Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1.
Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1.
复制标题
DOI：
10.3389/fmicb.2015.00149
复制
发表时间：
2015
影响因子：
5.2
通讯作者：
Ogorzalek Loo RR
中科院分区：
文献类型：
--
作者：
Leon DR;Ytterberg AJ;Boontheung P;Kim U;Loo JA;Gunsalus RP;Ogorzalek Loo RR
蛋白质组学工具识别复杂混合物的成分，通常提供一长串已识别的蛋白质。高通量方法擅长将串联质谱数据与从序列数据库预测的光谱相匹配。未分配的质谱被忽略，但原则上可以提供关于意外修饰的有价值的信息，并在消耗有限数量的材料的同时改进蛋白质注释。策略“挖掘”这些丢弃的信息，沿着的功能，当存在时，提供强有力的支持修改的讨论。在这项研究中，我们挖掘了来自Mazei甲烷八叠球菌Gö 1细胞裂解物的蛋白酶解消化伴刀豆球蛋白A下拉组分的LC-MS/MS数据集。分析鉴定了154种蛋白质。许多观察到的蛋白质显示出后修饰的形式，包括O-甲酰化和甲基酯化的片段，这些片段似乎是生物学相关的（即，而不是样品处理的人工产物）。有趣的裂解和修饰（例如，S-氰化和三甲基化）。在31个通过刀豆球蛋白A结合或从以前的研究中回收的甲烷八叠球菌蛋白N-末端中，只有M. Mazei S层蛋白MM 1976和M.食乙酸菌C2 A直向同源物MA 0829经历信号肽切除。实验结果与来自算法SignalP 3.0和Exprot的预测形成对比，这些算法被发现过度预测信号肽的存在。发现蛋白质MM 0002、MM 0716、MM 1364和MM 1976是糖基化的，采用专门针对糖肽的色谱法可能会揭示更多。这项研究补充了有限的，现有的成熟古细菌N-末端的实验数据集，包括存在或不存在的信号肽，翻译起始位点，和其他处理。甲烷八叠球菌的表面和膜蛋白被大量修饰。
Proteomic tools identify constituents of complex mixtures, often delivering long lists of identified proteins. The high-throughput methods excel at matching tandem mass spectrometry data to spectra predicted from sequence databases. Unassigned mass spectra are ignored, but could, in principle, provide valuable information on unanticipated modifications and improve protein annotations while consuming limited quantities of material. Strategies to “mine” information from these discards are presented, along with discussion of features that, when present, provide strong support for modifications. In this study we mined LC-MS/MS datasets of proteolytically-digested concanavalin A pull down fractions from Methanosarcina mazei Gö1 cell lysates. Analyses identified 154 proteins. Many of the observed proteins displayed post-translationally modified forms, including O-formylated and methyl-esterified segments that appear biologically relevant (i.e., not artifacts of sample handling). Interesting cleavages and modifications (e.g., S-cyanylation and trimethylation) were observed near catalytic sites of methanogenesis enzymes. Of 31 Methanosarcina protein N-termini recovered by concanavalin A binding or from a previous study, only M. mazei S-layer protein MM1976 and its M. acetivorans C2A orthologue, MA0829, underwent signal peptide excision. Experimental results contrast with predictions from algorithms SignalP 3.0 and Exprot, which were found to over-predict the presence of signal peptides. Proteins MM0002, MM0716, MM1364, and MM1976 were found to be glycosylated, and employing chromatography tailored specifically for glycopeptides will likely reveal more. This study supplements limited, existing experimental datasets of mature archaeal N-termini, including presence or absence of signal peptides, translation initiation sites, and other processing. Methanosarcina surface and membrane proteins are richly modified.
登录
查看更多内容
影响因子：
4.4
作者：
Falkner, Jayson A.;Falkner, Jarret W.;Andrews, Philip C.
通讯作者：
Andrews, Philip C.
影响因子：
4.8
作者：
Bäumer, S;Ide, T;Deppenmeier, U
通讯作者：
Deppenmeier, U
影响因子：
2.8
作者：
FISCHER, R;GARTNER, P;THAUER, RK
通讯作者：
THAUER, RK
DOI：
10.1126/science.1178535
发表时间：
2009-12-04
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Becker T;Bhushan S;Jarasch A;Armache JP;Funes S;Jossinet F;Gumbart J;Mielke T;Berninghausen O;Schulten K;Westhof E;Gilmore R;Mandon EC;Beckmann R
通讯作者：
Beckmann R
影响因子：
2.9
作者：
DEGANI, Y;PATCHORNIK, A
通讯作者：
PATCHORNIK, A