【目的】以新疆不同地域、不同人群来源的长双歧杆菌长亚种(Bifidobacterium longum subsp.longum)为研究对象,解析肠道专性共栖细菌在宿主人群中的系统发育和基因组多样性,为针对不同人群开发个性化功能益生菌提供理论依据。【方法】...【目的】以新疆不同地域、不同人群来源的长双歧杆菌长亚种(Bifidobacterium longum subsp.longum)为研究对象,解析肠道专性共栖细菌在宿主人群中的系统发育和基因组多样性,为针对不同人群开发个性化功能益生菌提供理论依据。【方法】从地理跨度较大的新疆喀什、伊犁的维吾尔族和哈萨克族母婴人群中分离出136株B.longum subsp.longum,并通过公共数据库整合来自国内其他地域人群的菌株进行比较基因组分析。【结果】B.longum subsp.longum基因组的平均大小、G+C含量、编码序列数量分别为2.38 Mb、59.91%、2160个。基于核心基因构建的系统发育树显示,来自新疆的所有菌株在系统发育树上属于4个进化支(clade),来自同一民族、不同地域人群的菌株其系统发育呈现不同的进化支,地理上更相近、不同人群来源的菌株存在一定程度的重叠。对更大地理范围(全中国)的分析显示,B.longum subsp.longum菌株呈现明显的东西部地理来源聚集特征和协同进化现象。基于附属基因和碳水化合物代谢功能基因的分析显示,来源于同一系统发育进化支的同一民族、不同地域人群菌株的功能基因谱丰度也差异较大;碳水化合物水解酶家族GH13(α-淀粉酶)和GH43(β-木糖苷酶)等在喀什地区菌株基因组中更为丰富;相反,地理上相近、即使来自不同民族人群的菌株,其基因组中蛋白质直系同源簇(cluster of orthologous groups of proteins,COG)功能基因谱、碳水化合物水解酶关联基因家族谱更相似。【结论】新疆不同地域人群来源的B.longum subsp.longum菌株系统发育呈现明显的地理和民族分布特征以及功能基因分布特征,地理尺度范围越大,菌株的地理分布特征越明显。需要基于更大范围菌株基因组的大数据进一步验证人群的地理分布尺度与菌株协同进化和特异性的关系。展开更多
Fusarium crown rot(FCR),predominantly caused by Fusarium pseudograminearum,has been listed as a Category Ⅱ disease in six provinces of China,posing a significant threat to wheat production.The phenylpyrrole fungicide...Fusarium crown rot(FCR),predominantly caused by Fusarium pseudograminearum,has been listed as a Category Ⅱ disease in six provinces of China,posing a significant threat to wheat production.The phenylpyrrole fungicide fludioxonil is a key agent for FCR control.Previous studies indicated that resistance to fludioxonil in F.pseudograminearum is primarily associated with altered expression levels of the FpOS1 gene,which encodes a hybrid histidine kinase.However,the roles of mutations in other FpOS genes and the molecular interactions between FpOS proteins and fludioxonil remain elusive.To address these gaps,we generated 16 fludioxonil-resistant mutants with heritable resistance traits by in vitro selection of four sensitive F.pseudograminearum isolates.These mutants exhibited high resistance levels,with resistance factors(RF)ranging from 633.73 to 8617.07.Compared to their parental isolates,the resistant mutants showed significantly reduced mycelial growth rate,sporulation capacity,and pathogenicity.They were also more sensitive to ionic,osmotic,and oxidative stresses and displayed compromised cell wall and membrane integrity.Fludioxonil demonstrated no cross-resistance with tebuconazole or pydiflumetofen;however,it exhibited weak positive crossresistance to pyraclostrobin and moderate positive cross-resistance to iprodione.Fludioxonil treatment significantly promoted glycerol synthesis and inhibited deoxynivalenol(DON)production in parental isolates,whereas these regulatory effects were markedly attenuated in the resistant mutants.Mutation analysis identified mutation sites in FpOS1,FpOS4,and FpOS5 genes,with a lower mutation frequency in FpOS1 and no mutations detected in FpOS2.Molecular docking indicated that amino acid substitutions in FpOS4 and FpOS5 significantly reduced the binding affinity of fludioxonil to these target proteins.In conclusion,F.pseudograminearum poses a moderate risk of resistance to fludioxonil.Point mutations in FpOS4 and FpOS5 genes emerge as key molecular drivers of resistance,likely by diminishing the binding affinity between the fungicide and its proteins.This study clarifies the molecular basis of fludioxonil resistance in F.pseudograminearum and provides a scientific rationale for the judicious use of this fungicide in managing FCR.展开更多
Small RNAs(sRNAs)are important non-coding RNAs that usually play crucial roles in gene expression at the post-transcriptional level.The sRNAs have mostly been investigated in model microorganisms such as Escherichia c...Small RNAs(sRNAs)are important non-coding RNAs that usually play crucial roles in gene expression at the post-transcriptional level.The sRNAs have mostly been investigated in model microorganisms such as Escherichia coli and some pathogens.Nevertheless,microbial sRNAs from extreme environments such as the polar regions and deep sea have recently been discovered and analyzed for their unique roles in stress response,metabolic regulation and adaptation to extreme environments.These sRNAs fine-tune gene expression during oxidative and radiation stress,and modulate temperature and osmotic pressure responses.Representative sRNAs and their functions in thermophilic,psychrophilic,halophilic and radiation-tolerant bacteria are summarized in this review.Despite challenges in sample collection,RNA isolation,and functional annotation,the study of sRNAs in extreme environments provides opportunities for discovering novel regulatory mechanisms,applying them to biotechnology,and advancing our understanding of evolutionary adaptations.Looking ahead,high-throughput sequencing,synthetic biology,and multi-omics integration will bring new breakthroughs in discovering novel sRNAs and their functions and regulatory mechanisms.Such advancements are poised to enable comprehensive characterization of sRNA-mediated regulatory networks in extremophiles and unlock their biotechnological potential through mechanism-driven applications.展开更多
文摘【目的】以新疆不同地域、不同人群来源的长双歧杆菌长亚种(Bifidobacterium longum subsp.longum)为研究对象,解析肠道专性共栖细菌在宿主人群中的系统发育和基因组多样性,为针对不同人群开发个性化功能益生菌提供理论依据。【方法】从地理跨度较大的新疆喀什、伊犁的维吾尔族和哈萨克族母婴人群中分离出136株B.longum subsp.longum,并通过公共数据库整合来自国内其他地域人群的菌株进行比较基因组分析。【结果】B.longum subsp.longum基因组的平均大小、G+C含量、编码序列数量分别为2.38 Mb、59.91%、2160个。基于核心基因构建的系统发育树显示,来自新疆的所有菌株在系统发育树上属于4个进化支(clade),来自同一民族、不同地域人群的菌株其系统发育呈现不同的进化支,地理上更相近、不同人群来源的菌株存在一定程度的重叠。对更大地理范围(全中国)的分析显示,B.longum subsp.longum菌株呈现明显的东西部地理来源聚集特征和协同进化现象。基于附属基因和碳水化合物代谢功能基因的分析显示,来源于同一系统发育进化支的同一民族、不同地域人群菌株的功能基因谱丰度也差异较大;碳水化合物水解酶家族GH13(α-淀粉酶)和GH43(β-木糖苷酶)等在喀什地区菌株基因组中更为丰富;相反,地理上相近、即使来自不同民族人群的菌株,其基因组中蛋白质直系同源簇(cluster of orthologous groups of proteins,COG)功能基因谱、碳水化合物水解酶关联基因家族谱更相似。【结论】新疆不同地域人群来源的B.longum subsp.longum菌株系统发育呈现明显的地理和民族分布特征以及功能基因分布特征,地理尺度范围越大,菌株的地理分布特征越明显。需要基于更大范围菌株基因组的大数据进一步验证人群的地理分布尺度与菌株协同进化和特异性的关系。
基金Supported by Funding from the Henan Provincial Scientific and Technological Breakthrough Project(No.242102111113).
文摘Fusarium crown rot(FCR),predominantly caused by Fusarium pseudograminearum,has been listed as a Category Ⅱ disease in six provinces of China,posing a significant threat to wheat production.The phenylpyrrole fungicide fludioxonil is a key agent for FCR control.Previous studies indicated that resistance to fludioxonil in F.pseudograminearum is primarily associated with altered expression levels of the FpOS1 gene,which encodes a hybrid histidine kinase.However,the roles of mutations in other FpOS genes and the molecular interactions between FpOS proteins and fludioxonil remain elusive.To address these gaps,we generated 16 fludioxonil-resistant mutants with heritable resistance traits by in vitro selection of four sensitive F.pseudograminearum isolates.These mutants exhibited high resistance levels,with resistance factors(RF)ranging from 633.73 to 8617.07.Compared to their parental isolates,the resistant mutants showed significantly reduced mycelial growth rate,sporulation capacity,and pathogenicity.They were also more sensitive to ionic,osmotic,and oxidative stresses and displayed compromised cell wall and membrane integrity.Fludioxonil demonstrated no cross-resistance with tebuconazole or pydiflumetofen;however,it exhibited weak positive crossresistance to pyraclostrobin and moderate positive cross-resistance to iprodione.Fludioxonil treatment significantly promoted glycerol synthesis and inhibited deoxynivalenol(DON)production in parental isolates,whereas these regulatory effects were markedly attenuated in the resistant mutants.Mutation analysis identified mutation sites in FpOS1,FpOS4,and FpOS5 genes,with a lower mutation frequency in FpOS1 and no mutations detected in FpOS2.Molecular docking indicated that amino acid substitutions in FpOS4 and FpOS5 significantly reduced the binding affinity of fludioxonil to these target proteins.In conclusion,F.pseudograminearum poses a moderate risk of resistance to fludioxonil.Point mutations in FpOS4 and FpOS5 genes emerge as key molecular drivers of resistance,likely by diminishing the binding affinity between the fungicide and its proteins.This study clarifies the molecular basis of fludioxonil resistance in F.pseudograminearum and provides a scientific rationale for the judicious use of this fungicide in managing FCR.
基金supported by the National Natural Science Foundation of China(Grant nos.42476264,41976224).
文摘Small RNAs(sRNAs)are important non-coding RNAs that usually play crucial roles in gene expression at the post-transcriptional level.The sRNAs have mostly been investigated in model microorganisms such as Escherichia coli and some pathogens.Nevertheless,microbial sRNAs from extreme environments such as the polar regions and deep sea have recently been discovered and analyzed for their unique roles in stress response,metabolic regulation and adaptation to extreme environments.These sRNAs fine-tune gene expression during oxidative and radiation stress,and modulate temperature and osmotic pressure responses.Representative sRNAs and their functions in thermophilic,psychrophilic,halophilic and radiation-tolerant bacteria are summarized in this review.Despite challenges in sample collection,RNA isolation,and functional annotation,the study of sRNAs in extreme environments provides opportunities for discovering novel regulatory mechanisms,applying them to biotechnology,and advancing our understanding of evolutionary adaptations.Looking ahead,high-throughput sequencing,synthetic biology,and multi-omics integration will bring new breakthroughs in discovering novel sRNAs and their functions and regulatory mechanisms.Such advancements are poised to enable comprehensive characterization of sRNA-mediated regulatory networks in extremophiles and unlock their biotechnological potential through mechanism-driven applications.
