Post-genomics of microsporidia, with emphasis on a model of minimal eukaryotic proteome: a review

The genome sequence of the microsporidian parasite Encephalitozoon cuniculi Levaditi, Nicolau et Schoen, 1923 contains about 2,000 genes that are representative of a non-redundant potential proteome composed of 1,909 protein chains. The purpose of this review is to relate some advances in the characterisation of this proteome through bioinformatics and experimental approaches. The reduced diversity of the set of E. cuniculi proteins is perceptible in all the compilations of predicted domains, orthologs, families and superfamilies, available in several public databases. The phyletic patterns of orthologs for seven eukaryotic organisms support an extensive gene loss in the fungal clade, with additional deletions in E. cuniculi. Most microsporidial orthologs are the smallest ones among eukaryotes, justifying an interest in the use of these compacted proteins to better discriminate between essential and non-essential regions. The three components of the E. cuniculi mRNA capping apparatus have been especially well characterized and the three-dimensional structure of the cap methyltransferase has been elucidated following the crystallisation of the microsporidial enzyme Ecm1. So far, our mass spectrometry-based analyses of the E. cuniculi spore proteome has led to the identification of about 170 proteins, one-quarter of these having no clearly predicted function. Immunocytochemical studies are in progress to determine the subcellular localisation of microsporidia-specific proteins. Post-translational modifications such as phosphorylation and glycosylation are expected to be soon explored.     

中国植物弹状病毒研究进展

弹状病毒含有单链负义RNA基因组,寄主范围比较广泛,能侵染无脊椎动物、脊椎动物以及植物等寄主,对人类的健康、农作物产量和自然生态系统造成严重威胁。植物弹状病毒主要根据复制场所分为细胞质弹状病毒属Cytorhabdovirus和细胞核弹状病毒属Nucleorhabdovirus,其基因组由单股负链RNA组成。此外,Dichorhavirus和Varicosavirus病毒属是两个新鉴定的植物弹状病毒属,其特征是具有二分体基因组。本文着重介绍危害我国农作物的几类植物弹状病毒,对它们的病理学、病害流行、基因组信息以及传播媒介进行概述,为中国植物弹状病毒病害的研究提供理论依据。     

小麦锈菌蛋白激酶基因家族的鉴定与生物信息学分析

为深入分析锈菌结构基因组,阐明锈菌毒性变异的分子机制,本研究通过生物信息分析方法,对3种小麦锈菌蛋白激酶(protein kinases,PKs)超家族预测基因进行了系统分析,利用COG(clusters of orthologous groups of proteins)、KEGG(Kyoto encyclopedia of genes and genomes)、GO(gene ontology)和PHI(pathogen-host interactions)数据库进行注释分析,并对小麦锈菌MAPK基因的蛋白质互作网络进行预测。结果表明,条锈菌Puccinia striiformis、叶锈菌P.triticina和秆锈菌P.graminis的PKs基因数量分别为221、159和159个,不同PKs基因家族类型在3种锈菌中的数量分布上表现出很高的保守性。注释分析表明,PKs家族预测功能涉及病原菌生长发育中的调控作用和病原菌-寄主互作机制,包括信号传导和致病因子等。PKs家族核心基因数目在蛋白激酶基因中占比大于1/3。MAPK基因的催化结构域序列呈现高度相似性。以STRING数据库的酿酒酵母蛋白质互作网络信息为参考,对小麦锈菌MAPK基因的蛋白质互作网络进行预测,共鉴定出25个互作关系,包含29个MAPK基因。研究表明这3种锈菌之间MAPK互作蛋白质分布不均衡,这可能反映了锈菌基因组进化的特殊复杂性。     

后生动物线粒体基因组基因次序重组规律分析

后生动物线粒体基因组由于其大小和基因数目的相对稳定,被认为是研究后生动物系统发育关系的一种理想模型。后生动物线粒体基因组大多有37个基因,包括22个tRNA编码基因和13个蛋白编码基因,它们的排列顺序也被认为是研究后生动物线粒体基因组很好的材料。通过对来自NCBI数据库的2 511种后生动物线粒体基因组提取的基因次序,包括对基因的倒置、共有基因簇、基因的缺失和重复、相邻位置的基因交换等重组形式的概述,综述了近年来对动物线粒体基因组基因次序重组的研究状况。     

Take-all of wheat

Take-all, caused by the soilborne fungus Gaeumannomyces graminis var. tritici, is arguably the most-studied root disease of any crop, yet remains the most important root disease of wheat worldwide. S. D. Garrett launched the study of root diseases and soilborne pathogens as an independent field of science starting in the middle of the 20th century, inspired by and based in large part on his research on take-all during the first half of the 20th century. Because there has been neither a source of host plant resistance nor an effective and economical fungicide for use against this disease, the focus for nearly a century has been on cultural and biological controls. In spite of the intensive and extensive works towards these controls, with mostly site-or soil-specific success, the only broadly and consistently effective controls require either crop rotation (break crops), or the converse, wheat monoculture to induce take-all decline. Take-all decline has become the model system for research on biological control of plant pathogens in the rhizosphere and provided the first proof to the scientific world after decades of debate that antibiotics are both produced in soils and play a role in the ecology of soil microorganisms. On the other hand, even the best yields following take-all decline are rarely equal to those achieved with crop rotation. Because of this, the continuing trends globally to shorten rather than lengthen the rotations in wheat-based cropping systems, and the growing use of direct-seed (no-till) trashy systems to reduce costs and protect soil and water resources, new methods to control take-all are needed more than ever. With high resolution maps of the genomes of cereals and other grasses now available, including a complete sequence of the rice genome, and the interesting differences as well as striking similarities among the genomes of cereals and related grasses, gene transfer to wheat from oats, rice, maize and other grass species resistant to G. graminis var. tritici should be pursued.     

Korean <Emphasis Type="Italic">Brassica oleracea</Emphasis> germplasm offers a novel source of qualitative resistance to blackleg disease

Blackleg disease, caused by the hemibiotrophic fungal pathogen Leptosphaeria maculans, is one of the most devastating disease of Brassica species worldwide. To date, a total of 20 race-specific blackleg resistance (R) genes have been reported and all of those loci are located in either the A or B genomes of various Brassica species. The B. oleracea genome (CC) shares a high ancestral synteny with the A genome of B. rapa, suggesting the presence of qualitative (race specific) resistance to blackleg disease is also possible in B. oleracea germplasm. In the present study the C genome of Korean B. oleracea germplasm was screened for the presence of blackleg R genes. Thirty-two inbred cabbage lines with unknown resistance profiles, along with five control B. napus lines with well-characterised race-specific R genes, were assessed for cotyledon resistance against two L. maculans isolates with known and highly-contrasting avirulence gene (Avr) profiles. Two cabbage accessions were identified which produced a strong resistance when challenged with either isolate, demonstrating the presence of effective blackleg R genes in the cabbage C genome. Additionally, 16 microsatellite markers linked to seven different R genes of the B. napus A genome were converted into markers for their homologous regions on the B. oleracea C genome. These markers were used to screen all B. oleracea lines to assess if the novel C genome R genes were syntenous to known R gene-homologous regions of the A genome. The resistant cabbage lines offer C genome R genes for the protection of B. oleracea varieties against incursion of blackleg disease, as well as novel additional resistance sources for introgression into B. napus and B. carinata breeding material.     

miRNA在植物病毒基因组中的靶基因预测及分析

microRNA(miRNA)是一类长约22nt的内源性的非编码小RNA,在植物的生长发育和胁迫响应中起重要调控作用。本文通过生物信息学的方法,在miRBase中下载了12种植物的miRNA序列;在DPVweb和VIDE病毒数据库中查找侵染这些植物的病毒,并在NCBI数据库中搜索其基因组序列,共获得173种病毒的基因组序列。用psRNATarget在线软件预测植物miRNA在植物病毒中的靶基因,发现植物miRNA可能参与调控包括聚合蛋白、衣壳蛋白、逆转录酶、复制相关基因、通读蛋白、依赖RNA的RNA聚合酶等多种植物病毒基因的表达。     

A review of the development of two types of human skeletal muscle infections from microsporidia associated with pathology in invertebrates and cold-blooded vertebrates

Traditionally, the Microsporidia were primarily studied in insects and fish. There were only a few human cases of microsporidiosis reported until the advent of AIDS, when the number of human microsporidian infections dramatically increased and the importance of these new pathogens to medicine became evident. Over a dozen different kinds of microsporidia infecting humans have been reported. While some of these infections were identified in new genera (Enterocytozoon, Vittaforma), there were also infections identified from established genera such as Pleistophora and Encephalitozoon. The genus Pleistophora, originally erected for a species described from fish muscle, and the genus Encephalitozoon, originally described from disseminated infection in rabbits, suggested a link between human infections and animals. In the 1980's, three Pleistophora sp. infections were described from human skeletal muscle without life cycles presented. Subsequently, the genus Trachipleistophora was established for a human-infecting microsporidium with developmental differences from species of the genus Pleistophora. Thus, the existence of a true Pleistophora sp. or spp. in humans was put into question. We have demonstrated the life-cycle stages of the original Pleistophora sp. infection from human muscle, confirming the existence of a true Pleistophora species in humans, P. ronneafiei Cali et Takvorian, 2003, the first demonstrated in a mammalian host. Another human infection, caused by a parasite from invertebrates, was Brachiola algerae Lowman, Takvorian et Cali, 2000. The developmental stages of this human muscle-infecting microsporidium demonstrate morphologically what we have also confirmed by molecular means, that B. algerae, the mosquito parasite, is the causative agent of this human skeletal muscle infection. B. algerae had previously been demonstrated in humans but only in surface infections, skin and eye. The diagnostic features of B. algerae and P. ronneafiei infections in human skeletal muscle are presented. While Encephalitozoon cuniculi has been known as both an animal (mammal) and human parasite, the idea of human microsporidial infections derived from cold-blooded vertebrates and invertebrates has only been suggested by microsporidian phylogeny based on small subunit ribosomal DNA sequences but has not been appreciated. The morphological data presented here demonstrate these relationships. Additionally, water, as a link that connects microsporidial spores in the environment to potential host organisms, is diagrammatically presented.     

36个小麦审定和区试品种(系)的抗白粉病基因推导

明确我国当前小麦审定和区试品种含有的抗白粉病基因, 可为这些品种在小麦抗病育种中的应用及品种合理布局和轮换提供依据。本研究采用24个不同毒性的小麦白粉菌菌株对36个小麦审定和区试品种(系)进行抗白粉病基因推导, 参试品种(系)与46个已知抗病基因小麦品种(系)抗谱比较的结果表明, 11个小麦审定品种中有5个品种对所有供试白粉菌菌株表现抗性, 结合亲本溯源, 推测其中有3个品种可能携有Pm21基因; 另外6个审定品种中有5个品种可能含有抗病基因Pm2, 且其对应的亲本或亲本组合中含有抗病基因Pm2。25个区试品种(系)中有3个可能含有Pm21, 10个含有Pm2, 1个含有Pm2+6,2个含有Pm4b,1个含有Pm8。另外, 参试的36个品种(系)中还有9个品种(系)和已知基因品种抗谱存在一定差异。总体上, 推导出已知基因的品种以含有Pm2基因的品种最多, Pm21基因的品种次之, 建议在生产上加强对Pm21基因品种(系)特别是已审定的携有Pm21基因品种的推广和应用, 应该注意一些省份在育种和生产上应慎用或少用含Pm2基因的品种(系)。     

Electrophoretic karyotypes of <Emphasis Type="Italic">Rhynchosporium commune,R. secalis and R. agropyri</Emphasis>

Pulsed-field gel electrophoresis was used to generate electrophoretic karyotypes for 15 strains representing the three closely related plant-pathogenic fungi Rhynchosporium commune, R. secalis and R. agropyri. Between 13 and 16 chromosomes ranging in size from 0.9 to 6.4 Mb were found among the strains, leading to estimated genome sizes ranging from 54 to 63 Mb. Southern hybridization was used to identify homologous chromosomes, allowing detection of chromosome-length polymorphisms. There were no obvious differences in genome sizes or structures among the three species. The avirulence gene NIP1 is present on a large chromosome that is not likely to be dispensable. Two strains of R. commune that were proposed in earlier studies to be aneuploid as a result of a parasexual cycle did not possess a larger number of chromosomes. The reported information on genome size and chromosome number will be useful for genome sequencing projects that aim to identify genes involved in speciation and host specialization.     

Population dynamics and pathogenic races of rice blast fungus, <Emphasis Type="Italic">Magnaporthe oryzae</Emphasis> in the Mekong Delta in Vietnam

In a study of the population dynamics of Magnaporthe oryzae in the Mekong Delta in Vietnam, 226 isolates were collected from various sites in December 2001, September and December 2004. The pathogenic races of isolates were determined using international differential rice varieties. Isolates with the same race number were not found, not even in the same field or on the same seedling, suggesting that the fungus in the Mekong Delta was dynamically changing. But focusing on the known major resistance genes in the Japanese differential varieties, some isolates in the area were found to be the same race. Phylogenetic analyses based on the transposable elements Pot2 and MGR586 in the genomes supported that the pathogenic races were critically variable in comparison with the genomic diversity. Isolates with MAT1-1 predominated in the Mekong Delta, but in some provinces those with MAT1-2 coexisted at low frequency with MAT1-1. However, no isolates produced perithecia and ascospores. Isolates in the Mekong Delta probably had hot spots in their genomes that are easily altered and associated with some avirulence genes.     

The Genomic Sequence of Pseudomonas fluorescens Pf-5: Insights Into Biological Control

ABSTRACT The complete sequence of the 7.07 Mb genome of the biological control agent Pseudomonas fluorescens Pf-5 is now available, providing a new opportunity to advance knowledge of biological control through genomics. P. fluorescens Pf-5 is a rhizosphere bacterium that suppresses seedling emergence diseases and produces a spectrum of antibiotics toxic to plant-pathogenic fungi and oomycetes. In addition to six known secondary metabolites produced by Pf-5, three novel secondary metabolite biosynthesis gene clusters identified in the genome could also contribute to biological control. The genomic sequence provides numerous clues as to mechanisms used by the bacterium to survive in the spermosphere and rhizosphere. These features include broad catabolic and transport capabilities for utilizing seed and root exudates, an expanded collection of efflux systems for defense against environmental stress and microbial competition, and the presence of 45 outer membrane receptors that should allow for the uptake of iron from a wide array of siderophores produced by soil microorganisms. As expected for a bacterium with a large genome that lives in a rapidly changing environment, Pf-5 has an extensive collection of regulatory genes, only some of which have been characterized for their roles in regulation of secondary metabolite production or biological control. Consistent with its commensal lifestyle, Pf-5 appears to lack a number of virulence and pathogenicity factors found in plant pathogens.     

Genetic Variation in Spiroplasma citri

Spiroplasmas are members of the Class Mollicutes, wall-less prokaryotes having a high adenosine–thymidine content in their small genomes. Spiroplasma citri is a plant pathogen that inhabits phloem. Like other phytopathogenic spiroplasmas and the related phytoplasmas, it is transmitted from plant to plant by phloem-feeding leafhoppers that serve as alternate hosts for the spiroplasma as well as vectors. Genetic information in spiroplasmas is carried on a circular chromosome, on plasmids and/or in virus genomes. A picture emerging from recent research on the S. citri genome is one of frequent and often extensive variation, resulting from a number of different mechanisms. Expansion and contraction events must continually be occurring in about equal proportions so that the net genome size varies within defined boundaries. Particularly impressive are large changes in genome size that can occur in only a few generations. As with most organisms, genetic variation in S. citri results from variation in extrachromosomal DNA content, changes due to DNA replication and repair processes and changes due to recombination. The implied flux of genetic information into and out of the S. citri genome should be beneficial to the bacterium, allowing it, with its small genome size, to adapt to new environments.     

基于线粒体全基因组解析华北地区棉铃虫种群遗传结构

为明确我国华北地区棉铃虫种群间遗传分化,通过高通量测序测定华北地区河北省廊坊市、河南省新乡市和山东省烟台市27份棉铃虫线粒体全基因组,并分析这3个市棉铃虫种群的遗传结构。结果表明,华北地区棉铃虫线粒体基因组全长15 345~15 375 bp,长度变异主要由基因间隔区的A+T富集区造成,所有样品的13个蛋白编码基因在长度上均无差异,总群体间遗传分化很小,遗传分化指数为0.025,基因流水平很高,为19.46。27份样品被聚为亚型I和亚型II两个遗传分支,但未形成明显的地理结构,其中亚型II比例较低,仅包含河北省和山东省的4份样品。表明我国华北地区棉铃虫种群存在线粒体亚型分化,不同区域种群之间存在广泛的基因交流,没有形成谱系遗传结构,推测棉铃虫在华北地区存在高迁飞现象。     

A novel type of Potato virus Y recombinant genome,determined for the genetic strain PVYE

Two Potato virus Y (PVY) isolates collected in Brazil, PVY‐AGA and PVY‐MON, were identified as recombinants between two parent genomes, PVY^NTN and PVY‐NE‐11, with a novel type of genomic pattern. The new recombinants had an ordinary PVY^NTN genome structure for approximately 6·7‐kb from the 5′‐end of the genome whereas the 3′‐terminal 3·0‐kb segment had two fragments of NE‐11‐like sequence separated by another small PVY^NTN‐like fragment. PVY strains are defined based on the hypersensitive resistance (HR) response in potato indicators. Both PVY‐AGA and PVY‐MON isolates did not induce the HR in potato cultivars carrying Ny, Nc, or (putative) Nz genes and thus were able to overcome all known resistance genes to PVY. Only one of the two isolates, PVY‐AGA, induced a vein necrosis reaction in tobacco. The biological responses of the potato indicators and tobacco defined PVY‐MON as an isolate of the PVY^E strain. To distinguish PVY‐AGA and PVY‐MON from other PVY^NTN isolates, an RT‐PCR test was developed utilizing new specific primers from the capsid protein gene area and producing a characteristic 955‐bp band. Serological profiling of these PVY isolates with three monoclonal antibodies revealed an unusual reactivity, where one of the two commercial PVY^N‐specific monoclonal antibodies did not recognize PVY‐AGA. The ability of these new PVY recombinants to overcome resistance genes in potato producing mild or no symptoms, combined with the lack of serological reactivity towards at least one PVY^N‐specific antibody may present a significant threat posed by these isolates to seed potato production areas.     

Cereal diseases caused by <Emphasis Type="Italic">Fusarium graminearum</Emphasis>: from biology of the pathogen to oxidative burst-related host defense responses

Small grain cereals, such as wheat, barley and oats are considered among the most important food sources. Plant-parasitic nematodes play a considerable role in decreasing cereal yields. The three-major species of cereal cyst nematodes (CCN) Heterodera avenae, H. latipons, and H. filipjevi are distributed worldwide and cause considerable damage. This review provides information regarding the global distribution of these nematode species, yield loss due to CCN, their biology and pathogenic relation to plants, identification and control through agricultural practices, biological agents and resistance breeding. As morphological identification of CCN is difficult and time-consuming, several molecular techniques for the identification of these CCN species have been developed in recent years. The restrictions on the use of nematicides demand for resistance to CCN. Resistance genes in several lines are known and are used in numerous breeding programmes against CCN; pyramiding these resistance genes into high yielding cultivars that could become commercially available for farmers is progressing.