Conners Shannon B, Montero Clemente I, Comfort Donald A, Shockley Keith R, Johnson Matthew R, Chhabra Swapnil R, Kelly Robert M
Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA.
J Bacteriol. 2005 Nov;187(21):7267-82. doi: 10.1128/JB.187.21.7267-7282.2005.
Comprehensive analysis of genome-wide expression patterns during growth of the hyperthermophilic bacterium Thermotoga maritima on 14 monosaccharide and polysaccharide substrates was undertaken with the goal of proposing carbohydrate specificities for transport systems and putative transcriptional regulators. Saccharide-induced regulons were predicted through the complementary use of comparative genomics, mixed-model analysis of genome-wide microarray expression data, and examination of upstream sequence patterns. The results indicate that T. maritima relies extensively on ABC transporters for carbohydrate uptake, many of which are likely controlled by local regulators responsive to either the transport substrate or a key metabolic degradation product. Roles in uptake of specific carbohydrates were suggested for members of the expanded Opp/Dpp family of ABC transporters. In this family, phylogenetic relationships among transport systems revealed patterns of possible duplication and divergence as a strategy for the evolution of new uptake capabilities. The presence of GC-rich hairpin sequences between substrate-binding proteins and other components of Opp/Dpp family transporters offers a possible explanation for differential regulation of transporter subunit genes. Numerous improvements to T. maritima genome annotations were proposed, including the identification of ABC transport systems originally annotated as oligopeptide transporters as candidate transporters for rhamnose, xylose, beta-xylan, and beta-glucans and identification of genes likely to encode proteins missing from current annotations of the pentose phosphate pathway. Beyond the information obtained for T. maritima, the present study illustrates how expression-based strategies can be used for improving genome annotation in other microorganisms, especially those for which genetic systems are unavailable.
对嗜热栖热菌（Thermotoga maritima）在14种单糖和多糖底物上生长期间的全基因组表达模式进行了综合分析，目的是提出转运系统和假定转录调节因子的碳水化合物特异性。通过比较基因组学、全基因组微阵列表达数据的混合模型分析以及上游序列模式的检查等互补方法，预测了糖类诱导的调控子。结果表明，嗜热栖热菌在很大程度上依赖ABC转运蛋白来摄取碳水化合物，其中许多可能受对转运底物或关键代谢降解产物有反应的局部调节因子控制。ABC转运蛋白的扩展Opp/Dpp家族成员在特定碳水化合物摄取中的作用得到了提示。在这个家族中，转运系统之间的系统发育关系揭示了可能的复制和分化模式，作为新摄取能力进化的一种策略。Opp/Dpp家族转运蛋白的底物结合蛋白与其他组分之间富含GC的发夹序列的存在，为转运蛋白亚基基因的差异调节提供了一种可能的解释。提出了对嗜热栖热菌基因组注释的许多改进，包括将最初注释为寡肽转运蛋白的ABC转运系统鉴定为鼠李糖、木糖、β-木聚糖和β-葡聚糖的候选转运蛋白，以及鉴定可能编码戊糖磷酸途径当前注释中缺失蛋白质的基因。除了从嗜热栖热菌获得的信息外，本研究还说明了基于表达的策略如何用于改进其他微生物的基因组注释，特别是那些缺乏遗传系统的微生物。
