Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function.
Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function.
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DOI：
10.1073/pnas.1801247115
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发表时间：
2018-05-08
影响因子：
11.1
通讯作者：
Murphy BT
中科院分区：
文献类型：
--
作者：
Clark CM;Costa MS;Sanchez LM;Murphy BT
质谱学是一种强大的技术，已被用于通过细菌的蛋白质含量来识别细菌，并通过分析其专门的代谢物来评估细菌的功能特征。然而，到目前为止，这些分析都是独立进行的，这导致无法快速将细菌系统发育鉴定与潜在的环境功能联系起来。为了弥补这一差距，我们设计了MALDI-TOF质谱学数据采集和生物信息学管道(IDBac)，以集成直接来自琼脂上生长的细菌细胞的完整蛋白质和专门代谢物光谱的数据。这项技术将细菌组织成高度相似的系统发育组，并允许在短短几个小时内比较数百个菌株的新陈代谢差异。几十年来，研究人员一直缺乏快速将微生物身份与细菌新陈代谢联系起来的能力。由于专门化代谢物对细菌在环境中的功能和生存至关重要，我们设计了一种数据采集和生物信息学技术(IDBac)，该技术利用原位基质辅助激光解吸/电离飞行时间质谱仪(MALDI-TOF MS)来分析从琼脂平板上采集的单个细菌菌落记录的蛋白质和专门化代谢物光谱。我们证明了我们的方法的力量，通过区分两个枯草芽孢杆菌菌株在-lt；30分钟仅基于他们的区别能力产生环肽抗生素表面素和普伐他汀，引起的单一移码突变。接下来，我们使用IDBac检测了一组8个淡水小单孢菌在16S rRNA基因序列上有99%的相似性的种内细微差异，它们产生的金属清除酰基去铁胺。最后，我们使用IDBac从从琼脂平板中分离的不明密歇根湖海绵相关细菌中同时提取蛋白质和专门的代谢物MS图谱。在短短3小时内，我们创建了11个环境分离物的分级蛋白质MS分组(每个MS重复10个，总共110个光谱)，准确地反映了系统发育分组。根据专化代谢物产生的种间和种内差异，我们进一步区分了这些组内的菌株，它们拥有几乎相同的16S rRNA基因序列同一性。IDBac是一种将蛋白质含量的原位MS分析与专门的代谢物产生相结合的尝试，以允许轻松地区分密切相关的细菌菌落。
Mass spectrometry is a powerful technique that has been used to identify bacteria by their protein content and to assess bacterial functional traits through analysis of their specialized metabolites. However, until now these analyses have operated independently, which has resulted in the inability to rapidly connect bacterial phylogenetic identity with potential environmental function. To bridge this gap, we designed a MALDI-TOF mass spectrometry data acquisition and bioinformatics pipeline (IDBac) to integrate data from both intact protein and specialized metabolite spectra directly from bacterial cells grown on agar. This technique organizes bacteria into highly similar phylogenetic groups and allows for comparison of metabolic differences of hundreds of isolates in just a few hours. For decades, researchers have lacked the ability to rapidly correlate microbial identity with bacterial metabolism. Since specialized metabolites are critical to bacterial function and survival in the environment, we designed a data acquisition and bioinformatics technique (IDBac) that utilizes in situ matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze protein and specialized metabolite spectra recorded from single bacterial colonies picked from agar plates. We demonstrated the power of our approach by discriminating between two Bacillus subtilis strains in <30 min solely on the basis of their differential ability to produce cyclic peptide antibiotics surfactin and plipastatin, caused by a single frameshift mutation. Next, we used IDBac to detect subtle intraspecies differences in the production of metal scavenging acyl-desferrioxamines in a group of eight freshwater Micromonospora isolates that share >99% sequence similarity in the 16S rRNA gene. Finally, we used IDBac to simultaneously extract protein and specialized metabolite MS profiles from unidentified Lake Michigan sponge-associated bacteria isolated from an agar plate. In just 3 h, we created hierarchical protein MS groupings of 11 environmental isolates (10 MS replicates each, for a total of 110 spectra) that accurately mirrored phylogenetic groupings. We further distinguished isolates within these groupings, which share nearly identical 16S rRNA gene sequence identity, based on interspecies and intraspecies differences in specialized metabolite production. IDBac is an attempt to couple in situ MS analyses of protein content and specialized metabolite production to allow for facile discrimination of closely related bacterial colonies.
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影响因子：
--
作者：
D'Onofrio A;Crawford JM;Stewart EJ;Witt K;Gavrish E;Epstein S;Clardy J;Lewis K
通讯作者：
Lewis K
影响因子：
7.4
作者：
Gowda, Harsha;Ivanisevic, Julijana;Johnson, Caroline H.;Kurczy, Michael E.;Benton, H. Paul;Rinehart, Duane;Thomas Nguyen;Ray, Jayashree;Kuehl, Jennifer;Arevalo, Bernardo;Westenskow, Peter D.;Wang, Junhua;Arkin, Adam P.;Deutschbauer, Adam M.;Patti, Gary J.;Siuzdak, Gary
通讯作者：
Siuzdak, Gary
影响因子：
5.2
作者：
Rahi P;Prakash O;Shouche YS
通讯作者：
Shouche YS
DOI：
10.1088/1742-5468/2008/10/p10008
发表时间：
2008-10-01
影响因子：
2.4
作者：
Blondel, Vincent D.;Guillaume, Jean-Loup;Lefebvre, Etienne
通讯作者：
Lefebvre, Etienne
影响因子：
4.2
作者：
Argueelles Arias, Anthony;Lambert, Stephany;Rigali, Sebastien
通讯作者：
Rigali, Sebastien