Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum
Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum
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DOI：
10.1128/jb.00176-15
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发表时间：
2015-08-01
影响因子：
3.2
通讯作者：
Mascher, Thorsten
中科院分区：
文献类型：
--
作者：
Huang, Xiaoluo;Pinto, Daniela;Mascher, Thorsten
信号转导是细菌感知复杂且不断变化的环境并做出相应适应的重要过程。信号转导蛋白 (STP) 可以分为三种不同的主要类型：单组分系统 (1CS)、双组分系统 (2CS) 和胞质外功能西格玛因子 (ECF)。由于放线菌中的STP特别丰富，我们根据微生物信号转导（MiST）数据库中存储的数据，全面研究了119个放线菌基因组中编码的STP的丰度和多样性。总体而言，我们观察到基因组大小和编码的 STP 总数之间存在近似线性相关性。所有膜锚定 1CS 中大约有一半是蛋白激酶。对于 1CS 和 2CS，对结构域结构的详细分析确定了仅在放线菌基因组中发现的新型蛋白质。许多放线菌基因组的 ECF 特别丰富。这项研究的结果是，近 500 个以前未分类的 ECF 可以分为 18 个新的 ECF 组。这项综合调查表明，放线菌基因组编码以前未知的 STP，这可能代表了信号转导和调节的新机制。这些信息不仅扩展了我们对细菌信号转导多样性的了解，而且还提供了关于其机制的清晰且可测试的假设，这些假设可以作为实验研究的起点。 重要性随着基因组时代的到来，随着可用序列信息量的巨大增加，现在的挑战已经转向理解和使用这个宝库。此类分析是提供有意义的信息的先决条件，这些信息可以帮助指导后续的实验工作，例如新型信号传导策略的机制研究。这项工作对 119 个放线菌基因组的信号转导蛋白进行了全面分析。我们识别、分类和描述了大量新颖且保守的信号装置。因此，我们的工作对于任何对这一重要细菌门的信号转导感兴趣的研究人员来说都是重要的资源，该细菌门包含与生态、生物技术和医学相关的生物体。
Signal transduction is an essential process that allows bacteria to sense their complex and ever-changing environment and adapt accordingly. Three distinct major types of signal-transducing proteins (STPs) can be distinguished: one-component systems (1CSs), two-component systems (2CSs), and extracytoplasmic-function sigma factors (ECFs). Since Actinobacteria are particularly rich in STPs, we comprehensively investigated the abundance and diversity of STPs encoded in 119 actinobacterial genomes, based on the data stored in the Microbial Signal Transduction (MiST) database. Overall, we observed an approximately linear correlation between the genome size and the total number of encoded STPs. About half of all membrane-anchored 1CSs are protein kinases. For both 1CSs and 2CSs, a detailed analysis of the domain architectures identified novel proteins that are found only in actinobacterial genomes. Many actinobacterial genomes are particularly enriched for ECFs. As a result of this study, almost 500 previously unclassified ECFs could be classified into 18 new ECF groups. This comprehensive survey demonstrates that actinobacterial genomes encode previously unknown STPs, which may represent new mechanisms of signal transduction and regulation. This information not only expands our knowledge of the diversity of bacterial signal transduction but also provides clear and testable hypotheses about their mechanisms, which can serve as starting points for experimental studies.IMPORTANCEIn the wake of the genomic era, with its enormous increase in the amount of available sequence information, the challenge has now shifted toward making sense and use of this treasure chest. Such analyses are a prerequisite to provide meaningful information that can help guide subsequent experimental efforts, such as mechanistic studies on novel signaling strategies. This work provides a comprehensive analysis of signal transduction proteins from 119 actinobacterial genomes. We identify, classify, and describe numerous novel and conserved signaling devices. Hence, our work serves as an important resource for any researcher interested in signal transduction of this important bacterial phylum, which contains organisms of ecological, biotechnological, and medical relevance.