scholarly journals The Copper-microRNA Pathway Is Integrated with Developmental and Environmental Stress Responses in Arabidopsis thaliana

2021 ◽  
Vol 22 (17) ◽  
pp. 9547
Author(s):  
Ana Perea-García ◽  
Amparo Andrés-Bordería ◽  
Peter Huijser ◽  
Lola Peñarrubia
Keyword(s):  
Arabidopsis Thaliana ◽  
Environmental Stress ◽  
Stress Responses ◽  
Signal Transduction Pathway ◽  
Regulatory Elements ◽  
Developmental Phase ◽  
Promoter Regions ◽  
Cu Deficiency ◽  
Essential Nutrient ◽  
Mirna Pathway

As an essential nutrient, copper (Cu) scarcity causes a decrease in agricultural production. Cu deficiency responses include the induction of several microRNAs, known as Cu-miRNAs, which are responsible for degrading mRNAs from abundant and dispensable cuproproteins to economize copper when scarce. Cu-miRNAs, such as miR398 and miR408 are conserved, as well as the signal transduction pathway to induce them under Cu deficiency. The Arabidopsis thaliana SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family member SPL7 binds to the cis-regulatory motifs present in the promoter regions of genes expressed under Cu deficiency, including Cu-miRNAs. The expression of several other SPL transcription factor family members is regulated by miR156. This regulatory miR156-SPL module plays a crucial role in developmental phase transitions while integrating internal and external cues. Here, we show that Cu deficiency also affects miR156 expression and that SPL3 overexpressing plants, resistant to miR156 regulation, show a severe decrease in SPL7-mediated Cu deficiency responses. These include the expression of Cu-miRNAs and their targets and is probably due to competition between SPL7 and miR156-regulated SPL3 in binding to cis-regulatory elements in Cu-miRNA promoters. Thus, the conserved SPL7-mediated Cu-miRNA pathway could generally be affected by the miR156-SPL module, thereby underscoring the integration of the Cu-miRNA pathway with developmental and environmental stress responses in Arabidopsis thaliana.

scholarly journals Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12617
Author(s):  
Yarui Wei ◽  
Shuliang Zhao ◽  
Na Liu ◽  
Yuxing Zhang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Systemic Acquired Resistance ◽  
Acquired Resistance ◽  
Signal Transduction Pathway ◽  
Promoter Regions ◽  
Systematic Analysis ◽  
Genome Wide ◽  
Pathogenesis Related ◽  
Genome Level

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.

scholarly journals Comparative Genome-wide Analysis and Expression Profiling of Histone Acetyltransferases and Histone Deacetylases Involved in the Response to Drought in Wheat

2020 ◽  
Author(s):  
Hua Li ◽  
Huajie Liu ◽  
Xinxin Pei ◽  
Hongyu Chen ◽  
Xiao Li ◽  
...  
Keyword(s):  
Drought Stress ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Gene Expression Analysis ◽  
Regulatory Elements ◽  
Wheat Genome ◽  
Histone Acetyltransferases ◽  
Promoter Regions ◽  
Conserved Domain ◽  
Genome Wide

Abstract Background: Histone acetyltransferases (HATs) and histone deacetylases (HDACs) contribute to plant growth, development, and stress responses. A number of HAT and HDAC genes have been identified in several plants. However, wheat HATs and HDACs have not been comprehensively characterized. In this study, we identified TaHATs and TaHDACs in the wheat genome using bioinformatics tools. Result: In total, 30 TaHAT genes and 53 TaHDAC genes were detected in the wheat genome. As described in other plants, TaHATs were classified into four subfamilies (i.e., GNAT, p300/CBP, MYST, and TAFII250) and TaHDACs were divided into three subfamilies (i.e., RPD3/HDA1, HD2, and SIR2). Phylogenetic and conserved domain analyses showed that TaHATs and TaHDACs are highly similar to those in Arabidopsis and rice; however, divergence and expansion from Arabidopsis and rice were also observed. We detected many stress-related cis-regulatory elements in the promoter regions of these genes (i.e., ABRE, STRE, MYB et al.). Further, based on a comparative expression analyses of three varieties with different degrees of drought resistance under drought stress, we found that TaHAG2, TaHAG3, TaHAC2, TaHDA18, TaHDT1, and TaHDT2 are likely regulate drought stress in wheat. Conclusions: In this study, TaHATs and TaHDACs from the wheat genome were identified. Three TaHATs and three TaHDACs were very likely to regulate drought stress based on a promoter analysis and gene expression analysis. These results provide a foundation for further research on the regulation of acetylation in wheat and its role in the response to drought stress.

scholarly journals In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Raju Mondal ◽  
Subhankar Biswas ◽  
Akanksha Srivastava ◽  
Suvajit Basu ◽  
Maitri Trivedi ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Abiotic Stress ◽  
Signaling Pathways ◽  
Differential Expression ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Light Stress ◽  
Regulatory Elements ◽  
Qrt Pcr

Abstract Background S-domain receptor-like kinases (SD-RLKs) are an important and multi-gene subfamily of plant receptor-like/pelle kinases (RLKs), which are known to play a significant role in the development and immune responses of Arabidopsis thaliana. The conserved cysteine residues in the extracellular domain of SD-RLKs make them interesting candidates for sensing reactive oxygen species (ROS), assisting oxidative stress mitigation and associated signaling pathways during abiotic stresses. However, how closely SD-RLKs are interrelated to abiotic stress mitigation and signaling remains unknown in A. thaliana. Results This study was initiated by examining the chromosomal localization, phylogeny, sequence and differential expression analyses of 37 SD-RLK genes using publicly accessible microarray datasets under cold, osmotic stress, genotoxic stress, drought, salt, UV-B, heat and wounding. Out of 37 SD-RLKs, 12 genes displayed differential expression patterns in both the root and the shoot tissues. Promoter structure analysis suggested that these 12 SD-RLK genes harbour several potential cis-regulatory elements (CREs), which are involved in regulating multiple abiotic stress responses. Based on these observations, we investigated the expression patterns of 12 selected SD-RLKs under ozone, wounding, oxidative (methyl viologen), UV-B, cold, and light stress at different time points using semi-qRT-PCR. Of these 12 SD-SRKs, the genes At1g61360, At1g61460, At1g61380, and At4g27300 emerged as potential candidates that maintain their expression in most of the stress treatments till exposure for 12 h. Expression patterns of these four genes were further verified under similar stress treatments using qRT-PCR. The expression analysis indicated that the gene At1g61360, At1g61380, and At1g61460 were mostly up-regulated, whereas the expression of At4g27300 either up- or down-regulated in these conditions. Conclusions To summarize, the computational analysis and differential transcript accumulation of SD-RLKs under various abiotic stresses suggested their association with abiotic stress tolerance and related signaling in A. thaliana. We believe that a further detailed study will decipher the specific role of these representative SD-RLKs in abiotic stress mitigation vis-a-vis signaling pathways in A. thaliana.

scholarly journals Characteristics of SlCML39, a Tomato Calmodulin-like Gene, and Its Negative Role in High Temperature Tolerance of Arabidopsis thaliana during Germination and Seedling Growth

2021 ◽  
Vol 22 (21) ◽  
pp. 11479
Author(s):  
Haidong Ding ◽  
Ying Qian ◽  
Yifang Fang ◽  
Yurong Ji ◽  
Jiarong Sheng ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
High Temperature ◽  
Seedling Growth ◽  
Stress Responses ◽  
Plant Stress ◽  
Temperature Tolerance ◽  
Signal Pathway ◽  
Negative Regulator ◽  
Growth Stages ◽  
Promoter Regions

Calmodulin-like (CML) proteins are primary calcium sensors and function in plant growth and response to stress stimuli. However, so far, the function of plant CML proteins, including tomato, is still unclear. Previously, it was found that a tomato (Solanum lycopersicum) CML, here named SlCML39, was significantly induced by high temperature (HT) at transcription level, but its biological function is scarce. In this study, the characteristics of SlCML39 and its role in HT tolerance were studied. SlCML39 encodes a protein of 201 amino acids containing four EF hand motifs. Many cis-acting elements related to plant stress and hormone response appear in the promoter regions of SlCML39. SlCML39 is mainly expressed in the root, stem, and leaf and can be regulated by HT, cold, drought, and salt stresses as well as ABA and H2O2. Furthermore, heterologous overexpression of SlCML39 reduces HT tolerance in Arabidopsis thaliana at the germination and seedling growth stages. To better understand the molecular mechanism of SlCML39, the downstream gene network regulated by SlCML39 under HT was analyzed by RNA-Seq. Interestingly, we found that many genes involved in stress responses as well as ABA signal pathway are down-regulated in the transgenic seedlings under HT stress, such as KIN1, RD29B, RD26, and MAP3K18. Collectively, these data indicate that SlCML39 acts as an important negative regulator in response to HT stress, which might be mediated by the ABA signal pathway.

scholarly journals Evolutionary insights into PtdIns3P signaling through FYVE and PHOX effector proteins from the moss Physcomitrella patens

2019 ◽  
Author(s):  
Patricia Agudelo-Romero ◽  
Ana Margarida Fortes ◽  
Trinidad Suárez ◽  
Hernán Ramiro Lascano ◽  
Laura Saavedra
Keyword(s):  
Stress Responses ◽  
Growth And Development ◽  
Physcomitrella Patens ◽  
Higher Plants ◽  
Regulatory Elements ◽  
Plant Evolution ◽  
Effector Proteins ◽  
Promoter Regions ◽  
Photosynthetic Organisms ◽  
Binding Domains

ABSTRACTPhosphatidylinositol 3-phosphate (PtdIns3P) is one of the five different phosphoinositides (PPIs) species in plant cells, which regulate several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3P mode of action, specifically through PtdIns3P-binding effectors such as FYVE and PHOX proteins have been partially explored in plants with main focus on Arabidopsis thaliana. Additionally, they have been underexplored in other plant organisms such as bryophytes, the earliest diverging group of terrestrial flora.In this study, we searched for genes coding for FYVE and PHOX domains containing sequences from different photosynthetic organisms in order to gather evolutionary insights on these PPI binding domains, followed by an in silico characterization of the FYVE and PHOX gene family in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis-acting regulatory elements and transcription factor binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens. The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2D to 3D growth, which could provide ancestral regulatory players undertaken during plant evolution.

scholarly journals Regulatory Network Identification, Promoter and Expression Analysis of Arabidopsis thaliana NPR1 in Defense Responses against Stresses

2018 ◽  
Vol 10 (3) ◽  
pp. 333-339
Author(s):  
Amir G. SHAHRIARI ◽  
Aminallah TAHMASEBI ◽  
Sima SAZEGARI
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Defense Responses ◽  
Wrky Transcription Factor ◽  
Microarray Data Analysis ◽  
Common Element ◽  
Biotic And Abiotic Stresses ◽  
Promoter Regions ◽  
Biotic Stresses

Salicylic acid (SA) and jasmonic acid (JA) phytohormones have been known for their roles in plant defense behaviour against biotic and abiotic stresses. They regulate defense pathways by antagonistic interaction. NPR1 as a key regulatory factor in the cross-talk between SA and JA, signaling is essential for the inhibition of JA-responsive gene expression by SA. In silico promoter analysis of 1.5 kb promoter regions of NPR1 gene revealed that NPR1 contains 23 MYB and 20 WRKY transcription factor binding sites. Different cis-elements associated with various stress responses were identified in Arabidopsis thaliana NPR1. The most common element was allocated to the defense responses against biotic stresses. Based on gene network analysis, NPR1, TGA2 and TGA3 were predicted to have functional cooperation with each other. Affymetrix microarray data analysis of A. thaliana under SA treatment demonstrated that most genes involved in NPR1 network are up-regulated under SA treatment. Therefore, interaction and cooperation between these factors might serve to fine-tune regulation of defense and immune responses against biotic and abiotic stresses.  

scholarly journals Comprehensive analysis of multiprotein bridging factor 1 family genes and SlMBF1c negatively regulate the resistance to Botrytis cinerea in tomato

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xu Zhang ◽  
Zhixuan Xu ◽  
Lichen Chen ◽  
Zhonghai Ren
Keyword(s):  
Botrytis Cinerea ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Regulatory Elements ◽  
Comprehensive Analysis ◽  
Promoter Regions ◽  
Functional Studies ◽  
Different Tissues

Abstract Background Multiprotein bridging factor 1 s (MBF1s) are members of the transcriptional co-activator family that have involved in plant growth, development and stress responses. However, little is known about the Solanum lycopersicum MBF1 (SlMBF1) gene family. Results In total, five SlMBF1 genes were identified based on the tomato reference genome, and these genes were mapped to five chromosomes. All of the SlMBF1 proteins were highly conserved, with a typical MBF1 domain and helix-turn-helix_3 domain. In addition, the promoter regions of the SlMBF1 genes have various stress and hormone responsive cis-regulatory elements. Encouragingly, the SlMBF1 genes were expressed with different expression profiles in different tissues and responded to various stress and hormone treatments. The biological function of SlMBF1c was further identified through its overexpression in tomato, and the transgenic tomato lines showed increased susceptibility to Botrytis cinerea (B. cinerea). Additionally, the expression patterns of salicylic acid (SA)-, jasmonic acid (JA)- and ethylene (ET)- mediated defense related genes were altered in the transgenic plants. Conclusions Our comprehensive analysis provides valuable information for clarifying the evolutionary relationship of the SlMBF1 members and their expression patterns in different tissues and under different stresses. The overexpression of SlMBF1c decreased the resistance of tomato to B. cinerea through enhancing the gene expression of the SA-mediated signaling pathway and depressing JA/ET-mediated signaling pathways. These results will facilitate future functional studies of the transcriptional co-activator family.

scholarly journals Genome-Wide Identification and Characterization of Cysteine-Rich Receptor-Like Protein Kinase Genes in Tomato and Their Expression Profile in Response to Heat Stress

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 258
Author(s):  
Yahui Liu ◽  
Zhengxiang Feng ◽  
Weimin Zhu ◽  
Junzhong Liu ◽  
Yingying Zhang
Keyword(s):  
Heat Stress ◽  
Abiotic Stress ◽  
Protein Kinases ◽  
Stress Responses ◽  
Plant Disease Resistance ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Multiple Sequence ◽  
Downstream Signaling ◽  
Essential Components

During plant growth, development and stress adaption, receptor-like protein kinases (RLKs) are essential components in perceiving and integrating extracellular stimuli and transmitting the signals to activate the downstream signaling pathways. Cysteine-rich receptor-like protein kinases (CRKs) are a large subfamily of RLKs and their roles in modulating plant disease resistance are well elucidated. However, the roles of CRKs in plant abiotic stress responses, especially heat stress, are largely unknown. In this study, 35 SlCRK genes were identified in tomato (Solanum lycopersicum) based on the multiple sequence alignment and phylogenetic relationships. SlCRK genes are tandemly distributed on seven chromosomes and have similar exon–intron organization and common conserved motifs. Various phytohormone responsive, stress responsive cis-regulatory elements and heat shock elements are predicted in the promoter regions of SlCRK genes. Transcriptome analysis of tomato fruits under heat stress revealed that most SlCRK genes were downregulated upon heat treatment. GO enrichment analyses of genes that were co-expressed with SlCRK members have identified various stress responses related and proteasomal protein catabolic process related genes, which may be involved in heat stress signaling. Overall, our results provide valuable information for further research on the roles of SlCRKs in response to abiotic stress, especially heat stress.

scholarly journals Genome-Wide Identification of Sultr Genes in Malus domestica and Low Sulfur-Induced MhSultr3;1a to Increase Cysteine-Improving Growth

2021 ◽  
Vol 12 ◽  
Author(s):  
Mi Xun ◽  
Jianfei Song ◽  
Junyuan Shi ◽  
Jiaqi Li ◽  
Yujia Shi ◽  
...  
Keyword(s):  
Malus Domestica ◽  
Higher Plants ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Specific Expression ◽  
Essential Nutrient ◽  
Function Characterization ◽  
Gene Structures ◽  
Low Sulfur

Sulfur is an essential nutrient for plant growth and development. Sulfate transporters (Sultrs) are critical for sulfate (SO42-) uptake from the soil by the roots in higher plants. However, knowledge about Sultrs in apples (Malus domestica) is scarce. Here, nine putative MdSultrs were identified and classified into two groups according to the their phylogenetic relationships, gene structures, and conserved motifs. Various cis-regulatory elements related to abiotic stress and plant hormone responsiveness were found in the promoter regions of MdSultrs. These MdSultrs exhibited tissue-specific expression patterns and responded to low sulfur (S), abscisic acid (ABA), indole-3-acetic acid (IAA), and methyl jasmonate (MeJA), wherein MdSultr3;1a was especially expressed in the roots and induced by low S. The uptake of SO42- in cultivated apples depends on the roots of its rootstock, and MhSultr3;1a was isolated from Malus hupehensis roots used as a rootstock. MhSultr3;1a shared 99.85% homology with MdSultr3;1a and localized on the plasma membrane and nucleus membrane. Further function characterization revealed that MhSultr3;1a complemented an SO42- transport-deficient yeast mutant and improved the growth of yeast and apple calli under low S conditions. The MhSultr3;1a-overexpressing apple calli had a higher fresh weight compared with the wild type (WT) under a low-S treatment because of the increased SO42- and cysteine (Cys) content. These results demonstrate that MhSultr3;1a may increase the content of SO42- and Cys to meet the demands of S-containing compounds and improve their growth under S-limiting conditions.

scholarly journals Gateway cloning and in-planta transformation of drought stress responsive Ecmyb1 gene isolated from Eleusine coracana var.PRM 6107

2021 ◽  
Vol 22 (1) ◽  
pp. 205-211
Author(s):  
Megha Bhatt ◽  
Prafull Salvi ◽  
Pushpa Lohani
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Drought Stress ◽  
Stress Responses ◽  
Anthocyanin Biosynthesis ◽  
Regulatory Protein ◽  
Regulatory Elements ◽  
Growth And Yield ◽  
Yield Potential ◽  
Gateway Cloning

Drought is one of the key abiotic stress that critically influences the crops by restraining their growth and yield potential. Being sessile, plants tackle the detrimental effects of drought stress via modulating the cellular state by changing the gene expression. Such alteration of gene expression is essentially driven by the transcriptional syndicate. Transcription factors (TF) are the key regulatory protein that controls the expression of their target gene by binding to the cis-regulatory elements present in the promoter region. Myb-TFs ubiquitously present in all eukaryotes belong to one of the largest TF family, and play wide array of biological functions in plants including anthocyanin biosynthesis, vasculature system, cell signaling, seed maturation and abiotc stress responses. In the present study the full length Myb TF from Eleusine corocana was subcloned using Gateway cloning system and further transformed into Arabidopsis thaliana through floral dip method. Transgenic Arabidopsis thaliana plants harbouring Ecmyb1 gene were screened and grown in transgenic glasshouse under controlled conditions.

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