Proteome profile and proteogenomics of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor
Proteome profile and proteogenomics of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor
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DOI：
10.1016/j.jprot.2013.12.009
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发表时间：
2014-02-26
影响因子：
3.3
通讯作者：
von Bergen, Martin
中科院分区：
文献类型：
--
作者：
Schiffmann, Christian L.;Jehmlich, Nico;von Bergen, Martin
Mccartyi Dehalococcoides菌株CBDB1是一种专性有机卤化物呼吸厌氧细菌，能够转化广泛的高度相关的卤代有机污染物，并已在自然和工程环境中检测到。为了了解分子原理，我们产生了一个蛋白质的CBDB1培养在合成的厌氧介质中，六氯苯作为唯一的电子受体。通过两种不同的蛋白质组学技术的蛋白质组表征导致8491个不同的肽对应于1023个蛋白质，覆盖70%的注释的1458个蛋白质编码序列。从32个注释的还原脱卤酶同源基因（rdhA），我们能够检测到16个RdhA蛋白。高质量的质谱数据进一步用于构建质谱数据库，为精确、快速的蛋白质组学检索提供平台，并将衍生的蛋白质组数据集应用于蛋白质基因组学方法，从而完善CBDB1的基因组注释。这主要是由于蛋白质延长（13例）和检测到翻译序列与现有注释无明显联系（5例）。这些数据超越了目前对细菌蛋白质组的认识，为更好地了解功能性细胞提供了一个扩展的平台。生物学意义氯代有机分子的厌氧还原脱卤是自然生境中卤代有机物循环利用的关键过程，与地下水生物修复高度相关。通过呼吸链将卤代化合物的还原脱卤与ATP生成偶联的能力是模式生物D中普遍存在的一种显著能力。Mccartyi菌株CBDB1。因此，通过全面的LC-MS分析生成参考蛋白质组图谱，并将其转化为SpectraST文库，为精确和快速的鸟枪蛋白质组搜索提供平台。蛋白质组学方法导致CBDB1基因注释的细化，并将扩展细菌蛋白质组的现有知识。该方法提供了一个扩展的平台，更好地了解功能性细胞代谢，从而构成了一个工具，蛋白质表达的比较研究，以及进一步研究有机卤化物呼吸。(C)2013爱思唯尔有限公司版权所有。
Dehalococcoides mccartyi strain CBDB1 is an obligate orgahohalide-respiring anaerobic bacterium that is able to transform a wide range of highly relevant halogenated organic contaminants and has been detected in natural and engineered environments. In order to understand the molecular principles, we generated a protein profile of CBDB1 cultivated in a synthetic anaerobic medium with hexachlorobenzene as the sole electron acceptor. The proteome characterization through two different proteomic techniques resulted in 8491 distinct peptides corresponding to 1023 proteins that covered 70% of the annotated 1458 protein-coding sequences. From the 32 annotated reductive dehalogenases homologous genes (rdhA) we were able to detect 16 RdhA proteins. High-quality MS spectra were further used to build a spectra library to provide a platform for precise and fast proteomic searches.In addition, the derived proteome data set was used to apply a proteogenomic approach that led to a refinement of genome annotation of CBDB1. This was mostly due to protein prolongation (13 cases) and detection of translated sequences without an obvious link to existing annotations (5 cases). These data go beyond the current knowledge of the bacterial proteome and provide an expanded platform for a better understanding of the functional cellular.Biological significanceAnaerobic reductive dehalogenation of chlorinated organic molecules is a key process for the recycling of halogenated organic substances in natural habitats and highly relevant for groundwater bioremediation. The ability to couple reductive dehalogenation of halogenated compounds to ATP-generation via a respiratory chain is one remarkable capability prevalent in the model organism D. mccartyi strain CBDB1. Therefore, a reference proteome map was generated by comprehensive LC-MS analysis and converted into a SpectraST library to provide a platform for precise and fast shotgun proteomic searches. A proteogenomics approach led to a refinement of gene annotation of CBDB1 and will extend the current knowledge of the bacterial proteome. The approach provides an expanded platform for a better understanding of the functional cellular metabolism and thereby constitutes a tool for comparative studies of protein expression as well as further research on organohalide respiration. (C) 2013 Elsevier B.V. All rights reserved.