临床患者血培养分离出卡明斯假谷氨酸杆菌的全基因组测序及基因功能分析  

Whole Genome Sequencing and Gene Function Analysis of Pseudoglutamicibacter Cumminsii Isolated from Blood Culture of Clinical Patients

作　　者：许楠[1] 杨旭东 田莹 刘泽世[1] 薛丽[1] 高宁[1] 耿燕[1] XU Nan;YANG Xu-dong;TIAN Ying;LIU Ze-shi;XUE Li;GAO Ning;GENG Yan(Department of Clinical Laboratory,the Second Affiliated Hospital of Xi’an Jiaotong University,Xi’an 710004,China;Department of Biochemistry and Molecular Biology,Basic Medicine College,Health Science Center of Xi’an Jiaotong University,Xi’an 710061,China)

机构地区：[1]西安交通大学第二附属医院检验科,西安710004 [2]西安交通大学医学部基础医学院生物化学与分子生物学系,西安710061

出　　处：《现代检验医学杂志》2023年第3期58-64,共7页Journal of Modern Laboratory Medicine

摘　　要：目的 应用全基因组测序及生物信息学分析方法对一株分离自腹膜间皮瘤患者血液标本中的卡明斯假谷氨酸杆菌菌株进行基因测序和功能分析。方法 于2018年8月2日~8月15日,两次从临床患者血液中分离出的微生物经基质辅助激光解析电离-飞行时间质谱(matrix-assisted laser desorption ionization time-of-flight mass spectrometry,MALDI-TOF)鉴定为卡明斯假谷氨酸杆菌。应用基因组测序软件构建、自组装的基因功能表注释器及anti SMASH等软件预测其次级代谢反应和产物蛋白生物合成调控相关的基因及基因簇。通过查询COG,KEGG,GO,NR,CAzy和SwissProt数据库对预测的基因进行功能注释。结果 卡明斯假谷氨酸杆菌基因组经过重组装、分析筛选及基因序列整合筛选和优化,得到了约300个Scaffolds,总长度约2 456 693bp,GC含量平均约为58.39%。分析发现其中约有2 097个编码基因,1 431个功能注释蛋白。其中427个蛋白功能未知,KEGG预测到的编码蛋白主要集中在碳水化合物代谢、氨基酸代谢、能量代谢、维生素代谢、脂类代谢和遗传信息传递和表达等通路。CAZy注释发现27个碳水化合物代谢相关酶,通过基因序列比对识别出21个与β-内酯合成有关的次级代谢基因,序列分析发现89个抗药性基因。结论 首次成功全面深入分析了卡明斯假谷氨酸杆菌的基因组序列,为今后研究该菌株的代谢特点、致病性及抗药性奠定了基础。Objective A Pseudoglutamicibacter cumminsii strain was isolated from blood samples of patients with peritoneal mesothelioma,and its genome was sequenced and its gene function was analyzed.Methods On 2 August and 15 August 2018,the microorganisms isolated from the blood of clinical patients were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry(MALDI-TOF)as Pseudoglutamicibacter cumminsii.Using genome sequencing software,selfassembled gene menu annotator and anti SMASH software,etc,the genes and gene clusters related to its secondary metabolic reaction and biosynthesis regulation of product protein were predicted respectively.The predicted genes were annotated by querying COG,KEGG,GO,NR,CAzy and Swiss-Prot databases.Results After reassembly,analysis and screening,gene sequence integration and screening and optimization of Pseudoglutamicibacter cumminsii genome,about 300 Scaffolds were obtained.The total length was roughly estimated to be about 2456693bp,and the average GC content was only about 58.39%.After analysis,it was predicted to contain about 2097 coding genes.By comparison,1431 proteins were annotated.Among them,427 had unknown functions.The encoded proteins predicted by KEGG were mainly enriched in the function of carbohydrate metabolism,amino acid metabolism,energy metabolism,vitamin metabolism,lipid metabolism and the transmission and expression of genetic information.Twenty-seven enzymes related to carbohydrate metabolism were identified by CAZy annotation.Twenty-one secondary metabolic genes related toβ-lactone synthesis were identified by gene sequence alignment,and the sequence analysis revealed 89 resistance genes.Conclusion The genome sequence of Pseudoglutamicibacter cumminsii was successfully analyzed for the first time,laiing a foundation for the future study of its metabolic characteristics,pathogenicity and drug resistance.

关 键 词：卡明斯假谷氨酸杆菌 全基因组测序 基因注释 

分 类 号：R378[医药卫生—病原生物学] Q786[医药卫生—基础医学]