Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
BMC Genomics. 2010 Apr 21;11:255. doi: 10.1186/1471-2164-11-255.
Many Firmicutes bacteria, including solvent-producing clostridia such as Clostridium acetobutylicum, are able to utilize xylose, an abundant carbon source in nature. Nevertheless, homology searches failed to recognize all the genes for the complete xylose and xyloside utilization pathway in most of them. Moreover, the regulatory mechanisms of xylose catabolism in many Firmicutes except Bacillus spp. still remained unclear.
A comparative genomic approach was used to reconstruct the xylose and xyloside utilization pathway and analyze its regulatory mechanisms in 24 genomes of the Firmicutes. A novel xylose isomerase that is not homologous to previously characterized xylose isomerase, was identified in C. acetobutylicum and several other Clostridia species. The candidate genes for the xylulokinase, xylose transporters, and the transcriptional regulator of xylose metabolism (XylR), were unambiguously assigned in all of the analyzed species based on the analysis of conserved chromosomal gene clustering and regulons. The predicted functions of these genes in C. acetobutylicum were experimentally confirmed through a combination of genetic and biochemical techniques. XylR regulons were reconstructed by identification and comparative analysis of XylR-binding sites upstream of xylose and xyloside utilization genes. A novel XylR-binding DNA motif, which is exceptionally distinct from the DNA motif known for Bacillus XylR, was identified in three Clostridiales species and experimentally validated in C. acetobutylicum by an electrophoretic mobility shift assay.
This study provided comprehensive insights to the xylose catabolism and its regulation in diverse Firmicutes bacteria especially Clostridia species, and paved ways for improving xylose utilization capability in C. acetobutylicum by genetic engineering in the future.
许多厚壁菌门细菌，包括产溶剂梭菌如丙酮丁醇梭菌，能够利用木糖，这是自然界中丰富的碳源。然而，同源搜索未能识别出大多数此类细菌中完整的木糖和木糖苷利用途径的所有基因。此外，许多厚壁菌门（除芽孢杆菌属外）中木糖分解代谢的调控机制仍不清楚。
采用比较基因组学方法重建了 24 个厚壁菌门基因组中的木糖和木糖苷利用途径，并分析了其调控机制。在丙酮丁醇梭菌和其他几种梭菌中鉴定出一种新型木糖异构酶，它与以前表征的木糖异构酶没有同源性。根据保守染色体基因聚类和调控子分析，明确地在所有分析的物种中分配了木酮糖激酶、木糖转运蛋白和木糖代谢的转录调节因子（XylR）的候选基因。通过遗传和生化技术的组合，实验证实了这些基因在丙酮丁醇梭菌中的预测功能。通过鉴定和比较分析木糖和木糖苷利用基因上游的 XylR 结合位点，重建了 XylR 调控子。在三个梭菌目中鉴定并实验验证了一种新型 XylR 结合 DNA 模体，它与芽孢杆菌属 XylR 的 DNA 模体明显不同，通过电泳迁移率变动分析在丙酮丁醇梭菌中得到了实验验证。
本研究提供了对不同厚壁菌门细菌，特别是梭菌属物种中木糖分解代谢及其调控的全面了解，并为未来通过遗传工程提高丙酮丁醇梭菌的木糖利用能力铺平了道路。
