Combined ESTs from Plant–Microbe Interactions: Using GC Counting to Determine the Species of Origin

Huitema, Edgar; Torto, Trudy A.; Styer, Allison; Kamoun, Sophien

doi:10.1385/1-59259-413-1:79

Cited by 8 publications

(7 citation statements)

References 6 publications

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“…Sequence Analyses-GC counting was performed as described elsewhere (31). PexFinder and signal peptide predictions were performed as described by Torto et al (32).…”

Section: Methodsmentioning

confidence: 99%

A Kazal-like Extracellular Serine Protease Inhibitor from Phytophthora infestans Targets the Tomato Pathogenesis-related Protease P69B

Tian

Huitema

Cunha

et al. 2004

Journal of Biological Chemistry

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292

268

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The oomycetes form one of several lineages within the eukaryotes that independently evolved a parasitic lifestyle and consequently are thought to have developed alternative mechanisms of pathogenicity. The oomycete Phytophthora infestans causes late blight, a ravaging disease of potato and tomato. Little is known about processes associated with P. infestans pathogenesis, particularly the suppression of host defense responses. We describe and functionally characterize an extracellular protease inhibitor, EPI1, from P. infestans. EPI1 contains two domains with significant similarity to the Kazal family of serine protease inhibitors. Database searches suggested that Kazal-like proteins are mainly restricted to animals and apicomplexan parasites but appear to be widespread and diverse in the oomycetes. Recombinant EPI1 specifically inhibited subtilisin A among major serine proteases and inhibited and interacted with the pathogenesis-related P69B subtilisin-like serine protease of tomato in intercellular fluids. The epi1 and P69B genes were coordinately expressed and up-regulated during infection of tomato by P. infestans. Inhibition of tomato proteases by EPI1 could form a novel type of defense-counterdefense mechanism between plants and microbial pathogens. In addition, this study points to a common virulence strategy between the oomycete plant pathogen P. infestans and several mammalian parasites, such as the apicomplexan Toxoplasma gondii.

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“…Sequence Analyses-GC counting was performed as described elsewhere (31). PexFinder and signal peptide predictions were performed as described by Torto et al (32).…”

Section: Methodsmentioning

confidence: 99%

A Kazal-like Extracellular Serine Protease Inhibitor from Phytophthora infestans Targets the Tomato Pathogenesis-related Protease P69B

Tian

Huitema

Cunha

et al. 2004

Journal of Biological Chemistry

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292

268

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“…Of the latter, 968 were predicted to be of P. infestans origin. This was based on their having a GC content >50%, which helps distinguish P. infestans from host transcripts (Huitema et al 2003;Ronning et al 2002), and lacking strong matches against potato or tomato sequences in GenBank (using a threshold BLASTN E value of 10 -45 ).…”

Section: Cdna Libraries and Cdna Sequencingmentioning

confidence: 99%

Large-Scale Gene Discovery in the Oomycete Phytophthora infestans Reveals Likely Components of Phytopathogenicity Shared with True Fungi

Randall¹,

Dwyer²,

Huitema³

et al. 2005

MPMI

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164

134

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To overview the gene content of the important pathogen Phytophthora infestans, large-scale cDNA and genomic sequencing was performed. A set of 75,757 high-quality expressed sequence tags (ESTs) from P. infestans was obtained from 20 cDNA libraries representing a broad range of growth conditions, stress responses, and developmental stages. These included libraries from P. infestans-potato and -tomato interactions, from which 963 pathogen ESTs were identified. To complement the ESTs, onefold coverage of the P. infestans genome was obtained and regions of coding potential identified. A unigene set of 18,256 sequences was derived from the EST and genomic data and characterized for potential functions, stage-specific patterns of expression, and codon bias. Cluster analysis of ESTs revealed major differences between the expressed gene content of mycelial and spore-related stages, and affinities between some growth conditions. Comparisons with databases of fungal pathogenicity genes revealed conserved elements of pathogenicity, such as class III pectate lyases, despite the considerable evolutionary distance between oomycetes and fungi. Thirty-seven genes encoding components of flagella also were identified. Several genes not anticipated to occur in oomycetes were detected, including chitin synthases, phosphagen kinases, and a bacterial-type FtsZ cell-division protein. The sequence data described are available in a searchable public database.

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“…The concept of an "interaction transcriptome" has been introduced as a means of describing overall transcriptional profiles of host and pathogen organisms occurring at an infection interface (Birch and Kamoun 2000). Sets of ESTs from mixed host-pathogen cDNA libraries represent a sample of the interaction transcriptome, and various methods for distinguishing host and pathogen genes have been developed (Hraber and Weller 2001;Huitema et al 2003a;Qutob et al 2000). A natural extension of this line of work would be to include both host and pathogen gene targets on a single microarray in order to simultaneously follow changes in the host and pathogen during the course of infection.…”

mentioning

confidence: 99%

Patterns of Gene Expression Upon Infection of Soybean Plants byPhytophthora sojae

Moy¹,

Qutob²,

Chapman³

et al. 2004

MPMI

206

151

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To investigate patterns of gene expression in soybean (Glycine max) and Phytophthora sojae during an infection time course, we constructed a 4,896-gene microarray of host and pathogen cDNA transcripts. Analysis of rRNA from soybean and P. sojae was used to estimate the ratio of host and pathogen RNA present in mixed samples. Large changes in this ratio occurred between 12 and 24 h after infection, reflecting the rapid growth and proliferation of the pathogen within host tissues. From the microarray analysis, soybean genes that were identified as strongly upregulated during infection included those encoding enzymes of phytoalexin biosynthesis and defense and pathogenesis-related proteins. Expression of these genes generally peaked at 24 h after infection. Selected lipoxygenases and peroxidases were among the most strongly downregulated soybean genes during the course of infection. The number of pathogen genes expressed during infection reached a maximum at 24 h. The results show that it is possible to use a single microarray to simultaneously probe gene expression in two interacting organisms. The patterns of gene expression we observed in soybean and P. sojae support the hypothesis that the pathogen transits from biotrophy to necrotrophy between 12 and 24 h after infection.

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Combined ESTs from Plant–Microbe Interactions: Using GC Counting to Determine the Species of Origin

Cited by 8 publications

References 6 publications

A Kazal-like Extracellular Serine Protease Inhibitor from Phytophthora infestans Targets the Tomato Pathogenesis-related Protease P69B

A Kazal-like Extracellular Serine Protease Inhibitor from Phytophthora infestans Targets the Tomato Pathogenesis-related Protease P69B

Large-Scale Gene Discovery in the Oomycete Phytophthora infestans Reveals Likely Components of Phytopathogenicity Shared with True Fungi

Patterns of Gene Expression Upon Infection of Soybean Plants byPhytophthora sojae

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