Identification of histone deacetylase genes in <i>Dendrobium officinale</i> and their expression profiles under phytohormone and abiotic stress treatments

Zhang, Mingze; Silva, Jaime A. Teixeira da; Yu, Zhenming; Wang, Haobin; Si, Can; Zhao, Conghui; He, Chunmei; Duan, Jun

doi:10.7717/peerj.10482

Cited by 12 publications

(6 citation statements)

References 83 publications

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Section: Resultssupporting

confidence: 62%

“…A similar situation also occurs for SmHDA1-3, and the results showed that they differ only in the terminal motifs. On the other hand, SmHDTs does not contain any motifs, a similar pattern has been observed in Dendrobium officinale SRTs [24]. The color of the inner ring represents the species: green, S. miltiorrhiza; red, S. lycopersicum; black, A. thaliana; brown, O. sativa; blue, Z. mays.…”

Section: Gene Structure and Motif Analysis Of Smhdacssupporting

confidence: 63%

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Genome-Wide Identification and Characterization of the Salvia miltiorrhiza Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses

Chen,

Ying,

Yao

et al. 2024

Plants

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Salvia miltiorrhiza is a plant commonly used in traditional Chinese medicine. Its material bases for treating diseases are tanshinones and phenolic acids, including salvianolic acids. Histone deacetylase proteins (HDACs) are a class of specific functional enzymes that interact with acetylation groups on the N-terminal lysine of histone proteins further regulate gene transcription through structural changes at the chromatin level. HDACs involved in the growth and development of various plants, and induced by plant hormones to regulate the internal environment of plants to resist stress, at the same time affect the accumulation of some secondary metabolites. However, the role of SmHDACs on the accumulation of salvianolic acid in S. miltiorrhiza remains unclear. In this study, 16 SmHDACs genes were identified from the high-quality S. miltiorrhiza genome, their physicochemical properties were predicted. In phylogenetic trees co-constructed with HDACs proteins from other plants, SmHDACs was divided into three subfamilies, each with similar motif and conserved domain composition. The distribution of the three subfamilies is similar to that of dicotyledonous plants. Chromosome localization analysis showed that SmHDACs genes were randomly located. Cis-acting element analysis predicted that SmHDACs gene expression may be related to and induced by various phytohormones, such as MeJA and ABA. By combining the expression pattern and co-expression network induced by phytohormones, we speculate that SmHDACs may further influence the synthesis of salvianolic acid, and identified SmHDA5, a potential functional gene, then speculate its downstream target based on the co-expression network. In summary, we analyzed the SmHDACs gene family of S. miltiorrhiza and screened out the potential functional gene SmHDA5. From the perspective of epigenetics, we proposed the molecular mechanism of plant hormone promoting salvianolic acid synthesis, which filled the gap in the subdivision of histone deacetylase in S. miltiorrhiza research, provided a theoretical basis for the culture and transformation of S. miltiorrhiza germplasm resources.

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Section: Resultssupporting

confidence: 62%

Section: Gene Structure and Motif Analysis Of Smhdacssupporting

confidence: 63%

Genome-Wide Identification and Characterization of the Salvia miltiorrhiza Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses

Chen,

Ying,

Yao

et al. 2024

Plants

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“…[95] Triticulum aestivum Drought stress downregulated 5 HDA genes and upregulated TaHAC2 in drought-resistant BL207 [96] Dendrobium hirsutum Under drought stress, the DoHDA10 and DoHDT4 genes are expressed in the roots, stems, and leaves. [97] Arabidopsis thaliana HDA9 reduces plant drought sensitivity via H3K9ac in 14 genes during water deficit [98] Table 2. Cont.…”

Section: Gossypium Hirsutummentioning

confidence: 99%

Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications

Abdulraheem,

Xiong,

Moshood

et al. 2024

Plants

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Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5–10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.

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“…HDAC genes also displayed different transcriptional level to respond to drought. For example, DoHDA10 and DoHDT4 were highly up-regulated after PEG-mediated drought treatment, while other HDAC genes were not changed [52]. Wei et al studied the roles of six HDACs in response to drought stress in kenaf and found up-regulation of all these HDACs after PEG treatments [74].…”

Section: Hdacsmentioning

confidence: 99%

Histone Acetylation Changes in Plant Response to Drought Stress

Gao

et al. 2021

Genes

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Drought stress causes recurrent damage to a healthy ecosystem because it has major adverse effects on the growth and productivity of plants. However, plants have developed drought avoidance and resilience for survival through many strategies, such as increasing water absorption and conduction, reducing water loss and conversing growth stages. Understanding how plants respond and regulate drought stress would be important for creating and breeding better plants to help maintain a sound ecosystem. Epigenetic marks are a group of regulators affecting drought response and resilience in plants through modification of chromatin structure to control the transcription of pertinent genes. Histone acetylation is an ubiquitous epigenetic mark. The level of histone acetylation, which is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), determines whether the chromatin is open or closed, thereby controlling access of DNA-binding proteins for transcriptional activation. In this review, we summarize histone acetylation changes in plant response to drought stress, and review the functions of HATs and HDACs in drought response and resistance.

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Identification of histone deacetylase genes in Dendrobium officinale and their expression profiles under phytohormone and abiotic stress treatments

Cited by 12 publications

References 83 publications

Genome-Wide Identification and Characterization of the Salvia miltiorrhiza Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses

Genome-Wide Identification and Characterization of the Salvia miltiorrhiza Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses

Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications

Histone Acetylation Changes in Plant Response to Drought Stress

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