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

Abstract Background: Sugarcane (Saccharum) is the most important sugar crop in the world. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes. Results: A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genome and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which MYB43, MYB53, MYB65, MYB78, and MYB99 were validated by qPCR. Allelic expression dominance in the stem was more significant than that in the leaf, implying the differential expression of alleles may be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C4 photosynthetic regulators by C4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively. Conclusions: A Genome-wide expression analysis demonstrated that SsMYB genes were involved in stem development and stress response. This study largely contributed to understanding the extent to which MYB transcription factors investigate regulatory mechanisms and functional divergence in sugarcane.

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Genome-Wide Investigation of WRKY Transcription Factors Involved in Terminal Drought Stress Response in Common Bean

Frontiers in Plant Science ◽

10.3389/fpls.2017.00380 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 17

Author(s):

Jing Wu ◽

Jibao Chen ◽

Lanfen Wang ◽

Shumin Wang

Keyword(s):

Transcription Factors ◽

Drought Stress ◽

Stress Response ◽

Common Bean ◽

Wrky Transcription Factors ◽

Terminal Drought ◽

Genome Wide ◽

Terminal Drought Stress

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

International Journal of Molecular Sciences ◽

10.3390/ijms22168793 ◽

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.

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Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon

BMC Genomics ◽

10.1186/s12864-016-2968-8 ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 29

Author(s):

Licao Cui ◽

Kewei Feng ◽

Mengxing Wang ◽

Meng Wang ◽

Pingchuan Deng ◽

...

Keyword(s):

Transcription Factors ◽

Expression Analysis ◽

Brachypodium Distachyon ◽

Genome Wide ◽

Erf Transcription Factors

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Increasing Oxygen Partial Pressures Induce a Distinct Transcriptional Response in Human PBMC: A Pilot Study on the “Normobaric Oxygen Paradox”

International Journal of Molecular Sciences ◽

10.3390/ijms22010458 ◽

2021 ◽

Vol 22 (1) ◽

pp. 458

Author(s):

Deborah Fratantonio ◽

Fabio Virgili ◽

Alessandro Zucchi ◽

Kate Lambrechts ◽

Tiziana Latronico ◽

...

Keyword(s):

Oxidative Stress ◽

Transcription Factors ◽

Stress Response ◽

Mononuclear Cells ◽

Human Peripheral Blood ◽

Oxidative Stress Response ◽

Molecular Characteristics ◽

Nuclear Factor ◽

Normobaric Oxygen ◽

Oxygen Paradox

The term “normobaric oxygen paradox” (NOP), describes the response to the return to normoxia after a hyperoxic event, sensed by tissues as oxygen shortage, and resulting in up-regulation of the Hypoxia-inducible factor 1α (HIF-1α) transcription factor activity. The molecular characteristics of this response have not been yet fully characterized. Herein, we report the activation time trend of oxygen-sensitive transcription factors in human peripheral blood mononuclear cells (PBMCs) obtained from healthy subjects after one hour of exposure to mild (MH), high (HH) and very high (VHH) hyperoxia, corresponding to 30%, 100%, 140% O2, respectively. Our observations confirm that MH is perceived as a hypoxic stress, characterized by the activation of HIF-1α and Nuclear factor (erythroid-derived 2)-like 2 (NRF2), but not Nuclear Factor kappa-light-chain-enhancer of activated B cells (NF-κB). Conversely, HH is associated to a progressive loss of NOP response and to an increase in oxidative stress leading to NRF2 and NF-kB activation, accompanied by the synthesis of glutathione (GSH). After VHH, HIF-1α activation is totally absent and oxidative stress response, accompanied by NF-κB activation, is prevalent. Intracellular GSH and Matrix metallopeptidase 9 (MMP-9) plasma levels parallel the transcription factors activation pattern and remain elevated throughout the observation time. In conclusion, our study confirms that, in vivo, the return to normoxia after MH is sensed as a hypoxic trigger characterized by HIF-1α activation. On the contrary, HH and VHH induce a shift toward an oxidative stress response, characterized by NRF2 and NF-κB activation in the first 24 h post exposure.

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Genome-wide identification of AP2/ERF transcription factors in mungbean (Vigna radiata) and expression profiling of the VrDREB subfamily under drought stress

Crop and Pasture Science ◽

10.1071/cp18180 ◽

2018 ◽

Vol 69 (10) ◽

pp. 1009 ◽

Cited By ~ 3

Author(s):

Abdullahi Muhammad Labbo ◽

Maryam Mehmood ◽

Malik Nadeem Akhtar ◽

Muhammad Jawad Khan ◽

Aamira Tariq ◽

...

Keyword(s):

Transcription Factors ◽

Drought Stress ◽

Stress Tolerance ◽

Vigna Radiata ◽

Critical Role ◽

Drought Stress Tolerance ◽

Legume Crop ◽

Genome Wide ◽

Responsive Element ◽

Major Factors

Mungbean (Vigna radiata L.) is a valuable legume crop grown in tropical and subtropical areas of Asia. Drought is one of the major factors hindering its growth globally. APETALA2/ethylene-responsive element factor binding proteins (AP2/ERF) are an important family of plant-specific transcription factors (TFs) involved in drought-stress tolerance. We identified 71 AP2/ERF TFs in the mungbean genome by using bioinformatics tools and classified them into subfamilies: AP2 (16 members), ERF (22), RAV (2), DREB (30) and soloist (other proteins with no domain, 1). Members of DREB play a critical role in drought-stress tolerance. Ten-day-old mungbean plants cv. AZRI-06 were exposed to drought stress by complete withholding of water for 7 days. Root samples were collected from control and drought-stressed plants, and the expression pattern of 30 identified VrDREB genes was determined by qPCR. Most VrDREB genes exhibited differential expression in response to drought. Five genes (VrDREB5, VrDREB12, VrDREB13, VrDREB22, VrDREB30) were highly expressed under drought stress and might be considered excellent candidates for further functional analysis and for improvement of mungbean drought tolerance.

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

Genes ◽

10.3390/genes12121867 ◽

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.

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