An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research
An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research
复制标题
DOI：
10.1093/femsec/fiy013
复制
发表时间：
2018-01
影响因子：
4.2
通讯作者：
Dominique Türkowsky;N. Jehmlich;G. Diekert;L. Adrian;M. von Bergen;Tobias Goris
中科院分区：
文献类型：
--
作者：
Dominique Türkowsky;N. Jehmlich;G. Diekert;L. Adrian;M. von Bergen;Tobias Goris
摘要有机卤化物呼吸作用（OHR）是全球卤素循环中的一个重要过程，也是生物修复的重要研究内容。然而，对OHR的研究受到许多有机卤化物呼吸细菌（OHRB）有限的遗传可及性和低生长产量的阻碍。因此，基因组学、转录组学和蛋白质组学常被用来研究OHRB。在一般情况下，这些基因表达的研究是更有用的，当不同的“组学”方法的数据进行整合，并在广泛的培养条件下进行比较，理想情况下涉及几个密切相关的OHRB。尽管有几个蛋白质组学和转录组学数据集处理人力资源管理局，这些方法目前没有包括在审查。因此，我们在这里提出了一个综合和比较概述的组学研究进行的OHRB多噬硫酸菌，Dehalococcoides mccartyi，脱硫杆菌属。和限制性脱卤菌。本文讨论了OHR的基因、转录本、蛋白质及其调控和生化过程，并对D.提供了Mccartyi，其是可能使用醌非依赖性呼吸链的少数细菌之一。OHRB的几个“组学”衍生的理论，如有机卤化物呼吸链，氢代谢，corrinoid生物合成或一碳代谢的基础上，这种综合性的方法进行了批判性的讨论。
ABSTRACT Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide‐respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different ‘omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB. Despite the availability of a couple of proteomic and transcriptomic datasets dealing with OHRB, such approaches are currently not covered in reviews. Therefore, we here present an integrative and comparative overview of omics studies performed with the OHRB Sulfurospirillum multivorans, Dehalococcoides mccartyi, Desulfitobacterium spp. and Dehalobacter restrictus. Genes, transcripts, proteins and the regulatory and biochemical processes involved in OHR are discussed, and a comprehensive view on the unusual metabolism of D. mccartyi, which is one of the few bacteria possibly using a quinone‐independent respiratory chain, is provided. Several ‘omics'‐derived theories on OHRB, e.g. the organohalide‐respiratory chain, hydrogen metabolism, corrinoid biosynthesis or one‐carbon metabolism are critically discussed on the basis of this integrative approach.