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

贝利斯实验室最近发表的一篇论文描述了脑膜炎奈瑟菌中编码疫苗抗原的基因上游基因间隔区的等位基因变异。这种抗原fHBP是Bexsero(4C-MenB)的一种成分，Bexsero(4C-MenB)是一种新的重组疫苗，用于预防脑膜炎奈瑟菌B群菌株的脑膜炎和败血症。对~1,000个基因组的分析表明，在~90%的脑膜炎奈瑟菌分离株中发现了该区域的9个序列。基因表达的实验量化与数学处理相结合，允许特定的变异核苷酸和遗传元件与基因表达差异相关联。通过结合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，该项目旨在对三种细菌病原体-脑膜炎奈瑟菌、淋病奈瑟菌和空肠弯曲菌-的基因表达进行全球分析。该项目的目标是确定具有一系列功能的多个基因在基因间区的遗传变异程度。遗传变异将通过生物信息学分析进行评估，并与实验确定的基因表达水平(由RNA-Seq和/或qPCR确定)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突变进行确认。进一步的工作可能涉及反式作用因子的机械测试(例如，RNA聚合酶结合)，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.