scholarly journals Global identification of full-length cassava lncRNAs unveils the role of CRIR1 in cold stress response

2021 ◽  
Author(s):  
shuxia li ◽  
Zhihao Cheng ◽  
Shiman Dong ◽  
Zhibo Li ◽  
Liangping Zou ◽  
...  
Keyword(s):  
Stress Response ◽  
Cold Stress ◽  
Cold Treatment ◽  
Cold Shock Protein ◽  
Translation Efficiency ◽  
Global Identification ◽  
Non Coding Rnas ◽  
Stress Related Genes ◽  
Rna Chaperones

Long non-coding RNAs (lncRNAs) have been considered to be important regulators of gene expression in a range of biological processes in plants. A large number of lncRNAs have been identified in plants. However, most of their biological functions still remain to be determined. Here, we identified total 3 004 lncRNAs in cassava under normal or cold-treated conditions from Iso-seq data. We further characterized a lincRNA, CRIR1, as a novel positive regulator of the plant response to cold stress. CRIR1 can be significantly induced by cold treatment. Overexpression of CRIR1 in cassava enhanced the cold tolerance of transgenic plants. Transcriptome analysis demonstrated that CRIR1 regulates a range of cold stress-related genes in a CBF-independent pathway. We further found that CRIR1 RNA can interact with MeCSP5, a homolog of the cold shock protein that acts as RNA chaperones, indicating that CRIR1 may recruit MeCSP5 to improve the translation efficiency of mRNA. In summary, our study greatly extends the repertoire of lncRNAs in plants as well as its responding to cold stress. Moreover, it reveals a sophisticated mechanism by which CRIR1 regulates plant cold stress response by modulating the expression of stress-responsive genes and increasing the translational yield.

GRAS-domain transcription factor PAT1 regulates jasmonic acid biosynthesis in grape cold stress response

2021 ◽  
Author(s):  
Zemin Wang ◽  
Darren Chern Jan Wong ◽  
Yi Wang ◽  
Guangzhao Xu ◽  
Chong Ren ◽  
...  
Keyword(s):  
Stress Response ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Cold Treatment ◽  
Ectopic Expression ◽  
Bimolecular Fluorescence Complementation ◽  
Luciferase Reporter ◽  
Vitis Amurensis ◽  
Mobility Shift

Abstract Cultivated grapevine (Vitis) is a highly valued horticultural crop, and cold stress affects its growth and productivity. Wild Amur grape (Vitis amurensis) PAT1 (Phytochrome A signal transduction 1, VaPAT1) is induced by low temperature, and ectopic expression of VaPAT1 enhances cold tolerance in Arabidopsis (Arabidopsis thaliana). However, little is known about the molecular mechanism of VaPAT1 during the cold stress response in grapevine. Here, we confirmed the overexpression of VaPAT1 in transformed grape calli enhanced cold tolerance. Yeast two-hybrid and bimolecular fluorescence complementation assays highlighted an interaction between VaPAT1 with INDETERMINATE-DOMAIN 3 (VaIDD3). A role of VaIDD3 in cold tolerance was also indicated. Transcriptome analysis revealed VaPAT1 and VaIDD3 overexpression and cold treatment coordinately modulate the expression of stress-related genes including lipoxygenase 3 (LOX3), a gene encoding a key jasmonate biosynthesis enzyme. Co-expression network analysis indicated LOX3 might be a downstream target of VaPAT1. Both electrophoretic mobility shift and dual luciferase reporter assays showed the VaPAT1-IDD3 complex binds to the IDD-box (AGACAAA) in the VaLOX3 promoter to activate its expression. Overexpression of both VaPAT1 and VaIDD3 increased the transcription of VaLOX3 and JA levels in transgenic grape calli. Conversely, VaPAT1-SRDX (dominant repression) and CRISPR/Cas9-mediated mutagenesis of PAT1-ED causing the loss of the C-terminus in grape calli dramatically prohibited the accumulation of VaLOX3 and JA levels during cold treatment. Together, these findings point to a pivotal role of VaPAT1 in the cold stress response in grape by regulating JA biosynthesis.

scholarly journals Transcriptomics of cryophilic Saccharomyces kudriavzevii reveals the key role of gene translation efficiency in cold stress adaptations

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 432 ◽  
Author(s):  
Jordi Tronchoni ◽  
Victor Medina ◽  
Jose Guillamón ◽  
Amparo Querol ◽  
Roberto Pérez-Torrado
Keyword(s):  
Cold Stress ◽  
Translation Efficiency ◽  
Saccharomyces Kudriavzevii

scholarly journals TrmB, a tRNA m7G46 methyltransferase, plays a role in hydrogen peroxide resistance and positively modulates the translation of katA and katB mRNAs in Pseudomonas aeruginosa

2019 ◽  
Vol 47 (17) ◽  
pp. 9271-9281 ◽  
Author(s):  
Narumon Thongdee ◽  
Juthamas Jaroensuk ◽  
Sopapan Atichartpongkul ◽  
Jurairat Chittrakanwong ◽  
Kamonchanok Chooyoung ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Pseudomonas Aeruginosa ◽  
Stress Response ◽  
Translational Regulation ◽  
Cellular Response ◽  
Oxidative Stress Response ◽  
Translation Efficiency ◽  
Trna Modification ◽  
Negative Effect

Abstract Cellular response to oxidative stress is a crucial mechanism that promotes the survival of Pseudomonas aeruginosa during infection. However, the translational regulation of oxidative stress response remains largely unknown. Here, we reveal a tRNA modification-mediated translational response to H2O2 in P. aeruginosa. We demonstrated that the P. aeruginosa trmB gene encodes a tRNA guanine (46)-N7-methyltransferase that catalyzes the formation of m7G46 in the tRNA variable loop. Twenty-three tRNA substrates of TrmB with a guanosine residue at position 46 were identified, including 11 novel tRNA substrates. We showed that loss of trmB had a strong negative effect on the translation of Phe- and Asp-enriched mRNAs. The trmB-mediated m7G modification modulated the expression of the catalase genes katA and katB, which are enriched with Phe/Asp codons at the translational level. In response to H2O2 exposure, the level of m7G modification increased, consistent with the increased translation efficiency of Phe- and Asp-enriched mRNAs. Inactivation of trmB led to decreased KatA and KatB protein abundance and decreased catalase activity, resulting in H2O2-sensitive phenotype. Taken together, our observations reveal a novel role of m7G46 tRNA modification in oxidative stress response through translational regulation of Phe- and Asp-enriched genes, such as katA and katB.

scholarly journals Potential Roles of Long Non-Coding RNAs (lncRNAs) in Stress Response Regulation

2020 ◽  
Vol 11 (SPL4) ◽  
pp. 2385-2389
Author(s):  
Shiv Swaroop ◽  
Thangminlal Vaiphei S
Keyword(s):  
Stress Response ◽  
Ionizing Radiation ◽  
Open Reading Frames ◽  
Biologically Active ◽  
Cellular Stress Response ◽  
Heterochromatin Formation ◽  
Cellular Expression ◽  
Wide Range ◽  
Non Coding Rnas

The non-coding RNAs (ncRNAs) are functional RNA transcripts involved in gene regulation at the level of transcription and post-transcription. There have been vital pieces of evidence to support the role of regulatory non-coding RNAs in the eukaryotic genome in recent years. The ncRNAs are also associated with post-translational modifications such as histone modification, heterochromatin formation, DNA methylation and other key molecules which are involved in regulating chromatin structures for gene expression. LncRNAs (long non-coding RNAs) are the most diverse, biologically active transcripts without significant open reading frames (ORFs) and represent the majority of ncRNAs populations in the human genome. Emerging pieces of evidence suggest the role of ncRNAs in a wide range of human diseases, including cardiovascular, Alzheimer, and cancer. Several reports in the recent past also supported their involvement in the modulation of various cellular responses, although the mechanisms of ncRNAs mediated gene regulations are still not fully understood. This review paper highlights the importance of lncRNAs in cellular stress response such as DNA damaging ionizing radiation that will encourage research in thrust areas of therapeutics and diagnostics. The involvement of important lncRNAs in regulating biological processes, responses to ionizing and non-ionizing radiation, as well as methods for the analysis of their cellular expression has been discussed.

Prolonged cold stress response of Escherichia coli O157 and the role of rpoS

2011 ◽  
Vol 146 (2) ◽  
pp. 163-169 ◽  
Author(s):  
Sinisa Vidovic ◽  
Anil K. Mangalappalli-Illathu ◽  
Darren R. Korber
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Cold Stress ◽  
Escherichia Coli O157

Role of geranylgeranyl reductase gene in organ development and stress response in olive (Olea europaea) plants

2009 ◽  
Vol 36 (4) ◽  
pp. 370 ◽  
Author(s):  
Leonardo Bruno ◽  
Adriana Chiappetta ◽  
Innocenzo Muzzalupo ◽  
Cinzia Gagliardi ◽  
Domenico Iaria ◽  
...  
Keyword(s):  
Stress Response ◽  
Olea Europaea ◽  
Developmental Stages ◽  
Cold Treatment ◽  
In Situ Hybridisation ◽  
Transit Peptide ◽  
Specific Cell ◽  
Reductase Gene ◽  
Olea Europaéa

The NADPH-dependent geranylgeranyl reductase gene (OeCHLP) was characterised in olive (Olea europaea L.). OeCHLP catalyses the formation of carbon double bonds in the phytolic side chain of chlorophyll, tocopherols and plastoquinones and, therefore, is involved in metabolic pathways related to plant productivity and stress response, besides to nutritional value of its products. The nuclear OeCHLP encodes a deduced product of 51 kDa, which harbours a transit peptide for cytoplasm-to-chloroplast transport and a nicotinamide binding domain. Two estimated identical copies of gene are harboured per haploid genome of the cv. ‘Carolea’ used in the present study. Levels and cytological pattern of OeCHLP transcription were investigated by quantitative RT–PCR and in situ hybridisation. In line with the presence of ubiquitous tocopherols and/or chlorophyll, OeCHLP transcripts were present in various organs of plants. In leaves and fruits at different developmental stages, OeCHLP was differentially expressed in relation to their morpho-physiological features. An early and transient enhancement of gene transcription was detected in leaves of different age exposed to cold treatment (4°C), as well as in fruits mechanically wounded. Moreover, OeCHLP transcripts locally increased in specific cell domains of fruits severely damaged by the pathogen Bactrocera olea. Combined, these data show that OeCHLP expression early responds to biotic and abiotic stressful factors. Levels of tocopherols also increased in leaves exposed to cold conditions and fruits severely damaged by pathogen. We suggest that gene activity under stress condition could be related to tocopherol action.

scholarly journals Characterization and Expression Analysis of Common BeanHistone Deacetylase 6during Development and Cold Stress Response

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Rita Kusi-Appiah Hayford ◽  
Ayalew Ligaba-Osena ◽  
Mayavan Subramani ◽  
Adrianne Brown ◽  
Kalpalatha Melmaiee ◽  
...  
Keyword(s):  
Stress Response ◽  
Cold Stress ◽  
Common Bean ◽  
Histone Deacetylases ◽  
Functional Characterization ◽  
Model Species ◽  
Cellular Processes ◽  
Stem Leaf

Histone deacetylases (HDACs) are important regulators of gene transcription thus controlling multiple cellular processes. Despite its essential role in plants,HDA6is yet to be validated in common bean. In this study, we show thatHDA6is involved in plant development and stress response. Differential expression ofHDA6was determined in various tissues and the expression was seen to be upregulated with plant age (seedling < flowering < maturity). Higher expression was observed in flowers and pods than in stem, leaf, and root. Upregulation ofHDA6gene during cold stress implies its prominent role in abiotic stress. Furthermore, theHDA6gene was isolated from three common bean genotypes and sequence analyses revealed homology with functionally characterized homologs in model species. The 53 kDa translated product was detected using anHDA6specific antibody and recombinant protein overexpressed inEscherichia colishowed HDAC activityin vitro. To our knowledge, this is the first report in the agriculturally important crop common bean describing the functional characterization and biological role ofHDA6.

scholarly journals Integrated RNA-seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots

2020 ◽  
Vol 21 (13) ◽  
pp. 4615 ◽  
Author(s):  
Weilong Kong ◽  
Chenhao Zhang ◽  
Yalin Qiang ◽  
Hua Zhong ◽  
Gangqing Zhao ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Stress Response ◽  
Cold Stress ◽  
Molecular Mechanisms ◽  
Oryza Sativa L ◽  
Growth And Yield ◽  
Rna Seq ◽  
Cold Tolerant ◽  
Stress Related Genes ◽  
Qtls Mapping

Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice’s cold–stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold–stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold–stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.

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