The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer
The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer
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DOI：
10.1093/molbev/msq333
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发表时间：
2011-04-01
影响因子：
10.7
通讯作者：
Pupko, Tal
中科院分区：
文献类型：
--
作者：
Cohen, Ofir;Gophna, Uri;Pupko, Tal
水平基因转移是微生物物种进化中普遍存在的一种重要现象。HGT研究的一个重要挑战是更好地理解决定基因在进化中成功转移和保留的趋势的因素（即，可转移性）。先前观察到，基因的可转移性取决于它们参与的细胞过程，其中参与转录或翻译的基因比代谢基因更不可能被转移。进一步表明，蛋白质-蛋白质相互作用网络中的基因连接性影响HGT。这两个因素被证明是相关的，它们对HGT的影响被统称为“复杂性假设”。在这项研究中，我们使用了一种随机映射方法，利用先进的似然性为基础的进化模型来量化基因家族收购事件的HGT。我们将我们的方法应用于广泛的跨物种全基因组数据集，使我们能够估计进化中转移事件的总体程度，并研究基因转移的趋势和障碍。通过对基因的生物学功能和连接性的研究，我们对“复杂性假说”有了新的认识。“具体来说，我们的目标是解开蛋白质连接，细胞功能和可转移性之间的关系，并量化这些因素中的每一个在确定可转移性方面的相对贡献。我们表明，一个基因家族的生物功能是一个微不足道的因素，在确定的可转移性时，蛋白质具有相似的连接水平进行比较。相比之下，我们发现，连接是一个重要的和统计学上显着的因素，在确定可转移性时，蛋白质具有相似的功能进行比较。
Horizontal gene transfer (HGT) is a prevalent and a highly important phenomenon in microbial species evolution. One of the important challenges in HGT research is to better understand the factors that determine the tendency of genes to be successfully transferred and retained in evolution (i.e., transferability). It was previously observed that transferability of genes depends on the cellular process in which they are involved where genes involved in transcription or translation are less likely to be transferred than metabolic genes. It was further shown that gene connectivity in the protein-protein interaction network affects HGT. These two factors were shown to be correlated, and their influence on HGT is collectively termed the "Complexity Hypothesis". In this study, we used a stochastic mapping method utilizing advanced likelihood-based evolutionary models to quantify gene family acquisition events by HGT. We applied our methodology to an extensive across-species genome-wide dataset that enabled us to estimate the overall extent of transfer events in evolution and to study the trends and barriers to gene transferability. Focusing on the biological function and the connectivity of genes, we obtained novel insights regarding the "complexity hypothesis." Specifically, we aimed to disentangle the relationships between protein connectivity, cellular function, and transferability and to quantify the relative contribution of each of these factors in determining transferability. We show that the biological function of a gene family is an insignificant factor in the determination of transferability when proteins with similar levels of connectivity are compared. In contrast, we found that connectivity is an important and a statistically significant factor in determining transferability when proteins with a similar function are compared.