1
|
Lai D, Zhang K, He Y, Fan Y, Li W, Shi Y, Gao Y, Huang X, He J, Zhao H, Lu X, Xiao Y, Cheng J, Ruan J, Georgiev MI, Fernie AR, Zhou M. Multi-omics identification of a key glycosyl hydrolase gene FtGH1 involved in rutin hydrolysis in Tartary buckwheat (Fagopyrum tataricum). Plant Biotechnol J 2024; 22:1206-1223. [PMID: 38062934 PMCID: PMC11022807 DOI: 10.1111/pbi.14259] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 04/18/2024]
Abstract
Rutin, a flavonoid rich in buckwheat, is important for human health and plant resistance to external stresses. The hydrolysis of rutin to quercetin underlies the bitter taste of Tartary buckwheat. In order to identify rutin hydrolysis genes, a 200 genotypes mini-core Tartary buckwheat germplasm resource was re-sequenced with 30-fold coverage depth. By combining the content of the intermediate metabolites of rutin metabolism with genome resequencing data, metabolite genome-wide association analyses (GWAS) eventually identified a glycosyl hydrolase gene FtGH1, which could hydrolyse rutin to quercetin. This function was validated both in Tartary buckwheat overexpression hairy roots and in vitro enzyme activity assays. Mutation of the two key active sites, which were determined by molecular docking and experimentally verified via overexpression in hairy roots and transient expression in tobacco leaves, exhibited abnormal subcellular localization, suggesting functional changes. Sequence analysis revealed that mutation of the FtGH1 promoter in accessions of two haplotypes might be necessary for enzymatic activity. Co-expression analysis and GWAS revealed that FtbHLH165 not only repressed FtGH1 expression, but also increased seed length. This work reveals a potential mechanism behind rutin metabolism, which should provide both theoretical support in the study of flavonoid metabolism and in the molecular breeding of Tartary buckwheat.
Collapse
Affiliation(s)
- Dili Lai
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- College of AgricultureGuizhou UniversityGuiyangChina
| | - Kaixuan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yuqi He
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yu Fan
- School of Food and Biological EngineeringChengdu UniversityChengduChina
| | - Wei Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yaliang Shi
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yuanfen Gao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xu Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jiayue He
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hui Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xiang Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yawen Xiao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | | | - Jingjun Ruan
- College of AgricultureGuizhou UniversityGuiyangChina
| | - Milen I. Georgiev
- Laboratory of Metabolomics, Institute of MicrobiologyBulgarian Academy of SciencesPlovdivBulgaria
- Center of Plant Systems Biology and BiotechnologyPlovdivBulgaria
| | - Alisdair R. Fernie
- Center of Plant Systems Biology and BiotechnologyPlovdivBulgaria
- Department of Molecular PhysiologyMax‐Planck‐Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Meiliang Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| |
Collapse
|
2
|
Liu M, Zhang F, Lu H, Xue H, Dong X, Li Z, Xu J, Wang W, Wei C. PPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome. BMC Genomics 2024; 25:405. [PMID: 38658835 DOI: 10.1186/s12864-024-10302-5] [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: 12/08/2023] [Accepted: 04/11/2024] [Indexed: 04/26/2024] Open
Abstract
Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated historically. With the fast-growing number of individual genomes and their annotations available, the demand for a genome browser to visualize genome annotation for many individuals together with a graph-based pangenome is getting higher and higher. Here we report a new pangenome browser PPanG, a precise pangenome browser enabling nucleotide-level comparison of individual genome annotations together with a graph-based pangenome. Nine rice genomes with annotations were provided by default as potential references, and any individual genome can be selected as the reference. Our pangenome browser provides unprecedented insights on genome variations at different levels from base to gene, and reveals how the structures of a gene could differ for individuals. PPanG can be applied to any species with multiple individual genomes available and it is available at https://cgm.sjtu.edu.cn/PPanG .
Collapse
Affiliation(s)
- Mingwei Liu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Fan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Huimin Lu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hongzhang Xue
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiaorui Dong
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zhikang Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jianlong Xu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Wensheng Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
| | - Chaochun Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| |
Collapse
|
3
|
Chen LA, Boyle K. The Role of the Gut Microbiome in Health and Disease in the Elderly. Curr Gastroenterol Rep 2024:10.1007/s11894-024-00932-w. [PMID: 38642272 DOI: 10.1007/s11894-024-00932-w] [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] [Accepted: 04/05/2024] [Indexed: 04/22/2024]
Abstract
PURPOSE OF REVIEW Growing evidence supports the contribution of age in the composition and function of the gut microbiome, with specific findings associated with health in old age and longevity. RECENT FINDINGS Current studies have associated certain microbiota, such as Butyricimonas, Akkermansia, and Odoribacter, with healthy aging and the ability to survive into extreme old age. Furthermore, emerging clinical and pre-clinical research have shown promising mechanisms for restoring a healthy microbiome in elderly populations through various interventions such as fecal microbiota transplant (FMT), dietary interventions, and exercise programs. Despite several conceptually exciting interventional studies, the field of microbiome research in the elderly remains limited. Specifically, large longitudinal studies are needed to better understand causative relationships between the microbiome and healthy aging. Additionally, individualized approaches to microbiome interventions based on patients' co-morbidities and the underlying functional capacity of their microbiomes are needed to achieve optimal results.
Collapse
Affiliation(s)
- Lea Ann Chen
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers, New Brunswick, NJ, USA.
| | - Kaitlyn Boyle
- Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| |
Collapse
|
4
|
Zhao S, Mo G, Wang Q, Xu J, Yu S, Huang Z, Liu W, Zhang W. Role of RB1 in neurodegenerative diseases: inhibition of post-mitotic neuronal apoptosis via Kmt5b. Cell Death Discov 2024; 10:182. [PMID: 38637503 PMCID: PMC11026443 DOI: 10.1038/s41420-024-01955-y] [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: 07/03/2023] [Revised: 12/04/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
During the development of the vertebrate nervous system, 50% of the nerve cells undergo apoptosis shortly after formation. This process is important for sculpting tissue during morphogenesis and removing transiently functional cells that are no longer needed, ensuring the appropriate number of neurons in each region. Dysregulation of neuronal apoptosis can lead to neurodegenerative diseases. However, the molecular events involved in activating and regulating the neuronal apoptosis program are not fully understood. In this study, we identified several RB1 mutations in patients with neurodegenerative diseases. Then, we used a zebrafish model to investigate the role of Rb1 in neuronal apoptosis. We showed that Rb1-deficient mutants exhibit a significant hindbrain neuronal apoptosis, resulting in increased microglia infiltration. We further revealed that the apoptotic neurons in Rb1-deficient zebrafish were post-mitotic neurons, and Rb1 inhibits the apoptosis of these neurons by regulating bcl2/caspase through binding to Kmt5b. Moreover, using this zebrafish mutant, we verified the pathogenicity of the R621S and L819V mutations of human RB1 in neuronal apoptosis. Collectively, our data indicate that the Rb1-Kmt5b-caspase/bcl2 axis is crucial for protecting post-mitotic neurons from apoptosis and provides an explanation for the pathogenesis of clinically relevant mutations.
Collapse
Affiliation(s)
- Shuang Zhao
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Guiling Mo
- Guangzhou KingMed Diagnostics Group Co., Ltd., International Biotech Island, Guangzhou, 510005, China
| | - Qiang Wang
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Jin Xu
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Shihui Yu
- Guangzhou KingMed Diagnostics Group Co., Ltd., International Biotech Island, Guangzhou, 510005, China
| | - Zhibin Huang
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Wei Liu
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, 510006, China.
| | - Wenqing Zhang
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, 510006, China.
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, 518055, China.
| |
Collapse
|
5
|
Wang YF, Zhang WL, Li ZX, Liu Y, Tan J, Yin HZ, Zhang ZC, Piao XJ, Ruan MH, Dai ZH, Wang SJ, Mu CY, Yuan JH, Sun SH, Liu H, Yang F. METTL14 downregulation drives S100A4 + monocyte-derived macrophages via MyD88/NF-κB pathway to promote MAFLD progression. Signal Transduct Target Ther 2024; 9:91. [PMID: 38627387 PMCID: PMC11021505 DOI: 10.1038/s41392-024-01797-1] [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: 10/07/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Without intervention, a considerable proportion of patients with metabolism-associated fatty liver disease (MAFLD) will progress from simple steatosis to metabolism-associated steatohepatitis (MASH), liver fibrosis, and even hepatocellular carcinoma. However, the molecular mechanisms that control progressive MAFLD have yet to be fully determined. Here, we unraveled that the expression of the N6-methyladenosine (m6A) methyltransferase METTL14 is remarkably downregulated in the livers of both patients and several murine models of MAFLD, whereas hepatocyte-specific depletion of this methyltransferase aggravated lipid accumulation, liver injury, and fibrosis. Conversely, hepatic Mettl14 overexpression alleviated the above pathophysiological changes in mice fed on a high-fat diet (HFD). Notably, in vivo and in vitro mechanistic studies indicated that METTL14 downregulation decreased the level of GLS2 by affecting the translation efficiency mediated by YTHDF1 in an m6A-depedent manner, which might help to form an oxidative stress microenvironment and accordingly recruit Cx3cr1+Ccr2+ monocyte-derived macrophages (Mo-macs). In detail, Cx3cr1+Ccr2+ Mo-macs can be categorized into M1-like macrophages and S100A4-positive macrophages and then further activate hepatic stellate cells (HSCs) to promote liver fibrosis. Further experiments revealed that CX3CR1 can activate the transcription of S100A4 via CX3CR1/MyD88/NF-κB signaling pathway in Cx3cr1+Ccr2+ Mo-macs. Restoration of METTL14 or GLS2, or interfering with this signal transduction pathway such as inhibiting MyD88 could ameliorate liver injuries and fibrosis. Taken together, these findings indicate potential therapies for the treatment of MAFLD progression.
Collapse
Affiliation(s)
- Yue-Fan Wang
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital Affiliated to Naval Medical University, 200438, Shanghai, China
- The Department of Medical Genetics, Naval Medical University, 200433, Shanghai, China
| | - Wen-Li Zhang
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital Affiliated to Naval Medical University, 200438, Shanghai, China
| | - Zhi-Xuan Li
- Translational Medicine Research Center, Medical Innovation Research Division and Fourth Medical Center of the Chinese PLA General Hospital, 100048, Beijing, China
| | - Yue Liu
- The Department of Pharmaceutical Analysis, School of Pharmacy, Naval Medical University, 200433, Shanghai, China
| | - Jian Tan
- The Department of Medical Genetics, Naval Medical University, 200433, Shanghai, China
| | - Hao-Zan Yin
- The Department of Medical Genetics, Naval Medical University, 200433, Shanghai, China
| | - Zhi-Chao Zhang
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital Affiliated to Naval Medical University, 200438, Shanghai, China
| | - Xian-Jie Piao
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital Affiliated to Naval Medical University, 200438, Shanghai, China
| | - Min-Hao Ruan
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital Affiliated to Naval Medical University, 200438, Shanghai, China
| | - Zhi-Hui Dai
- The Department of Medical Genetics, Naval Medical University, 200433, Shanghai, China
| | - Si-Jie Wang
- The Department of Medical Genetics, Naval Medical University, 200433, Shanghai, China
| | - Chen-Yang Mu
- The Department of Medical Genetics, Naval Medical University, 200433, Shanghai, China
| | - Ji-Hang Yuan
- The Department of Medical Genetics, Naval Medical University, 200433, Shanghai, China
| | - Shu-Han Sun
- The Department of Medical Genetics, Naval Medical University, 200433, Shanghai, China
| | - Hui Liu
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital Affiliated to Naval Medical University, 200438, Shanghai, China.
| | - Fu Yang
- The Department of Medical Genetics, Naval Medical University, 200433, Shanghai, China.
- Key Laboratory of Biosafety Defense, Ministry of Education, 200433, Shanghai, China.
- Shanghai Key Laboratory of Medical Biodefense, 200433, Shanghai, China.
| |
Collapse
|
6
|
Tong J, Chen X, Wang X, Men S, Liu Y, Sun X, Yan D, Wang L. Novel KMT5B variant associated with neurodevelopmental disorder in a Chinese family: A case report. Heliyon 2024; 10:e28686. [PMID: 38571636 PMCID: PMC10988039 DOI: 10.1016/j.heliyon.2024.e28686] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
Background We report here the clinical and genetic features of KMT5B-related neurodevelopmental disorder caused by a novel heterozygous frameshift variant in KMT5B in a Chinese family. Case presentation A 7-year-old Chinese boy with mild-to-moderate intellectual disability, significant language impairment, motor disability, and coordination difficulties presented to our hospital because he "could not speak and did not look at others." He was diagnosed with autism spectrum disorder previously owing to developmental delays in cognition, language expression, and understanding. The child also had variable nonspecific features including macrocephaly, wide button-hole space and nasal bridge, low ear, social behavior disorder, and foot deformities. Exome sequencing (ES) revealed that both the proband and his younger brother had inherited a novel heterozygous frameshift variant c.438_439ins[ASD; KT192064.1:1_310] of the KMT5B gene from their father. Bioinformatics analysis showed that the novel mutation affected the structure of the KMT5B pre-SET domain, mainly in the α-helix region. According to the American College of Medical Genetics and Genomics (ACMG) guidelines, this type of variant was eventually determined to be likely pathogenic (PVS1+PM2_P). Conclusions Our investigation expands the mutation spectrum of KMT5B to help us to better understand KMT5B-related neurodevelopmental disorder.
Collapse
Affiliation(s)
| | | | - Xin Wang
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Shuai Men
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yuan Liu
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Xun Sun
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Dongmei Yan
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Leilei Wang
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| |
Collapse
|
7
|
Cao H, Song K, Hu Y, Li Q, Ma T, Li R, Chen N, Zhu S, Liu W. The role of exogenous hydrogen sulfide in mitigating cadmium toxicity in plants: A comprehensive meta-analysis. Environ Sci Pollut Res Int 2024:10.1007/s11356-024-33298-7. [PMID: 38613761 DOI: 10.1007/s11356-024-33298-7] [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] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Reducing the accumulation of cadmium (Cd) and mitigating its toxicity are pivotal strategies for addressing Cd pollution's threats to agriculture and human health. Hydrogen sulfide (H2S) serves as a signaling molecule, playing a crucial role in plant stress defense mechanisms. Nevertheless, a comprehensive assessment of the impact of exogenous H2S on plant growth, antioxidant properties, and gene expression under Cd stress remains lacking. In this meta-analysis, we synthesized 575 observations from 27 articles, revealing that exogenous H2S significantly alleviates Cd-induced growth inhibition in plants. Specifically, it enhances root length (by 8.71%), plant height (by 15.67%), fresh weight (by 15.15%), dry weight (by 22.54%), and chlorophyll content (by 27.99%) under Cd stress conditions. H2S boosts antioxidant enzyme activity, particularly catalase (CAT), by 39.51%, thereby reducing Cd-induced reactive oxygen species (ROS) accumulation. Moreover, it impedes Cd translocation from roots to shoots, resulting in a substantial 40.19% reduction in stem Cd content. Additionally, H2S influences gene expression in pathways associated with antioxidant enzymes, metal transport, heavy metal tolerance, H2S biosynthesis, and energy metabolism. However, the efficacy of exogenous H2S in alleviating Cd toxicity varies depending on factors such as plant species, concentration of the H2S donor sodium hydrosulfide (NaHS), application method, and cultivation techniques. Notably, NaHS concentrations exceeding 200 μM may adversely affect plants. Overall, our study underscores the role of exogenous H2S in mitigating Cd toxicity and elucidates its mechanism, providing insights for utilizing H2S to combat Cd pollution in agriculture.
Collapse
Affiliation(s)
- Hanping Cao
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, 401331, China
| | - Kejin Song
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, 401331, China
| | - Yingying Hu
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, 401331, China
| | - Qingxiao Li
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, 401331, China
| | - Tengfei Ma
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, 401331, China
| | - Rui Li
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, 401331, China
| | - Nan Chen
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, 401331, China
| | - Shunqin Zhu
- School of Life Science, Southwest University, Chongqing, 400715, China
| | - Wanhong Liu
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, 401331, China.
| |
Collapse
|
8
|
Feng DC, Zhu WZ, Wang J, Li DX, Shi X, Xiong Q, You J, Han P, Qiu S, Wei Q, Yang L. The implications of single-cell RNA-seq analysis in prostate cancer: unraveling tumor heterogeneity, therapeutic implications and pathways towards personalized therapy. Mil Med Res 2024; 11:21. [PMID: 38605399 PMCID: PMC11007901 DOI: 10.1186/s40779-024-00526-7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
In recent years, advancements in single-cell and spatial transcriptomics, which are highly regarded developments in the current era, particularly the emerging integration of single-cell and spatiotemporal transcriptomics, have enabled a detailed molecular comprehension of the complex regulation of cell fate. The insights obtained from these methodologies are anticipated to significantly contribute to the development of personalized medicine. Currently, single-cell technology is less frequently utilized for prostate cancer compared with other types of tumors. Starting from the perspective of RNA sequencing technology, this review outlined the significance of single-cell RNA sequencing (scRNA-seq) in prostate cancer research, encompassing preclinical medicine and clinical applications. We summarize the differences between mouse and human prostate cancer as revealed by scRNA-seq studies, as well as a combination of multi-omics methods involving scRNA-seq to highlight the key molecular targets for the diagnosis, treatment, and drug resistance characteristics of prostate cancer. These studies are expected to provide novel insights for the development of immunotherapy and other innovative treatment strategies for castration-resistant prostate cancer. Furthermore, we explore the potential clinical applications stemming from other single-cell technologies in this review, paving the way for future research in precision medicine.
Collapse
Affiliation(s)
- De-Chao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Division of Surgery & Interventional Science, University College London, London, WC1E 6BT, UK.
| | - Wei-Zhen Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Deng-Xiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xu Shi
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiao Xiong
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jia You
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ping Han
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shi Qiu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Lu Yang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
9
|
Bernal-Gallardo JJ, de Folter S. Plant genome information facilitates plant functional genomics. Planta 2024; 259:117. [PMID: 38592421 PMCID: PMC11004055 DOI: 10.1007/s00425-024-04397-z] [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] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
MAIN CONCLUSION In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.
Collapse
Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
| |
Collapse
|
10
|
Nagle MF, Yuan J, Kaur D, Ma C, Peremyslova E, Jiang Y, Niño de Rivera A, Jawdy S, Chen JG, Feng K, Yates TB, Tuskan GA, Muchero W, Fuxin L, Strauss SH. GWAS supported by computer vision identifies large numbers of candidate regulators of in planta regeneration in Populus trichocarpa. G3 (Bethesda) 2024; 14:jkae026. [PMID: 38325329 PMCID: PMC10989874 DOI: 10.1093/g3journal/jkae026] [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] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 02/09/2024]
Abstract
Plant regeneration is an important dimension of plant propagation and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. Association mapping methods such as genome-wide association studies (GWAS) have long demonstrated abilities to help uncover the genetic basis of trait variation in plants; however, the performance of these methods depends on the accuracy and scale of phenotyping. To enable a large-scale GWAS of in planta callus and shoot regeneration in the model tree Populus, we developed a phenomics workflow involving semantic segmentation to quantify regenerating plant tissues over time. We found that the resulting statistics were of highly non-normal distributions, and thus employed transformations or permutations to avoid violating assumptions of linear models used in GWAS. We report over 200 statistically supported quantitative trait loci (QTLs), with genes encompassing or near to top QTLs including regulators of cell adhesion, stress signaling, and hormone signaling pathways, as well as other diverse functions. Our results encourage models of hormonal signaling during plant regeneration to consider keystone roles of stress-related signaling (e.g. involving jasmonates and salicylic acid), in addition to the auxin and cytokinin pathways commonly considered. The putative regulatory genes and biological processes we identified provide new insights into the biological complexity of plant regeneration, and may serve as new reagents for improving regeneration and transformation of recalcitrant genotypes and species.
Collapse
Affiliation(s)
- Michael F Nagle
- Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR 97311, USA
| | - Jialin Yuan
- Department of Electrical Engineering and Computer Science, Oregon State University, 1148 Kelley Engineering Center, Corvallis, OR 97331, USA
| | - Damanpreet Kaur
- Department of Electrical Engineering and Computer Science, Oregon State University, 1148 Kelley Engineering Center, Corvallis, OR 97331, USA
| | - Cathleen Ma
- Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR 97311, USA
| | - Ekaterina Peremyslova
- Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR 97311, USA
| | - Yuan Jiang
- Statistics Department, Oregon State University, 239 Weniger Hall, Corvallis, OR 97331, USA
| | - Alexa Niño de Rivera
- Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR 97311, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee-Knoxville, 310 Ferris Hall 1508 Middle Dr, Knoxville, TN 37996, USA
| | - Kai Feng
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
| | - Timothy B Yates
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee-Knoxville, 310 Ferris Hall 1508 Middle Dr, Knoxville, TN 37996, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee-Knoxville, 310 Ferris Hall 1508 Middle Dr, Knoxville, TN 37996, USA
| | - Li Fuxin
- Department of Electrical Engineering and Computer Science, Oregon State University, 1148 Kelley Engineering Center, Corvallis, OR 97331, USA
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR 97311, USA
| |
Collapse
|
11
|
Zhang P, Gou L, Murugan DD, Zhang H. Editorial: Epigenetic and genetic mechanisms underlying cardiovascular diseases and neurodevelopmental disorders. Front Genet 2024; 15:1401354. [PMID: 38633404 PMCID: PMC11021750 DOI: 10.3389/fgene.2024.1401354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Affiliation(s)
- Peng Zhang
- Shenzhen Key Laboratory of ENT, Institute of ENT and Longgang ENT Hospital, Shenzhen, China
| | - Lingshan Gou
- Center for Genetic Medicine, Xuzhou Maternity and Child Healthcare Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Dharmani Devi Murugan
- Department of Pharmacology, Faculty of Medicine, Universiti of Malaya, Kuala Lumpur, Malaysia
| | - Hongsong Zhang
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| |
Collapse
|
12
|
Sun J, Li M, Sun H, Lin Z, Shi B, Jia Z. Genetic association and functional validation of ZFP36L2 in non-syndromic orofacial cleft subtypes. J Hum Genet 2024; 69:139-144. [PMID: 38321215 DOI: 10.1038/s10038-024-01222-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Non-syndromic orofacial cleft (NSOC) is one of the most common craniofacial malformations with complex etiology. This study aimed to explore the role of specific SNPs in ZFP36L2 and its functional relevance in zebrafish models. METHODS We analyzed genetic data of the Chinese Han population from two previous GWAS, comprising of 2512 cases and 2255 controls. Based on the Hardy-Weinberg Equilibrium (HWE) and minor allele frequency (MAF), SNPs in the ZFP36L2 were selected for association analysis. In addition, zebrafish models were used to clarify the in-situ expression pattern of zfp36l2 and the impact of its Morpholino-induced knockdown. RESULTS Via association analysis, rs7933 in ZFP36L2 was significantly associated with various non-syndromic cleft lip-only subtypes, potentially conferring a protective effect. Zebrafish embryos showed elevated expression of zfp36l2 in the craniofacial region during critical stages of oral cavity formation. Furthermore, Morpholino-induced knockdown of zfp36l2 led to craniofacial abnormalities, including cleft lip, which was partially rescued by the addition of zfp36l2 mRNA. CONCLUSION Our findings highlight the significance of ZFP36L2 in the etiology of NSOC, supported by both human genetic association data and functional studies in zebrafish. These results pave the way for further exploration of targeted interventions for craniofacial malformations.
Collapse
Affiliation(s)
- Jialin Sun
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Mujia Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Huaqin Sun
- SCU-CUHK Joint Laboratory for Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyuan Lin
- SCU-CUHK Joint Laboratory for Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
| |
Collapse
|
13
|
Khan F, Pandey P, Verma M, Ramniwas S, Lee D, Moon S, Park MN, Upadhyay TK, Kim B. Emerging trends of phytochemicals as ferroptosis modulators in cancer therapy. Biomed Pharmacother 2024; 173:116363. [PMID: 38479184 DOI: 10.1016/j.biopha.2024.116363] [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: 12/27/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
Ferroptosis, a novel form of regulated cell death characterized by dependence on iron and lipid peroxidation, has been implicated in a wide range of clinical conditions including neurological diseases, cardiovascular disorders, acute kidney failure, and various types of cancer. Therefore, it is critical to suppress cancer progression and proliferation. Ferroptosis can be triggered in cancer cells and some normal cells by synthetic substances, such as erastin, Ras-selective lethal small molecule-3, or clinical pharmaceuticals. Natural bioactive compounds are traditional drug discovery tools, and some have been therapeutically used as dietary additives or pharmaceutical agents against various malignancies. The fact that natural products have multiple targets and minimal side effects has led to notable advances in anticancer research. Research has indicated that ferroptosis can also be induced by natural compounds during cancer treatment. In this review, we focused on the most recent developments in emerging molecular processes and the significance of ferroptosis in cancer. To provide new perspectives on the future development of ferroptosis-related anticancer medications, we also provide a summary of the implications of natural phytochemicals in triggering ferroptosis through ROS production and ferritinophagy induction in a variety of malignancies.
Collapse
Affiliation(s)
- Fahad Khan
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Pratibha Pandey
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, India.
| | - Meenakshi Verma
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413, India; Department of Chemistry, University Institute of Sciences, Chandigarh University, Gharuan, Mohali, Punjab 140413, India
| | - Seema Ramniwas
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413, India
| | - Dain Lee
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemun-gu, Seoul 02447, the Republic of Korea
| | - Seungjoon Moon
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemun-gu, Seoul 02447, the Republic of Korea; Chansol Hospital of Korean Medicine, 290, Buheung-ro, Bupyeong-gu, Incheon 21390, the Republic of Korea
| | - Moon Nyeo Park
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemun-gu, Seoul 02447, the Republic of Korea
| | - Tarun Kumar Upadhyay
- Department of Biotechnology, Parul Institute of Applied Sciences and Research and Development Cell, Parul University, Vadodara 391760, India
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemun-gu, Seoul 02447, the Republic of Korea.
| |
Collapse
|
14
|
Liu C, Mao B, Zhang Y, Tian L, Ma B, Chen Z, Wei Z, Li A, Shao Y, Cheng G, Li L, Li W, Zhang D, Ding X, Peng J, Peng Y, He J, Ye N, Yuan D, Chu C, Duan M. The OsWRKY72-OsAAT30/OsGSTU26 module mediates reactive oxygen species scavenging to drive heterosis for salt tolerance in hybrid rice. J Integr Plant Biol 2024; 66:709-730. [PMID: 38483018 DOI: 10.1111/jipb.13640] [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] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/23/2024] [Indexed: 04/11/2024]
Abstract
Hybrid rice (Oryza sativa) generally outperforms its inbred parents in yield and stress tolerance, a phenomenon termed heterosis, but the underlying mechanism is not completely understood. Here, we combined transcriptome, proteome, physiological, and heterosis analyses to examine the salt response of super hybrid rice Chaoyou1000 (CY1000). In addition to surpassing the mean values for its two parents (mid-parent heterosis), CY1000 exhibited a higher reactive oxygen species scavenging ability than both its parents (over-parent heterosis or heterobeltiosis). Nonadditive expression and allele-specific gene expression assays showed that the glutathione S-transferase gene OsGSTU26 and the amino acid transporter gene OsAAT30 may have major roles in heterosis for salt tolerance, acting in an overdominant fashion in CY1000. Furthermore, we identified OsWRKY72 as a common transcription factor that binds and regulates OsGSTU26 and OsAAT30. The salt-sensitive phenotypes were associated with the OsWRKY72paternal genotype or the OsAAT30maternal genotype in core rice germplasm varieties. OsWRKY72paternal specifically repressed the expression of OsGSTU26 under salt stress, leading to salinity sensitivity, while OsWRKY72maternal specifically repressed OsAAT30, resulting in salinity tolerance. These results suggest that the OsWRKY72-OsAAT30/OsGSTU26 module may play an important role in heterosis for salt tolerance in an overdominant fashion in CY1000 hybrid rice, providing valuable clues to elucidate the mechanism of heterosis for salinity tolerance in hybrid rice.
Collapse
Affiliation(s)
- Citao Liu
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Bigang Mao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Yanxia Zhang
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Lei Tian
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Biao Ma
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhuo Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongwei Wei
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Aifu Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ye Shao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Gongye Cheng
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Lingling Li
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Wenyu Li
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Di Zhang
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaoping Ding
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | | | - Yulin Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Jiwai He
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Nenghui Ye
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Dingyang Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Chengcai Chu
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Meijuan Duan
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| |
Collapse
|
15
|
Bai H, He LY, Gao FZ, Yao KS, Zhang M, Qiao LK, Chen ZY, He LX, Liu YS, Zhao JL, Ying GG. Airborne antibiotic resistome and microbiome in pharmaceutical factories. Environ Int 2024; 186:108639. [PMID: 38603815 DOI: 10.1016/j.envint.2024.108639] [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: 01/26/2024] [Revised: 03/24/2024] [Accepted: 04/06/2024] [Indexed: 04/13/2024]
Abstract
Antimicrobial resistance is considered to be one of the biggest public health problems, and airborne transmission is an important but under-appreciated pathway for the spread of antibiotic resistance genes (ARGs) in the environment. Previous research has shown pharmaceutical factories to be a major source of ARGs and antibiotic resistant bacteria (ARB) in the surrounding receiving water and soil environments. Pharmaceutical factories are hotspots of antibiotic resistance, but the atmospheric transmission and its environmental risk remain more concerns. Here, we conducted a metagenomic investigation into the airborne microbiome and resistome in three pharmaceutical factories in China. Soil (average: 38.45%) and wastewater (average: 28.53%) were major contributors of airborne resistome. ARGs (vanR/vanS, blaOXA, and CfxA) conferring resistance to critically important clinically used antibiotics were identified in the air samples. The wastewater treatment area had significantly higher relative abundances of ARGs (average: 0.64 copies/16S rRNA). Approximately 28.2% of the detected airborne ARGs were found to be associated with plasmids, and this increased to about 50% in the wastewater treatment area. We have compiled a list of high-risk airborne ARGs found in pharmaceutical factories. Moreover, A total of 1,043 viral operational taxonomic units were identified and linked to 47 family-group taxa. Different CRISPR-Cas immune systems have been identified in bacterial hosts in response to phage infection. Similarly, higher phage abundance (average: 2451.70 PPM) was found in the air of the wastewater treatment area. Our data provide insights into the antibiotic resistance gene profiles and microbiome (bacterial and non-bacterial) in pharmaceutical factories and reveal the potential role of horizontal transfer in the spread of airborne ARGs, with implications for human and animal health.
Collapse
Affiliation(s)
- Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
| | - Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Kai-Sheng Yao
- Aquatic Ecology and Water Quality Management group, Wageningen University, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Min Zhang
- Pearl River Water Resources Research Institute, Pearl River Water Resources Commission of the Ministry of Water Resources, Guangzhou 510610, China
| | - Lu-Kai Qiao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Zi-Yin Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Jian-Liang Zhao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
| |
Collapse
|
16
|
Zhou X, Fang K, Liu Y, Li W, Tan Y, Zhang J, Yu X, Wang G, Zhang Y, Shang Y, Zhang L, Chen CD, Wang S. ZFP541 and KCTD19 regulate chromatin organization and transcription programs for male meiotic progression. Cell Prolif 2024; 57:e13567. [PMID: 37921559 PMCID: PMC10984108 DOI: 10.1111/cpr.13567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
The successful progression of meiosis prophase I requires integrating information from the structural and molecular levels. In this study, we show that ZFP541 and KCTD19 work in the same genetic pathway to regulate the progression of male meiosis and thus fertility. The Zfp541 and/or Kctd19 knockout male mice show various structural and recombination defects including detached chromosome ends, aberrant localization of chromosome axis components and recombination proteins, and globally altered histone modifications. Further analyses on RNA-seq, ChIP-seq, and ATAC-seq data provide molecular evidence for the above defects and reveal that ZFP541/KCTD19 activates the expression of many genes by repressing several major transcription repressors. More importantly, we reveal an unexpected role of ZFP541/KCTD19 in directly modulating chromatin organization. These results suggest that ZFP541/KCTD19 simultaneously regulates the transcription cascade and chromatin organization to ensure the coordinated progression of multiple events at chromosome structural and biochemical levels during meiosis prophase I.
Collapse
Affiliation(s)
- Xu Zhou
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
| | - Kailun Fang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell Biology, Chinese Academy of SciencesShanghaiChina
| | - Yanlei Liu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive MedicineShandong UniversityJinanShandongChina
| | - Weidong Li
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
| | - Yingjin Tan
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
| | - Jiaming Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive MedicineShandong UniversityJinanShandongChina
| | - Xiaoxia Yu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive MedicineShandong UniversityJinanShandongChina
| | - Guoqiang Wang
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
| | - Yanan Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive MedicineShandong UniversityJinanShandongChina
| | - Yongliang Shang
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
| | - Liangran Zhang
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life SciencesShandong Normal UniversityJinanShandongChina
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell Biology, Chinese Academy of SciencesShanghaiChina
| | - Shunxin Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive MedicineShandong UniversityJinanShandongChina
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive GeneticsShandong UniversityJinanShandongChina
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive HealthShandong Technology Innovation Center for Reproductive HealthJinanShandongChina
| |
Collapse
|
17
|
Chen L, Chen K, Xi X, Du X, Zou X, Ma Y, Song Y, Luo C, Weining S. The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome. Int J Mol Sci 2024; 25:3883. [PMID: 38612691 PMCID: PMC11011394 DOI: 10.3390/ijms25073883] [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: 02/22/2024] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Plant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, comprising 12 reference genomes, including cultivated barley, landraces, and wild barley. Their chromosomal locations, physical-chemical characteristics, gene structures, conserved domains, and subcellular localizations were systematically analyzed to reveal the certain differences between wild and cultivated populations. Through a cis-acting element analysis, co-expression network, and large-scale transcriptome analysis, their involvement in growth, development, and responses to various stressors was highlighted. It is worth noting that HvMOREXann5 is only expressed in pistils and anthers, indicating its crucial role in reproductive development. Based on the resequencing data from 282 barley accessions worldwide, genetic variations in thefamily were investigated, and the results showed that 5 out of the 12 identified HvMOREXanns were affected by selection pressure. Genetic diversity and haplotype frequency showed notable reductions between wild and domesticated barley, suggesting that a genetic bottleneck occurred on the annexin family during the barley domestication process. Finally, qRT-PCR analysis confirmed the up-regulation of HvMOREXann7 under drought stress, along with significant differences between wild accessions and varieties. This study provides some insights into the genome organization and genetic characteristics of the annexin gene family in barley at the pan-genome level, which will contribute to better understanding its evolution and function in barley and other crops.
Collapse
Affiliation(s)
- Liqin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
| | - Kunxiang Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
| | - Xi Xi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
| | - Xianghong Du
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.D.); (X.Z.)
| | - Xinyi Zou
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.D.); (X.Z.)
| | - Yujia Ma
- College of Landscape Architecture and Art, Northwest A&F University, Xianyang 712100, China;
| | - Yingying Song
- College of Plant Protection, Northwest A&F University, Xianyang 712100, China;
| | - Changquan Luo
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China;
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
| |
Collapse
|
18
|
Lim TW, Huang S, Zhang Y, Burrow MF, McGrath C. A comparison of the prevalence of respiratory pathogens and opportunistic respiratory pathogenic profile of 'clean' and 'unclean' removable dental prostheses. J Dent 2024; 145:104968. [PMID: 38561038 DOI: 10.1016/j.jdent.2024.104968] [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] [Received: 10/06/2023] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVES To determine and compare the opportunistic respiratory pathogenic index (ORPI) and prevalence of respiratory pathogens between clean and unclean removable prostheses. METHODS A cross-sectional study was conducted among 97 removable prosthesis wearers at a teaching dental hospital. Participants' prosthesis hygiene was grouped into clean and unclean. After prosthesis plaque samples were sequenced using the Type IIB Restriction-site Associated DNA Sequencing for Microbiome method, the prevalence was assessed for the presence of respiratory pathogens on each sample. The ORPIs for clean and unclean prostheses were quantified based on the sum of the relative abundance of respiratory pathogenic bacteria in a microbiome using a reference database that contains opportunistic respiratory pathogens and disease-associated information. RESULTS A total of 30 opportunistic respiratory pathogens were identified on the removable prostheses. Eighty-one (83.5 %) removable prostheses harboured respiratory pathogenic bacteria. Stenotrophomonas maltophilia (34.0 %), Pseudomonas aeruginosa (27.8 %), and Streptococcus agalactiae (27.8 %) were the top three prevalent respiratory pathogens detected in plaque samples. There was a significantly higher prevalence of respiratory pathogens residing on unclean than clean prostheses (P = 0.046). However, the ORPIs in both groups showed no statistically significant difference (P = 0.516). CONCLUSIONS The ORPIs for both clean and unclean prostheses demonstrated a similar abundance of respiratory pathogens. However, the high prevalence of respiratory pathogens residing on unclean prostheses should not be underestimated. Therefore, maintaining good prosthesis hygiene is still important for overall oral and systemic health, even though the direct link between prosthesis cleanliness and reduced abundance of respiratory pathogens has not been established. CLINICAL SIGNIFICANCE The association between the prevalence of respiratory pathogens and unclean removable prostheses has been demonstrated and might increase the theoretical risk of respiratory disease development.
Collapse
Affiliation(s)
- Tong Wah Lim
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR
| | - Shi Huang
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR
| | - Yufeng Zhang
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR
| | - Michael Francis Burrow
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR
| | - Colman McGrath
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR.
| |
Collapse
|
19
|
Zheng YY, Chen LH, Fan BL, Xu Z, Wang Q, Zhao BY, Gao M, Yuan MH, Tahir Ul Qamar M, Jiang Y, Yang L, Wang L, Li W, Cai W, Ma C, Lu L, Song JM, Chen LL. Integrative multiomics profiling of passion fruit reveals the genetic basis for fruit color and aroma. Plant Physiol 2024; 194:2491-2510. [PMID: 38039148 DOI: 10.1093/plphys/kiad640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 12/03/2023]
Abstract
Passion fruit (Passiflora edulis) possesses a complex aroma and is widely grown in tropical and subtropical areas. Here, we conducted the de novo assembly, annotation, and comparison of PPF (P. edulis Sims) and YPF (P. edulis f. flavicarpa) reference genomes using PacBio, Illumina, and Hi-C technologies. Notably, we discovered evidence of recent whole-genome duplication events in P. edulis genomes. Comparative analysis revealed 7.6∼8.1 million single nucleotide polymorphisms, 1 million insertions/deletions, and over 142 Mb presence/absence variations among different P. edulis genomes. During the ripening of yellow passion fruit, metabolites related to flavor, aroma, and color were substantially accumulated or changed. Through joint analysis of genomic variations, differentially expressed genes, and accumulated metabolites, we explored candidate genes associated with flavor, aroma, and color distinctions. Flavonoid biosynthesis pathways, anthocyanin biosynthesis pathways, and related metabolites are pivotal factors affecting the coloration of passion fruit, and terpenoid metabolites accumulated more in PPF. Finally, by heterologous expression in yeast (Saccharomyces cerevisiae), we functionally characterized 12 terpene synthases. Our findings revealed that certain TPS homologs in both YPF and PPF varieties produce identical terpene products, while others yield distinct compounds or even lose their functionality. These discoveries revealed the genetic and metabolic basis of unique characteristics in aroma and flavor between the 2 passion fruit varieties. This study provides resources for better understanding the genome architecture and accelerating genetic improvement of passion fruits.
Collapse
Affiliation(s)
- Yu-Yu Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin-Hua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Bing-Liang Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhenni Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Qiuxia Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Bo-Yuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Min Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Min-Hui Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Muhammad Tahir Ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuanyuan Jiang
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Liu Yang
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Wenguo Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Chongjian Ma
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Li Lu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Hongshan Laboratory, Wuhan 430071, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| |
Collapse
|
20
|
Hua X, Zhao T, Gui X, Jin B. A NiFe PBA/AuNPs nanocomposite sensitive immunosensor for electrochemical detection of PSA. Anal Methods 2024; 16:1923-1933. [PMID: 38497295 DOI: 10.1039/d3ay02184j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
In this paper, a label-free electrochemical immunosensor for sensitive detection of prostate antigen (PSA) was developed based on a NiFe PBA/AuNPs composite. The prostate antigen antibody was immobilized and the immunosensor was constructed by using a glassy carbon electrode modified with a nanocomposite consisting of nickel-iron Prussian blue analog (NiFe PBA) and gold nanoparticles (AuNPs). Due to the good biological affinity of AuNPs for biomolecules, as well as the porous nanostructure and regular shape of NiFe PBA, NiFe PBA/AuNPs nanocomposites significantly improve the electron transport rate, while achieving excellent performance for the sensor. Due to the interaction between the antibody and the antigen on the modified electrode, the current signal of the NiFe PBA itself is reduced due to the redox changes in Fe2+ and Fe3+, which can be determined by differential pulse voltammetry (DPV). Therefore, the monitoring of prostate antigen detection is realized. Under optimal experimental conditions, the immunosensor exhibited excellent detection performance with a dynamic response range from 0.5 pg mL-1 to 1000 pg mL-1 for the PSA concentration and a detection limit of 0.23 pg mL-1 (S/N = 3). In addition, the PSA aptasensor has good selectivity, high stability, and satisfactory reproducibility and has broad potential in clinical research and diagnostic applications.
Collapse
Affiliation(s)
- Xin Hua
- Department of Chemistry, Anhui University, Hefei 230601, China.
| | - Tongxiao Zhao
- Department of Chemistry, Anhui University, Hefei 230601, China.
| | - Xueqin Gui
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Baokang Jin
- Department of Chemistry, Anhui University, Hefei 230601, China.
| |
Collapse
|
21
|
Ma G, Zhang Y, Li X. Overexpression of OsDUF6 increases salt stress tolerance in rice. BMC Plant Biol 2024; 24:216. [PMID: 38532340 DOI: 10.1186/s12870-024-04921-z] [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] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Soil salinity is one of the primary environmental stresses faced in rice production. When plants are exposed to salt stress, a series of cellular balances will be disrupted. Dufulin is an immune-induced antiviral agent used in plants. The DUF gene family influences plant response to abiotic stress, and the functional role of OsDUF6(ABA98726.1) in rice response to salt stress is being investigated here. RESULTS Based on the transcriptome analysis of Dufulin treatment in inducing salt tolerance in rice, we selected the OsDUF6 protein located on the cell membrane and studied its molecular function by overexpressing OsDUF6. Salt-induced decreases in root, stem, and leaf length and increased leaf yellowing rate and Na+ concentration in the wild-type plant were mitigated in the overexpressed lines. OsDUF6 overexpression increased the enzymatic antioxidant activities of superoxide dismutase, peroxidase, catalase, and phenylalanine ammonia-lyase. OsDUF6 also played a positive role in Na+ transport as reflected by the increased growth of a salt-sensitive yeast mutant complemented with OsDUF6 in the presence of salt stress. In addition, Reverse transcription quantitative PCR analysis confirmed that the overexpression of OsDUF6 significantly changed the expression level of other genes related to growth and stress tolerance. CONCLUSIONS Combined with previously published data, our results supported the observation that OsDUF6 is an important functional factor in Dufulin-induced promotion of salt stress tolerance in rice.
Collapse
Affiliation(s)
- Guangming Ma
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticides and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Yong Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticides and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Xiangyang Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticides and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China.
| |
Collapse
|
22
|
Wang N, Que H, Luo Q, Zheng W, Li H, Wang Q, Gu J. Mechanisms of ferroptosis in nonalcoholic fatty liver disease and therapeutic effects of traditional Chinese medicine: a review. Front Med (Lausanne) 2024; 11:1356225. [PMID: 38590315 PMCID: PMC10999571 DOI: 10.3389/fmed.2024.1356225] [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: 12/15/2023] [Accepted: 02/22/2024] [Indexed: 04/10/2024] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is characterized by excessive accumulation of fat in hepatocytes (nonalcoholic fatty liver (NAFL)), and lobular inflammation and hepatocyte damage (which characterize nonalcoholic steatohepatitis (NASH) are found in most patients). A subset of patients will gradually develop liver fibrosis, cirrhosis, and eventually hepatocellular carcinoma, which is a deadly disease that threatens human life worldwide. Ferroptosis, a novel nonapoptotic form of programmed cell death (PCD) characterized by iron-dependent accumulation of reactive oxygen radicals and lipid peroxides, is closely related to NAFLD. Traditional Chinese medicine (TCM) has unique advantages in the prevention and treatment of NAFLD due to its multicomponent, multipathway and multitarget characteristics. In this review, we discuss the effect of TCM on NAFLD by regulating ferroptosis, in order to provide reference for the further development and application of therapeutic drugs to treat NAFLD.
Collapse
Affiliation(s)
- Nan Wang
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Hanyun Que
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Qiulin Luo
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Wenxin Zheng
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Hong Li
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Qin Wang
- College of Pharmacy, Southwest Minzu University, Chengdu, China
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Jian Gu
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| |
Collapse
|
23
|
Liu L, Zhan J, Yan J. Engineering the future cereal crops with big biological data: toward an intelligence-driven breeding by design. J Genet Genomics 2024:S1673-8527(24)00058-4. [PMID: 38531485 DOI: 10.1016/j.jgg.2024.03.005] [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] [Received: 10/30/2023] [Revised: 03/17/2024] [Accepted: 03/17/2024] [Indexed: 03/28/2024]
Abstract
How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades, especially under an unpredicted climate change. Crop breeding, initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding, has played a critical role in securing the global food supply. However, regarding the changing environment and ever-increasing human population, can we breed outstanding crop varieties fast enough to achieve high productivity, good quality, and widespread adaptability? This review outlines the recent achievements in understanding cereal crop breeding, including the current knowledge about crop agronomic traits, newly developed techniques, crop big biological data research, and the possibility of integrating them for intelligence-driven breeding by design, which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops. This review focuses on the major cereal crops, including rice, maize, and wheat, to explain how intelligence-driven breeding by design is becoming a reality.
Collapse
Affiliation(s)
- Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Jimin Zhan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| |
Collapse
|
24
|
Liu MM, Fan CQ, Zhang GL. A Single-Cell Landscape of Spermioteleosis in Mice and Pigs. Cells 2024; 13:563. [PMID: 38607002 PMCID: PMC11011153 DOI: 10.3390/cells13070563] [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: 12/01/2023] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
(1) Background: Spermatozoa acquired motility and matured in epididymis after production in the testis. However, there is still limited understanding of the specific characteristics of sperm development across different species. In this study, we employed a comprehensive approach to analyze cell compositions in both testicular and epididymal tissues, providing valuable insights into the changes occurring during meiosis and spermiogenesis in mouse and pig models. Additionally, we identified distinct gene expression signatures associated with various spermatogenic cell types. (2) Methods: To investigate the differences in spermatogenesis between mice and pigs, we constructed a single-cell RNA dataset. (3) Results: Our findings revealed notable differences in testicular cell clusters between these two species. Furthermore, distinct gene expression patterns were observed among epithelial cells from different regions of the epididymis. Interestingly, regional gene expression patterns were also identified within principal cell clusters of the mouse epididymis. Moreover, through analysing differentially expressed genes related to the epididymis in both mouse and pig models, we successfully identified potential marker genes associated with sperm development and maturation for each species studied. (4) Conclusions: This research presented a comprehensive single-cell landscape analysis of both testicular and epididymal tissues, shedding light on the intricate processes involved in spermatogenesis and sperm maturation, specifically within mouse and pig models.
Collapse
Affiliation(s)
| | | | - Guo-Liang Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China; (M.-M.L.); (C.-Q.F.)
| |
Collapse
|
25
|
Yu H, Li Y, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S. Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach. Nat Protoc 2024:10.1038/s41596-024-00966-4. [PMID: 38514839 DOI: 10.1038/s41596-024-00966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/20/2023] [Indexed: 03/23/2024]
Abstract
The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.
Collapse
Affiliation(s)
- Hongwei Yu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Wentao Han
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Fuyun Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuanting Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
- Laboratory for Marine Fisheries and Aquaculture, Laoshan Laboratory, Qingdao, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
| |
Collapse
|
26
|
Olbrich M, Bartels L, Wohlers I. Sequencing technologies and hardware-accelerated parallel computing transform computational genomics research. Front Bioinform 2024; 4:1384497. [PMID: 38567256 PMCID: PMC10985184 DOI: 10.3389/fbinf.2024.1384497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Affiliation(s)
- Michael Olbrich
- Center for Biotechnology, Khalifa University for Science and Technology, Abu Dhabi, United Arab Emirates
| | - Lennart Bartels
- Biomolecular Data Science in Pneumology, Research Center Borstel, Borstel, Germany
| | - Inken Wohlers
- Biomolecular Data Science in Pneumology, Research Center Borstel, Borstel, Germany
- University of Lübeck, Lübeck, Germany
| |
Collapse
|
27
|
Chen R, Ye Y, Ding Y, Wan Z, Ye X, Liu J. Potential biomarkers of acute myocardial infarction based on the composition of the blood microbiome. Clin Chim Acta 2024; 556:117843. [PMID: 38387830 DOI: 10.1016/j.cca.2024.117843] [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: 01/29/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND It is difficult to distinguish between acute myocardial infarction (AMI) and unstable angina (UA) due to their similar clinical features. In recent years, studies have shown that microbiomes have great potential in distinguishing diseases. The purpose of this study is to describe the composition of serum microbiome in the AMI and UA by 16S rDNA sequencing. METHODS Based on the high-throughput detection platform and 16S rDNA amplification sequencing technology, this study detected the blood microbial composition of 55 patients with AMI and 62 patients with UA. Alpha diversity and Beta diversity analysis were used to compare the differences in microbial composition and bacterial colony structure between AMI and UA groups. We perform PCoA (Principal Co-ordinates Analysis) based on Unweighted Unifrac distance. In addition, various statistical methods were employed to examine the significance of differences in microbial composition and genus between the two groups. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was employed to predict KEGG (Kyoto Encyclopedia of Genes and Genomes) function from 16S sequencing data. Random forest was applied to identify biomarkers and construct the diagnostic model. Subsequently, the stability of the model was verified by 10-fold cross and the diagnostic effectiveness was evaluated through ROC (Receiver Operating Characteristic). RESULTS In this study, we found that alpha diversity index of serum microbiome in AMI group was significantly higher than in UA group. T-test analysis demonstrated that the UA group presented a higher abundance of Ralstonia, Faecalibaculum and Gammaproteobacteria, while Bacteroides, Sphingomonas, Faecalibaculum, Haemophilus, Serratia, Bifidobacterium and Chloroplast were more abundant in the AMI group. The LefSe (LDA Effect Size) analysis showed that the Gammaproteobacteria, Proteobacteria, Ralstonia pickettli, Ralstonia, Burkholderiaceae and Burkholderiales were enriched in UA group, and Bacteroidales, Bacteroidia, Bacteroidota, Clostridia and Firmicutes were more abundant in the AMI group. Ten bacterial diagnostic models were constructed in the random forest. The area under the curve (AUC) in the training set was 88.01%, and the AUC value in the test set was 95.04%. CONCLUSION In this study, the composition of blood microorganisms in the groups of patients with AMI and UA has been analyzed, providing novel insights for understanding the pathogenesis of AMI; Blood microbiome may serve as novel diagnostic biomarkers of AMI.
Collapse
Affiliation(s)
- Rishou Chen
- Department of Laboratory Medicine, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan 523127, China
| | - Yonglong Ye
- Department of Laboratory Medicine, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan 523127, China
| | - Yali Ding
- Department of Laboratory Medicine, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan 523127, China
| | - Zhidong Wan
- Department of Laboratory Medicine, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan 523127, China
| | - Xinyu Ye
- Department of Laboratory Medicine, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan 523127, China
| | - Jun Liu
- Department of Laboratory Medicine, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan 523127, China.
| |
Collapse
|
28
|
Zong X, Lou Y, Xia M, Zhao K, Chen J, Huang J, Yang S, Wang L. Recombination and repeat-induced point mutation landscapes reveal trade-offs between the sexual and asexual cycles of Magnaporthe oryzae. J Genet Genomics 2024:S1673-8527(24)00056-0. [PMID: 38490361 DOI: 10.1016/j.jgg.2024.03.003] [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] [Received: 01/30/2024] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
The fungal disease caused by Magnaporthe oryzae is one of the most devastating diseases that endanger many crops worldwide. Evidence shows that sexual reproduction can be advantageous for fungal diseases as hybridization facilitates host-jumping. However, the pervasive clonal lineages of M. oryzae observed in natural fields contradict this expectation. A better understanding of the roles of recombination and the fungi-specific repeat-induced point mutation (RIP) in shaping its evolutionary trajectory is essential to bridge this knowledge gap. Here we systematically investigate the RIP and recombination landscapes in M. oryzae using a whole genome sequencing data from 252 population samples and 92 cross progenies. Our data reveal that the RIP can robustly capture the population history of M. oryzae, and we provide accurate estimations of the recombination and RIP rates across different M. oryzae clades. Significantly, our results highlight a parent-of-origin bias in both recombination and RIP rates, tightly associating with their sexual potential and variations of effector proteins. This bias suggests a critical trade-off between generating novel allelic combinations in the sexual cycle to facilitate host-jumping and stimulating transposon-associated diversification of effectors in the asexual cycle to facilitate host coevolution. These findings provide unique insights into understanding the evolution of blast fungus.
Collapse
Affiliation(s)
- Xifang Zong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Yaxin Lou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Mengshuang Xia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Kunyang Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Jingxuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Ju Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210000, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210000, China.
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China.
| |
Collapse
|
29
|
Liu B, Yi D, Xia X, Ramirez K, Zhao H, Cao Y, Tripathi A, Dong R, Gao A, Ding H, Qiu S, Kalinichenko VV, Fallon MB, Dai Z. General Capillary Endothelial Cells Undergo Reprogramming into Arterial Endothelial Cells in Pulmonary Hypertension through HIF-2α/Notch4 Pathway. bioRxiv 2024:2024.02.13.580227. [PMID: 38464011 PMCID: PMC10925079 DOI: 10.1101/2024.02.13.580227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Pulmonary arterial hypertension (PAH) is characterized by a progressive increase of pulmonary vascular resistance and obliterative pulmonary vascular remodeling that result in right heart hypertrophy, failure, and premature death. The underlying mechanisms of loss of distal capillary endothelial cells (ECs) and obliterative vascular lesion formation remain unclear. Our recent single-cell RNA sequencing, spatial transcriptomics analysis, RNASCOPE, and immunostaining analysis showed that arterial ECs accumulation and loss of capillary ECs were evident in human PAH patients and pulmonary hypertension (PH) rodents. Pseudotime trajectory analysis of the single-cell RNA sequencing data suggest that lung capillary ECs transit to arterial ECs during the development of PH. Our study also identified CXCL12 as the marker for arterial ECs in PH. Capillary EC lineage tracing approach using capillary specific-Dre;Tdtomato reporter mice demonstrated that capillary ECs gave rise to arterial ECs during PH development. Genetic deletion of HIF-2a or pharmacological inhibition of Notch4 normalized the arterial programming in PH. In conclusion, our study demonstrates that capillary endothelium transits to arterial endothelium through the HIF-2a-Notch4 pathway during the development of PAH. Thus, targeting arterial EC transition might be a novel approach for treating PAH patients.
Collapse
Affiliation(s)
- Bin Liu
- Division of Pulmonary, Critical Care and Sleep, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Dan Yi
- Division of Pulmonary, Critical Care and Sleep, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Xiaomei Xia
- Division of Pulmonary, Critical Care and Sleep, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Karina Ramirez
- Division of Pulmonary, Critical Care and Sleep, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Hanqiu Zhao
- Division of Pulmonary, Critical Care and Sleep, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Yanhong Cao
- Division of Pulmonary, Critical Care and Sleep, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Ankit Tripathi
- Division of Pulmonary, Critical Care and Sleep, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Ryan Dong
- Division of Pulmonary, Critical Care and Sleep, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Anton Gao
- Division of Pulmonary, Critical Care and Sleep, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Hongxu Ding
- Department of Pharmacy Practice & Science, College of Pharmacy, University of Arizona, Tucson, Arizona, USA
| | - Shenfeng Qiu
- Department of Basic Medical Science, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Vladimir V. Kalinichenko
- Division of Neonatology, Phoenix Children’s Hospital, Phoenix, Arizona, USA
- Phoenix Children’s Health Research Institute, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Michael B. Fallon
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Zhiyu Dai
- Division of Pulmonary, Critical Care and Sleep, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Sarver Heart Center, University of Arizona, Tucson, Arizona, USA
| |
Collapse
|
30
|
Yuan H, Cheng M, Wang R, Wang Z, Fan F, Wang W, Si F, Gao F, Li S. miR396b/GRF6 module contributes to salt tolerance in rice. Plant Biotechnol J 2024. [PMID: 38454780 DOI: 10.1111/pbi.14326] [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] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Salinity, as one of the most challenging environmental factors restraining crop growth and yield, poses a severe threat to global food security. To address the rising food demand, it is urgent to develop crop varieties with enhanced yield and greater salt tolerance by delving into genes associated with salt tolerance and high-yield traits. MiR396b/GRF6 module has previously been demonstrated to increase rice yield by shaping the inflorescence architecture. In this study, we revealed that miR396b/GRF6 module can significantly improve salt tolerance of rice. In comparison with the wild type, the survival rate of MIM396 and OE-GRF6 transgenic lines increased by 48.0% and 74.4%, respectively. Concurrent with the increased salt tolerance, the transgenic plants exhibited reduced H2 O2 accumulation and elevated activities of ROS-scavenging enzymes (CAT, SOD and POD). Furthermore, we identified ZNF9, a negative regulator of rice salt tolerance, as directly binding to the promoter of miR396b to modulate the expression of miR396b/GRF6. Combined transcriptome and ChIP-seq analysis showed that MYB3R serves as the downstream target of miR396b/GRF6 in response to salt tolerance, and overexpression of MYB3R significantly enhanced salt tolerance. In conclusion, this study elucidated the potential mechanism underlying the response of the miR396b/GRF6 network to salt stress in rice. These findings offer a valuable genetic resource for the molecular breeding of high-yield rice varieties endowed with stronger salt tolerance.
Collapse
Affiliation(s)
- Huanran Yuan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Mingxing Cheng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhikai Wang
- College of Life Science, Yangtze University, Jingzhou, China
| | - Fengfeng Fan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Wei Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fengfeng Si
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
| | - Feng Gao
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| |
Collapse
|
31
|
Wang C, Wang Z, Cai Y, Zhu Z, Yu D, Hong L, Wang Y, Lv W, Zhao Q, Si L, Liu K, Han B. A higher-yield hybrid rice is achieved by assimilating a dominant heterotic gene in inbred parental lines. Plant Biotechnol J 2024. [PMID: 38450899 DOI: 10.1111/pbi.14295] [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] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 03/08/2024]
Abstract
The exploitation of heterosis to integrate parental advantages is one of the fastest and most efficient ways of rice breeding. The genomic architecture of heterosis suggests that the grain yield is strongly correlated with the accumulation of numerous rare superior alleles with positive dominance. However, the improvements in yield of hybrid rice have shown a slowdown or even plateaued due to the limited availability of complementary superior alleles. In this study, we achieved a considerable increase in grain yield of restorer lines by inducing an alternative splicing event in a heterosis gene OsMADS1 through CRISPR-Cas9, which accounted for approximately 34.1%-47.5% of yield advantage over their corresponding inbred rice cultivars. To achieve a higher yield in hybrid rice, we crossed the gene-edited restorer parents harbouring OsMADS1GW3p6 with the sterile lines to develop new rice hybrids. In two-line hybrid rice Guang-liang-you 676 (GLY676), the yield of modified hybrids carrying the homozygous heterosis gene OsMADS1GW3p6 significantly exceeded that of the original hybrids with heterozygous OsMADS1. Similarly, the gene-modified F1 hybrids with heterozygous OsMADS1GW3p6 increased grain yield by over 3.4% compared to the three-line hybrid rice Quan-you-si-miao (QYSM) with the homozygous genotype of OsMADS1. Our study highlighted the great potential in increasing the grain yield of hybrid rice by pyramiding a single heterosis gene via CRISPR-Cas9. Furthermore, these results demonstrated that the incomplete dominance of heterosis genes played a major role in yield-related heterosis and provided a promising strategy for breeding higher-yielding rice varieties above what is currently achievable.
Collapse
Affiliation(s)
- Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ziqun Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yunxiao Cai
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhou Zhu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Danheng Yu
- Department of Life Sciences, Imperial College London, South Kensington, London, UK
| | - Lei Hong
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yongchun Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wei Lv
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Lizhen Si
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Kun Liu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
32
|
Shu P, Li Y, Sheng J, Shen L. Recent Advances in Dissecting the Function of Ethylene in Interaction between Host and Pathogen. J Agric Food Chem 2024; 72:4552-4563. [PMID: 38379128 DOI: 10.1021/acs.jafc.3c07978] [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: 02/22/2024]
Abstract
Pathogens influence the growth and development of plants, resulting in detrimental damage to their yields and quality. Ethylene, a gaseous phytohormone, serves a pivotal function in modulating diverse physiological processes in plants, including defense mechanisms against pathogen invasion. Ethylene biosynthesis is involved in both plants and pathogens. Recent empirical research elucidates the intricate interactions and regulatory mechanisms between ethylene and pathogens across various plant species. In this review, we provide a comprehensive overview of the latest findings concerning ethylene's role and its regulatory networks in host-pathogen interactions. Additionally, we explore the crosstalk between ethylene and other phytohormones. Points regarding ethylene emission and its modulation by pathogens are also emphasized. Moreover, we also discuss potential unresolved issues in the field that warrant further investigation.
Collapse
Affiliation(s)
- Pan Shu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
| | - Yujing Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
| | - Jiping Sheng
- School of Agricultural Economics and Rural Development, Renmin University of China, Beijing 100872, P. R. China
| | - Lin Shen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
| |
Collapse
|
33
|
Sun Y, Zhou Y, Long Q, Xing J, Guo P, Liu Y, Zhang C, Zhang Y, Fernie AR, Shi Y, Luo Y, Luo J, Jin C. OsBCAT2, a gene responsible for the degradation of branched-chain amino acids, positively regulates salt tolerance by promoting the synthesis of vitamin B5. New Phytol 2024; 241:2558-2574. [PMID: 38258425 DOI: 10.1111/nph.19551] [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] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
Salt stress negatively affects rice growth, development and yield. Metabolic adjustments contribute to the adaptation of rice under salt stress. Branched-chain amino acids (BCAA) are three essential amino acids that cannot be synthesized by humans or animals. However, little is known about the role of BCAA in response to salt stress in plants. Here, we showed that BCAAs may function as scavengers of reactive oxygen species (ROS) to provide protection against damage caused by salinity. We determined that branched-chain aminotransferase 2 (OsBCAT2), a protein responsible for the degradation of BCAA, positively regulates salt tolerance. Salt significantly induces the expression of OsBCAT2 rather than BCAA synthesis genes, which indicated that salt mainly promotes BCAA degradation and not de novo synthesis. Metabolomics analysis revealed that vitamin B5 (VB5) biosynthesis pathway intermediates were higher in the OsBCAT2-overexpressing plants but lower in osbcat2 mutants under salt stress. The salt stress-sensitive phenotypes of the osbcat2 mutants are rescued by exogenous VB5, indicating that OsBCAT2 affects rice salt tolerance by regulating VB5 synthesis. Our work provides new insights into the enzymes involved in BCAAs degradation and VB5 biosynthesis and sheds light on the molecular mechanism of BCAAs in response to salt stress.
Collapse
Affiliation(s)
- Yangyang Sun
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
- Sanya Research Institute of Hainan Academy of Agricultural Sciences, Sanya, 572025, China
| | - Yutong Zhou
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Qiyuan Long
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Junwei Xing
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Peizhen Guo
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Yanchen Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Changjian Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Yuanyuan Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Yuheng Shi
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Yuehua Luo
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Jie Luo
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Cheng Jin
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| |
Collapse
|
34
|
Xu H, Yang N, Wang BY, Zhou L, Xu LL, Chen Y, Wang DJ, Ge WH. Phenylacetyl glutamine (PAGln) enhances cardiomyocyte death after myocardial infarction through β1 adrenergic receptor. Environ Toxicol 2024; 39:1682-1699. [PMID: 38041472 DOI: 10.1002/tox.24063] [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: 11/03/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
This study aims to explore the roles of phenylacetyl glutamine (PAGln) on myocardial infarction (MI) pathogenesis. Here, using targeted metabolomics analysis, it was found that the plasma metabolite PAGln was upregulated in coronary artery disease (CAD) patients and MI mice and could be an independent risk factor for CAD. In vivo and in vitro functional experiments revealed that PAGln pretreatment enhanced MI-induced myocardial injury and cardiac fibrosis, as evident by the increased infarct size, cardiomyocyte death, and the upregulated expression of cardiac fibrosis markers (Col1a1 and α-SMA). Combined with RNA-sequencing analysis and G protein-coupled receptor (GPCR) inhibitor, we found that the GPCR signaling activation is essential for PAGln-mediated effects on cardiomyocyte death. Furthermore, drug affinity responsive target stability and cellular thermal shift assay demonstrated that PAGln could interact with β1-adrenergic receptor (AR). Moreover, β1-AR blocker treatment indeed extended the cardiac remodeling after PAGln-enhanced MI. These results suggest that PAGln might be a potential therapeutic target for extending the cardiac remodeling window in MI patients that signals via β1-AR.
Collapse
Affiliation(s)
- Hang Xu
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China
- Department of Pharmacy, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Na Yang
- Department of Pharmacy, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Bao-Yan Wang
- Department of Pharmacy, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Lin Zhou
- Department of Pharmacy, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Li-Li Xu
- Department of Pharmacy, China Pharmaceutical University Nanjing Drum Tower Hospital, Nanjing, China
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yan Chen
- Department of Pharmacy, China Pharmaceutical University Nanjing Drum Tower Hospital, Nanjing, China
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Dong-Jin Wang
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Wei-Hong Ge
- Department of Pharmacy, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| |
Collapse
|
35
|
Zhang J, Chen X, Song Y, Gong Z. Integrative regulatory mechanisms of stomatal movements under changing climate. J Integr Plant Biol 2024; 66:368-393. [PMID: 38319001 DOI: 10.1111/jipb.13611] [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] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024]
Abstract
Global climate change-caused drought stress, high temperatures and other extreme weather profoundly impact plant growth and development, restricting sustainable crop production. To cope with various environmental stimuli, plants can optimize the opening and closing of stomata to balance CO2 uptake for photosynthesis and water loss from leaves. Guard cells perceive and integrate various signals to adjust stomatal pores through turgor pressure regulation. Molecular mechanisms and signaling networks underlying the stomatal movements in response to environmental stresses have been extensively studied and elucidated. This review focuses on the molecular mechanisms of stomatal movements mediated by abscisic acid, light, CO2 , reactive oxygen species, pathogens, temperature, and other phytohormones. We discussed the significance of elucidating the integrative mechanisms that regulate stomatal movements in helping design smart crops with enhanced water use efficiency and resilience in a climate-changing world.
Collapse
Affiliation(s)
- Jingbo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Xuexue Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yajing Song
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Institute of Life Science and Green Development, School of Life Sciences, Hebei University, Baoding, 071001, China
| |
Collapse
|
36
|
Li J, Xu Y, Zhang J, Zhang Z, Guo H, Wei D, Wu C, Hai T, Sun HX, Zhao Y. Single-cell transcriptomic analysis reveals transcriptional and cell subpopulation differences between human and pig immune cells. Genes Genomics 2024; 46:303-322. [PMID: 37979077 DOI: 10.1007/s13258-023-01456-9] [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: 08/16/2023] [Accepted: 09/26/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND The pig is a promising donor candidate for xenotransplantation. Understanding the differences between human and swine immune systems is critical for addressing xenotransplant rejection and hematopoietic reconstitution. The gene transcriptional profile differences between human and pig immune cell subpopulations have not been studied. To assess the similarities and differences between pigs and humans at the levels of gene transcriptional profiles or cell subpopulations are important for better understanding the cross-species similarity of humans and pigs, and it would help establish the fundamental principles necessary to genetically engineer donor pigs and improve xenotransplantation. OBJECTIVE To assess the gene transcriptional similarities and differences between pigs and humans. METHODS Two pigs and two healthy humans' PBMCs were sorted for 10 × genomics single-cell sequence. We generated integrated human-pig scRNA-seq data from human and pig PBMCs and defined the overall gene expression landscape of pig peripheral blood immune cell subpopulations by updating the set of human-porcine homologous genes. The subsets of immune cells were detected by flow cytometry. RESULTS There were significantly less T cells, NK cells and monocytes but more B cells in pig peripheral blood than those in human peripheral blood. High oxidative phosphorylation, HIF-1, glycolysis, and lysosome-related gene expressions in pig CD14+ monocytes were observed, whereas pig CD14+ monocytes exhibited lower levels of cytokine receptors and JAK-STAT-related genes. Pig activated CD4+T cells decreased cell adhesion and inflammation, while enriched for migration and activation processes. Porcine GNLY+CD8+T cells reduced cytotoxicity and increased proliferation compared with human GNLY+CD8+T cells. Pig CD2+CD8+γδT cells were functionally homologous to human CD2+CD4+ γδT cells. Pig CD2-CD8-γδT cells expressed genes with quiescent and precursor characteristics, while CD2-CD8+γδT cells expressed migration and memory-related molecules. Pig CD24+ and CD5+B cells are associated with inflammatory responses. CONCLUSION Our research with integrated scRNA-seq assays identified the different distribution of pig immune cell subpopulations and the different transcriptional profiles of human and pig immune cells. This study enables a deeper understanding of the development and function of porcine immune cells.
Collapse
Affiliation(s)
- Jie Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
- BGI-Beijing, Beijing, 102601, China
| | - Yanan Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Jiayu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Immunology, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Zhaoqi Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Han Guo
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changhong Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Tang Hai
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hai-Xi Sun
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- BGI-Beijing, Beijing, 102601, China.
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
| |
Collapse
|
37
|
Lim TW, Huang S, Jiang Y, Zhang Y, Burrow MF, McGrath C. Characterization of pathogenic microbiome on removable prostheses with different levels of cleanliness using 2bRAD-M metagenomic sequencing. J Oral Microbiol 2024; 16:2317059. [PMID: 38410192 PMCID: PMC10896157 DOI: 10.1080/20002297.2024.2317059] [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: 09/26/2023] [Accepted: 02/03/2024] [Indexed: 02/28/2024] Open
Abstract
Background The microbiomes on the surface of unclean removable prostheses are complex and yet largely underexplored using metagenomic sequencing technology. Objectives To characterize the microbiome of removable prostheses with different levels of cleanliness using Type IIB Restriction-site Associated DNA for Microbiome (2bRAD-M) sequencing and compare the Microbial Index of Pathogenic Bacteria (MIP) between clean and unclean prostheses. Materials and Methods Ninety-seven removable prostheses were classified into 'clean' and 'unclean' groups. All prosthesis plaque samples underwent 2bRAD metagenomic sequencing to characterize the species-resolved microbial composition. MIPs for clean and unclean prostheses were calculated based on the sum of the relative abundance of pathogenic bacteria in a microbiome using a reference database that contains opportunistic pathogenic bacteria and disease-associated information. Results Beta diversity analyses based on Jaccard qualitative and Bray-Curtis quantitative distance matrices identified significant differences between the two groups (p < 0.05). There was a significant enrichment of many pathogenic bacteria in the unclean prosthesis group. The MIP for unclean prostheses (0.47 ± 0.25) was significantly higher than for clean prostheses (0.37 ± 0.29), p = 0.029. Conclusions The microbial community of plaque samples from 'unclean' prostheses demonstrated compositional differences compared with 'clean' prostheses. In addition, the pathogenic microbiome in the 'unclean' versus 'clean' group differed.
Collapse
Affiliation(s)
- Tong Wah Lim
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Shi Huang
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yuesong Jiang
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yufeng Zhang
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Michael Francis Burrow
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Colman McGrath
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
38
|
Ashraf H, Ghouri F, Baloch FS, Nadeem MA, Fu X, Shahid MQ. Hybrid Rice Production: A Worldwide Review of Floral Traits and Breeding Technology, with Special Emphasis on China. Plants (Basel) 2024; 13:578. [PMID: 38475425 DOI: 10.3390/plants13050578] [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] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/26/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024]
Abstract
Rice is an important diet source for the majority of the world's population, and meeting the growing need for rice requires significant improvements at the production level. Hybrid rice production has been a significant breakthrough in this regard, and the floral traits play a major role in the development of hybrid rice. In grass species, rice has structural units called florets and spikelets and contains different floret organs such as lemma, palea, style length, anther, and stigma exsertion. These floral organs are crucial in enhancing rice production and uplifting rice cultivation at a broader level. Recent advances in breeding techniques also provide knowledge about different floral organs and how they can be improved by using biotechnological techniques for better production of rice. The rice flower holds immense significance and is the primary focal point for researchers working on rice molecular biology. Furthermore, the unique genetics of rice play a significant role in maintaining its floral structure. However, to improve rice varieties further, we need to identify the genomic regions through mapping of QTLs (quantitative trait loci) or by using GWAS (genome-wide association studies) and their validation should be performed by developing user-friendly molecular markers, such as Kompetitive allele-specific PCR (KASP). This review outlines the role of different floral traits and the benefits of using modern biotechnological approaches to improve hybrid rice production. It focuses on how floral traits are interrelated and their possible contribution to hybrid rice production to satisfy future rice demand. We discuss the significance of different floral traits, techniques, and breeding approaches in hybrid rice production. We provide a historical perspective of hybrid rice production and its current status and outline the challenges and opportunities in this field.
Collapse
Affiliation(s)
- Humera Ashraf
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin 33100, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Xuelin Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
39
|
Ran Y, Sun D, Liu X, Zhang L, Niu Z, Chai T, Hu Z, Qiao K. Chlorella pyrenoidosa as a potential bioremediator: Its tolerance and molecular responses to cadmium and lead. Sci Total Environ 2024; 912:168712. [PMID: 38016561 DOI: 10.1016/j.scitotenv.2023.168712] [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: 09/04/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Heavy metal contamination negatively affects plants and animals in water as well as soils. Some microalgae can remove heavy metal contaminants from wastewater. The aim of this study was to screen green microalgae (GM) to identify those that tolerate high concentrations of toxic heavy metals in water as possible candidates for phytoremediation. Analyses of the tolerance, physiological parameters, ultrastructure, and transcriptomes of GM under Cd/Pb treatments were conducted. Compared with the other GM, Chlorella pyrenoidosa showed stronger tolerance to high concentrations of Cd/Pb. The reduced glutathione content and peroxidase activity were higher in C. pyrenoidosa than those in the other GM. Ultrastructural observations showed that, compared with other GM, C. pyrenoidosa had less damage to the cell surface and interior under Cd/Pb toxicity. Transcriptome analyses indicated that the "peroxisome" and "sulfur metabolism" pathways were enriched with differentially expressed genes under Cd/Pb treatments, and that CpSAT, CpSBP, CpKAT2, Cp2HPCL, CpACOX, CpACOX2, and CpACOX4, all of which encode antioxidant enzymes, were up-regulated under Cd/Pb treatments. These results show that C. pyrenoidosa has potential applications in the remediation of polluted water, and indicate that antioxidant enzymes contribute to Cd/Pb detoxification. These findings will be useful for producing algal strains for the purpose of bioremediation in water contamination.
Collapse
Affiliation(s)
- Ye Ran
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, PR China
| | - Dexiang Sun
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, PR China
| | - Xiang Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, PR China
| | - Ling Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, PR China
| | - Zhiyong Niu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, PR China
| | - Tuanyao Chai
- College of Life Science, University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zhangli Hu
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, PR China.
| | - Kun Qiao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, PR China.
| |
Collapse
|
40
|
Wang C, Yu X, Wang J, Zhao Z, Wan J. Genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice. J Genet Genomics 2024:S1673-8527(24)00029-8. [PMID: 38325701 DOI: 10.1016/j.jgg.2024.01.007] [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] [Received: 12/13/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Heterosis, also known as hybrid vigor, is commonly observed in rice crosses. The hybridization of rice species or subspecies exhibits robust hybrid vigor, however, the direct harnessing of this vigor is hindered by reproductive isolation. Here, we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific hybrids. This review encompasses the genetic model of reproductive isolation within and among Oryza sativa species, emphasizing the essential role of mitochondria in this process. Additionally, we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes, elucidating their significant contribution to reproductive isolation. Furthermore, our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in rice. Building on these advances, we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.
Collapse
Affiliation(s)
- Chaolong Wang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowen Yu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhigang Zhao
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
41
|
Ameen M, Zafar A, Mahmood A, Zia MA, Kamran K, Javaid MM, Yasin M, Khan BA. Melatonin as a master regulatory hormone for genetic responses to biotic and abiotic stresses in model plant Arabidopsis thaliana: a comprehensive review. Funct Plant Biol 2024; 51:FP23248. [PMID: 38310885 DOI: 10.1071/fp23248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 02/06/2024]
Abstract
Melatonin is a naturally occurring biologically active amine produced by plants, animals and microbes. This review explores the biosynthesis of melatonin in plants, with a particular focus on its diverse roles in Arabidopsis thaliana , a model species. Melatonin affects abiotic and biotic stress resistance in A. thaliana . Exogenous and endogenous melatonin is addressed in association with various conditions, including cold stress, high light stress, intense heat and infection with Botrytis cinerea or Pseudomonas , as well as in seed germination and lateral root formation. Furthermore, melatonin confers stress resistance in Arabidopsis by initiating the antioxidant system, remedying photosynthesis suppression, regulating transcription factors involved with stress resistance (CBF, DREB, ZAT, CAMTA, WRKY33, MYC2, TGA) and other stress-related hormones (abscisic acid, auxin, ethylene, jasmonic acid and salicylic acid). This article additionally addresses other precursors, metabolic components, expression of genes (COR , CBF , SNAT , ASMT , PIN , PR1 , PDF1.2 and HSFA ) and proteins (JAZ, NPR1) associated with melatonin and reducing both biological and environmental stressors. Furthermore, the future perspective of melatonin rich agri-crops is explored to enhance plant tolerance to abiotic and biotic stresses, maximise crop productivity and enhance nutritional worth, which may help improve food security.
Collapse
Affiliation(s)
- Muaz Ameen
- Department of Botany, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Asma Zafar
- Department of Botany, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Anjum Zia
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Kashif Kamran
- Department of Physics, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Mansoor Javaid
- Department of Agronomy, College of Agriculture, University of Sargodha, Sargodha 40100, Pakistan
| | - Muhammad Yasin
- Department of Agronomy, College of Agriculture, University of Sargodha, Sargodha 40100, Pakistan
| | - Bilal Ahmad Khan
- Department of Agronomy, College of Agriculture, University of Sargodha, Sargodha 40100, Pakistan
| |
Collapse
|
42
|
Pandey S. Agronomic potential of plant-specific Gγ proteins. Physiol Mol Biol Plants 2024; 30:337-347. [PMID: 38623166 PMCID: PMC11016034 DOI: 10.1007/s12298-024-01428-7] [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] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/17/2024] [Accepted: 02/28/2024] [Indexed: 04/17/2024]
Abstract
The vascular plant-specific type III Gγ proteins have emerged as important targets for biotechnological applications. These proteins are exemplified by Arabidopsis AGG3, rice Grain Size 3 (GS3), Dense and Erect Panicle 1 (DEP1), and GGC2 and regulate plant stature, seed size, weight and quality, nitrogen use efficiency, and multiple stress responses. These Gγ proteins are an integral component of the plant heterotrimeric G-protein complex and differ from the canonical Gγ proteins due to the presence of a long, cysteine-rich C-terminal region. Most cereal genomes encode three or more of these proteins, which have similar N-terminal Gγ domains but varying lengths of the C-terminal domain. The C-terminal domain is hypothesized to give specificity to the protein function. Intriguingly, many accessions of cultivated cereals have natural deletion of this region in one or more proteins, but the mechanistic details of protein function remain perplexing. Distinct, sometimes contrasting, effects of deletion of the C-terminal region have been reported in different crops or under varying environmental conditions. This review summarizes the known roles of type III Gγ proteins, the possible action mechanisms, and a perspective on what is needed to comprehend their full agronomic potential.
Collapse
Affiliation(s)
- Sona Pandey
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132 USA
| |
Collapse
|
43
|
Liu P, Zhang Z, Cai Y, Li Z, Zhou Q, Chen Q. Ferroptosis: Mechanisms and role in diabetes mellitus and its complications. Ageing Res Rev 2024; 94:102201. [PMID: 38242213 DOI: 10.1016/j.arr.2024.102201] [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: 05/29/2023] [Revised: 01/06/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
Diabetes mellitus (DM) and its complications are major diseases that affect human health and pose a serious threat to global public health. Although the prevention and treatment of DM and its complications are constantly being revised, optimal treatment strategies remain unavailable. Further exploration of new anti-diabetic strategies is an arduous task. Revealing the pathological changes and molecular mechanisms of DM and its complications is the cornerstone for exploring new therapeutic strategies. Ferroptosis is a type of newly discovered iron-dependent regulated cell death. Notably, the role of ferroptosis in the occurrence, development, and pathogenesis of DM and its complications has gradually been revealed. Numerous studies have shown that ferroptosis plays an important role in the pathophysiology and pathogenesis of DM and its associated complications. The aim of this review is to discuss the known underlying mechanisms of ferroptosis, the relationship between ferroptosis and DM, and the relationship between ferroptosis as a mode of cell death and diabetic kidney disease, diabetic retinopathy, diabetic cardiomyopathy, diabetic osteoporosis, diabetes-associated cognitive dysfunction, DM-induced erectile dysfunction, and diabetic atherosclerosis.
Collapse
Affiliation(s)
- Pan Liu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan, PR China
| | - Zhengdong Zhang
- School of Clinical Medicine, Chengdu Medical College, Chengdu 610500, Sichuan, PR China; Department of Orthopedics, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan, PR China
| | - Yichen Cai
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan, PR China
| | - Zhaoying Li
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan, PR China
| | - Qian Zhou
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan, PR China
| | - Qiu Chen
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan, PR China.
| |
Collapse
|
44
|
Knight AK, Spencer JB, Smith AK. DNA methylation as a window into female reproductive aging. Epigenomics 2024; 16:175-188. [PMID: 38131149 PMCID: PMC10841041 DOI: 10.2217/epi-2023-0298] [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: 08/24/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
People with ovaries experience reproductive aging as their reproductive function and system declines. This has significant implications for both fertility and long-term health, with people experiencing an increased risk of cardiometabolic disorders after menopause. Reproductive aging can be assessed through markers of ovarian reserve, response to fertility treatment or molecular biomarkers, including DNA methylation. Changes in DNA methylation with age associate with poorer reproductive outcomes, and epigenome-wide studies can provide insight into genes and pathways involved. DNA methylation-based epigenetic clocks can quantify biological age in reproductive tissues and systemically. This review provides an overview of hallmarks and theories of aging in the context of the reproductive system, and then focuses on studies of DNA methylation in reproductive tissues.
Collapse
Affiliation(s)
- Anna K Knight
- Research Division, Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jessica B Spencer
- Reproductive Endocrinology & Infertility Division, Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alicia K Smith
- Research Division, Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Reproductive Endocrinology & Infertility Division, Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Psychiatry & Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
45
|
Zhang J, Li L, Zhang Z, Han L, Xu L. The Effect of Ethephon on Ethylene and Chlorophyll in Zoysia japonica Leaves. Int J Mol Sci 2024; 25:1663. [PMID: 38338942 PMCID: PMC10855035 DOI: 10.3390/ijms25031663] [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: 12/29/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Zoysia japonica (Zoysia japonica Steud.) is a kind of warm-season turfgrass with many excellent characteristics. However, the shorter green period and longer dormancy caused by cold stress in late autumn and winter are the most limiting factors affecting its application. A previous transcriptome analysis revealed that ethephon regulated genes in chlorophyll metabolism in Zoysia japonica under cold stress. Further experimental data are necessary to understand the effect and underlying mechanism of ethephon in regulating the cold tolerance of Zoysia japonica. The aim of this study was to evaluate the effects of ethephon by measuring the enzyme activity, intermediates content, and gene expression related to ethylene biosynthesis, signaling, and chlorophyll metabolism. In addition, the ethylene production rate, chlorophyll content, and chlorophyll a/b ratio were analyzed. The results showed that ethephon application in a proper concentration inhibited endogenous ethylene biosynthesis, but eventually promoted the ethylene production rate due to its ethylene-releasing nature. Ethephon could promote chlorophyll content and improve plant growth in Zoysia japonica under cold-stressed conditions. In conclusion, ethephon plays a positive role in releasing ethylene and maintaining the chlorophyll content in Zoysia japonica both under non-stressed and cold-stressed conditions.
Collapse
Affiliation(s)
| | | | | | - Liebao Han
- College of Grassland Science, Beijing Forestry University, Beijing 100083, China; (J.Z.); (L.L.); (Z.Z.)
| | - Lixin Xu
- College of Grassland Science, Beijing Forestry University, Beijing 100083, China; (J.Z.); (L.L.); (Z.Z.)
| |
Collapse
|
46
|
Zhang H, Wang X, Yang Z, Bai Y, Chen L, Wu T. Transcriptome analysis reveals the potential mechanism of the response to scale insects in Camellia sasanqua Thunb. BMC Genomics 2024; 25:106. [PMID: 38267855 PMCID: PMC10807073 DOI: 10.1186/s12864-024-09980-y] [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: 11/29/2023] [Accepted: 01/06/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Camellia sasanqua Thunb. is an essential woody ornamental plant. Our continuous observation found that scale insects often infest C. sasanqua all year round in Kunming, China, resulting in poor growth. Scientifically preventing and controlling the infestation of scale insects should be paid attention to, and the mechanism of scale insects influencing C. sasanqua should be used as the research basis. RESULTS The scale insect was identified as Pseudaulacaspis sasakawai Takagi. We analyzed transcriptome sequencing data from leaves of C. sasanqua infested with scale insects. A total of 1320 genes were either up-regulated or down-regulated and differed significantly in response to scale insects. GO (Gene Ontology) annotation analysis showed that the pathway of catalytic activity, binding, membrane part, cell part, and cellular process were affected. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that most DEGs (differentially expressed genes) involved in plant hormone signal transduction, MAPK signaling pathway, flavonoid biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis. We also observed that the expression of galactose metabolism and carotenoid biosynthesis were significantly influenced. In addition, qRT-PCR (quantitative real-time PCR) validated the expression patterns of DEGs, which showed an excellent agreement with the transcriptome sequencing. CONCLUSIONS Our transcriptomic analysis revealed that the C. sasanqua had an intricate resistance strategy to cope with scale insect attacks. After sensing the attack signal of scale insects, C. sasanqua activated the early signal MAPK (mitogen-activated protein kinase) to activate further transcription factors and Auxin, ET, JA, ABA, and other plant hormone signaling pathways, ultimately leading to the accumulation of lignin, scopolin, flavonoids and other secondary metabolites, produces direct and indirect resistance to scale insects. Our results suggested that it provided some potential resources of defense genes that would benefit the following resistance breeding in C. sasanqua to scale insects.
Collapse
Affiliation(s)
- Hongye Zhang
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Xubo Wang
- Yunnan Biodiversity Research Institute, Southwest Forestry University, Kunming, 650224, China
| | - Ziyun Yang
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Yan Bai
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Longqing Chen
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Tian Wu
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China.
| |
Collapse
|
47
|
Wang Y, Xie Y, Mahara G, Xiong Y, Xiong Y, Zheng Q, Chen J, Zhang W, Zhou H, Li Q. Intestinal microbiota and metabolome perturbations in ischemic and idiopathic dilated cardiomyopathy. J Transl Med 2024; 22:89. [PMID: 38254195 PMCID: PMC10804607 DOI: 10.1186/s12967-023-04605-6] [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: 06/17/2023] [Accepted: 10/06/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Various clinical similarities are present in ischemic (ICM) and idiopathic dilated cardiomyopathy (IDCM), leading to ambiguity on some occasions. Previous studies have reported that intestinal microbiota appeared dysbiosis in ICM, whether implicating in the IDCM remains unclear. The aim of this study was to assess the alterations in intestinal microbiota and fecal metabolites in ICM and IDCM. METHODS ICM (n = 20), IDCM (n = 22), and healthy controls (HC, n = 20) were enrolled in this study. Stool samples were collected for 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS) analysis. RESULTS Both ICM and IDCM exhibited reduced alpha diversity and altered microbial community structure compared to HC. At the genus level, nine taxa including Blautia, [Ruminococcus]_torques_group, Christensenellaceae_R-7_group, UCG-002, Corynebacterium, Oceanobacillus, Gracilibacillus, Klebsiella and Citrobacter was specific to ICM, whereas one taxa Alistipes uniquely altered in IDCM. Likewise, these changes were accompanied by significant metabolic differences. Further differential analysis displayed that 18 and 14 specific metabolites uniquely changed in ICM and IDCM, respectively. The heatmap was generated to display the association between genera and metabolites. Receiver operating characteristic curve (ROC) analysis confirmed the predictive value of the distinct microbial-metabolite features in disease status. The results showed that microbial (area under curve, AUC = 0.95) and metabolic signatures (AUC = 0.84) were effective in discriminating ICM from HC. Based on the specific microbial and metabolic features, the patients with IDCM could be separated from HC with an AUC of 0.80 and 0.87, respectively. Furthermore, the gut microbial genus (AUC = 0.88) and metabolite model (AUC = 0.89) were comparable in predicting IDCM from ICM. Especially, the combination of fecal microbial-metabolic features improved the ability to differentiate IDCM from ICM with an AUC of 0.96. CONCLUSION Our findings highlighted the alterations of gut microbiota and metabolites in different types of cardiomyopathies, providing insights into the pathophysiological mechanisms of myocardial diseases. Moreover, multi-omics analysis of fecal samples holds promise as a non-invasive tool for distinguishing disease status.
Collapse
Affiliation(s)
- Yusheng Wang
- Department of Cardiovascular Internal Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Yandan Xie
- Department of Cardiovascular Internal Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Gehendra Mahara
- Clinical Research Center, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Yanling Xiong
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yalan Xiong
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qifang Zheng
- Department of Cardiovascular Internal Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Jianqin Chen
- Department of Cardiovascular Internal Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| |
Collapse
|
48
|
Zhou R, Wang S, Zhan N, He W, Deng G, Dou T, Zhu XT, Xie WZ, Zheng YY, Hu C, Bi F, Gao H, Dong T, Liu S, Li C, Yang Q, Wang L, Song JM, Dang J, Guo Q, Yi G, Chen LL, Sheng O. High-quality genome assemblies for two Australimusa bananas (Musa spp.) and insights into regulatory mechanisms of superior fiber properties. Plant Commun 2024; 5:100681. [PMID: 37660253 PMCID: PMC10811375 DOI: 10.1016/j.xplc.2023.100681] [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: 01/18/2023] [Revised: 08/19/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
Bananas (Musa spp.) are monocotyledonous plants with high genetic diversity in the Musaceae family that are cultivated mainly in tropical and subtropical countries. The fruits are a popular food, and the plants themselves have diverse uses. Four genetic groups (genomes) are thought to have contributed to current banana cultivars: Musa acuminata (A genome), Musa balbisiana (B genome), Musa schizocarpa (S genome), and species of the Australimusa section (T genome). However, the T genome has not been effectively explored. Here, we present the high-quality TT genomes of two representative accessions, Abaca (Musa textilis), with high-quality natural fiber, and Utafun (Musa troglodytarum, Fe'i group), with abundant β-carotene. Both the Abaca and Utafun assemblies comprise 10 pseudochromosomes, and their total genome sizes are 613 Mb and 619 Mb, respectively. Comparative genome analysis revealed that the larger size of the T genome is likely attributable to rapid expansion and slow removal of transposons. Compared with those of Musa AA or BB accessions or sisal (Agava sisalana), Abaca fibers exhibit superior mechanical properties, mainly because of their thicker cell walls with a higher content of cellulose, lignin, and hemicellulose. Expression of MusaCesA cellulose synthesis genes peaks earlier in Abaca than in AA or BB accessions during plant development, potentially leading to earlier cellulose accumulation during secondary cell wall formation. The Abaca-specific expressed gene MusaMYB26, which is directly regulated by MusaMYB61, may be an important regulator that promotes precocious expression of secondary cell wall MusaCesAs. Furthermore, MusaWRKY2 and MusaNAC68, which appear to be involved in regulating expression of MusaLAC and MusaCAD, may at least partially explain the high accumulation of lignin in Abaca. This work contributes to a better understanding of banana domestication and the diverse genetic resources in the Musaceae family, thus providing resources for Musa genetic improvement.
Collapse
Affiliation(s)
- Run Zhou
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuo Wang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ni Zhan
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Weidi He
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Tongxin Dou
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Xi-Tong Zhu
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wen-Zhao Xie
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Yu Zheng
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunhua Hu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Fangcheng Bi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Huijun Gao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Tao Dong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Siwen Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Qiaosong Yang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jiangbo Dang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| |
Collapse
|
49
|
Ai Y, Meng Y, Yan B, Zhou Q, Wang X. The biochemical pathways of apoptotic, necroptotic, pyroptotic, and ferroptotic cell death. Mol Cell 2024; 84:170-179. [PMID: 38181758 DOI: 10.1016/j.molcel.2023.11.040] [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: 08/20/2023] [Revised: 10/16/2023] [Accepted: 11/30/2023] [Indexed: 01/07/2024]
Abstract
Apoptosis, the first regulated form of cell death discovered in mammalian cells, is executed by caspase-3/7, which are dormant in living cells but become activated by upstream caspase-8 or caspase-9 in responding to extracellular cytokines or intracellular stress signals, respectively. The same cell death-inducing cytokines also cause necroptosis when caspase-8 is inhibited, resulting in the activation of receptor-interacting protein kinase 3 (RIPK3), which phosphorylates pseudokinase MLKL to trigger its oligomerization and membrane-disrupting activity. Caspase-1/4/5/11, known as inflammatory caspases, instead induce pyroptosis by cleaving gasdermin D, whose caspase-cleaved N terminus forms pores on the plasma membrane. The membrane protein NINJ1 amplifies the extent of membrane rupture initiated by gasdermin D. Additionally, disturbance of peroxidation of polyunsaturated fatty acid tails of membrane phospholipids triggers ferroptosis, an iron-dependent and caspases-independent necrotic death. This review will discuss how these regulated cell death pathways act individually and interconnectively in particular cell types to carry out specific physiological and pathological functions.
Collapse
Affiliation(s)
- Youwei Ai
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yutong Meng
- National Institute of Biological Sciences, Beijing and Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, No. 7 Life Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Bo Yan
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qinyi Zhou
- National Institute of Biological Sciences, Beijing and Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, No. 7 Life Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Xiaodong Wang
- National Institute of Biological Sciences, Beijing and Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, No. 7 Life Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
| |
Collapse
|
50
|
Tian Y, Chen X, Xu P, Wang Y, Wu X, Wu K, Fu X, Chin Y, Liao Y. Rapid Visual Detection of Elite Erect Panicle Dense and Erect Panicle 1 Allele for Marker-Assisted Improvement in Rice ( Oryza sativa L.) Using the Loop-Mediated Isothermal Amplification Method. Curr Issues Mol Biol 2024; 46:498-512. [PMID: 38248334 PMCID: PMC10814556 DOI: 10.3390/cimb46010032] [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: 11/30/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Molecular-assisted breeding is an effective way to improve targeted agronomic traits. dep1 (dense and erect panicle 1) is a pleiotropic gene that regulates yield, quality, disease resistance, and stress tolerance, traits that are of great value in rice (Oryza sativa L.) breeding. In this study, a colorimetric LAMP (loop-mediated isothermal amplification) assay was developed for the detection of the dep1 allele and tested for the screening and selection of the heavy-panicle hybrid rice elite restorer line SHUHUI498, modified with the allele. InDel (Insertion and Deletion) primers (DEP1_F and DEP1_R) and LAMP primers (F3, B3, FIP, and BIP) for genotyping were designed using the Primer3 Plus (version 3.3.0) and PrimerExplore (version 5) software. Our results showed that both InDel and LAMP markers could be used for accurate genotyping. After incubation at a constant temperature of 65 °C for 60 min with hydroxynaphthol blue (HNB) as a color indicator, the color of the LAMP assay containing the dep1 allele changed to sky blue. The SHUHUI498 rice line that was detected in our LAMP assay displayed phenotypes consistent with the dep1 allele such as having a more compact plant architecture, straight stems and leaves, and a significant increase in the number of effective panicles and spikelets, demonstrating the effectiveness of our method in screening for the dep1 allele in rice breeding.
Collapse
Affiliation(s)
- Yonghang Tian
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Xiyi Chen
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Yuping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Xianjun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Kun Wu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, China; (K.W.); (X.F.)
| | - Xiangdong Fu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, China; (K.W.); (X.F.)
| | - Yaoxian Chin
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Yongxiang Liao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| |
Collapse
|