Genes
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2025
·Vol. 16
·期 2
·184
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IF 2.8
Ruipeng Liu,Tingting Sun,Pengyu Du,Zengcai Liu,Yawei Li,Xinyu Tong,Li Zou
Background: Basic helix–loop–helix (bHLH) transcription factors (TFs) widely exist in eukaryotic organisms and play a key role in plant growth and development in response to environmental stresses.Sanghuangporus baumii, an important medicinal mushroom known for its anticancer properties, has limited research on the bHLH gene family. Methods: This research utilized the genomic data fromS. baumiito identify bHLH family members, and their gene structure, conserved motifs, and phylogenetic relationship were characterized. Additionally, we conducted an analysis of promoter cis-elements and predicted protein interaction networks. We also examined the expression profiles of bHLH genes during different developmental stages and in response to four abiotic stresses: heat, cold, oxidative stress, and heavy metal exposure. Finally, we overexpressed the candidate geneSbbHLH3in yeast to assess its tolerance to these different stress conditions. Results: A total of 12SbbHLHgenes were identified inS. baumii, and the members of the bHLH gene family displayed a variety of physicochemical characteristics, reflecting their diverse array of functions. Based on homology, the SbbHLH proteins are more closely related to those found inLentinula edodesandPleurotus ostreatus. The analysis of promoter cis-elements showed thatSbbHLHs contain several elements associated with abiotic stress response, and a network prediction identified 28 bHLH-interacting proteins. Expression pattern analysis revealed that mostSbbHLHgenes exhibited a positive response to different developmental stages and abiotic stresses. Notably, the overexpression ofSbbHLH3significantly enhanced stress tolerance in yeast. Conclusions: This study provides a comprehensive assessment of the bHLH family inS. baumii, delivering new genetic resources for breeding resistant varieties.
研究领域:
真菌学
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分子生物学
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遗传学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
MOLECULES
·
2022
·Vol. 27
·期 9
·2809
·
IF 4.927
Qi-Ting Fang,Wen-Wen Luo,Ya-Nan Zheng,Ying Ye,Mei-Juan Hu,Xin-Qiang Zheng,Jian-Liang Lu,Yue-Rong Liang,Jian-Hui Ye
Chemicals underlying the floral aroma of dry teas needs multi-dimensional investigations. Green, black, and freeze-dried tea samples were produced from five tea cultivars, and only ‘Chunyu2’ and ‘Jinguanyin’ dry teas had floral scents. ‘Chunyu2’ green tea contained the highest content of total volatiles (134.75 μg/g) among green tea samples, while ‘Jinguanyin’ black tea contained the highest content of total volatiles (1908.05 μg/g) among black tea samples. The principal component analysis study showed that ‘Chunyu2’ and ‘Jinguanyin’ green teas and ‘Chunyu2’ black tea were characterized by the abundant presence of certain alcohols with floral aroma, while ‘Jinguanyin’ black tea was discriminated due to the high levels of certain alcohols, esters, and aldehydes. A total of 27 shared volatiles were present in different tea samples, and the contents of 7 floral odorants in dry teas had correlations with those in fresh tea leaves (p< 0.05). Thus, the tea cultivar is crucial to the floral scent of dry tea, and these seven volatiles could be promising breeding indices.Keywords:floral scent;tea cultivars;processing;volatiles;alcohols;principal component analysis;co-expression analysis
研究领域:
食品科学
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植物化学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
STAR Protocols
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2021
·
IF 0
Lidia Wrobel,Farah H. Siddiqi,David C. Rubinsztein
Summary We present a protocol for in vivo siRNA-mediated knockdown of a gene of interest in mouse liver using systemic delivery via intravenous injection. We describe a step-by-step protocol for delivery of siRNA particles, with tips on how to optimize dosage. We detail steps for feeding/starving cycles as well as for liver tissue isolation, followed by gene expression analysis, measured at the mRNA and protein levels. For complete information on the generation and use of this protocol, please refer to Wrobel et al. (2020) .
研究领域:
分子生物学
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遗传学
✓ 已验证
DOI
PubMed
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
·
2024
·Vol. 91
·期 1
·
IF 3.9
Ji Zeng,Hao Wang,Yuxi Xu,Jianying Han,Yannan Li,Shu'an Wen,Changbu Wu,Dani Li,Zheng Liu,Xiaokang Zhang,Guo-Bao Tian,Min Dong
Clostridioides difficile is an obligate anaerobic, Gram-positive bacterium that produces toxins. Despite technological progress, conducting gene expression analysis of C. difficile under different conditions continues to be labor-intensive. Therefore, there is a demand for simplified tools to investigate the transcriptional and translational regulation of C. difficile. The cell-free gene expression (CFE) system has demonstrated utility in various applications, including prototyping, protein production, and in vitro screening. In this study, we developed a C. difficile CFE system capable of in vitro transcription and translation (TX-TL) in the presence of oxygen. Through optimization of cell extract preparation and reaction systems, we increased the protein yield significantly. Furthermore, our observations indicated that this system exhibited higher protein yield using linear DNA templates than circular plasmids for in vitro expression. The prototyping capability of the C. difficile CFE system was assessed using a series of synthetic Clostridium promoters, demonstrating a good correlation between in vivo and in vitro expression. Additionally, we tested the expression of tcdB and tcdR from clinically relevant C. difficile strains using the CFE system, confirming higher toxin expression of the hypervirulent strain R20291. We believe that the CFE system can not only serve as a platform for in vitro protein synthesis and genetic part prototyping but also has the potential to be a simplified model for studying metabolic regulations in Clostridioides difficile.
研究领域:
微生物学
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分子生物学
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生物技术
✓ 已验证
DOI
高影响因子
Frontiers in Plant Science
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2025
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IF 4.8
Zhangting Xu,Guihua Zhang,Feixiong Zheng,Xiaoji Deng,Yiming Sun,Jaime A Teixeira da Silva,Xiaoxia Shen,Zhenming Yu
Introduction Dendrobium is a multi-purpose medicinal orchid that grows on the edge of highaltitude cliffs. The content of water-soluble polysaccharides (WSPs), which primarily play a pharmacological role, is the main criterion for evaluating the quality of Dendrobium orchid. Therefore, it is necessary to study the regulatory manner involved in the accumulation of WSPs. Methods D. officinale were treated with methyl jasmonate (MeJA), and WSPs content was measured at different time points to assess the dynamic accumulation pattern. To clarify the role of one finger (Dof) family genes in the MeJA-mediated WSP metabolic pathway, a bioinformatics analysis identified Dof members in D. huoshanense , D. nobile and D. officinale . Based on expression patterns and co-expression analysis, a regulatory factor, DoDof4 was identified. Results In this study, the elicitation of D. officinale by methyl jasmonate (MeJA) increased WSP production, which was further amplified by extending the treatment period. Analysis of transcriptomic data revealed that members of the DNA-binding with Dof gene family members accounted for 4% of all differentially expressed genes coding for transcription factors, following MeJA induction. To clarify the role of Dof family genes in the MeJA-mediated WSP metabolic pathway, a bioinformatics analysis identified 29, 29 and 22 Dof members in D. huoshanense , D. nobile and D. officinale , respectively and these were divided into four groups. DoDof4 was encoded a 31.16 kDa protein composed of 292 amino acids, and was targeted on chromosome 3. Furthermore, DoDof4 was a typical transcription factor that localized in the nucleus, displayed transcriptional activity and increased the WSPs accumulation. DoDof4 was co-expressed with 15 genes involved in the WSP metabolic pathway, eight of which displayed a positive Pearson's correlation coefficient. Additionally, correlation analysis revealed the possible downstream targets ( KM980199 and KP203853 ) of DoDof4 . Discussion The results of the present study suggest that DoDof4 acts as an important regulator in the WSPs metabolic pathway, exhibiting potential values for the improvement of WSPs in Dendrobium species.
研究领域:
植物学
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分子生物学
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遗传学
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生药学
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植物生理学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
Discover Oncology
·
2024
·Vol. 15
·期 1
·1-18
·
IF 2.8
Feng Rui,Li Haolin,Meng Tong,Fei Mingtian,Yang Cheng
Purpose This study aimed to construct an m6A and cuproptosis-related long non-coding RNAs (lncRNAs) signature to accurately predict the prognosis of kidney clear cell carcinoma (KIRC) patients using the information acquired from The Cancer Genome Atlas (TCGA) database. Methods First, the co-expression analysis was performed to identify lncRNAs linked with N6-methyladenosine (m6A) and cuproptosis in ccRCC. Then, a model encompassing four candidate lncRNAs was constructed via univariate, least absolute shrinkage together with selection operator (LASSO), and multivariate regression analyses. Furthermore, Kaplan–Meier, principal component, functional enrichment annotation, and nomogram analyses were performed to develop a risk model that could effectively assess medical outcomes for ccRCC cases. Moreover, the cellular function of NFE4 in Caki-1/OS-RC-2 cultures was elucidated through CCK-8/EdU assessments and Transwell experiments. Dataset outcomes indicated that NFE4 can have possible implications in m6A and cuproptosis, and may promote ccRCC progression. Results We constructed a panel of m6A and cuproptosis-related lncRNAs to construct a prognostic prediction model. The Kaplan–Meier and ROC curves showed that the feature had acceptable predictive validity in the TCGA training, test, and complete groups. Furthermore, the m6A and cuproptosis-related lncRNA model indicated higher diagnostic efficiency than other clinical features. Moreover, the NFE4 function analysis indicated a gene associated with m6A and cuproptosis-related lncRNAs in ccRCC. It was also revealed that the proliferation and migration of Caki-1 /OS-RC-2 cells were inhibited in the NFE4 knockdown group. Conclusion Overall, this study indicated that NFE4 and our constructed risk signature could predict outcomes and have potential clinical value.
研究领域:
生物信息学
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癌症生物学
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分子生物学
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基因组学
✓ 已验证
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）