病原体毒力的进化

病原体毒力的进化是进化生物学和传染病预防控制中的重要课题。最具有进化优势的病原体应该是能够最大限度传播自身,对宿主造成的危害越小,越有利于病原体的长期传播。但根据“交易模型”,病原体在具有传播能力的同时,不可避免地造成宿主适应性的降低。由这一模型预测的病原体毒力进化,会在传播率最大和对宿主影响最小之间取得平衡,以便病原体的基本繁殖率最大化。本文介绍了近年来对这一模型的研究结果、其可能的使用意义和存在的争议,以及进一步完善模型的必要性．     

多重感染与寄生物致病性的进化

对于寄生物致病性进化方向问题的研究,是近些年才开始重视的。目前主要还停留在利用数学模型对寄生物在多重感染情况下致病性进化方向的研究,实验的研究还不多见。从理论研究以及不多的实验来看,寄生物的致病性并不只向对宿主无害的方向进化。但是要了解多重感染情况下,寄生物致病性的进化方向;则需要对特定寄生物及其宿主进行大量的实验研究,阐明多重感染的发生率、它们的流行病学,以及特定的寄生物和宿主关系共同进化所取决的主要因素。     

肠道微生态系统及其与宿主的协同进化

肠道微生态系统是寄生在宿主肠道内的微生物的总和。微生物进入肠道后,通过一个复杂的过程形成群落,与宿主之间相互作用,形成共生关系。宿主客观上为微生物提供生存和进化场所,微生态系统为宿主提供营养物质、刺激肠道组织的发育、刺激宿主肠道免疫系统的发育、影响宿主能量代谢、协助宿主降解有毒物质、影响宿主生殖活动和寿命等功能。作为一个进化的系统,微生态系统的物种多样性和丰富度对维持宿主正常生理功能具有重要作用,但同时又受宿主的影响,物种间相互作用和宿主-微生物间的相互作用是微生态系统进化的动力。进化主要表现在微生物和宿主基因组上发生适应性变化。因此,系统生态学的理论对理解肠道微生态系统的运行机制和临床应用具有重要指导作用。     

寄生虫及其宿主协同进化的研究进展

本文对寄生虫及其宿主协同进化的研究进行了回顾,将其发展分为三个阶段：1．寄生虫-宿主协同进化的初步认识;2．协同进化模式及其内在机制的探索;3．协同进化机制研究方法的发展。目前的研究主要集中于协同进化生物学意义的进一步深入探讨。同时,对协同进化的有关概念、方法和本学科的发展进行了简单阐述和讨论。     

巢寄生的协同进化

巢寄生现象一直是鸟类学专家探讨的热点问题,对于协同进化的问题又有许多不同理论。从宿主的2种对待寄生卵的行为出发,对于巢寄生协同进化的各种理论做了简单的归纳。其中宿主的拒卵行为被认为是一种适应性的表现,这导致和寄生鸟的进化竞争。而对宿主接受卵的行为却有2种不同的观点,即进化滞后说和进化平衡说,这2种学说从不同的方面都能解释宿主接受卵的行为。关于巢寄生的协同进化问题还需要进一步的研究和更多的实例证明．     

昆虫专性内共生细菌及其基因组研究进展

昆虫专性内共生细菌是一类与宿主昆虫长期协同进化的共生微生物,在许多昆虫体内均有发现,主要存在于昆虫特化的器官(含菌体)内,以垂直传播的方式由母系遗传。专性内共生细菌与昆虫的生存、繁殖以及进化等方面息息相关,其主要功能是为宿主提供必需氨基酸等营养物质。因其长期生活在宿主细胞内处于封闭的高营养的环境中,其基因组的特征与普通细菌基因组有很大区别,包括基因组大小、GC含量、基因缺失等方面。通过对共生细菌基因水平上的深入研究,有助于理解专性内共生细菌在宿主昆虫协同进化过程中的作用。目前,昆虫内共生细菌基因的生物学功能、内共生细菌之间以及内共生细菌与宿主之间的互作机制还不是很清楚,有待进一步的研究和探索。     

慢病毒与哺乳动物宿主的协同进化

选取部分哺乳动物代表类群为例,构建病毒及宿主因子基因树并与宿主物种树进行拓扑结构比较,探讨感染哺乳动物的慢病毒与宿主的协同进化.结果表明慢病毒Pol酶基因以及部分宿主因子的进化与宿主的进化历史相同,提示慢病毒可能随哺乳动物的基因组垂直进化,或其首次感染哺乳动物是一次较古老的事件.     

噬菌体的"关闭宿主"功能

噬菌体基因组编码产生某些特殊的蛋白质分子,可与宿主菌生长、代谢的重要调控性蛋白质结合,并使其钝化,从而阻断宿主的生长与繁殖,将宿主菌大分子合成机制和能量装置转向噬菌体自身的复制与增殖。目前研究所获得的有关噬菌体“关闭宿主”功能的证据,主要涉及噬菌体编码的某些蛋白质分子与宿主菌的DNA复制及转录相关因子的相互作用,而这些蛋白质-蛋白质分子间的相互作用将为我们提供新的抗菌药物或抗菌药物作用的靶点,也有助于生物系统进化关系及蛋白质-蛋白质相互作用关系的研究。     

植物病毒适应性机制研究进展

植物病毒是一类专性寄生生物,其生存和繁衍依赖于宿主植物和传播介体.植物病毒通过适应性进化来对抗宿主的防御系统,响应环境的变化,确保病毒的顺利传播和扩大种群数量,其适应性机制的研究不仅有助于我们对病毒的变异和进化、病毒与宿主及传播介体间的互作有更深刻的理解,更重要的是为植物病毒病的防治提供了新的思路和途径.主要从RNA沉默抑制子、快速进化、病毒的传播3个方面,就近年来在植物病毒适应性机制研究领域的一些进展进行概述.     

寄生虫对宿主种群的调节

寄生虫寄生于宿主 ,组成了宿主 寄生虫系统 ,它们之间是否已经通过长期的选择进化形成了一种稳定的关系呢 ?寄生虫对宿主是否还具有种群调节能力呢?Price1认为寄生虫是一种开拓性物种 ,具有高度的进化和形成物种速率 ,有较广的适应范围 ,从而形成了不稳定的宿主 寄生虫系统 ,寄生虫和宿主种群之间仍然产生相互作用。       

Evolution and consequences of transposable elements

Recent studies on transposable elements (TEs) have shed light on the mechanisms that have shaped their evolution. In addition to accumulating nucleotide substitutions over evolutionary time, TEs appear to be especially prone to genetic rearrangements and vertical transmissions across even distantly related species. As a consequence of replicating in host genomes, TEs have a significant mutational effect on their hosts. Although most TE-insertion mutations seem to exert a negative effect on host fitness, a growing body of evidence indicates that some TE-mediated genetic changes have become established features of host species genomes indicating that TEs can contribute significantly to organismic evolution.     

Transposable elements and host genome evolution

Several recent reports have challenged the idea that transposable elements (TEs) are mainly 'selfish' or 'junk' DNA with little importance for host evolution. It has been proposed that TEs have the potential to provide host genomes with the ability to enhance their own evolution. They might also be a major source of genetic diversity, allowing response to environmental changes. Because the relationships between TEs and host genomes are highly variable, and because the selfish, junk and beneficial DNA hypotheses are by no means mutually exclusive, a single label for these relationships appears to be inappropriate and potentially misleading.     

Transposable elements donate lineage-specific regulatory sequences to host genomes

The evolutionary implications of transposable element (TE) influences on gene regulation are explored here. An historical perspective is presented to underscore the importance of TE influences on gene regulation with respect to both the discovery of TEs and the early conceptualization of their potential impact on host genome evolution. Evidence that points to a role for TEs in host gene regulation is reviewed, and comparisons between genome sequences are used to demonstrate the fact that TEs are particularly lineage-specific components of their host genomes. Consistent with these two properties of TEs, regulatory effects and evolutionary specificity, human-mouse genome wide sequence comparisons reveal that the regulatory sequences that are contributed by TEs are exceptionally lineage specific. This suggests a particular mechanism by which TEs may drive the diversification of gene regulation between evolutionary lineages.     

The influence of transposable elements on animal colouration

Transposable elements (TEs) are mobile genetic sequences present within host genomes. TEs can contribute to the evolution of host traits, since transposition is mutagenic and TEs often contain host regulatory and protein coding sequences. We review cases where TEs influence animal colouration, reporting major patterns and outstanding questions. TE-induced colouration phenotypes typically arise via introduction of novel regulatory sequences and splice sites, affecting pigment cell development or pigment synthesis. We discuss if particular TE types may be more frequently involved in the evolution of colour variation in animals, given that examples involving long terminal repeat (LTR) elements appear to dominate. Currently, examples of TE-induced colouration phenotypes in animals mainly concern model and domesticated insect and mammal species. However, several influential recent examples, coupled with increases in genome sequencing, suggest cases reported from wild species will increase considerably.     

The evolution of retrotransposon regulatory regions and its consequences on the Drosophila melanogaster and Homo sapiens host genomes

It has now been established that transposable elements (TEs) make up a variable, but significant proportion of the genomes of all organisms, from Bacteria to Vertebrates. However, in addition to their quantitative importance, there is increasing evidence that TEs also play a functional role within the genome. In particular, TE regulatory regions can be viewed as a large pool of potential promoter sequences for host genes. Studying the evolution of regulatory region of TEs in different genomic contexts is therefore a fundamental aspect of understanding how a genome works. In this paper, we first briefly describe what is currently known about the regulation of TE copy number and activity in genomes, and then focus on TE regulatory regions and their evolution. We restrict ourselves to retrotransposons, which are the most abundant class of eukaryotic TEs, and analyze their evolution and the subsequent consequences for host genomes. Particular attention is paid to much-studied representatives of the Vertebrates and Invertebrates, Homo sapiens and Drosophila melanogaster, respectively, for which high quality sequenced genomes are available.     

The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution

Pack-TYPE transposable elements (TEs) are a group of non-autonomous DNA transposons found in plants. These elements can efficiently capture and shuffle coding DNA across the host genome, accelerating the evolution of genes. Despite their relevance for plant genome plasticity, the detection and study of Pack-TYPE TEs are challenging due to the high similarity these elements have with genes. Here, we produced an automated annotation pipeline designed to study Pack-TYPE elements and used it to successfully annotate and analyse more than 10,000 new Pack-TYPE TEs in the rice and maize genomes. Our analysis indicates that Pack-TYPE TEs are an abundant and heterogeneous group of elements. We found that these elements are associated with all main superfamilies of Class II DNA transposons in plants and likely share a similar mechanism to capture new chromosomal DNA sequences. Furthermore, we report examples of the direct contribution of these TEs to coding genes, suggesting a generalised and extensive role of Pack-TYPE TEs in plant genome evolution.     

Transposable element recruitments in the mammalian placenta: impacts and mechanisms

Transposable elements (TEs) are mobile DNA elements found at high frequency in mammalian genomes. Although these elements are generally perceived as genomic parasites, they have the potential to influence host genome function in many beneficial ways. This article discusses the role TEs have played in the evolution of the placenta and pregnancy in viviparous mammals. Using examples from our own research and the literature, we argue that frequent recruitment of TEs, in particular of retroelements, has facilitated the extreme diversification of tissues at the maternal-fetal interface. We also discuss the mechanisms by which TEs have been recruited for functions during pregnancy. We argue that retroelements are pre-adapted to becoming cis-regulatory elements for host genomes because they need to utilize host regulatory signals for their own life cycle. However, although TEs contain some of the signals necessary for host functions upon insertion, they often require modification before acquiring a biological role in a host tissue. We discuss the process by which one TE was transformed into a promoter for prolactin expression in the endometrium, describing a model for TE domestication called 'epistatic capture'.     

The evolution of retrotransposon regulatory regions and its consequences on the Drosophila melanogaster and Homo sapiens host genomes

It has now been established that transposable elements (TEs) make up a variable, but significant proportion of the genomes of all organisms, from Bacteria to Vertebrates. However, in addition to their quantitative importance, there is increasing evidence that TEs also play a functional role within the genome. In particular, TE regulatory regions can be viewed as a large pool of potential promoter sequences for host genes. Studying the evolution of regulatory region of TEs in different genomic contexts is therefore a fundamental aspect of understanding how a genome works. In this paper, we first briefly describe what is currently known about the regulation of TE copy number and activity in genomes, and then focus on TE regulatory regions and their evolution. We restrict ourselves to retrotransposons, which are the most abundant class of eukaryotic TEs, and analyze their evolution and the subsequent consequences for host genomes. Particular attention is paid to much-studied representatives of the Vertebrates and Invertebrates, Homo sapiens and Drosophila melanogaster, respectively, for which high quality sequenced genomes are available.     

Turning gold into ‘junk’: transposable elements utilize central proteins of cellular networks

The numerous discovered cases of domesticated transposable element (TE) proteins led to the recognition that TEs are a significant source of evolutionary innovation. However, much less is known about the reverse process, whether and to what degree the evolution of TEs is influenced by the genome of their hosts. We addressed this issue by searching for cases of incorporation of host genes into the sequence of TEs and examined the systems-level properties of these genes using the Saccharomyces cerevisiae and Drosophila melanogaster genomes. We identified 51 cases where the evolutionary scenario was the incorporation of a host gene fragment into a TE consensus sequence, and we show that both the yeast and fly homologues of the incorporated protein sequences have central positions in the cellular networks. An analysis of selective pressure (Ka/Ks ratio) detected significant selection in 37% of the cases. Recent research on retrovirus-host interactions shows that virus proteins preferentially target hubs of the host interaction networks enabling them to take over the host cell using only a few proteins. We propose that TEs face a similar evolutionary pressure to evolve proteins with high interacting capacities and take some of the necessary protein domains directly from their hosts.