Rediers Hans, Rainey Paul B, Vanderleyden Jos, De Mot René
Centre of Microbial and Plant Genetics, Heverlee, Belgium.
Microbiol Mol Biol Rev. 2005 Jun;69(2):217-61. doi: 10.1128/MMBR.69.2.217-261.2005.
A major challenge for microbiologists is to elucidate the strategies deployed by microorganisms to adapt to and thrive in highly complex and dynamic environments. In vitro studies, including those monitoring genomewide changes, have proven their value, but they can, at best, mimic only a subset of the ensemble of abiotic and biotic stimuli that microorganisms experience in their natural habitats. The widely used gene-to-phenotype approach involves the identification of altered niche-related phenotypes on the basis of gene inactivation. However, many traits contributing to ecological performance that, upon inactivation, result in only subtle or difficult to score phenotypic changes are likely to be overlooked by this otherwise powerful approach. Based on the premise that many, if not most, of the corresponding genes will be induced or upregulated in the environment under study, ecologically significant genes can alternatively be traced using the promoter trap techniques differential fluorescence induction and in vivo expression technology (IVET). The potential and limitations are discussed for the different IVET selection strategies and system-specific variants thereof. Based on a compendium of genes that have emerged from these promoter-trapping studies, several functional groups have been distinguished, and their physiological relevance is illustrated with follow-up studies of selected genes. In addition to confirming results from largely complementary approaches such as signature-tagged mutagenesis, some unexpected parallels as well as distinguishing features of microbial phenotypic acclimation in diverse environmental niches have surfaced. On the other hand, by the identification of a large proportion of genes with unknown function, these promoter-trapping studies underscore how little we know about the secret lives of bacteria and other microorganisms.
微生物学家面临的一个主要挑战是阐明微生物在高度复杂和动态的环境中适应并茁壮成长所采用的策略。包括监测全基因组变化的体外研究已证明了其价值，但它们充其量只能模拟微生物在自然栖息地所经历的非生物和生物刺激集合中的一个子集。广泛使用的基因到表型方法涉及基于基因失活来鉴定与生态位相关的改变的表型。然而，许多对生态性能有贡献的性状，在失活时只会导致细微或难以评分的表型变化，很可能会被这种原本强大的方法所忽视。基于这样一个前提，即许多（如果不是大多数）相应的基因将在研究的环境中被诱导或上调，生态上重要的基因可以使用启动子捕获技术差异荧光诱导和体内表达技术（IVET）来追踪。讨论了不同IVET选择策略及其系统特异性变体的潜力和局限性。基于这些启动子捕获研究中出现的基因汇编，区分了几个功能组，并通过对选定基因的后续研究说明了它们的生理相关性。除了证实来自如签名标签诱变等基本互补方法的结果外，在不同环境生态位中微生物表型适应的一些意想不到的相似之处以及独特特征也浮出水面。另一方面，通过鉴定很大一部分功能未知的基因，这些启动子捕获研究强调了我们对细菌和其他微生物的隐秘生活了解得多么少。
