Comparative Analysis Of Completely Sequenced Genomes

细菌、古生物、真核生物和病毒的完全和几乎完全测序的基因组数据库迅速增长(已有数千个基因组，还有更多的基因组正在进行中)，为基因组研究创造了广泛的新机遇，也带来了重大的新挑战。在过去的一年里，我们进行了各种研究，利用基因组信息来建立基因组进化的基本原则。 我们的大部分工作都是为了了解病毒和移动元素的进化。病毒基因组容易发生广泛的基因丢失、获得和交换，并且不共享通用基因。因此，在病毒进化的大范围研究中，基因和基因组网络分析可以补充传统的系统发育学。我们使用二部网络方法对双链DNA(DsDNA)病毒的基因组进行了详尽的比较分析，发现dsDNA病毒圈中存在一个健壮的层次模块化。二部网络由两类节点组成，其中一类节点，在这种情况下是基因组，通过第二类节点，在这种情况下是基因。这样的网络可以被划分为组合来自两个类的节点的模块。DsDNA病毒的两部分网络包括19个模块，形成5个主要和3个次要的超级模块。在这些模块中，有11个包括尾部噬菌体，反映了这一最大病毒组的多样性。该模块分析定量地验证和提炼了先前提出的非平凡进化关系。一个扩展的超级模块将假定的“超级病毒目”的大型和巨型病毒与各种中等大小的病毒和相关的移动元素结合起来。这个超级模块中的所有病毒都共享一个独特的形态发生工具包，带有一个双糖冻卷主要衣壳蛋白。疱疹病毒和尾随噬菌体组成另一个超级模块，由一组不同的以HK97类主要衣壳蛋白为中心的形态发生蛋白结合在一起。这两个超级模块一起覆盖了目前已知的绝大多数dsDNA病毒。我们正式确定了一组14个病毒标志基因，这些基因组成了网络的枢纽，并解释了大部分模块间的连接。 对病毒基因组之间进化关系的实证研究得到了病毒-宿主共同进化的理论建模的补充，并用比较基因组数据对模型预测进行了检验。几乎所有的细胞生命形式都是具有不同程度自主性的不同遗传寄生虫的宿主，包括质粒、转座子和病毒。原始复制子进化的理论模型表明，寄生虫(‘作弊者’)必然在这样的系统中进化，并可以主要通过分隔来阻止它们。考虑到遗传寄生虫(几乎)无处不在、丰富性和多样性，这个问题变得切中要害：这种寄生虫是生命固有的吗？至少在原核生物中，寄生虫的持久性与水平基因转移(HGT)的速度有关。我们从数学上推导出自私元素持久化所需的最小传输速率的阈值，这取决于元素复制率和丢失率以及主机的成本。对多组不同细菌和古菌中转座子、质粒和病毒相关元件的特征基因复制、丢失和转移速率的估计表明，这些速率中的大多数与寄生虫的长期存在是相容的。值得注意的是，非寄生基因的持久性也需要少量但非零比率的HGT。我们假设，细胞无法将其水平转移率调整到低于寄生虫持久性所需的阈值，而不会经历非常有害的副作用。作为细胞所能承受的最低DNA转移率的下限，我们考虑了通过穆勒棘轮的种群基因组退化和突变熔毁的过程。对这一假说的数字评估表明，微生物种群在逃脱穆勒棘轮的同时无法清除寄生虫。因此，遗传寄生虫似乎在细胞生物体中几乎是不可避免的。 Casposon是我们在研究CRISPR-Cas系统的进化过程中发现的一个假定的自合成转座子超家族。据预测，这些酪蛋白使用Cas1蛋白的同系物作为重组酶，可能有助于古细菌和细菌中CRISPR-Cas适应性免疫系统的起源。Casposon在实验上仍然没有特征，除了最近证明了Cas1同源物的整合酶活性，并且考虑到它们在古菌和细菌中的相对稀有性，最初的比较基因组分析没有提供它们迁移性的直接迹象。我们通过比较62株玛氏甲烷八叠球菌的基因组发现了酪蛋白迁移率的证据。在这些基因组中，酪蛋白被可变地插入三个不同的位置，表示多个、最近的得和失。一些酪蛋白被插入到其他可移动的遗传元件中，这些基因可能为酪蛋白的水平转移提供载体。此外，许多Mazei基因组包含以前未检测到的单一末端反向重复序列，这些重复序列显然来自酪蛋白，可能类似于CRISPR进化的中间产物。我们进一步证明了Casposon插入的序列特异性，并注意到与CRISPR-Cas的适应机制明显相似。最后，除了确定最初定义的三个家族中的其他代表外，我们还描述了一个新的、第四个赌场家族。 综上所述，这些研究促进了对不同生命形式，特别是病毒和移动元素中基因组进化的现有理解，并为基因组进化的一般原理提供了新的见解。

The rapidly growing database of completely and nearly completely sequenced genomes of bacteria, archaea, eukaryotes and viruses (several thousand genomes already available and many more in progress) creates both extensive new opportunities and major new challenges for genome research. During the last year, we performed a variety of studies that took advantage of the genomic information to establish fundamental principles of genome evolution. Much of our work aimed at understanding evolution of viruses and mobile elements. Virus genomes are prone to extensive gene loss, gain, and exchange and share no universal genes. Therefore, in a broad-scale study of virus evolution, gene and genome network analyses can complement traditional phylogenetics. We performed an exhaustive comparative analysis of the genomes of double-stranded DNA (dsDNA) viruses by using the bipartite network approach and found a robust hierarchical modularity in the dsDNA virosphere. Bipartite networks consist of two classes of nodes, with nodes in one class, in this case genomes, being connected via nodes of the second class, in this case genes. Such a network can be partitioned into modules that combine nodes from both classes. The bipartite network of dsDNA viruses includes 19 modules that form 5 major and 3 minor supermodules. Of these modules, 11 include tailed bacteriophages, reflecting the diversity of this largest group of viruses. The module analysis quantitatively validates and refines previously proposed nontrivial evolutionary relationships. An expansive supermodule combines the large and giant viruses of the putative order "Megavirales" with diverse moderate-sized viruses and related mobile elements. All viruses in this supermodule share a distinct morphogenetic tool kit with a double jelly roll major capsid protein. Herpesviruses and tailed bacteriophages comprise another supermodule, held together by a distinct set of morphogenetic proteins centered on the HK97-like major capsid protein. Together, these two supermodules cover the great majority of currently known dsDNA viruses. We formally identify a set of 14 viral hallmark genes that comprise the hubs of the network and account for most of the intermodule connections. The empirical research into the evolutionary relationships between viral genomes was complemented by theoretical modeling of virus-host coevolution, with the model predictions tested against comparative genomic data. Almost all cellular life forms are hosts to diverse genetic parasites with various levels of autonomy including plasmids, transposons and viruses. Theoretical modeling of the evolution of primordial replicators indicates that parasites ('cheaters') necessarily evolve in such systems and can be kept at bay primarily via compartmentalization. Given the (near) ubiquity, abundance and diversity of genetic parasites, the question becomes pertinent: are such parasites intrinsic to life? At least in prokaryotes, the persistence of parasites is linked to the rate of horizontal gene transfer (HGT). We mathematically derive the threshold value of the minimal transfer rate required for selfish element persistence, depending on the element duplication and loss rates as well as the cost to the host. Estimation of the characteristic gene duplication, loss and transfer rates for transposons, plasmids and virus-related elements in multiple groups of diverse bacteria and archaea indicates that most of these rates are compatible with the long term persistence of parasites. Notably, a small but non-zero rate of HGT is also required for the persistence of non-parasitic genes. We hypothesize that cells cannot tune their horizontal transfer rates to be below the threshold required for parasite persistence without experiencing highly detrimental side-effects. As a lower boundary to the minimum DNA transfer rate that a cell can withstand, we consider the process of genome degradation and mutational meltdown of populations through Muller's ratchet. A numerical assessment of this hypothesis suggests that microbial populations cannot purge parasites while escaping Muller's ratchet. Thus, genetic parasites appear to be virtually inevitable in cellular organisms. Casposons are a superfamily of putative self-synthesizing transposable elements that we discovered during our studies into the evolution of CRISPR-Cas systems. The casposons are predicted to employ a homolog of Cas1 protein as a recombinase and could have contributed to the origin of the CRISPR-Cas adaptive immunity systems in archaea and bacteria. Casposons remain uncharacterized experimentally, except for the recent demonstration of the integrase activity of the Cas1 homolog, and given their relative rarity in archaea and bacteria, original comparative genomic analysis has not provided direct indications of their mobility. We found evidence of casposon mobility obtained by comparison of the genomes of 62 strains of the archaeon Methanosarcina mazei. In these genomes, casposons are variably inserted in three distinct sites indicative of multiple, recent gains, and losses. Some casposons are inserted into other mobile genetic elements that might provide vehicles for horizontal transfer of the casposons. Additionally, many M. mazei genomes contain previously undetected solo terminal inverted repeats that apparently are derived from casposons and could resemble intermediates in CRISPR evolution. We further demonstrated the sequence specificity of casposon insertion and note clear parallels with the adaptation mechanism of CRISPR-Cas. Finally, besides identifying additional representatives in each of the three originally defined families, we describe a new, fourth, family of casposons. Taken together, these studies advance the existing understanding of the genome evolution in diverse life forms, in particular viruses and mobile elements, and provide new insights into general principles of genome evolution.