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Zhang Y, Wei Y, Wu M, Liu M, Liang S, Zhu X, Liu X, Lin F. Cand2 inhibits CRL-mediated ubiquitination and suppresses autophagy to facilitate pathogenicity of phytopathogenic fungi. Plant Commun 2024; 5:100720. [PMID: 37718510 PMCID: PMC10873881 DOI: 10.1016/j.xplc.2023.100720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
The ubiquitin-proteasome system and the autophagy system are the two primary mechanisms used by eukaryotes to maintain protein homeostasis, and both are closely related to the pathogenicity of the rice blast fungus. In this research, we identified MoCand2 as an inhibitor of ubiquitination in Magnaporthe oryzae. Through this role, MoCand2 participates in the regulation of autophagy and pathogenicity. Specifically, we found that deletion of MoCand2 increased the ubiquitination level in M. oryzae, whereas overexpression of MoCand2 inhibited the accumulation of ubiquitinated proteins. Interaction analyses showed that MoCand2 is a subunit of Cullin-RING ligases (CRLs). It suppresses ubiquitination by blocking the assembly of CRLs and downregulating the expression of key CRL subunits. Further research indicated that MoCand2 regulates autophagy through ubiquitination. MoCand2 knockout led to over-ubiquitination and over-degradation of MoTor, and we confirmed that MoTor content was negatively correlated with autophagy level. In addition, MoCand2 knockout accelerated the K63 ubiquitination of MoAtg6 and strengthened the assembly and activity of the phosphatidylinositol-3-kinase class 3 complex, thus enhancing autophagy. Abnormal ubiquitination and autophagy in ΔMocand2 resulted in defects in growth, conidiation, stress resistance, and pathogenicity. Finally, sequence alignment and functional analyses in other phytopathogenic fungi confirmed the high conservation of fungal Cand2s. Our research thus reveals a novel mechanism by which ubiquitination regulates autophagy and pathogenicity in phytopathogenic fungi.
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Affiliation(s)
- Yunran Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Yunyun Wei
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China
| | - Minghua Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengyu Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shuang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaohong Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fucheng Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Xu PX, Ren HY, Zhao N, Jin XJ, Wen BH, Qin T. Distribution characteristics of the Legionella CRISPR-Cas system and its regulatory mechanism underpinning phenotypic function. Infect Immun 2024; 92:e0022923. [PMID: 38099659 PMCID: PMC10790817 DOI: 10.1128/iai.00229-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/10/2023] [Indexed: 01/17/2024] Open
Abstract
Legionella is a common intracellular parasitic bacterium that infects humans via the respiratory tract, causing Legionnaires' disease, with fever and pneumonia as the main symptoms. The emergence of highly virulent and azithromycin-resistant Legionella pneumophila is a major challenge in clinical anti-infective therapy. The CRISPR-Cas acquired immune system provides immune defense against foreign nucleic acids and regulates strain biological functions. However, the distribution of the CRISPR-Cas system in Legionella and how it regulates gene expression in L. pneumophila remain unclear. Herein, we assessed 915 Legionella whole-genome sequences to determine the distribution characteristics of the CRISPR-Cas system and constructed gene deletion mutants to explore the regulation of the system based on growth ability in vitro, antibiotic sensitivity, and intracellular proliferation of L. pneumophila. The CRISPR-Cas system in Legionella was predominantly Type II-B and was mainly concentrated in the genome of L. pneumophila ST1 strains. The Type II-B CRISPR-Cas system showed no effect on the strain's growth ability in vitro but significantly reduced resistance to azithromycin and decreased proliferation ability due to regulation of the lpeAB efflux pump and the Dot/Icm type IV secretion system. Thus, the Type II-B CRISPR-Cas system plays a crucial role in regulating the virulence of L. pneumophila. This expands our understanding of drug resistance and pathogenicity in Legionella, provides a scientific basis for the prevention of Legionnaires' disease outbreaks and the rational use of clinical drugs, and facilitates effective treatment of Legionnaires' disease.
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Affiliation(s)
- Pei-Xing Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hong-Yu Ren
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Na Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiao-Jing Jin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bo-Hai Wen
- Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tian Qin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Deng J, Wang L, Zhang L, Yang C, Huang J, Zhu L, Chen Q, Meng Z, Cai F, Shi T. Tartary Buckwheat ( Fagopyrum tataricum) FtTT8 Inhibits Anthocyanin Biosynthesis and Promotes Proanthocyanidin Biosynthesis. Int J Mol Sci 2023; 24:17368. [PMID: 38139196 PMCID: PMC10743629 DOI: 10.3390/ijms242417368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/21/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Tartary buckwheat (Fagopyrum tataricum) is an important plant, utilized for both medicine and food. It has become a current research hotspot due to its rich content of flavonoids, which are beneficial for human health. Anthocyanins (ATs) and proanthocyanidins (PAs) are the two main kinds of flavonoid compounds in Tartary buckwheat, which participate in the pigmentation of some tissue as well as rendering resistance to many biotic and abiotic stresses. Additionally, Tartary buckwheat anthocyanins and PAs have many health benefits for humans and the plant itself. However, little is known about the regulation mechanism of the biosynthesis of anthocyanin and PA in Tartary buckwheat. In the present study, a bHLH transcription factor (TF) FtTT8 was characterized to be homologous with AtTT8 and phylogenetically close to bHLH proteins from other plant species. Subcellular location and yeast two-hybrid assays suggested that FtTT8 locates in the nucleus and plays a role as a transcription factor. Complementation analysis in Arabidopsis tt8 mutant showed that FtTT8 could not recover anthocyanin deficiency but could promote PAs accumulation. Overexpression of FtTT8 in red-flowering tobacco showed that FtTT8 inhibits anthocyanin biosynthesis and accelerates proanthocyanidin biosynthesis. QRT-PCR and yeast one-hybrid assay revealed that FtTT8 might bind to the promoter of NtUFGT and suppress its expression, while binding to the promoter of NtLAR and upregulating its expression in K326 tobacco. This displayed the bidirectional regulating function of FtTT8 that negatively regulates anthocyanin biosynthesis and positively regulates proanthocyanidin biosynthesis. The results provide new insights on TT8 in Tartary buckwheat, which is inconsistent with TT8 from other plant species, and FtTT8 might be a high-quality gene resource for Tartary buckwheat breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Taoxiong Shi
- School of Life Sciences, Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang 550025, China; (J.D.); (L.W.); (L.Z.); (C.Y.); (J.H.); (L.Z.); (Q.C.); (Z.M.); (F.C.)
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Wei YY, Liang S, Zhu XM, Liu XH, Lin FC. Recent Advances in Effector Research of Magnaporthe oryzae. Biomolecules 2023; 13:1650. [PMID: 38002332 PMCID: PMC10669146 DOI: 10.3390/biom13111650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Recalcitrant rice blast disease is caused by Magnaporthe oryzae, which has a significant negative economic reverberation on crop productivity. In order to induce the disease onto the host, M. oryzae positively generates many types of small secreted proteins, here named as effectors, to manipulate the host cell for the purpose of stimulating pathogenic infection. In M. oryzae, by engaging with specific receptors on the cell surface, effectors activate signaling channels which control an array of cellular activities, such as proliferation, differentiation and apoptosis. The most recent research on effector identification, classification, function, secretion, and control mechanism has been compiled in this review. In addition, the article also discusses directions and challenges for future research into an effector in M. oryzae.
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Affiliation(s)
- Yun-Yun Wei
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China;
| | - Shuang Liang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.L.); (X.-M.Z.)
| | - Xue-Ming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.L.); (X.-M.Z.)
| | - Xiao-Hong Liu
- Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.L.); (X.-M.Z.)
- Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Zhang W, Chen SJ, Guo LY, Zhang Z, Zhang JB, Wang XM, Meng XB, Zhang MY, Zhang KK, Chen LL, Li YW, Wen Y, Wang L, Hu JH, Bai YY, Zhang XJ. Nitric oxide synthase and its function in animal reproduction: an update. Front Physiol 2023; 14:1288669. [PMID: 38028794 PMCID: PMC10662090 DOI: 10.3389/fphys.2023.1288669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Nitric oxide (NO), a free radical labile gas, is involved in the regulation of various biological functions and physiological processes during animal reproduction. Recently, increasing evidence suggests that the biological role and chemical fate of NO is dependent on dynamic regulation of its biosynthetic enzyme, three distinct nitric oxide synthase (NOS) according to their structure, location and function. The impact of NOS isoforms on reproductive functions need to be timely elucidated. Here, we focus on and the basic background and latest studies on the development, structure, importance inhibitor, location pattern, complex functions. Moreover, we summarize the exactly mechanisms which involved some cell signal pathways in the regulation of NOS with cellular and molecular level in the animal reproduction. Therefore, this growing research area provides the new insight into the important role of NOS male and female reproduction system. It also provides the treatment evidence on targeting NOS of reproductive regulation and diseases.
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Affiliation(s)
- Wei Zhang
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Su juan Chen
- Department of Life Science and Technology, Xinxiang Medical College, Xinxiang, Henan, China
| | - Li ya Guo
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Jia bin Zhang
- College of Veterinary Medicine, Jilin Agriculture University, Changchun, China
| | - Xiao meng Wang
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xiang bo Meng
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Min ying Zhang
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Ke ke Zhang
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Lin lin Chen
- College of Veterinary Medicine, Jilin Agriculture University, Changchun, China
| | - Yi wei Li
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Yuliang Wen
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Lei Wang
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Jian he Hu
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Yue yu Bai
- Animal Health Supervision in Henan Province, Zhengzhou, Henan, China
| | - Xiao jian Zhang
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan, China
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Mi K, Zeng L, Chen Y, Yang S. Integrative Analysis of Single-Cell and Bulk RNA Sequencing Reveals Prognostic Characteristics of Macrophage Polarization-Related Genes in Lung Adenocarcinoma. Int J Gen Med 2023; 16:5031-5050. [PMID: 37942473 PMCID: PMC10629586 DOI: 10.2147/ijgm.s430408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a group of cancers with poor prognosis. The combination of single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (RNA-seq) can identify important genes involved in cancer development and progression from a broader perspective. Methods The scRNA-seq data and bulk RNA-seq data of LUAD were downloaded from the Gene Expression Omnibus (GEO) database and the Cancer Genome Atlas (TCGA) database. Analyzing scRNA-seq for core cells in the GSE131907 dataset, and the uniform manifold approximation and projection (UMAP) was used for dimensionality reduction and cluster identification. Macrophage polarization-associated subtypes were acquired from the TCGA-LUAD dataset after analysis, followed by further identification of differentially expressed genes (DEGs) in the TCGA-LUAD dataset (normal/LUAD tissue samples, two subtypes). Venn diagrams were utilized to visualize differentially expressed and highly variable macrophage polarization-related genes. Subsequently, a prognostic risk model for LUAD patients was constructed by univariate Cox and Least Absolute Shrinkage and Selection Operator (LASSO), and the model was investigated for stability in the external data GSE72094. After analyzing the correlation between the trait genes and significantly mutated genes, the immune infiltration between the high/low-risk groups was then examined. The Monocle package was applied to analyze the pseudo-temporal trajectory analysis of different cell clusters in macrophage clusters. Subsequently, cell clusters of data macrophages were selected as key cell clusters to explore the role of characteristic genes in different cell populations and to identify transcription factors (TFs) that affect signature genes. Finally, qPCR were employed to validate the expression levels of prognosis signature genes in LUAD. Results 424 macrophage highly variable genes, 3920 DEGs, and 9561 DEGs were obtained from macrophage clusters, the macrophage polarization-related subtypes, and normal/LUAD tissue samples, respectively. Twenty-eight differentially expressed and highly mutated MPRGs were obtained. A prognostic risk model with 7 DE-MPRGs (RGS13, ADRB2, DDIT4, MS4A2, ALDH2, CTSH, and PKM) was constructed. This prognostic model still has a good prediction effect in the GSE72094 dataset. ZNF536 and DNAH9 were mutated in the low-risk group, while COL11A1 was mutated in the high-risk group, and they were highly correlated with the characteristic genes. A total of 11 immune cells were significantly different in the high/low-risk groups. Five cell types were again identified in the macrophage cluster, and then NK cells: CD56hiCD62L+ differentiated earlier and were present mainly on 2 branches. While macrophages were present on 2 branches and differentiated later. It was found that the expression levels of BCLAF1 and MAX were higher in cluster 1, which might be the TFs affecting the expression of the characteristic genes. Moreover, qPCR confirmed that the expression of the prognosis genes was generally consistent with the results of the bioinformatic analysis. Conclusion Seven MPRGs (RGS13, ADRB2, DDIT4, MS4A2, ALDH2, CTSH, and PKM) were identified as prognostic genes for LUAD and revealed the mechanisms of MPRGs at the single-cell level.
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Affiliation(s)
- Ke Mi
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Lizhong Zeng
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Yang Chen
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Shuanying Yang
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
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Abstract
Ferroptosis suppressor protein 1 (FSP1) is one of the main regulatory molecules of ferroptosis. FSP1 functions through the FSP1-coenzyme Q10 (CoQ10)-NAD(P)H axis and the vitamin K redox cycle. FSP1 is regulated by upstream factors, including transcription factors and noncoding RNA (ncRNA), and is subject to epigenetic modifications, which affect the progress of FSP1-related diseases. FSP1 is closely associated with the poor prognosis of malignant tumors and plays an important role in disease treatment. This review aims to provide a comprehensive understanding of the role of FSP1 in ferroptosis regulation by summarizing regulatory pathways, possible mechanisms involving FSP1, and the relationship between FSP1 and disease prognosis and treatment.
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Affiliation(s)
- Wentao Li
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center of Geriatric Disorders, Xiangya Hospital of Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, Hunan 410011, China
| | - Lin Liang
- Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, Hunan 410011, China
| | - Siyi Liu
- Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, Hunan 410011, China
| | - Hong Yi
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center of Geriatric Disorders, Xiangya Hospital of Central South University, Changsha, Hunan 410008, China.
| | - Yanhong Zhou
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center of Geriatric Disorders, Xiangya Hospital of Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, Hunan 410011, China.
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Hu L, Brito LF, Luo H, Chen S, Johnson JS, Sammad A, Guo G, Xu Q, Wang Y. Differential Responses of Physiological Parameters, Production Traits, and Blood Metabolic Profiling between First- and Second-Parity Holstein Cows in the Comparison of Spring versus Summer Seasons. J Agric Food Chem 2023; 71:11902-11920. [PMID: 37490609 DOI: 10.1021/acs.jafc.3c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Heat stress (HS) negatively influences cows' welfare and productivity. Therefore, a better understanding of the physiological and molecular mechanisms of HS responses from multiple parities is paramount for the development of effective management and breeding strategies. In comparison with first-parity cows in the spring (Spring-1), first-parity cows in the summer (Summer-1) had a significantly higher rectal temperature (RT), respiration rate (RR), drooling score (DS), and daily activity (DA), while lower (P < 0.05) daily rumination (DR), seven-day average milk yield (7AMY), milk yield on sampling day (MY_S), milk yield on test day (MY_T), and lactose percentage (LP) were observed. When comparing the spring (Spring-2) and summer (Summer-2) of the second-parity cows, significant differences were also found in RT, RR, DS, DA, and DR (P < 0.05), corresponding to similar trends with the first parity while having smaller changes. Moreover, significantly negative impacts on performance traits were only observed on fat percentage (FP) and LP. These results showed that there were different biological responses between first- and second-parity Holstein cows. Further, 18 and 17 metabolites were involved in the seasonal response of first- and second-parity cows, respectively. Nine differential metabolites were shared between the two parities, and pathway analyses suggested that cows had an inhibited tricarboxylic acid cycle, increased utilization of lipolysis, and a dysregulated gut microbiome during the summer. The metabolites identified exclusively for each parity highlighted the differences in microbial response and host amino acid metabolism between two parities in response to HS. Moreover, glucose, ethanol, and citrate were identified as potential biomarkers for distinguishing individuals between Spring-1 and Summer-1. Ethanol and acetone were better predictors for distinguishing individuals between Spring-2 and Summer-2. Taken together, the present study demonstrated the impact of naturally induced HS on physiological parameters, production traits, and the blood metabolome of Holstein cows. There are different biological responses and regulation mechanisms between first- and second-parity Holstein cows.
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Affiliation(s)
- Lirong Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hanpeng Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shaokan Chen
- Beijing Sunlon Livestock Development Co. Ltd, Beijing 100176, China
| | - Jay S Johnson
- USDA-ARS Livestock Behavior Research Unit, West Lafayette, Indiana 47907, United States
| | - Abdul Sammad
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co. Ltd, Beijing 100176, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Li J, Li L. Physical modification of vegetable protein by extrusion and regulation mechanism of polysaccharide on the unique functional properties of extruded vegetable protein: a review. Crit Rev Food Sci Nutr 2023:1-14. [PMID: 37548410 DOI: 10.1080/10408398.2023.2239337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Development and utilization of high quality vegetable protein resources has become a hotspot. Food extrusion as a key technology can efficiently utilize vegetable protein. By changing the extrusion conditions, vegetable protein can obtain unique functional properties, which can meet the different needs of food processing. However, extrusion of single vegetable protein also exposes many disadvantages, such as low degree functional properties, poor quality stability and lower tissue fibrosis. Therefore, addition of polysaccharide has become a new development trend to compensate for the shortcomings of extruded vegetable protein. The unique functional properties of vegetable protein-polysaccharide conjugates (Maillard reaction products) can be achieved after extrusion due to regulation of polysaccharides and adjustment of extrusion parameters. However, the physicochemical changes caused by the intermolecular interactions between protein and polysaccharide during extrusion are complex, so control of these changes is still challenging, and further studies are needed. This review summarizes extrusion modification of vegetable proteins or polysaccharides. Next, the effect of different types of polysaccharides on vegetable proteins and its regulation mechanism during extrusion is mainly introduced, including the extrusion of starch polysaccharide-vegetable protein, and non-starch polysaccharide-vegetable protein. Finally, it also outlines the development perspectives of extruded vegetable protein-polysaccharide.
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Affiliation(s)
- Jinpeng Li
- College of Food Science, Northeast Agricultural University, Harbin, P.R. China
| | - Liang Li
- College of Food Science, Northeast Agricultural University, Harbin, P.R. China
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Jiang P, Chen D, Chang X, Zhang C, Fan X, Qin X. Study on the Regulation Mechanism of Quality Deterioration Due to Chilling Stress and Dry Exposure during Anhydrous Storage and Transportation of Yesso Scallop Patinopecten yessoensis. Foods 2023; 12:2902. [PMID: 37569171 PMCID: PMC10418722 DOI: 10.3390/foods12152902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
In this paper, the quality change of Yesso scallop (Patinopecten yessoensis) in the process of anhydrous storage and transportation after cold acclimation and induced dormancy was studied, and the regulation mechanism of quality degradation during storage and transportation in the process of gradient chilling stress and drying exposure was further explored. The results show that, when transferred from hydrous to anhydrous states, the breathing pattern of the scallops changed from aerobic to anaerobic. Their gill filaments were altered and their apparent vitality constantly declined, which was reflected by the edge shrinkage of the pallium and the direct proportions of the edge reduction rate and the stimulus response period. After being in the anhydrous state for 4 d, the AEC value dropped to 67.59%. At this time, if they were placed under hydration again, the scallops resumed a good growth state. By proteomics analysis, it was revealed that cold acclimation and dry exposure mainly led to changes in biological functions and pathways, such as mitochondrial inner membrane and ATP hydrolysis activity. In addition, it can be seen from the functional annotation and enrichment analysis of the metabolite KEGG that cold acclimation promoted the purine metabolism of scallops, while dry exposure inhibited the metabolism of saturated fatty acids. In this study, the infrared sensing mode was used for the first time, too, in order to record the heart-rate changes of the scallops during circulation, which shows that non-destructive vitality monitoring of Lamellibranchia is feasible.
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Affiliation(s)
- Peihong Jiang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Guangdong Province Engineering Laboratory for Marine Biological Products, Zhanjiang 524088, China; (P.J.)
- Shandong Provincial Key Laboratory of Agricultural Products Storage, Transportation and Preservation Technology, Shandong Institute of Commerce and Technology, National Engineering Research Center for Agricultural Products Logistics, Shandong Guonong Logistics Technology Co., Ltd., Jinan 250103, China
| | - Dongjie Chen
- Shandong Provincial Key Laboratory of Agricultural Products Storage, Transportation and Preservation Technology, Shandong Institute of Commerce and Technology, National Engineering Research Center for Agricultural Products Logistics, Shandong Guonong Logistics Technology Co., Ltd., Jinan 250103, China
| | - Xiangyang Chang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Guangdong Province Engineering Laboratory for Marine Biological Products, Zhanjiang 524088, China; (P.J.)
| | - Changfeng Zhang
- Shandong Provincial Key Laboratory of Agricultural Products Storage, Transportation and Preservation Technology, Shandong Institute of Commerce and Technology, National Engineering Research Center for Agricultural Products Logistics, Shandong Guonong Logistics Technology Co., Ltd., Jinan 250103, China
| | - Xiuping Fan
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Guangdong Province Engineering Laboratory for Marine Biological Products, Zhanjiang 524088, China; (P.J.)
| | - Xiaoming Qin
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Guangdong Province Engineering Laboratory for Marine Biological Products, Zhanjiang 524088, China; (P.J.)
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Li F, Li PF, Hao XD. Circular RNAs in ferroptosis: regulation mechanism and potential clinical application in disease. Front Pharmacol 2023; 14:1173040. [PMID: 37332354 PMCID: PMC10272566 DOI: 10.3389/fphar.2023.1173040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/25/2023] [Indexed: 06/20/2023] Open
Abstract
Ferroptosis, an iron-dependent non-apoptotic form of cell death, is reportedly involved in the pathogenesis of various diseases, particularly tumors, organ injury, and degenerative pathologies. Several signaling molecules and pathways have been found to be involved in the regulation of ferroptosis, including polyunsaturated fatty acid peroxidation, glutathione/glutathione peroxidase 4, the cysteine/glutamate antiporter system Xc-, ferroptosis suppressor protein 1/ubiquinone, and iron metabolism. An increasing amount of evidence suggests that circular RNAs (circRNAs), which have a stable circular structure, play important regulatory roles in the ferroptosis pathways that contribute to disease progression. Hence, ferroptosis-inhibiting and ferroptosis-stimulating circRNAs have potential as novel diagnostic markers or therapeutic targets for cancers, infarctions, organ injuries, and diabetes complications linked to ferroptosis. In this review, we summarize the roles that circRNAs play in the molecular mechanisms and regulatory networks of ferroptosis and their potential clinical applications in ferroptosis-related diseases. This review furthers our understanding of the roles of ferroptosis-related circRNAs and provides new perspectives on ferroptosis regulation and new directions for the diagnosis, treatment, and prognosis of ferroptosis-related diseases.
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12
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Lyu M, Lai H, Wang Y, Zhou Y, Chen Y, Wu D, Chen J, Ying B. Roles of alternative splicing in infectious diseases: from hosts, pathogens to their interactions. Chin Med J (Engl) 2023; 136:767-779. [PMID: 36893312 PMCID: PMC10150853 DOI: 10.1097/cm9.0000000000002621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT Alternative splicing (AS) is an evolutionarily conserved mechanism that removes introns and ligates exons to generate mature messenger RNAs (mRNAs), extremely improving the richness of transcriptome and proteome. Both mammal hosts and pathogens require AS to maintain their life activities, and inherent physiological heterogeneity between mammals and pathogens makes them adopt different ways to perform AS. Mammals and fungi conduct a two-step transesterification reaction by spliceosomes to splice each individual mRNA (named cis -splicing). Parasites also use spliceosomes to splice, but this splicing can occur among different mRNAs (named trans -splicing). Bacteria and viruses directly hijack the host's splicing machinery to accomplish this process. Infection-related changes are reflected in the spliceosome behaviors and the characteristics of various splicing regulators (abundance, modification, distribution, movement speed, and conformation), which further radiate to alterations in the global splicing profiles. Genes with splicing changes are enriched in immune-, growth-, or metabolism-related pathways, highlighting approaches through which hosts crosstalk with pathogens. Based on these infection-specific regulators or AS events, several targeted agents have been developed to fight against pathogens. Here, we summarized recent findings in the field of infection-related splicing, including splicing mechanisms of pathogens and hosts, splicing regulation and aberrant AS events, as well as emerging targeted drugs. We aimed to systemically decode host-pathogen interactions from a perspective of splicing. We further discussed the current strategies of drug development, detection methods, analysis algorithms, and database construction, facilitating the annotation of infection-related splicing and the integration of AS with disease phenotype.
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Affiliation(s)
- Mengyuan Lyu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongli Lai
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yili Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yi Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dongsheng Wu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jie Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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13
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Qin A, Aluko OO, Liu Z, Yang J, Hu M, Guan L, Sun X. Improved cotton yield: Can we achieve this goal by regulating the coordination of source and sink? Front Plant Sci 2023; 14:1136636. [PMID: 37063185 PMCID: PMC10090392 DOI: 10.3389/fpls.2023.1136636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Cotton is one of the major cash crops globally. It is characterized by determinate growth and multiple fruiting, which makes the source-sink contradiction more obvious. Coordination between source and sink is crucial for normal growth, yield, and quality of cotton. Numerous studies reported how the assimilate transport and distribution under varying environmental cues affected crop yields. However, less is known about the functional mechanism underlying the assimilate transport between source and sink, and how their distribution impacts cotton growth. Here, we provided an overview of the assimilate transport and distribution mechanisms , and discussed the regulatory mechanisms involved in source-sink balance in relation to cotton yield. Therefore, this review enriched our knowledge of the regulatory mechanism involved in source-sink relationship for improved cotton yield.
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Liu Z, Yuan Y, Wang L, Zhao X, Wang L, Wang L, Zhao Z, Zhao X, Chu Y, Gao Y, Yang F, Wang Y, Zhang Q, Zhao J, Liu M. Three Novel Adenylate Cyclase Genes Show Significant Biological Functions in Plant. J Agric Food Chem 2023; 71:1149-1161. [PMID: 36601683 DOI: 10.1021/acs.jafc.2c07683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Adenylate cyclase is the key enzyme solely synthesizing cAMP which participates in cell metabolism regulations and functions as an intracellular second messenger. However, the biological functions of plant ACs have not been elucidated clearly for their poor conservative sequences and low detectable cAMP. We performed a systematic study of plant ACs by using Chinese jujube, whose fruit exhibits the highest cAMP content among plants. Three novel ACs were identified from Chinese jujube, and two types of methods including in vitro and in vivo were used to certificate ZjAC1-3 which can catalyze the conversion of ATP into cAMP. The biological functions of significant accelerations of seed germination, root growth, and flowering were found via overexpression of these AC genes in Arabidopsis, and these functions of ACs were further demonstrated by treating the AC-overexpressing transgenic lines and wild type Arabidopsis with bithionol and dibutyryl-cAMP. At last, transcriptome data revealed that the underlying mechanism of the biological functions of ACs might be regulation of the key genes involved in the circadian rhythm pathway and the hormone signal transduction pathway. This research established a foundation for further investigating plant AC genes and provided strong evidence for cAMP serving as a signaling molecule in plants.
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Affiliation(s)
- Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
- Jujube Industry Technology Research Institute of Hebei, Baoding, Hebei 071001, China
| | - Ye Yuan
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Lili Wang
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xuan Zhao
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
- "Dongzao" Research Institute of Zhanhua District, Binzhou, Shandong 256800, China
| | - Lixin Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, China
| | - Zhihui Zhao
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xin Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Yuetong Chu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Yaning Gao
- Beijing Pharma and Biotech Center, Beijing 100176, China
| | - Fangyuan Yang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Yulu Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Qiong Zhang
- Shandong Institute of Pomology, Tai'an, Shandong 271000, China
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
- Jujube Industry Technology Research Institute of Hebei, Baoding, Hebei 071001, China
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15
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Zhao Y, Zhao J, Hu M, Sun L, Liu Q, Zhang Y, Li Q, Wang P, Ma W, Li H, Gao H, Zhang Y. Transcriptome and Proteome Analysis Revealed the Influence of High-Molecular-Weight Glutenin Subunits (HMW-GSs) Deficiency on Expression of Storage Substances and the Potential Regulatory Mechanism of HMW-GSs. Foods 2023; 12:foods12020361. [PMID: 36673453 PMCID: PMC9857648 DOI: 10.3390/foods12020361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
The processing quality of wheat is affected by seed storage substances, such as protein and starch. High-molecular-weight glutenin subunits (HMW-GSs) are the major components of wheat seed storage proteins (SSPs); they are also key determinators of wheat end-use quality. However, the effects of HMW-GSs absence on the expression of other storage substances and the regulation mechanism of HMW-GSs are still limited. Previously, a wheat transgenic line LH-11 with complete deletions of HMW-GSs was obtained through introducing an exogenous gene Glu-1Ebx to the wild-type cultivar Bobwhite by transgenic approach. In this study, comparative seed transcriptomics and proteomics of transgenic and non-transgenic lines at different seed developmental stages were carried out to explore the changes in genes and proteins and the underlying regulatory mechanism. Results revealed that a number of genes, including genes related to SSPs, carbohydrates metabolism, amino acids metabolism, transcription, translation, and protein process were differentially enriched. Seed storage proteins displayed differential expression patterns between the transgenic and non-transgenic line, a major rise in the expression levels of gliadins were observed at 21 and 28 days post anthesis (DPA) in the transgenic line. Changes in expressions of low-molecular-weight glutenins (LMW-GSs), avenin-like proteins (ALPs), lipid transfer proteins (LTPs), and protease inhibitors (PIs) were also observed. In addition, genes related to carbohydrate metabolism were differentially expressed, which probably leads to a difference in starch component and deposition. A list of gene categories participating in the accumulation of SSPs was proposed according to the transcriptome and proteome data. Six genes from the MYB and eight genes from the NAC transcription families are likely important regulators of HMW-GSs accumulation. This study will provide data support for understanding the regulatory network of wheat storage substances. The screened candidate genes can lay a foundation for further research on the regulation mechanism of HMW-GSs.
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Affiliation(s)
- Yun Zhao
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Jie Zhao
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Mengyun Hu
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Lijing Sun
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Qian Liu
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Yelun Zhang
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Qianying Li
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Peinan Wang
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
| | - Hui Li
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Huimin Gao
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
- Correspondence: (H.G.); (Y.Z.)
| | - Yingjun Zhang
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
- Correspondence: (H.G.); (Y.Z.)
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16
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Wei Z, Shi Y, Xue C, Li M, Wei J, Li G, Xiong W, Zhou M. Understanding the Dual Roles of CircHIPK3 in Tumorigenesis and Tumor Progression. J Cancer 2022; 13:3674-3686. [PMID: 36606192 PMCID: PMC9809309 DOI: 10.7150/jca.78090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/06/2022] [Indexed: 12/12/2022] Open
Abstract
CircHIPK3 is a type of endogenous circular RNA, which contains a covalently closed circular structure and cannot encode protein or polypeptide. CircHIPK3 is unusually expressed in varieties of tumors and plays dual roles of tumor promotion or tumor inhibition in tumorigenesis and development of tumors by serving as the sponge for miRNA in multiple tumors. Here, we reviewed the differential expression, the dual functions, the regulation mechanism, and the network in a variety of tumors as well as the potential value for the diagnosis and treatment of tumors, which are of great significance for our comprehensive understanding of the roles and mechanisms of circHIPK3 in tumors.
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Affiliation(s)
- Zeyu Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China.,Xiangya Stomatological Hospital, Central South University, Changsha, Hunan 410078, China.,Cancer Research Institute, Central South University, Changsha, Hunan 410078, China
| | - Yijia Shi
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China.,Xiangya Stomatological Hospital, Central South University, Changsha, Hunan 410078, China.,Cancer Research Institute, Central South University, Changsha, Hunan 410078, China
| | - Changning Xue
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China.,Cancer Research Institute, Central South University, Changsha, Hunan 410078, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan 410078, China
| | - Mengna Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China.,Cancer Research Institute, Central South University, Changsha, Hunan 410078, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan 410078, China
| | - Jianxia Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China.,Cancer Research Institute, Central South University, Changsha, Hunan 410078, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan 410078, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China.,Cancer Research Institute, Central South University, Changsha, Hunan 410078, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan 410078, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China.,Cancer Research Institute, Central South University, Changsha, Hunan 410078, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan 410078, China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China.,Cancer Research Institute, Central South University, Changsha, Hunan 410078, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan 410078, China.,✉ Corresponding author: Ming Zhou, E-mail:
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Shen ZJ, Xu SX, Huang QY, Li ZY, Xu YD, Lin CS, Huang YJ. TMT proteomics analysis of a pseudocereal crop, quinoa ( Chenopodium quinoa Willd.), during seed maturation. Front Plant Sci 2022; 13:975073. [PMID: 36426144 PMCID: PMC9678934 DOI: 10.3389/fpls.2022.975073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.), an Andean native crop, is increasingly popular around the world due to its high nutritional content and stress tolerance. The production and the popularity of this strategic global food are greatly restricted by many limiting factors, such as seed pre-harvest sprouting, bitter saponin, etc. To solve these problems, the underlying mechanism of seed maturation in quinoa needs to be investigated. In this study, based on the investigation of morphological characteristics, a quantitative analysis of its global proteome was conducted using the combinational proteomics of tandem mass tag (TMT) labeling and parallel reaction monitoring (PRM). The proteome changes related to quinoa seed maturation conversion were monitored to aid its genetic improvement. Typical changes of morphological characteristics were discovered during seed maturation, including mean grain diameter, mean grain thickness, mean hundred-grain weight, palea, episperm color, etc. With TMT proteomics analysis, 581 differentially accumulated proteins (DAPs) were identified. Functional classification analysis and Gene Ontology enrichment analysis showed that most DAPs involved in photosynthesis were downregulated, indicating low levels of photosynthesis. DAPs that participated in glycolysis, such as glyceraldehyde-3-phosphate dehydrogenase, pyruvate decarboxylase, and alcohol dehydrogenase, were upregulated to fulfill the increasing requirement of energy consumption during maturation conversion. The storage proteins, such as globulins, legumins, vicilins, and oleosin, were also increased significantly during maturation conversion. Protein-protein interaction analysis and function annotation revealed that the upregulation of oleosin, oil body-associated proteins, and acyl-coenzyme A oxidase 2 resulted in the accumulation of oil in quinoa seeds. The downregulation of β-amyrin 28-oxidase was observed, indicating the decreasing saponin content, during maturation, which makes the quinoa "sweet". By the PRM and qRT-PCR analysis, the expression patterns of most selected DAPs were consistent with the result of TMT proteomics. Our study enhanced the understanding of the maturation conversion in quinoa. This might be the first and most important step toward the genetic improvement of quinoa.
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Affiliation(s)
- Zhi-Jun Shen
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Su-Xia Xu
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Qing-Yun Huang
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Zi-Yang Li
- Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Yi-Ding Xu
- Landscape Architecture and Landscape Research Branch, China Academy of Urban Planning and Design, Beijing, China
| | - Chun-Song Lin
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Yi-Jin Huang
- Department of Dermatology, The First Affiliated Hospital of Xiamen University, Xiamen, China
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18
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Tang D, Shen Y, Li F, Yue R, Duan J, Ye Z, Lin Y, Zhou W, Yang Y, Chen L, Wang H, Zhao J, Li P. Integrating metabolite and transcriptome analysis revealed the different mechanisms of characteristic compound biosynthesis and transcriptional regulation in tea flowers. Front Plant Sci 2022; 13:1016692. [PMID: 36247612 PMCID: PMC9557745 DOI: 10.3389/fpls.2022.1016692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
The flowers of tea plants (Camellia sinensis), as well as tea leaves, contain abundant secondary metabolites and are big potential resources for the extraction of bioactive compounds or preparation of functional foods. However, little is known about the biosynthesis and transcriptional regulation mechanisms of those metabolites in tea flowers, such as terpenoid, flavonol, catechins, caffeine, and theanine. This study finely integrated target and nontarget metabolism analyses to explore the metabolic feature of developing tea flowers. Tea flowers accumulated more abundant terpenoid compounds than young leaves. The transcriptome data of developing flowers and leaves showed that a higher expression level of later genes of terpenoid biosynthesis pathway, such as Terpene synthases gene family, in tea flowers was the candidate reason of the more abundant terpenoid compounds than in tea leaves. Differently, even though flavonol and catechin profiling between tea flowers and leaves was similar, the gene family members of flavonoid biosynthesis were selectively expressed by tea flowers and tea leaves. Transcriptome and phylogenetic analyses indicated that the regulatory mechanism of flavonol biosynthesis was perhaps different between tea flowers and leaves. However, the regulatory mechanism of catechin biosynthesis was perhaps similar between tea flowers and leaves. This study not only provides a global vision of metabolism and transcriptome in tea flowers but also uncovered the different mechanisms of biosynthesis and transcriptional regulation of those important compounds.
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Affiliation(s)
- Dingkun Tang
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yihua Shen
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Fangdong Li
- College of Science, Anhui Agricultural University, Hefei, China
| | - Rui Yue
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Jianwei Duan
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zhili Ye
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Ying Lin
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Wei Zhou
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yilin Yang
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Lixiao Chen
- Municipal Research Institute for Processing of Agricultural and Featured Products, Shiyan Academy of Agricultural Science, Shiyan, China
| | - Hongyan Wang
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
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19
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Feng WM, Liu P, Yan H, Yu G, Zhang S, Jiang S, Shang EX, Qian DW, Duan JA. Investigation of Enzymes in the Phthalide Biosynthetic Pathway in Angelica sinensis Using Integrative Metabolite Profiles and Transcriptome Analysis. Front Plant Sci 2022; 13:928760. [PMID: 35845641 PMCID: PMC9286521 DOI: 10.3389/fpls.2022.928760] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
The roots of Angelica sinensis (Oliv.) Diels are well known for their efficacy in promoting blood circulation. Although many studies have indicated that phthalides are the main chemical components responsible for the pharmacological properties of A. sinensis, the phthalide biosynthetic pathway and enzymes that transform different phthalides are still poorly understood. We identified 108 potential candidate isoforms for phthalide accumulation using transcriptome and metabolite profile analyses. Then, six enzymes, including phospho-2-dehydro-3-deoxyheptonate aldolase 2, shikimate dehydrogenase, primary amine oxidase, polyphenol oxidase, tyrosine decarboxylase, and shikimate O-hydroxycinnamoyl transferase, were identified and proven to be involved in phthalide accumulation by heterologously expressing these proteins in Escherichia coli. We proposed a possible mechanism underlying phthalide transformation and biosynthetic pathways in A. sinensis based on our findings. The results of our study can provide valuable information for understanding the mechanisms underlying phthalide accumulation and transformation and enable further development of quality control during the cultivation of A. sinensis.
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Affiliation(s)
- Wei-Meng Feng
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Pei Liu
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Yan
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Guang Yu
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Sen Zhang
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shu Jiang
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Er-Xin Shang
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Da-Wei Qian
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Ao Duan
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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20
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Gao G, Jin R, Liu D, Zhang X, Sun X, Zhu P, Mao H. CmWRKY15-1 Promotes Resistance to Chrysanthemum White Rust by Regulating CmNPR1 Expression. Front Plant Sci 2022; 13:865607. [PMID: 35574103 PMCID: PMC9094113 DOI: 10.3389/fpls.2022.865607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/16/2022] [Indexed: 06/15/2023]
Abstract
Chrysanthemum white rust (CWR), a disease caused by the fungus Puccinia horiana Henn., seriously impairs the production and ornamental value of chrysanthemums. We previously isolated the disease-resistance gene CmWRKY15-1 from the chrysanthemum and generated CmWRKY15-1 transgenic plants. Here, we determined that CmWRKY15-1-overexpressing lines of the susceptible cultivar 'Jinba' show higher defensive enzyme activity and lower H2O2 levels than a wild type after inoculation with P. horiana, indicating that CmWRKY15-1 positively regulates plant responses to P. horiana. To further explore the mechanism underlying this effect, we performed RNA sequencing using the leaves of wild-type and CmWRKY15-1-RNA interference lines of the resistant cultivar 'C029' after treatment with P. horiana. We identified seven differentially expressed genes in the salicylic acid (SA) pathway, including CmNPR1 (Non-expressor of pathogenesis-related genes 1), encoding an important regulator of this pathway. We isolated the CmNPR1 promoter by hiTAIL-PCR and predicted that it contains pathogen-induced W-box elements. The promoter region of CmNPR1 was activated by P. horiana in a β-glucuronidase activity assay. Yeast one-hybrid assays showed that CmWRKY15-1 binds to the CmNPR1 promoter region to regulate its expression. Finally, we confirmed the interaction between CmWRKY15-1 and CmNPR1 in a bimolecular fluorescence complementation assay. We propose that CmWRKY15-1 interacts with CmNPR1 to activate the expression of downstream pathogenesis-related genes that enhance resistance to P. horiana through the SA pathway. These findings shed light on the mechanism underlying resistance to CWR.
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Affiliation(s)
- Ge Gao
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Ruibing Jin
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Di Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xin Zhang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xiaomei Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Pengfang Zhu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Hongyu Mao
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, China
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21
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Han G, Qiao Z, Li Y, Yang Z, Wang C, Zhang Y, Liu L, Wang B. RING Zinc Finger Proteins in Plant Abiotic Stress Tolerance. Front Plant Sci 2022; 13:877011. [PMID: 35498666 PMCID: PMC9047180 DOI: 10.3389/fpls.2022.877011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/22/2022] [Indexed: 05/03/2023]
Abstract
RING zinc finger proteins have a conserved RING domain, mainly function as E3 ubiquitin ligases, and play important roles in plant growth, development, and the responses to abiotic stresses such as drought, salt, temperature, reactive oxygen species, and harmful metals. RING zinc finger proteins act in abiotic stress responses mainly by modifying and degrading stress-related proteins. Here, we review the latest progress in research on RING zinc finger proteins, including their structural characteristics, classification, subcellular localization, and physiological functions, with an emphasis on abiotic stress tolerance. Under abiotic stress, RING zinc finger proteins on the plasma membrane may function as sensors or abscisic acid (ABA) receptors in abiotic stress signaling. Some RING zinc finger proteins accumulate in the nucleus may act like transcription factors to regulate the expression of downstream abiotic stress marker genes through direct or indirect ways. Most RING zinc finger proteins usually accumulate in the cytoplasm or nucleus and act as E3 ubiquitin ligases in the abiotic stress response through ABA, mitogen-activated protein kinase (MAPK), and ethylene signaling pathways. We also highlight areas where further research on RING zinc finger proteins in plants is needed.
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Affiliation(s)
- Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
- Dongying Institute, Shandong Normal University, Dongying, China
| | - Ziqi Qiao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Yuxia Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Zongran Yang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Chengfeng Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Yuanyuan Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Lili Liu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
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22
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Zhao D, Wang Q, Meng F, Lu F, Bie X, Lu Z, Lu Y. TetR-Type Regulator Lp_2642 Positively Regulates Plantaricin EF Production Based on Genome-Wide Transcriptome Sequencing of Lactiplantibacillus plantarum 163. J Agric Food Chem 2022; 70:4362-4372. [PMID: 35311254 DOI: 10.1021/acs.jafc.2c00206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Whole-genome and transcriptome sequences of Lactiplantibacillus plantarum 163 are provided. There was one circular chromosome and four circular plasmids, with sizes of 3,131,367; 56,674; 49,140; 43,628; and 36,387 bp, respectively, in L. plantarum 163. The regulator Lp_2642 was selected from the genome data, the overexpression of which increased the transcriptional levels of related genes in plantaricin EF biosynthesis and enhanced plantaricin EF production. Its production was 17.30 mg/L in 163 (Lp_2642), which was 1.29-fold higher than that of the original strain. The regulation mechanism demonstrated that Lp_2642 can bind to three sites of plnA promoter, which enhances its transcription and expression, thereby increasing plantaricin EF production. Amino acids Asn-100, Asn-64, and Thr-69 may play a key role in the binding of Lp_2642. These results provide a novel strategy for mass production of plantaricin EF, which facilitates its large-scale production and application in the agriculture and food industries as a preservative.
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Affiliation(s)
- Deyin Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fanqiang Meng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yingjian Lu
- College of Food Science & Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
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23
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Huang Y, Zang X, Yang C, Deng H, Ma X, Xie M, Zhou M, Song J, Xue X. Gene, virulence and related regulatory mechanisms in Cryptococcus gattii. Acta Biochim Biophys Sin (Shanghai) 2022; 54:593-603. [PMID: 35593469 DOI: 10.3724/abbs.2022029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Cryptococcus gattii is a kind of basidiomycetous yeast, which grows in human and animal hosts. C. gattii has four distinct genomes, VGI/AFLP4, VGII/AFLP6, VGIII/AFLP5, and VGIV/AFLP7. The virulence of C. gattii is closely associated with genotype and related stress-signaling pathways, but the pathogenic mechanism of C. gattii has not been fully identified. With the development of genomics and transcriptomics, the relationship among genes, regulatory mechanisms, virulence, and treatment is gradually being recognized. In this review, to better understand how C. gattii causes disease and to characterize hypervirulent C. gattii strains, we summarize the current understanding of C. gattii genotypes, phenotypes, virulence, and the regulatory mechanisms.
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24
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Zhang Y, Fu J, Zhou Q, Li F, Shen Y, Ye Z, Tang D, Chi N, Li L, Ma S, Inayat MA, Guo T, Zhao J, Li P. Metabolite Profiling and Transcriptome Analysis Revealed the Conserved Transcriptional Regulation Mechanism of Caffeine Biosynthesis in Tea and Coffee Plants. J Agric Food Chem 2022; 70:3239-3251. [PMID: 35245048 DOI: 10.1021/acs.jafc.1c06886] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Caffeine is a characteristic bioactive compound in tea and coffee plants, which is synthesized and accumulated extensively in leaves and seeds. However, little is known about the regulatory mechanism of caffeine synthesis in plants. This study compared the caffeine metabolite between tea and coffee plants. We found that tea leaves contained significantly higher caffeine than coffee leaves, which is perhaps due to more members of N-methyltransferase (NMT) genes as well as higher expression levels in tea plants. Substantial numbers of transcription factors were predicted to be involved in caffeine biosynthesis regulation, combining weighted gene co-expression network analysis and the cis-element of NMT promoter analysis in tea and coffee plants. Furthermore, analysis of the transcription factors from the caffeine-related modules suggested that the regulatory mechanism of caffeine biosynthesis was probably partly conservative in tea and coffee plants. This study provides an essential resource for the regulatory mechanism of caffeine biosynthesis in plants.
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Affiliation(s)
- Yanrui Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Jiamin Fu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Qiying Zhou
- Henan Key Laboratory of Tea Plant Biology, College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yihua Shen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Zhili Ye
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Dingkun Tang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Ning Chi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Lanqing Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Shuyu Ma
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Mallano Ali Inayat
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Tieying Guo
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili 679600, China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
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25
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Yang K, Han H, Li Y, Ye J, Xu F. Significance of miRNA in enhancement of flavonoid biosynthesis. Plant Biol (Stuttg) 2022; 24:217-226. [PMID: 34806280 DOI: 10.1111/plb.13361] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/15/2021] [Indexed: 05/20/2023]
Abstract
Flavonoid metabolism shows very strong plasticity in plant development and coping with the changing environment. Flavonoid biosynthesis is regulated by many metabolic pathways, including transcriptional regulation, post-transcriptional control, post-translational regulationand epigenetic regulation. miRNA is a form of endogenous noncoding single-strand small molecule RNA that primarily regulates the expression of target genes horizontally after transcription through splicing and translational suppression. It also plays an important role in regulating plant growth and development, secondary metabolism and biotic and abiotic stress. miRNA can regulate the formation of flavonoids by acting on structural genes or indirectly by using an MBW transcription complex comprising MYB-bHLH-WD40. This study summarizes the biosynthesis and mechanisms of miRNA, and provides a summary of the mechanisms of miRNAs involved in production of flavonoids, in order to elucidate the biosynthesis pathway and complex regulatory network of plant flavonoids. We aim to provide new insights into improving the content of flavonoid active ingredients in plants.
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Affiliation(s)
- K Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - H Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Y Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - J Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - F Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
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26
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Affiliation(s)
- Jinwei Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Research Center of Chemical Kinomics, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- School of Medicine, Institute of Cardiovascular Diseases, Xiamen Cardiovascular Hospital Xiamen University, Xiamen University, Xiamen, China
- Hatherly Laboratories, College of Medicine and Health, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Streatham Campus, Exeter, United Kingdom
- *Correspondence: Jinwei Zhang,
| | - Jing Yao
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Department of Anesthesiology, College of Life Sciences, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Mingqiang Rong
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, China
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27
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Shi S, Liu J, Dong J, Hu J, Liu Y, Feng J, Zhou D. Research progress on the regulation mechanism of probiotics on the microecological flora of infected intestines in livestock and poultry. Lett Appl Microbiol 2021; 74:647-655. [PMID: 34882816 DOI: 10.1111/lam.13629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022]
Abstract
The animal intestine is a complex ecosystem composed of host cells, gut microbiota and available nutrients. Gut microbiota can prevent the occurrence of intestinal diseases in animals by regulating the homeostasis of the intestinal environment. The intestinal microbiota is a complex and stable microbial community, and the homeostasis of the intestinal environment is closely related to the invasion of intestinal pathogens, which plays an important role in protecting the host from pathogen infections. Probiotics are strains of microorganisms that are beneficial to health, and their potential has recently led to a significant increase in studies on the regulation of intestinal flora. Various potential mechanisms of action have been proposed on probiotics, especially mediating the regulation mechanism of the intestinal flora on the host, mainly including competitive inhibition of pathogens, stimulation of the host's adaptive immune system and regulation of the intestinal flora. The advent of high-throughput sequencing technology has given us a clearer understanding and has facilitated the development of research methods to investigate the intestinal microecological flora. This review will focus on the regulation of probiotics on the microbial flora of intestinal infections in livestock and poultry and will depict future research directions.
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Affiliation(s)
- S Shi
- College of Life Sciences, Anqing Normal University and Anhui Key Laboratory of Biodiversity Research and Ecological Protection in Southwest Anhui Province, Anqing, P. R. China
| | | | - J Dong
- College of Life Sciences, Anqing Normal University and Anhui Key Laboratory of Biodiversity Research and Ecological Protection in Southwest Anhui Province, Anqing, P. R. China
| | - J Hu
- College of Life Sciences, Anqing Normal University and Anhui Key Laboratory of Biodiversity Research and Ecological Protection in Southwest Anhui Province, Anqing, P. R. China
| | - Y Liu
- College of Life Sciences, Anqing Normal University and Anhui Key Laboratory of Biodiversity Research and Ecological Protection in Southwest Anhui Province, Anqing, P. R. China
| | - J Feng
- Susong Chunrun Food Co., Ltd, Anqing, P. R. China
| | - D Zhou
- College of Life Sciences, Anqing Normal University and Anhui Key Laboratory of Biodiversity Research and Ecological Protection in Southwest Anhui Province, Anqing, P. R. China
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28
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Ru JN, Hou ZH, Zheng L, Zhao Q, Wang FZ, Chen J, Zhou YB, Chen M, Ma YZ, Xi YJ, Xu ZS. Genome-Wide Analysis of DEAD-box RNA Helicase Family in Wheat ( Triticum aestivum) and Functional Identification of TaDEAD-box57 in Abiotic Stress Responses. Front Plant Sci 2021; 12:797276. [PMID: 34956297 PMCID: PMC8699334 DOI: 10.3389/fpls.2021.797276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/01/2021] [Indexed: 05/29/2023]
Abstract
DEAD-box RNA helicases constitute the largest subfamily of RNA helicase superfamily 2 (SF2), and play crucial roles in plant growth, development, and abiotic stress responses. Wheat is one of the most important cereal crops in worldwide, and abiotic stresses greatly restrict its production. So far, the DEAD-box RNA helicase family has yet to be characterized in wheat. Here, we performed a comprehensive genome-wide analysis of the DEAD-box RNA helicase family in wheat, including phylogenetic relationships, chromosomal distribution, duplication events, and protein motifs. A total of 141 TaDEAD-box genes were identified and found to be unevenly distributed across all 21 chromosomes. Whole genome/segmental duplication was identified as the likely main driving factor for expansion of the TaDEAD-box family. Expression patterns of the 141 TaDEAD-box genes were compared across different tissues and under abiotic stresses to identify genes to be important in growth or stress responses. TaDEAD-box57-3B was significantly up-regulated under multiple abiotic stresses, and was therefore selected for further analysis. TaDEAD-box57-3B was localized to the cytoplasm and plasma membrane. Ectopic expression of TaDEAD-box57-3B in Arabidopsis improved tolerance to drought and salt stress as measured by germination rates, root lengths, fresh weights, and survival rates. Transgenic lines also showed higher levels of proline and chlorophyll and lower levels of malonaldehyde (MDA) than WT plants in response to drought or salt stress. In response to cold stress, the transgenic lines showed significantly better growth and higher survival rates than WT plants. These results indicate that TaDEAD-box57-3B may increase tolerance to drought, salt, and cold stress in transgenic plants through regulating the degree of membrane lipid peroxidation. This study provides new insights for understanding evolution and function in the TaDEAD-box gene family.
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Affiliation(s)
- Jing-Na Ru
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ze-Hao Hou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Lei Zheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Qi Zhao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Feng-Zhi Wang
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement/Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Jun Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yong-Bin Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ya-Jun Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
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29
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Wu H, Tong Y, Zhou R, Wang Y, Wang Z, Ding T, Huang B. Mr-AbaA Regulates Conidiation by Interacting with the Promoter Regions of Both Mr-veA and Mr-wetA in Metarhizium robertsii. Microbiol Spectr 2021; 9:e0082321. [PMID: 34494863 DOI: 10.1128/Spectrum.00823-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conidiation is a pivotal strategy for fungi to resist adverse environments and disperse to new habitats, which is especially important for entomopathogenic fungi whose conidia are infective as fungal pesticide propagules. However, the molecular mechanism for regulating conidiation in entomopathogenic fungi is not fully understood. Here, we characterized the regulatory mechanism of the key developmental transcription factor Mr-AbaA. Bioinformatic analysis, transcriptional profiles, and subcellular localization of Mr-abaA indicated that AbaA functioned as a transcription factor in the conidiophore development and conidium stages. Microscopic examination showed that the null mutant of Mr-abaA differentiated into defective phialides to produce an abacus structure instead of conidia. Loss of Mr-abaA resulted in the inhibition of submerged blastospore separation in vitro. Moreover, yeast (Saccharomyces cerevisiae) one-hybrid assays of interactions between genes and deletion of Mr-veA showed that Mr-AbaA regulates conidiation by interacting with the promoter regions of Mr-veA and Mr-wetA. These results demonstrate that Mr-AbaA positively regulates conidiation in Metarhizium robertsii by regulating the velvet family ortholog gene Mr-veA and contributes to the separation of blastospores in submerged culture. IMPORTANCE Metarhizium robertsii is an emerging model entomopathogenic fungus for developing biopesticides; therefore, a comprehensive understanding of its conidiation is very important for its application. In this study, we revealed that the transcription factor Mr-AbaA is involved in the control of aerial conidiation and blastospore separation in submerged culture. Further yeast one-hybrid assays demonstrated that Mr-AbaA interacts with the promoter regions of Mr-veA and Mr-wetA, which code for proteins involved in the control of conidiation. This finding provides new insight into the regulation of the conidiation of this important entomopathogenic fungi.
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Tang J, He H, Li Y, Liu Z, Xia Z, Cao L, Zhu Z, Shuai L, Liu Y, Wan Q, Luo Y, Zhang Y, Rang J, Xia L. Comparative Proteomics Reveals the Effect of the Transcriptional Regulator Sp13016 on Butenyl-Spinosyn Biosynthesis in Saccharopolyspora pogona. J Agric Food Chem 2021; 69:12554-12565. [PMID: 34657420 DOI: 10.1021/acs.jafc.1c03654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Butenyl-spinosyn is a highly effective and broad-spectrum biopesticide produced by Saccharopolyspora pogona. However, the yield of this compound is difficult to increase because the regulatory mechanism of secondary metabolism is still unknown. Here, the transcriptional regulator Sp13016 was discovered to be highly associated with butenyl-spinosyn synthesis and bacterial growth. Overexpression of sp13016 improved butenyl-spinosyn production to a level that was 2.84-fold that of the original strain, while deletion of sp13016 resulted in a significant decrease in yield and growth inhibition. Comparative proteomics revealed that these phenotypic changes were attributed to the influence of Sp13016 on the central carbon metabolism pathway to regulate the supply of precursors. Our research helps to reveal the regulatory mechanism of butenyl-spinosyn biosynthesis and provides a reference for increasing the yield of natural products of Actinomycetes.
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Affiliation(s)
- Jianli Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Yunlong Li
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Zhudong Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Li Cao
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Zirong Zhu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Ling Shuai
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Yang Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Qianqian Wan
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Yuewen Luo
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Youming Zhang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Lushan Road 36, Changsha 410081, China
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He M, Hu F. TF-RBP-AS Triplet Analysis Reveals the Mechanisms of Aberrant Alternative Splicing Events in Kidney Cancer: Implications for Their Possible Clinical Use as Prognostic and Therapeutic Biomarkers. Int J Mol Sci 2021; 22:8789. [PMID: 34445498 DOI: 10.3390/ijms22168789] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Aberrant alternative splicing (AS) is increasingly linked to cancer; however, how AS contributes to cancer development still remains largely unknown. AS events (ASEs) are largely regulated by RNA-binding proteins (RBPs) whose ability can be modulated by a variety of genetic and epigenetic mechanisms. In this study, we used a computational framework to investigate the roles of transcription factors (TFs) on regulating RBP-AS interactions. A total of 6519 TF–RBP–AS triplets were identified, including 290 TFs, 175 RBPs, and 16 ASEs from TCGA–KIRC RNA sequencing data. TF function categories were defined according to correlation changes between RBP expression and their targeted ASEs. The results suggested that most TFs affected multiple targets, and six different classes of TF-mediated transcriptional dysregulations were identified. Then, regulatory networks were constructed for TF–RBP–AS triplets. Further pathway-enrichment analysis showed that these TFs and RBPs involved in triplets were enriched in a variety of pathways that were associated with cancer development and progression. Survival analysis showed that some triplets were highly associated with survival rates. These findings demonstrated that the integration of TFs into alternative splicing regulatory networks can help us in understanding the roles of alternative splicing in cancer.
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Wang J, Wang C, Li L, Yang L, Wang S, Ning X, Gao S, Ren L, Chaulagain A, Tang J, Wang T. Alternative splicing: An important regulatory mechanism in colorectal carcinoma. Mol Carcinog 2021; 60:279-293. [PMID: 33629774 DOI: 10.1002/mc.23291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/01/2021] [Accepted: 02/11/2021] [Indexed: 12/17/2022]
Abstract
Alternative splicing (AS) is a process that produces various mRNA splicing isoforms via different splicing patterns of mRNA precursors (pre-mRNAs). AS is the primary mechanism for increasing the types and quantities of proteins to improve biodiversity and influence multiple biological processes, including chromatin modification, signal transduction, and protein expression. It has been reported that AS is involved in the tumorigenesis and development of colorectal carcinoma (CRC). In this review, we delineate the concept, types, regulatory processes, and technical advances of AS and focus on the role of AS in CRC initiation, progression, treatment, and prognosis. This summary of the current knowledge about AS will contribute to our understanding of CRC initiation and development. This study will help in the discovery of novel biomarkers and therapeutic targets for CRC prognosis and treatment.
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Affiliation(s)
- Jianyi Wang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Chuhan Wang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Le Li
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Lirui Yang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Shuoshuo Wang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Xuelian Ning
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Shuangshu Gao
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Lili Ren
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Anita Chaulagain
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Jing Tang
- Department of Pathology, Harbin Medical University, Harbin, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Tianzhen Wang
- Department of Pathology, Harbin Medical University, Harbin, China
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33
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Xue JY, Takken FLW, Nepal MP, Maekawa T, Shao ZQ. Editorial: Evolution and Functional Mechanisms of Plant Disease Resistance. Front Genet 2020; 11:593240. [PMID: 33133173 PMCID: PMC7573559 DOI: 10.3389/fgene.2020.593240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 08/31/2020] [Indexed: 11/24/2022] Open
Affiliation(s)
- Jia-Yu Xue
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China.,College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Frank L W Takken
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Takaki Maekawa
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Zhu-Qing Shao
- School of Life Sciences, Nanjing University, Nanjing, China
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Li X, Jiang Y, Ma L, Ma X, Liu Y, Shan J, Ma K, Xing F. Comprehensive Transcriptome and Proteome Analyses Reveal the Modulation of Aflatoxin Production by Aspergillus flavus on Different Crop Substrates. Front Microbiol 2020; 11:1497. [PMID: 32760360 PMCID: PMC7371938 DOI: 10.3389/fmicb.2020.01497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 06/09/2020] [Indexed: 01/26/2023] Open
Abstract
As a natural severe contaminant of stored grains and other crops worldwide, Aspergillus flavus can produce aflatoxins (AFs), the most powerful naturally producing toxic and hepatocarcinogenic compounds. AFs production is regulated by diverse factors including AFs cluster genes, transcription factors, regulators, and environmental factors. Among them, crop substrate is one of the most important factors. Here, we found that AFB1 production was significantly higher in maize and rice broth than in peanut broth. To clarify the mechanisms involved, complementary transcriptomic and proteomic analyses were performed to identify changes in A. flavus incubated in the three crop substrates. The results indicated that fewer genes and proteins were differentially expressed between maize and rice substrates, whereas more differentially expressed genes were observed between maize/rice broth and peanut broth. In particular, the genes involved in the initial step of AFs biosynthesis (aflA, aflB, and aflC) and the ACCase-encoding gene accA were significantly upregulated on the maize and rice substrates. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses indicated that carbon-metabolism-related genes were obviously enriched in the maize broth, and the genes involved in acetyl-CoA accumulation and consumption were up- and downregulated, respectively. Several genes involved in the regulation of AFs biosynthesis, including veA, ppoB, snf1, and the G-protein-coupled receptor (GPCR) genes, were differentially expressed on the three substrates, suggesting that these genes may be also involved in sugar signal sensing, transfer, and regulation. Interestingly, by the correlation analyses of transcriptome and proteome, trehalose metabolism genes, aldehyde dehydrogenase gene, and tryptophan synthase gene were found to be relevant with the regulation of AFs production on different crop substrates. Taken together, the differential expressions of the AFs cluster genes, several regulatory genes, and carbon metabolism genes were involved in the comprehensive modulation of AFs production on different crop substrates.
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Affiliation(s)
- Xu Li
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiran Jiang
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longxue Ma
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun Ma
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Liu
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.,School of Food Science and Engineering, Foshan University, Foshan, China
| | - Jihao Shan
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kang Ma
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, China
| | - Fuguo Xing
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
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35
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Sun CF, Li YQ, Mao XM. Regulation of Protein Post-Translational Modifications on Metabolism of Actinomycetes. Biomolecules 2020; 10:E1122. [PMID: 32751230 DOI: 10.3390/biom10081122] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022] Open
Abstract
Protein post-translational modification (PTM) is a reversible process, which can dynamically regulate the metabolic state of cells through regulation of protein structure, activity, localization or protein–protein interactions. Actinomycetes are present in the soil, air and water, and their life cycle is strongly determined by environmental conditions. The complexity of variable environments urges Actinomycetes to respond quickly to external stimuli. In recent years, advances in identification and quantification of PTMs have led researchers to deepen their understanding of the functions of PTMs in physiology and metabolism, including vegetative growth, sporulation, metabolite synthesis and infectivity. On the other hand, most donor groups for PTMs come from various metabolites, suggesting a complex association network between metabolic states, PTMs and signaling pathways. Here, we review the mechanisms and functions of PTMs identified in Actinomycetes, focusing on phosphorylation, acylation and protein degradation in an attempt to summarize the recent progress of research on PTMs and their important role in bacterial cellular processes.
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Abstract
Ferroptosis is a kind of regulated cell death (RCD) caused by the redox state disorder of intracellular microenvironment controlled by glutathione (GSH) peroxidase 4 (GPX4), which is inhibited by iron chelators and lipophilic antioxidants. In addition to classical regulatory mechanisms, new regulatory factors for ferroptosis have been discovered in recent years, such as the P53 pathway, the activating transcription factor (ATF)3/4 pathway, Beclin 1 (BECN1) pathway, and some non-coding RNA. Ferroptosis is closely related to cancer treatment, neurodegenerative diseases, ischemia–reperfusion of organ, neurotoxicity, and others, in particular, in the field of neurodegenerative diseases treatment has aroused people’s interest. The nuclear factor E2 related factor 2 (Nrf2/NFE2L2) has been proved to play a key role in neurodegenerative disease treatment and ferroptosis regulation. Ferroptosis promotes the progression of neurodegenerative diseases, while the expression of Nrf2 and its target genes (Ho-1, Nqo-1, and Trx) has been declined with aging; therefore, there is still insufficient evidence for ferroptosis and Nrf2 regulatory networks in the field of neurodegenerative diseases. In this review, we will provide a brief overview of ferroptosis regulatory mechanisms, as well as an emphasis on the mechanism of Nrf2 regulating ferroptosis. We also highlight the role of ferroptosis and Nrf2 during the process of neurodegenerative diseases and investigate a theoretical basis for further research on the relationship between Nrf2 and ferroptosis in the process of neurodegenerative diseases treatment.
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Affiliation(s)
- Xiaohua Song
- School of Public Health, University of South China, Hengyang, China
| | - Dingxin Long
- School of Public Health, University of South China, Hengyang, China
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Shen L, Yuan Y, Guo Y, Li M, Li C, Pu X. Probing the Druggablility on the Interface of the Protein-Protein Interaction and Its Allosteric Regulation Mechanism on the Drug Screening for the CXCR4 Homodimer. Front Pharmacol 2019; 10:1310. [PMID: 31787895 PMCID: PMC6855241 DOI: 10.3389/fphar.2019.01310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/15/2019] [Indexed: 12/19/2022] Open
Abstract
Modulating protein–protein interactions (PPIs) with small drug-like molecules targeting it exhibits great promise in modern drug discovery. G protein-coupled receptors (GPCRs) are the largest family of targeted proteins and could form dimers in living biological cells through PPIs. However, compared to drug development of the orthosteric site, there has been lack of investigations on the druggability of the PPI interface for GPCRs and its functional implication on experiments. Thus, in order to address these issues, we constructed a novel computational strategy, which involved in molecular dynamics simulation, virtual screening and protein structure network (PSN), to study one representative GPCR homodimer (CXCR4). One druggable pocket was identified in the PPI interface and one small molecule targeting it was screened, which could strengthen PPI mainly through hydrophobic interaction between the benzene rings of the PPI molecule and TM4 of the receptor. The PSN results further reveals that the PPI molecule could increase the number of the allosteric regulation pathways between the druggable pocket of the dimer interface to the orthostatic site for the subunit A but only play minor role for the other subunit B, leading to the asymmetric change in the volume of the binding pockets for the two subunits (increase for the subunit A and minor change for the subunit B). Consequently, the screening performance of the subunit A to the antagonists is enhanced while the subunit B is unchanged nearly, implying that the PPI molecule may be beneficial to enhance the drug efficacies of the antagonists. In addition, one main regulation pathway with the highest frequency was identified for the subunit A, which consists of Trp1955.34–Tyr190ECL2–Val1965.35–Gln2005.39–Asp2626.58–Cys28N-term, revealing their importance in the allosteric regulation from the PPI molecule. The observations from the work could provide valuable information for the development of the PPI drug-like molecule for GPCRs.
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Affiliation(s)
- Liting Shen
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Chuan Li
- College of Computer Science, Sichuan University, Chengdu, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, China
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Lv C, Niu S, Yan S, Bai C, Yu X, Hou J, Gao W, Zhang J, Zhao Z, Yang C, Zhang Y. Low-density lipoprotein receptor-related protein 1 regulates muscle fiber development in cooperation with related genes to affect meat quality. Poult Sci 2019; 98:3418-3425. [PMID: 30982888 DOI: 10.3382/ps/pez168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/13/2019] [Indexed: 12/30/2022] Open
Abstract
Low-density lipoprotein receptor-related protein 1 (LRP1) is an important signal protein that is widely involved in physiological processes, such as lipid metabolism, cell movement, and disease processes. However, the relationship between LRP1 and meat quality remains unknown in chickens. The present study aimed to investigate the correlation between LRP1 and meat quality that builds on our preliminary research, as well as to reveal the underlying molecular mechanism of LRP1 on meat-quality traits. The results showed that LRP1 was significantly correlated with shear force (P < 0.05). Several key genes involved in muscle growth and development, including IGF-1, IGFBP-5, IGF-1R, IGF-2, and MyoD, were down-regulated significantly (P < 0.05 or P < 0.01), and MSTN was up-regulated significantly (P < 0.01) in the presence of LRP1 interference. Cell proliferation- or apoptosis-related genes, including PMP22, CDKN2C, and p53, increased significantly (P < 0.05 or P < 0.01), whereas Bcl-x decreased significantly (P < 0.05) in the RNAi group. We conclude that LRP1 regulates muscle fiber development in cooperation with related genes that affect myoblast proliferation and apoptosis, thereby impacting shear force in chickens. This study will provide a valuable resource for biological investigations of muscle growth and meat-quality-related genes in chickens. The results could be useful in identifying candidate genes that could be used for selective breeding to improve meat quality.
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Affiliation(s)
- Chao Lv
- College of Animal Science, Jilin University, Changchun 130062, P. R. China
| | - Shuling Niu
- College of Animal Science, Jilin University, Changchun 130062, P. R. China.,Department of Animal Science and Technology, Changchun Sci-Tech University, Changchun 130600, P. R. China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun 130062, P. R. China
| | - Chunyan Bai
- College of Animal Science, Jilin University, Changchun 130062, P. R. China
| | - Xi Yu
- College of Animal Science, Jilin University, Changchun 130062, P. R. China
| | - Jiani Hou
- Department of Animal Science and Technology, Changchun Sci-Tech University, Changchun 130600, P. R. China
| | - Wenjing Gao
- College of Animal Science, Jilin University, Changchun 130062, P. R. China
| | - Jinyu Zhang
- College of Animal Science, Jilin University, Changchun 130062, P. R. China
| | - Zhihui Zhao
- College of Animal Science, Jilin University, Changchun 130062, P. R. China
| | - Caini Yang
- College of Animal Science, Jilin University, Changchun 130062, P. R. China
| | - Yonghong Zhang
- College of Animal Science, Jilin University, Changchun 130062, P. R. China
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Guo T, Ho CT, Zhang X, Cao J, Wang H, Shao X, Pan D, Wu Z. Oolong Tea Polyphenols Ameliorate Circadian Rhythm of Intestinal Microbiome and Liver Clock Genes in Mouse Model. J Agric Food Chem 2019; 67:11969-11976. [PMID: 31583884 DOI: 10.1021/acs.jafc.9b04869] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Our present study focused on the regulating effect of oolong tea polyphenols (OTPs) on the circadian rhythm of liver and intestinal microbiome. OTP significantly alleviated the disrupted diurnal oscillation and phase shift of the specific intestinal microbiota and liver clock genes in mice induced by constant dark (CD) treatment. Transcriptomics revealed that 1114 genes in the control group and 647 genes in the CD group showed circadian rhythm while 723 genes were rhythmic in the CD-OTP group. The Gene Ontology (GO) database provided significant differences in differentially expressed genes (DEGs) in response to OTP treatment. In addition, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched the most DEGs after OTP intervention including "Focal adhesion" (9 DEGs) and "PI3K-Akt signaling pathway" (9 DEGs). The present study provided a global view that OTP may alleviate the circadian rhythm disorder of the host, contributing to the improvement of microecology and health.
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Affiliation(s)
| | - Chi-Tang Ho
- Department of Food Science , Rutgers University , New Brunswick , New Jersey 08901 , United States
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Toma-Fukai S, Shimizu T. Structural Insights into the Regulation Mechanism of Small GTPases by GEFs. Molecules 2019; 24:E3308. [PMID: 31514408 DOI: 10.3390/molecules24183308] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Small GTPases are key regulators of cellular events, and their dysfunction causes many types of cancer. They serve as molecular switches by cycling between inactive guanosine diphosphate (GDP)-bound and active guanosine triphosphate (GTP)-bound states. GTPases are deactivated by GTPase-activating proteins (GAPs) and are activated by guanine-nucleotide exchange factors (GEFs). The intrinsic GTP hydrolysis activity of small GTPases is generally low and is accelerated by GAPs. GEFs promote GDP dissociation from small GTPases to allow for GTP binding, which results in a conformational change of two highly flexible segments, called switch I and switch II, that enables binding of the gamma phosphate and allows small GTPases to interact with downstream effectors. For several decades, crystal structures of many GEFs and GAPs have been reported and have shown tremendous structural diversity. In this review, we focus on the latest structural studies of GEFs. Detailed pictures of the variety of GEF mechanisms at atomic resolution can provide insights into new approaches for drug discovery.
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41
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Sun Z, Yan B. Multiple roles and regulatory mechanisms of the transcription factor GATA6 in human cancers. Clin Genet 2019; 97:64-72. [PMID: 31437305 DOI: 10.1111/cge.13630] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/13/2019] [Accepted: 08/20/2019] [Indexed: 12/24/2022]
Abstract
Cancer is a common type of non-communicable disease, and its morbidity and mortality are rapidly increasing. It is expected to become the largest obstacle to the promotion of global human health in the future. Some transcription factors that play important regulatory roles in embryogenesis and subsequent tissue maintenance can be selectively amplified during tumorigenesis. Due to its high expression in the embryonic endoderm and mesoderm, GATA6 plays a crucial role in the normal development of early human heart, lung, digestive system, adrenal glands, breasts, ovaries, retina, skin, and nervous system. Up to now, overexpression of the GATA6 gene has been shown to play an important role in several cancers, including lung cancer, digestive system tumors, breast cancer, and ovarian cancer. However, the human body is a complex organism, which causes the transcription factor GATA6 to have multiple roles in cancer. In this review, we summarize the multiple roles of transcription factor GATA6 in various cancers and its regulatory mechanisms. The aim is to better understand the relationship between GATA6 gene expression and cancer development and to provide new insights for exploring potential therapeutic targets.
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Affiliation(s)
- Zhaoqing Sun
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Bo Yan
- Shandong Provincial Key Laboratory of Cardiac Disease Diagnosis and Treatment, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China.,The Center for Molecular Genetics of Cardiovascular Diseases, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China.,Shandong Provincial Sino-US Cooperation Research Center for Translational Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
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Hong Z, Zhang X. [Role of cytokine signal suppressor 3 in the regulatory mechanism of colon cancer invasion and proliferation]. Nan Fang Yi Ke Da Xue Xue Bao 2019; 39:43-48. [PMID: 30692065 DOI: 10.12122/j.issn.1673-4254.2019.01.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the expression of cytokine signal suppressor 3 (SOCS3) in colon cancer tissue and the mechanism by which SOCS3 regulates the proliferation and invasion of colon cancer. METHODS We collected the specimens of tumor tissues and paired adjacent tissues from 80 patients with colon cancer undergoing radical resection in our hospital between July, 2014 and May, 2017, and the expression of SOCS3 in the tissue samples was analyzed using Western blotting. We also transfected colon cancer cell line SW480 with a SOCS3-overexpressing plasmid or a small interference RNA (siRNA) for SOCS3 knockdown, and the changes in the cell proliferation and invasion capacity were evaluated using CCK-8 assay and Transwell assay, respectively. The effect of demethylation and IL-6 treatment on SOCS3 expression and the proliferation and invasion of SW480 cells were observed. RESULTS Colon cancer tissues showed a lowered expression of SOCS3 compared with the adjacent tissues. Over-expression of SOCS3 significantly inhibited while SOCS3 knockdown obviously promoted the proliferation and invasion of SW480 cells in vitro. Demethylation treatment up-regulated SOCS3 expression and inhibited the proliferation and invasion capacity of SW480 cells; IL-6 treatment of the cells caused the reverse changes. CONCLUSIONS SOCS3 participates in the development and progression of colon cancer and serves as a potential target for colon cancer treatment. In patients with colon cancer, the low expression of SOCS3 possibly as a result of methylation may promote the proliferation and invasion of the cancer cells.
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Affiliation(s)
- Zhu Hong
- Department of Anal and Intestinal Surgery, Tianjin Union Medical Center (Nankai University Affiliated Hospital), Tianjin 300121, China
| | - Xipeng Zhang
- Department of Anal and Intestinal Surgery, Tianjin Union Medical Center (Nankai University Affiliated Hospital), Tianjin 300121, China
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Zhang LQ, Li QZ. Estimating the effects of transcription factors binding and histone modifications on gene expression levels in human cells. Oncotarget 2018; 8:40090-40103. [PMID: 28454114 PMCID: PMC5522221 DOI: 10.18632/oncotarget.16988] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/11/2017] [Indexed: 12/22/2022] Open
Abstract
Transcription factors and histone modifications are vital for the regulation of gene expression. Hence, to estimate the effects of transcription factors binding and histone modifications on gene expression, we construct a statistical model for the genome-wide 15 transcription factors binding data, 10 histone modifications profiles and DNase-I hypersensitivity data in three mammalian. Remarkably, our results show POLR2A and H3K36me3 can highly and consistently predict gene expression in three cell lines. And H3K4me3, H3K27me3 and H3K9ac are more reliable predictors than other histone modifications in human embryonic stem cells. Moreover, genome-wide statistical redundancies exist within and between transcription factors and histone modifications, and these phenomena may be caused by the regulation mechanism. In further study, we find that even though transcription factors and histone modifications offer similar effects on expression levels of genome-wide genes, the effects of transcription factors and histone modifications on predictive abilities are different for genes in independent biological processes.
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Affiliation(s)
- Lu-Qiang Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, China
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, China
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Zhang H, Xie F, Gong H, Huang H, Chen S, Kang M, Fu Y. [Effects of heat-sensitive moxibustion on HPA axis in rats with irritable bowel syndrome]. Zhongguo Zhen Jiu 2017; 37:1315-21. [PMID: 29354998 DOI: 10.13703/j.0255-2930.2017.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To observe the effects of heat-sensitive moxibustion on corticotropin releasing hormone (CRH), adrenocorticotrophic hormone (ACTH) and corticosterone (CORT) in rats with irritable bowel syndrome (IBS), and to explore the possible mechanism of heat-sensitive moxibustion on IBS. METHODS According to random number table, 56 SD male rats were randomly divided into a blank group (n=8), a model group (n=8), a moxibustion group (n=32), and a mifepristone group (RU-486 group, n=8). The rats in the blank group were treated with normal feeding; the rats in the model group, RU-486 group and moxibustion group were treated with chronic non-predictable stimulation for 21 days to establish IBS model. After model establishment, the rats in the moxibustion group were treated with moxibustion at "Mingmen" (GV 4) for 40 min, once a day for 14 days; the tail temperature was recorded every 5 min; according to the change of tail temperature, the rats were divided into a heat-sensitive moxibustion group and a non-heat-sensitive moxibustion group, and 8 rats were randomly selected in the two groups. The rats in the RU-486 group were treated with gastric administration of RU-486 for 14 days, while the rats in the blank group, model group and moxibustion groups were treated with identical volume of 0.9% NaCl. The rat general condition, body mass, behavioristics, intestinal propulsive rate and visceral sensitivity were observed in each group; ELISA method was used to detect serum CRH, ACTH and CORT; optical microscope was applied to observe the morphological changes of colon. RESULTS (1) After model establishment, rats were in rest state, fatigued, with withered hair and dim ear; the stool was dry or watery; the body mass were slowly increased; the number of crossed grid and standing frequency were significantly reduced; visceral sensitivity was increased and intestinal propulsion rate was decreased; no obvious inflammatory cell infiltration was observed under microscope. (2) After intervention, compared with the blank group, the body mass and visceral sensitivity in the RU-486 group were not significantly different (both P>0.05), but the intestinal propulsion rate was decreased significantly (P<0.01). Compared with the blank group, the body mass of heat-sensitive moxibustion group and non-heat-sensitive moxibustion group was lower (both P<0.01), but the visceral sensitivity and intestinal propulsion rate were similar (both P>0.05). Compared with the model group, the body mass and visceral sensitivity were improved in the RU-486 group (P<0.05, P<0.01), but the intestinal propulsion rate was similar (P>0.05). The body mass, visceral sensitivity and intestinal propulsion rate of the heat-sensitive moxibustion group and the non-heat-sensitive moxibustion group were superior to those of the model group (P<0.05, P<0.01), and the body mass and intestinal propulsion rate of heat-sensitive moxibustion group were superior to those of non-heat-sensitive moxibustion group (both P<0.05). (3) After intervention, compared with the blank group, the contents of CRH, ACTH and CORT in the model group were significantly increased (P<0.05, P<0.01). Compared with the model group, the contents of CRH, ACTH and CORT of the heat-sensitive moxibustion group were statistically reduced (P<0.05, P<0.01), and the contents of CRH and ACTH in the non-heat-sensitive moxibustion group were statistically reduced (P<0.05, P<0.01); the content of CRH in the RU-486 group was reduced (P<0.05), but the contents of ACTH and CORT were increased (P<0.05, P<0.01). Compared with the non-heat-sensitive moxibustion group, the heat-sensitive moxibustion group was better in the improvement of CRH (P<0.05), but there was no significant difference of ACTH and CORT between the two groups (both P>0.05). CONCLUSION Heat-sensitive moxibustion could reduce the contents of CRH, ACTH and CORT through the HPA axis, and improve the function of gastrointestinal motility to treat IBS.
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Affiliation(s)
- Haifeng Zhang
- Department of Acupuncture and Moxibustion, the Affiliated Hospital of Jiangxi University of TCM, Nanchang 330006, China
| | - Fangshen Xie
- Department of Acupuncture and Moxibustion, Xingguo County Hospital of TCM
| | - Hongbin Gong
- Department of Acupuncture and Moxibustion, the Affiliated Hospital of Jiangxi University of TCM, Nanchang 330006, China
| | - Hui Huang
- Graduate School of Jiangxi University of TCM
| | - Shutao Chen
- Graduate School of Jiangxi University of TCM
| | - Mingfei Kang
- Department of Acupuncture and Moxibustion, the Affiliated Hospital of Jiangxi University of TCM, Nanchang 330006, China
| | - Yong Fu
- Department of Acupuncture and Moxibustion, the Affiliated Hospital of Jiangxi University of TCM, Nanchang 330006, China
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Abstract
Chloride channel 2 (ClC-2) is one of the nine mammalian members of the ClC family. The present review discusses the molecular properties of ClC‑2, including CLCN2, ClC‑2 promoter and the structural properties of ClC‑2 protein; physiological properties; functional properties, including the regulation of cell volume. The effects of ClC‑2 on the digestive, respiratory, circulatory, nervous and optical systems are also discussed, in addition to the mechanisms involved in the regulation of ClC‑2. The review then discusses the diseases associated with ClC‑2, including degeneration of the retina, Sjögren's syndrome, age‑related cataracts, degeneration of the testes, azoospermia, lung cancer, constipation, repair of impaired intestinal mucosa barrier, leukemia, cystic fibrosis, leukoencephalopathy, epilepsy and diabetes mellitus. It was concluded that future investigations of ClC‑2 are likely to be focused on developing specific drugs, activators and inhibitors regulating the expression of ClC‑2 to treat diseases associated with ClC‑2. The determination of CLCN2 is required to prevent and treat several diseases associated with ClC‑2.
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Affiliation(s)
- Hongwei Wang
- Department of Ophthalmology, People's Hospital of Jingjiang, Jingjiang, Jiangsu 214500, P.R. China
| | - Minghui Xu
- Library, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Qingjie Kong
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, Jilin 130024, P.R. China
| | - Peng Sun
- Department of Ophthalmology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang 154000, P.R. China
| | - Fengyun Yan
- Assets Division, Harbin University of Science and Technology, Harbin, Heilongjiang 150080, P.R. China
| | - Wenying Tian
- Library, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Xin Wang
- Library, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, P.R. China
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Luan M, Tang RJ, Tang Y, Tian W, Hou C, Zhao F, Lan W, Luan S. Transport and homeostasis of potassium and phosphate: limiting factors for sustainable crop production. J Exp Bot 2017; 68:3091-3105. [PMID: 27965362 DOI: 10.1093/jxb/erw444] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Potassium (K) and phosphate (Pi) are both macronutrients essential for plant growth and crop production, but the unrenewable resources of phosphorus rock and potash have become limiting factors for food security. One critical measure to help solve this problem is to improve nutrient use efficiency (NUE) in plants by understanding and engineering genetic networks for ion uptake, translocation, and storage. Plants have evolved multiple systems to adapt to various nutrient conditions for growth and production. Within the NUE networks, transport proteins and their regulators are the primary players for maintaining nutrient homeostasis and could be utilized to engineer high NUE traits in crop plants. A large number of publications have detailed K+ and Pi transport proteins in plants over the past three decades. Meanwhile, the discovery and validation of their regulatory mechanisms are fast-track topics for research. Here, we provide an overview of K+ and Pi transport proteins and their regulatory mechanisms, which participate in the uptake, translocation, storage, and recycling of these nutrients in plants.
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Affiliation(s)
- Mingda Luan
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, PR China
| | - Ren-Jie Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Yumei Tang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, PR China
| | - Wang Tian
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Congong Hou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Fugeng Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, PR China
| | - Wenzhi Lan
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, PR China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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Gov E, Arga KY. Interactive cooperation and hierarchical operation of microRNA and transcription factor crosstalk in human transcriptional regulatory network. IET Syst Biol 2016; 10:219-228. [PMID: 27879476 PMCID: PMC8687357 DOI: 10.1049/iet-syb.2016.0001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/14/2016] [Accepted: 04/27/2016] [Indexed: 01/26/2024] Open
Abstract
Transcriptional regulation of gene expression is an essential cellular process that is arranged by transcription factors (TFs), microRNAs (miRNA) and their target genes through a variety of mechanisms. Here, we set out to reconstruct a comprehensive transcriptional regulatory network of Homo sapiens consisting of experimentally verified regulatory information on miRNAs, TFs and their target genes. We have performed topological analyses to elucidate the transcriptional regulatory roles of miRNAs and TFs. When we thoroughly investigated the network motifs, different gene regulatory scenarios were observed; whereas, mutual TF-miRNA regulation (interactive cooperation) and hierarchical operation where miRNAs were the upstream regulators of TFs came into prominence. Otherwise, biological process specific subnetworks were also constructed and integration of gene and miRNA expression data on ovarian cancer was achieved as a case study to observe dynamic patterns of the gene expression. Meanwhile, both co-operation and hierarchical operation types were determined in active ovarian cancer and process-specific subnetworks. In addition, the analysis showed that multiple signals from miRNAs were integrated by TFs. Our results demonstrate new insights on the architecture of the human transcriptional regulatory network, and here we present some lessons we gained from deciphering the reciprocal interplay between miRNAs, TFs and their target genes.
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Affiliation(s)
- Esra Gov
- Department of Bioengineering, Marmara University, 34722 Goztepe, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, 34722 Goztepe, Istanbul, Turkey.
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Xu Z, Jiang Y, Jia B, Zhou G. Elevated-CO2 Response of Stomata and Its Dependence on Environmental Factors. Front Plant Sci 2016; 7:657. [PMID: 27242858 PMCID: PMC4865672 DOI: 10.3389/fpls.2016.00657] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 04/29/2016] [Indexed: 05/18/2023]
Abstract
Stomata control the flow of gases between plants and the atmosphere. This review is centered on stomatal responses to elevated CO2 concentration and considers other key environmental factors and underlying mechanisms at multiple levels. First, an outline of general responses in stomatal conductance under elevated CO2 is presented. Second, stomatal density response, its development, and the trade-off with leaf growth under elevated CO2 conditions are depicted. Third, the molecular mechanism regulating guard cell movement at elevated CO2 is suggested. Finally, the interactive effects of elevated CO2 with other factors critical to stomatal behavior are reviewed. It may be useful to better understand how stomata respond to elevated CO2 levels while considering other key environmental factors and mechanisms, including molecular mechanism, biochemical processes, and ecophysiological regulation. This understanding may provide profound new insights into how plants cope with climate change.
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Affiliation(s)
- Zhenzhu Xu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Yanling Jiang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Bingrui Jia
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Guangsheng Zhou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
- Chinese Academy of Meteorological SciencesBeijing, China
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Xu Z, Jiang Y, Jia B, Zhou G. Elevated-CO2 Response of Stomata and Its Dependence on Environmental Factors. Front Plant Sci 2016. [PMID: 27242858 DOI: 10.3389/fpls.20116.00657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Stomata control the flow of gases between plants and the atmosphere. This review is centered on stomatal responses to elevated CO2 concentration and considers other key environmental factors and underlying mechanisms at multiple levels. First, an outline of general responses in stomatal conductance under elevated CO2 is presented. Second, stomatal density response, its development, and the trade-off with leaf growth under elevated CO2 conditions are depicted. Third, the molecular mechanism regulating guard cell movement at elevated CO2 is suggested. Finally, the interactive effects of elevated CO2 with other factors critical to stomatal behavior are reviewed. It may be useful to better understand how stomata respond to elevated CO2 levels while considering other key environmental factors and mechanisms, including molecular mechanism, biochemical processes, and ecophysiological regulation. This understanding may provide profound new insights into how plants cope with climate change.
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Affiliation(s)
- Zhenzhu Xu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Yanling Jiang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Bingrui Jia
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Guangsheng Zhou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China; Chinese Academy of Meteorological SciencesBeijing, China
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Yang H, Ma Y, Wang Y, Yang H, Shen W, Chen X. Transcription regulation mechanisms of bacteriophages: recent advances and future prospects. Bioengineered 2015; 5:300-4. [PMID: 25482231 DOI: 10.4161/bioe.32110] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Phage diversity significantly contributes to ecology and evolution of new bacterial species through horizontal gene transfer. Therefore, it is essential to understand the mechanisms underlying phage-host interactions. After initial infection, the phage utilizes the transcriptional machinery of the host to direct the expression of its own genes. This review presents a view on the transcriptional regulation mechanisms of bacteriophages, and its contribution to phage diversity and classification. Through this review, we aim to broaden the understanding of phage-host interactions while providing a reference source for researchers studying the regulation of phage transcription.
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Affiliation(s)
- Haiquan Yang
- a Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi, China
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