Skeletal muscle regeneration is a complex process where various cell types and cytokines are involved.Single-cell RNA-sequencing (scRNA-seq) provides the opportunity to deconvolute heterogeneous tissue into individual...Skeletal muscle regeneration is a complex process where various cell types and cytokines are involved.Single-cell RNA-sequencing (scRNA-seq) provides the opportunity to deconvolute heterogeneous tissue into individual cells based on their transcriptomic profiles.Recent scRNA-seq studies on mouse muscle regeneration have provided insights to understand the transcriptional dynamics that underpin muscle regeneration.However,a database to investigate gene expression profiling during skeletal muscle regeneration at the single-cell level is lacking.Here,we collected over 105 000 cells at 7 key regenerative time-points and non-injured muscles and developed a database,the Singlecell Skeletal Muscle Regeneration Database (SCSMRD).SCSMRD allows users to search the dynamic expression profiles of genes of interest across different cell types during the skeletal muscle regeneration process.It also provides a network to show the activity of regulons in different cell types at different time points.Pesudotime analysis showed the state changes trajectory of muscle stem cells (MuSCs) during skeletal muscle regeneration.This database is freely available at https://scsmrd.fengs-lab.com.展开更多
Glycerol may be converted to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae under anaerobic conditions and glycerol dismutation involves two parallel pathways controlled by the dha regulon. In this study, a fourtee...Glycerol may be converted to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae under anaerobic conditions and glycerol dismutation involves two parallel pathways controlled by the dha regulon. In this study, a fourteen-dimensional nonlinear dynamic system is presented to describe the continuous culture and multiplicity analysis, in which two regulated negative-feedback mechanisms of repression and enzyme inhibition are investigated. The model describing the expression of gene-mRNA-enzyme-product was established according to the repression of the dha regulon by 3-hydroxypropionaldehy (3-HPA). Comparisons between simulated and experimental results indicate that the model can be used to describe the production of 1,3-PD under continuous fermentation. The new model is translated into the corresponding S-system version. The robustness of this model is discussed by using the S-system model and the sensitivity analysis shows that the model is sufficiently robust. The influences of initial glycerol concentration and dilution rate on the biosynthesis of 1,3-PD and the stability of the dha regulon model are investigated. The intracellular concentrations of glycerol, 1,3-PD, 3-HPA, repressor mRNA, repressor, mRNA and protein levels of glycerol dehydratase (GDHt) and 1,3-PD oxydoreductase (PDOR) can be predicted for continuous cultivation. The results of simulation and analysis indicate that 3-HPA accumulation will repress the expression of the dha regulon at the transcriptional level. This model gives new insights into the regulation of glycerol metabolism in K. pneumoniae and explain some of the experimental observations.展开更多
The Escherichia coil fadR protein product, a paradigm/ prototypical FadR regulator, positively regulates fabA and fabB, the two critical genes for unsaturated fatty acid （UFA） biosynthesis. However the scenario in t...The Escherichia coil fadR protein product, a paradigm/ prototypical FadR regulator, positively regulates fabA and fabB, the two critical genes for unsaturated fatty acid （UFA） biosynthesis. However the scenario in the other γ- proteobacteria, such as Shewanella with the marine ori- gin, is unusual in that Rodionov and coworkers predicted that only fabA （not fabB） has a binding site for FadR pro- tein. It raised the possibility of fad regulon contraction. Here we report that this is the case. Sequence alignment of the FadR homologs revealed that the N-terminal DNA- binding domain exhibited remarkable similarity, whereas the ligand-accepting motif at C-terminus is relatively-less conserved. The FadR homologue of S. oneidensis （re- ferred to FadR_she） was over-expressed and purified to homogeneity. Integrative evidence obtained by FPLC （fast protein liquid chromatography） and chemical cross. linking analyses elucidated that FadR_she protein can dimerize in solution, whose identity was determined by MALDI-TOF-MS. In vitro data from electrophoretic mobil. ity shift assays suggested that FadR_she is almost functionally-exchangeable/equivalent to E. coil FadR （FadR_ec） in the ability of binding the E. coil fabA （and fabB） promoters. In an agreement with that of E. coil fabA, S. oneidensis fabA promoter bound both FadR_she andFadR_ec, and was disassociated specifically with the FadR regulatory protein upon the addition of long-chain acyI-CoA thioesters. To monitor in vivo effect exerted by FadR on Shewanella fabA expression, the native pro- moter of S. oneidensis fabA was fused to a LacZ reporter gene to engineer a chromosome fabA-lacZtranscriptional fusion in E. coil. As anticipated, the removal of fadR gene gave about 2-fold decrement of Shewanella fabA expression by β-gal activity, which is almost identical to the inhibitory level by the addition of oleate. Therefore, we concluded that fabA is contracted to be the only one member of fad regulon in the context of fatty acid syn- thesis in the marine bacteria Shewanella genus.展开更多
【背景】OpaR是副溶血弧菌群体感应系统的核心调控因子;QsvR是AraC家族转录调控因子,与OpaR之间具有相互调控作用;此外,QsvR对基因表达的调控作用受OpaR的影响,但是影响程度并未完全阐明。【目的】探究在野生株(wild-type,WT)和opaR基...【背景】OpaR是副溶血弧菌群体感应系统的核心调控因子;QsvR是AraC家族转录调控因子,与OpaR之间具有相互调控作用;此外,QsvR对基因表达的调控作用受OpaR的影响,但是影响程度并未完全阐明。【目的】探究在野生株(wild-type,WT)和opaR基因突变株(ΔopaR)的遗传背景下QsvR的转录调控元,分析Opa R对QsvR基因表达调控的影响。【方法】分别以WT和ΔopaR为参照,采用Illumina HiSeq测序平台进行比较转录组学研究,分析生物膜形成条件下qsv R基因突变株(Δqsv R)和Δqsv RΔopaR的基因表达情况。【结果】在WT遗传背景下,QsvR共调控1735个基因的转录(调控元1),其中被激活的基因有855个,被抑制的基因有880个;在ΔopaR遗传背景下,QsvR共调控1 187个基因的转录(调控元2),其中被激活的基因有533个,被抑制的基因有654个。调控元1和调控元2之间共有517个重叠基因,且QsvR对绝大多数重叠基因的调控关系相反。基因属性分类(gene ontology, GO)数据库富集分析结果显示,调控元1和调控元2中分别有467个和204个基因注释到分子功能、细胞组分和生物学过程3个一级分类和30个二级分类;京都基因和基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)对代谢途径的分析结果显示,调控元1和调控元2中分别有372和678个基因归到30个代谢通路中(Q value<0.05),调控元1中的基因主要集中在代谢、基因信息处理和环境信息处理上,而调控元2中的基因主要集中在细胞代谢通路上。蛋白相邻类的聚簇(cluster of orthologous groups of proteins, COG)数据库分类结果显示,调控元1和调控元2中的基因主要涉及氨基酸转运与代谢、信号转导、能量产生与转换、一般功能预测基因和未知功能基因等。此外,调控元1和调控元2中还含有大量调控因子基因和推定的c-di-GMP代谢基因,以及若干极生鞭毛基因、荚膜多糖基因、胞外多糖合成基因、Ⅳ型菌毛合成基因、Ⅲ型分泌系统基因和Ⅵ型分泌系统基因等。【结论】QsvR是副溶血弧菌中的全局性调控因子,控制着大量基因的转录。QsvR对靶基因的调控关系及QsvR调控元组成均受OpaR的影响。展开更多
基金supported by the National Natural Science Foundation of China(31972539 and 32102513)the Science,Technology,and Innovation Commission of Shenzhen Municipality,China(JCYJ20180306173644635)+2 种基金the Fundamental Research Funds for the Central Universities,China(G2020KY05109)the Natural Science Basic Research Program of Shaanxi Province,China(2022JQ-644)the Basic Research Programs of Taicang,China(TC2021JC14)。
文摘Skeletal muscle regeneration is a complex process where various cell types and cytokines are involved.Single-cell RNA-sequencing (scRNA-seq) provides the opportunity to deconvolute heterogeneous tissue into individual cells based on their transcriptomic profiles.Recent scRNA-seq studies on mouse muscle regeneration have provided insights to understand the transcriptional dynamics that underpin muscle regeneration.However,a database to investigate gene expression profiling during skeletal muscle regeneration at the single-cell level is lacking.Here,we collected over 105 000 cells at 7 key regenerative time-points and non-injured muscles and developed a database,the Singlecell Skeletal Muscle Regeneration Database (SCSMRD).SCSMRD allows users to search the dynamic expression profiles of genes of interest across different cell types during the skeletal muscle regeneration process.It also provides a network to show the activity of regulons in different cell types at different time points.Pesudotime analysis showed the state changes trajectory of muscle stem cells (MuSCs) during skeletal muscle regeneration.This database is freely available at https://scsmrd.fengs-lab.com.
基金Supported by the National High Technology Research and Development Program of China (2007AA02Z208)the State Key Development Program for Basic Research of China (2007CB714304)
文摘Glycerol may be converted to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae under anaerobic conditions and glycerol dismutation involves two parallel pathways controlled by the dha regulon. In this study, a fourteen-dimensional nonlinear dynamic system is presented to describe the continuous culture and multiplicity analysis, in which two regulated negative-feedback mechanisms of repression and enzyme inhibition are investigated. The model describing the expression of gene-mRNA-enzyme-product was established according to the repression of the dha regulon by 3-hydroxypropionaldehy (3-HPA). Comparisons between simulated and experimental results indicate that the model can be used to describe the production of 1,3-PD under continuous fermentation. The new model is translated into the corresponding S-system version. The robustness of this model is discussed by using the S-system model and the sensitivity analysis shows that the model is sufficiently robust. The influences of initial glycerol concentration and dilution rate on the biosynthesis of 1,3-PD and the stability of the dha regulon model are investigated. The intracellular concentrations of glycerol, 1,3-PD, 3-HPA, repressor mRNA, repressor, mRNA and protein levels of glycerol dehydratase (GDHt) and 1,3-PD oxydoreductase (PDOR) can be predicted for continuous cultivation. The results of simulation and analysis indicate that 3-HPA accumulation will repress the expression of the dha regulon at the transcriptional level. This model gives new insights into the regulation of glycerol metabolism in K. pneumoniae and explain some of the experimental observations.
文摘The Escherichia coil fadR protein product, a paradigm/ prototypical FadR regulator, positively regulates fabA and fabB, the two critical genes for unsaturated fatty acid （UFA） biosynthesis. However the scenario in the other γ- proteobacteria, such as Shewanella with the marine ori- gin, is unusual in that Rodionov and coworkers predicted that only fabA （not fabB） has a binding site for FadR pro- tein. It raised the possibility of fad regulon contraction. Here we report that this is the case. Sequence alignment of the FadR homologs revealed that the N-terminal DNA- binding domain exhibited remarkable similarity, whereas the ligand-accepting motif at C-terminus is relatively-less conserved. The FadR homologue of S. oneidensis （re- ferred to FadR_she） was over-expressed and purified to homogeneity. Integrative evidence obtained by FPLC （fast protein liquid chromatography） and chemical cross. linking analyses elucidated that FadR_she protein can dimerize in solution, whose identity was determined by MALDI-TOF-MS. In vitro data from electrophoretic mobil. ity shift assays suggested that FadR_she is almost functionally-exchangeable/equivalent to E. coil FadR （FadR_ec） in the ability of binding the E. coil fabA （and fabB） promoters. In an agreement with that of E. coil fabA, S. oneidensis fabA promoter bound both FadR_she andFadR_ec, and was disassociated specifically with the FadR regulatory protein upon the addition of long-chain acyI-CoA thioesters. To monitor in vivo effect exerted by FadR on Shewanella fabA expression, the native pro- moter of S. oneidensis fabA was fused to a LacZ reporter gene to engineer a chromosome fabA-lacZtranscriptional fusion in E. coil. As anticipated, the removal of fadR gene gave about 2-fold decrement of Shewanella fabA expression by β-gal activity, which is almost identical to the inhibitory level by the addition of oleate. Therefore, we concluded that fabA is contracted to be the only one member of fad regulon in the context of fatty acid syn- thesis in the marine bacteria Shewanella genus.
文摘【背景】OpaR是副溶血弧菌群体感应系统的核心调控因子;QsvR是AraC家族转录调控因子,与OpaR之间具有相互调控作用;此外,QsvR对基因表达的调控作用受OpaR的影响,但是影响程度并未完全阐明。【目的】探究在野生株(wild-type,WT)和opaR基因突变株(ΔopaR)的遗传背景下QsvR的转录调控元,分析Opa R对QsvR基因表达调控的影响。【方法】分别以WT和ΔopaR为参照,采用Illumina HiSeq测序平台进行比较转录组学研究,分析生物膜形成条件下qsv R基因突变株(Δqsv R)和Δqsv RΔopaR的基因表达情况。【结果】在WT遗传背景下,QsvR共调控1735个基因的转录(调控元1),其中被激活的基因有855个,被抑制的基因有880个;在ΔopaR遗传背景下,QsvR共调控1 187个基因的转录(调控元2),其中被激活的基因有533个,被抑制的基因有654个。调控元1和调控元2之间共有517个重叠基因,且QsvR对绝大多数重叠基因的调控关系相反。基因属性分类(gene ontology, GO)数据库富集分析结果显示,调控元1和调控元2中分别有467个和204个基因注释到分子功能、细胞组分和生物学过程3个一级分类和30个二级分类;京都基因和基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)对代谢途径的分析结果显示,调控元1和调控元2中分别有372和678个基因归到30个代谢通路中(Q value<0.05),调控元1中的基因主要集中在代谢、基因信息处理和环境信息处理上,而调控元2中的基因主要集中在细胞代谢通路上。蛋白相邻类的聚簇(cluster of orthologous groups of proteins, COG)数据库分类结果显示,调控元1和调控元2中的基因主要涉及氨基酸转运与代谢、信号转导、能量产生与转换、一般功能预测基因和未知功能基因等。此外,调控元1和调控元2中还含有大量调控因子基因和推定的c-di-GMP代谢基因,以及若干极生鞭毛基因、荚膜多糖基因、胞外多糖合成基因、Ⅳ型菌毛合成基因、Ⅲ型分泌系统基因和Ⅵ型分泌系统基因等。【结论】QsvR是副溶血弧菌中的全局性调控因子,控制着大量基因的转录。QsvR对靶基因的调控关系及QsvR调控元组成均受OpaR的影响。
