Viral proteomics: global evaluation of viruses and their interaction with the host

Viruses constantly adapt to and modulate the host environment during replication and propagation. Both DNA and RNA viruses encode multifunctional proteins that interact with and modify host cell proteins. While viral genomes were the first complete sequences known, the corresponding proteomes are only now elucidated, with some surprising results. Even more daunting is the task to globally monitor the impact of viral infection on the proteome of the host cell and many technical hurdles must still be overcome in order to facilitate robust and reproducible measurements. Further complicating the picture is the dynamic nature of proteins, including post-translational modifications, enzymatic cleavage and activation or destruction by proteolytic events. Nevertheless, several promising studies have been published using high-throughput methods directly measuring protein abundance. Particularly, quantitative or semiquantitative mass spectrometry-based analysis of viral and cellular proteomes are now being used to characterize viruses and their host interaction. In addition, the full set of interactions between viral and host proteins, the interactome, is beginning to emerge, with often unexpected interactions that need to be carefully validated. In this review, we will discuss two major areas of viral proteomics: first, virion proteomics (such as the protein characterization of viral particles) and second, proteoviromics, including the viral protein interactomics and the quantitative analysis of host cell proteome during viral infection.     

The reactions of bacterial viruses with their host cells

The Botanical Review -     

全球气候变暖对“植物-害虫-天敌”互作系统的影响

全球气候变化是近来人类关注的焦点问题,其最显著的特征是气候变暖。因为昆虫具有生活周期短、繁殖率高等特点,所以,气候变暖对昆虫的发育、繁殖和存活会产生强烈的直接影响。气候变暖促使一些昆虫提前春天的物候现象,向高纬度或高海拔地区迁移。然而,昆虫在自然界并非孤立地存在,它们与寄主植物和自然天敌相互联系、相互作用,并在长期的进化过程中逐渐适应特定区域的气候条件。因此,全球气候变暖对"植物-害虫-天敌"的种间关系必然产生直接或间接的影响,导致不同昆虫之间以及昆虫与其相关营养层的物种之间的相互关系在气候变化下呈现出时间上的异步性和空间上的错位,从而影响植物的适应性和抗虫性、害虫的发生规律和危害程度以及天敌的种群消长和控害效能。昆虫除了可以通过休眠或滞育的方式在时间上避开高温的影响外,还可以通过迁飞或移动的方式在空间上避开高温的影响,在这种迁移和扩散不同步的情况下可能使害虫食性和取食植物的害虫及其天敌的种类发生变化,从而改变生物群落的组成与结构,影响生态系统的服务和功能。     

Impacts of global warming on the interaction between host plants,insect pests and their natural enemies

全球气候变化是近来人类关注的焦点问题,其最显著的特征是气候变暖.因为昆虫具有生活周期短、繁殖率高等特点,所以,气候变暖对昆虫的发育、繁殖和存活会产生强烈的直接影响.气候变暖促使一些昆虫提前春天的物候现象,向高纬度或高海拔地区迁移.然而,昆虫在自然界并非孤立地存在,它们与寄主植物和自然天敌相互联系、相互作用,并在长期的进化过程中逐渐适应特定区域的气候条件.因此,全球气候变暖对“植物-害虫-天敌”的种间关系必然产生直接或间接的影响,导致不同昆虫之间以及昆虫与其相关营养层的物种之间的相互关系在气候变化下呈现出时间上的异步性和空间上的错位,从而影响植物的适应性和抗虫性、害虫的发生规律和危害程度以及天敌的种群消长和控害效能.昆虫除了可以通过休眠或滞育的方式在时间上避开高温的影响外,还可以通过迁飞或移动的方式在空间上避开高温的影响,在这种迁移和扩散不同步的情况下可能使害虫食性和取食植物的害虫及其天敌的种类发生变化,从而改变生物群落的组成与结构,影响生态系统的服务和功能.     

The plasmids of Acetobacter xylinum and their interaction with the host chromosome

Summary Acetobacter xylinum contains a complex system of plasmid DNA molecules. Plasmids of molecular weights or copy numbers different from the original wild-type, are found in different types of mutants. Restriction endonuclease digestion and DNA/DNA hybridization analysis, showed that the plasmids often contained partly, but not completely the same DNA sequences. Two of these plasmid classes were analysed in more detail, and could be shown to differ in size by about 5 kb. Hybridization analysis using cloned DNA fragments as probes, showed that sequences lacking in the smallest plasmid were still present in a DNA fraction co-migrating with linearized chromosomal DNA. In addition, at least part of the DNA in the smallest plasmid was present both in the plasmid and chromosomal DNA fraction. Analysis of a particular strain containing an insertion of transposon Tn1, also indicated the existence of complex interactions between plasmids and chromosomal DNA. Together with experiments on conjugative transfer and curing of the plasmids, the results indicate that at least part of the genetic system of A. xylinum is unusual when compared to that of other genetically characterized bacteria.     

Phaeocystis and its interaction with viruses

Over the years, viruses have been shown to be mortality agents for a wide range of phytoplankton species, including species within the genus Phaeocystis (Prymnesiophyceae). With its polymorphic life cycle, its worldwide distribution, and the capacity of several of the Phaeocystis species to form dense blooms, this genus is a key player for our understanding of biogeochemical cycling of elements. This paper provides an overview of what is know to date about the ecological role of viruses in regulating Phaeocystis population dynamics. It explores which variables affect the algal host–virus interactions, and examines the impact of virally induced cell lysis of Phaeocystis on the function and structure of the pelagic food web as well as on the flow of organic carbon and nutrients.     

Viral proteomics: The emerging cutting-edge of virus research

Viruses replicate and proliferate in host cells while continuously adjusting to and modulating the host environment. They encode a wide spectrum of multifunctional proteins, which interplay with and modify proteins in host cells. Viral genomes were chronologically the first to be sequenced. However, the corresponding viral proteomes, the alterations of host proteomes upon viral infection, and the dynamic nature of proteins, such as post-translational modifications, enzymatic cleavage, and activation or destruction by proteolysis, remain largely unknown. Emerging high-throughput techniques, in particular quantitative or semi-quantitative mass spectrometry-based proteomics analysis of viral and cellular proteomes, have been applied to define viruses and their interactions with their hosts. Here, we review the major areas of viral proteomics, including virion proteomics, structural proteomics, viral protein interactomics, and changes to the host cell proteome upon viral infection.     

Virion proteomics of large DNA viruses

Large DNA viruses normally have complex structures with many of protein components derived from both viral and host origins. The development in proteomics, especially mass spectrometry identification techniques provide powerful tools for analyzing large viruses. In this review, we have summarized the recent achievements on proteomic studies of large DNA viruses, such as herpesvirus, poxvirus, nimavirus and baculoviruse. The proteomics of baculovirus occlusion-derived virions (ODV) were emphasized. Different mass spectrometry techniques used on ,carious baculoviruses were introduced, and the identified structurally associated proteins of baculoviruses are summarized.     

Vaccination againstBoophilus microplus: Localization of antigens on tick gut cells and their interaction with the host immune system

Cattle have been vaccinated againstBoophilus microplus with antigens derived from partially fed female ticks. The immune response of the host lyses the gut cells of adult ticks, causing a reduction in the number, weight and reproductive capacity of engorging ticks. This response is different from the immunity that cattle acquire after repeated tick infestation. Evidence is presented that the antigens used in vaccination are located on the plasma membrane of the gut cells and it is unlikely that these antigens are secreted into the host during feeding. Vaccination using such concealed antigens may not encounter the mechanisms of immune evasion that parasites usually demonstrate.In-vitro assays suggest that vaccination immunity is not dependent on the need to stimulate cell-mediated responses. Immunoglobulin G alone, or with the aid of complement, is enough to damage tick gut.The normal function of the one protein antigen isolated so far is unknown but we speculate that it serves some vital function on the cell plasma membrane.     

Viral security proteins: counteracting host defences

Interactions with host defences are key aspects of viral infection. Various viral proteins perform counter-defensive functions, but a distinct class, called security proteins, is dedicated specifically to counteracting host defences. Here, the properties of the picornavirus security proteins L and 2A are discussed. These proteins have well-defined positions in the viral polyprotein, flanking the capsid precursor, but they are structurally and biochemically unrelated. Here, we consider the impact of these two proteins, as well as that of a third security protein, L(*), on viral reproduction, pathogenicity and evolution. The concept of security proteins could serve as a paradigm for the dedicated counter-defensive proteins of other viruses.     

Viral invasion and host defense: strategies and counter-strategies

The outcome of infection of plants by viruses is determined by the net effects of compatibility functions and defense responses. Recent advances reveal that viruses have the capacity to modulate host compatibility and defense functions by a variety of mechanisms.     

Challenges and rewards of interaction proteomics

The recent explosion of high throughput experimental technologies for characterizing protein interactions has generated large amounts of data describing interactions between thousands of proteins and producing genome scale views of protein assemblies. The systems level views afforded by these data hold great promise of leading to new knowledge but also involve many challenges. Deriving meaningful biological conclusions from these views crucially depends on our understanding of the approximation and biases that enter into deriving and interpreting the data. The challenges and rewards of interaction proteomics are reviewed here using as an example the latest comprehensive high throughput analyses of protein interactions in yeast.     

Building protein-protein interaction networks with proteomics and informatics tools

The systematic characterization of the whole interactomes of different model organisms has revealed that the eukaryotic proteome is highly interconnected. Therefore, biological research is progressively shifting away from classical approaches that focus only on a few proteins toward whole protein interaction networks to describe the relationship of proteins in biological processes. In this minireview, we survey the most common methods for the systematic identification of protein interactions and exemplify different strategies for the generation of protein interaction networks. In particular, we will focus on the recent development of protein interaction networks derived from quantitative proteomics data sets.