Common and contrasting themes in host cell-targeted effectors from bacterial,fungal, oomycete and nematode plant symbionts described using the Gene Ontology

A wide diversity of plant-associated symbionts, including microbes, produce proteins that can enter host cells, or are injected into host cells in order to modify the physiology of the host to promote colonization. These molecules, termed effectors, commonly target the host defense signaling pathways in order to suppress the defense response. Others target the gene expression machinery or trigger specific modifications to host morphology or physiology that promote the nutrition and proliferation of the symbiont. When recognized by the host's surveillance machinery, which includes cognate resistance (R) gene products, defense responses are engaged to restrict pathogen proliferation. Effectors from diverse symbionts may be delivered into plant cells via varied mechanisms, including whole organism cellular entry (viruses, some bacteria and fungi), type III and IV secretion (in bacteria), physical injection (nematodes and insects) and protein translocation signal sequences (oomycetes and fungi). This mini-review will summarize both similarities and differences in effectors and effector delivery systems found in diverse plant-associated symbionts as well as how these are described with Plant-Associated Microbe Gene Ontology (PAMGO) terms.     

Common processes in pathogenesis by fungal and oomycete plant pathogens,described with Gene Ontology terms

Plant diseases caused by fungi and oomycetes result in significant economic losses every year. Although phylogenetically distant, the infection processes by these organisms share many common features. These include dispersal of an infectious particle, host adhesion, recognition, penetration, invasive growth, and lesion development. Previously, many of these common processes did not have corresponding Gene Ontology (GO) terms. For example, no GO terms existed to describe processes related to the appressorium, an important structure for infection by many fungi and oomycetes. In this mini-review, we identify common features of the pathogenic processes of fungi and oomycetes and create a pathogenesis model using 256 newly developed and 38 extant GO terms, with an emphasis on the appressorium and signal transduction. This set of standardized GO terms provides a solid base to further compare and contrast the molecular underpinnings of fungal and oomycete pathogenesis.     

On the modeling paradigm of plant root nutrient acquisition

Plant and Soil - This study investigated maize-soil biota interactions as well as the soil legacy effects of continuous monoculture (CM) on maize performance. We conducted a glasshouse experiment...     

Knowledge acquisition,consistency checking and concurrency control for Gene Ontology (GO)

MOTIVATION: A critical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge. The Gene Ontology (GO; http://www.geneontology.org) provides a taxonomy of concepts and their attributes for annotating gene products. As GO increases in size, its ongoing construction and maintenance becomes more challenging. In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protégé-2000, to the maintenance and development of GO. RESULTS: We transferred GO to Protégé-2000 in order to evaluate its suitability for GO. The graphical user interface supported browsing and editing of GO. Tools for consistency checking identified minor inconsistencies in GO and opportunities to reduce redundancy in its representation. The Protégé Axiom Language proved useful for checking ontological consistency. The PROMPT tool allowed us to track changes to GO. Using Protégé-2000, we tested our ability to make changes and extensions to GO to refine the semantics of attributes and classify more concepts. AVAILABILITY: Gene Ontology in Protégé-2000 and the associated code are located at http://smi.stanford.edu/projects/helix/gokbms/. Protégé-2000 is available from http://protege.stanford.edu.     

土壤微生物在植物获得养分中的作用

大量施用化肥是当今农业的一个重要特征。化肥为粮食增产做出了巨大贡献,同时也带来一系列问题,如土壤酸化、水体富营养化、温室气体排放、资源耗竭等,直接威胁着农业可持续发展。土壤微生物是陆地生态系统植物多样性和生产力的重要驱动者,直接参与了植物获得养分和土壤养分循环两个过程。因此,通过调控土壤微生物的功能,有望降低农业对化肥的过分依赖。介绍了共生固氮菌、菌根真菌和根际促生菌对植物获得养分能力的影响及其机制,分析了土壤微生物对土壤氮、磷循环的影响及其与土壤养分生物有效性、养分损失的关系。依据这些知识,提出了改善植物营养、降低化肥施用的土壤微生物途径。虽然大量试验已证明了土壤微生物在改善植物营养中的重要作用,但是大面积应用土壤微生物技术来改善植物营养还存在不少问题。随着以后对这方面研究的加强以及上述问题的不断解决,土壤微生物有望在降低化肥施用量和维持农业可持续发展中做出重要贡献。     

Common themes in the genome strategies of pathogens

Genomes of pathogenic bacteria evolve by large-scale changes in gene inventory. The continual acquisition of genomic islands, which refines their metabolic arsenal, is offset by gene loss. Far from this being a passive deletion of genes no longer useful to pathogens, the removal of genes encoding problematic metabolic process and immunogenic surface antigens might be strongly beneficial. Genomes of virulent eukaryotes show the footprint of similar genomic alterations, including acquisition of genes by lateral transfer, and genome degradation in obligate pathogens. These common features suggest that unicellular pathogens share common strategies for adaptation.     

Common themes and variations in the rhodanese superfamily

The rhodanese homology domain is a ubiquitous fold found in several phylogenetically related proteins encoded by eubacterial, archeal, and eukaryotic genomes. Although rhodanese-like proteins share evolutionary relationships, analysis of their sequences highlights that they are so heterogeneous to form the rhodanese superfamily. The variability occurs at different levels including sequence, active site loop length, presence of a critical catalytic Cys residue, and domain arrangement. Even within the same genome, multiple genes encode rhodanese-like proteins presenting with variably arranged rhodanese domain(s): as single or tandem domain(s), or combined with other protein domain(s). Given the highly variable organization of the rhodanese domain(s) and the context where it is found, here we review the structural organization and function of the rhodanese-like proteins. The overview of the most recent findings about rhodanese allow us to depict a superfamily of versatile proteins relying on persulfide chemistry to accomplish cellular functions spanning from resistance to environmental threats, such as cyanide, and key cellular reactions related to sulfur metabolism and progression of cell cycle.     

Plant invasions facilitated by suppression of root nutrient acquisition rather than by disruption of mycorrhizal association in the native plant

Invasive species have profound negative impacts on native ranges. Unraveling the mechanisms employed by invasive plant species is crucial to controlling invasions. One important approach that invasive plants use to outcompete native plants is to disrupt mutualistic interactions between native roots and mycorrhizal fungi. However, it remains unclear how differences in the competitive ability of invasive plants affect native plant associations with mycorrhizae. Here, we examined how a native plant, Xanthium strumarium, responds to invasive plants that differed in competitive abilities (i.e., as represented by aboveground plant biomass) by measuring changes in root nitrogen concentration (root nutrient acquisition) and mycorrhizal colonization rate. We found that both root nitrogen concentration and mycorrhizal colonization rate in the native plant were reduced by invasive plants. The change in mycorrhizal colonization rate of the native plant was negatively correlated with both aboveground plant biomass of the invasive plants and the change in aboveground plant biomass of the native plant in monocultures relative to mixed plantings. In contrast, the change in root nitrogen concentration of the native plant was positively correlated with aboveground plant biomass of the invasive plants and the change in aboveground plant biomass of the native plant. When we compared the changes in mycorrhizal colonization rate and root nitrogen concentration in the native plant grown in monocultures with those of native plants grown with invasive plants, we observed a significant tradeoff. Our study shows that invasive plants can suppress native plants by reducing root nutrient acquisition rather than by disrupting symbiotic mycorrhizal associations, a novel finding likely attributable to a low dependence of the native plant on mycorrhizal fungi.     

Growth, respiration and nutrient acquisition by the arbuscular mycorrhizal fungus Glomus mosseae and its host plant Plantago lanceolata in cooled soil

Although plant phosphate uptake is reduced by low soil temperature, arbuscular mycorrhizal (AM) fungi are responsible for P uptake in many plants. We investigated growth and carbon allocation of the AM fungus Glomus mosseae and a host plant (Plantago lanceolata) under reduced soil temperature. Plants were grown in compartmented microcosm units to determine the impact on both fungus and roots of a constant 2.7 °C reduction in soil temperature for 16 d. C allocation was measured using two (13)CO(2) pulse labels. Although root growth was reduced by cooling, AM colonization, growth and respiration of the extraradical mycelium (ERM) and allocation of assimilated (13)C to the ERM were all unaffected; the frequency of arbuscules increased. In contrast, root respiration and (13)C content and plant P and Zn content were all reduced by cooling. Cooling had less effect on N and K, and none on Ca and Mg content. The AM fungus G. mosseae was more able to sustain activity in cooled soil than were the roots of P. lanceolata, and so enhanced plant P content under a realistic degree of soil cooling that reduced plant growth. AM fungi may therefore be an effective means to promote plant nutrition under low soil temperatures.     

How symbiotic bacteria influence plant utilisation by the polyphagous aphid, Aphis fabae

To explore the effect of rearing-plant species on the contribution of the symbiotic bacterium, Buchnera, to aphid performance, larvae of Aphis fabae that contained the bacteria (symbiotic aphids) and larvae experimentally deprived of the bacteria (aposymbiotic aphids) were reared on 16 plant species. Mortality of aphids was low on most plant species. The relative growth rate (RGR) of the larvae varied with plant species, and was generally depressed by elimination of the bacteria; the mean values of RGR varied between 0 and 0.29 μg μg⁻¹ day⁻¹ for symbiotic aphids and 0 and 0.17 μg μg⁻¹ day⁻¹ for aposymbiotic aphids. The extent to which RGR was depressed by aposymbiosis varied significantly between plant species, suggesting that aphid host plant may influence the contribution of the bacteria to plant utilisation. It is proposed that the bacteria may be particularly important on plants with phloem sap of high amino acid content of low quality, i.e. low concentrations of essential amino acids. Received: 18 August 1996 / Accepted: 13 January 1997     

低等白蚁肠道共生微生物的多样性及其功能

低等白蚁肠道里存在着复杂的微生物区系,包括真核微生物鞭毛虫和原核生物,细菌及古细菌。低等白蚁的后肠以特别膨大的囊形胃及其氢氧浓度的明显梯度分布和丰富的微生物区系为特征,是白蚁进行木质纤维素消化的主要器官。后肠内的鞭毛虫能将纤维素水解并发酵为乙酸,二氧化碳和氢,为白蚁提供营养和能源。系统发育研究表明,低等白蚁肠道共生细菌的主要类群为白蚁菌群1、螺旋体、拟杆菌,低G C mol%含量的革兰氏阳性菌和紫细菌等。而古细菌主要为甲烷短杆菌属的产甲烷菌。共生原核生物与二氧化碳的还原和氮的循环等代谢有关。但肠道共生微生物的具体功能和作用机制还有待进一步的揭示。     

Cost efficiency of nutrient acquisition and the advantage of mycorrhizal symbiosis for the host plant

Mycorrhizal symbiosis involves reciprocal transfer of carbon and nutrients between shoots on the one hand and roots colonized by symbiotic fungi on the other. Mycorrhizas may improve the mineral nutrient acquisition rates, but simultaneously increase the belowground demand for carbon. Mycorrhizal plants will have a selective advantage over non-mycorrhizal ones if they are more cost-efficient in terms of carbon cost per unit of acquired mineral nutrient. However, we demonstrate here in a simple model system that this is not a necessary condition. Mycorrhizas may evolve even when they are less cost-efficient, provided that photosynthesis and/or growth are strongly nutrient-limited. This result implies a unique hypothesis for the evolution of mycorrhizal associations which may be inherently cost-inefficient as compared to plant roots. Such symbioses may have evolved when the superior nutrient acquisition rate of fungi combines with the relatively high photosynthetic nutrient use efficiency of the host plant. Consequently, provided that mycorrhizas are really cost-inefficient, the selective advantage of mycorrhizal plants will disappear when an increase in the nutrient acquisition rate is not associated with a sufficiently high nutrient use efficiency of photosynthesis, as at high soil nutrient levels or due to a loss of leaf area, shading or low temperatures.     

Common themes in the assembly and architecture of activating immune receptors

Each of the many different cell types of the immune system expresses one or several activating receptors which serve a central role in the cell's surveillance function. Many of these cell-surface receptors share a distinctive modular design that consists of a ligand-binding module with no intrinsic signalling capability that is non-covalently associated with one or more dimeric signalling modules. Receptor assembly is directed by unique polar contacts within the transmembrane domains, whereas extracellular contacts can contribute to stability and specificity. This Review discusses the structural basis of receptor assembly and the implications of these findings for the mechanisms of receptor triggering.     

Plant species diversity affects plant nutrient pools by affecting plant biomass and nutrient concentrations in high-nitrogen ecosystems

Plant species diversity affects plant nutrient pools, however, previous studies have not considered plant nutrient concentrations and biomass simultaneously. In this study, we conducted an experimental system with 90 microcosms simulating constructed wetlands (CWs). Four species were selected to set up a plant species richness gradient (1, 2, 3, 4 species) and fifteen species compositions. The plant biomass, plant N, phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) concentrations and pools were analyzed. Results showed that, (1) plant species richness increased plant biomass, and the presence of Oenanthe javanicae increased while the presence of Reineckia carnea decreased plant biomass; (2) plant species richness only increased plant K and Mg concentrations of the communities and plant Mg concentration of the species, and the presence of O. Javanica increased while the presence of R. Japonicus decreased plant N and P concentrations of the communities; (3) plant species richness increased plant N, P, K, Ca, and Mg pools, and the presence of O. Javanica increased while the presence of R. Carnea decreased plant N, P, K, Ca and Mg pools; (4) the four-species mixture produced more biomass and nutrient pools than the corresponding highest specific species monocultures. In case the plant uptake can remove nutrients from CWs through harvesting, the results suggest that both nutrient concentrations and biomass must be considered when evaluating the accumulation of nutrients. Assembling plant communities with high species richness (four species) or certain species (such as O. Javanica) is recommended to remove more nutrients from CWs through harvesting.     

Programmed cell death in host-symbiont associations,viewed through the Gene Ontology

Manipulation of programmed cell death (PCD) is central to many host microbe interactions. Both plant and animal cells use PCD as a powerful weapon against biotrophic pathogens, including viruses, which draw their nutrition from living tissue. Thus, diverse biotrophic pathogens have evolved many mechanisms to suppress programmed cell death, and mutualistic and commensal microbes may employ similar mechanisms. Necrotrophic pathogens derive their nutrition from dead tissue, and many produce toxins specifically to trigger programmed cell death in their hosts. Hemibiotrophic pathogens manipulate PCD in a most exquisite way, suppressing PCD during the biotrophic phase and stimulating it during the necrotrophic phase. This mini-review will summarize the mechanisms that have evolved in diverse microbes and hosts for controlling PCD and the Gene Ontology terms developed by the Plant-Associated Microbe Gene Ontology (PAMGO) Consortium for describing those mechanisms.     

A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium,Microcoleus vaginatus

Microcoleus vaginatus plays a prominent role as both primary producer and pioneer in biocrust communities from dryland soils. And yet, it cannot fix dinitrogen, essential in often nitrogen-limited drylands. But a diazotroph-rich “cyanosphere” has been described in M. vaginatus, hinting that there exists a C for N exchange between the photoautotroph and heterotrophic diazotrophs. We provide evidence for this by establishing such a symbiosis in culture and by showing that it is selective and dependent on nitrogen availability. In natural populations, provision of nitrogen resulted in loss of diazotrophs from the cyanosphere of M. vaginatus compared to controls, but provision of phosphorus did not. Co-culturing of pedigreed cyanosphere diazotroph isolates with axenic M. vaginatus resulted in copious growth in C and N-free medium, but co-culture with non-cyanosphere diazotrophs or other heterotrophs did not. Unexpectedly, bundle formation in M. vaginatus, diacritical to the genus but not seen in axenic culture, was restored in vitro by imposed nitrogen limitation or, even more strongly, by co-culture with diazotrophic partners, implicating this trait in the symbiosis. Our findings provide direct evidence for a symbiotic relationship between M. vaginatus and its cyanosphere and help explain how it can be a global pioneer in spite of its genetic shortcomings.Subject terms: Microbial ecology, Soil microbiology     

Nutrient uptake estimates for woody species as described by the NST 3.0, SSAND, and PCATS mechanistic nutrient uptake models

The effect of soil acidity on root and rhizosheath development in wheat and barley seedlings was investigated in an acid Ferrosol soil to which various amounts of lime (CaCO₃) were applied to modify soil Al concentrations (pH (CaCl₂): 4.22 to 5.35 and Al (CaCl₂ extract): 17.7 to 0.4 mg kg^?1 soil; respectively), and Ferrosol soil from an adjacent location at the same site which had a higher Al concentration (pH 4.19; 29.2 mg kg^?1 Al). The cereal lines were selected on the basis of differences in their rate of root growth, Al-resistance and root hair morphology. Root morphology was assessed after 7 days of growth. The length of fine (mainly lateral) roots of Al-sensitive genotypes was more sensitive to soil Al concentrations than that of the coarse (mainly primary) roots. The experiments demonstrated that even where root growth was protected by expression of the TaALMT1 gene for Al-resistance, root-soil contact was diminished by soil acidity because root hair length (in many lines), and root hair density and rhizosheath formation (all lines) were adversely affected by soil acidity. In the case of Al-sensitive lines, fine root growth and rhizosheath mass were reduced over much the same range of soil Al concentrations (i.e. >3–6 mg kg^?1 Al). Although Al-resistant lines could maintain fine root length under these conditions, they were similarly unable to maintain rhizosheath mass. This finding may help to explain why Al-resistant wheats which yield relatively well in deep acid soils, may also benefit from application of lime to the surface layers of the soil.