limited amount of studies have focused on sugarcane. This review summarizes the potential functions of major TF families, such as WRKY, NAC, MYB and AP2/ERF, in regulating gene expression in the response of plants to abiotic and biotic stresses, which provides important clues for the engineering of stress-tolerant cultivars in sugarcane.

scholarly journals VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development

2020 ◽  
Author(s):  
Haley S. Toups ◽  
Noé Cochetel ◽  
Dennis Gray ◽  
Grant R. Cramer
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Berry Development ◽  
Rna Seq ◽  
Abiotic And Biotic Stresses ◽  
Vitis Species ◽  
Biotic Stresses ◽  
Similar Expression

Abstract Background: VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress responses. To better understand this highly duplicated, conserved clade, additional members of the clade were identified in four Vitis genotypes. A meta-data analysis was performed on publicly available microarray and RNA-Seq data (confirmed and expanded with RT-qPCR), and Vitis VviERF6L1 overexpression lines were established and characterized with phenotyping and RNA-Seq. Results: A total of 18 PN40024 VviERF6Ls were identified; additional VviERF6Ls were identified in Cabernet Sauvignon, Chardonnay, and Carménère. The amino acid sequences of VviERF6Ls were found to be highly conserved. VviERF6L transcripts were detected in numerous plant organs and were differentially expressed in response to numerous abiotic stresses including water deficit, salinity, and cold as well as biotic stresses such as red blotch virus, N. parvum , and E. necator . VviERF6Ls were differentially expressed across stages of berry development, peaking in the pre-veraison/veraison stage and retaining conserved expression patterns across different vineyards, years, and Vitis cultivars. Co-expression network analysis identified a scarecrow-like transcription factor and a calmodulin-like gene with highly similar expression profiles to the VviERF6L clade. Overexpression of VviERF6L1 in a Seyval Blanc background did not result in detectable morphological phenotypes. Genes differentially expressed in response to VviERF6L1 overexpression were associated with abiotic and biotic stress responses. Conclusions: VviERF6Ls represent a large and distinct clade of ERF transcription factors in grapevine. The high conservation of protein sequence between these 18 transcription factors may indicate these genes originate from a duplication event in Vitis . Despite high sequence similarity and similar expression patterns, VviERF6Ls demonstrate unique levels of expression supported by similar but heterogeneous promoter sequences. VviERF6L gene expression differed between Vitis species, cultivars and organs including roots, leaves and berries. These genes respond to berry development and abiotic and biotic stresses. VviERF6L1 overexpression in Vitis vinifera results in differential expression of genes related to phytohormone and immune system signaling. Further investigation of this interesting gene family is warranted.

scholarly journals Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 771 ◽  
Author(s):  
Baillo ◽  
Kimotho ◽  
Zhang ◽  
Xu
Keyword(s):  
Transcription Factors ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Biotic Stress ◽  
Crop Improvement ◽  
Abiotic And Biotic Stress ◽  
Crop Species ◽  
Biotic Stresses ◽  
Wide Range ◽  
Tf Gene

In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses can have a marked effect on crop yield. The present and future effects of climate change necessitate the improvement of crop stress tolerance. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) that are master regulators of stress-responsive genes are excellent candidates for crop improvement. Related examples in recent studies include TF gene modulation and overexpression approaches in crop species to enhance stress tolerance. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families, only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. Moreover, although significant progress has been made in deciphering the roles of TFs in important cereal crops, fewer TF genes have been elucidated in sorghum. As a model drought-tolerant crop, sorghum research warrants further focus. This review summarizes recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement, particularly in sorghum. Other TF families and non-coding RNAs that regulate gene expression are discussed briefly. Despite the emphasis on sorghum, numerous examples from wheat, rice, maize, and barley are included. Collectively, the aim of this review is to illustrate the potential application of TF genes for stress tolerance improvement and the engineering of resistant crops, with an emphasis on sorghum.

scholarly journals CHARACTERISTICS OF miRNA INTERACTION WITH mRNA GENES OF T. AESTIVUM C2H2, ERF, GRAS TRANSCRIPTION FACTORS FAMILIES

2020 ◽  
Vol 2 (338) ◽  
pp. 5-11
Author(s):  
A. K. Rakhmetullina ◽  
S. K. Turasheva ◽  
A. A. Bolshoy ◽  
A. T. Ivashchenko
Keyword(s):  
Transcription Factors ◽  
Binding Sites ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Gras Family ◽  
Physiological Processes ◽  
Nucleotide Interactions

The molecular mechanisms for increasing plant productivity remain poorly understood. Genes of C2H2, GRAS, ERF transcription factors (TFs) families play a key role in the physiological processes of plants, including wheat. In recent years, the important role of miRNAs in the regulation of the expression of many genes involved in the formation of productivity has been established. Wheat miRNA (mRNA-inhibiting RNA) target genes are involved in the regulation of the development of flowers, seeds, root, shoots, and responses to abiotic and biotic stresses. The miRNAs binding sites in mRNAs of C2H2, ERF, GRAS TFs families were performed using the MirTarget program, which calculates the free energy of miRNA binding with mRNA, the schemes and positions of nucleotide interactions with binding sites. Wheat genes were used as the object of the study, since wheat is one of the main grain crops in Kazakhstan and in many other countries. The presence of miRNA binding sites with high nucleotide complementarity in mRNA of C2H2, ERF, GRAS TF genes of wheat was shown. All binding sites of these miRNAs were located in the CDS of mRNA target genes. Of the 125 miRNAs of T. aestivum, miR319-3p efficiently bound with mRNA of C2H2 family genes with the value of ΔG/ΔGm equal 91 %. miR7757-5p interacted with mRNA of ERF and GRAS family genes with the value of ΔG/ΔGm equal to 92 % and 90 % respectively. miR9778-5p bound with mRNA of C2H2, ERF, GRAS family genes to varying degrees. Each of the miR408-3p, miR9780-3p, and miR9778-5p had four target genes with the value of ΔG/ΔGm equal to 87 % and 89 %. These data indicate the dependency of C2H2, GRAS, ERF TFs families expression on miRNA. The obtained results expand the fundamental ideas about the regulatory mechanisms of miRNA in the process of plant growth and development.

scholarly journals VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development

2020 ◽  
Author(s):  
Haley S. Toups ◽  
Noé Cochetel ◽  
Dennis Gray ◽  
Grant R. Cramer
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Berry Development ◽  
Rna Seq ◽  
Abiotic And Biotic Stresses ◽  
Vitis Species ◽  
Biotic Stresses ◽  
Similar Expression

Abstract Background VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress responses. To better understand this highly duplicated, conserved clade, additional members of the clade were identified in four Vitis genotypes. A meta-data analysis was performed on publicly available microarray and RNA-Seq data (confirmed and expanded with RT-qPCR), and a Vitis VviERF6L1 overexpression line was established and characterized with phenotyping and RNA-Seq. Results A total of 18 PN40024 VviERF6Ls were identified; additional VviERF6Ls were identified in Cabernet Sauvignon, Chardonnay, and Carménère. The amino acid sequences of VviERF6Ls were found to be highly conserved. VviERF6L transcripts were detected in numerous plant organs and were differentially expressed in response to numerous abiotic stresses including water deficit, salinity, and cold as well as biotic stresses such as red blotch virus, N. parvum , and E. necator . VviERF6Ls were differentially expressed across stages of berry development, peaking in the pre-veraison/veraison stage, and retaining conserved expression patterns across different vineyards, years, and Vitis cultivars. Co-expression network analysis identified a scarecrow-like transcription factor and a calmodulin-like gene with highly similar expression profiles to the VviERF6L clade. Overexpression of VviERF6L1 in a Seyval Blanc background did not result in detectable morphological phenotypes. Genes differentially expressed in response to VviERF6L1 overexpression were associated with abiotic and biotic stress responses. Conclusions VviERF6Ls represent a large and distinct clade of ERF transcription factors in grapevine. The high conservation of protein sequence between these 18 transcription factors may indicate these genes originate from a duplication event in Vitis . Despite high sequence similarity and similar expression patterns, VviERF6Ls demonstrate unique levels of expression supported by similar but heterogeneous promoter sequences. VviERF6L gene expression differed between Vitis species, cultivars and organs including roots, leaves and berries. These genes respond to berry development and abiotic and biotic stresses. VviERF6L1 overexpression in Vitis vinifera results in differential expression of genes related to phytohormone and immune system signaling. Further investigation of this interesting gene family is warranted.

scholarly journals The Interplay among Polyamines and Nitrogen in Plant Stress Responses

Plants ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 315 ◽  
Author(s):  
Konstantinos Paschalidis ◽  
Georgios Tsaniklidis ◽  
Bao-Quan Wang ◽  
Costas Delis ◽  
Emmanouil Trantas ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Stress Responses ◽  
Plant Stress ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
N Assimilation ◽  
Major Player ◽  
Key Factor ◽  
Plant Stress Responses ◽  
N Metabolism

The interplay between polyamines (PAs) and nitrogen (N) is emerging as a key factor in plant response to abiotic and biotic stresses. The PA/N interplay in plants connects N metabolism, carbon (C) fixation, and secondary metabolism pathways. Glutamate, a pivotal N-containing molecule, is responsible for the biosynthesis of proline (Pro), arginine (Arg) and ornithine (Orn) and constitutes a main common pathway for PAs and C/N assimilation/incorporation implicated in various stresses. PAs and their derivatives are important signaling molecules, as they act largely by protecting and preserving the function/structure of cells in response to stresses. Use of different research approaches, such as generation of transgenic plants with modified intracellular N and PA homeostasis, has helped to elucidate a plethora of PA roles, underpinning their function as a major player in plant stress responses. In this context, a range of transgenic plants over-or under-expressing N/PA metabolic genes has been developed in an effort to decipher their implication in stress signaling. The current review describes how N and PAs regulate plant growth and facilitate crop acclimatization to adverse environments in an attempt to further elucidate the N-PAs interplay against abiotic and biotic stresses, as well as the mechanisms controlling N-PA genes/enzymes and metabolites.

scholarly journals Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guiomar Martín ◽  
Yamile Márquez ◽  
Federica Mantica ◽  
Paula Duque ◽  
Manuel Irimia
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Alternative Splicing ◽  
Stress Responses ◽  
Target Genes ◽  
Intron Retention ◽  
Single Gene ◽  
Exon Skipping ◽  
Environmental Response ◽  
Biotic Stresses

Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. Results We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. Conclusions Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.

scholarly journals OsNAC45 is Involved in ABA Response and Salt Tolerance in Rice

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Xiang Zhang ◽  
Yan Long ◽  
Jingjing Huang ◽  
Jixing Xia
Keyword(s):  
Transcription Factors ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Stress Responses ◽  
Crop Yields ◽  
Plant Stress ◽  
Root Cells ◽  
Nac Transcription Factors ◽  
Rice Plants ◽  
Plant Stress Responses

Abstract Background Salt stress threatens crop yields all over the world. Many NAC transcription factors have been reported to be involved in different abiotic stress responses, but it remains unclear how loss of these transcription factors alters the transcriptomes of plants. Previous reports have demonstrated that overexpression of OsNAC45 enhances salt and drought tolerance in rice, and that OsNAC45 may regulate the expression of two specific genes, OsPM1 and OsLEA3–1. Results Here, we found that ABA repressed, and NaCl promoted, the expression of OsNAC45 in roots. Immunostaining showed that OsNAC45 was localized in all root cells and was mainly expressed in the stele. Loss of OsNAC45 decreased the sensitivity of rice plants to ABA and over-expressing this gene had the opposite effect, which demonstrated that OsNAC45 played an important role during ABA signal responses. Knockout of OsNAC45 also resulted in more ROS accumulation in roots and increased sensitivity of rice to salt stress. Transcriptome sequencing assay found that thousands of genes were differently expressed in OsNAC45-knockout plants. Most of the down-regulated genes participated in plant stress responses. Quantitative real time RT-PCR suggested that seven genes may be regulated by OsNAC45 including OsCYP89G1, OsDREB1F, OsEREBP2, OsERF104, OsPM1, OsSAMDC2, and OsSIK1. Conclusions These results indicate that OsNAC45 plays vital roles in ABA signal responses and salt tolerance in rice. Further characterization of this gene may help us understand ABA signal pathway and breed rice plants that are more tolerant to salt stress.

scholarly journals Recent Development on Plant Aldehyde Dehydrogenase Enzymes and Their Functions in Plant Development and Stress Signaling

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 51
Author(s):  
Adesola J. Tola ◽  
Amal Jaballi ◽  
Hugo Germain ◽  
Tagnon D. Missihoun
Keyword(s):  
Plant Development ◽  
Critical Analysis ◽  
Current Knowledge ◽  
Stress Signaling ◽  
Oxygen Species ◽  
Abiotic And Biotic Stresses ◽  
Aldehyde Dehydrogenases ◽  
Biotic Stresses ◽  
Wide Range ◽  
Excessive Accumulation

Abiotic and biotic stresses induce the formation of reactive oxygen species (ROS), which subsequently causes the excessive accumulation of aldehydes in cells. Stress-derived aldehydes are commonly designated as reactive electrophile species (RES) as a result of the presence of an electrophilic α, β-unsaturated carbonyl group. Aldehyde dehydrogenases (ALDHs) are NAD(P)+-dependent enzymes that metabolize a wide range of endogenous and exogenous aliphatic and aromatic aldehyde molecules by oxidizing them to their corresponding carboxylic acids. The ALDH enzymes are found in nearly all organisms, and plants contain fourteen ALDH protein families. In this review, we performed a critical analysis of the research reports over the last decade on plant ALDHs. Newly discovered roles for these enzymes in metabolism, signaling and development have been highlighted and discussed. We concluded with suggestions for future investigations to exploit the potential of these enzymes in biotechnology and to improve our current knowledge about these enzymes in gene signaling and plant development.

Versatile physiological functions of the Nudix Hydrolase family in berry development and stress response in grapevine

2020 ◽  
Author(s):  
Zhaoke Wang ◽  
Peipei Wang ◽  
Le Guan ◽  
Muhammad Salman Haider ◽  
Maazullah Nasim ◽  
...  
Keyword(s):  
Stress Response ◽  
Expression Patterns ◽  
Leaf Roll ◽  
Pcr Analysis ◽  
Berry Development ◽  
Abiotic And Biotic Stresses ◽  
Physiological Functions ◽  
Biotic Stresses ◽  
Wide Range ◽  
Nudix Hydrolases

Abstract Background Nudix hydrolases are widely distributed across all classes of organisms and provide the potential capacity to hydrolyze a wide range of organic pyrophosphates. Although Nudix hydrolases are involved in plants detoxification processes in response to abiotic and biotic stresses, the biological functions of Nudix hydrolases remain largely unclear in grapevine. Results A total of 25 putative grapevine Nudix hydrolases ( VvNUDXs ) were identified by bioinformatics analysis and classified into eight subfamilies based to their preferred substrates. Both tandem and segmental duplications were responsible for the evolution and expansion of NUDX gene family in grapevine. To investigate into their regulatory roles of VvNUDX genes during growth and development as well as in response to abiotic and biotic stress in grapevine, the expression patterns were revealed in publicly available microarray data. The spatial and temporal expression patterns of VvNUDX genes indicated that these genes might play important roles in multiple developmental processes. Transcriptome and qRT-PCR analysis exhibited that ten VvNUDX genes were specifically expressed in grapevine berries, suggesting the potential roles in grapevine berry development. Expression and phylogenetic analysis demonstrated that VvNUDX1 and VvNUDX3 might be involved in terpenoid biosynthesis in grapevine. Futhermore, most VvNUDX genes toward the ADP-ribose/NADH were different patterns in response to various abiotic and biotic stresses, such as salinity and drought, as well as different types of biotic treatments, such as Erysiphe necator , Bois Noir phytoplasma and leaf-roll-associated virus-3 (GLRaV-3). Conclusions These results showed that VvNUDX were associated with plant detoxification processes in response to abiotic and biotic stresses, and regulate disease immunity and resistance pathways. The present informations may provide good opportunities to explore the physiological functions of VvNUDX genes in berry development and stress response networks in grapevine.

scholarly journals An R1R2R3 MYB Transcription Factor, MnMYB3R1, Regulates the Polyphenol Oxidase Gene in Mulberry (Morus notabilis)

2019 ◽  
Vol 20 (10) ◽  
pp. 2602 ◽  
Author(s):  
Dan Liu ◽  
Shuai Meng ◽  
Zhonghuai Xiang ◽  
Guangwei Yang ◽  
Ningjia He
Keyword(s):  
Transcription Factor ◽  
Polyphenol Oxidase ◽  
Stress Responses ◽  
Promoter Region ◽  
Plant Stress ◽  
Luciferase Reporter ◽  
Myb Transcription Factor ◽  
Oxidase Gene ◽  
Cis Acting ◽  
Plant Stress Responses

The aim of this study was to determine how the mulberry (Morus notabilis) polyphenol oxidase 1 gene (MnPPO1) is regulated during plant stress responses by exploring the interaction between its promoter region and regulatory transcription factors. First, we analyzed the cis-acting elements in the MnPPO1 promoter. Then, we used the MnPPO1 promoter region [(1268 bp, including an MYB3R-binding cis-element (MSA)] as a probe to capture proteins in DNA pull-down assays. These analyses revealed that the MYB3R1 transcription factor in M. notabilis (encoded by MnMYB3R1) binds to the MnPPO1 promoter region. We further explored the interaction between the MnPPO1 promoter and MYB3R1 with the dual luciferase reporter, yeast one-hybrid, and chromatin immunoprecipitation assays. These analyses verified that MnMYB3R1 binds to the MSA in the MnPPO1 promoter region. The overexpression of MnMYB3R1 in tobacco upregulated the expression of the tobacco PPO gene. This observation as well as the quantitative real-time PCR results implied that MnMYB3R1 and PPO are involved in the abscisic acid-responsive stress response pathway.

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