Analysis of an abscisic acid (ABA)-responsive gene promoter  belonging to the Asr gene family from tomato in homologous  and heterologous systems

Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

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In silico study shows arsenic induces P1B ATPase gene family as cation transporter by abscisic acid signaling pathway in seedling of Sorghum bicolor

Acta Physiologiae Plantarum ◽

10.1007/s11738-017-2472-z ◽

2017 ◽

Vol 39 (8) ◽

Author(s):

Seyed Ahmad Shafiei Darabi ◽

Abbas Almodares ◽

Mansour Ebrahimi

Keyword(s):

Abscisic Acid ◽

Sorghum Bicolor ◽

Gene Family ◽

Signaling Pathway ◽

In Silico ◽

Abscisic Acid Signaling ◽

Atpase Gene ◽

In Silico Study

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Arabidopsis Calcium-Dependent Protein Kinase AtCPK32 Interacts with ABF4, a Transcriptional Regulator of Abscisic Acid-Responsive Gene Expression, and Modulates Its Activity

PLANT PHYSIOLOGY ◽

10.1104/pp.105.069757 ◽

2005 ◽

Vol 139 (4) ◽

pp. 1750-1761 ◽

Cited By ~ 217

Author(s):

Hyung-in Choi ◽

Hee-Jin Park ◽

Ji Hye Park ◽

Sunmi Kim ◽

Min-Young Im ◽

...

Keyword(s):

Gene Expression ◽

Abscisic Acid ◽

Protein Kinase ◽

Transcriptional Regulator ◽

Dependent Protein Kinase ◽

Calcium Dependent ◽

Dependent Protein ◽

Responsive Gene ◽

Calcium Dependent Protein Kinase

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Genome-Wide Identification of the Expansin Gene Family and Its Potential Association with Drought Stress in Moso Bamboo

International Journal of Molecular Sciences ◽

10.3390/ijms21249491 ◽

2020 ◽

Vol 21 (24) ◽

pp. 9491

Author(s):

Kang-Ming Jin ◽

Ren-Ying Zhuo ◽

Dong Xu ◽

Yu-Jun Wang ◽

Hui-Jin Fan ◽

...

Keyword(s):

Cell Wall ◽

Abscisic Acid ◽

Abiotic Stress ◽

Gene Family ◽

Moso Bamboo ◽

Structure Evolution ◽

Dependent Manner ◽

Cell Wall Loosening ◽

Expansin Gene ◽

Wall Loosening

Expansins, a group of cell wall-loosening proteins, are involved in cell-wall loosening and cell enlargement in a pH-dependent manner. According to previous study, they were involved in plant growth and abiotic stress responses. However, information on the biological function of the expansin gene in moso bamboo is still limited. In this study, we identified a total of 82 expansin genes in moso bamboo, clustered into four subfamilies (α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA) and expansin-like B (EXPB)). Subsequently, the molecular structure, chromosomal location and phylogenetic relationship of the expansin genes of Phyllostachys edulis (PeEXs) were further characterized. A total of 14 pairs of tandem duplication genes and 31 pairs of segmented duplication genes were also identified, which may promote the expansion of the expansin gene family. Promoter analysis found many cis-acting elements related to growth and development and stress response, especially abscisic acid response element (ABRE). Expression pattern revealed that most PeEXs have tissue expression specificity. Meanwhile, the expression of some selected PeEXs was significantly upregulated mostly under abscisic acid (ABA) and polyethylene glycol (PEG) treatment, which implied that these genes actively respond to expression under abiotic stress. This study provided new insights into the structure, evolution and function prediction of the expansin gene family in moso bamboo.

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Crosstalk among stress responses in plants: Pathogen defense overrides UV protection through an inversely regulated ACE/ACE type of light-responsive gene promoter unit

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.042692199 ◽

2002 ◽

Vol 99 (4) ◽

pp. 2428-2432 ◽

Cited By ~ 36

Author(s):

E. Logemann ◽

K. Hahlbrock

Keyword(s):

Stress Responses ◽

Gene Promoter ◽

Uv Protection ◽

Pathogen Defense ◽

Responsive Gene

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Regulation of the mdm2 Oncogene by Thyroid Hormone Receptor

Molecular and Cellular Biology ◽

10.1128/mcb.19.1.864 ◽

1999 ◽

Vol 19 (1) ◽

pp. 864-872 ◽

Cited By ~ 37

Author(s):

Jian-Shen Qi ◽

Yaping Yuan ◽

Vandana Desai-Yajnik ◽

Herbert H. Samuels

Keyword(s):

Cell Cycle ◽

Thyroid Hormone ◽

Gene Family ◽

Thyroid Hormone Receptor ◽

Retinoic Acid Receptor ◽

Receptor Gene ◽

Gene Promoter ◽

Orphan Nuclear Receptor ◽

Retinoid Receptor ◽

Dna Elements

ABSTRACT The mdm2 gene is positively regulated by p53 through a p53-responsive DNA element in the first intron of the mdm2gene. mdm2 binds p53, thereby abrogating the ability of p53 to activate the mdm2 gene, and thus forming an autoregulatory loop ofmdm2 gene regulation. Although the mdm2 gene is thought to act as an oncogene by blocking the activity of p53, recent studies indicate that mdm2 can act independently of p53 and block the G1 cell cycle arrest mediated by members of the retinoblastoma gene family and can activate E2F1/DP1 and the cyclin A gene promoter. In addition, factors other than p53 have recently been shown to regulate the mdm2 gene. In this article, we report that thyroid hormone (T3) receptors (T3Rs), but not the closely related members of the nuclear thyroid hormone/retinoid receptor gene family (retinoic acid receptor, vitamin D receptor, peroxisome proliferation activation receptor, or retinoid X receptor), regulate mdm2 through the same intron sequences that are modulated by p53. Chicken ovalbumin upstream promoter transcription factor I, an orphan nuclear receptor which normally acts as a transcriptional repressor, also activatesmdm2 through the same intron region of the mdm2gene. Two T3R-responsive DNA elements were identified and further mapped to sequences within each of the p53 binding sites of themdm2 intron. A 10-amino-acid sequence in the N-terminal region of T3Rα that is important for transactivation and interaction with TFIIB was also found to be important for activation of themdm2 gene response element. T3 was found to stimulate the endogenous mdm2 gene in GH4C1 cells. These cells are known to express T3Rs, and T3 is known to stimulate replication of these cells via an effect in the G1 phase of the cell cycle. Our findings, which indicate that T3Rs can regulate the mdm2gene independently of p53, provide an explanation for certain known effects of T3 and T3Rs on cell proliferation. In addition, these findings provide further evidence for p53-independent regulation of mdm2 which could lead to the development of tumors from cells that express low levels of p53 or that express p53 mutants defective in binding to and activating the mdm2 gene.

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