scholarly journals Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

2020 ◽  
Author(s):  
Mohammad Aslam ◽  
Kenji Sugita ◽  
Yuan Qin ◽  
Abidur Rahman
Keyword(s):  
Stress Response ◽  
Cold Stress ◽  
Expression Analysis ◽  
Stress Responses ◽  
Auxin Signaling ◽  
Potential Candidate ◽  
Wild Type ◽  
Gene Expressions ◽  
Significant Differential Expression ◽  
Genome Wide

Abstract Background: The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators for plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. Results: To better understand the role of microRNA in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4°C revealed that the auxin signaling mutant, solitary root 1 ( slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRNA in wild-type and slr1 mutant roots using next-generation sequencing revealed 180 known and 71 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26 nt-31 nt small RNA population in slr1 compared with wild-type. Comparative analysis of microRNA expression shows significant differential expression of 13 known and 7 novel miRNAs in slr1 at 4°C compared with wild-type. Target gene expression analysis of the members from one potential candidate miRNAs, miR169 revealed the possible involvement of miR169- NF-YA module in the auxin-mediated cold stress response. Conclusions: Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRNA in auxin and cold responses.

scholarly journals Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

2020 ◽  
Author(s):  
Mohammad Aslam ◽  
Kenji Sugita ◽  
Yuan Qin ◽  
Abidur Rahman
Keyword(s):  
Stress Response ◽  
Cold Stress ◽  
Expression Analysis ◽  
Stress Responses ◽  
Auxin Signaling ◽  
Potential Candidate ◽  
Wild Type ◽  
Gene Expressions ◽  
Genome Wide

Abstract The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators for plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. To better understand the role of microRNA in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4°C revealed that the auxin signaling mutant, solitary root 1 ( slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRNA in wild-type and slr1 mutant roots using next-generation deep sequencing revealed 180 known and 86 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26nt-31nt small RNA population in slr1 compared with wild-type. Comparative analysis of microRNA expression shows differential expression of 13 miRNAs in slr1 compared with wild-type. Target gene expression analysis of one of the potential candidate miRNAs, miR169 revelaed the possible involvement of miR169- NF-YA module in the auxin-mediated cold stress response. Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRNA in auxin and cold responses.

scholarly journals Aux/IAA14 Regulates microRNA-Mediated Cold Stress Response in Arabidopsis Roots

2020 ◽  
Vol 21 (22) ◽  
pp. 8441
Author(s):  
Mohammad Aslam ◽  
Kenji Sugita ◽  
Yuan Qin ◽  
Abidur Rahman
Keyword(s):  
Stress Response ◽  
Cold Stress ◽  
Expression Analysis ◽  
Stress Responses ◽  
Auxin Signaling ◽  
Potential Candidate ◽  
Wild Type ◽  
Gene Expressions ◽  
Significant Differential Expression ◽  
In The Wild

The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators of plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. To better understand the role of microRNA (miR) in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4 °C revealed that the auxin signaling mutant, solitary root 1 (slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRs in the wild-type and slr1 mutant roots using next-generation sequencing revealed 180 known and 71 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26–31 nt small RNA population in slr1 compared with wild type. Comparative analysis of microRNA expression shows significant differential expression of 13 known and 7 novel miRs in slr1 at 4 °C compared with wild type. Target gene expression analysis of the members from one potential candidate miR, miR169, revealed the possible involvement of miR169/NF-YA module in the Aux/IAA14-mediated cold stress response. Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRs in auxin and cold responses.

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

Plant Omics ◽  
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.

scholarly journals Genome-Wide Identification and Expression Analysis of BBX Transcription Factors in Iris germanica L.

2021 ◽  
Vol 22 (16) ◽  
pp. 8793
Author(s):  
Yinjie Wang ◽  
Yongxia Zhang ◽  
Qingquan Liu ◽  
Ting Zhang ◽  
Xinran Chong ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Gene Family ◽  
Expression Analysis ◽  
Stress Responses ◽  
Transcriptional Activation ◽  
Transcript Abundance ◽  
Response Patterns ◽  
Genome Wide ◽  
Iris Germanica

The family of B-box (BBX) transcription factors contains one or two B-BOX domains and sometimes also features a highly conserved CCT domain, which plays important roles in plant growth, development and stress response. Nevertheless, no systematic study of the BBX gene family in Iris germanica L. has been undertaken. In this study, a set of six BBX TF family genes from I. germanica was identified based on transcriptomic sequences, and clustered into three clades according to phylogenetic analysis. A transient expression analysis revealed that all six BBX proteins were localized in the nucleus. A yeast one-hybrid assay demonstrated that IgBBX3 has transactivational activity, while IgBBX1, IgBBX2, IgBBX4, and IgBBX5 have no transcriptional activation ability. The transcript abundance of IgBBXs in different tissues was divided into two major groups. The expression of IgBBX1, IgBBX2, IgBBX3 and IgBBX5 was higher in leaves, whereas IgBBX4 and IgBBX6 was higher in roots. The stress response patterns of six IgBBX were detected under phytohormone treatments and abiotic stresses. The results of this study lay the basis for further research on the functions of BBX gene family members in plant hormone and stress responses, which will promote their application in I. germanica breeding.

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

2008 ◽  
Vol 68 (4) ◽  
pp. 572-578 ◽  
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.

scholarly journals Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1867
Author(s):  
Yan Li ◽  
Xiang Li ◽  
Jiatong Wei ◽  
Kewei Cai ◽  
Hongzhi Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Cold Stress ◽  
Gene Family ◽  
Gene Families ◽  
Regulatory Function ◽  
Wrky Gene ◽  
Wrky Transcription Factors ◽  
Biotic Stresses ◽  
Genome Wide

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

Genome-wide identification, phylogeny and expression analysis of HSF gene family in barley during abiotic stress response and reproductive development

Plant Gene ◽  
2020 ◽  
Vol 23 ◽  
pp. 100231
Author(s):  
Sumit Kumar Mishra ◽  
Anuj Kumar Poonia ◽  
Reeku Chaudhary ◽  
Vinay K. Baranwal ◽  
Deepanksha Arora ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Family ◽  
Expression Analysis ◽  
Reproductive Development ◽  
Abiotic Stress Response ◽  
Genome Wide

scholarly journals Genome-wide characterization and expression analysis of citrus NUCLEAR FACTOR-Y (NF-Y) transcription factors identified a novel NF-YA gene involved in drought-stress response and tolerance

PLoS ONE ◽  
2018 ◽  
Vol 13 (6) ◽  
pp. e0199187 ◽  
Author(s):  
Suzam L. S. Pereira ◽  
Cristina P. S. Martins ◽  
Aurizangela O. Sousa ◽  
Luciana R. Camillo ◽  
Caroline P. Araújo ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Stress Response ◽  
Expression Analysis ◽  
Nuclear Factor ◽  
Nuclear Factor Y ◽  
Genome Wide

Identification and expression analysis of chloroplast ribonucleoproteins (cpRNPs) in Arabidopsis and rice

Genome ◽  
2020 ◽  
Author(s):  
Jiawen Wu ◽  
Huimin Liu ◽  
Shan Lu ◽  
Jian Hua ◽  
Baohong Zou
Keyword(s):  
Expression Analysis ◽  
Stress Responses ◽  
Expression Patterns ◽  
Tissue Expression ◽  
Stability Control ◽  
Rna Recognition Motif ◽  
Chloroplast Targeting ◽  
Genome Wide ◽  
A Genome ◽  
Targeting Signal

Chloroplast ribonucleoproteins (cpRNPs) are implicated in splicing, editing and stability control of chloroplast RNAs as well as in regulating development and stress tolerance. To facilitate a comprehensive understanding of their functions, we carried out a genome-wide identification, curation, and phylogenetic analysis of cpRNP genes in Oryza sativa (rice) and Arabidopsis thaliana (Arabidopsis). Ten cpRNP genes were identified in each of Arabidopsis and rice genomes based on the presence of two RRM (RNA recognition motif) domains and an N-terminal chloroplast targeting signal peptide in the predicted proteins. These proteins are localized to chloroplasts. Gene expression analysis revealed that cpRNPs have differential tissue expression patterns and some cpRNPs are induced by abiotic stresses such as cold, heat and drought. Taken together, our study provides a comprehensive annotation of the cpRNP gene family and their expression patterns in Arabidopsis and rice which will facilitate further studies on their roles in plant growth and stress responses.

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