新根瘤菌属(Neorhizobium)隶属于根瘤菌科(Rhizobiaceae),目前有效发布了8个种。为了探究该属下不同模式菌株的全基因组分子机理和遗传特征,本文采用Prodigal等软件对这8个模式菌株的全基因组序列进行基因预测、功能注释和系统发育分析...新根瘤菌属(Neorhizobium)隶属于根瘤菌科(Rhizobiaceae),目前有效发布了8个种。为了探究该属下不同模式菌株的全基因组分子机理和遗传特征,本文采用Prodigal等软件对这8个模式菌株的全基因组序列进行基因预测、功能注释和系统发育分析,并在此基础上进行了基因组比较分析。基因组预测结果显示,这8个模式菌株的CDS(Coding Sequences)数量为4471~6669个,GC含量在60.0%至61.6%之间,rRNA数量为3至9个,tRNA数量为43至51个。通过比较基因组分析发现,所有菌株共享的直系同源基因簇有2563个,独立拥有的基因簇数量少。通过平均核苷酸一致性(ANI)、数字DNA-DNA杂交(dDDH)和系统发育树的分析,发现菌株CCBAU 05176^(T)和菌株T17_20^(T)具有最高的同源性,而菌株T786^(T)和NTR19^(T)的遗传距离最远。COG(Cluster of Orthologous Groups of Proteins)和KEGG(Kyoto Encyclopedia of Genes and Genomes)分类的比较分析显示,注释的基因功能整体差异较小,但在SL-1T中,异种生物的生物降解和代谢的注释比例和数量明显高于其他模式菌株。本研究为新根瘤菌属的系统分类以及在生态系统中的应用奠定了理论基础。展开更多
Acetobacteraceae has garnered significant attention because of its unique properties and the broad applications of the bacterial cellulose it produces.However,unlike model strains,Acetobacteraceae have few synthetic b...Acetobacteraceae has garnered significant attention because of its unique properties and the broad applications of the bacterial cellulose it produces.However,unlike model strains,Acetobacteraceae have few synthetic biology applications because they are difficult to manipulate genetically and have insufficient genetic regulatory elements,among other factors.To address this limitation,this study characterized the fundamental properties and synthetic biology elements of three commonly used bacterial cellulose-producing strains.First,the basic characteristics of the three strains,including their cellulose film production ability,division time,antibiotic susceptibility,and plasmid features,were analyzed.Two inducible promoters(pTrc and pLux101)were subsequently characterized within the three strains.The inducibility of the pTrc promoter was relatively low across the three strains(induction ratio:1.98–6.39),whereas the pLux101 promoter demonstrated a significantly greater level of inducibility within the three strains(induction ratio:87.28–216.71).Finally,through gene knockout experiments,this study identified four genes essential for bacterial cellulose film production in the genome of the Gluconacetobacter hansenii ATCC 5358 strain.This study not only enriches the library of synthetic biology elements in nonmodel strains,but also lays the foundation for the synthetic biology applications of Acetobacteraceae.展开更多
文摘新根瘤菌属(Neorhizobium)隶属于根瘤菌科(Rhizobiaceae),目前有效发布了8个种。为了探究该属下不同模式菌株的全基因组分子机理和遗传特征,本文采用Prodigal等软件对这8个模式菌株的全基因组序列进行基因预测、功能注释和系统发育分析,并在此基础上进行了基因组比较分析。基因组预测结果显示,这8个模式菌株的CDS(Coding Sequences)数量为4471~6669个,GC含量在60.0%至61.6%之间,rRNA数量为3至9个,tRNA数量为43至51个。通过比较基因组分析发现,所有菌株共享的直系同源基因簇有2563个,独立拥有的基因簇数量少。通过平均核苷酸一致性(ANI)、数字DNA-DNA杂交(dDDH)和系统发育树的分析,发现菌株CCBAU 05176^(T)和菌株T17_20^(T)具有最高的同源性,而菌株T786^(T)和NTR19^(T)的遗传距离最远。COG(Cluster of Orthologous Groups of Proteins)和KEGG(Kyoto Encyclopedia of Genes and Genomes)分类的比较分析显示,注释的基因功能整体差异较小,但在SL-1T中,异种生物的生物降解和代谢的注释比例和数量明显高于其他模式菌株。本研究为新根瘤菌属的系统分类以及在生态系统中的应用奠定了理论基础。
文摘Acetobacteraceae has garnered significant attention because of its unique properties and the broad applications of the bacterial cellulose it produces.However,unlike model strains,Acetobacteraceae have few synthetic biology applications because they are difficult to manipulate genetically and have insufficient genetic regulatory elements,among other factors.To address this limitation,this study characterized the fundamental properties and synthetic biology elements of three commonly used bacterial cellulose-producing strains.First,the basic characteristics of the three strains,including their cellulose film production ability,division time,antibiotic susceptibility,and plasmid features,were analyzed.Two inducible promoters(pTrc and pLux101)were subsequently characterized within the three strains.The inducibility of the pTrc promoter was relatively low across the three strains(induction ratio:1.98–6.39),whereas the pLux101 promoter demonstrated a significantly greater level of inducibility within the three strains(induction ratio:87.28–216.71).Finally,through gene knockout experiments,this study identified four genes essential for bacterial cellulose film production in the genome of the Gluconacetobacter hansenii ATCC 5358 strain.This study not only enriches the library of synthetic biology elements in nonmodel strains,but also lays the foundation for the synthetic biology applications of Acetobacteraceae.
