Finding new overlapping genes and their theory

寻找新的重叠基因及其理论

• 批准号: 150058393
• 负责人: Professor Dr.-Ing. Martin Bossert
• 金额: --
• 依托单位: Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL)
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2010
• 资助国家: 德国
• 起止时间: 2009-12-31 至 2018-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/150058393?language=en
• 关键词: Finding; new; overlapping; genes; their

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.

新的重叠蛋白质编码的DNA序列在原核生物中被发现和验证。使用模型从信息和通信理论的基本机制进行检查。基于以前的项目结果，我们假设：（i）重叠基因（OLG）是由重叠印刷引起的;（ii）孤儿是新出现的OLG的后代。这些假设应按以下方式进行检验：1.细菌基因组将进行统计建模，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的从头进化中起着什么作用？我们将研究是否有一个连续体之间的非编码重叠的原基因对“真正的”OLG。这些研究将揭示OLG可能起源的随机过程的细节。2.我们预计竞争选择压力作用于OLG对，这导致Ka/Ks比偏离单基因。目前测量Ka/Ks比的方法需要许多数据才能足够准确。利用信息论的知识，我们将开发一个模型，使用较少的参数，因此，需要较少的数据来确定Ka/Ks。测序的生物体提供了一个大的数据库，以确定OLG的遗传。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。使用这些工具，可以回答上述孤儿假设。为此，使用BLAST鉴定相关基因，并将同源性可视化，从而可以显示前OLG的解偶联。为了评估重叠的持续演变，选择压力和序列相似性也应可视化。这些工具将有助于回答OLG如何进一步发展功能的问题。4. OLG的假设进化历史应重建（见上文）并进行实验测试。为此，OLG的祖先和中间序列应通过系统发育工具重建，合成并插入适当的敲除突变体中，从而允许测量它们对适应性的影响。mRNA的核糖体足迹可以有效地发现不同细菌中的OLG。此类实验应用于确定依赖于GC含量和密码子使用的OLG的预测。足迹数据提供了确定所使用的阅读帧的可能性。该方法将使用信息论方法进行改进，使得可以检测单个基因的阅读框架。此外，还应检测前一项目中已检测的肠出血性大肠杆菌的亲属。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，OLG可以被预测或被实验发现，其中一些已经被链特异性地突变以测试它们的适应性。这将继续进行，并将使用分子生物学方法对一些进一步的OLG进行功能表征。