Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes

Rice (Oryza sativa L.), a staple crop plant that is a major source of calories for approximately 50% of the human population, exhibits various physiological responses against temperature stress. These responses are known mechanisms of flexible adaptation through crosstalk with the intrinsic circadian clock. However, the molecular regulatory network underlining this crosstalk remains poorly understood. Therefore, we performed systematic transcriptome data analyses to identify the genes involved in both cold stress responses and diurnal rhythmic patterns. Here, we first identified cold-regulated genes and then identified diurnal rhythmic genes from those (119 cold-upregulated and 346 cold-downregulated genes). We defined cold-responsive diurnal rhythmic genes as CD genes. We further analyzed the functional features of these CD genes through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses and performed a literature search to identify functionally characterized CD genes. Subsequently, we found that light-harvesting complex proteins involved in photosynthesis strongly associate with the crosstalk. Furthermore, we constructed a protein–protein interaction network encompassing four hub genes and analyzed the roles of the Stay-Green (SGR) gene in regulating crosstalk with sgr mutants. We predict that these findings will provide new insights in understanding the environmental stress response of crop plants against climate change.

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Acute cold stress in rheumatoid arthritis inadequately activates stress responses and induces an increase of interleukin 6

Annals of the Rheumatic Diseases ◽

10.1136/ard.2008.089458 ◽

2008 ◽

Vol 68 (4) ◽

pp. 572-578 ◽

Cited By ~ 16

Author(s):

R H Straub ◽

G Pongratz ◽

H Hirvonen ◽

T Pohjolainen ◽

M Mikkelsson ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Stress Response ◽

Cold Stress ◽

Stress Responses ◽

Plasma Levels ◽

Acute Stress ◽

Whole Body ◽

Cold Therapy ◽

Before And After ◽

Sympathetic Stress

Objective:Acute stress in patients with rheumatoid arthritis (RA) should stimulate a strong stress response. After cryotherapy, we expected to observe an increase of hormones of the adrenal gland and the sympathetic nervous system.Methods:A total of 55 patients with RA were recruited for whole-body cryotherapy at −110°C and −60°C, and local cold therapy between −20°C and −30°C for 7 days. We measured plasma levels of steroid hormones, neuropeptide Y (sympathetic marker), and interleukin (IL)6 daily before and after cryotherapy.Results:In both therapy groups with/without glucocorticoids (GC), hormone and IL6 levels at baseline and 5 h after cold stress did not change over 7 days of cryotherapy. In patients without GC, plasma levels of cortisol and androstenedione were highest after −110°C cold stress followed by −60°C or local cold stress. The opposite was found in patients under GC therapy, in whom, unexpectedly, −110°C cold stress elicited the smallest responses. In patients without GC, adrenal cortisol production increased relative to other adrenal steroids, and again the opposite was seen under GC therapy with a loss of cortisol and an increase of dehydroepiandrosterone. Importantly, there was no sympathetic stress response in both groups. Patients without GC and −110°C cold stress demonstrated higher plasma IL6 compared to the other treatment groups (not observed under GC), but they showed the best clinical response.Conclusions:We detected an inadequate stress response in patients with GC. It is further shown that the sympathetic stress response was inadequate in patients with/without GC. Paradoxically, plasma levels of IL6 increased under strong cold stress in patients without GC. These findings confirm dysfunctional stress axes in RA.

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OsDIRP1, a Putative RING E3 Ligase, Plays an Opposite Role in Drought and Cold Stress Responses as a Negative and Positive Factor, Respectively, in Rice (Oryza sativa L.)

Frontiers in Plant Science ◽

10.3389/fpls.2018.01797 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 7

Author(s):

Li Hua Cui ◽

Hye Jo Min ◽

Mi Young Byun ◽

Hyeong Geun Oh ◽

Woo Taek Kim

Keyword(s):

Oryza Sativa ◽

Cold Stress ◽

Stress Responses ◽

Oryza Sativa L ◽

E3 Ligase ◽

Ring E3 Ligase ◽

Ring E3 ◽

Positive Factor

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Identification and Expression Analysis of the NAC Gene Family in Coffea canephora

Agronomy ◽

10.3390/agronomy9110670 ◽

2019 ◽

Vol 9 (11) ◽

pp. 670 ◽

Cited By ~ 4

Author(s):

Dong ◽

Jiang ◽

Yang ◽

Xiao ◽

Bai ◽

...

Keyword(s):

Cold Stress ◽

Gene Family ◽

Stress Responses ◽

Developmental Stages ◽

Expression Patterns ◽

Coffea Canephora ◽

Coffee Bean ◽

Systematic Analysis ◽

Nac Gene Family ◽

Basic Features

The NAC gene family is one of the largest families of transcriptional regulators in plants, and it plays important roles in the regulation of growth and development as well as in stress responses. Genome-wide analyses have been performed in diverse plant species, but there is still no systematic analysis of the NAC genes of Coffea canephora Pierre ex A. Froehner. In this study, we identified 63 NAC genes from the genome of C. canephora. The basic features and comparison analysis indicated that the NAC gene members increased via duplication events during the evolution of the plant. Phylogenetic analysis divided the NAC proteins from C. canephora, Arabidopsis and rice into 16 subgroups. Analysis of the expression patterns of CocNACs under cold stress and coffee bean development indicated that 38 CocNACs were differentially expressed under cold stress; six genes may play important roles in the process of cold acclimation, and four genes among 54 CocNACs showing a variety of expression patterns during different developmental stages of coffee beans may be positively related to the bean development. This study can expand our understanding of the functions of the CocNAC gene family in cold responses and bean development, thereby potentially intensifying the molecular breeding programs of Coffea spp. plants.

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Short- and Long-Term Transcriptomic Responses of Escherichia coli to Biocides: a Systems Analysis

Applied and Environmental Microbiology ◽

10.1128/aem.00708-20 ◽

2020 ◽

Vol 86 (14) ◽

Author(s):

Beatriz Merchel Piovesan Pereira ◽

Xiaokang Wang ◽

Ilias Tagkopoulos

Keyword(s):

Escherichia Coli ◽

Stress Response ◽

Stress Responses ◽

Zinc Homeostasis ◽

Cross Resistance ◽

Transcriptional Responses ◽

Systematic Analysis ◽

Content Type ◽

Short Term Exposure

ABSTRACT The mechanisms of the bacterial response to biocides are poorly understood, despite their broad application. To identify the genetic basis and pathways implicated in the biocide stress response, we exposed Escherichia coli populations to 10 ubiquitous biocides. By comparing the transcriptional responses between a short-term exposure (30 min) and a long-term exposure (8 to 12 h) to biocide stress, we established the common gene and pathway clusters that are implicated in general and biocide-specific stress responses. Our analysis revealed a temporal choreography, starting from the upregulation of chaperones to the subsequent repression of motility and chemotaxis pathways and the induction of an anaerobic pool of enzymes and biofilm regulators. A systematic analysis of the transcriptional data identified a zur-regulated gene cluster to be highly active in the stress response against sodium hypochlorite and peracetic acid, presenting a link between the biocide stress response and zinc homeostasis. Susceptibility assays with knockout mutants further validated our findings and provide clear targets for downstream investigation of the implicated mechanisms of action. IMPORTANCE Antiseptics and disinfectant products are of great importance to control and eliminate pathogens, especially in settings such as hospitals and the food industry. Such products are widely distributed and frequently poorly regulated. Occasional outbreaks have been associated with microbes resistant to such compounds, and researchers have indicated potential cross-resistance with antibiotics. Despite that, there are many gaps in knowledge about the bacterial stress response and the mechanisms of microbial resistance to antiseptics and disinfectants. We investigated the stress response of the bacterium Escherichia coli to 10 common disinfectant and antiseptic chemicals to shed light on the potential mechanisms of tolerance to such compounds.

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Comprehensive transcriptome resource for response to phytohormone-induced signaling in Capsicum annuum L.

BMC Research Notes ◽

10.1186/s13104-020-05281-1 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Junesung Lee ◽

Jae-Young Nam ◽

Hakgi Jang ◽

Nayoung Kim ◽

Yong-Min Kim ◽

...

Keyword(s):

Rna Sequencing ◽

Stress Responses ◽

Molecular Networks ◽

Response To Treatment ◽

Pepper Plant ◽

Transcriptome Data ◽

Biotic And Abiotic Stress ◽

Data Description ◽

Growth Development ◽

Transcriptome Resource

Abstract Objectives Phytohormones are small signaling molecules with crucial roles in plant growth, development, and environmental adaptation to biotic and abiotic stress responses. Despite several previously published molecular studies focused on plant hormones, our understanding of the transcriptome induced by phytohormones remains unclear, especially in major crops. Here, we aimed to provide transcriptome dataset using RNA sequencing for phytohormone-induced signaling in plant. Data description We used high-throughput RNA sequencing profiling to investigate the pepper plant response to treatment with four major phytohormones (salicylic acid, jasmonic acid, ethylene, and abscisic acid). This dataset yielded 78 samples containing three biological replicates per six different time points for each treatment and the control, constituting 187.8 Gb of transcriptome data (2.4 Gb of each sample). This comprehensive parallel transcriptome data provides valuable information for understanding the relationships and molecular networks that regulate the expression of phytohormone-related genes involved in plant developments and environmental stress adaptation.

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Meta-analysis of transcriptome data clarified hormonal regulation of cold stress response in Arabidopsis thaliana L.

Bioinformatics of Genome Regulation and Structure/ Systems Biology ◽

10.18699/bgrs/sb-2020-210 ◽

2020 ◽

Keyword(s):

Arabidopsis Thaliana ◽

Stress Response ◽

Cold Stress ◽

Hormonal Regulation ◽

Meta Analysis ◽

Transcriptome Data

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OsCBE1, a Substrate Receptor of Cullin4-Based E3 Ubiquitin Ligase, Functions as a Regulator of Abiotic Stress Response and Productivity in Rice

International Journal of Molecular Sciences ◽

10.3390/ijms22052487 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2487

Author(s):

Juyoung Choi ◽

Wonkyung Lee ◽

Gynheung An ◽

Seong-Ryong Kim

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Cold Stress ◽

Stress Tolerance ◽

Ubiquitin Ligase ◽

E3 Ubiquitin Ligase ◽

In Silico Analysis ◽

Wild Type ◽

Abiotic Stress Response ◽

Environmental Stress Response

Ubiquitination is an important environmental stress response, and E3 ubiquitin ligases play a major role in the process. T-DNA insertion mutants of rice, Oscbe1-1, and Oscbe1-2, were identified through the screening of cold stress tolerance at seedling stage. Oscbe1 mutants showed a significantly higher cold stress tolerance in the fresh weight, chlorophyll content, and photosynthetic efficiency than wild type. Molecular prediction showed that OsCBE1 (Oryza sativa Cullin4-Based E3 ubiquitin ligase1) encoded a novel substrate receptor of Cullin4-based E3 ubiquitin ligase complex (C4E3). Whereas Oscbe1 mutants had fewer panicles and grains than wild type in the paddy field, the overexpression lines of OsCBE1 had more panicles and grains, suggesting that OsCBE1 is involved in the regulation of both abiotic stress response and development. Oscbe1 mutants also showed ABA hypersensitivity during seed germination, suggesting OsCBE1 function for the stress response via ABA signaling. In silico analysis of OsCBE1 activity predicted a CCCH-type transcription factor, OsC3H32, as a putative substrate. Co-IP (Co-immunoprecipitation) study showed that OsCBE1 interacts with OsDDB1, an expected binding component of OsCBE1 and OsC3H32. Additionally, expression of OsOLE16, OsOLE18, and OsBURP5 were negatively related with expression of OsCBE1. These results suggest that OsCBE1 functions as a regulator of the abiotic stress response via CCCH as a member of the C4E3.

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Genome-wide identification of miRNAs targets involved in cold response in cassava

Plant Omics ◽

10.21475/poj.13.01.20.p2337 ◽

2020 ◽

pp. 57-64

Author(s):

Shuxia Li ◽

Zhihao Cheng ◽

Ming Peng

Keyword(s):

Stress Response ◽

Cold Stress ◽

Stress Responses ◽

High Throughput Sequencing ◽

Target Genes ◽

Cold Response ◽

Mirna Targets ◽

Genome Wide ◽

A Genome ◽

Growth Development

MicroRNAs (miRNAs) are recognized as essential transcriptional or post-transcriptional regulators, and play versatile roles in plants growth, development and stress responses. Cassava (Manihot esculenta) is a major root crop widely grown worldwide. Cold stress seriously affects cassava plants growth, development and yield. MiRNAs and their targets have been extensively studied in model plants, but a genome-wide identification of miRNAs’ targets is still lacking in cassava. In this study, two degradome libraries were constructed using cold-treated and control cassava seedlings to identify the roles of miRNAs and their targets in response to cold stress. Following high-throughput sequencing and comparing with miRNA database, degradome data allowed us to identify a total of 151 non-redundant miRNA-target pairs. We revealed that ~ 42% of miRNA targets are conserved across plant species. However, 83 novel miRNA targets were identified in the two libraries. Gene ontology analyses showed that many target genes involved in cellular and metabolic process. In addition, 12 miRNAs and 31 corresponding targets of them were further found to be involved in cold stress response. Particularly, miR159, 164 and 396 participated in cold stress response by up-regulating certain transcription factors that were involved in the regulation of downstream gene expression. The work helps identifing cold-responsive miRNA targets in cassava and increases the number of novel targets involved in cold stress response. Furthermore, the findings of this study might provide valuable reference and new insights for understanding the functions of miRNA in stress response in plants.

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Quantitative Proteomic Analysis of Castor (Ricinus communis L.) Seeds During Early Imbibition Provided Novel Insights into Cold Stress Response

International Journal of Molecular Sciences ◽

10.3390/ijms20020355 ◽

2019 ◽

Vol 20 (2) ◽

pp. 355 ◽

Cited By ~ 3

Author(s):

Xiaoyu Wang ◽

Min Li ◽

Xuming Liu ◽

Lixue Zhang ◽

Qiong Duan ◽

...

Keyword(s):

Fatty Acid ◽

Stress Response ◽

Cold Stress ◽

Cold Tolerance ◽

Stress Responses ◽

Fatty Acid Biosynthesis ◽

Ricinus Communis ◽

Seedling Emergence ◽

Proteomics Data ◽

Castor Seeds

Early planting is one of the strategies used to increase grain yield in temperate regions. However, poor cold tolerance in castor inhibits seed germination, resulting in lower seedling emergence and biomass. Here, the elite castor variety Tongbi 5 was used to identify the differential abundance protein species (DAPS) between cold stress (4 °C) and control conditions (30 °C) imbibed seeds. As a result, 127 DAPS were identified according to isobaric tag for relative and absolute quantification (iTRAQ) strategy. These DAPS were mainly involved in carbohydrate and energy metabolism, translation and posttranslational modification, stress response, lipid transport and metabolism, and signal transduction. Enzyme-linked immunosorbent assays (ELISA) demonstrated that the quantitative proteomics data collected here were reliable. This study provided some invaluable insights into the cold stress responses of early imbibed castor seeds: (1) up-accumulation of all DAPS involved in translation might confer cold tolerance by promoting protein synthesis; (2) stress-related proteins probably protect the cell against damage caused by cold stress; (3) up-accumulation of key DAPS associated with fatty acid biosynthesis might facilitate resistance or adaptation of imbibed castor seeds to cold stress by the increased content of unsaturated fatty acid (UFA). The data has been deposited to the ProteomeXchange with identifier PXD010043.

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