Genomic islands in Photorhabdus

Genomic islands are responsible for unique aspects of bacterial behavior such as symbiosis and pathogenicity. Photorhabdus luminescens is a pathogen of insects that spends part of its lifecycle in symbiosis with a nematode. Here, we describe novel genomic islands from Photorhabdus that are involved in symbiosis and pathogenicity, and discuss the inter-relationship between virulence factors used against invertebrates and vertebrates.     

Insect pathogenicity islands in the insect pathogenic bacterium Photorhabdus

Abstract. Genomic islands are regions of the bacterial genome responsible for unique aspects of bacterial behaviour, such as host symbiosis and pathogenicity. Where such regions are involved in pathogenesis, they are termed pathogenicity islands (PAIs). Photorhabdus luminescens is an insect pathogen that spends part of its life in symbiosis with a nematode and part of its life as an insect pathogen. Here, several novel PAIs from P. luminescens ssp. akhurstii strain W14 are described that encode factors involved apparently in both nematode symbiosis and insect pathogenicity. The structures of these islands are compared with those found in mammalian pathogens, and the potential cross‐talk between virulence factors used against invertebrates and those used against vertebrates is discussed.     

Photorhabdus: towards a functional genomic analysis of a symbiont and pathogen

Pathogenicity and symbiosis are central to bacteria-host interactions. Although several human pathogens have been subjected to functional genomic analysis, we still understand little about bacteria-invertebrate interactions despite their ecological prevalence. Advances in our knowledge of this area are often hindered by the difficulty of isolating and working with invertebrate pathogenic bacteria and their hosts. Here we review studies on pathogenicity and symbiosis in an insect pathogenic bacterium Photorhabdus and its entomopathogenic nematode vector and model insect hosts. Whilst switching between these hosts, Photorhabdus changes from a state of symbiosis with its nematode vector to one of pathogenicity towards its new insect host and both the bacteria and the nematode then cooperatively exploit the dying insect. We examine candidate genes involved in symbiosis and pathogenicity, their secretion and expression patterns in culture and in the host, and begin to dissect the extent of their genetic coregulation. We describe the presence of several large genomic islands, putatively involved in pathogenicity or symbiosis, within the otherwise Yersinia-like backbone of the Photorhabdus genome. Finally, we examine the emerging comparative genomics of the Photorhabdus group and begin to describe the interrelationship between anti-invertebrate virulence factors and those used against vertebrates.     

PIPS: pathogenicity island prediction software

The adaptability of pathogenic bacteria to hosts is influenced by the genomic plasticity of the bacteria, which can be increased by such mechanisms as horizontal gene transfer. Pathogenicity islands play a major role in this type of gene transfer because they are large, horizontally acquired regions that harbor clusters of virulence genes that mediate the adhesion, colonization, invasion, immune system evasion, and toxigenic properties of the acceptor organism. Currently, pathogenicity islands are mainly identified in silico based on various characteristic features: (1) deviations in codon usage, G+C content or dinucleotide frequency and (2) insertion sequences and/or tRNA genetic flanking regions together with transposase coding genes. Several computational techniques for identifying pathogenicity islands exist. However, most of these techniques are only directed at the detection of horizontally transferred genes and/or the absence of certain genomic regions of the pathogenic bacterium in closely related non-pathogenic species. Here, we present a novel software suite designed for the prediction of pathogenicity islands (pathogenicity island prediction software, or PIPS). In contrast to other existing tools, our approach is capable of utilizing multiple features for pathogenicity island detection in an integrative manner. We show that PIPS provides better accuracy than other available software packages. As an example, we used PIPS to study the veterinary pathogen Corynebacterium pseudotuberculosis, in which we identified seven putative pathogenicity islands.     

Natural occurrence of Bacillus thuringiensis and Bacillus cereus in eukaryotic organisms: a case for symbiosis

Bacillus thuringiensis and Bacillus cereus, two members of the Bacillus cereus sensu lato group, are most noted for their virulence in, respectively, arthropods and mammals including humans. Because of their pathogenicity to insects in particular, and their narrow host range, strains of B. thuringiensis have been utilised successfully as biocontrol agents of insect pests. Whereas B. cereus is not an established entomopathogen, certain strains of this species are well known to be etiological agents of gastrointestinal and emetic syndromes in humans. While much is known about the taxonomic properties and molecular basis for virulence of B. thuringiensis and B. cereus, comparatively less is known about their ecology in natural environments. Thus, there are limited data regarding their resilience, i.e. recycling of vegetative and sporulated phases of growth in soil, ecolgical niches including symbiotic interactions with other organisms, and the impact on ecosystems in which they proliferate. Nevertheless, based on recent data, a picture is beginning to emerge that B. thuringiensis and B. cereus are capable of establishing mutual and commensal relationships with both animals and plants. In this regard, these bacilli can proliferate in the digestive tracts of animals, where upon defecation they form dormant spores in the soil, and to a lesser extent on the phylloplane and rhizospheres of plants. Altogether, current evidence strongly suggests that B. thuringiensis and B. cereus are capable of completing their life cycles and recycling through various reservoirs, including animals, plants, and soil. This review focuses on the current knowledge pertaining to the ecologic interactions between B. thuringiensis and B. cereus and eukaryotic hosts, with special emphasis on symbiosis.     

基于样带的唐古特白刺灌丛沙包空间格局尺度研究

黄河河岸与库布齐沙漠之间生态过渡带上的唐古特白刺(Nitraria Tangutorum)灌丛沙包由于遭受到不同程度的破坏而表现出一定程度的退化,空间格局尺度从一定程度上表征了其破碎化程度。我们分别应用样方方差法,小波分析,分维,谱分析以及空隙度分析等方法对鄂尔多斯高原北缘唐古特白刺灌丛沙包的空间格局尺度进行了比较研究,旨在选出适合分析干旱半干旱区白刺灌丛沙包空间格局尺度的方法,并确定研究区内唐古特白刺灌丛沙包的空间格局尺度,为保护唐古特白刺灌丛沙包提供科学依据。结果表明:(1)TTLQV法得到的格局尺度过大,而小波分析得到的格局尺度过小,分维分析得到的格局尺度除了相对较小之外,趋势也不明显,因此都不适合分析干旱半干旱区白刺灌丛沙包的空间格局尺度;(2)而3TLQV,tQV,谱分析和空隙度分析所得到的结果则相对容易接受,其大小顺序是:3TLQV>tQV>空隙度分析>谱分析;(3)独贵塔拉、呼和木独和巴拉贡唐古特白刺灌丛沙包的空间格局尺度分别为16.7～27.1m,10.2～25.0m和8.8～17.0m,这一结果将有助于在今后的研究中合理地确定研究范围和尺度。     

Experimental Evolution of a Plant Pathogen into a Legume Symbiont

Rhizobia are phylogenetically disparate α- and β-proteobacteria that have achieved the environmentally essential function of fixing atmospheric nitrogen in symbiosis with legumes. Ample evidence indicates that horizontal transfer of symbiotic plasmids/islands has played a crucial role in rhizobia evolution. However, adaptive mechanisms that allow the recipient genomes to express symbiotic traits are unknown. Here, we report on the experimental evolution of a pathogenic Ralstonia solanacearum chimera carrying the symbiotic plasmid of the rhizobium Cupriavidus taiwanensis into Mimosa nodulating and infecting symbionts. Two types of adaptive mutations in the hrpG-controlled virulence pathway of R. solanacearum were identified that are crucial for the transition from pathogenicity towards mutualism. Inactivation of the hrcV structural gene of the type III secretion system allowed nodulation and early infection to take place, whereas inactivation of the master virulence regulator hrpG allowed intracellular infection of nodule cells. Our findings predict that natural selection of adaptive changes in the legume environment following horizontal transfer has been a major driving force in rhizobia evolution and diversification and show the potential of experimental evolution to decipher the mechanisms leading to symbiosis.     

Legume growth-promoting rhizobia: An overview on the Mesorhizobium genus

The need for sustainable agricultural practices is revitalizing the interest in biological nitrogen fixation and rhizobia-legumes symbioses, particularly those involving economically important legume crops in terms of food and forage. The genus Mesorhizobium includes species with high geographical dispersion and able to nodulate a wide variety of legumes, including important crop species, like chickpea or biserrula. Some cases of legume-mesorhizobia inoculant introduction represent exceptional opportunities to study the rhizobia genomes evolution and the evolutionary relationships among species. Complete genome sequences revealed that mesorhizobia typically harbour chromosomal symbiosis islands. The phylogenies of symbiosis genes, such as nodC, are not congruent with the phylogenies based on core genes, reflecting rhizobial host range, rather than species affiliation. This agrees with studies showing that Mesorhizobium species are able to exchange symbiosis genes through lateral transfer of chromosomal symbiosis islands, thus acquiring the ability to nodulate new hosts. Phylogenetic analyses of the Mesorhizobium genus based on core and accessory genes reveal complex evolutionary relationships and a high genomic plasticity, rendering the Mesorhizobium genus as a good model to investigate rhizobia genome evolution and adaptation to different host plants. Further investigation of symbiosis genes as well as stress response genes will certainly contribute to understand mesorhizobia-legume symbiosis and to develop more effective mesorhizobia inoculants.     

Sip,an integrase protein with excision,circularization and integration activities,defines a new family of mobile Staphylococcus aureus pathogenicity islands

We report the complete sequence of Staphylococcal pathogenicity island bovine 2 (SaPIbov2), encoding the biofilm-associated protein Bap. SaPIbov2 contains 24 open reading frames, including sip, which encodes a functional staphylococcal integrase protein. SaPIbov2 is bordered by 18 bp direct repeats. The integration site into the chromosome lies at the 3' end of a gene encoding GMP synthase. SaPIbov2 has extensive similarity to previously described pathogenicity islands of Staphylococcus aureus. The principal difference is that toxin genes present in the other pathogenicity islands are exchanged for a transposon-like element that carries the bap gene and genes encoding an ABC transporter and a transposase. Also, SaPIbov2 can be excised to form a circular element and can integrate site-specifically and RecA-independently at a chromosomal att site in a Sip-dependent manner. This was demonstrated both in S. aureus and with plasmid substrates ectopically in Escherichia coli. Thus, SaPIbov2 encodes a functional recombinase of the integrase family that promotes element excision and insertion/integration. In addition, we demonstrated that the presence of SaPIbov2 facilitated the persistence of S. aureus in an intramammary gland infection model. Finally, different bovine isolates of S. aureus were found to carry islands related to SaPIbov2, suggesting the existence of a family of related pathogenicity islands.     

Functional analysis of pyochelin-/enantiopyochelin-related genes from a pathogenicity island of Pseudomonas aeruginosa strain PA14

Genomic islands are foreign DNA blocks inserted in so-called regions of genomic plasticity (RGP). Depending on their gene content, they are classified as pathogenicity, symbiosis, metabolic, fitness or resistance islands, although a detailed functional analysis is often lacking. Here we focused on a 34-kb pathogenicity island of Pseudomonas aeruginosa PA14 (PA14GI-6), which is inserted at RGP5 and carries genes related to those for pyochelin/enantiopyochelin biosynthesis. These enantiomeric siderophores of P. aeruginosa and certain strains of Pseudomonas protegens are assembled by a thiotemplate mechanism from salicylate and two molecules of cysteine. The biochemical function of several proteins encoded by PA14GI-6 was investigated by a series of complementation analyses using mutants affected in potential homologs. We found that PA14_54940 codes for a bifunctional salicylate synthase/salicyl-AMP ligase (for generation and activation of salicylate), that PA14_54930 specifies a dihydroaeruginoic acid (Dha) synthetase (for coupling salicylate with a cysteine-derived thiazoline ring), that PA14_54910 produces a type II thioesterase (for quality control), and that PA14_54880 encodes a serine O-acetyltransferase (for increased cysteine availability). The structure of the PA14GI-6-specified metabolite was determined by mass spectrometry, thin-layer chromatography, and HPLC as (R)-Dha, an iron chelator with antibacterial, antifungal and antitumor activity. The conservation of this genomic island in many clinical and environmental P. aeruginosa isolates of different geographical origin suggests that the ability for Dha production may confer a selective advantage to its host.     

链格孢柑橘致病型过氧化物酶体对接复合体蛋白AaPex13和AaPex14的生物学功能

过氧化物酶体是存在于真核细胞中的一类单层膜细胞器,参与多种生理生化代谢过程,而Pex13和Pex14是过氧化物酶体膜上的对接复合体蛋白,参与基质蛋白-受体复合体的跨膜运输。目前,Pex13和Pex14在大多数植物病原真菌中的生物学功能尚不清楚。本研究鉴定了柑橘褐斑病菌链格孢柑橘致病型(the tangerine pathotype of Alternaria alternata)的对接复合体蛋白Pex13和Pex14,并构建基因敲除突变体与回补菌株,探究其生物学功能。结果表明,与野生型和回补菌株相比,ΔAaPex13和ΔAaPex14营养生长、分生孢子形成显著下降,分生孢子的萌发率显著降低,抗氧化能力和抗细胞壁胁迫能力也显著减弱,病菌的ACT毒素产量分别降低30%和33%,在离体叶片上丧失致病力。此外,AaPex13和AaPex14的缺失导致基质蛋白无法定位到过氧化物酶体,过氧化物酶体生物发生存在缺陷。本研究明确了AaPex13和AaPex14在病菌生长发育、过氧化物酶体形成、ACT毒素产生以及维持致病力方面都具有重要的调控作用。     

Bacterial pathogenicity islands

The information on the key pathogenicity factors of uropathogenic and enteropathogenic Escherichia coli, Shigella, Salmonella, Vibrio cholerae, Yersinia, Listeria and Helicobacter pylori is reviewed. The analysis of data on pathogenicity "islands" and "islets" of infective agents is given. The problems of the genetic control of pathogenicity factors and the functions of pathogenicity "islands", found in infective agents, are discussed.     

千岛湖片段化栖息地地栖哺乳动物的红外相机监测及最小监测时长

作为典型的陆桥岛屿, 千岛湖成为检验栖息地片段化理论的自然研究平台。2011年5月1日至2014年3月31日, 我们在千岛湖32个岛屿和1个大陆对照样点布设了60台红外相机, 对千岛湖体型较大的地栖兽类及其最小监测时长进行了监测和研究。在27,798个相机日的监测中, 共获得动物影像照片23,639张, 照片清晰、可进行物种鉴定的有2,414张, 占照片总数的10.2%; 其中体型较大的地栖兽类独立照片988张, 识别为9个物种: 穿山甲(Manis pentadactyla)、黄麂(Muntiacus reevesi)、野猪(Sus scrofa)、华南兔(Lepus sinensis)、马来豪猪(Hystrix brachyuran)、猪獾(Arctonyx collaris)、鼬獾(Melogale moschata)、花面狸(Paguma larvata)和豹猫(Prionailurus bengalensis), 平均独立照片拍摄率为40.9%。种-面积曲线研究表明, 岛屿上的地栖兽类物种丰富度随着岛屿面积的增大而增大, 曲线的z值为0.27。大岛(>10 ha)中, 最小监测时长随面积增加而增加, 而小岛没有明显趋势; 最小监测时长随隔离度增加而减小, 但关系不显著(d.f. = 20, F = 3.067, P = 0.095), 表明建湖后栖息地的片段化与岛屿化导致了一些对面积或栖息地较为敏感的大型兽类在小岛屿上的局部灭绝。因此, 我们建议对于面积较大的片段化栖息地, 红外相机应保证较长的最小监测时长, 而面积较小的片段化栖息地在监测中应根据隔离度、基质性质、物种种类适时调整调查强度, 以完整反映当地物种实际情况。     

Characterization and expression analysis of Staphylococcus aureus pathogenicity island 3. Implications for the evolution of staphylococcal pathogenicity islands

We describe the complete sequence of the 15.9-kb staphylococcal pathogenicity island 3 encoding staphylococcal enterotoxin serotypes B, K, and Q. The island, which meets the generally accepted definition of pathogenicity islands, contains 24 open reading frames potentially encoding proteins of more than 50 amino acids, including an apparently functional integrase. The element is bordered by two 17-bp direct repeats identical to those found flanking staphylococcal pathogenicity island 1. The island has extensive regions of homology to previously described pathogenicity islands, particularly staphylococcal pathogenicity islands 1 and bov. The expression of 22 of the 24 open reading frames contained on staphylococcal pathogenicity island 3 was detected either in vitro during growth in a laboratory medium or serum or in vivo in a rabbit model of toxic shock syndrome using DNA microarrays. The effect of oxygen tension on staphylococcal pathogenicity island 3 gene expression was also examined. By comparison with the known staphylococcal pathogenicity islands in the context of gene expression described here, we propose a model of pathogenicity island origin and evolution involving specialized transduction events and addition, deletion, or recombination of pathogenicity island "modules."     

大丽轮枝菌VdSCH9基因的功能研究

大丽轮枝菌是一种土传性植物病原真菌,可侵染多种植物并引发黄萎病。目前,人们关于大丽轮枝菌的侵染和致病机制的了解还很不深入。本文通过敲除大丽轮枝菌编码丝氨酸/苏氨酸的蛋白激酶基因VdSCH9,阐明了其在大丽轮枝菌生长发育及致病过程中的作用。SCH9基因在酵母中的表达与cAMP-PKA途径和TOR信号通路相关,对酵母的生长、压力响应和寿命等有重要作用。大丽轮枝菌VdSCH9敲除突变体的生长速率显著下降,菌落边缘菌丝更为稀疏,菌丝分枝减少,对棉花植株为害的平均病情指数为56.6,显著低于野生型和互补突变体的平均病情指数90.5和82.8,对茄子植株为害的平均病情指数为65.9,也显著低于野生型和互补突变体的平均病情指数91.1和89.8。另外,敲除突变体对于高渗透压、氧化还原压力、细胞膜和细胞壁完整性等压力条件的敏感性增强。因此,VdSCH9对于大丽轮枝菌的生长、压力响应及致病力均有重要作用。     

Direct observations of the association between a deep-sea fish and a giant scyphomedusa

This is a report of evidence of a close symbiotic relationship between the scyphomedusa, Stygiomedusa gigantea and the fish, Thalassobathia pelagica. Images from remotely operated vehicles (ROV) were obtained of the fish swimming on and around the large scyphomedusa. This is the first ever documented symbiosis between an Ophidiform fish and a medusa.     

组蛋白去乙酰化酶CfSnt2调控果生刺盘孢生长发育和致病力

炭疽病是油茶Camellia oleifera的重要病害,该病害的优势致病菌是刺盘孢属Colletotrichum的果生刺盘孢C. fructicola,在全国的油茶产区普遍发生。我们前期发现组蛋白乙酰转移酶CfGcn5调控油茶果生刺盘孢的生长发育和致病过程,但组蛋白去乙酰化酶在该病菌中的生物学功能尚不清楚。本研究以组蛋白去乙酰化酶CfSnt2为研究对象,利用反向遗传学的方法,通过对野生型、CfSNT2基因敲除突变体及互补菌株的生物学表型进行比较分析,发现CfSNT2基因敲除突变体的菌丝生长速率明显减缓、分生孢子的产量显著减少、附着胞形成率降低、对细胞壁胁迫剂的响应异常,同时对油茶致病力显著减弱。以上现象说明CfSnt2调控果生刺盘孢的生长、产孢、附着胞的形成、对细胞壁完整性胁迫剂的耐受性及致病力。     

Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes

The compositions of bacterial genomes can be changed rapidly and dramatically through a variety of processes including horizontal gene transfer. This form of change is key to bacterial evolution, as it leads to ‘evolution in quantum leaps’. Horizontal gene transfer entails the incorporation of genetic elements transferred from another organism—perhaps in an earlier generation—directly into the genome, where they form ‘genomic islands’, i.e. blocks of DNA with signatures of mobile genetic elements. Genomic islands whose functions increase bacterial fitness, either directly or indirectly, have most likely been positively selected and can be termed ‘fitness islands’. Fitness islands can be divided into several subtypes: ‘ecological islands’ in environmental bacteria and ‘saprophytic islands’, ‘symbiosis islands’ or ‘pathogenicity islands’ (PAIs) in microorganisms that interact with living hosts. Here we discuss ways in which PAIs contribute to the pathogenic potency of bacteria, and the idea that genetic entities similar to genomic islands may also be present in the genomes of eukaryotes.     

The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival.

Pathogenicity islands are chromosomal clusters of horizontally acquired virulence genes that are often found at tRNA loci. The selC tRNA locus of Escherichia coli has served as the site of integration of two distinct pathogenicity islands which are responsible for converting benign strains into uro- and enteropathogens. Because virulence genes are targeted to the selC locus of E.coli, we investigated the homologous region of the Salmonella typhimurium chromosome for the presence of horizontally acquired sequences. At this site, we identified a 17 kb DNA segment that is both unique to Salmonella and necessary for virulence. This segment harbors a gene, mgtC, that is required for intramacrophage survival and growth in low Mg2+ media. The mgtC locus is regulated by the PhoP/PhoQ two-component system, a major regulator of virulence functions present in both pathogenic and non-pathogenic bacterial species. Cumulatively, our experiments indicate that the ability to replicate in low Mg2+ environments is necessary for Salmonella virulence, and suggest that a similar mechanism is responsible for the dissemination and acquisition of pathogenicity islands in enteric bacteria.