An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima
An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima
复制标题
DOI：
10.1128/jb.187.21.7267-7282.2005
复制
发表时间：
2005-11-01
影响因子：
3.2
通讯作者：
Kelly, RM
中科院分区：
文献类型：
--
作者：
Conners, SB;Montero, CI;Kelly, RM
对超嗜热菌Thermotoga maritima在14种单糖和多糖底物上生长过程中的全基因组表达模式进行了全面的分析，目的是提出运输系统和假定的转录调节因子的碳水化合物特异性。通过互补使用比较基因组学、全基因组微阵列表达数据的混合模型分析和上游序列模式检查来预测糖诱导的调节基因。结果表明，毛滴虫对碳水化合物的摄取广泛依赖于ABC转运蛋白，其中许多转运蛋白可能受当地调节因子的控制，这些转运蛋白对运输底物或关键代谢降解产物做出反应。ABC转运蛋白OPP/DPP家族成员在特定碳水化合物摄取中的作用被提出。在这个家族中，运输系统之间的系统发育关系揭示了可能的复制和分歧模式，作为新摄取能力进化的一种策略。底物结合蛋白和OPP/DPP家族转运蛋白的其他组分之间富含GC的发夹序列的存在，为转运蛋白亚单位基因的差异调控提供了可能的解释。许多对毛滴虫基因组注释的改进被提出，包括鉴定最初被注释为寡肽转运体的ABC运输系统作为鼠李糖、木糖、β-木聚糖和β-葡聚糖的候选转运体，以及鉴定可能编码从当前的戊糖磷酸途径注释中缺失的蛋白质的基因。除了为毛滴虫获得的信息外，本研究还说明了如何使用基于表达的策略来改进其他微生物的基因组注释，特别是那些没有遗传系统的微生物。
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.