Understanding the Functional Effects of Genetic Variation in the Promoters of Bacterial Pathogens

Bayliss实验室最近发表的一篇论文描述了脑膜炎奈瑟氏球菌编码疫苗抗原基因上游基因间区域的等位基因变异。该抗原fHbp是Bexsero（4C-MenB）的组分，Bexsero是一种新的重组疫苗，用于预防由血清群B菌株引起的脑膜炎和败血症。脑膜炎对约1,000个基因组的分析表明，在约90%的N.脑膜炎分离株基因表达的实验定量结合数学处理允许特定变异核苷酸和遗传元件与基因表达差异的关联。通过采用基因组序列的生物信息学分析、数据集的数学处理和预测的实验测试的组合，该项目旨在产生三种细菌病原体-脑膜炎奈瑟氏菌、脑膜炎奈瑟氏菌和脑膜炎奈瑟氏菌中基因表达的全局分析。淋病奈瑟菌和空肠弯曲菌。该项目旨在确定具有一系列功能的多个基因的基因间区域的遗传变异程度。将通过生物信息学分析评估遗传变异，并将其与实验测定的基因表达水平（通过RNA-Seq和/或qPCR测定）相关联。将利用数学测试来确定控制表达的特定序列，并通过关键核苷酸的定点诱变进行确认。进一步的工作可能涉及反式作用因子（例如RNA聚合酶结合）的机械测试或通过生物信息学和数学测试外推到其他启动子和物种。

A recently published paper by the Bayliss lab described the allelic variation in Neisseria meningitidis for the intergenic region upstream of a gene coding a vaccine antigen. This antigen fHbp is a component of Bexsero (4C-MenB), a new recombinant vaccine for preventing meningitis and septicaemia by serogroup B strains of N. meningitidis. Analysis of ~1,000 genomes determined that nine sequences of this region were found in ~90% of N. meningitidis isolates. Experimental quantification of gene expression combined with mathematical treatments allowed association of specific variant nucleotides and genetic elements with difference in gene expression.By employing a combination of bioinformatic analyses of genome sequences, mathematical treatments of datasets and experimental tests of predictions this project aims to produce a global analysis of gene expression in three bacterial pathogens - Neisseria meningitidis, Neisseria gonorrhoeae and Campylobaster jejuni. The project will aim to determine the extent of genetic variation in the intergenic regions for multiple genes with a range of functions. Genetic variation will be assessed by bioinformatic analyses and correlated with experimentally determined gene expression levels (determined by RNA-Seq and/or qPCR). Mathematical testing will be utilised to determine the specific sequences controlling expression with confirmation by site-directed mutagenesis of key nucleotides. Further work may involve mechanistic testing of the trans-acting factors (e.g. RNA polymerase binding) or extrapolation to other promoters and species through bioinformatic and mathematical testing.