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首页> 外文期刊>Journal of bacteriology >An Expression-Driven Approach to the Prediction of Carbohydrate Transport and Utilization Regulons in the Hyperthermophilic Bacterium Thermotoga maritima
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An Expression-Driven Approach to the Prediction of Carbohydrate Transport and Utilization Regulons in the Hyperthermophilic Bacterium Thermotoga maritima

机译：一种表达驱动的预测嗜热嗜热菌中糖类转运和利用调节子的方法。

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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, β-xylan, andβ -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.
机译：全面分析了全嗜热细菌 Thermotoga maritima 在14种单糖和多糖底物上的生长过程中的全基因组表达模式，旨在为运输系统和推定的转录调节子提出碳水化合物特异性的目标。通过比较基因组学的互补使用，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，可以预测糖诱导的调控因子。结果表明 T。 maritima 广泛依赖于ABC转运蛋白来吸收碳水化合物，其中许多可能是由对转运基质或关键的代谢降解产物有反应的局部调节剂控制的。建议在ABC转运蛋白的扩展Opp / Dpp家族成员中吸收特定碳水化合物。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重复和分化模式，作为新的吸收能力进化的策略。在底物结合蛋白和Opp / Dpp家族转运蛋白的其他组分之间存在富含GC的发夹序列，这为转运蛋白亚基基因的差异调控提供了可能的解释。 T的许多改进。提出了maritima基因组注释，包括鉴定最初被标记为寡肽转运蛋白的ABC转运系统，作为鼠李糖，木糖，β-木聚糖和β-葡聚糖的候选转运蛋白，并鉴定可能编码当前注释中缺失的蛋白质的基因。磷酸戊糖途径。除了为 T获得的信息。 maritima ，本研究说明了如何将基于表达的策略用于改善其他微生物的基因组注释，尤其是那些没有遗传系统的微生物。

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