Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome

The identification of the whole set of protein interactions taking place in an organism is one of the main tasks in genomics, proteomics and systems biology. One of the computational techniques used by many investigators for studying and predicting protein interactions is the comparison of evolutionary histories (phylogenetic trees), under the hypothesis that interacting proteins would be subject to a similar evolutionary pressure resulting in a similar topology of the corresponding trees. Here, we present a new approach to predict protein interactions from phylogenetic trees, which incorporates information on the overall evolutionary histories of the species (i.e. the canonical "tree of life") in order to correct by the expected background similarity due to the underlying speciation events. We test the new approach in the largest set of annotated interacting proteins for Escherichia coli. This assessment of co-evolution in the context of the tree of life leads to a highly significant improvement (P(N) by sign test approximately 10E-6) in predicting interaction partners with respect to the previous technique, which does not incorporate information on the overall speciation tree. For half of the proteins we found a real interactor among the 6.4% top scores, compared with the 16.5% by the previous method. We applied the new method to the whole E.coli proteome and propose functions for some hypothetical proteins based on their predicted interactors. The new approach allows us also to detect non-canonical evolutionary events, in particular horizontal gene transfers. We also show that taking into account these non-canonical evolutionary events when assessing the similarity between evolutionary trees improves the performance of the method predicting interactions.     

植物UGTs的功能、应用与分子改造研究进展

植物尿苷二磷酸糖基转移酶（uridinediphosphate,UGTs）,在次生代谢产物生物合成、激素平衡、免疫防御、脱毒反应等生理过程中发挥重要作用。随着酶功能表征和结构研究的不断深入,具有催化高效性、区域/立体选择性和底物宽容性的植物UGTs可用于天然/非天然糖苷的酶法直接合成及异源生物合成,植物UGTs酶分子理性改造与定向进化的成功例子也在不断增加。围绕生物学功能、糖基化应用与酶分子改造三个方面,对近几年来植物UGTs的相关研究进行系统综述。同时,对植物UGTs基因的准确预测与筛选、系统功能分析及酶分子理性设计等方面的发展趋势进行展望。     

The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer

The primary plant cell wall comprises the most abundant polysaccharides on the Earth and represents a rich source of energy for organisms which have evolved the ability to digest them. Enzymes able to degrade plant cell wall polysaccharides are widely distributed in micro-organisms but are generally absent in animals, although their presence in insects, especially phytophagous beetles from the superfamilies Chrysomeloidea and Curculionoidea, has recently begun to be appreciated. The observed patchy distribution of endogenous genes encoding these enzymes in animals has raised questions about their evolutionary origins. Recent evidence suggests that endogenous plant cell wall degrading enzymes-encoding genes have been acquired by animals through a mechanism known as horizontal gene transfer (HGT). HGT describes how genetic material is moved by means other than vertical inheritance from a parent to an offspring. Here, we provide evidence that the mustard leaf beetle, Phaedon cochleariae, possesses in its genome genes encoding active xylanases from the glycoside hydrolase family 11 (GH11). We also provide evidence that these genes were originally acquired by P. cochleariae from a species of gammaproteobacteria through HGT. This represents the first example of the presence of genes from the GH11 family in animals.     

玉米螟P450基因cDNA的克隆及植物次生物质对其诱导表达

昆虫细胞色素P450是一类在生物代谢中起重要作用的基因家族,承担着许多重要的生 理功能,包括对植物次生物质代谢和杀虫剂解毒等.本研究以玉米螟5龄幼虫中肠的总RNA为 模板,根据不同昆虫P450基因家族保守氨基酸序列,设计并合成简并引物,利用RT-PCR扩 增出了玉米螟细胞色素P450基因cDNA片段,将其克隆到pMD19 T载体进行序列测定.测序获得了编码213个氨基酸残基的641 bp的DNA片段,命名为OfP450(GenBank登录号：EU807990) ;与已公布的棉铃虫、家蚕、欧洲防风草结网毛虫、小菜蛾和黑腹果蝇等的细胞色素P450氨基酸序列进行比较,其一致性分别为55％、50％、49％、44％和31％.将植物次生物质棉酚、丁布添加入人工饲料中,对玉米螟进行了饲喂实验,采用优化半定量RT-PCR,以18S rRNA为内标,RT-PCR检测进食棉酚、丁布植物化合物的玉米螟中肠P450基因的转录. 结果表明,其转录水平能被棉酚、丁布显著诱导. 提示本实验克隆的玉米螟细胞色素P450对植物次生物质的代谢作用与P450表达量呈正相关.该研究为下一步将植物介导的RNA干扰技术应用于害虫生物防治提供坚实的基础.     

Medicinal plant cell suspension cultures: pharmaceutical applications and high-yielding strategies for the desired secondary metabolites

The development of plant tissue (including organ and cell) cultures for the production of secondary metabolites has been underway for more than three decades. Plant cell cultures with the production of high-value secondary metabolites are promising potential alternative sources for the production of pharmaceutical agents of industrial importance. Medicinal plant cell suspension cultures (MPCSC), which are characterized with the feature of fermentation with plant cell totipotency, could be a promising alternative “chemical factory”. However, low productivity becomes an inevitable obstacle limiting further commercialization of MPCSC and the application to large-scale production is still limited to a few processes. This review generalizes and analyzes the recent progress of this bioproduction platform for the provision of medicinal chemicals and outlines a range of trials taken or underway to increase product yields from MPCSC. The scale-up of MPCSC, which could lead to an unlimited supply of pharmaceuticals, including strategies to overcome and solution of the associated challenges, is discussed.     

A fragment of chloroplast DNA was transferred horizontally,probably from non-eudicots,to mitochondrial genome of <Emphasis Type="Italic">Phaseolus</Emphasis>

The mitochondrial genomes of some Phaseolus species contain a fragment of chloroplast trnA gene intron, named pvs-trnA for its location within the Phaseolus vulgaris sterility sequence (pvs). The purpose of this study was to determine the type of transfer (intracellular or horizontal) that gave rise to pvs-trnA. Using a PCR approach we could not find the respective portion of the trnA gene as a part of pvs outside the Phaseolus genus. However, a BLAST search revealed longer fragments of trnA present in the mitochondrial genomes of some Citrus species, Helianthus annuus and Zea mays. Basing on the identity or near-identity between these mitochondrial sequences and their chloroplast counterparts we concluded that they had relocated from chloroplasts to mitochondria via recent, independent, intracellular DNA transfers. In contrast, pvs-trnA displayed a relatively higher sequence divergence when compared with its chloroplast counterpart from Phaseolus vulgaris. Alignment of pvs-trnA with corresponding trnAfragments from 35 plant species as well as phylogenetic analysis revealed that pvs-trnA grouped with non-eudicot sequences and was well separated from all Fabalessequences. In conclusion, we propose that pvs-trnA arose via horizontal transfer of a trnA intron fragment from chloroplast of a non-eudicot plant to Phaseolus mitochondria. This is the first example of horizontal transfer of a chloroplast sequence to the mitochondrial genome in higher plants.     

Frequent,independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes

Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes—as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.     

植物防卫的碳-养分平衡假说

碳-养分平衡假说(carbon-nutrient balance hypothesis,CNBH)认为,植物组织中次生代谢物浓度受环境碳-资源有效性控制;植物体内次生代谢物按照化学计量的要求进行分配;资源分配给防卫物的必要条件是资源供应量满足植物生长需求后仍过剩。CNBH自提出以来,其适用范围不断受到限制,解释与预测研究结果的能力逐渐显现不足。期间,对CNBH进行过优化和修改,设置了多种限制条件,以期能使CNBH得到补救,继续成为指导植物-草食动物间相互作用和植物体内资源分配的相关理论。然而,随着研究的逐渐深入,CNBH被证实缺乏逻辑性和内在一致性;CNBH不能满足假说本身的发展要求,缺乏明确可行的量化指标体系,也没有明确地标识出理论预测范围与可测试范围之间的界限。研究表明,CNBH的基本假设本身是错误的;随着人们对植物-草食动物间相互作用的认知能力加强,更深刻地认识到资源在植物体内的分配模式,意识到CNBH假说的严重缺陷。在现有的植物防卫理论中,生长-分化平衡假说(growth-differentiation balance hypothesis)较为成熟,不但具有CNBH的优点,而且更具有植物生理学和进化...     

Plant‐like bacterial expansins play contrasting roles in two tomato vascular pathogens

Expansin proteins, which loosen plant cell walls, play critical roles in normal plant growth and development. The horizontal acquisition of functional plant‐like expansin genes in numerous xylem‐colonizing phytopathogenic bacteria suggests that bacterial expansins may also contribute to virulence. To investigate the role of bacterial expansins in plant diseases, we mutated the non‐chimeric expansin genes (CmEXLX2 and RsEXLX) of two xylem‐inhabiting bacterial pathogens, the Actinobacterium Clavibacter michiganensis ssp. michiganensis (Cmm) and the β‐proteobacterium Ralstonia solanacearum (Rs), respectively. The Cmm Δ CmEXLX2 mutant caused increased symptom development on tomato, which was characterized by more rapid wilting, greater vascular necrosis and abundant atypical lesions on distant petioles. This increased disease severity correlated with larger in planta populations of the Δ CmEXLX2 mutant, even though the strains grew as well as the wild‐type in vitro. Similarly, when inoculated onto tomato fruit, Δ CmEXLX2 caused significantly larger lesions with larger necrotic centres. In contrast, the Rs Δ RsEXLX mutant showed reduced virulence on tomato following root inoculation, but not following direct petiole inoculation, suggesting that the RsEXLX expansin contributes to early virulence at the root infection stage. Consistent with this finding, Δ RsEXLX attached to tomato seedling roots better than the wild‐type Rs, which may prevent mutants from invading the plant's vasculature. These contrasting results demonstrate the diverse roles of non‐chimeric bacterial expansins and highlight their importance in plant–bacterial interactions.