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

Gene Ontology annotation highlights shared and divergent pathogenic strategies of type III effector proteins deployed by the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic Escherichia coli strains

Genome-informed identification and characterization of Type III effector repertoires in various bacterial strains and species is revealing important insights into the critical roles that these proteins play in the pathogenic strategies of diverse bacteria. However, non-systematic discipline-specific approaches to their annotation impede analysis of the accumulating wealth of data and inhibit easy communication of findings among researchers working on different experimental systems. The development of Gene Ontology (GO) terms to capture biological processes occurring during the interaction between organisms creates a common language that facilitates cross-genome analyses. The application of these terms to annotate type III effector genes in different bacterial species – the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic strains of Escherichia coli – illustrates how GO can effectively describe fundamental similarities and differences among different gene products deployed as part of diverse pathogenic strategies. In depth descriptions of the GO annotations for P. syringae pv tomato DC3000 effector AvrPtoB and the E. coli effector Tir are described, with special emphasis given to GO capability for capturing information about interacting proteins and taxa. GO-highlighted similarities in biological process and molecular function for effectors from additional pathosystems are also discussed

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

The Plant Pathogen Pseudomonas syringae pv. tomato Is Genetically Monomorphic and under Strong Selection to Evade Tomato Immunity

Recently, genome sequencing of many isolates of genetically monomorphic bacterial human pathogens has given new insights into pathogen microevolution and phylogeography. Here, we report a genome-based micro-evolutionary study of a bacterial plant pathogen, Pseudomonas syringae pv. tomato. Only 267 mutations were identified between five sequenced isolates in 3,543,009 nt of analyzed genome sequence, which suggests a recent evolutionary origin of this pathogen. Further analysis with genome-derived markers of 89 world-wide isolates showed that several genotypes exist in North America and in Europe indicating frequent pathogen movement between these world regions. Genome-derived markers and molecular analyses of key pathogen loci important for virulence and motility both suggest ongoing adaptation to the tomato host. A mutational hotspot was found in the type III-secreted effector gene hopM1. These mutations abolish the cell death triggering activity of the full-length protein indicating strong selection for loss of function of this effector, which was previously considered a virulence factor. Two non-synonymous mutations in the flagellin-encoding gene fliC allowed identifying a new microbe associated molecular pattern (MAMP) in a region distinct from the known MAMP flg22. Interestingly, the ancestral allele of this MAMP induces a stronger tomato immune response than the derived alleles. The ancestral allele has largely disappeared from today's Pto populations suggesting that flagellin-triggered immunity limits pathogen fitness even in highly virulent pathogens. An additional non-synonymous mutation was identified in flg22 in South American isolates. Therefore, MAMPs are more variable than expected differing even between otherwise almost identical isolates of the same pathogen strain

Information Management of Genome Enabled Data Streams for Pseudomonas syringae on the Pseudomonas-Plant Interaction (PPI) Website

Genome enabled research has led to a large and ever-growing body of data on Pseudomonas syringae genome variation and characteristics, though systematic capture of this information to maximize access by the research community remains a significant challenge. Major P. syringae data streams include genome sequence data, newly identified type III effectors, biological characterization data for type III effectors, and regulatory feature characterization. To maximize data access, the Pseudomonas-Plant Interaction (PPI) website [1] is primarily focused on categorization of type III effectors and curation of effector functional data represented in the Hop database and Pseudomonas-Plant Interaction Resource, respectively. The PPI website further serves as a conduit for incorporation of new genome characterization data into the annotation records at NCBI and other data repositories, and clearinghouse for additional data sets and updates in response to the evolving needs of the research community

Sequencing and annotation of the Wolbachia endosymbiont of Diaphorina citri by the CG-HLB Genome Resources group reveals candidate sources of interaction with the insect host

The Citrus Greening – Huanglongbing (CG-HLB) Genome Resources group serves as a bioinformatics resource for diverse projects related to the biology of CG-HLB.  A major recent project concerns the generation and annotation of a draft genome sequence for the Wolbachia endosymbiont (wDi) of the Asian citrus psyllid, of particular interest given the potential for control of psyllid behavior through manipulation of its bacterial endosymbionts.   The Wolbachia draft genome was assembled and contigs aligned using the wPip strain from mosquito, its closest relative among completed Wolbachia genome sequences.  OrthoMCL analysis of the annotated draft genome sequence confirmed the presence of 670 genes common to all sequenced Wolbachia genomes. Candidate host interaction factors include 54 predicted ankyrin proteins hypothesized to play a role in host reproductive manipulation, a Type IV secretion system linked to ankyrin protein export, and a bacterioferritin linked to host iron homeostasis.  Several metabolic capabilities were identified in wDi that are absent from Liberibacter. FtsZ and Wsp phylogenies indicate that the Wolbachia strain in the Florida D. citri isolate falls into a sub-clade of supergroup B, distinct from Wolbachia present in Chinese D. citri isolates, supporting the hypothesis that the D. citri introduced into Florida did not originate from China. The Wolbachia sequence and annotation can be viewed on the CG-HLB Genome Resources Website (http://citrusgreening.org/), together with the sequences of publically available Liberibacter genomes sequenced to date. Future plans involve development of a searchable Liberibacter diagnostic sequence database using the over 1700 publically available Ca. Liberibacter gene sequences

Sequencing and annotation of the Wolbachia endosymbiont of Diaphorina citri by the CG-HLB Genome Resources group reveals candidate sources of interaction with the insect host

The Citrus Greening – Huanglongbing (CG-HLB) Genome Resources group serves as a bioinformatics resource for diverse projects related to the biology of CG-HLB.  A major recent project concerns the generation and annotation of a draft genome sequence for the Wolbachia endosymbiont (wDi) of the Asian citrus psyllid, of particular interest given the potential for control of psyllid behavior through manipulation of its bacterial endosymbionts.   The Wolbachia draft genome was assembled and contigs aligned using the wPip strain from mosquito, its closest relative among completed Wolbachia genome sequences.  OrthoMCL analysis of the annotated draft genome sequence confirmed the presence of 670 genes common to all sequenced Wolbachia genomes. Candidate host interaction factors include 54 predicted ankyrin proteins hypothesized to play a role in host reproductive manipulation, a Type IV secretion system linked to ankyrin protein export, and a bacterioferritin linked to host iron homeostasis.  Several metabolic capabilities were identified in wDi that are absent from Liberibacter. FtsZ and Wsp phylogenies indicate that the Wolbachia strain in the Florida D. citri isolate falls into a sub-clade of supergroup B, distinct from Wolbachia present in Chinese D. citri isolates, supporting the hypothesis that the D. citri introduced into Florida did not originate from China. The Wolbachia sequence and annotation can be viewed on the CG-HLB Genome Resources Website (http://citrusgreening.org/), together with the sequences of publically available Liberibacter genomes sequenced to date. Future plans involve development of a searchable Liberibacter diagnostic sequence database using the over 1700 publically available Ca. Liberibacter gene sequences

Bioinformatic characterization of the reduced genome citrus pathogen Ca. Liberibacter asiaticus

<p><em>Ca</em>. Liberibacter asiaticus (Las) is an alpha-proteobacteria vectored by psyllid insects and believed to be the causal agent of citrus greening or Huanglongbing. However, given the difficulty in culturing this organism, much about its biology remains a mystery. Availability of genome sequence data for a single isolate of Las (Duan, 2009), provides an opportunity to gain insights into its biology and mechanisms of adaptation to host and vector through sequence analysis. Using hidden Markov models based on data from related bacteria, transcription factor binding site predictions have been generated to identify genes with potentially coordinated response to various stimuli. Subcellular localization of annotated gene products based on SignalP and LipoP predictions of signal peptide cleavage sites has been an additional focus given the potential importance of exported and surface proteins in physical interactions with the host and vector. Repetitive regions, mapped using RepeatScout and Repeat Masker, are of use in designing diagnostic probes. Future work will involve characterization of genome architecture through identification of genomic regions orthologous to better studied relatives. Data related to Las characterization can be found on the Citrus Greening - HLB Genome Resources website (http://www.citrusgreening.org). This website is designed as a comprehensive online resource and data sharing platform for the citrus greening research community. In addition to the predicted signal peptides, lipoproteins and transcription factor binding sites, links to off-site analyses such as KEGG pathway maps are also included. Users can explore above mentioned features and add novel annotations on the Las genome using the Artemis or GBrowse genome browsers. Guides for genome viewing and links to other genome analysis tools are also available.</p