Finding new overlapping genes and their theory

新的重叠的蛋白质编码dna序列在原核生物中被发现和验证。使用来自信息和通信理论的模型来检查潜在的机制。基于以往的项目成果，我们假设：(1)重叠基因（OLG）是叠印造成的；(2)孤儿是新出现的OLG的后代。这些假设的检验方法如下：1。将对细菌基因组进行统计学建模，并与自然基因组进行比较：遗传密码、gc含量和密码子使用在蛋白质编码OLG的从头进化中起什么作用？我们将研究在非编码重叠原基因之间是否存在“真正的”OLG连续体。这些研究将揭示OLG可能起源于的随机过程的细节。2. 我们预计竞争选择压力作用于OLG对，这导致Ka/Ks比偏离单一基因。目前测量Ka/Ks比率的方法需要大量的数据才能足够准确。利用信息论知识，我们将开发一个使用较少参数的模型，因此需要较少的数据来确定Ka/ ks。测序的生物体为确定OLG的系统发育提供了一个庞大的数据库。为了理解和解释许多OLG的这些数据，需要可视化和可视化分析。利用这些工具，可以回答上述孤儿假说。为此，使用BLAST对相关基因进行鉴定，并将系统发育可视化，以显示前OLG的解偶联。为了评估重叠的持续进化，选择压力和序列相似性也应该可视化。这些工具将有助于回答OLG如何发展进一步功能的问题。4. 假设的OLG进化历史将被重建（见上文）并进行实验验证。为此，应通过系统发育工具重建OLG的祖先和中间序列，合成并插入适当的敲除突变体中，从而测量其对适应度的影响。mRNA的核糖体足迹可以有效地在不同的细菌中找到OLG。这样的实验应使用确定预测的OLG依赖于gc含量和密码子的使用。占用数据提供了确定所使用的读取框架的可能性。这种方法将使用信息论方法进行改进，从而可以检测到单个基因的阅读框。此外，对以往项目中检测过的肠出血性大肠杆菌的亲属进行检测。这将证实或反驳孤儿对生态位适应很重要的假设。在之前的项目阶段，可以预测或通过实验发现OLG。其中一些已经发生了突变——专门为了测试它们的适应性。这将继续进行，并使用分子生物学方法对一些进一步的OLG进行功能表征。

New overlapping protein-coding DNA-sequences in prokaryotes are to be found and verified. The underlying mechanisms are examined using models from information and communication theory. Based on former project results, we hypothesize that (i) overlapping genes (OLG) result from overprinting and (ii) orphans are descendants of newly arisen OLG. These hypotheses shall be tested as follows: 1. Bacterial genomes will be modelled statistically and compared to the natural genomes: Which role plays the genetic code, the GC-content and the codon usage in the de novo evolution of protein-coding OLG? We will examine if there is a continuum between non-coding overlapping proto-genes towards 'true' OLG. These studies will reveal details about the stochastic processes from which OLG potentially originate. 2. We expect competing selection pressures acting on OLG pairs, which cause Ka/Ks ratios to deviate from single genes. Current methods to measure Ka/Ks ratios need many data to be sufficient accurate. Using information theoretic knowledge, we will develop a model which uses less parameters and, thus, needs less data to determine Ka/Ks.3. Sequenced organisms provide a large data base to determine the phylogeny of OLG. To understand and interpret these data for many OLG, visualisations and visual analytics are needed. Using such tools, the above mentioned orphan hypothesis can be answered. Towards this end, related genes are identified using BLAST and the phylogeny shall be visualized, such that the uncoupling of former OLG can be shown. To assess the on-going evolution of overlaps, selection pressures and sequence similarities shall be visualized as well. These tools will help to answer the question of how OLG potentially evolve further functions. 4. Hypothetical evolutionary histories of OLG shall be reconstructed (see above) and tested experimentally. Towards this end, ancestral and intermediate sequences of OLG shall be reconstructed by phylogenetic tools, synthesized and inserted in appropriate knock out mutants, thus allowing to measure their influence on fitness.5. Ribosomal footprints of mRNA are efficient to find OLG in different bacteria. Such experiments shall be used to determine the prediction of OLG in dependence of the GC-content and codon usage. Footprint data provide the possibility to determine the reading frame used. This approach will be improved using information theoretic methods such that the reading frame of single genes can be detected. Furthermore, relatives of EHEC, which has been examined in former project, shall be tested. This will corroborate or refute the hypothesis that orphans are important for niche adaptation.6. In the previous project phases, OLG could be predicted or were experimentally found. Some of these have been mutated strand-specifically to test their fitness. This shall be continued and a functional characterization of some further OLG shall be conducted using methods of molecular biology.