Liu Jiajian, Xu Xing, Stormo Gary D
Department of Genetics, Washington University School of Medicine, 660 S Euclid, Box 8232, St Louis, MO 63110, USA.
Nucleic Acids Res. 2008 Sep;36(16):5376-90. doi: 10.1093/nar/gkn515. Epub 2008 Aug 13.
While hundreds of microbial genomes are sequenced, the challenge remains to define their cis-regulatory maps. Here, we present a comparative genomic analysis of the cis-regulatory map of Shewanella oneidensis, an important model organism for bioremediation because of its extraordinary abilities to use a wide variety of metals and organic molecules as electron acceptors in respiration. First, from the experimentally verified transcriptional regulatory networks of Escherichia coli, we inferred 24 DNA motifs that are conserved in S. oneidensis. We then applied a new comparative approach on five Shewanella genomes that allowed us to systematically identify 194 nonredundant palindromic DNA motifs and corresponding regulons in S. oneidensis. Sixty-four percent of the predicted motifs are conserved in at least three of the seven newly sequenced and distantly related Shewanella genomes. In total, we obtained 209 unique DNA motifs in S. oneidensis that cover 849 unique transcription units. Besides conservation in other genomes, 77 of these motifs are supported by at least one additional type of evidence, including matching to known transcription factor binding motifs and significant functional enrichment or expression coherence of the corresponding target genes. Using the same approach on a more focused gene set, 990 differentially expressed genes derived from published microarray data of S. oneidensis during exposure to metal ions, we identified 31 putative cis-regulatory motifs (16 with at least one type of additional supporting evidence) that are potentially involved in the process of metal reduction. The majority (18/31) of those motifs had been found in our whole-genome comparative approach, further demonstrating that such an approach is capable of uncovering a large fraction of the regulatory map of a genome even in the absence of experimental data. The integrated computational approach developed in this study provides a useful strategy to identify genome-wide cis-regulatory maps and a novel avenue to explore the regulatory pathways for particular biological processes in bacterial systems.
虽然已有数百种微生物基因组被测序，但确定它们的顺式调控图谱仍然是一项挑战。在此，我们对希瓦氏菌（Shewanella oneidensis）的顺式调控图谱进行了比较基因组分析，希瓦氏菌是生物修复的重要模式生物，因为它具有非凡的能力，能够在呼吸作用中使用多种金属和有机分子作为电子受体。首先，我们从经过实验验证的大肠杆菌转录调控网络中推断出24个在希瓦氏菌中保守的DNA基序。然后，我们对五个希瓦氏菌基因组应用了一种新的比较方法，该方法使我们能够系统地识别出希瓦氏菌中194个非冗余的回文DNA基序和相应的调控子。预测的基序中有64%在七个新测序的、亲缘关系较远的希瓦氏菌基因组中的至少三个中保守。我们总共在希瓦氏菌中获得了209个独特的DNA基序，这些基序覆盖了849个独特的转录单元。除了在其他基因组中的保守性外，这些基序中的77个还得到了至少一种其他类型证据的支持，包括与已知转录因子结合基序的匹配以及相应靶基因的显著功能富集或表达一致性。对一组更聚焦的基因集采用相同方法，即来自已发表的希瓦氏菌暴露于金属离子期间的微阵列数据的990个差异表达基因，我们鉴定出31个推定的顺式调控基序（16个有至少一种其他类型的支持证据），它们可能参与金属还原过程。这些基序中的大多数（18/31）已在我们的全基因组比较方法中被发现，这进一步证明即使在没有实验数据的情况下，这种方法也能够揭示基因组调控图谱的很大一部分。本研究中开发的综合计算方法为识别全基因组顺式调控图谱提供了一种有用的策略，并为探索细菌系统中特定生物学过程的调控途径提供了一条新途径。
