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Pang S, Zheng H, Zhang J, Ren X, Zong X, Zou J, Wang L. Function Analysis of a Maize Endo-1,4-β-xylanase Gene ZmHSL in Response to High-Temperature Stress. Int J Mol Sci 2024; 25:8834. [PMID: 39201520 PMCID: PMC11354693 DOI: 10.3390/ijms25168834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 08/03/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
Rising temperature is a major threat to the normal growth and development of maize, resulting in low yield production and quality. The mechanism of maize in response to heat stress remains uncertain. In this study, a maize mutant Zmhsl-1 (heat sensitive leaves) with wilting and curling leaves under high temperatures was identified from maize Zheng 58 (Z58) mutant lines generated by ethyl methanesulfonate (EMS) mutagenesis. The Zmhsl-1 plants were more sensitive to increased temperature than Z58 in the field during growth season. The Zmhsl-1 plants had lower plant height, lower yield, and lower content of photosynthetic pigments. A bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) enabled the identification of the corresponding gene, named ZmHSL, which encodes an endo-β-1,4-xylanase from the GH10 family. The loss-of-function of ZmHSL resulted in reduced lignin content in Zmhsl-1 plants, leading to defects in water transport and more severe leaf wilting with the increase in temperature. RNA-seq analysis revealed that the differentially expressed genes identified between Z58 and Zmhsl-1 plants are mainly related to heat stress-responsive genes and unfolded protein response genes. All these data indicated that ZmHSL plays a key role in lignin synthesis, and its defective mutation causes changes in the cell wall structure and gene expression patterns, which impedes water transport and confers higher sensitivity to high-temperature stress.
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Affiliation(s)
- Shengyan Pang
- Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.P.); (H.Z.); (X.R.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (J.Z.); (X.Z.)
| | - Hongyan Zheng
- Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.P.); (H.Z.); (X.R.)
| | - Jiankui Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (J.Z.); (X.Z.)
| | - Xiaotian Ren
- Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.P.); (H.Z.); (X.R.)
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing 102206, China
| | - Xuefeng Zong
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (J.Z.); (X.Z.)
| | - Junjie Zou
- Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.P.); (H.Z.); (X.R.)
| | - Lei Wang
- Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.P.); (H.Z.); (X.R.)
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Chen C, Zhang M, Ma X, Meng Q, Zhuang K. Differential heat-response characteristics of two plastid isoforms of triose phosphate isomerase in tomato. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:650-661. [PMID: 37878418 PMCID: PMC10893939 DOI: 10.1111/pbi.14212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/29/2023] [Accepted: 10/07/2023] [Indexed: 10/27/2023]
Abstract
Heat stress causes dysfunction of the carbon-assimilation metabolism. As a member of Calvin-Benson-Bassham (CBB) cycle, the chloroplast triose phosphate isomerases (TPI) catalyse the interconversion of glyceraldehyde 3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP). The tomato (Solanum lycopersicum) genome contains two individual SlTPI genes, Solyc10g054870 and Solyc01g111120, which encode the chloroplast-located proteins SlTPI1 and SlTPI2, respectively. The tpi1 and tpi2 single mutants had no visible phenotypes, but the leaves of their double mutant lines tpi1tpi2 had obviously reduced TPI activity and displayed chlorotic variegation, dysplasic chloroplasts and lower carbon-assimilation efficiency. In addition to altering carbon metabolism, proteomic data showed that the loss of both SlTPI1 and SlTPI2 severely affected photosystem proteins, reducing photosynthetic capacity. None of these phenotypes was evident in the tpi1 or tpi2 single mutants, suggesting that SlTPI1 and SlTPI2 are functionally redundant. However, the two proteins differed in their responses to heat stress; the protein encoded by the heat-induced SlTPI2 showed a higher level of thermotolerance than that encoded by the heat-suppressed SlTPI1. Notably, heat-induced transcription factors, SlWRKY21 and SlHSFA2/7, which negatively regulated SlTPI1 expression and positively regulated SlTPI2 expression, respectively. Our findings thus reveal that SlTPI1 and SlTPI2 have different thermostabilities and expression patterns in response to heat stress, which have the potential to be applied in thermotolerance strategies in crops.
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Affiliation(s)
- Chong Chen
- State Key Laboratory of Crop Biology, College of Life SciencesShandong Agricultural UniversityTai’anShandongChina
- College of Agriculture and BioengineeringHeze UniversityHe'zeShandongChina
| | - Meng Zhang
- State Key Laboratory of Crop Biology, College of Life SciencesShandong Agricultural UniversityTai’anShandongChina
| | - Xiaocui Ma
- College of ForestryShandong Agricultural UniversityTai'anShandongChina
| | - Qingwei Meng
- State Key Laboratory of Crop Biology, College of Life SciencesShandong Agricultural UniversityTai’anShandongChina
| | - Kunyang Zhuang
- State Key Laboratory of Crop Biology, College of Life SciencesShandong Agricultural UniversityTai’anShandongChina
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Li R, Song M, Yin D, Ye X, Yu J, Chen X. Indole-3-acetic acid mediated removal of sludge toxicity by microalgae: Focus on the role of extracellular polymeric substances. BIORESOURCE TECHNOLOGY 2023; 387:129700. [PMID: 37604255 DOI: 10.1016/j.biortech.2023.129700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
The use of indole-3-acid (IAA) as an additive aided in achieving the objectives of reducing sludge extract toxicity, increasing Tetradesmus obliquus biomass yield, and enhancing extracellular polysaccharide production. Proteomics analysis can unveil the microalgae's response mechanism to sludge toxicity stress. With 10-6 M IAA addition, microalgae biomass reached 3.426 ± 0.067 g/L. Sludge extract demonstrated 78.3 ± 3.2% total organic carbon removal and 72.2 ± 2.1% toxicity removal. Extracellular polysaccharides and proteins witnessed 2.08 and 1.76-fold increments, respectively. Proteomic analysis indicated that Tetradesmus obliquus directed carbon sources towards glycogen accumulation and amino acid synthesis, regulating pathways associated with carbon metabolism (glycolysis, TCA cycle, and amino acid metabolism) to adapt to the stressful environment. These findings lay the groundwork for future waste sludge treatment and offer novel insights into microalgae cultivation and extracellular polysaccharide enrichment in sludge.
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Affiliation(s)
- Renjie Li
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Meijing Song
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Danning Yin
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoyun Ye
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiayu Yu
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xiurong Chen
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
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Zhou Y, Zhang F, Mao L, Feng T, Wang K, Xu M, Lv B, Wang X. Bifico relieves irritable bowel syndrome by regulating gut microbiota dysbiosis and inflammatory cytokines. Eur J Nutr 2023; 62:139-155. [PMID: 35918555 PMCID: PMC9899748 DOI: 10.1007/s00394-022-02958-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/08/2022] [Indexed: 02/07/2023]
Abstract
PURPOSE Gut microbiota dysbiosis, a core pathophysiology of irritable bowel syndrome (IBS), is closely related to immunological and metabolic functions. Gut microbiota-based therapeutics have been recently explored in several studies. Bifico is a probiotic cocktail widely used in gastrointestinal disorders which relate to the imbalance of gut microbiota. However, the efficacy and potential mechanisms of Bifico treatment in IBS remains incompletely understood. METHODS Adopting a wrap restraint stress (WRS) -induced IBS mice model. Protective effect of Bifico in IBS mice was examined through abdominal withdrawal reflex (AWR) scores. 16S rDNA, 1H nuclear magnetic resonance (1H-NMR) and western blot assays were performed to analyze alterations of gut microbiota, microbiome metabolites and inflammatory cytokines, respectively. RESULTS Bifico could decrease intestinal visceral hypersensitivity. Although gut microbiota diversity did not increase, composition of gut microbiota was changed after treatment of Bifico, which were characterized by an increase of Proteobacteria phylum and Actinobacteria phylum, Muribaculum genus, Bifidobacterium genus and a decrease of Parabacteroides genus, Sutterella genus and Lactobacillus genus. Moreover, Bifico elevated the concentration of short-chain fatty acids (SCFAs) and reduced protein levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α). From further Spearman's correlation analysis, Bifidobacterium genus were positively correlated with SCFAs including propionate, butyrate, valerate and negatively correlated with IL-6 and TNF-α. CONCLUSION Bifico could alleviate symptoms of IBS mice through regulation of the gut microbiota, elevating production of SCFAs and reducing the colonic inflammatory response.
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Affiliation(s)
- Yanlin Zhou
- grid.417400.60000 0004 1799 0055Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310003 Zhejiang China ,grid.268505.c0000 0000 8744 8924The First Clinical College of Zhejiang Chinese Medical University, Hangzhou, 310053 Zhejiang China ,Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Chinese Medical University, Hubin Campus, Hangzhou, 310006 China
| | - Fan Zhang
- grid.268505.c0000 0000 8744 8924The First Clinical College of Zhejiang Chinese Medical University, Hangzhou, 310053 Zhejiang China ,Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Chinese Medical University, Hubin Campus, Hangzhou, 310006 China ,grid.417400.60000 0004 1799 0055Department of Radiology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310003 Zhejiang China
| | - Liqi Mao
- grid.411440.40000 0001 0238 8414Department of Gastroenterology, The First People’s Hospital of Huzhou, The First Affiliated Hospital of Huzhou Teachers College, Huzhou, 313000 Zhejiang China
| | - Tongfei Feng
- grid.417400.60000 0004 1799 0055Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310003 Zhejiang China ,Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Chinese Medical University, Hubin Campus, Hangzhou, 310006 China
| | - Kaijie Wang
- grid.417400.60000 0004 1799 0055Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310003 Zhejiang China ,Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Chinese Medical University, Hubin Campus, Hangzhou, 310006 China
| | - Maosheng Xu
- grid.417400.60000 0004 1799 0055Department of Radiology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310003 Zhejiang China
| | - Bin Lv
- grid.417400.60000 0004 1799 0055Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310003 Zhejiang China ,Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Chinese Medical University, Hubin Campus, Hangzhou, 310006 China
| | - Xi Wang
- Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Chinese Medical University, Hubin Campus, Hangzhou, 310006 China
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Zha G, Yin J, Cheng F, Song M, Zhang M, Obel HO, Wang Y, Chen J, Lou Q. Fine mapping of CscpFtsY, a gene conferring the yellow leaf phenotype in cucumber (Cucumis sativus L.). BMC PLANT BIOLOGY 2022; 22:570. [PMID: 36471240 PMCID: PMC9724417 DOI: 10.1186/s12870-022-03922-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Leaf color mutants are ideal materials to study pigment metabolism and photosynthesis. Leaf color variations are mainly affected by chlorophylls (Chls) and carotenoid contents and chloroplast development in higher plants. However, the regulation of chlorophyll metabolism remains poorly understood in many plant species. The chloroplast signal-recognition particle system is responsible for the insertion of the light-harvesting chlorophyll a/b proteins (LHCPs) to thylakoid membranes, which controls the chloroplast development as well as the regulation of Chls biosynthesis post-translationally in higher plants. RESULTS In this study, the yellow leaf cucumber mutant, named yl, was found in an EMS-induced mutant library, which exhibited a significantly reduced chlorophyll content, abnormal chloroplast ultrastructure and decreased photosynthetic capacity. Genetic analysis demonstrated that the phenotype of yl was controlled by a recessive nuclear gene. Using BSA-seq technology combined with the map-based cloning method, we narrowed the locus to a 100 kb interval in chromosome 3. Linkage analysis and allelism test validated the candidate SNP residing in CsaV3_3G009150 encoding one homolog of chloroplast signal-recognition particle (cpSRP) receptor in Arabidopsis, cpFtsY, could be responsible for the yellow leaf phenotype of yl. The relative expression of CscpFtsY was significantly down-regulated in different organs except for the stem, of yl compared with that in the wild type (WT). Subcellular localization result showed that CscpFtsY located in the chloroplasts of mesophyll cells. CONCLUSIONS The yl mutant displayed Chls-deficient, impaired chloroplast ultrastructure with intermittent grana stacks and significantly decreased photosynthetic capacity. The isolation of CscpFtsY in cucumber could accelerate the progress on chloroplast development by cpSRP-dependant LHCP delivery system and regulation of Chls biosynthesis in a post-translational way.
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Affiliation(s)
- Gaohui Zha
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095 China
| | - Juan Yin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095 China
| | - Feng Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095 China
| | - Mengfei Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095 China
| | - Mengru Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095 China
| | - Hesbon Ochieng Obel
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095 China
| | - Yi Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095 China
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095 China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095 China
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Zhang T, Dong X, Yuan X, Hong Y, Zhang L, Zhang X, Chen S. Identification and characterization of CsSRP43, a major gene controlling leaf yellowing in cucumber. HORTICULTURE RESEARCH 2022; 9:uhac212. [PMID: 36479584 PMCID: PMC9719040 DOI: 10.1093/hr/uhac212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/14/2022] [Indexed: 06/17/2023]
Abstract
Mutants are crucial to extending our understanding of genes and their functions in higher plants. In this study a spontaneous cucumber mutant, yf, showed yellow color leaves, had significant decreases in related physiological indexes of photosynthesis characteristics, and had more abnormal chloroplasts and thylakoids. Inheritance analysis indicated that the yellow color of the leaf was controlled by a recessive nuclear locus, yf. A candidate gene, CsSRP43, encoding a chloroplast signal recognition particle 43 protein, was identified through map-based cloning and whole-genome sequence analysis. Alignment of the CsSRP43 gene homologs between both parental lines revealed a 7-kb deletion mutation including the promoter region and the coding sequence in the yf mutant. In order to determine if the CsSRP43 gene was involved in the formation of leaf color, the CRISPR/Cas9-mediate system was used to modify CsSRP43 in the 9930 background; two independent transgenic lines, srp43-1 and srp43-2, were generated, and they showed yellow leaves with abnormal chloroplasts and thylakoids. Transcriptomic analysis revealed that differentially expressed genes associated with the photosynthesis-related pathway were highly enriched between srp43-1 and wild type, most of which were significantly downregulated in line srp43-1. Furthermore, yeast two-hybrid and biomolecular fluorescence complementation assays were used to confirm that CsSRP43 directly interacted with LHCP and cpSRP54 proteins. A model was established to explain the molecular mechanisms by which CsSRP43 participates in the leaf color and photosynthesis pathway, and it provides a valuable basis for understanding the molecular and genetic mechanisms of leaf color in cucumber.
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Affiliation(s)
- Tingting Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Shaanxi Engineering Research Center for Vegetables, Yangling 712100, China
| | - Xiangyu Dong
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Shaanxi Engineering Research Center for Vegetables, Yangling 712100, China
| | - Xin Yuan
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Shaanxi Engineering Research Center for Vegetables, Yangling 712100, China
| | - Yuanyuan Hong
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Shaanxi Engineering Research Center for Vegetables, Yangling 712100, China
| | - Lingling Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Shaanxi Engineering Research Center for Vegetables, Yangling 712100, China
| | - Xuan Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Shaanxi Engineering Research Center for Vegetables, Yangling 712100, China
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The distance distribution of human microRNAs in MirGeneDB database. Sci Rep 2022; 12:17696. [PMID: 36271017 PMCID: PMC9587017 DOI: 10.1038/s41598-022-22253-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/12/2022] [Indexed: 01/18/2023] Open
Abstract
MicroRNAs (miRNAs) are small single-stranded non-coding RNAs around 22 nucleotide lengths found in organisms, playing an important role in cell differentiation, development, gene regulation, and apoptosis. The distance of disease miRNA biomarkers has been used to explore the association between various diseases as well as the association between virus and disease in the literature. To date, there have been no studies on deriving the distribution of the pairwise distance of human miRNAs. As the pairwise distance of miRNA biomarkers might be a useful tool in studying the disease association, in this paper, the distance distributions of human miRNAs were derived such that they could be used to measure the closeness between miRNAs. Two distance models were used to calculate the pairwise distances of 567 Homo sapiens miRNA genes accessed from the MirGeneDB database. These miRNA pairwise distances were fitted by the normal distribution, gamma distribution, empirical cumulative distribution, and the kernel density estimation method. This is the first study to provide the distance distribution of human miRNAs. The similarity of miRNA biomarkers for several diseases was examined using the derived distributions.
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Zhu Y, Yuan G, Wang Y, An G, Li W, Liu J, Sun D. Mapping and functional verification of leaf yellowing genes in watermelon during whole growth period. FRONTIERS IN PLANT SCIENCE 2022; 13:1049114. [PMID: 36340411 PMCID: PMC9627507 DOI: 10.3389/fpls.2022.1049114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Increasing light energy utilization efficiency is an effective way to increase yield and improve quality of watermelon. Leaf is the main place for photosynthesis, and the color of leaf is directly related to the change of photosynthesis. In addition, leaf yellowing can be used as a marker trait to play an important role in watermelon hybrid breeding and improve seed breeding. It can not only be used to eliminate hybrids at seedling stage, but also be used to determine seed purity. In this study, transcriptome analysis was first carried out using the whole growth period leaf yellowing watermelon mutant w-yl and inbred line ZK, and identified 2,471 differentially expressed genes (DEGs) in the comparison group w-yl-vs-ZK. Among the top 20 terms of the gene ontology (GO) enrichment pathway, 17 terms were related to photosynthesis. KEGG pathway enrichment analysis showed that the most abundant pathway was photosynthesis-antenna proteins. The F2 population was constructed by conventional hybridization with the inbred line ZK. Genetic analysis showed that leaf yellowing of the mutant was controlled by a single recessive gene. The leaf yellowing gene of watermelon located between Ind14,179,011 and InD16,396,362 on chromosome 2 by using indel-specific PCR markers, with a region of 2.217 Mb. In the interval, it was found that five genes may have gene fragment deletion in w-yl, among which Cla97C02G036010, Cla97C02G036030, Cla97C02G036040, Cla97C02G036050 were the whole fragment loss, and Cla97C02G0360 was the C-terminal partial base loss. Gene function verification results showed that Cla97C02G036040, Cla97C02G036050 and Cla97C02G036060 may be the key factors leading to yellowing of w-yl leaves.
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Affiliation(s)
- Yingchun Zhu
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Gaopeng Yuan
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Yifan Wang
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Guolin An
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Weihua Li
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Junpu Liu
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Dexi Sun
- The Key Laboratory of Genetic Resource Evaluation and Application of Horticultural Crops (Fruit), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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Wang S, Wang Y, Yu R, Yuan D, Ni Y, Wang L, Sun M, Wang X. Association of lipid profile and reported edentulism in the elder population: data from the China Health and Retirement Longitudinal Study. BMC Oral Health 2022; 22:445. [PMID: 36243707 PMCID: PMC9571461 DOI: 10.1186/s12903-022-02492-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
Objectives Relationship between lipid profile and periodontitis has been reported. However, the association between lipid parameters and edentulism is unclear. This study aimed to investigate the association between lipid profile and reported edentulism in the elder population using a national cohort. Methods A total of 3 100 participants aged 65 or above were enrolled in 2011 from China Health and Retirement Longitudinal Study, which was a national population-based survey. We used adjusted logistics models to investigate the relationship between lipid profile and reported edentulism before and after propensity score matching. Results The mean (SD) age was 71.96 (5.63) years, and 1 581 (51.0%) were men. There were 254 (8.2%) individuals reporting edentulism, and the low-density lipoprotein cholesterol (LDL-C) was significantly higher in the reported edentulism group, compared with the non-edentulism (122.48 vs. 116.91 mg/dl, P = 0.015). In the multivariable model, LDL-C was significantly associated with a higher odds of reported edentulism (adjusted OR [95% CI], 1.004 [1.001–1.008]). In the matched population, LDL-C, non high-density lipoprotein cholesterol, remnant cholesterol, total cholesterol and triglycerides were positively associated with reported edentulism, while HDL-C was negatively associated. Conclusions Lipid profiles are probably associated with edentulism, indicating the interaction between oral health and metabolic status in the elder population.
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Affiliation(s)
- Shuping Wang
- Department of Stomatology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yutao Wang
- Shanghai Fufan Information Technology Co., Ltd, No.323 Guoding Road, Yangpu District, Shanghai, 200433, China
| | - Riyue Yu
- Department of Stomatology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Dingxiang Yuan
- Department of Stomatology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yaofeng Ni
- Department of Stomatology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Lixin Wang
- Department of Stomatology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Man Sun
- Community Health Service Center, Huangcun Town, Daxing District, Beijing, China
| | - Xin Wang
- Department of VIP Dental Service, Beijing Stomatological Hospital, Capital Medical University, Beijing, China.
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10
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Feng J, Lu M, Li W, Li J, Meng P, Li Z, Gao X, Zhang Y. PPARγ alleviates peritoneal fibrosis progression along with promoting GLUT1 expression and suppressing peritoneal mesothelial cell proliferation. Mol Cell Biochem 2022; 477:1959-1971. [PMID: 35380292 PMCID: PMC9206601 DOI: 10.1007/s11010-022-04419-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 03/17/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Peritoneal fibrosis (PF) is commonly induced by bioincompatible dialysate exposure during peritoneal dialysis, but the underlying mechanisms remain elusive. This study aimed to investigate the roles of peroxisome proliferator-activated receptor gamma (PPARγ) in PF pathogenesis. METHODS Rat and cellular PF models were established by high glucose dialysate and lipopolysaccharide treatments. Serum creatinine, urea nitrogen, and glucose contents were detected by ELISA. Histological evaluation was done through H&E and Masson staining. GLUT1, PPARγ, and other protein expression were measured by qRT-PCR, western blotting, and IHC. PPARγ and GLUT1 subcellular distribution were detected using confocal microscopy. Cell proliferation was assessed by MTT and Edu staining. RESULTS Serum creatinine, urea nitrogen and glucose, and PPARγ and GLUT1 expression in rat PF model were reduced by PPARγ agonists Rosiglitazone or 15d-PGJ2 and elevated by antagonist GW9662. Rosiglitazone or 15d-PGJ2 repressed and GW9662 aggravated peritoneal fibrosis in rat PF model. PPARγ and GLUT1 were mainly localized in nucleus and cytosols of peritoneal mesothelial cells, respectively, which were reduced in cellular PF model, enhanced by Rosiglitazone or 15d-PGJ2, and repressed by GW9662. TGF-β and a-SMA expression was elevated in cellular PF model, which was inhibited by Rosiglitazone or 15d-PGJ2 and promoted by GW9662. PPARγ silencing reduced GLUT1, elevated a-SMA and TGF-b expression, and promoted peritoneal mesothelial cell proliferation, which were oppositely changed by PPARγ overexpression. CONCLUSION PPARγ inhibited high glucose-induced peritoneal fibrosis progression through elevating GLUT1 expression and repressing peritoneal mesothelial cell proliferation.
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Affiliation(s)
- Junxia Feng
- Department of Nephrology, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), 48 Xinhua Road, 510800, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Meizhi Lu
- Department of Nephrology, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), 48 Xinhua Road, 510800, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Wenhao Li
- Department of Nephrology, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), 48 Xinhua Road, 510800, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jingchun Li
- Department of Nephrology, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), 48 Xinhua Road, 510800, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Ping Meng
- Department of Nephrology, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), 48 Xinhua Road, 510800, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zukai Li
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xuejuan Gao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China.
| | - Yunfang Zhang
- Department of Nephrology, Affiliated Huadu Hospital, Southern Medical University (People's Hospital of Huadu District), 48 Xinhua Road, 510800, Guangzhou, China.
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China.
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11
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Xu H, Ye W, Shi B. LncRNA MALAT1 Regulates USP22 Expression Through EZH2-Mediated H3K27me3 Modification to Accentuate Sepsis-Induced Myocardial Dysfunction. Cardiovasc Toxicol 2022; 22:813-830. [PMID: 35726125 DOI: 10.1007/s12012-022-09758-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/03/2022] [Indexed: 11/29/2022]
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long non-coding RNA (lncRNA), has been confirmed to recruit enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) to regulate cardiomyocyte apoptosis in diabetic cardiomyopathy. However, whether the similar regulatory axis exists in sepsis-induced myocardial dysfunction (SIMD) has not been clearly established. The current study sought to define the mechanism governing MALAT1-mediated EZH2 in SIMD. MALAT1 was significantly upregulated in lipopolysaccharide-induced cardiomyocytes. Depletion of MALAT1 by caudal vein injection of small interfering RNA targeting MALAT1 alleviated myocardial injury in SIMD rats, restored cardiac function, reduced oxidative stress production and fibrosis, and inhibited inflammatory factors and apoptosis in myocardial tissues. Moreover, MALAT1 bound to EZH2 and promoted EZH2 activity in the nucleus of cardiomyocytes. EZH2 repressed ubiquitin-specific peptidase 22 (USP22) expression through H3K27me3 modification. EZH2 elevation aggravated the cardiac injury in SIMD rats, while USP22 upregulation inhibited the effect of EZH2, which reduced the cardiac injury in SIMD rats. Taken together, MALAT1 decreased USP22 expression by interacting with EZH2, thereby worsening SIMD, highlighting an attractive therapeutic strategy for SIMD.
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Affiliation(s)
- Hong Xu
- Department of Cardiovascular Division, Shandong Provincial Third Hospital, Jinan, 250031, Shandong, People's Republic of China
| | - Wei Ye
- Department of Respiratory Medicine, Shandong Provincial Third Hospital, Jinan, 250031, Shandong, People's Republic of China
| | - Baochang Shi
- Department of Hepatobiliary Surgery, Shandong Provincial Third Hospital, No. 12, WuYingShan Middle Road, Tianqiao District, Jinan, 250031, Shandong, People's Republic of China.
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12
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Choublier N, Taghi M, Menet MC, Le Gall M, Bruce J, Chafey P, Guillonneau F, Moreau A, Denizot C, Parmentier Y, Nakib S, Borderie D, Bouzinba-Segard H, Couraud PO, Bourdoulous S, Declèves X. Exposure of human cerebral microvascular endothelial cells hCMEC/D3 to laminar shear stress induces vascular protective responses. Fluids Barriers CNS 2022; 19:41. [PMID: 35658915 PMCID: PMC9164338 DOI: 10.1186/s12987-022-00344-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/23/2022] [Indexed: 01/01/2023] Open
Abstract
Endothelial cells (ECs) are constantly submitted in vivo to hemodynamical forces derived from the blood circulation, including shear stress (SS). ECs are able to detect SS and consequently adapt their phenotype, thus affecting many endothelial functions. If a plethora of shear stress-regulated molecular networks have been described in peripheral ECs, less is known about the molecular responses of microvascular brain ECs which constitute the blood-brain barrier (BBB). In this work, we investigated the response of human cerebral microvascular ECs to laminar physiological shear stress using the well characterized hCMEC/D3 cell line. Interestingly, we showed that hCMEC/D3 cells responded to shear stress by aligning perpendicularly to the flow direction, contrary to peripheral endothelial cells which aligned in the flow direction. Whole proteomic profiles were compared between hCMEC/D3 cells cultured either in static condition or under 5 or 10 dyn.cm-2 SS for 3 days. 3592 proteins were identified and expression levels were significantly affected for 3% of them upon both SS conditions. Pathway analyses were performed which revealed that most proteins overexpressed by SS refer to the antioxidant defense, probably mediated by activation of the NRF2 transcriptional factor. Regarding down-regulated proteins, most of them participate to the pro-inflammatory response, cell motility and proliferation. These findings confirm the induction of EC quiescence by laminar physiological SS and reveal a strong protective effect of SS on hCMEC/D3 cells, suggesting a similar effect on the BBB. Our results also showed that SS did not significantly increase expression levels nor did it affect the localization of junctional proteins and did not afect either the functional activity of several ABC transporters (P-glycoprotein and MRPs). This work provides new insights on the response of microvascular brain ECs to SS and on the importance of SS for optimizing in vitro BBB models.
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Affiliation(s)
- Nina Choublier
- INSERM, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, 75006, Paris, France.
| | - Meryam Taghi
- INSERM, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, 75006, Paris, France
| | - Marie-Claude Menet
- Institut de Chimie Physique, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Morgane Le Gall
- 3P5 Proteom'IC Facility, Institut Cochin, INSERM, CNRS, Université de Paris, F-75014, Paris, France
| | - Johanna Bruce
- 3P5 Proteom'IC Facility, Institut Cochin, INSERM, CNRS, Université de Paris, F-75014, Paris, France
| | - Philippe Chafey
- 3P5 Proteom'IC Facility, Institut Cochin, INSERM, CNRS, Université de Paris, F-75014, Paris, France
| | - François Guillonneau
- 3P5 Proteom'IC Facility, Institut Cochin, INSERM, CNRS, Université de Paris, F-75014, Paris, France
| | | | | | | | - Samir Nakib
- Service de Biochimie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, 75014, Paris, France
| | - Didier Borderie
- Service de Biochimie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, 75014, Paris, France
| | - Haniaa Bouzinba-Segard
- CNRS, INSERM, Institut Cochin, Inserm, CNRS, Université Paris Cité, 75014, Paris, France
| | - Pierre-Olivier Couraud
- CNRS, INSERM, Institut Cochin, Inserm, CNRS, Université Paris Cité, 75014, Paris, France
| | - Sandrine Bourdoulous
- CNRS, INSERM, Institut Cochin, Inserm, CNRS, Université Paris Cité, 75014, Paris, France
| | - Xavier Declèves
- INSERM, Optimisation Thérapeutique en Neuropsychopharmacologie, Université Paris Cité, 75006, Paris, France.
- Biologie du Médicament Et Toxicologie, AP-HP, Hôpital Cochin, 75014, Paris, France.
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13
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Choi W, Kim J, Ko JW, Choi A, Kwon YH. Effects of maternal branched-chain amino acid and alanine supplementation on growth and biomarkers of protein metabolism in dams fed a low-protein diet and their offspring. Amino Acids 2022; 54:977-988. [PMID: 35353249 DOI: 10.1007/s00726-022-03157-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/13/2022] [Indexed: 11/24/2022]
Abstract
A considerable number of studies have reported that maternal protein restriction may disturb fetal growth and organ development due to a lower availability of amino acids. Leucine, one of branched-chain amino acid (BCAA) promotes protein synthesis through mechanistic target of rapamycin signaling. Here, we investigated the effects of BCAA supplementation in the dams fed a low-protein diet on serum and hepatic biochemical parameters of protein metabolism of dams and their offspring. Female ICR mice were fed a control (20% casein), a low-protein (10% casein), a low-protein with 2% BCAAs or a low-protein with 2% alanine diet for 2 weeks before mating and then throughout pregnancy and lactation. Alanine was used as an amino nitrogen control for the BCAA. Dams and their male offspring were sacrificed at postnatal day 21. There were no changes in body weight and fat mass in low-protein fed dams; however, BCAA supplementation significantly increased fat mass and serum leptin levels. Low-protein diet consumption reduced maternal protein synthesis based on biochemical analysis of serum albumin and hepatic protein levels and immunoblotting of S6 protein, which were increased by BCAA and alanine supplementation. Offspring from dams fed a low-protein diet exhibited lower body and organ weights. Body weight and hepatic protein levels of the offspring were increased by alanine supplementation. However, the decreased serum biochemical parameters, including glucose, triglyceride, total protein and albumin levels in the low-protein offspring group were not changed in response to BCAA or alanine supplementation. A reduced density of the hepatic vessel system in the offspring from dams fed a low-protein diet was restored in the offspring from dams fed either BCAA and alanine-supplemented diet. These results suggest that supplementation of amino nitrogen per se may be responsible for inducing hepatic protein synthesis in the dams fed a low-protein diet and alleviating the distorted growth and liver development of their offspring.
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Affiliation(s)
- Wooseon Choi
- Department of Food and Nutrition, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea.,Department of Pharmacology, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Juhae Kim
- Department of Food and Nutrition, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Je Won Ko
- Department of Food and Nutrition, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Alee Choi
- Department of Food and Nutrition, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Young Hye Kwon
- Department of Food and Nutrition, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea. .,Research Institute of Human Ecology, Seoul National University, Seoul, South Korea.
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14
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Ebrahimnejad M, Azizi P, Alipour V, Zarrindast MR, Vaseghi S. Complicated Role of Exercise in Modulating Memory: A Discussion of the Mechanisms Involved. Neurochem Res 2022; 47:1477-1490. [PMID: 35195832 DOI: 10.1007/s11064-022-03552-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/15/2022]
Abstract
Evidence has shown the beneficial effects of exercise on learning and memory. However, many studies have reported controversial results, indicating that exercise can impair learning and memory. In this article, we aimed to review basic studies reporting inconsistent complicated effects of exercise on memory in rodents. Also, we discussed the mechanisms involved in the effects of exercise on memory processes. In addition, we tried to find scientific answers to justify the inconsistent results. In this article, the role of brain-derived neurotrophic factor (BDNF) and tropomyosin receptor kinase B (involved in synaptic plasticity and neurogenesis), and vascular endothelial growth factor, nerve growth factor, insulin-like growth factor 1, inflammatory markers, apoptotic factors, and antioxidant system was discussed in the modulation of exercise effects on memory. The role of intensity and duration of exercise, and type of memory task was also investigated. We also mentioned to the interaction of exercise with the function of neurotransmitter systems, which complicates the prediction of exercise effect via altering the level of BDNF. Eventually, we suggested that changes in the function of neurotransmitter systems following different types of exercise (depending on exercise intensity or age of onset) should be investigated in further studies. It seems that exercise-induced changes in the function of neurotransmitter systems may have a stronger role than age, type of memory task, or exercise intensity in modulating memory. Importantly, high levels of interactions between neurotransmitter systems and BDNF play a critical role in the modulation of exercise effects on memory performance.
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Affiliation(s)
- Mahshid Ebrahimnejad
- Department of Physiology, Faculty of Veterinary Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Paniz Azizi
- School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Vahide Alipour
- Department of Physical Education and Sport Sciences, Faculty of Humanities, Rasht Branch, Islamic Azad University, Rasht, Iran
| | - Mohammad-Reza Zarrindast
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Salar Vaseghi
- Medicinal Plants Research Center, Institute of Medicinal Plants, ACECR, P.O. Box: 1419815477, Karaj, Iran.
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15
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Li L, Chen Z, von Scheidt M, Li S, Steiner A, Güldener U, Koplev S, Ma A, Hao K, Pan C, Lusis AJ, Pang S, Kessler T, Ermel R, Sukhavasi K, Ruusalepp A, Gagneur J, Erdmann J, Kovacic JC, Björkegren JLM, Schunkert H. Transcriptome-wide association study of coronary artery disease identifies novel susceptibility genes. Basic Res Cardiol 2022; 117:6. [PMID: 35175464 PMCID: PMC8852935 DOI: 10.1007/s00395-022-00917-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/18/2022] [Accepted: 02/01/2022] [Indexed: 01/31/2023]
Abstract
The majority of risk loci identified by genome-wide association studies (GWAS) are in non-coding regions, hampering their functional interpretation. Instead, transcriptome-wide association studies (TWAS) identify gene-trait associations, which can be used to prioritize candidate genes in disease-relevant tissue(s). Here, we aimed to systematically identify susceptibility genes for coronary artery disease (CAD) by TWAS. We trained prediction models of nine CAD-relevant tissues using EpiXcan based on two genetics-of-gene-expression panels, the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) and the Genotype-Tissue Expression (GTEx). Based on these prediction models, we imputed gene expression of respective tissues from individual-level genotype data on 37,997 CAD cases and 42,854 controls for the subsequent gene-trait association analysis. Transcriptome-wide significant association (i.e. P < 3.85e-6) was observed for 114 genes. Of these, 96 resided within previously identified GWAS risk loci and 18 were novel. Stepwise analyses were performed to study their plausibility, biological function, and pathogenicity in CAD, including analyses for colocalization, damaging mutations, pathway enrichment, phenome-wide associations with human data and expression-traits correlations using mouse data. Finally, CRISPR/Cas9-based gene knockdown of two newly identified TWAS genes, RGS19 and KPTN, in a human hepatocyte cell line resulted in reduced secretion of APOB100 and lipids in the cell culture medium. Our CAD TWAS work (i) prioritized candidate causal genes at known GWAS loci, (ii) identified 18 novel genes to be associated with CAD, and iii) suggested potential tissues and pathways of action for these TWAS CAD genes.
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Affiliation(s)
- Ling Li
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
- Fakultät für Informatik, Technische Universität München, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Zhifen Chen
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Moritz von Scheidt
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Shuangyue Li
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Andrea Steiner
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Ulrich Güldener
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Simon Koplev
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Angela Ma
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Calvin Pan
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Aldons J Lusis
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Shichao Pang
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Thorsten Kessler
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Raili Ermel
- Department of Cardiac Surgery, The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Katyayani Sukhavasi
- Department of Cardiac Surgery, The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Arno Ruusalepp
- Department of Cardiac Surgery, The Heart Clinic, Tartu University Hospital, Tartu, Estonia
- Clinical Gene Networks AB, Stockholm, Sweden
| | - Julien Gagneur
- Fakultät für Informatik, Technische Universität München, Munich, Germany
| | - Jeanette Erdmann
- DZHK (German Research Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Jason C Kovacic
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, Australia
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY, 10029-6574, USA
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
- Clinical Gene Networks AB, Stockholm, Sweden
- Department of Medicine, Huddinge, Karolinska Institutet, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Heribert Schunkert
- Department of Cardiology, German Heart Center Munich, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany.
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany.
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16
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Zhang N, Pan H, Liang X, Xie J, Han W. The roles of transmembrane family proteins in the regulation of store-operated Ca 2+ entry. Cell Mol Life Sci 2022; 79:118. [PMID: 35119538 PMCID: PMC11071953 DOI: 10.1007/s00018-021-04034-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022]
Abstract
Store-operated Ca2+ entry (SOCE) is a major pathway for calcium signaling, which regulates almost every biological process, involving cell proliferation, differentiation, movement and death. Stromal interaction molecule (STIM) and ORAI calcium release-activated calcium modulator (ORAI) are the two major proteins involved in SOCE. With the deepening of studies, more and more proteins are found to be able to regulate SOCE, among which the transmembrane (TMEM) family proteins are worth paying more attention. In addition, the ORAI proteins belong to the TMEM family themselves. As the name suggests, TMEM family is a type of proteins that spans biological membranes including plasma membrane and membrane of organelles. TMEM proteins are in a large family with more than 300 proteins that have been already identified, while the functional knowledge about the proteins is preliminary. In this review, we mainly summarized the TMEM proteins that are involved in SOCE, to better describe a picture of the interaction between STIM and ORAI proteins during SOCE and its downstream signaling pathways, as well as to provide an idea for the study of the TMEM family proteins.
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Affiliation(s)
- Ningxia Zhang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Xiaojing Liang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiansheng Xie
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
- Laboratory of Cancer Biology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
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17
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Vitória JJM, Trigo D, da Cruz E Silva OAB. Revisiting APP secretases: an overview on the holistic effects of retinoic acid receptor stimulation in APP processing. Cell Mol Life Sci 2022; 79:101. [PMID: 35089425 PMCID: PMC11073327 DOI: 10.1007/s00018-021-04090-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 01/03/2023]
Abstract
Alzheimer's disease (AD) is the leading cause of dementia worldwide and is characterized by the accumulation of the β-amyloid peptide (Aβ) in the brain, along with profound alterations in phosphorylation-related events and regulatory pathways. The production of the neurotoxic Aβ peptide via amyloid precursor protein (APP) proteolysis is a crucial step in AD development. APP is highly expressed in the brain and is complexly metabolized by a series of sequential secretases, commonly denoted the α-, β-, and γ-cleavages. The toxicity of resulting fragments is a direct consequence of the first cleaving event. β-secretase (BACE1) induces amyloidogenic cleavages, while α-secretases (ADAM10 and ADAM17) result in less pathological peptides. Hence this first cleavage event is a prime therapeutic target for preventing or reverting initial biochemical events involved in AD. The subsequent cleavage by γ-secretase has a reduced impact on Aβ formation but affects the peptides' aggregating capacity. An array of therapeutic strategies are being explored, among them targeting Retinoic Acid (RA) signalling, which has long been associated with neuronal health. Additionally, several studies have described altered RA levels in AD patients, reinforcing RA Receptor (RAR) signalling as a promising therapeutic strategy. In this review we provide a holistic approach focussing on the effects of isoform-specific RAR modulation with respect to APP secretases and discuss its advantages and drawbacks in subcellular AD related events.
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Affiliation(s)
- José J M Vitória
- Department of Medical Sciences, Neurosciences and Signalling Group, Institute of Biomedicine, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Diogo Trigo
- Department of Medical Sciences, Neurosciences and Signalling Group, Institute of Biomedicine, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Odete A B da Cruz E Silva
- Department of Medical Sciences, Neurosciences and Signalling Group, Institute of Biomedicine, University of Aveiro, 3810-193, Aveiro, Portugal.
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Zhang Z, Wang J, Xing G, Li M, Li S. Integrating physiology, genetics, and transcriptome to decipher a new thermo-sensitive and light-sensitive virescent leaf gene mutant in cucumber. FRONTIERS IN PLANT SCIENCE 2022; 13:972620. [PMID: 36051299 PMCID: PMC9424728 DOI: 10.3389/fpls.2022.972620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/25/2022] [Indexed: 05/08/2023]
Abstract
Chloroplasts are the material basis of photosynthesis, and temperature and light severely affect chloroplast development and thus influence photosynthetic efficiency. This study identified a spontaneous virescent leaf mutant, SC311Y, whose cotyledons and true leaves were yellow and gradually turned green. However, temperature and light affected the process of turning green. In addition, this mutant (except at the seedling stage) had ruffled leaves with white stripes, sterile males, and poorly fertile female flowers. Genetic characteristics analysis revealed that the recessive gene controlled the virescent leaf. Two F2 populations mapped v-3 to the interval of 33.54-35.66 Mb on chromosome 3. In this interval, BSA-Seq, RNA-Seq, and cDNA sequence analyses revealed only one nonsynonymous mutation in the Csa3G042730 gene, which encoded the RNA exosome supercomplex subunit resurrection1 (RST1). Csa3G042730 was predicted to be the candidate gene controlling the virescent leaf, and the candidate gene may regulate chloroplast development by regulating plastid division2 (PDV2). A transcriptome analysis showed that different factors caused the reduced chlorophyll and carotenoid content in the mutants. To our knowledge, this study is the first report of map-based cloning related to virescent leaf, male-sterile, and chloroplast RNA regulation in cucumber. The results could accelerate the study of the RNA exosome supercomplex for the dynamic regulation of chloroplast RNA.
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Affiliation(s)
- Zhipeng Zhang
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving Quality and Increase of Protected Vegetables in Shanxi Province, Jinzhong, China
| | - Jinyao Wang
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving Quality and Increase of Protected Vegetables in Shanxi Province, Jinzhong, China
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving Quality and Increase of Protected Vegetables in Shanxi Province, Jinzhong, China
| | - Meilan Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving Quality and Increase of Protected Vegetables in Shanxi Province, Jinzhong, China
- *Correspondence: Meilan Li,
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving Quality and Increase of Protected Vegetables in Shanxi Province, Jinzhong, China
- Sen Li,
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Hwang S, Chung KW. Targeting fatty acid metabolism for fibrotic disorders. Arch Pharm Res 2021; 44:839-856. [PMID: 34664210 DOI: 10.1007/s12272-021-01352-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023]
Abstract
Fibrosis is defined by abnormal accumulation of extracellular matrix, which can affect virtually every organ system under diseased conditions. Fibrotic tissue remodeling often leads to organ dysfunction and is highly associated with increased morbidity and mortality. The disease burden caused by fibrosis is substantial, and the medical need for effective antifibrotic therapies is essential. Significant progress has been made in understanding the molecular mechanism and pathobiology of fibrosis, such as transforming growth factor-β (TGF-β)-mediated signaling pathways. However, owing to the complex and dynamic properties of fibrotic disorders, there are currently no therapeutic options that can prevent or reverse fibrosis. Recent studies have revealed that alterations in fatty acid metabolic processes are common mechanisms and core pathways that play a central role in different fibrotic disorders. Excessive lipid accumulation or defective fatty acid oxidation is associated with increased lipotoxicity, which directly contributes to the development of fibrosis. Genetic alterations or pharmacologic targeting of fatty acid metabolic processes have great potential for the inhibition of fibrosis development. Furthermore, mechanistic studies have revealed active interactions between altered metabolic processes and fibrosis development. Several well-known fibrotic factors change the lipid metabolic processes, while altered metabolic processes actively participate in fibrosis development. This review summarizes the recent evidence linking fatty acid metabolism and fibrosis, and provides new insights into the pathogenesis of fibrotic diseases for the development of drugs for fibrosis prevention and treatment.
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Affiliation(s)
- Seonghwan Hwang
- College of Pharmacy, Pusan National University, Busan, 46214, Republic of Korea
| | - Ki Wung Chung
- College of Pharmacy, Pusan National University, Busan, 46214, Republic of Korea.
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Kurt F, Filiz E, Aydın A. Genome-wide identification of serine acetyltransferase (SAT) gene family in rice (Oryza sativa) and their expressions under salt stress. Mol Biol Rep 2021; 48:6277-6290. [PMID: 34389920 DOI: 10.1007/s11033-021-06620-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/03/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Assimilation of sulfur to cysteine (Cys) occurs in presence of serine acetyltransferase (SAT). Drought and salt stresses are known to be regulated by abscisic acid, whose biosynthesis is limited by Cys. Cys is formed by cysteine synthase complex depending on SAT and OASTL enzymes. Functions of some SAT genes were identified in Arabidopsis; however, it is not known how SAT genes are regulated in rice (Oryza sativa) under salt stress. METHODS AND RESULTS Sequence, protein domain, gene structure, nucleotide, phylogenetic, selection, gene duplication, motif, synteny, digital expression and co-expression, secondary and tertiary protein structures, and binding site analyses were conducted. The wet-lab expressions of OsSAT genes were also tested under salt stress. OsSATs have underwent purifying selection. Segmental and tandem duplications may be driving force of structural and functional divergences of OsSATs. The digital expression analyses of OsSATs showed that jasmonic acid (JA) was the only hormone inducing the expressions of OsSAT1;1, OsSAT2;1, and OsSAT2;2 whereas auxin and ABA only triggered OsSAT1;1 expression. Leaf blade is the only plant organ where all OsSATs but OsSAT1;1 were expressed. Wet-lab expressions of OsSATs indicated that OsSAT1;1, OsSAT1;2 and OsSAT1;3 genes were upregulated at different exposure times of salt stress. CONCLUSIONS OsSAT1;1, expressed highly in rice roots, may be a hub gene regulated by cross-talk of JA, ABA and auxin hormones. The cross-talk of the mentioned hormones and the structural variations of OsSAT proteins may also explain the different responses of OsSATs to salt stress.
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Affiliation(s)
- Fırat Kurt
- Department of Plant Production and Technologies, Faculty of Applied Sciences, Mus Alparslan University, Mus, Turkey
| | - Ertugrul Filiz
- Department of Crop and Animal Production, Cilimli Vocational School, Duzce University, Cilimli, Duzce, Turkey.
| | - Adnan Aydın
- Department of Agricultural Biotechnology, Faculty of Agriculture, Iğdır University, Iğdır, Turkey
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Lew SQ, Lin CH. N-acetylglucosamine-mediated morphological transition in Candida albicans and Candida tropicalis. Curr Genet 2021; 67:249-254. [PMID: 33388851 DOI: 10.1007/s00294-020-01138-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Abstract
Morphological transitions in Candida species are key factors in facilitating invasion and adapting to environmental changes. N-acetylglucosamine (GlcNAc) is a monosaccharide signalling molecule that can regulate morphological transitions in Candida albicans and Candida tropicalis. Interestingly, although the uptake and metabolic pathways of GlcNAc and GlcNAc-mediated white-to-opaque cell switching are similar between the two Candida species, GlcNAc induces hyphal development in C. albicans, whereas it suppresses hyphal development in C. tropicalis. These findings indicate that the characteristics of C. albicans and C. tropicalis in response to GlcNAc are remarkably different. Here, we compare the conserved and divergent GlcNAc-mediated signalling pathways and catabolism between the two Candida species. Deletion of NGT1, a GlcNAc transportation gene, inhibited hyphal formation in C. albicans but promoted hyphal development in C. tropicalis. To further understand these opposite effects on filamentous growth in response to GlcNAc in the two Candida species, the cyclic adenosine monophosphate/protein kinase A (cAMP/PKA) signalling pathways in both C. albicans and C. tropicalis were compared. Interestingly, GlcNAc activated the cAMP/PKA signalling pathway of the two Candida species, suggesting that the hyphal development-regulated circuit is remarkably diverse between the two species. Indeed, the Ndt80-like gene REP1, which is critical for regulating GlcNAc catabolism, exhibits distinct roles in the hyphal development of C. albicans and C. tropicalis. These data suggest possible reasons for the divergent hyphal growth response in C. albicans and C. tropicalis upon GlcNAc induction.
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Affiliation(s)
- Shi Qian Lew
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ching-Hsuan Lin
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan.
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